Science Literature

In their paper in Nature, Thewissen et al explain that the whale evolution story lacks a significant anchor point: "the link to the ancestor of cetaceans has been missing". It is not just a case of not knowing, but the focus of fundamental differences between researchers. Some emphasise morphology and some molecular evidence - and it should not be surprising to learn of a lack of harmony about the meaning of these data. Now, Thewissen and colleagues think they have an answer:

"It was known that whales are related to even-toed ungulates (artiodactyls), but until now no artiodactyls were morphologically close to early whales. Here we show that the Eocene south Asian raoellid artiodactyls are the sister group to whales. The raoellid Indohyus is similar to whales, and unlike other artiodactyls, in the structure of its ears and premolars, in the density of its limb bones and in the stable-oxygen-isotope composition of its teeth."

They use cladistic techniques to show the closeness of the raoellids and the cetaceans (although we should note that the cetaceans are represented by Pakicetus, Ambulocetus, Rodhocetus and Artiocetus - all supposedly transitional walking whales). Cladistics is not a straightforward tool to use for the purposes of tracing ancestries. This is because there are many shared characters to consider and it is necessary for researchers to select the character sets they use in the cladograms. Great stress is placed on finding the most parsimonious trees: the one with the minimum number of evolutionary changes needed to explain the data (a criterion that strikes me as unrealistic with the evolution of cetaceans, a process which necessarily requires an extraordinary number of changes). These shared characters do not always fit neatly into the cladistic framework of analysis: many animals (living and extinct) exhibit a puzzling mosaic of characters. The researchers identified four characters which they deem significant: the structure of ears and molars, the density of its limb bones, and the stable-oxygen-isotope composition of its teeth. From this they conclude:

"Raoellids are the sister group to cetaceans, and this implies that aquatic habitats originated before the Order Cetacea. The great evolutionary change that occurred at the origin of cetaceans is thus not the adoption of an aquatic lifestyle."

Whilst these particular characters may be used to defend the idea that the animals were aquatic waders, the claim that they represent the transition from artiodactyls to whales belongs to the realm of speculation. Hypotheses must be tested, and the researchers should evaluate their own hypothesis against alternatives. As a suggestion, consider the hypothesis that Indohyus was a specialised artiodactyl gathering its food in aqueous environments. Furthermore, the researchers must guard against the possibility that they are cherry-picking characters that allow them to reach a favoured decision. A report by Stokstad put a question mark against the claim that the long-lost relative of whales has been found. He concluded:

"Not everyone is convinced that Indohyus is the closest cetacean relative, however. Another analysis, in press at Cladistics, suggests that an extinct group of carnivorous mammals, called mesonychids, were more closely related to cetaceans."

The reference to this paper is given below.
Thewissen et al provide an adaptationist scenario for the pathway to cetaceans. The nearest analogy is suggested to be the African mousedeer which lives near streams, feeds on land, but flees into the water when danger occurs.

"Our working hypothesis for the origin of whales is that raoellid ancestors, although herbivores or omnivores on land, took to fresh water in times of danger. Aquatic habits were increased in Indohyus (as suggested by osteosclerosis and oxygen isotopes), although it did not necessarily have an aquatic diet (as suggested by carbon isotopes). Cetaceans originated from an Indohyus-like ancestor and switched to a diet of aquatic prey."

One newspaper report continues the tale:
"However, no one knows why some mammals returned to the water. Some may have started to wade in rivers and lakes to avoid predators or in search of better food. As they spent longer in the water, their legs evolved into flippers - while their noses developed into the blow holes found in the top of whales' heads."

This sounds like a good lead for a Rudyard Kipling story!

Whales originated from aquatic artiodactyls in the Eocene epoch of India
J. G. M. Thewissen, Lisa Noelle Cooper, Mark T. Clementz, Sunil Bajpai & B. N. Tiwari
Nature 450, 1190-1194 (20 December 2007) | doi:10.1038/nature06343

Abstract: Although the first ten million years of whale evolution are documented by a remarkable series of fossil skeletons, the link to the ancestor of cetaceans has been missing. It was known that whales are related to even-toed ungulates (artiodactyls), but until now no artiodactyls were morphologically close to early whales. Here we show that the Eocene south Asian raoellid artiodactyls are the sister group to whales. The raoellid Indohyus is similar to whales, and unlike other artiodactyls, in the structure of its ears and premolars, in the density of its limb bones and in the stable-oxygen-isotope composition of its teeth. We also show that a major dietary change occurred during the transition from artiodactyls to whales and that raoellids were aquatic waders. This indicates that aquatic life in this lineage occurred before the origin of the order Cetacea.

See also:

Stokstad. E. Long-Lost Relative of Whales Found? ScienceNOW Daily News, 19 December 2007

O'Leary, M.A. and Gatesy, J. Impact of increased character sampling on the phylogeny of Cetartiodactyla (Mammalia): combined analysis including fossils, Cladistics (OnlineEarly Articles). | doi:10.1111/j.1096-0031.2007.00187.x

Derbyshire, D. Revealed: The deer that grew into a whale, Daily Mail, 19th December 2007

It has long been recognised by the horseracing community that loving care and a good jockey are important factors in winning prizes. However, such is the hunger for success that breeders seek out every possible advantage for their next generation of hopefuls. The lure of 'good genes' has proved remarkably strong, turning stud farms into multi-million pound (dollar) industries. By combining the genes of a successful mare with those of a winning stallion, the progeny should be well-equipped genetically to compete. The racing industry effectively runs an equidian eugenics programme to improve the genetic qualities of competing animals.
Unfortunately for the participants, genes are not all they are made out to be. We have been exposed to the 'Genes-R-Us' emphasis for so long that it is very hard for people to correct their thinking. Nevertheless, major corrections are warranted, according to Wilson and Rambaut, who have just published their study of over 4000 racehorses. "Only 10 per cent of a horse's winnings can be attributed to parentage. [snip] The majority - up to 90 per cent - of a horse's lifetime winnings rest on how the horse is reared, trained and ridden and not to its genetic inheritance." Nurture, rather than nature, provides the primary factors affecting success. Furthermore, the authors could find no correlation between stud fees and the horse's lifetime earnings.
The surprise expressed at the research findings is an indication of just how entrenched the genocentric view of life has become. Why do we put so much emphasis on genes? The simple answer is that this derives from the origins story we have been fed for most of the 20th Century: the organism is just the vehicle for genes to reproduce themselves.
Research findings that contradict this dogma have been accumulating steadily and we are now overdue for a change. For more on this, go here. Unfortunately for Darwinists, the nurture factors do not change the genome: if nurture effects become significant, they undermine the efficacy of Darwin's mechanism of variation and natural selection. In a Nature news report, Kaplan cites the figures 91.5 percent nurture and 8.5 percent nature. He also cites Wilson saying:

"8.5% may seem small, but for those of us studying the benefits generated by genetics in wild animals this is huge [. . .] In the wild, where environmental conditions vary a lot and survival can depend on luck as much as anything else, genetics usually account for about 1-2% of survival rates."

These figures ought to be more widely discussed in the context of natural selection. Do models of natural selection do justice to the revelation that genetics usually account for about 1-2% of survival rates? Should students be taught about these figures, or are they deemed unable to handle them judiciously?

Breeding racehorses: what price good genes?
Alastair J. Wilson, Andrew Rambaut
Biology Letters, FirstCite, Dec 18 2007, doi 10.1098/rsbl.2007.0588

Abstract: Horse racing is a multi-million pound industry, in which genetic information is increasingly used to optimize breeding programmes. To maximize the probability of producing a successful offspring, the owner of a mare should mate her with a high-quality stallion. However, stallions with big reputations command higher stud fees and paying these is only a sensible strategy if, (i) there is a genetic variation for success on the racecourse and (ii) stud fees are an honest signal of a stallion's genetic quality. Using data on thoroughbred racehorses, and lifetime earnings from prize money (LE) as a measure of success, we performed quantitative genetic analyses within an animal model framework to test these two conditions. Although LE is heritable (VA=0.299 +- 0.108, Pr=0.002), there is no genetic variance for stud fee and the genetic correlation between traits is therefore zero. This result is supported by an absence of any relationship between stud fees for currently active stallions and the predicted LE for their (hypothetical) offspring. Thus, while there are good genes to be bought, a stallion's fees are not an honest signal of his genetic quality and are a poor predictor of a foal's prize winning potential.

See also:

Highfield, R. High price may not make champion horse, The Daily Telegraph: 19/12/2007.

Kaplan, M. Good genes help racehorses to be winners, news@nature.com, 18 December 2007 | doi:10.1038/news.2007.387

The human race, with its apparently inexhaustible variants, never ceases to engage our attention and fascination. Explaining the diversity, however, is not at all trivial, with academic controversy never far away.
Take, for example, explanations of the origin of human pygmies. "Traditional hypotheses assume that the small body size of human pygmies is an adaptation to special challenges, such as thermoregulation, locomotion in dense forests, or endurance against starvation." Since most pygmies live in the tropics, small size is perceived as an adaptive response to avoid overheating. An alternative explanation is that most pygmies live and hunt in jungles, where small size assists moving through undergrowth to catch prey. The third option is to emphasise the potential for scarcity of food supply for hunter gatherers, where small bodies have the advantage of needing less food. These are all Darwinian 'just-so stories' which are defended by creating various virtual scenarios around the favoured causal mechanism. However, say the authors of a new study:

"None of these explanations account for the worldwide distribution of human pygmies - some pygmy-sized populations are found outside forests, and many live in cool and dry areas; furthermore, long-standing poor nutrition does not necessarily lead to pygmy size, as shown by groups who, like certain pygmies, experience frequent food shortages and yet are among the tallest populations in the world."

Last year, Robert Walker, Andrea Migliano and others showed that environmental factors appear to be affecting growth rates of small human social groups. Some tribes exhibit fast child-juvenile growth, early puberty and first reproduction, and have lower overall life spans. This has now been followed up (with Migliano as lead author) to present environmental factors as crucial for the origin of pygmies.

"We argue that human pygmy populations and adaptations evolved independently as the result of a life history tradeoff between the fertility benefits of larger body size against the costs of late growth cessation, under circumstances of significant young and adult mortality. Human pygmies do not appear to have evolved through positive selection for small stature - this was a by-product of selection for early onset of reproduction."

In other words, the short pygmy stature is a spandrel. The real factors driving miniaturisation are related to significant mortality rates in young and adult members of a tribe. A report in The Economist expresses this very clearly:

"By adding pre-existing data for African pygmies to new information they have collected about the Aeta and the Batak of the Philippines, they show that at the beginnings of their lives all these pygmy populations follow the same growth curves as taller people, including Turkana and Americans. This demonstrates that pygmyism is not a result of early malnutrition, as another hypothesis has it. At the age of about 12, however, pygmies stop growing. That is also the age at which they become sexually mature - about three years earlier than taller people." [snip]

The argument is that "a short life exerts pressure to mature early, and thus switch resources from growth to reproduction. A mathematical model used by the team confirms that, given pygmy life expectancies, their growth and reproduction patterns have indeed been optimised by natural selection. The various pygmy groups are thus the products of harsh circumstances."

Two points are worth highlighting here.
1. The temptation for Darwinists to find an adaptationist story is very strong, but proposing a plausible story is not in itself science. Most of these 'just-so' stories thrive on limited data, and more rigorous analyses reveal frequently that these imaginative scenarios are just illusions. For more on this, go here.
2. Although the terms "evolution" and "evolutionary change" are liberally used by writers, there is no support (in this case) for the Blind Watchmaker theory of evolutionary transformation. What we have here are changes in growth rates and reproduction patterns which add nothing to biological complexity. Whereas the rest of mankind exhibit reversible traits relating to size, the onset of puberty, etc, pygmies have undergone permanent genetic change. Most probably, this represents a loss of genetic variability within the population. The Economist report has the title "Darwin's Children", but this is misleading. Rather than demonstrating the branching pattern associated with Darwin's vision of life's unfolding, the pygmy tribes are telling us that harsh circumstances have forced a tradeoff with a significant genetic cost. These evidences of variation are by no means the exclusive domain of Darwinism. Journalists, by and large, appear unable to put the record straight. Consequently, it is long overdue for the community of scientists to put its own house in order about the e-word. For more recent examples of this being a significant problem, go here and here and here.

Life history trade-offs explain the evolution of human pygmies
Andrea Bamberg Migliano, Lucio Vinicius, and Marta Mirazon Lahr
Proc. Natl. Acad. Sci. USA, week of December 10, 2007 | 10.1073/pnas.0708024105

Abstract: Explanations for the evolution of human pygmies continue to be a matter of controversy, recently fuelled by the disagreements surrounding the interpretation of the fossil hominin Homo floresiensis. Traditional hypotheses assume that the small body size of human pygmies is an adaptation to special challenges, such as thermoregulation, locomotion in dense forests, or endurance against starvation. Here, we present an analysis of stature, growth, and individual fitness for a large population of Aeta and a smaller one of Batak from the Philippines and compare it with data on other pygmy groups accumulated by anthropologists for a century. The results challenge traditional explanations of human pygmy body size. We argue that human pygmy populations and adaptations evolved independently as the result of a life history tradeoff between the fertility benefits of larger body size against the costs of late growth cessation, under circumstances of significant young and adult mortality. Human pygmies do not appear to have evolved through positive selection for small stature - this was a by-product of selection for early onset of reproduction.

See also:

Walker, R., et al. Growth Rates and Life Histories in Twenty-Two Small-Scale Societies, American Journal of Human Biology, 18:295-311, 2006.

Darwin's children, The Economist, Dec 13th 2007

The human species exhibits the phenomenon of sexual dimorphism in a multitude of subtle ways. A fascinating study by Whitcome et al allows a closer look at one of these differences - relating to the base of the spine. The shapes of these vertebrae are critical for bipedalism, and those of us who do not look after our backs will learn the hard way that posture and appropriate exercise are important. Particular challenges face pregnant women:

"Pregnancy augments the mass of the human female abdomen by as much as 31% (6.8 kg), translating the position of the maternal COM [Centre of Mass] forward and increasing the torque exerted by the upper body around the hip joints. Although this shift in mass does not disrupt postural stability in quadrupeds, it uniquely destabilizes bipeds whose supporting joints and twofooted support base lie solely under the hips. Such gravid instability can be counteracted by muscles, but sustained recruitment risks muscle fatigue and increases the likelihood of spinal injury.
Pregnant mothers habitually compensate positionally to fetal load by extending the lower back. Our longitudinal study of 19 pregnant human females shows that adjustments to lumbar lordosis permit mothers to maintain a stable anteroposterior position of the COM as gestation progresses and fetal mass increases."

It is found that men and women have differences in the morphology of the lower vertebrae, and the research paper links these to pregnancy. Men have two wedged vertebrae where women have three. Whilst this may not sound much, with all the other minor adjustments, pregnant women have the ability to adjust their posture so that the COM is in the right position and the shearing forces on the back are not excessive.
The instinctive reaction of some of us is to recognise lumbar lordosis as a design feature. However, the authors approach their research from within the Darwinian paradigm:

"Given the demands of fetal load and the importance of pregnancy for fitness, one predicts that natural selection has operated on the unique anatomy of the hominin lumbar region to mitigate the biomechanical problems that females confront."
and:
"The evidence for lumbar sexual dimorphism in humans which improves maternal performance in posture and locomotion suggests that the distinctive hominin lumbar curve has been subject to strong selection pressures."

To illustrate how these words are paradigm-driven, they have been rewritten below from a design perspective:

"Given the demands of fetal load and the importance of pregnancy for fitness, one predicts that design modifications have been made to the unique anatomy of the hominin lumbar region to mitigate the biomechanical problems that females confront."
and:
"The evidence for lumbar sexual dimorphism in humans which improves maternal performance in posture and locomotion suggests that the distinctive hominin lumbar curve is the result of intelligent design engineering."

As a result of the authors presupposing a Darwinian adaptationist story, they feel no need for rigour in defending their interpretation of the data. They comment:

"It is reasonable to hypothesize that fatigue and pain in the lower back muscle affected early hominin mothers just as they do modern mothers, possibly limiting foraging efficiency and the ability to escape from predators, leaving the gravid female at risk of nutritional stress and injury or death."

There is no attempt here to move beyond storytelling, no assessment of what a coherent Darwinian explanation should look like, and no consideration of behavioural modifications that might be adopted as an alternative to normal practice. The reviewers of the paper should have objected to the phrase "It is reasonable . . ." because it is not. When all the other morphological and hormonal changes in pregnancy are taken into account, the inference to design remains compelling.

Fetal load and the evolution of lumbar lordosis in bipedal hominins
Katherine K. Whitcome, Liza J. Shapiro & Daniel E. Lieberman
Nature 450, 1075-1078 (13 December 2007) | doi:10.1038/nature06342

As predicted by Darwin, bipedal posture and locomotion are key distinguishing features of the earliest known hominins. Hominin axial skeletons show many derived adaptations for bipedalism, including an elongated lumbar region, both in the number of vertebrae and their lengths, as well as a marked posterior concavity of wedged lumbar vertebrae, known as a lordosis. The lordosis stabilizes the upper body over the lower limbs in bipeds by positioning the trunk's centre of mass (COM) above the hips. However, bipedalism poses a unique challenge to pregnant females because the changing body shape and the extra mass associated with pregnancy shift the trunk's COM anterior to the hips. Here we show that human females have evolved a derived curvature and reinforcement of the lumbar vertebrae to compensate for this bipedal obstetric load. Similarly dimorphic morphologies in fossil vertebrae of Australopithecus suggest that this adaptation to fetal load preceded the evolution of Homo.

See also:

Quill, E. Keeping Mom in a Full, Upright Position, ScienceNOW Daily News, 12 December 2007

Coppedge, D. Walking Upright Is Not Just for Pregnant Females, Creation-Evolution Headlines (12/13/2007)

Sandeman-Allen, C. Question of balance, The Times (Letter, 14 December 2007)

"Science develops too fast for morality" is described by Mary Warnock as the cliche of the 20th Century. But this cannot be correct. Morality is concerned with how we use science and where we should be putting our efforts in research. At best, the cliche can be understood to mean that scientific research throws up novel issues for consideration, but this is to make a different (and non-controversial) point. At worst, it implies that morality should be understood as an inherently subjective framework for the guidance of human conduct.
The Committee of Enquiry into Human Fertilization and Embryology was set up by the UK Government to provide advice prior to legislation relating to in vitro fertilization (IVF). Morality is concerned with what we ought to do, but it is significant that the Committee focused on legislation without making any statements about the moral obligations of researchers.

"We were not a group of 'moral experts', with particular moral authority derived from our expertise. Rather, our entitlement to propose legislation derived from the fact that we had been set up by government and that we had been given the time and resources to do so. The only other requirement was that we should all be capable of formulating and listening to arguments."

Ever since the possibility of IVF emerged in the 1970s, there have been calls for a public debate about the ethical and moral implications. Some groups with a clear moral agenda contributed to this debate, but their representations were regarded as partisan. Warnock refers to the Roman Catholic Church and its opposition to the destruction of human embryos in research. The RC Church based this view on its understanding of the sanctity of human life from its beginning. The response of the Committee was significant:

"The Church claimed a right to regulate science in this area, because of its superior knowledge of morality. In sharp contrast, the committee's entitlement to issue moral advice to ministers derived from its having been set up to do so, and from its having a wide and non-partisan membership."

The Committee recognised that claims about the sanctity of human life and the status of the human embryo presuppose an authority. This is what delivers the 'ought' to morality. Where did the Committee find its authority? Not in any metaphysical foundations, but in the warrant they had from the UK Government to give advice. Thus, their authority has been socially constructed. Their approach is tacit acknowledgement that morality per se cannot be an outworking of the scientific method.
How did Warnock's team address the crucial question of the status of the human embryo?

"One of the most difficult tasks the committee faced was to get parliament to understand that the status of the embryo in vitro was a matter not of science but of moral decision. The novelty of the embryo in vitro meant that there could be no appeal to precedent or existing moral convention or to religious laws."

What is missing here is the acknowledgement that, biologically, the single-celled embryo is a human being at its earliest stage of development. This should be a point of agreement by all who contribute to this debate, and it is worth highlighting at the outset. The status of the embryo was considered by the Committee to be a matter of "moral decision", and a decision that Society must take through its elected representatives (and those it delegates to consider the issues). "Occasionally . . . those at the interface between science and politics are called on to define moral standards for society". Thus Parliament becomes the source of moral authority - the will of government prevails.
From the above comments, it is clear that all the characteristics of postmodernism are present in the way the Committee has handled its business. The moral obligation is socially constructed through the elected representatives and quangos. Moral decisions are made by those in positions of power on behalf of the community they govern. These decisions are ultimately subjective and they could change with the social context. Appeals to external authority may be admitted to public discourse but they are quickly dismissed as "partisan" and a matter of "private morality". Determining public morality is the business of Society and Government, not God as Law-Giver.
Curiously, one element of positivistic science has crept into this essay. The description of the Committee as having a "non-partisan membership" is one that relates closely to the concept of the researcher as an impartial, objective observer of the world. However, this is a complete delusion! No one is non-partisan on issues of ethics and morality. Everyone has an agenda that they bring to the discussion.
What we have here is a vivid demonstration of the fragmentation of knowledge and research philosophy within materialistic science. Humans, with our sense of 'ought' and 'duty', just do not fit into the materialistic worldview. The problems identified by the Romanticists of the 18th Century are still with us! Materialists today seeking to address the embryo research issue have found it necessary to adopt the mindset of postmodernism. They have tacitly acknowledged that no answers will emerge from within science. They have accepted that our rulers have authority to determine public morality. History suggests that this is a dangerous strategy. We need leaders who know themselves to be accountable to a higher authority. We need an underlying epistemology of knowledge that unifies the public and private arenas of life, and integrates the natural and the social sciences.

The ethical regulation of science
Mary Warnock
Nature 450, 615 (29 November 2007) | doi:10.1038/450615a

Abstract: Occasionally science makes procedures possible that are so radical that those at the interface between science and politics are called on to define moral standards for society.

In his book Insectivorous plants, Charles Darwin wrote of Dionaea muscipula: "This plant, commonly called Venus' fly-trap, from the rapidity and force of its movements, is one of the most wonderful in the world" and that it "is one of the most beautifully adapted plants in the vegetable kingdom". The trap closure mechanism is activated by the mechanical stimulation of triggers hairs on the leaf surface, although the details are not understood as well as we would like. Research into post-stimulation mechanical closure has been published in various places by Forterre et al (2005), showing that "snap-buckling instability" is the key. The leaf surface snaps from a concave curvature to a convex with 60% of the displacement occurring in 1/10 second. The researchers write: "by squeezing the leaves with our fingers we were able to induce a snap transition mechanically, indicating that the leaf was indeed in a bistable configuration."
This biological example of a process leading to rapid movement has inspired others to achieve biomimetic goals. Holmes and Crosby report on their research as follows:

"This snap-transition is due to the onset of an elastic, snap-through instability similar to the capture mechanism of the Venus flytrap. The response rates can be over two orders of magnitude faster than the typical response of shape-memory polymers, and the sensitivity and rate of the response can be tuned with predictable geometric and/or material property changes. Based on materials choice, a wide variety of external stimuli can trigger this stress development, such as temperature, pH, solvent swelling, magnetism, electric current, and light. This strategy has great potential for the design of responsive surfaces, which will impact a variety of applications including: release-on-command coatings and adhesives, on-command frictional changes, instant modification of optical properties at an interface, rapid response drug delivery, chemical sensing, and antimicrobial devices."

The concluding comment from Forterre et al was this:

"This ingenious solution to the problem of scaling up movements and speed from the cellular to the organ level in plants, nature's consummate hydraulic engineers, shows how controlling elastic instabilities in geometrically slender objects provides an alternative to the more common muscle-powered movements in animals."

The use of anthropomorphic language by researchers is typical whenever systems that exhibit exquisite design are being studied: this "ingenious solution" and plants as "nature's consummate hydraulic engineers". Our scientific culture precludes any reference to evidence for the handiwork of an intelligent designer. It is always worth remembering that the pioneers of biological research, including John Ray the botanist, had no inhibitions about attributing such evidences of design to a Person rather than an impersonal process.
It should not escape the attention of readers that the Venus Flytrap has all the elements of a mouse trap: the mechanical closure system involving snap-through instability, the activation mechanism resulting from the stimulation of triggers hairs by insects, the requirement for very rapid closure if the device is to be successful at all, and so on. Added to which, this trap opens again automatically, has a built-in digestion system and more. Take away any of these elements, and the mechanism ceases to perform any useful function. One day, this "most wonderful" plant may be written up as an IC system, refuting Darwin's claim that it is a product of adaptation.

Snapping Surfaces
D. P. Holmes, A. J. Crosby
Advanced Materials, November 2007, 19(21), 3589-3593 | DOI: 10.1002/adma.200700584

First paragraph: The responsive mechanism of the Venus flytrap has captured the interest of scientists for centuries. Although a complete understanding of the mechanism controlling the Venus flytrap movement has yet to be determined, a recent publication by Forterre et al.[1] demonstrates the importance of geometry and material properties for this fast, stimuli-responsive movement. Specifically, the movement is attributed to a snap-through elastic instability whose sensitivity is dictated by the length scale, geometry, and materials properties of the features.[2] Here, we use lessons from the Venus flytrap to design surfaces that dynamically modify their topography. We present a simple, robust, biomimetic responsive surface based on an array of microlens shells that snap from one curvature (e.g., concave) to another curvature (e.g., convex) (Fig. 1) when a critical stress develops in the shell structure. This snap-transition is due to the onset of an elastic, snap-through instability similar to the capture to the capture mechanism of the Venus flytrap.

See also:

Forterre Y, Skotheim JM, Dumais J, Mahadevan L., How the Venus flytrap snaps, Nature 2005, 433, 421-425.

Narayan, A.L., Venus flytrap inspires adaptive optics, PhysicsWorld.com, 4 December 2007

Mary Midgley is a respected (retired) philosopher who has made some significant contributions to thinking about science. We owe a debt of gratitude to her for explaining that, for some people, evolutionary thinking has become a religious movement. This is the take-home message of her books: Evolution as Religion and Science as Salvation. Earlier this year, she spoke at Durham University on Intelligent Design Theory, and the substance of her talk has now appeared in the current issue of Philosophy Now. She says of ID that "considered as science it is apparently vacuous" - which is not a good start. However, some of the issues in her essay are useful to discuss further.

There are significant problems with the way Midgley perceives ID. Here are some examples: ID "claims to provide a scientific rationale for Creationism"; ID's "central point is that living things are so 'irreducibly complex' that they cannot have evolved gradually by natural selection"; ID "tries to reactivate the old idea of a stark epistemological cold war, a contest for dominance between science and religion." If it is not obvious why these statements are caricatures, please read on. It is worth prefacing my comments with the note that these misrepresentations are all found in the literature of those who oppose ID as anti-science.

First, ID does not claim to provide a scientific rationale for Creationism. It does claim that science needs ID methodologies in order to avoid pre-empting the outcomes of research questions. Science incorporating ID concepts is science as it should be! If researchers do not have the tools for recognising design, how could anyone know if this world and living things were designed or not? What we have today are large numbers of atheists who are using science to justify their atheism and claiming that design inferences are out-of-bounds. However, science should be interested in truth, and if the possibility is granted that intelligent agency could be involved in origins, then we have to consider ways of researching that question within science. This is not about proving creationism but about being open to evidence, wherever it leads.

Second, what is ID's central point? Fundamentally, it concerns the legitimacy of making design inferences within science. This is the thrust of Bill Dembski's research, and Phillip Johnson has championed this message in his numerous books. Irreducible complexity has emerged as a critical issue because of Michael Behe's opening of Darwin's Black Box. But IC is a special case of Complex Specified Information, which is what Dembski works with. Furthermore, Behe's new book has little about IC, not because the argument is lacking in any way, but because Behe sets out to show that the empirical data (about mutations and natural selection) reveals that Darwinian mechanisms are totally incapable of building CSI.

Thirdly, what about this "old idea" of an "epistemological cold war, a contest for dominance between science and religion"? It is fair to say that there are serious issues for epistemology - but we are not dealing with an old idea. The contest is about the nature of science itself. It is about metaphysics: naturalistic science and theistic science. It is about philosophy: methodological materialism and methodological realism. The issues are highlighted in two sentences from Midgley's essay:

"Sensible students have therefore increasingly agreed with the great evolutionist Theodosius Dobzhansky that science and religion cannot clash because their functions are different. Science, said Dobzhansky, deals in facts, while religion deals in meaning."

The first sentence reveals that Midgley has adopted the NOMA principle championed by Stephen Jay Gould. The basic idea is that science and religion occupy different domains and cannot clash - by definition. But this understanding of the issues is contrived and it only works if religion is excluded from having anything to do with history (including origins) and knowledge (objective truth). There are obvious clashes here with Christianity, which is rooted in history and which is concerned with universal truths. The second sentence promotes the fact/value distinction, associated with the Enlightenment philosopher David Hume. This again is a pre-emptive epistemological strike, because there are many aspects of Christianity that are of a factual nature but are rejected as facts by atheists and sceptics. For more on this, go here.
At the end of her essay, Midgley writes: "Unless something like this can be done, it seems to me that ID is going to give us a great deal of trouble." She asks for people to seek out better ways of interacting on these issues. As a first step, I would advise that we recognise that there is a real struggle concerning the the nature of science. It is not the tired old battle of 'science versus religion'. The new concern is whether science is open to truth, wherever it leads or whether science should insist that every effect must have a natural cause. The contrast today is between the integration of all knowledge and the perpetual compartmentalisation of cognitive activity. ID is not the troubler of science! That dubious honour belongs to the advocates of philosophical materialism who have usurped science as a tool to further their own agendas.

A Plague On Both Their Houses
Mary Midgley
Philosophy Now, Nov/Dec 2007, No.64.

Abstract: Mary Midgley thinks creationists and evolutionists need to overcome the bewitchment of their own thinking and learn how to talk to each other.

See also:

Gene, M., Midgley Misfires, (Dec 1 2007)

Jigsaw buffs will enjoy the "Pore Puzzle" essay by Aitchison and Wozniak cited below. How do we approach the challenge of putting together a 1,000 piece picture?

"We solve the puzzle by considering each piece and ruling out those that don't fit physical restraints, such as colour patterns, the overall shape of the picture and the potential for interlocking. This is the basic premise for the multidisciplinary approach taken by Alber et al. to solve the structure of a large molecular machine, the yeast nuclear pore complex. But, in their case, the pieces were proteins, the various restraints were of a biochemical and morphological nature, and computers explored the placement of each protein into a single ensemble solution."

Within the cell, many thousands of different molecules are produced to accomplish the various tasks that need to be done. The nuclear envelope sets up a special environment within the cell. The enabling mechanism is the nuclear pore complex (NPC) which regulates the movement of molecules into and out of the nucleus. It is the architecture of this complex that has now been published for the first time. By all accounts, the authors' achievement is remarkable.
It is not surprising that striking patterns emerge in the detailed structure of the complex. However, the authors use this to suggest that their work provides pointers to an evolutionary origin from an ancestral structure. The relevant paragraph comes in their concluding remarks:

"Although the NPC is a complex structure, our analysis reveals underlying simplicities in its architecture. At its heart, the NPC contains a highly connected scaffold that attaches to and coats the curved pore membrane. The fold composition of the nucleoporins forming the scaffold is remarkably simple, consisting of only two different domain folds, the configurations of which resemble those found in vesicle-coating complexes - to which the NPC may therefore be evolutionarily related. [. . .] thus, the NPC is another example of how a complicated structure can evolve from the duplication, divergence and elaboration of simple ancestral modules."

This paragraph reveals one of the fundamental premises of Darwinism: as we come to understand the inner workings of organisms, things are supposed to get simpler. This simplicity then allows step-by-step transformation. Darwinists look for underlying simplicity - and let us know whenever they find it! Simplicity, however, can also be a design feature - particularly when NPCs have to be manufactured quickly by the cell every time it divides. Everyone involved with new product development knows that "simplification" is one of the keywords describing their (intelligent) activities. Having said this, it should be noted that the authors are referring only to structural simplification: the arrangement of the component parts. The real complexity of the NPC is to be found in the regulation work it has to do. This is where the information content of the NPC goes off scale! A biologist commented on this as follows:

The claim of underlying simplicity "ignores the chaperones and gatekeepers that are involved in the transport process. It ignores that there is one way and two way trafficking through the pore. Just the idea that the pore can discriminate between different nucleic acids, (which includes many different size heterogeneous RNAs, mRNA, primary transcript RNA and DNA), which are very similar suggests a certain basal level of complexity. In light of this, this pore in my estimation could be one of the most complex in the cell!"

The authors can be credited with some excellent science, but they have spoilt it by some parting comments about the evolution of the NPC that can only be described as speculative. Far better is to propose testable hypotheses. If the Darwinian approach is valid, further research will reveal further evidences of underlying simplicity relating to the information processing capabilities of the structure. Conversely, if further research reinforces complexity, the Darwinian paradigm should be discarded as unproductive. There is already enough evidence in the NPC to infer design, and the "underlying simplicity" of the structure communicates "evolution" only to those who are predisposed to receive it.

The molecular architecture of the nuclear pore complex
Frank Alber, Svetlana Dokudovskaya, Liesbeth M. Veenhoff, Wenzhu Zhang, Julia Kipper, Damien Devos, Adisetyantari Suprapto, Orit Karni-Schmidt, Rosemary Williams, Brian T. Chait, Andrej Sali & Michael P. Rout.
Nature 450, 695-701 (29 November 2007) | doi:10.1038/nature06405

Abstract: Nuclear pore complexes (NPCs) are proteinaceous assemblies of approximately 50 MDa that selectively transport cargoes across the nuclear envelope. To determine the molecular architecture of the yeast NPC, we collected a diverse set of biophysical and proteomic data, and developed a method for using these data to localize the NPC's 456 constituent proteins (see the accompanying paper). Our structure reveals that half of the NPC is made up of a core scaffold, which is structurally analogous to vesicle-coating complexes. This scaffold forms an interlaced network that coats the entire curved surface of the nuclear envelope membrane within which the NPC is embedded. The selective barrier for transport is formed by large numbers of proteins with disordered regions that line the inner face of the scaffold. The NPC consists of only a few structural modules that resemble each other in terms of the configuration of their homologous constituents, the most striking of these being a 16-fold repetition of 'columns'. These findings provide clues to the evolutionary origins of the NPC.

Pore puzzle
John D. Aitchison & Richard W. Wozniak
Nature 450, 621 (29 November 2007) | doi:10.1038/450621a

Abstract: Where would you start in trying to work out the structure of a macromolecular machine consisting of 456 proteins? Taking a combined experimental and computational approach is one answer.

In a report of a scientific meeting, Stokstad drew attention to the characters of the duck-billed platypus that baffled researchers at the end of the 18th Century. He went on: "Modern researchers have uncovered other implausible features, including 40,000 tiny glands in the broad bill that sense electric currents, which may help the platypus catch prey underwater." Nevertheless, the platypus has never quite escaped being regarded as primitive from an evolutionary perspective. Earlier this year, ARN's Denyse O'Leary asked these questions:

"Primitive? Most highly evolved? Or just different? A question that lurks just below the surface (and will likely stay there a long time) is, how much time was required for the evolution of this unique electrolocation sense? How likely is it to have been random?"

It is now possible to say more about the time question. The surprise is that there is evidence for this complex structure from the Early Cretaceous.

"A reanalysis of fossil jaws from Australia, reported at the meeting, suggests it belonged to a platypus that lived at least 112 million years ago. "It's really, really old for a monotreme," Timothy Rowe of the University of Texas (UT), Austin, told the audience."

Rowe is a palaeontologist who runs a computed tomography-scanning facility at UT Austin.

"Scans of three specimens revealed a large internal canal along the entire length of the jaw, like the canal in a modern platypus that carries nerve fibers from the electrosensory glands in the bill to the brain. "There's no other mammal that has a canal this size," Rowe said. Even back in the early Cretaceous, it seems, the platypus was using electrosensation."

Stokstad points out that the age of the fossil is "much older than current estimates from DNA of when platypuses and echidnas diverged from their most recent common ancestor. Molecular clocks put that date somewhere between 17 million and 80 million years ago." However, palaeontologists have grown used to mismatches like this and do not give too much weight to the figures emerging from molecular clocks. What this does show is that there are extreme constraints on time for any evolutionary story of the origin of platypuses and their electrolocation device. We appear to have a situation where intelligent design is demanded by the evidence of short timescales and the complexity of the "implausible" electrosensory system.

Jaw Shows Platypus Goes Way Back
Erik Stokstad
Science 318, 23 November 2007: 1237.

When scientists first laid eyes on the duckbilled platypus and the echidnas in the late 18th century, they were so baffled by these bizarre egg-laying mammals that some considered the specimens a hoax. Modern researchers have uncovered other implausible features, including 40,000 tiny glands in the broad bill that sense electric currents, which may help the platypus catch prey underwater. [snip]

An insect in Burmese amber, found within Cretaceous strata, has a "body structure and wing venation nearly identical to those of the recent Compsocidae". There are only two extant species, and both of these live in Central America. The authors say: "The small family Compsocidae has been unknown in the fossil record hitherto" and "the discovery of this group in the Late Albian Burmese amber is of great interest for its age and biogeography."
Findings like this serve to remind us that stasis is a distinctive feature of the fossil record and we have to do justice to this in our thinking about origins.
For earlier comments along these lines, go here and here and here.

The first fossil Compsocidae from Cretaceous Burmese amber (Insecta, Psocoptera, Troctomorpha)
A. Nel and A. Waller
Cretaceous Research, Volume 28, Issue 6, December 2007, Pages 1039-1041

Abstract: The first fossil record of the Compsocidae, Burmacompsocus perreaui gen. et sp. nov., is described from Late Albian Burmese amber. Its strong similarity to the two extant compsocid genera suggests a remarkable morphological stability within this group of 100 Ma. This family, now known only in Central America, was certainly more widespread in the past.

According to a recent study, there is "evidence for a basic human preference to understand the world in terms of purpose. When faced with an object that supports a plausible function, humans make an immediate but defeasible inference to design, and assume a teleological explanation is warranted."
The authors advance a model of human cognition that starts with "promiscuous teleology" in children, develops with the retreat of teleology resulting from "causal beliefs typically acquired through formal education", but sometimes advancing again with the onset of senility and the impairment of the causal belief system. Thus, teleological explanations are presented as "compelling and pervasive because they reflect an explanatory default."
To support this conceptual model, the authors (psychologists) constructed 10 "why" questions, each with a mechanistic answer and a teleological answer. The 41 participants in the study (including 17 Alzheimer's patients) were asked first about "acceptance" of the various answers, second about their "preferred" answer, and third they were asked to complete a "causal-beliefs task".
As part of their analytical framework, the authors introduced a categorisation of responses received: "warranted items, those that typically warrant teleological explanations (artifacts, biological traits), and unwarranted items, those that typically do not (biological organisms, nonliving natural objects, natural phenomena)". The word "unwarranted" raises many issues with me, because many of us have made design inferences about biological organisms (based on complex specified information), about nonliving natural objects (for example, water), and about natural phenomenon (such as the fine tuning of fundamental constants). Whilst these inferences go far beyond the questions asked of the participants, I cannot help thinking that the chosen analytical methodology has provided an opportunity for bias to be introduced to this research (for more on this, go here). However, based on the questions asked, the authors found that the Alzheimer's patients scored higher on teleological explanations than their healthy peers, suggesting the conclusion outlined above.
A surprise comes with the causal-beliefs tasks. About 66% of the participants identified an impersonal process as the causal agent for "unwarranted" items. The rest mostly invoked God. "But does the tendency to infer design also require an inference to a designer? The current results suggest not." Whatever the authors are measuring (and that is debateable), their work does not endorse the idea that people always see purpose and meaning from within a framework of Theism. An alternative hypothesis is that the reported perceptions involve an anthropocentric view of the world, with 'self' at the centre. This is, of course, a big contrast to Theism, where meaning and purpose is found only in relation to God.
On the positive side, this study could help promote a meaningful debate about what constitutes a legitimate design inference: "Inferring the appropriateness of a teleological explanation from an apparent function, which we call the inference to design, is often quite reasonable." What is needed here is not a pre-emptive judgment about what is warranted design and what is unwarranted, but a recognition that design inferences are evidence-based and probabilistic.
On the negative side, the authors make some wild extrapolations of their thesis to debates about origins. "Finally, the appeal of intelligent-design creationism, ultra-adaptationism in evolutionary biology, and widespread misunderstanding of evolution as a goal-directed process provide further evidence of the human tendency to view the world in terms of design." Space does not permit discussion here of ultra-adaptationism or evolution as a goal-directed process. But to interpret either ID or creationism as psychological phenomena, and in particular argue the persistence of teleology because advocates have not imbibed the "causal beliefs" that education supplies, is a travesty. The discussion of these issues has to be first about the interpretation of evidences. Both ID and creationism are interested in making truth claims, and people who do not understand this rule themselves out of meaningful debate. There are certainly psychological issues (and cultural issues) to address. The authors might make better use of their time by considering how the "Blind Watchmaker" version of evolutionary theory makes people blind to the significance of basic facts (like the evidence for profound limits to variation and the evidences for design in living things based on complex specified information).

Inferring Design
Tania Lombrozo, Deborah Kelemen, and Deborah Zaitchik
Psychological Science, 18 (11) 2007, 999-1006

ABSTRACT: Unlike educated adults, young children demonstrate a "promiscuous" tendency to explain objects and phenomena by reference to functions, endorsing what are called teleological explanations. This tendency becomes more selective as children acquire increasingly coherent beliefs about causal mechanisms, but it is unknown whether a widespread preference for teleology is ever truly outgrown. The study reported here investigated this question by examining explanatory judgments in patients with Alzheimer's disease (AD), whose dementia affects the rich causal beliefs adults typically consult in evaluating explanations. The results indicate that unlike healthy adults, AD patients systematically and promiscuously prefer teleological explanations, suggesting that an underlying tendency to construe the world in terms of functions persists throughout life. This finding has broad relevance not only to understanding conceptual impairments in AD, but also to theories of development, learning, and conceptual change. Moreover, this finding sheds light on the intuitive appeal of creationism.

The journal Trends in Ecology and Evolution, normally a good source of stimulating and thought-provoking articles, has decided to carry a review by Nicholas Matzke of Behe's The Edge of Evolution. The tone of the review is one of exasperation - as though Matzke finds it incomprehensible that anyone could be so dumb as to write this book.
However, like so many other reviews, there are signs that the reviewer has not digested the key arguments of the book. Behe is looking at what the data is telling us about the mechanisms of mutation and natural selection that are so beloved by Darwinists. He first shows that our best data sets are all underlining the implausibility that these mechanisms have anything to do with constructing the elegant molecular machinery of cells. Compare this with Matzke's initial salvo: "Behe begins by trying to shore up his argument that 'irreducibly complex' multiprotein systems, such as flagella, are unevolvable." But Behe's comments on this come later in the book! (Furthermore, my reading of Behe is not that he says these structures are unevolvable, but they are unevolvable by Darwinism mechanisms).
Matzke does not like Behe's mutation-rate statistics at all. He claims: "The argument collapses at every step. Behe obtains the crucial 10^20 number from an offhand estimate in the literature that considered only the few CQR [chloroquine resistance] alleles that have been detected because they have taken over regional populations." The correct response to a statistical argument is to present better statistics, or to point to literature that sets out a more rigorous analysis. Matzke does not do this, but uses many words to reach the general conclusion that chloroquine resistance "is both more complex and vastly more probable than Behe thinks." There is no attempt to put some substance into these words. Behe has responded (here) with discussion of the studies identified by Matzke as significant and concluding: "the number for resistance events of 1 in 10^20 seems to be a very good approximation". In my view, Behe ought to have the right to reply to this review, because TREE readers are being presented with a contrived and contentious argument by Matzke.

In the latter part of Matzke's review, he claims: "It is clear that Behe is driven not by a truly scientific investigation, but instead by metaphysics." This is not impressive from a philosophy of science perspective, as metaphysics underpins all scientific investigation. You cannot have science without metaphysics! The important questions relate to the dynamic between them, and how the metaphysics constrains the science. It has long been a concern of the ID Movement that philosophical naturalism is putting blinkers on science: a metaphysical commitment to naturalism leads to a demarcationist agenda and ends up declaring what the world must be like. In particular, it rules out all possibility that intelligent design can have anything to do with nature. Consequently, there is little interest in how to make design inferences in science, and lots of interest in explaining highly improbable data in terms of unknowable multiverses. In my own review of Behe's book, I present him as the real empiricist, and the Darwinians as people governed by their particular dogma.

The edge of creationism
Review of: Michael J. Behe, The Edge of Evolution: The Search for the Limits of Darwinism
Nicholas J. Matzke
Trends in Ecology & Evolution, Volume 22, Issue 11, November 2007, Pages 566-567

First para: Michael Behe is the leading advocate of 'intelligent design' (ID), which has been on the ropes since the 2005 Kitzmiller v. Dover trial. There, Behe's effort to show that ID is science and not creationism failed [1], [2] and [3]. The Edge of Evolution is Behe's rather scattered comeback attempt. The title refers to his thesis: that is, that anything as complex as a three-protein complex is beyond the reach of random mutation aided by natural selection.

See also:

Michael Behe's Amazon Blog
Trends in Ecology and Evolution follows the trend, Part I (2 November 2007)
Trends in Ecology and Evolution follows the trend, Part 2 (5 November 2007)
Trends in Ecology and Evolution follows the trend, Part 3 (6 November 2007)

Whereas non-human primate females are fertile almost until the end of their lives, human females of about 50 years of age experience the menopause and go through the rest of their lives with no prospect of conceiving any more children. The authors of recent research into the subject explain that these differences have "prompted interest in the evolutionary factors that might explain menopause". It is known that genetic factors are at least partly responsible, and this "suggests the idea that selection may have acted to optimise the length of the fertile portion of the life cycle."
It should be noted that the link between genetic factors and selection is only possible because of the prior assumption of Darwinism. However, even allowing this, the genetic link cannot be said to "support" the idea of the menopause being a product of selection, because it may have been a spandrel effect of humans evolving from ape-like ancestors.
Explanatory concepts used to structure the research are as follows:

"The two major hypotheses to explain the evolution of menopause are based on (i) the extremely protracted dependency of human infants on protection and provisioning by adults, particularly the mother, and (ii) the opportunities for intergenerational cooperation within kin groups."

The option that the menopause points to design influences is not even considered by the authors. In fact, the two major hypotheses (above) identified by the authors to explain the evolution of menopause are equally relevant to design. This maintains that caring for dependants is a designed behaviour and that close relatives all have a part to play. Confirming the two hypotheses does not discriminate between a Darwinian explanation and a design explanation.
The authors develop a test of the two hypotheses using data from 4 villages in The Gambia and a theoretical model. They show that there is a fitness benefit of the menopause with an optimum at 50 years of age.

This paper warrants two comments:
1. Since there is a perfectly reasonable design rationale for caring grandmas having experienced the menopause, the findings can be used as a vindication of the two hypotheses but not as a vindication of the relevance of Darwinism.
2. No attempt has been made to give any account of the genetic/physiological and other changes that are needed for the menopause to occur. This is 'black box' biology, with natural selection being asked to do an amazing number of things in a short period of time to achieve the (relatively small) fitness benefits. It should be noted that genetic changes are not directly passed on to offspring, as in the normal portrayal of the way Darwinism works. We are dealing here with complex changes in females that marginally affect the survival of grandchildren. Additionally, one wonders how many caring grandmothers there actually were in the hypothetical social groups of early man where life expectancies were low.
"Testing hypotheses of menopause" would be a better title, leaving open the issue of causation and theoretical models. The Darwinian elements of this paper can be understood in terms of bias. The adoption of Darwinism to the exclusion of any other conceptual approach is an example of Availability Bias, and the way all the evidences are claimed to support the Darwinian thesis of the research is an example of Confirmation Bias. For more on bias in scholarship, go here.

Testing evolutionary theories of menopause
Daryl P. Shanley, Rebecca Sear, Ruth Mace, Thomas B.L. Kirkwood
Proceedings of the Royal Society B, 274, December 7 2007, 2943-2949 | doi: 10.1098/rspb.2007.1028

Abstract: Why do women cease fertility rather abruptly through menopause at an age well before generalized senescence renders child rearing biologically impossible? The two main evolutionary hypotheses are that menopause serves either (i) to protect mothers from rising age-specific maternal mortality risks, thereby protecting their highly dependent younger children from death if the mother dies or (ii) to provide post-reproductive grandmothers who enhance their inclusive fitness by helping to care and provide for their daughters' children. Recent theoretical work indicates that both factors together are necessary if menopause is to provide an evolutionary advantage. However, these ideas need to be tested using detailed data from actual human life histories lived under reasonably 'natural' conditions; for obvious reasons, such data are extremely scarce. We here describe a study based on a remarkably complete dataset from The Gambia. The data provided quantitative estimates for key parameters for the theoretical model, which were then used to assess the actual effects on fitness. Empirically based numerical analysis of this nature is essential if the enigma of menopause is to be explained satisfactorily in evolutionary terms. Our results point to the distinctive (and perhaps unique) role of menopause in human evolution and provide important support for the hypothesized evolutionary significance of grandmothers.

See also:

MacKenzie, D. Caring grandmas explain evolutionary role of menopause, New Scientist, 19 September 2007

Cohen, J. Menopause in Chimps? ScienceNOW Daily News, 13 December 2007

An exercise to document "conceptual uncertainty" in the interpretation of seismic images is deserving of wider discussion. Few readers of this blog will know anything about seismic sections, but the reported research addresses principles that are relevant to us all.
Seismic data can be used to provide 3D models of rocks and geological structures below the ground. Seismic imaging is a standard tool of petroleum geologists, but many other geoscientists find the technique invaluable. There is a major constraint: "All geological data sets are spatially limited and have limited resolution. Geoscientists who interpret such data sets must, therefore, rely upon their previous experience and apply a limited set of geological concepts." The researchers set out to understand more about the human factors involved in the process of interpretation. Geologically-alert readers can consult the original paper to read about the findings and their significance. We shall focus on more generic issues raised in the discussion section.
Three main sources of bias were identified in the participants (all of whom were geoscientists with some expertise with seismic sections, but with varying lengths of experience). It must be emphasised that "bias" has no connotations of unprofessional behaviour or unethical practice. It relates to identifiable influences on human judgment. The three categories are as follows.
1. Availability bias. This refers to the recent experiences of subjects, who tend to employ models that have contemporary application in their own thinking.
2. Anchoring bias. Subjects were reluctant to move away from an initial framing of the problem where the views of experts provided contextualisation and reassurance.
3. Confirmation bias. This "involves actively seeking out opinions and facts that support one's own beliefs or hypotheses" (that is, the reverse of pursuing falsification).

These three types of bias were not at all rare. "Examples of bias based on dominant tectonic setting expertise can be found at all levels of experience. Individual participants with 15+ years experience anecdotally show evidence of availability and anchoring bias in the same way students do." "Many" participants were considered to exhibit confirmation bias.
Why is this relevant? It is because these geoscientists are representative of the scientific community as a whole, wherever human judgment/interpretation is involved in their work. Many of the issues aired in this blog relate to popular biological models (genetic reductionism, common ancestry, Darwinism, etc) that involve the interpretation of data and which can be favoured because of availability bias. The influence of opinion formers often goes far beyond the content of their words. This is anchoring bias. And the tendency to seek out support for one's personal views (rather than challenge them) is widespread (perhaps exemplified in the way Darwinists indulge in imaginative story-telling). This is confirmation bias.
There's plenty of "conceptual uncertainty" in all matters relating to origins. It would be healthy if some researchers could do for the biological community what the seismic modeling team has done for geoscience.

What do you think this is? "Conceptual uncertainty" in geoscience interpretation
C.E. Bond, A.D. Gibbs, Z.K. Shipton, S. Jones
GSA Today, 17(11), (November 2007), 4-10 . DOI: 10.1130/GSAT01711A.1

Interpretations of seismic images are used to analyze sub-surface geology and form the basis for many exploration and extraction decisions, but the uncertainty that arises from human bias in seismic data interpretation has not previously been quantified. [. . .] We have documented the range of interpretations to a single data set, and in doing so have quantified the "conceptual uncertainty" inherent in seismic interpretation. In this experiment, 412 interpretations of a synthetic seismic image were analyzed. Only 21% of the participants interpreted the "correct" tectonic setting of the original model, and only 23% highlighted the three main fault strands in the image. [. . .] [O]ur results demonstrate that conceptual uncertainty has a critical influence on resource exploration and other areas of geoscience. Practices should be developed to minimize the effects of conceptual uncertainty, and it should be accounted for in risk analysis.

Evidence showing the limitations of genetic reductionism continues to be published. The latest involves the development of the mammalian heart. Using the mouse as a model system, the researchers noted that the early stage heart reveals symmetrical development of the branchial arch arteries. In the space of just one day, these arch arteries are remodelled so that blood flows predominantly through the left arch arteries. Previous work had identified the likely role of a transcription factor Pitx2 and a signalling molecule Nodal, but "the overall mechanisms - or genetic pathways - that govern asymmetric development of the artery arches remained elusive."
Apparently, evidence has been accumulating "to suggest that the mechanical force created by blood flow affects gene expression in the developing embryo" and it is this hypothesis that has stimulated the reported research. In essence, (1) the transcription factor Pitx2 induces morphological change to the outflow tract of the heart, (2) the blood flow becomes asymmetric, (3) the uneven blood flow triggers a signalling response - (4) resulting in the asymmetric remodelling of the great arteries.
This cascade of cause and effect involves a remarkable collaboration between genetics and haemodynamics. According to the accompanying News & Views essay, the researchers' results "provide a useful model for converting physical forces into genetic information - that is, the maintenance by haemodynamics of the expression of vessel-stabilization factors that shape the asymmetrical cardiovascular system of mammals."
As is often the case when faced with complex specified systems like this, academic writers resort to anthropomorphic language. Nature is portrayed as the creator and even the artist:

"Compared with the masterpiece crafted by nature, even Leonardo da Vinci's anatomical drawings of the cardiovascular system seem primitive. In creating this system, nature seems to use blood flow as its paintbrush."

These writers are recognising that there is a richness before them that needs expression. It is a richness that they know cannot be captured by talking about evolutionary "tinkering" (which is what their naturalistic evolutionary worldview demands). What they need is a worldview that allows design to be the product of an intelligent agent. They need to allow the paintbrush to be held by a real artist. This is what Intelligent Design offers.

Haemodynamics determined by a genetic programme govern asymmetric development of the aortic arch
Kenta Yashiro, Hidetaka Shiratori & Hiroshi Hamada
Nature 450, 285-288 (8 November 2007) | doi:10.1038/nature06254

Abstract: [. . .] The cellular and molecular bases of asymmetric morphogenesis remain largely unknown, however. Here we show that ablation of unilateral Pitx2 expression in mice impairs asymmetric remodelling of the branchial arch artery (BAA) system, resulting in randomized laterality of the aortic arch. Pitx2-positive cells were found not to contribute to asymmetrically remodelled arteries. Instead, Pitx2 functions in the secondary heart field5 and induces a dynamic morphological change in the outflow tract of the heart, which results in the provision of an asymmetric blood supply to the sixth BAA. This uneven distribution of blood flow results in differential signalling by both the platelet-derived growth factor receptor and vascular endothelial growth factor receptor 2. The consequent stabilization of the left sixth BAA and regression of its right counterpart underlie left-sided formation of the aortic arch. Our results therefore indicate that haemodynamics, generated by a Pitx2-induced morphological change in the outflow tract, is responsible for the asymmetric remodelling of the great arteries.

See also:

Snider, P. & Conway, S.J. The power of blood, Nature 450, 180-181 (8 November 2007) | doi:10.1038/450180a

The past week has seen two cases of atheists flexing their ideological muscles in science journals. The first, in Current Biology, is a news report that is effectively a propaganda piece for Richard Dawkins.

"Britain's champion atheist, Richard Dawkins, is spearheading a campaign to challenge the dominance of religion in everyday life and in politics, insisting that the atheists deserve to be heard too. Atheists in the US "have been downtrodden for a very long time. So I think some sort of political organisation is what they need," he says. Religion is noticeable in US schools, places of work and public institutions in a way that would seem inappropriate in countries like the UK."

There are many aspects of this piece that make it unfit to be published in a science journal, not the least of which is the presumption that Dawkins' crusade will be welcomed by scientists. I will comment on just one other point: atheists are not a downtrodden group. Since the Enlightenment, it has been customary to distinguish sharply between "facts" and "values", with science grabbing the domain of facts, leaving the values to individuals: our very personal and private views. As a result, the intelligentsia has developed (in the US and the UK) within a framework of tacit atheism. Consequently, atheists feel perfectly at home within the intellectual milieu of these countries, and it is Christians who are hounded if they say anything in public forums that implies accountability to God or ethical/moral principles that relate to humanity as a whole (rather than expressing a personal conviction). The fact/value split (also known as the faith/knowledge dichotomy) is not just Enlightenment epistemology, it has become a major strategy for demarcating science and maintaining power - see Johnson's 1995 review (below).

The other case of atheist flag-waving is in a book review in today's Nature. Adam Rutherford, who is podcast producer for Nature, contributes an over-enthusiastic review of the PBS/NOVA documentary: Judgment Day: Intelligent Design on Trial. This is yet another telling of the story of the "Intelligent Design" trial in Dover, Pennsylvania, in 2005. Rutherford's battle cry on 18 June 2007 was "I call upon atheists everywhere to stand up and be counted." He wanted his readers to know he is a humanist and a Darwinian. This is a reviewer who needs to be very careful not to allow his ideology to spoil his judgment. Unfortunately, he fails badly. The review is full of smears and innuendo. Here is a sampling: ID is a "pseudo-intellectual fundamentalist fig-leaf"; "one feels almost sorry for the intelligent-design team, they're so inept"; "its champions take comments from scientists out of context and even lied under oath"; the trial "marked the official neutering of this unpleasant, sneaky movement". He wants sensible people to "use science and reason to combat fundamentalism." Unfortunately, his review uses neither science nor reason to counter the influence of Intelligent Design and it is very regrettable that the editors of Nature have allowed this example of ideological invective to be printed.

Since the documentary is soon to be released, it would be advisable for viewers to check out an ID website www.intelligentdesign.org that is designed to be a portal for people to learn about ID as well as responses to the Judgment Day documentary. A short Youtube video gives the gist of how the program is perceived.

Call to atheists
Nigel Williams
Current Biology, Vol 17, R899-R900, 06 November 2007

Summary: Britain's most plangent critic of religion has set up a new campaign to support atheists, particularly in the US. Nigel Williams reports.

Dover trial documentary screens
Adam Rutherford
Nature, 450, 170 (8 November 2007) | doi:10.1038/450170a

EXHIBIT REVIEWED-Judgment Day: Intelligent Design on Trial, produced by NOVA & Vulcan Productions for PBS, broadcast on 13 November on PBS

See also:

Johnson, P.E. The Soul of the American University, First Things (March 1995).

Excerpt: The crucial issue in the universities [. . .] is the faith/knowledge dichotomy. From a scientific point of view, "knowledge" is inherently empirical, coming from sense experience and scientific investigation. This is the legacy of positivism, a philosophy that achieved its culminating triumph in the Darwinian theory of evolution. In modern universities professors take for granted that the universe began with something like particles in mindless motion governed by impersonal laws, and that everything that has appeared since is the product of a purely naturalistic process of physical, chemical, and biological evolution. "Everything that has appeared since" includes things like human religious and ethical beliefs, which are themselves presumed to be products of things like brain chemistry and natural selection. The worldview of scientific naturalism preserves a place for religious beliefs: a place, that is, among the things to be explained by scientific methodology. [. . .] All efforts to assert Christianity in the university ended in futility because of the inability or unwillingness of the Christians to challenge naturalism's monopoly over the production of knowledge.

It is becoming increasingly apparent that evolutionists do not like being quoted by those who like something they have written but who do not share their evolutionary perspective on origins. The cry "out of context" is regularly heard, although rarely does this mean more than "I did not write these words to support their position!"
A more radical reaction is to formally retract the words that have been quoted. This response appears in the current issue of American Scientist. In a letter to the Editors, former chemistry professor Homer Jacobson identifies two passages in a 1955 paper he wrote for that journal, explains why he no longer agrees with them, and concludes by saying why he is requesting the paragraphs to be retracted:

"Retraction this untimely is not normally undertaken, but in this case I request it because of continued irresponsible contemporary use by creationists who have quoted my not merely out-of-context, but incorrect, statements, to support their dubious viewpoint. I am deeply embarrassed to have been the originator of such misstatements, allowing bad science to have come into the purview of those who use it for anti-science ends."

It is of interest to look at the specific passages he is retracting. The first is:

On page 121: "Directions for the reproduction of plans, for energy and the extraction of parts from the current environment, for the growth sequence, and for the effector mechanisms translating instructions into growth - all had to be simultaneously present at that moment [of life's birth]."

Informed readers will recognise this immediately as a description of an irreducibly complex system. Writing in 1955, Jacobson did not have the terminology to call it IC, although he recognised the problem. He gives the reason for his retraction: "use of the requirement of simultaneity was a conjecture, unsupported by any proof. Separate developments of partial structures might well have occurred in an environment of randomly reacting molecules, eventually to join into one or more self-reproducing structures." Does it need to be said that these words are also conjectural! Saying something "might well have occurred" is hardly a substantial comment. He offers no supporting reasoning and effectively waves a magic wand. This retraction is a recognition that he had described an IC system (which we recognise today cannot form without intelligent agency). Since he does not accept intelligent agency, he must of necessity postulate a natural route for assembly of the system and deny that it is actually IC.
The second retraction also addresses an issue that is receiving much contemporary attention:

On page 125: "From the probability standpoint, the ordering of the present environment into a single amino acid molecule would be utterly improbable in all the time and space available for the origin of terrestrial life."

Jacobson explains that his probability calculation was flawed and adds: "Molecules of increased complexity have been found, however, when necessary components are available, with the aid of ambient energy from natural or experimental systems, e.g. electrical discharges, substantial temperature gradients or contiguous compounds or elements whose chemical reactions produce free energy. All of these could have existed under early Earth conditions, and thus this passage is completely inapplicable."
This response recalls the Miller-Urey experiments (which are currently regarded as peripheral by most OOL researchers). The element of conjecture is apparent here also, as Jacobson can only argue that the right conditions "could have existed under early Earth conditions". The empirical support for this is highly controversial. More generally, it is worth noting that evolutionists are very reluctant to calculate probabilities - because some regard it as very high (but we don't yet know the mechanism) whereas others regard it as very very low (but think it was a lucky chance anyway). Based on what we know, the probabilities are extraordinarily low, as Koonin has demonstrated. For more on this, go here.
Jacobson is perfectly entitled to make a retraction, but the issues are not going to go away. Jacobson may gain some personal satisfaction, but the challenge of IC systems remains and the improbability of chemical evolution appears insuperable. Far better for Jacobson and those who think like him to face up to these challenges and address the data as we know it (rather than indulge in fantasies about "might well have occurred" and what conditions "could have existed").

LETTER TO THE EDITORS
Homer Jacobson
American Scientist, November-December 2007

To the Editors: In January 1955, American Scientist published my article, "Information, Reproduction and the Origin of Life" (Vol. 43, No. 1). I ask you to honor my request to retract two brief passages, as follows: [snip]

See also:
Scientist distances himself from creationist claims, New Scientist, 04 November 2007

For another example of someone who does not like being quoted:
Luskin, C. Human-Chimp Evolution Dialogue (Part 1): An Exchange with Jon Cohen, Author of Science's "The Myth of 1%" Article, Evolution News & Views, October 24 2007

Behe cuts through the arguments to discover the fine tapestry of life

Review of:
The Edge of Evolution: The Search for the Limits of Darwinism
By Michael J. Behe
Free Press, 2007

Michael Behe's new book has been disowned as a work of science by numerous reviewers in Science, Nature and a host of other publications. Only after reading the book could I understand why the reaction has been so intense! It is not because Behe is betraying science (indeed, he is pre-eminently an empiricist) but because the implications of the data he discusses completely undermine the evolutionary consensus that has long been nurtured by opinion-formers within the scientific community. Furthermore, Behe takes all their best arguments and shows that the evidence actually supports the case for non-random, purposeful explanations of the natural world.

Richard Dawkins' carefully crafted arguments are faced head-on by Behe, with devastating effect. For example, Behe considers several evidences of Darwinism in action (notably sickle cell anaemia providing resistance to malaria, antibiotic resistance in bacteria, antifreeze proteins in Antarctic fish) and completely confounds those who say that ID scientists do not accept the Darwinian mechanisms of mutations and natural selection. Not only does Behe endorse the view that these data are good examples of Darwinism in action, but he goes on to show (using the research of the past decade or so) that these mechanisms are utterly incapable of building the complexity that we observe permeating living things. The phenomenon of mutation and natural selection is uncontroversial. The case presented by Behe using the empirical evidence is that the central Darwinian mechanisms cannot deliver the outcomes required by evolutionary theory.

Another example Dawkins favours is the "arms race" metaphor to describe the struggle for survival in the living world. Behe looks at what is actually happening from his own perspective as a biochemist and shows that a better metaphor is "trench warfare". This is because there is no development of more sophisticated arms but only the exploitation of short-term advantages that fortuitously arise. In most cases, these are examples of malfunctions and genetic loss (more like blowing up a bridge than developing a new weapon).

Dawkins (deducing from theory, p.41): "The arms-race idea remains by far the most satisfactory explanation for the existence of the advanced and complex machinery that animals and plants possess."
Behe (induction from data, p.42): "Far and away the most extensive relevant data we have on the subject of evolution's effects on competing organisms is that accumulated on interactions between humans and our parasites. As with the example of malaria, the data show trench warfare, with acts of desperate destruction, not arms races, with mutual improvements."

Thirdly, Behe concludes that the Blind Watchmaker is a figment of Dawkins vivid imagination. The argument is drawn from the best databases we have of Darwinian processes in action. These are malaria (P. falciparum), the HIV virus and an important intestinal bacterium (Escherichia coli). Both Dawkins and Behe describe the need, within Darwinism, for climbing a mountain step by step up a continuous path. The both recognise the same problems but come to totally different conclusions.

"P. falciparum, HIV and E.coli are all very, very different from each other. They range from the simple to the complex, have very different life cycles, and represent three different fundamental domains of life: eukaryote, virus, and prokaryote. Yet they all tell the same tale of Darwinian evolution. Single simple changes to old cellular machinery that can help in dire circumstances are easy to come by. This is where Darwin rules, in the land of antibiotic resistance and single tiny steps. Burning a bridge that can stop an invading army or breaking a lock that can slow a burglar are easy and effective. But if just one or a few steps have to be jumped to gain a beneficial effect, as with chloroquine resistance, random mutation starts breathing hard. Skipping a few more steps appears to be beyond the edge of evolution." (p.162)
"Why no trace of the fabled blind watchmaker? The simplest explanation is that [. . .] the blind watchmaker does not exist." (p.164)

It is customary to portray Darwinian evolution using the term "tinkering". There is some merit in this, as the mechanisms of Darwinism are both stochastic and opportunistic. Behe recognises tinkering in the way the human body fights malaria.

"The defense of vertebrates from invasion by microscopic predators is the job of the immune system, yet hemoglobin is not part of the immune system. Hemoglobin's main job is as part of the respiratory system, to carry oxygen to tissues. Using hemoglobin to fight off malaria is an act of utter desperation, like using a TV set to plug a hole in the Hoover Dam. Even leaving aside the question of where the dam and TV set came from - which is no small question - it must be conceded that this Darwinian process is a tradeoff of least-bad alternatives. The army in its trenches is suffering loss upon loss. No matter which way it turns, in this war fought by random mutation and natural selection, it is losing function, not gaining." (p.29-30)

Although "tinkering" is a widely used term in evolutionary biology, it is not a term that fits well into biology in general. However, a Gordian Knot tethers most biological thinking to a neodarwinian anchor, because biologists have been taught from infancy that nothing in biology makes sense except in the light of evolution. Behe has cut this Gordian Knot and the effect of this is liberating. Now, we can recognise the pervasiveness of coherent complex systems and exquisitely fabricated structures and we do not need to force-fit these into being the products of "tinkering". (For a recent example, go here). There are various avenues to explore to explain all this, but Behe is quite clear where his thinking is going:

"I conclude that another possibility is more likely: The elegant, coherent, functional systems upon which life depends are the result of deliberate intelligent design". (p.166)

Whilst the mammalian embryo is still in the womb, electrical activity can be detected in the developing ears (and eyes). "This spontaneous activity is required for maturation of auditory neurons and to establish auditory pathways in the brain." Recently, a big step forward has been made in understanding how this activity is generated in the ear. It involves cells in Kolliker's organ, which is a transient epithelial structure in the developing cochlea. These cells spontaneously release ATP, which goes on to activate the inner hair cells and auditory nerve fibres. It must be emphasised that this process effectively ceases at birth: "Spontaneous ATP-dependent signalling rapidly subsides after the onset of hearing, thereby preventing this experience-independent activity from interfering with accurate encoding of sound."
The research has pioneered in several ways. It has brought development into the way neuroscientists study hearing. It has identified function in an organ that was a mystery: "These [supporting cells] are cells that, until now, we thought weren't doing a hell of a lot," said Jonathan Gale, a coauthor of the study. It has shown that hearing can be stimulated by ATP: "What we were struck with was that ATP was doing the job that sound would eventually do in the developed cochlea," said Dwight Bergles of Johns Hopkins School of Medicine, corresponding author of the study. "Before the ear is mature enough to detect sound, hair cells respond to ATP." (The authors suggest that this may be the key needed to understand the onset of tinnitus). According to one commentator, the study is "essentially opening up a new area, and actually underscoring the importance of cells we normally ignore".
This appears to be a good example of how the reductionist approach to science creates blinkers. Those working in this area had a mental model of the relevant components and they were untroubled by the fact that they ignored some parts of the system. The new research shows a longitudinal dimension: cellular activity occurs in development that is relevant to maturing the system but this activity ceases and appears irrelevant in the functioning of the mature organ. However, "spontaneous activity in auditory nerve fibres before the onset of hearing is essential for the survival of target neurons in the cochlear nucleus, accurate wiring of auditory pathways, and the refinement of tonotopic maps in auditory nuclei." [emphasis added]
This is great research, moving beyond reductionism towards a holistic approach. I liked the accompanying News & Views essay which referred to a "fantasia" and to the cells of Kolliker's organ "generating their own 'virtual' music". This is a melodious sound in the biologist's ear, but it is music deriving from the beauty and complexity of the living world, not from evolutionary theory (without which, say some, nothing makes sense).
The research does have some relevance to theories of evolution. In The Edge of Evolution, Michael Behe sets out two criteria by which to judge whether random mutation hitched to natural selection is a biologically reasonable explanation for any given molecular phenomenon. These are on page 104: steps (simply the number that must be taken to reach a beneficial state) and coherence (whether those steps are random or ordered). The new role discovered for Kolliker's organ demands an extraordinarily high degree of coherence, because of its transient - but essential - contribution, whatever else may be said about steps. This points to a non-random explanation for the origin of the ear: naturally occuring mutations cannot deliver it.

The origin of spontaneous activity in the developing auditory system
Nicolas X. Tritsch, Eunyoung Yi, Jonathan E. Gale, Elisabeth Glowatzki & Dwight E. Bergles
Nature 450, 50-55 (1 November 2007) | doi:10.1038/nature06233

Abstract: Spontaneous activity in the developing auditory system is required for neuronal survival as well as the refinement and maintenance of tonotopic maps in the brain. However, the mechanisms responsible for initiating auditory nerve firing in the absence of sound have not been determined. Here we show that supporting cells in the developing rat cochlea spontaneously release ATP, which causes nearby inner hair cells to depolarize and release glutamate, triggering discrete bursts of action potentials in primary auditory neurons. This endogenous, ATP-mediated signalling synchronizes the output of neighbouring inner hair cells, which may help refine tonotopic maps in the brain. Spontaneous ATP-dependent signalling rapidly subsides after the onset of hearing, thereby preventing this experience-independent activity from interfering with accurate encoding of sound. These data indicate that supporting cells in the organ of Corti initiate electrical activity in auditory nerves before hearing, pointing to an essential role for peripheral, non-sensory cells in the development of central auditory pathways.

See also:

Forsythe, I.D., Hearing: A fantasia on Kolliker's organ, Nature 450, 43-44, (1 November 2007) | doi:10.1038/450043a

Scheff, J., Sensing through non-sensory cells, The Scientist, 31st October 2007

Although the number of reports of Cambrian jellyfish has greatly increased in the past few years, "there have been no previous reports of fossils possessing preserved characters diagnostic of particular medusozoan clades". New fossils from the Middle Cambrian of Utah "have very well preserved soft tissue, which the authors interpret as evidence that representatives of modern jellyfish existed by the middle Cambrian period."
How have they concluded they are "modern"? The fossils are entombed in fine-grained sediment so that fine details have been preserved. "Given the available character information, they also may comprise representatives of three separate classes of modern medusozoans: Cubozoa; Hydrozoa; and Scyphozoa. This suggests that an important aspect of modern marine pelagic ecosystems was in place shortly after the Cambrian radiation."
The authors also comment on biological complexity:

"the living cubozoan Tripedalia cystophora has sophisticated reproductive behavior that includes mate recognition and courtship, involving the indirect transfer of sperm through spermatophores. Cubozoans also have complex eyes and nervous systems. The existence of our newly described fossil material may suggest that these complex traits could have evolved within the Cnidaria by the Middle Cambrian."

In a press release the implications for rapid species diversification were described as follows:

"Lieberman said the jellyfish the group describes, found in Utah, offer insights into the puzzle of rapid species diversification and development that occurred during the Cambrian radiation, a time when most animal groups appear in the fossil record, beginning roughly 540 million years ago. [. . .]
With the discovery of the four different types of jellyfish in the Cambrian, however, the researchers said that there is enough detail to assert that the types can be related to the modern orders and families of jellyfish. The specimens show the same complexity. That means that either the complexity of modern jellyfish developed rapidly roughly 500 million years ago, or that the group is even older and existed long before then."

The most interesting aspect is the ability to identify modern orders and families. Here is another case of sudden appearance of complex life forms followed by stasis. This is evidence against the gradualist emphasis of Darwinism and it adds weight to the question asked by Steve Meyer ("The Origin of Biological Information and the Higher Taxonomic Categories", Proceedings of the Biological Society of Washington, 117(2004): 213-239.): "Can neo-Darwinism explain the discontinuous increase in CSI that appears in the Cambrian explosion--either in the form of new genetic information or in the form of hierarchically organized systems of parts?"

Exceptionally Preserved Jellyfishes from the Middle Cambrian
Cartwright P, Halgedahl SL, Hendricks JR, Jarrard RD, Marques AC, Collins, AG, Lieberman BS.
PLoS ONE, 2007, 2(10): e1121. doi:10.1371/journal.pone.0001121

Abstract: Cnidarians represent an early diverging animal group and thus insight into their origin and diversification is key to understanding metazoan evolution. Further, cnidarian jellyfish comprise an important component of modern marine planktonic ecosystems. Here we report on exceptionally preserved cnidarian jellyfish fossils from the Middle Cambrian (~505 million years old) Marjum Formation of Utah. These are the first described Cambrian jellyfish fossils to display exquisite preservation of soft part anatomy including detailed features of structures interpreted as trailing tentacles and subumbrellar and exumbrellar surfaces. If the interpretation of these preserved characters is correct, their presence is diagnostic of modern jellyfish taxa. These new discoveries may provide insight into the scope of cnidarian diversity shortly after the Cambrian radiation, and would reinforce the notion that important taxonomic components of the modern planktonic realm were in place by the Cambrian period.

See also:

Fossil record reveals elusive jellyfish more than 500 million years old, EurekAlert, 30 October 2007.

The earliest fossil evidence of comb jellies, ARN literature blog.

Soon after Darwin published On the Origin of Species, a claim was made by two Canadian geologists that they had found the first signs of life on Earth: Eozoon canadense or the "Dawn animal of Canada". They announced the find at a meeting of the British Association of the Advancement of Science in 1864. The president of the BAAA, Sir Charles Lyell, referred to Eozoon as "one of the greatest geological discoveries of his time". The two Canadians and "their primary London-based ally, William Benjamin Carpenter, pursued the support of an elite community of geologists by presenting to scientific societies and publishing papers in prestigious scientific journals." So, for example, Carpenter's paper appeared in the Proceedings of the Royal Society in 1864. Charles Darwin welcomed the find and brought it into the 4th edition of the Origin in 1866. He wrote: "After reading Dr Carpenter's description of this remarkable fossil, it is impossible to feel any doubt regarding its organic nature". The problem for Darwin was that the earliest known fossils were complex, and his theory required something much simpler to precede the forms of the Cambrian Explosion. It was a relief when Eozoon appeared to provide evidence supporting gradualism.
In the 6th edition, Darwin modified the text to read: "The existence of the Eozoon in the Laurentian formation of Canada is generally admitted". This perhaps recognises that there were some dissenting voices: Professor William King (a geologist) and Thomas Rowney (a chemist) at Queen's College, Galway. The characteristics of the ensuing controversy are the subject of an interesting paper by Adelman. She points out that the Canadian geologists adopted a "diffusion" model of communication: "scientific facts were confirmed within the scientific community and then presented to the public." London was the focus of their attention, because the opinion-formers were located there. "The 'Eozoonists' felt that the fossil's credibility was established once the leaders of the scientific community in London had accepted it." The dissenters, however, chose not to play this game.

"King and Rowney, by contrast, did not accept that the prestige of Eozoonists had any bearing on the credibility of the finding. Instead of pursuing the support of scientific elites, they sought maximum publicity for their claims that Eozoon was not a fossil through a sensational letter in a popular journal."

The establishment figures, who had endorsed the authenticity of Eozoon, did not take kindly to the way dissent was being handled - it was outside their control. They cast doubt on the competence of the dissenters to contribute to the discussion about the fossils.

"Carpenter responded by parading his disdain for King, claiming that he awaited not proof of the inorganic nature of Eozoon, but 'proof of his competence to estimate the value of the evidence in this branch of scientific inquiry'. According to Carpenter, King's powers of observation were so poor that he ranked him 'in the same category with those sagacious persons who still maintain that the flint implements were shaped out by a fortuitous succession of accidental blows, and not by human handiwork'. In addition, he dismissed Rowney by saying that a chemist could not claim any authority on the subject of fossils."

There was also a 'provincial versus urban' agenda. Adelman thus documents an instructive case study, giving insight into the power struggles within science and the way science leaders have sought to establish their authority within the community of science and with the public at large.

"The manner in which the Eozoon controversy was conducted shows that the present tensions between scientists, the media and the public are nothing new."

In case it needs saying, Eozoon was not a fossil and the dissenters were correct to challenge the consensus. Clearly there are parallels with today: the role of scientific elites, the status of peer publication, the protocols required to be accepted as members of the scientific community, the way debated issues can be presented as fact to the public, the disdain shown to dissenters, the lobbying of editors to restrict access by critics of the Establishment, and the exploration of alternative ways of communicating minority views to peers and the public. This is the very human face of science. We are seeing these characteristics today in numerous areas where scientists have reached different conclusions. No prizes for identifying at least one example!

Eozoon: debunking the dawn animal
Juliana Adelman
Endeavour, 31(3), September 2007, 94-98 | doi:10.1016/j.endeavour.2007.07.002

Abstract: Discovered in the nineteenth century by the Canadian Geological Survey, the Eozoon canadense fossil, or 'dawn animal of Canada', created a sensation in the geological community. Only a few initially challenged its status as a fossil organism, including two professors in the remote Irish town of Galway. These men claimed that Eozoon was nothing more than a mineral formation and did not represent the discovery of the primordial organism. Supporters of Eozoon closed ranks and a heated debate soon broke out in a range of periodicals. The story of Eozoon lays bare the construction of scientific credibility, a process that was threatened in the second half of the nineteenth century by the proliferation of popular science.

Despite natural selection's central role within the neodarwinian synthesis, there are important limitations to the empirical research that has been undertaken. In particular, "long-term morphological time series with information on the selective regime are exceedingly rare." Drake and Klingenberg have sought to extend the time-span of available data by looking at skeletons of dogs in museums. "Domestic dogs are a unique system for the study of phenotypic evolution, because there not only is a considerable amount of morphological variation, but the history of breeds and the breed standards also provide a documented record of the selection regime that has been applied by breeders". One museum has provided skeletal material for the St Bernard breed spanning 120 years. Their paper documents morphological change over this period and provides an analysis.
Originally, these dogs were working animals and breeding was designed to enhance function. However, in the 1880s, the focus shifted so that the animals were bred as pets and show dogs. Significantly, "the breed standard describes the perfect St Bernard in terms of its appearance, but not its behaviour". Morphological variations are documented in the paper, and it is not surprising to read that "the shape changes [. . .] correspond to the features specified in the breed standard for St Bernards".
There are two interesting findings. First, the changes show intelligent agency at work. "The close agreement between the observed changes and the features described as desirable in the breed standard, and therefore favoured by breeders, suggests that the observed change was brought about by selective breeding." Second, there is no evidence that allometry has been a factor. "Previous research has suggested that morphological diversity in dogs may be due in large part to allometric shape changes. Our data indicate that this is not the case for the historical change in St Bernards." In particular, there was "no consistent trend of skull size in the time period covered by our study."
Since Mendel's pioneering work, there has always been a question mark over the relevance of artificial selection, because breeders are working with innate variation rather than new mutations. Did their study cast any light on this issue? The answer appears to be no:

"Unfortunately, the available data do not allow us to decide whether a sufficient amount of genetic variation still persists from the initial, heterogeneous breeding stock or whether genetic variation is replenished continuously by new mutation".

As the paper stands, it is a useful addition to the literature. However, outside the paper, a spin is being put on the findings that are completely unjustified. This is illustrated by the EurekAlert! headline: "St Bernard study casts doubt on creationism". Also, the last sentence of the news release: "this research once again demonstrates how selection - whether natural or, in this case, artificially influenced by man - is the fundamental driving force behind the evolution of life on the planet." These words are attributed to Dr Klingenberg, one of the co-authors. In order to make this claim, it is necessary to paint creationists and ID advocates as deniers of both natural selection and artificial selection - which is as untrue today as it was in Darwin's day. We do not deny natural selection; we deny that it has the capability to make complex specified information in living things. The changes documented in this paper are trivial:

"The upper jaw and palate have tilted, raising the anterior and lowering the posterior part, which contributes to the shortened and relatively high muzzle. This tilting of the upper jaw and palate, together with the upward shifts of landmarks on the frontal bone, contribute to the pronounced stop, the angle between the muzzle and the forehead, which the breed standard specifies as desirable. [snip]"

"Once again", studies of minor variations in peppered moths, Galapagos finch beaks, beach mice in Florida, etc., are used to claim that natural selection is "the fundamental driving force behind the evolution of life on the planet." Once again, this illustrates the bankruptcy of Darwinism.

The pace of morphological change: historical transformation of skull shape in St Bernard dogs
Abby Grace Drake and Christian Peter Klingenberg
Proceedings of the Royal Society B: Biological Sciences, 275, 7 January 2008, 71-76 | doi:10.1098/rspb.2007.1169 | doi:10.1098/rspb.2007.1169

Abstract: Owing to the great morphological diversity of domestic dogs, the study of historical shape change in dog skulls provides an excellent opportunity for investigating the dynamics of morphological evolution. Breed standards make known which features were selected by breeders. Here we use the methods of geometric morphometrics to study change of skull shape in a series of purebred St Bernard dogs spanning nearly 120 years. A regression of shape on time was highly significant and revealed a consistent trend of shape change that corresponded to the features deemed desirable by the breed standard. Historical shape change in St Bernards involves a broadening of the skull and a tilting of the palate and upper jaw relative to the rest of the skull. This trend appears to be linear throughout the entire period and appears to be continuing. Allometry was ruled out as a contributing factor to this change because there was no consistent trend of historical change in skull size and because neither the patterns of static nor ontogenetic allometry corresponded to the historical shape change. The dramatic modification of the St Bernard skull demonstrates that selection can achieve sustained and substantial change and can completely overcome constraints such as allometry.

See also:
St Bernard study casts doubt on creationism, EurekAlert! 23 October 2007.

Back in June, Science published a review authored by Sean Carroll which was a very negative response to Mike Behe's new book. This was the subject of comment here where I concluded:

The real issue is: will a debate within science be allowed? If Behe is not allowed the right of reply, this review should be treated as an exercise in polemics, designed to protect the world of science from ever having to face up to evidences of ID. If there is the opportunity to reply, readers will enjoy a genuine scientific debate.

Well, an exchange of sorts has been permitted within the pages of Science - in the correspondence section of the 12 October 2007 issue. Behe was allowed less than 200 words to refute the claim that he failed to discuss pyrimethamine resistance in malarial parasites and to explain that his book illustrated "the crucial difference between beneficial intermediate mutations and deleterious intermediate ones."
Carroll had nearly 500 words of response. This disparity is worthy of note, because Behe has since pointed out that his letter was edited to remove at least one significant paragraph.
Carroll conceded that Behe did not fail to discuss pyrimethamine resistance in malarial parasites. But instead of apologising for implying that Behe had overlooked this data, he changed the charge to say that Behe had misread the data. "My criticism is that Behe omitted the clear evidence for the cumulative selection of multiple changes in the drug target protein in nature and that he invoked an altogether different and unsupported explanation in an attempt to bolster his main premise."
The normal flow of academic exchange after Behe's correspondence would be for Carroll to graciously admit he had made a mistake and apologise for making a false claim. Then, it would be appropriate for any new charge to be discussed so as to allow both parties to explore the issue rationally. This was not how the editors of Science saw fit to conduct the exchange. Rather, Behe has had to resort to the internet to post his further response to Carroll.
The reality seems to be that Carroll is reading the evidence through Darwinian spectacles. He finds it incomprehensible that anyone could read things in any other way. As an illustration, consider this section of his letter:

He [Behe] speculates that "two further, simultaneous mutations seem to be necessary" for the evolution of pyrimethamine resistance, despite the fact that the authors I cited (2) explicitly demonstrated two different pathways to triple and quadruple mutants via stepwise processes. Behe does not cite this work and he obfuscates the clear but inconvenient message in this body of data.

Compare this with Behe's internet response:

It was hypothesized that multiple mutations in different genes might be required:
"Because concurrent mutations in two different genes occur at reduced frequency, this would help explain the rarity with which resistance has evolved." (Nair, S., et al. 2003. A selective sweep driven by pyrimethamine treatment in southeast asian malaria parasites. Mol. Biol. Evol. 20:1526-1536)
(By the way, Hayton and Su 2004 also remark that, "Based on the mutant pfcrt haplotypes known so far, it is likely that simultaneous multipoint changes in pfcrt are necessary to confer [chloroquine resistance]".)

Carroll implies I'm somehow less than honest for passing on the thinking of workers in the field in this area, while he passes off as near-conclusive ambiguous work done in vitro.

Some of us think that there is scope for a genuine academic debate here, but it is hard work interacting with people who appear to have a deductive agenda (i.e. some advocates of Darwinian evolution). We need editors who can manage these debates and provide forums for genuine exchanges about the implications of evidence.

Letters: Addressing Cumulative Selection
Michael J Behe, with response by Sean B. Carroll
Science 12 October 2007: 318, 196 | DOI: 10.1126/science.318.5848.196

See also:
Behe, M.J. Back and forth with Sean Carroll in Science, Amazon Blog, October 17, 2007

In 1998, Ian Tattersall wrote: "All of which brings us back to the question of whether Neanderthals had language. To which the answer is almost certainly no, at least in the form in which we are familiar with it." (Becoming Human: Evolution and Human Uniqueness, p172). He provided many other arguments to justify the conclusion that Neanderthals are really different from humans. However, in the following years, archaeological finds have chipped away at this position and today Neanderthals look a lot more like humans than they appeared then. But disputes continue over language.
A genetic link with language has been identified. "So the speculation was that [the FOXP2 variations] were unique to humans and not there in Neandertals," says evolutionary geneticist Svante Paabo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, who traced FOXP2's ancestry. "If there was one single gene I really wanted to see in Neandertals, it was this one." Culotta writes:

"Paabo appears to have gotten his wish: His team extracted ancient DNA from two 43,000-year-old Neandertal bones found in a cave in northern Spain. Genetic analysis revealed that the FOXP2 sequence in both Neandertals matched that in living people. It harbored the two mutations that help set the human gene apart from those of all other animals. This doesn't necessarily prove that Neandertals could speak, because many other, unknown genes probably influence language ability. But "with respect to FOXP2, there's nothing to say that Neandertals could not speak just like we do," says Paabo. He now suggests that the gene was favored by selection much earlier, before Neandertals and modern humans had completely diverged, perhaps 300,000 or 400,000 years ago."

The recent controversy over the issue of contamination is one the authors claim to have addressed. Allowing that the genetic link is only one element of the language question, this new evidence can be used to trigger an alternative hypothesis about Neanderthals. Instead of a common ancestor of humans and Neanderthals, another possible hypothesis is that Neanderthals is a descendant species of humanity. They buried their dead and had a variety of aesthetic practices because they were human. They spoke because they were human. Surely we have now reached the stage where this hypothesis can be tested alongside evolutionary options?

The Derived FOXP2 Variant of Modern Humans Was Shared with Neandertals
Johannes Krause, Carles Lalueza-Fox, Ludovic Orlando, Wolfgang Enard, Richard E. Green, Hernan A. Burbano, Jean-Jacques Hublin, Catherine Hanni, Javier Fortea, Marco de la Rasilla, Jaume Bertranpetit, Antonio Rosas, and Svante Paabo.
Current Biology, online October 18 2007 | doi 10.1016/j.cub.2007.10.008

Summary: Although many animals communicate vocally, no extant creature rivals modern humans in language ability. Therefore, knowing when and under what evolutionary pressures our capacity for language evolved is of great interest. Here, we find that our closest extinct relatives, the Neandertals, share with modern humans two evolutionary changes in FOXP2, a gene that has been implicated in the development of speech and language. We furthermore find that in Neandertals, these changes lie on the common modern human haplotype, which previously was shown to have been subject to a selective sweep. These results suggest that these genetic changes and the selective sweep predate the common ancestor (which existed about 300,000-400,000 years ago) of modern human and Neandertal populations. This is in contrast to more recent age estimates of the selective sweep based on extant human diversity data. Thus, these results illustrate the usefulness of retrieving direct genetic information from ancient remains for understanding recent human evolution.

See also:

Culotta, E. Talk Like a Man, ScienceNOW Daily News, 18 October 2007

The evolutionary agenda for the human appendix was set by Charles Darwin in The Descent of Man (1871). In Chapter 1, he presented several evidences for our animal ancestry, some of which went under the name of 'Rudiments'. On pages 27-28, he has this to say:

"With respect to the alimentary canal I have met with an account of only a single rudiment, namely the vermiform appendage of the caecum. The caecum is a branch or diverticulum of the intestine, ending in a cul-de-sac, and it is extremely long in many of the lower vegetable-feeding mammals [. . .] It appears as if, in consequence of changed diet or habits, the caecum had become much shortened in various animals, the vermiform appendage being left as a rudiment of the shortened part. [. . .] Not only is it useless, but it is sometimes the cause of death, of which fact I have lately heard two instances: this is due to small hard bodies, such as seeds, entering the passage and causing inflammation."

This was the story that was passed to subsequent generations of biologists. It was endorsed by Ernst Mayr as recently as 2001: "Every shift into a new adaptive zone leaves a residue of no longer needed morphological features that then become an impediment. One only needs to think of the many weaknesses in humans that are remnants of our quadrupedal and more vegetarian past, for instance [. . .] the caecal appendix." (p. 143, What Evolution Is, Basic Books).
For many years, the only dissenting voices have been from creationists, who found some evidence of functionality. However, it would appear that those with specialist knowledge had quietly buried this 'evidence' for evolution, as is witnessed by this comment in a recent study of its functionality: "[The appendix was] often considered to be a vestige of evolutionary development despite evidence to the contrary based on comparative primate anatomy." The research is summarised thus in a news report:

The function of the appendix seems related to the large amount of bacteria populating the human digestive system, according to the study in the Journal of Theoretical Biology. There are more bacteria than human cells in the typical body. Most of it is good and helps digest food.
But sometimes the bacteria in the intestines die or are purged. Diseases such as cholera or amoebic dysentery would clear the gut of useful bacteria. The appendix's job is to reboot the digestive system in that case.
The appendix "acts as a good safe house for bacteria," said Duke surgery professor Bill Parker, a study co-author. Its location -- just below the normal one-way flow of food and germs in the large intestine in a sort of gut cul-de-sac -- helps support the theory, he said.

It might be hoped that Darwinian evolutionary biologists would acknowledge that errors have been made; that Darwin's claim for the appendix being useless was a claim made from ignorance rather than knowledge; that their theory had coloured their understanding of the data; etc. But no - what we get is this response to the new research:

The idea "seems by far the most likely" explanation for the function of the appendix, said Brandeis University biochemistry professor Douglas Theobald. "It makes evolutionary sense."

It makes evolutionary sense ONLY because evolutionary theory is apparently infinitely adaptable to data and the storytelling mentality prevails.
It should be remembered that functionality was the prediction of biologists with a creation or design mentality, and it was not the prediction of evolutionary biologists. On this occasion, the people with a design perspective were right and the Darwinians were wrong. Let's remember this next time we hear creation or ID being decried as being unable to make any scientific predictions!

Biofilms in the large bowel suggest an apparent function of the human vermiform appendix
R. Randal Bollinger, Andrew S. Barbas, Errol L. Bush, Shu S. Lin and William Parker
Journal of Theoretical Biology, 249(4), 21 December 2007, 826-831.

Abstract: The human vermiform ("worm-like") appendix is a 5 to 10 cm long and 0.5 to 1 cm wide pouch that extends from the cecum of the large bowel. The architecture of the human appendix is unique among mammals, and few mammals other than humans have an appendix at all. The function of the human appendix has long been a matter of debate, with the structure often considered to be a vestige of evolutionary development despite evidence to the contrary based on comparative primate anatomy. The appendix is thought to have some immune function based on its association with substantial lymphatic tissue, although the specific nature of that putative function is unknown. Based (a) on a recently acquired understanding of immune-mediated biofilm formation by commensal bacteria in the mammalian gut, (b) on biofilm distribution in the large bowel, (c) the association of lymphoid tissue with the appendix, (d) the potential for biofilms to protect and support colonization by commensal bacteria, and (e) on the architecture of the human bowel, we propose that the human appendix is well suited as a "safe house" for commensal bacteria, providing support for bacterial growth and potentially facilitating re-inoculation of the colon in the event that the contents of the intestinal tract are purged following exposure to a pathogen.

See also:

Borenstein, S., Appendix is a refuge for good germs, study says, The Associated Press, Oct 06, 2007.

Materials scientists are actively researching biological materials, surfaces and functionalities. All forms of life are inspiring innovation and influencing the direction of development. The adhesive mechanisms of climbing animals have also guided materials scientists.

"Climbing animals have many abilities that are the envy of materials scientists. First, they have remarkable powers of adhesion. Even a large gecko can run across a ceiling; a tree frog jumping from branch to branch does not fall so long as a single toe pad makes good contact with the tree; ants can carry more than 100 times their own weight while walking upside-down. Second, the adhesive mechanisms are reversible (geckos can walk at more than 10 steps a second), and detachment is effortless. Third, animal adhesive pads can have self-cleaning properties and thus do not get fouled. Finally, the adhesive pads of geckos only stick when required."

The outcome of some research in this area is provided by Majumder and colleagues in today's Science. "Inspired by the complex subsurface structure of the smooth adhesive pads of tree frogs and insects such as grasshoppers and ants, they show that adhesive force can be increased by up to a factor of 30 by subsurface structures such as air-or fluid-filled pockets."
It is interesting to note the impact made by these biological surfaces on Majumder et al: the feet "show a remarkable ability to attach to almost any surface"; "man-made pressure-sensitive adhesives lack these amazing qualities"; they attribute "the extraordinary ability of naturally occurring adhesives" to "the complex and hierarchal structural morphologies of their attachment pads". Clearly, something significant is going on here.
When mankind produces "future smart adhesives" like those reported, the materials are described as "designed to do particular tasks". They are the product of intelligent agency. However, when superior materials occur in animals (and plants), they are "remarkable mechanisms developed by climbing animals over millions of years of evolution." The problem is that the ability of evolutionary processes to deliver anything that looks like complex specified information, let alone anything inspiring human designers, has yet to be demonstrated. Proofs of evolution based on industrial melanism of peppered moths or changing beak shapes of Galapagos finches are utterly trivial compared with what is being claimed here. We have a situation where evolution is part of the scientific culture, useful only to frame research by showing allegiance to the prevailing philosophy of naturalism. But we need to recognise that this appeal to evolution adds nothing to the research and is irrelevant to the way science is done. We desperately need a more appropriate methodological underpinning for biomimetics. For more on this, go here.

Microfluidic Adhesion Induced by Subsurface Microstructures
Abhijit Majumder, Animangsu Ghatak, and Ashutosh Sharma
Science 318, 12 October 2007: 258-261.

Abstract: Natural adhesives in the feet of different arthropods and vertebrates show strong adhesion as well as excellent reusability. Whereas the hierarchical structures on the surface are known to have a substantial effect on adhesion, the role of subsurface structures such as the network of microchannels has not been studied. Inspired by these bioadhesives, we generated elastomeric layers with embedded air- or oil-filled microchannels. These adhesives showed remarkable enhancement of adhesion (~30 times), which results from the crack-arresting properties of the microchannels, together with the surface stresses caused by the capillary force. The importance of the thickness of the adhesive layer, channel diameter, interchannel spacing, and vertical position within the adhesive has been examined for developing an optimal design of this microfluidic adhesive.

See also:

Barnes, W.J.P., Biomimetic Solutions to Sticky Problems, Science 318, 12 October 2007: 203-204.

Two papers in Nature have documented patterns of change that have affected contemporary languages. "Both concern language change, and come from laboratories of well-established evolutionary theorists. Both analyse historical linguistic data to show that patterns of change depend strongly on the frequency with which words are used in discourse, as measured from large contemporary databases." The first paper finds that "verbs evolve and homogenize at a rate inversely proportional to their prevalence in the English language". The second paper looked at words more broadly and found that "less-frequently-used words evolved faster, and that frequency can explain half of the rate of evolution." Taken together, this is the same trend: "frequently used words are resistant to change".
As Fitch points out, "Documenting these relationships remains descriptive, not explanatory". Significantly, both these papers frame their reported research using evolutionary language and concepts. This is pointed out by Marris: "Both papers were written by teams with evolutionary biology backgrounds, and both call attention to the similarities between language change and the evolution of species. Leiberman even refers to early English as a "primordial soup" of verb forms in his paper." From a design perspective, we ask whether this is helpful or confusing.
The first thing we can say is that neo-Darwinism is not appropriate, because words are used by intelligent agents, and the changes occur because intelligent agents choose to change. Consequently, a more appropriate conceptual framework is provided by Intelligent Design.
Secondly, the changes being reported relate to vocabulary, not syntax or grammar. If we are looking for an analogy with Darwinism, it is with micro-evolution - with no significant change in complexity of the language. This is a relatively non-controversial area, where evolutionary theory and design theory often converge.
Third, the reported changes in regular/irregular verb usage are all in one direction: towards regularity. Thus, the language becomes simplified with time. Early languages are not like a "primordial soup" - they were more sophisticated than their descendants! Marris' report makes this clear: "Brian Joseph, a historical linguist at Ohio State University in Columbus and the editor of the journal Language, says that's going too far. Early English, he says, was "just as regular and rule-based" as modern language - it just had more complicated rules."
Consequently, whilst the reported research is interesting and thought-provoking, the Darwinian gloss is superficial. Stephen Pinker gets close with this comment: "The analogy with darwinian evolution is crude, although not useless".

Quantifying the evolutionary dynamics of language
Erez Lieberman, Jean-Baptiste Michel, Joe Jackson, Tina Tang & Martin A. Nowak
Nature 449, 713-716 (11 October 2007) | doi:10.1038/nature06137

Human language is based on grammatical rules. Cultural evolution allows these rules to change over time. Rules compete with each other: as new rules rise to prominence, old ones die away. To quantify the dynamics of language evolution, we studied the regularization of English verbs over the past 1,200 years. [snip] We study how the rate of regularization depends on the frequency of word usage. The half-life of an irregular verb scales as the square root of its usage frequency: a verb that is 100 times less frequent regularizes 10 times as fast. Our study provides a quantitative analysis of the regularization process by which ancestral forms gradually yield to an emerging linguistic rule.

Frequency of word-use predicts rates of lexical evolution throughout Indo-European history
Mark Pagel, Quentin D. Atkinson & Andrew Meade
Nature 449, 717-720 (11 October 2007) | doi:10.1038/nature06176

[snip] Here we use four large and divergent language corpora (English, Spanish, Russian and Greek) and a comparative database of 200 fundamental vocabulary meanings in 87 Indo-European languages to show that the frequency with which these words are used in modern language predicts their rate of replacement over thousands of years of Indo-European language evolution. Across all 200 meanings, frequently used words evolve at slower rates and infrequently used words evolve more rapidly. This relationship holds separately and identically across parts of speech for each of the four language corpora, and accounts for approximately 50% of the variation in historical rates of lexical replacement. We propose that the frequency with which specific words are used in everyday language exerts a general and law-like influence on their rates of evolution. Our findings are consistent with social models of word change that emphasize the role of selection, and suggest that owing to the ways that humans use language, some words will evolve slowly and others rapidly across all languages.

See also:

Marris, E., How 'holp' became 'helped', news@nature.com, 10 October 2007 | doi:10.1038/news.2007.152

Fitch, W.T. Linguistics: An invisible hand, Nature 449, 665-667, (11 October 2007) | doi:10.1038/449665a

One does not have to go very deep into the evidences for variation in living things to find that gradualism does not fit the data. It should not be a controversial matter to say that Darwin's portrayal of a branching "Tree of Life" (TOL) is erroneous. However, allegiance to this metaphor has been fundamental for generations of Darwinists. Koonin writes: "Nevertheless, it is generally assumed that, in principle, the TOL exists and is resolvable although, in practice, full resolution might never be attained and, furthermore, might not even be particularly important for understanding the actual events that transpired during the respective transitional stages." Living with the theoretical model, in tension with the empirical data, has had a negative influence on evolutionary biologists, who appear to prefer fitting data into their theoretical models rather than testing their models against the evidence.
Koonin has made a radical and controversial contribution to the debate.

I argue for a fundamentally different solution, i.e., that a single, uninterrupted TOL does not exist, although the evolution of large divisions of life for extended time intervals can be adequately described by trees. I suggest that evolutionary transitions follow a general principle that is distinct from the regular cladogenesis. I denote this principle the Biological Big Bang ( BBB ) Model. Under this model, each of the biological transitions is, indeed, a transition in a more specific, technical sense, i.e., a switch between two phases of evolution, a phase of rapid evolution (inflation) characterized by rampant exchange and recombination of genetic material, followed by congealing into a relatively slow phase governed by the tree pattern.

This BBB model draws inspiration from cosmology. In particular, Koonin is impressed by inflation as the vehicle by which complexity (in the form of stars and galaxies) was generated.

However, the nature of the Big Bang event had not received a coherent explanation before the advent, in 1981, of a new generation of cosmological models that stem from the concept of inflation. Inflation is the exponentially fast initial expansion of a universe. Inflation is in an excellent agreement with several crucial results of observational cosmology. In the most plausible, self-consistent inflationary models, inflation is eternal, with an infinite number of island (pocket, bubble) universes (hereinafter, simply, universes) emerging through the decay of small regions of the primordial "sea" of false vacuum and comprising the infinite multiverse.

In the BBB model, there were biological analogues to inflation, whereby complexity emerged from precursors. This involves extensive genetic exchanges and structural reorganisations that are essentially unpredictable and therefore have the corollary that "there is no TOL". Indeed, "the BBB model defies the TOL paradigm". Darwinism can have a place in understanding the "slow phase" of biological variation, but not those that are abrupt: "understanding the inflationary phases and the exact processes occurring during BBBs emerges as a major goal of evolutionary biology."
One reviewer of this paper noted the words: "In each major class of biological objects, the principal types emerge "ready-made", and intermediate grades cannot be identified" and commented: "Ouch, that will be up on ID websites faster than one can bat an eye." All credit to Koonin for his response:

Here I do not really understand the concern. I changed "ready-made" to "abruptly", to avoid any ID allusions and added clarifications but, beyond that, there is little I can do because this is an important sentence that accurately and clearly portrays a crucial and, to the very best of my understanding, real feature of evolutionary transitions. Will this be used by the ID camp? Perhaps - if they read that far into the paper. However, I am afraid that, if our goal as evolutionary biologists is to avoid providing any grist for the ID mill, we should simply claim that Darwin, "in principle", solved all the problems of the origin of biological complexity in his eye story, and only minor details remain to be filled in.

There's some good advice here! Let's hope the debaters take this challenge seriously.

The Biological Big Bang model for the major transitions in evolution
Eugene V Koonin
Biology Direct 2007, 2:21doi:10.1186/1745-6150-2-21 [open access]

From the Abstract:
Hypothesis: I propose that most or all major evolutionary transitions that show the "explosive" pattern of emergence of new types of biological entities correspond to a boundary between two qualitatively distinct evolutionary phases. The first, inflationary phase is characterized by extremely rapid evolution driven by various processes of genetic information exchange, such as horizontal gene transfer, recombination, fusion, fission, and spread of mobile elements. These processes give rise to a vast diversity of forms from which the main classes of entities at the new level of complexity emerge independently, through a sampling process. In the second phase, evolution dramatically slows down, the respective process of genetic information exchange tapers off, and multiple lineages of the new type of entities emerge, each of them evolving in a tree-like fashion from that point on. [snip]
Conclusion: A Biological Big Bang ( BBB ) model is proposed for the major transitions in life's evolution. According to this model, each transition is a BBB such that new classes of biological entities emerge at the end of a rapid phase of evolution (inflation) that is characterized by extensive exchange of genetic information which takes distinct forms for different BBBs. The major types of new forms emerge independently, via a sampling process, from the pool of recombining entities of the preceding generation. This process is envisaged as being qualitatively different from tree-pattern cladogenesis.

Quote from the Background: "There seems to be a striking commonality between all major transitions in the evolution of life. In each new class of biological objects, the principal types emerge abruptly, and intermediate grades (e.g., intermediates between the precellular stage of evolution and prokaryotic cells or between prokaryotic and eukaryotic cells), typically, cannot be identified."

See also:
Crowther, R., Darwin Doubting Heretic Reveals Himself at National Center for Biotechnology, Evolution News & Views, 9 October 2007.

There has long been a quest for evolutionary explanations of altruistic human behaviour and various mechanisms have been proposed (kin selection, reciprocal altruism). However, these have not done justice to the range of cooperative behaviours exhibited by humans. Animals, particularly chimpanzees, have been extensively studied to gain insights into the evolution of human behaviour. The public are treated to stories of tool use and non-verbal communication and many think that the gulf between humans and the great apes is not a big one to jump. So it is of interest to note a recent study that demonstrates that chimpanzees have no detectable sense of fairness.
The researchers developed an experimental programme based on an exercise known as the ultimatum game. With humans, an individual presents a proposal to share money with a second player. If the second player accepts, the proposal is implemented. If the second player declines, no one gets anything. It is found that if the proposer is not generous enough in the proposal, the responder thinks the deal is unfair and declines, so the proposer gets no benefit.
With chimps, raisins rather than money were used as currency. Also, the 'proposer' chimps were not expected to choose the division of raisins in their proposal - this was controlled by the researchers. It was found that the 'responder' chimps accepted any offer that brought them a finite number of raisins, and the researchers detected no trace of the chimps refusing proposals that were unfair. Traditional models of economic behaviour describe these responders as "rational maximizers" - who make judgments based on self-interest, without reference to other parties.
The researchers conclude: "It thus would seem that in this context, one of humans' closest living relatives behaves according to traditional economic models of self-interest, unlike humans, and that this species does not share the human sensitivity to fairness."
The paper suggests this research makes "an important contribution to the debate on evolution and possible uniqueness of human cooperation", but does not comment further. The sense of fairness implies a sense of right and wrong (morality) and an ability to analyse the situation abstractly (an aspect of consciousness). Evolutionary theorists have struggled with both these elements. Their discussion revolves around genetics and the environment (nature and nurture), but this is as far as their conceptual model permits them to go. A design perspective does not place restrictions on the explanatory framework adopted, allowing a richer set of hypotheses to be explored.

Chimpanzees Are Rational Maximizers in an Ultimatum Game
Keith Jensen, Josep Call, and Michael Tomasello
Science 318, 5 October 2007: 107-109.

Traditional models of economic decision-making assume that people are self-interested rational maximizers. Empirical research has demonstrated, however, that people will take into account the interests of others and are sensitive to norms of cooperation and fairness. In one of the most robust tests of this finding, the ultimatum game, individuals will reject a proposed division of a monetary windfall, at a cost to themselves, if they perceive it as unfair. Here we show that in an ultimatum game, humans' closest living relatives, chimpanzees (Pan troglodytes), are rational maximizers and are not sensitive to fairness. These results support the hypothesis that other-regarding preferences and aversion to inequitable outcomes, which play key roles in human social organization, distinguish us from our closest living relatives.

See also:

Fair Play in Chimpanzees, Max Planck Press Release, 5 October 2007

Patience, fairness and the human condition, The Economist, Oct 4th 2007

Visual adaptation in humans provides us with the ability to see in a wide range of conditions, from the darkness of night to the brightness of the midday sun. Adaptation means that the signals from our photoreceptors are processed so as to amplify weak signals and also to damp strong signals thereby preventing saturation. "Past physiological work has shown that ganglion cells, the output cells of the retina, adapt at lower light levels than cones and one of the downstream targets of the cones, horizontal cells. Such studies provide evidence for adaptation in the retinal circuitry and in the cone photoreceptors." This mechanism is known as "receptor adaptation". New research reveals a second mechanism where there is a convergence of signals from multiple cones within the retinal circuitry. This is described as "post-receptor adaptation". The two mechanisms are complementary to each other. As light levels increase, the main site of adaptation switches from the retinal circuitry to the cone photoreceptors.
The research paper concludes:

"Receptor and post-receptor adaptation permit the amplification required to see objects in shadows while avoiding saturation from the sky. The combination of these adaptive mechanisms allows the visual system to encode details in a scene with greater fidelity than a standard camera at a single exposure setting. The strategy the retina employs - shifting the dominant site of adaptation to match the reliability of the input signals - demonstrates an elegant principle for accurate information processing in sensory perception."

This blog has, in the past, drawn attention to the differences between tinkering evolution and exquisite design. This new research appears to fall into the latter category.

Light adaptation in cone vision involves switching between receptor and post-receptor sites
Felice A. Dunn, Martin J. Lankheet & Fred Rieke
Nature 449, 603-606 (4 October 2007) | doi:10.1038/nature06150

We see over an enormous range of mean light levels, greater than the range of output signals retinal neurons can produce. Even highlights and shadows within a single visual scene can differ ~10,000-fold in intensity-exceeding the range of distinct neural signals by a factor of ~100. The effectiveness of daylight vision under these conditions relies on at least two retinal mechanisms that adjust sensitivity in the ~200 ms intervals between saccades1. One mechanism is in the cone photoreceptors (receptor adaptation)2, 3, 4, 5 and the other is at a previously unknown location within the retinal circuitry that benefits from convergence of signals from multiple cones (post-receptor adaptation)6, 7. Here we find that post-receptor adaptation occurs as signals are relayed from cone bipolar cells to ganglion cells. Furthermore, we find that the two adaptive mechanisms are essentially mutually exclusive: as light levels increase the main site of adaptation switches from the circuitry to the cones. These findings help explain how human cone vision encodes everyday scenes, and, more generally, how sensory systems handle the challenges posed by a diverse physical environment.

The fossil record of pycnogonids (sea spiders) is sparse, to say the least. Until recently, there were only 5 named species from 3 localities: one Silurian specimen, some larval instars from the late Cambrian and the rest are Devonian. The fossil record between these Palaeozoic Systems and the present was quiet.
However, a French team has broken the silence by announcing some spectacularly preserved specimens from Jurassic rocks. They point out that the discovery "fill[s] a 400Myr gap of knowledge in the evolutionary history of this enigmatic group of marine arthropods."
So, what can now be said about their "evolutionary history"? The authors write: "They reveal very close morphological and functional (locomotion, feeding) similarities with present-day pycnogonids." Bear in mind that there are over 1100 species of modern pycnogonids, so variation is extensive within this group of animals. The implication is that the fossil record of sea spiders reveals stasis: minor variations about a central theme.
The authors also say that there are "marked differences with all Palaeozoic representatives of the group". However, whilst it has been suggested that a greater diversity of body plans existed among the Palaeozoic pycnogonid taxa, it has not been obvious what is primitive and what is derived. The Devonian forms have suggested this diversity, but the geologically earlier Silurian specimen was placed "near the base of the pycnogonid crown group". This implies that stasis continues back into the Palaeozoic, with various specialized forms emerging as localized variant species.
Here is yet another life form, stretching from the lower Palaeozoic to the present, that displays stasis in its morphology with relatively minor differences over time. Why is it that the dominant feature (stasis) gets so little attention, when "evolutionary history" gets so much?

New sea spiders from the Jurassic La Voulte-sur-Rhone Lagerstatte
Charbonnier, S., Vannier, J. & Riou, B.
Proceedings of the Royal Society B, October 2007, 274, 2555-2561 | doi 10.1098/rspb.2007.0848

Abstract: The diverse and exceptionally well-preserved pycnogonids described herein from the Middle Jurassic La Voulte Lagerstatte fill a 400Myr gap of knowledge in the evolutionary history of this enigmatic group of marine arthropods. They reveal very close morphological and functional (locomotion, feeding) similarities with present-day pycnogonids and, by contrast, marked differences with all Palaeozoic representatives of the group. This suggests a relatively recent, possibly Mesozoic origin for at least three major extant lineages of pycnogonids (Ammotheidae, Colossendeidae, Endeidae). Combined evidence from depositional environment, faunal associates and recent analogues indicate that the La Voulte pycnogonids probably lived in the upper bathyal zone (ca 200m). Our results point to a remarkable morphological and ecological stability of this arthropod group over at least 160Myr and suggest that the colonization of the deep sea by pycnogonids occurred before the Jurassic.

See also:

Jaggard, V. Photo in the News: New Sea Spider Fossils Found, National Geographic News, August 16, 2007.

Siveter, D.J. et al., A Silurian sea spider, Nature, 431, 978-980 (21 October 2004)

By studying the formation of embryonic molar teeth, researchers developed a model linking dentition patterns of rodents to the influence of signalling molecules secreted by the surrounding tissues. They identified both inhibitor (i) and activator (a) molecules and found that the balance between them determines when and if an additional molar will form. This model was examined to see if it was generic. "If this developmental system is shared by all mammals, different dental phenotypes could be generated simply by varying the a/i ratio. Kavanagh et al. argue that the system has influenced the evolution of functional diversity in mammalian dentition. To test that possibility, they compile data on the proportional area of the molars of 29 species of murine rodents - close relatives of the mice in which the authors discovered the regulatory system." Did the test prove positive? "The predictive mathematical model they derive from the developmental experiments explains nearly 75% of the diversity in molar proportions in these rodents."
In a News & Views article, Polly writes: "The predictive power of their model is impressive, but will it hold for all mammals? From my further analyses, the answer is a qualified 'yes'. The results are shown in Figure 3, which depicts the 'morphological space' (morphospace) for different combinations of relative molar size. Nearly 70% of the variation from 35 additional species, representing 13 mammalian orders, is explained by Kavanagh and colleagues' model."
This research is described as establishing "a remarkable connection between developmental and evolutionary biology." It is this claimed link with evolutionary biology that we now need to consider. If evolutionary biology is described as "variation", then we are all evolutionary biologists. But that definition is naive and unproductive. The interesting questions come when we ask whether there are limits to variation. It is significant that the proposed model does not involve variations via mutations, but variations stimulated and controlled by environmental factors. These variations are not neodarwinian, but emerge via a dynamic developmental system. The different dental structures do not imply different genetic programs, nor do they imply the emergence of new biological information. The developmental model is more suited to a design framework because the same fundamental program yields numerous different dentition patterns that are adapted to the lifestyle of the relevant organisms. The real evolutionary challenge is to explain the origin of the developmental system, the activator-inhibitor mechanism and the program logic.
Within the constraints of the developmental system, adaptive variation is possible. This research can be used to illustrate the concept of 'limits to variation' because the variation is pre-programmed and not open-ended. Development creates a limited range of options for potential variation. If evolutionary biologists were more familiar with thinking like this, they would not be so disturbed by Behe's new book, which is concerned with the limits of what neodarwinism can achieve.

Predicting evolutionary patterns of mammalian teeth from development
Kathryn D. Kavanagh, Alistair R. Evans & Jukka Jernvall
Nature 449, 427-432 (27 September 2007) | doi:10.1038/nature06153

Abstract: One motivation in the study of development is the discovery of mechanisms that may guide evolutionary change. Here we report how development governs relative size and number of cheek teeth, or molars, in the mouse. We constructed an inhibitory cascade model by experimentally uncovering the activator-inhibitor logic of sequential tooth development. The inhibitory cascade acts as a ratchet that determines molar size differences along the jaw, one effect being that the second molar always makes up one-third of total molar area. By using a macroevolutionary test, we demonstrate the success of the model in predicting dentition patterns found among murine rodent species with various diets, thereby providing an example of ecologically driven evolution along a developmentally favoured trajectory. In general, our work demonstrates how to construct and test developmental rules with evolutionary predictability in natural systems.

See also:

Polly, P.D., Development with a bite, Nature 449, 413-415, (27 September 2007) | doi:10.1038/449413a

Fact: human males have a voice pitch in the range 90-160 Hz, with a mean of 120 Hz. The range for women is 180-280 Hz. There is a significant difference - this is vocal sexual dimorphism.
Hypothesis: a Darwinian explanation suggests that there is a link between voice pitch and reproductive success.
Testing the hypothesis: an association has been found, in the Hazda tribe of Tanzania, between the depth of pitch of male voices and the number of children the subjects father.
Conclusion: "These findings suggest that the association between voice pitch and reproductive success in men is mediated by differential access to fecund women. Furthermore, they show that there is currently selection pressure for low-pitch voices in men."

Whilst this sounds like the authors are using the scientific method, the details are not so clear. The authors admit: "we don't know the exact reason that these men with deeper voices have fathered more children". They draw from the work of others to suggest possible mechanisms: "Previous studies have also shown a relationship between testosterone and deeper vocal pitch, and so increased testosterone may contribute to the male's ability to hunt." Successful hunters are likely to be recognised by the tribe, and these men may then be regarded as desirable husbands, perhaps marry earlier and thereby have greater opportunity to father children. None of these steps of the explanation appear to have been validated.
There appears to be no questions rising in the minds of researchers about extrapolating from the Hadza, a Tanzanian hunter-gatherer tribe, to humans in general. The press release comments:

Because of their similarity to the hunter-gatherer lifestyle of our ancestors, the reproductive success of the Hadza could be indicative the way that human beings evolved. "It's possible that vocal dimorphism has evolved over thousands of years, partly due to mate selection," says Apicella. "Perhaps at one time, men and women's voices were closer in pitch than they are today."

These comments deserve to be handled more critically, because although the Hazda are hunter-gatherers, they are not characterised as carnivores. They eat a starchy diet heavy in roots and tubers. How do we know they are not descendants of farming ancestors and no more representative of our ancestors than any other human community?
Can a design framework for research help us here? This framework would posit advantages for sexual dimorphism (including vocal characteristics) that would go beyond reproductive success by predicting a variety of other benefits for individuals and for society. The design framework is not inconsistent with reproductive success, but it would suggest that focusing on this one consequence is a case of trivialising the phenomenon.

Voice pitch predicts reproductive success in male hunter-gatherers
C.L. Apicella, D.R. Feinberg, F.W. Marlowe
Biology Letters, FirstCite, September 25 2007 | doi 10.1098/rsbl.2007.0410

Abstract: The validity of evolutionary explanations of vocal sexual dimorphism hinges upon whether or not individuals with more sexually dimorphic voices have higher reproductive success than individuals with less dimorphic voices. However, due to modern birth control methods, these data are rarely described, and mating success is often used as a second-rate proxy. Here, we test whether voice pitch predicts reproductive success, number of children born and child mortality in an evolutionarily relevant population of hunter-gatherers. While we find that voice pitch is not related to reproductive outcomes in women, we find that men with low voice pitch have higher reproductive success and more children born to them. However, voice pitch in men does not predict child mortality. These findings suggest that the association between voice pitch and reproductive success in men is mediated by differential access to fecund women. Furthermore, they show that there is currently selection pressure for low-pitch voices in men.

See also:

Male voice pitch predicts reproductive success in hunter-gatherers, EurekAlert, 25 September 2007.

"Mitosis and meiosis are the most exciting and elaborate processes that occur during the life of dividing cells. Over the course of little more than an hour (for mitosis), macromolecular structures throughout the cell are reorganized, signalling pathways are activated and silenced, proteins are degraded and, at the end of each division, two daughter cells are born. Not only are mitosis and meiosis wonderfully elaborate, it is also essential that they proceed without error, as mistakes can result in the death of the organism."

The authors of a significant review article ask: "How are all of these processes coordinated?" and go on to review the knowledge that has emerged to date. In particular, they focus attention on chromosomal passenger proteins. Previous suspicions that these passenger proteins "might regulate key mitotic processes by moving from place to place in the dividing cell" have been confirmed "and studies of these proteins comprise a major area of ongoing mitosis and meiosis research." What emerges is a fascinating picture of coordinated activity, with events "orchestrated with a precision that is worthy of a classical symphony, with different activities being switched on and off at precise times and locations throughout the cell." In this musical analogy, the chromosomal passenger complex (CPC) is the conductor.

"We now understand that the CPC orchestrates mitosis and meiosis at several different levels to ensure that two daughter cells are generated with an accurate distribution of genetic material. The regulation of kinetochore-microtubule attachments in a bipolar spindle, the delay of anaphase onset when spindle tension is aberrant, the regulation of sister chromatid cohesion and the completion of cytokinesis are among the crucial mitotic functions that require CPC activity."

The authors conclude by utilising the analogy again: "The score for the elaborate and wonderful symphonies that are mitosis and meiosis therefore remains unfinished, with much more to be written." This comment is worthy of further thought. An unfinished symphony implies that the composer ended the work prematurely. However, we would not be here if mitosis and meiosis were not working smoothly during our personal experience of life. The symphony IS already written, but we have not yet fully read the score. We have heard the music in part - much more awaits us! The control systems within cells evoke aesthetic feelings akin to hearing a skilled orchestra led by a gifted and inspirational conductor. The important point is that the awe and wonder is our response to what we find in the natural world. We discover a score (we do not write it) and the more we discover, the more we put the music back into our mechanistic models of the world. Contrast this with the much-quoted words of Richard Dawkins:

"The universe we observe has precisely the properties we should expect if there is, at bottom, no design, no purpose, no evil and no good, nothing but blind, pitiless indifference. As that unhappy poet A.E. Housman put it: 'For Nature, heartless, witless Nature Will neither care nor know.' DNA neither cares nor knows. DNA just is. And we dance to its music."
(Dawkins R., "River out of Eden: A Darwinian View of Life," Phoenix: London, 1996, p.155.)

We are not dancing to music that is heartless and witless! We are dancing to music that has a depth of meaning we are only beginning to grasp.

Chromosomal passengers: conducting cell division
Sandrine Ruchaud, Mar Carmena and William C. Earnshaw
Nature Reviews Molecular Cell Biology, 8, 798-812 (October 2007) | doi:10.1038/nrm2257

Abstract: Mitosis and meiosis are remarkable processes during which cells undergo profound changes in their structure and physiology. These events are orchestrated with a precision that is worthy of a classical symphony, with different activities being switched on and off at precise times and locations throughout the cell. One essential 'conductor' of this symphony is the chromosomal passenger complex (CPC), which comprises Aurora-B protein kinase, the inner centromere protein INCENP, survivin and borealin (also known as Dasra-B ). Studies of the CPC are providing insights into its functions, which range from chromosome-microtubule interactions to sister chromatid cohesion to cytokinesis, and constitute one of the most dynamic areas of ongoing mitosis and meiosis research.

Quote:
"Perhaps the problem is that for some scientists reductionism functions as a security blanket. It avoids the need to ask too many questions, to stare into the abyss of fundamental uncertainty. If we abandoned the universality of the reductionist approach, who knows what would happen? For sure, the nature of biological science would change. But so it should!"
Denis Noble, The Music of Life: Biology beyond the Genome. Oxford UP, 2006, p. 66.

Homo erectus bones from Dmanisi, Georgia, have been identified as the "earliest known hominins to have lived outside of Africa in the temperate zones of Eurasia." Differences between them and other representatives of H. erectus have been carefully scrutinised. Some have commented that the differences suggest the Dmanisi bones are transitional between habilis and erectus, but others emphase the highly variable nature of early erectus fossil material.
In a News & Views essay, Daniel Lieberman wrote: "When viewed close up, however, the Australopithecus-Homo transition has always been murky. One problem is that we don't know enough about Homo habilis, the putative ancestor of H. erectus."
Also, "In some respects, H. habilis looks like a good candidate as the ancestor of H. erectus; it has a vertical face, teeth of intermediate size between those of australopithecus and H. erectus, and an intermediate sized brain. But the oldest fossils definitively attributed to H. habilis are 1.9 million years old and thus no older than the oldest H. erectus fossils. Moreover, Spoor et al also report a new H. habilis upper jaw dated to 1.44 million years ago, extending the species' temporal overlap with H. erectus. (For more on Spoor et al., go here).
Lieberman introduced his essay with these words: "The fossil record of human evolution is like a pointillist painting: one sees a different picture close up from when one stands back." This analogy is actually very helpful. Normally, in science, gaining more data helps to fill in the picture so that the details can be seen more clearly. However, this is not so in human evolution. Gaining more data frequently leads to headlines that suggest a radical rethink of previous "knowledge". In this case, we have more data implying a mosaic of characters and greater variability. Zooming in on the picture is not revealing the details of a transformation story. Like a pointillist painting, evolution is only apparent from a distant vantage point. Close up, we see masses of data, but no coherent picture. In situations like this, it is particularly important not to impose theory (of evolutionary transformation) on the data.

Postcranial evidence from early Homo from Dmanisi, Georgia
David Lordkipanidze, Tea Jashashvili, Abesalom Vekua, Marcia S. Ponce de Leon, Christoph P. E. Zollikofer, G. Philip Rightmire, Herman Pontzer, Reid Ferring, Oriol Oms, Martha Tappen, Maia Bukhsianidze, Jordi Agusti, Ralf Kahlke, Gocha Kiladze, Bienvenido Martinez-Navarro, Alexander Mouskhelishvili, Medea Nioradze & Lorenzo Rook.
Nature, 449, 305-310 (20 September 2007) | doi:10.1038/nature06134

Abstract: The Plio-Pleistocene site of Dmanisi, Georgia, has yielded a rich fossil and archaeological record documenting an early presence of the genus Homo outside Africa. Although the craniomandibular morphology of early Homo is well known as a result of finds from Dmanisi and African localities, data about its postcranial morphology are still relatively scarce. Here we describe newly excavated postcranial material from Dmanisi comprising a partial skeleton of an adolescent individual, associated with skull D2700/D2735, and the remains from three adult individuals. This material shows that the postcranial anatomy of the Dmanisi hominins has a surprising mosaic of primitive and derived features. The primitive features include a small body size, a low encephalization quotient and absence of humeral torsion; the derived features include modern-human-like body proportions and lower limb morphology indicative of the capability for long-distance travel. Thus, the earliest known hominins to have lived outside of Africa in the temperate zones of Eurasia did not yet display the full set of derived skeletal features.

See also:

Dalton, R., Treasure trove of Homo erectus found, news@nature.com: 19 September 2007; | doi:10.1038/news070917-6

Lieberman, D.E., Homing in on early Homo, Nature, 449, 291 - 292 (20 September 2007) | doi:10.1038/449291a

Luskin, C. Human Origins Update: Harvard Scientist and New York Times Reporter Get the "Plug Evolution Memo"...Sort of
Evolution News & Views, September 22, 2007

Most people interested in human evolution have learned that australopithecenes gave rise to Homo habilis which in turn gave rise to Homo erectus. Also, that Homo erectus is the ancestor to all the other Homo species including H. sapiens. This linear picture was undermined by recent finds east of Lake Turkana in Kenya. The research team discovered habilis and erectus fossils in the same rock formation. "The new fossils confirm the distinctiveness of H. habilis and H. erectus, independently of overall cranial size, and suggest that these two early taxa were living broadly sympatrically in the same lake basin for almost half a million years." This lengthy coexistence means that the species occupied distinct ecological niches. According to the lead author: "the easiest way to interpret these fossils is that there was an ancestral species that gave rise to both of them somewhere between two and three million years ago."
In a news report, Minkel writes: "The late evolutionary biologist Stephen Jay Gould used to rail against the notion of a ladder of perfection rising from early humanlike species to Neandertals to Homo sapiens at the pinnacle. Two new fossils unearthed near a lake in Kenya bear out Gould's preferred metaphor for human evolution - that of a bush with many branches." Whilst the new finds do undermine the popular "linear" view of human evolution, they are not necessarily support for a "bush with many branches" view. The latter results from the data being viewed with the premise that evolutionary transformation must have occurred and that apelike animals did turn into Homo sapiens. Without this premise, the data are not compelling.

Implications of new early Homo fossils from Ileret, east of Lake Turkana, Kenya
F. Spoor, M. G. Leakey, P. N. Gathogo, F. H. Brown, S. C. Anton, I. McDougall, C. Kiarie, F. K. Manthi and L. N. Leakey.
Nature 448, 688-691 (9 August 2007) | doi:10.1038/nature05986

Sites in eastern Africa have shed light on the emergence and early evolution of the genus Homo1, 2, 3, 4, 5, 6. The best known early hominin species, H. habilis and H. erectus, have often been interpreted as time-successive segments of a single anagenetic evolutionary lineage3, 7, 8, 9, 10. The case for this was strengthened by the discovery of small early Pleistocene hominin crania from Dmanisi in Georgia that apparently provide evidence of morphological continuity between the two taxa11, 12. Here we describe two new cranial fossils from the Koobi Fora Formation, east of Lake Turkana in Kenya, that have bearing on the relationship between species of early Homo. A partial maxilla assigned to H. habilis reliably demonstrates that this species survived until later than previously recognized, making an anagenetic relationship with H. erectus unlikely. The discovery of a particularly small calvaria of H. erectus indicates that this taxon overlapped in size with H. habilis, and may have shown marked sexual dimorphism. The new fossils confirm the distinctiveness of H. habilis and H. erectus, independently of overall cranial size, and suggest that these two early taxa were living broadly sympatrically in the same lake basin for almost half a million years.

See also:
Minkel, J.R. New Fossils Illustrate "Bushiness" of Human Evolution, Scientific American News, 8 August 2007

Luskin, C. Paleoanthropologists Disown Homo habilis from Our Direct Family Tree, Evolution News & Views, August 9, 2007

"Several years ago, paleontologist Jennifer Clack of the University of Cambridge in the U.K. proposed that hearing evolved [in the Mesozoic] to help vertebrates catch the buzzing insects that were undergoing an evolutionary explosion around the same time." However, a report has now been published demonstrating the presence of true tympanic ears in reptiles from the Permian Period, reputed to be 60 million years earlier, when "buzzing insects were not as prevalent". "The researchers were able to identify six apparently closely related species, all of which showed clear evidence of large, eardrumlike structures covering much of their cheeks. In the better preserved specimens, inner ear bones similar to those of modern ears were found, including a stapes."
The researchers "examined the functional performance of this unique and unexpected auditory arrangement, and discovered that these little reptiles were able to hear at least as well as a modern lizard." New data like this is a stimulus to new hypotheses and the authors have suggested "that the auditory sense might have arisen among vertebrates that lived in dimly lit niches."
Rather than discuss the Darwinian tendency to explain origins via selection for functionality (hearing buzzing insects enhances survival/hearing allows hunting in the night and enhances survival), I want to draw attention to the early appearance of all the important complex organs: "By the end of the Paleozoic many of the major adaptive features characterizing amniote evolution had evolved; important examples include the ability for flight, secondary aquatic lifestyle, and high-fiber herbivory. The discovery of a highly-evolved auditory apparatus in Middle Permian parareptiles even further emphasizes that the entire groundplan for the impressive evolutionary history of amniotes was already largely in place by the end of the Paleozoic; what followed was in fact only a subsequent tinkering of earlier inventions." Darwinism needs time, but the fossil record no longer provides it. Complexity appears abruptly and most of the subsequent variations are adaptations. Welcome the day when evolutionary theorists appreciate that the origin of complexity and the "subsequent tinkering" are two distinct issues to address.

Impedance-Matching Hearing in Paleozoic Reptiles: Evidence of Advanced Sensory Perception at an Early Stage of Amniote Evolution
Johannes Muller, Linda A. Tsuji
PLoS ONE, 2007, 2(9): e889. doi:10.1371/journal.pone.0000889

Background: Insights into the onset of evolutionary novelties are key to the understanding of amniote origins and diversification. The possession of an impedance-matching tympanic middle ear is characteristic of all terrestrial vertebrates with a sophisticated hearing sense and an adaptively important feature of many modern terrestrial vertebrates. Whereas tympanic ears seem to have evolved multiple times within tetrapods, especially among crown-group members such as frogs, mammals, squamates, turtles, crocodiles, and birds, the presence of true tympanic ears has never been recorded in a Paleozoic amniote, suggesting they evolved fairly recently in amniote history.
Conclusions/Significance: Using modern amniotes as analogues, the possession of an impedance-matching middle ear in these parareptiles suggests unique ecological adaptations potentially related to living in dim-light environments. More importantly, our results demonstrate that already at an early stage of amniote diversification, and prior to the Permo-Triassic extinction event, the complexity of terrestrial vertebrate ecosystems had reached a level that proved advanced sensory perception to be of notable adaptive significance.

See also:

Balter, M., Let's Hear It for the First Ears, ScienceNOW Daily News, 12 September 2007.

Prehistoric Reptiles From Russia Possessed The First Modern Ears, Science Daily, September 12, 2007.

It is interesting to find a biological article referring to "mountains of data" challenging "old views" that is not concerned with the supposed "mountains of evidence" against the concept of design in nature! In this case, the focus is on genes: "Only 6 years later, the landscape of the genome is already proving to be dramatically different than most scientists had expected."
The trigger for the new views has been a project called the Encyclopedia of DNA Elements (ENCODE), previously noted here for contributing to the overthrow of the Junk DNA paradigm. Barry: "Even more surprisingly, the junk DNA may not be junk after all. Most of this supposedly useless DNA now appears to produce transcriptions of its genetic code, boosting the raw information output of the genome to about 62 times what genes alone would produce."
However, this is only part of the challenge to the "old views". There is a need for some radical thinking about genes themselves. Barry summarises the situation in his useful online article. An academic paper developing these new ideas is by Gingeras. He writes: "studies focused on noncoding transcripts of known biological function have begun to reveal a complexity in genome organization not captured by the current collection of annotations, prompting a reconsideration of what constitutes the fundamental functional element of the genome and how it relates to phenotypic variation." He argues the case for the definition of a new operational unit which will supersede the gene in our thinking. "If each of the transcripts sharing sequence space with a protein-coding gene are capable of effecting the same phenotype/function, then a gene can consist of multiple (coding and noncoding) transcripts and regulatory regions (Fig. 1D). This increased complexity of both the components of a gene and its boundaries begs for a simpler operational unit that can be used to link a specific DNA sequence to phenotype/function. Individual RNA transcripts provide these fundamental operational elements."
Whilst this conclusion appears eminently justified by the evidence, there are dramatic implications for evolutionary theory, which has so often been developed using concepts that are now out-of-date. We have to discard not only Junk DNA, but also the "Central Dogma", the "selfish gene" and the conceptual model of characters controlled by single genes and under the influence of natural selection forces. Barry puts his finger on a significant challenge this brings to neoDarwinian evolutionary theory:

"The same sequences are being used for multiple functions," says Thomas R. Gingeras of Affymetrix. That introduces complications into the evolution of the genome, which had until recently been assumed to act through single DNA mutations affecting single genes. Now, "a mutation in one of those sequences has to be interpreted not only in terms of [one gene], but [of] all the other transcripts going through the region," Gingeras explains.
The implications of this single mutation-multiple consequence model are still a matter of debate. In some cases, the RNA transcripts from DNA that overlaps a protein-coding gene regulate that same gene, so a mutation could affect both the structure and the regulation of a protein. But often, those transcripts regulate genes that are far away, or even on different chromosomes. This complex interweaving of genes, transcripts, and regulation makes the net effect of a single mutation on an organism much more difficult to predict, Gingeras says.

Nickerson has some significant comments on the significance of these findings:

The discoveries have one common theme: Cellular processes long assumed to be "genetic" appear quite often to be the result of highly complex interactions occurring in regions of DNA void of genes. This is roughly akin to Wall Street waking to the realization that money doesn't make the world go 'round, after all.
"It's a radical concept, one that a lot of scientists aren't very happy with," said Francis S. Collins, director of the National Human Genome Research Institute. "But the scientific community is going to have to rethink what genes are, what they do and don't do, and how the genome's functional elements have evolved." "I think we're all pretty awed by what we're seeing," Collins said. "It amounts to a scientific revolution."

The complexity discovered has been difficult to describe. One researcher is quoted as saying: "The picture that's emerging [of how living cells actually operate and evolve] is so immensely more complicated than anyone imagined, it's almost depressing". Casual observers might say they find chaos in the emerging picture of the genome, but systems biology is tracking down extraordinary sophistication at the molecular biology level, indicating that theories (like Darwinism) that are undirected and stochastic have little to offer 21st Century biology.

Genome 2.0 - Mountains of new data are challenging old views
Patrick Barry
Science News, September 8, 2007; 172(10), p. 154

First para: When scientists unveiled a draft of the human genome in early 2001, many cautioned that sequencing the genome was only the beginning. The long list of the four chemical components that make up all the strands of human DNA would not be a finished book of life, but a road map of an undiscovered country that would take decades to explore. Only 6 years later, the landscape of the genome is already proving to be dramatically different than most scientists had expected.

Origin of phenotypes: Genes and transcripts
Thomas R. Gingeras
Genome Research, 2007 17: 682-690. [Open Access]

Abstract: While the concept of a gene has been helpful in defining the relationship of a portion of a genome to a phenotype, this traditional term may not be as useful as it once was. Currently, "gene" has come to refer principally to a genomic region producing a polyadenylated mRNA that encodes a protein. However, the recent emergence of a large collection of unannotated transcripts with apparently little protein coding capacity, collectively called transcripts of unknown function (TUFs), has begun to blur the physical boundaries and genomic organization of genic regions with noncoding transcripts often overlapping protein-coding genes on the same (sense) and opposite strand (antisense). Moreover, they are often located in intergenic regions, making the genic portions of the human genome an interleaved network of both annotated polyadenylated and nonpolyadenylated transcripts, including splice variants with novel 5' ends extending hundreds of kilobases. This complex transcriptional organization and other recently observed features of genomes argue for the reconsideration of the term "gene" and suggests that transcripts may be used to define the operational unit of a genome.

See also:

Nickerson, C. DNA unraveled, Boston Globe, September 24, 2007

The quest for signs of life in the Earth's oldest rocks shows no signs of diminishing. Wen-Long Zang is concerned with information coming from metamorphosed rocks, where there is growing evidence for the preservation of single-celled animals in metamorphosed chert. Newly published is his discovery of spinose acritarchs in the Harris Greenstone Domain in South Australia. This is dated as Late Archaean, around 2500 million years, and part of the first supercontinent Kenorland.
The significance of his report is that these particular fossils are eukaryotes, not the bacterial cells that we normally associate with the Archaean. Previous to this finding, eukaryotes were suspected in the Archaean because researchers had detected biomarkers, but the "oldest confirmed macroscopic eukaryotic algae were reported from the 2100-1900 Ma Neganee Iron Formation, Michigan." This led many to link the evolution of eukaryotes with the rise of oxygen in the Earth's atmosphere (the Great Oxidation Event is dated about 2.4 Ga). However, there have been several significant and related finds: Archaean oil, eukaryotic biomarkers in the Archaean, and reinterpretation of evidences relating to lack of atmospheric oxygen prior to 2.4 Ga. Dutkiewicz et al (2006) write: "The presence of abundant biomarkers for cyanobacteria and eukaryotes derived from and trapped in rocks deposited before the Great Oxidation Event is consistent with an earlier evolution of oxygenic photosynthesis than previously thought and suggests that some aquatic settings had become sufficiently oxygenated for sterol biosynthesis by this time."
The picture emerging of the Late Archaean is one that includes prokaryotes and eukaryotes, photosynthesis, an oxygenated atmosphere and lots of biological activity. This is a big contrast from the picture even 10 years ago. The significance for our thinking about origins is that the eons of time demanded by Darwinian processes are not available. Eukaryotic life appears to be irreducibly complex, yet these life forms appear as body fossils in the Late Archaean and their origin is still one of the greatest mysteries of biology. This constitutes evidence that Darwinism is not a good way to gain understanding, and also evidence that an information-rich approach is the only viable way forward.

Deposition and deformation of late Archaean sediments and preservation of microfossils in the Harris Greenstone Domain, Gawler Craton, South Australia
Wen-Long Zang
Precambrian Research, June 2007, 156(1-2): 107-124.

Abstract: Late Archaean sediments, felsic, mafic and ultramafic volcanics in the Harris Greenstone Domain, central Gawler Craton, South Australia are interpreted to have been deposited at ~2520 Ma in back arc settings and were metamorphosed at ~2440 Ma. Sedimentary evidence suggests that the metasediments in the Domain might have been deposited in fluvial/estuarine to deltaic-shelf environments and deformed by intermediate amphibolite facies metamorphism accompanying the Sleafordian Orogeny at ~2440 Ma. Microfossils are preserved in metachert layers that had been boudinaged into lenses. These microfossils, including spinose acritarchs, are organic-walled as evidenced by Laser-Raman microscopy. Fossil-bearing off-cuts were then treated by HF and similar microfossils, degraded organic matter and acid-resistant minerals, such as zircon, were exposed in situ on the etched surface. Their morphologically complex forms and detailed wall structures suggest that these microfossils are of primary biological origin. The microfossils in foliated metachert lenses, either from original deposition or from post-depositional quartz veins, are older than the ~2440 Ma age of the Sleafordian Orogeny, which provides a minimum age for the host rocks. In either case, these spinose acritarchs are the oldest protists known to date.

See also:

Dutkiewicz, A., et al. Biomarkers from Huronian oil-bearing fluid inclusions: An uncontaminated record of life before the Great Oxidation Event. Geology: 2006, Vol. 34, No. 6, pp. 437-440.

Geneticist Michael Majerus has had a long-standing interest in melanism and specifically the peppered moth example of industrial melanism.

At a recent meeting of the European Society for Evolutionary Biology in Uppsala, he reported on experiments he has been carrying out since the year 2000 that were designed with a more rigorous methodology than was used by Bernard Kettlewell in the 1950s. "He released black or white moths into cylindrical cages on branches at dusk. Before dawn, he removed the cages and counted how many moths subsequently disappeared from their resting places. He showed that selection now favors pale moths, with 21% eaten by birds, compared with 29% of the black ones." It is possible to look critically at the methodology and at the statistics dealing with significance, but this only qualifies the conclusions. I am happy to accept that the evidence is now stronger that there is differential predation by birds. Where does this take us?
The concluding words of Majerus' lecture are these: "If the rise and fall of the peppered moth is one of the most visually impacting and easily understood examples of Darwinian evolution in action, it should be taught. It provides after all: The Proof of Evolution." This quote explains why the issue is still important: Darwinists have always sought to use the peppered moth story as a proof of Darwinian evolution. This is a burden that cannot be carried by the evidence. Even with Majerus' new improved methodology, we have an example of natural selection within the peppered moth population with differential predation being the causal mechanism. It is an extraordinary mental leap to go from this to the origin of novelty, complexity and new body plans - which remain the central challenges for any theory of evolutionary transformation.
According to the report, Majerus says that the new research will "conclusively rebut creationist claims." It is sad that Majerus and the Science reporter do not see this as an issue that must be faced by scientists. Is it scientifically defensible to find an example of natural selection within a population of an animal, and then use this as an evidence for evolutionary transformation from the first single cell to the extraordinary diversity of life that we find in the biosphere? When this simple question is answered with a negative, then we can have a more constructive dialogue. In the meantime, let's teach the peppered moth story, but without overloading it with Darwinian dogma. Kettlewell did make mistakes, and Majerus has made progress in correcting them. But Majerus has a long way to go before he addresses the real mistakes that still permeate our educational system.

Last Word on Moths
Random Samples
Science, 317, 7 September 2007, 1301.

A Cambridge University professor has completed a 6-year experiment with peppered moths that he says should conclusively rebut creationist claims. [snip].

See also:

Nelson, P. Michael Majerus: Peppered Moths DO Rest On Tree Trunks, And Incidentally, God Doesn't Exist
Uncommon Descent, 28 August 2007

Wells, J. Exhuming the Peppered Mummy, Discovery Institute, August 30, 2007

de Roode, J., Reclaiming the peppered moth for science, New Scientist, 08 December 2007.

Quotation from Fodor, J. Why Pigs Don't Have Wings, London Review of Books, 18 October 2007:
"It wouldn't be unreasonable for a biologist of the Darwinist persuasion to argue like this: 'Bother conceptual issues and bother those who raise them. We can't do without biology and biology can't do without Darwinism. So Darwinism must be true.' Darwinists do often argue this way; and the fear of hyperbole seems not to inhibit them. The biologist Theodosius Dobzhansky said that nothing in biology makes sense without Darwinism, and he is widely paraphrased. The philosopher Daniel Dennett says that 'in a single stroke, the idea of evolution by natural selection unifies the realm of life, meaning and purpose with the realm of space and time, cause and effect, mechanism and physical law.' (Phew!) Richard Dawkins says, 'If superior creatures from space ever visit earth, the first question they will ask, in order to assess the level of our civilisation, is: "Have they discovered evolution yet?"' Shake a stick at a Darwinist treatise and you're sure to find, usually in the first chapter, claims for the indispensability of adaptationism. Well, if adaptationism really is the only game in town, if the rest of biology really does presuppose it, we had better cleave to it warts and all. What is indispensable therefore cannot be dispensed with, as Wittgenstein might have said. The breaking news, however, is that serious alternatives to adaptationism have begun to emerge; ones that preserve the essential claim that phenotypes evolve, but depart to one degree or other from Darwin's theory that natural selection is the mechanism by which they do."

Roger White is interested in the way scientists think, in particular, those researching the origins of life (OOL). As is appropriate for a philosopher, he has no axe to grind regarding the technical details.

"Let me be clear at the outset about the aim and scope of this paper. It is not my purpose to evaluate specific scientific proposals on the origin of life. My discussion will be very abstract, not entering into any of the details of cutting edge research. The reason for this, as I hope will become clear, is that my concern is with an abstract epistemological question which arises prior to detailed investigation, and does not hinge on the details of research."

He introduces his argument by considering three pebble patterns: scattered in a disorderly fashion, ordered on a beach according to size, and arranged to form a smiling stick figure. This allows him to discuss Chance, Law and Design as causal explanations (those familiar with Dembski's design filter will not struggle to grasp this).

Some OOL researchers belong to the "Chance" school, described here as the "Almost a Miracle Camp". Quotes are provided from Crick, Mayr and Monod. But this group is in the minority.

"What interests me is just why the 'Almost a Miracle' camp is so small. Why is it that the vast majority of researchers in the field agree with Dawkins that we cannot credibly suppose that life arose by spontaneous random generation if the chance of this happening was extremely small."

So White develops his argument by looking at the grounds for thinking that Law ("non-intentional biasing") must be invoked. This involves some logic analysis and a critical appraisal of what the OOL researchers are saying. Very quickly, this leads to comparisons with "intentional biasing" by an external agent. Interestingly, White does not give much credence to those who declare this option to be a science-stopper and alien to the scientific mind. Philosophically, it is a perfectly reasonable option to consider. The major objection to it is identified as the Preference Problem: how can we possibly know how such an external agent might act?

But non-intentional biasing does not fare well either. White looks first at physical parameters: "Does the fact that certain values are necessary for life make them more likely to be favored by laws? [. . .] Blind physical laws are no more naturally drawn toward states of affairs with value than blind chance is." He then goes on to discuss complexity.

"What has struck scientists with such awe is that even the very simplest cell is an enormously complicated piece of machinery, more intricate and complex than any machine made by humans. No doubt life began in a somewhat simpler form, but it is widely held that the kind of systems required for a process of natural selection to get going would also have to be extraordinarily intricate and complex. It might seem that this alone is what stands in need of explanation, whether or not the machinery happens to be living or life-producing."

The ensuing argument is highly reminiscent of Behe's definition of irreducible complexity. The conclusion is that non-intentional biasing does not take us beyond Chance in the discussion of causation. "Why then are most scientists so reluctant to allow too much chance into their accounts of life's emergence?" The explanation offered is that they have a "gut reaction to the data".

As far as the overall conclusion is concerned, White comments:

"That molecular replicating systems appear to be designed by an agent is sufficient to convince us that they didn't arise by chance. But in scientific reasoning, non-intentional explanations are to be preferred, if possible (some would say at all costs), to intentional ones - hence the motivation to find a non-intentional explanation of life. [. . .] If the reason we doubt the Chance Hypothesis is that we suspect that life is due in part to intelligent agency, this by itself gives us no reason to expect there to be a non-intentional explanation for life. If on reflection we do not find the hypothesis of intentional biasing acceptable, then we are left with no reason at all to doubt that life arose by chance."

White's paper covers ground that is familiar to ID advocates and it is refreshing to read the analysis and conclusions. White cannot be dismissed as a mere philosopher, for there are a number of biologists who are coming to similar conclusions. One of these is Koonin, who has recognised that explaining the OOL is "a puzzle that defeats conventional evolutionary thinking". He appeals to infinities embedded in multiverse theory to find a mechanistic answer, thereby avoiding the need to make design inferences. I wonder what White would make of Koonin's argument?

Does Origins of Life Research Rest on a Mistake?
Roger White
Nous, 41(3),(September 2007) , 453-477. | doi:10.1111/j.1468-0068.2007.00655.x

No abstract. From the Introduction: What puzzles me is why, if appeals to intelligent agency are not on the table, we should be so reluctant to attribute the origin of life largely to chance. My purpose is to question a common approach to the subject of life's origin. Very roughly, this approach consists in an aversion to appeals to chance in accounting for life's origin prior to an evaluation of alternative hypotheses.

Massimo Pigliucci goes on the offensive when he writes: "I have little patience for the pretense of a "fair and balanced view," when we all know that balance comes out of discussions and disagreements among peers, not from the point of view of a single individual". In this case, the individual is Michael Lynch, author of The Origins of Genome Architecture and Pigliucci is reviewing the book as one of his peers.
Lynch represents an 'evolved modern synthesis' position. He accepts that the modern synthesis needed developing: "One of the central theses of the book is that natural selection is not necessarily the central evolutionary mechanism, as quite a bit of the details of genomic structures and evolution can be accounted for by invoking the neutral mechanisms of mutation, recombination, and drift." With this framework, the explanatory tools are to hand and the remaining task is to use them to systematise the genetic information that we are able to gather. "Lynch's thesis [. . .] is that the theoretical apparatus of evolutionary theory is complete and that people should stop whining about missing pieces and the need for a new synthesis: just study your population genetics and everything will be all right."
Pigliucci presents this as a "rather uninspiring theme". Furthermore, "what the modern synthesis has not given us is a theory of form, and applying population genetics to genomics - as valuable an exercise as that is in its own right - isn't going to give us one either. As much as genes are fundamental to the evolutionary process, there is much more to biology than genes and their dynamics." This is interesting territory to explore, as readers of Why is a Fly not a Horse? will agree.
The review closes with this paragraph: "Ultimately, the main reason we need an expansion of the modern synthesis was pointed out by Popper several years ago: "[the Darwinian theory] is strictly a theory of genes, yet the phenomenon that has to be explained is that of the transmutation of form". Lynch's contribution in The Origins of Genome Architecture goes a long way toward completing our explanation of how genes (and genomes) change over time. Nonetheless, although indeed necessary, population genetics is not even close to sufficient for understanding how phenotypes evolve. There is much more to do, and a large undiscovered country lies out there. Let's take a look." This is the kind of emphasis that ID scientists welcome!

Postgenomic Musings
Massimo Pigliucci
Science 317, 31 August 2007, 1172-1173. DOI: 10.1126/science.1146047

Book Reviewed:
The Origins of Genome Architecture, by Michael Lynch
Sinauer Associates, Sunderland, MA, 2007. 510 pp. ISBN 9780878934843.

Everyone in biology keeps predicting that the next few years will bring answers to some of the major open questions in evolutionary biology, but there seems to be disagreement on what, exactly, those questions are. Enthusiasts of the various "-omics" (genomics, proteomics, transcriptomics, metabolomics, and even phenomics) believe, as Michael Lynch puts it in the final chapter of The Origins of Genome Architecture, that "we can be confident of two things: the basic theoretical machinery for understanding the evolutionary process is well established, and we will soon be effectively unlimited by the availability of information at the DNA level." [snip]

See also:

scordova, Michael Lynch: Darwinism is a caricature of evolutionary biology
Uncommon Descent, 1 September 2007

The cover story of today's Nature is concerned with the first unambiguous finding of fossilised orchid pollen. This is very exciting for evolutionary botanists, who have long been "fascinated by the spectacular adaptations to insect pollination exhibited by orchids".
The discovery involves an extinct worker stingless bee (Meliorchis caribea) preserved in Dominican amber that carries an orchid pollinarium (the male reproductive structure that is transferred as a single unit during pollination). The researchers have analysed the morphology of this structure and assign it to "the extant subtribe Goodyerinae (subfamily Orchidoideae)". This means that an essentially modern orchid was living at the time when the amber was formed (Miocene, considered to be 15-20 million years old). Thus far, there is little here for evolutionary biologists to work with, because the pollinarium does not reveal anything about origins - only that a modern orchid was also present in the Miocene.
In this case, evolutionary theory is imported in order to frame the find and to allow a transformist interpretation. "We use the ages of other fossil monocots and M. caribea to calibrate a molecular phylogenetic tree of the Orchidaceae. Our results indicate that the most recent common ancestor of extant orchids lived in the Late Cretaceous (76-84 Myr ago), and [. . .] support the hypothesis of an ancient origin for Orchidaceae." The report by Ledford adds: "To investigate, the team used genetic information from 55 genera of living orchids to make a family tree, determining which plants are most related to each other today and then working backwards to see when they probably split apart. By dating the amber of their new fossil find to 15-20 million years ago, they could then start to put dates onto the various branches of this tree." The Late Cretaceous age was arrived at by "assuming a relatively constant rate of orchid evolution".
It is important to realise that that these conclusions have not emerged naturally from the empirical data, but are the product of an evolutionary framework adopted by the researchers. With different assumptions and a different methodology, it should not be deemed surprising if the same data can lead to contrasting conclusions. However, on the basis that the "rate of orchid evolution" exhibited by the subtribe Goodyerinae is almost zero, the comment of the lead author is probably correct: "The dinosaurs could have walked among orchids".

Dating the origin of the Orchidaceae from a fossil orchid with its pollinator
Santiago R. Ramirez, Barbara Gravendeel, Rodrigo B. Singer, Charles R. Marshall and Naomi E. Pierce
Nature 448, 1042-1045 (30 August 2007) | doi:10.1038/nature06039

Since the time of Darwin1, evolutionary biologists have been fascinated by the spectacular adaptations to insect pollination exhibited by orchids. However, despite being the most diverse plant family on Earth2, the Orchidaceae lack a definitive fossil record and thus many aspects of their evolutionary history remain obscure. Here we report an exquisitely preserved orchid pollinarium (of Meliorchis caribea gen. et sp. nov.) attached to the mesoscutellum of an extinct stingless bee, Proplebeia dominicana, recovered from Miocene amber in the Dominican Republic, that is 15-20 million years (Myr) old3. This discovery constitutes both the first unambiguous fossil of Orchidaceae4 and an unprecedented direct fossil observation of a plant-pollinator interaction5, 6. By applying cladistic methods to a morphological character matrix, we resolve the phylogenetic position of M. caribea within the extant subtribe Goodyerinae (subfamily Orchidoideae). We use the ages of other fossil monocots and M. caribea to calibrate a molecular phylogenetic tree of the Orchidaceae. Our results indicate that the most recent common ancestor of extant orchids lived in the Late Cretaceous (76-84 Myr ago), and also suggest that the dramatic radiation of orchids began shortly after the mass extinctions at the K/T boundary. These results further support the hypothesis of an ancient origin for Orchidaceae.

See also:

Ledford, H. Amber preserves rare orchid pollen,
news@nature.com: 29 August 2007; | doi:10.1038/news070827-4

Here's some good holiday reading - at least this proved to be the case for me!
According to some contemporary Earth scientists, "Kelvin's famous calculations, coupled with denial of observational data, impeded geoscience for ~100 yr." They are referring, of course, to Lord Kelvin"s 1863 calculations of the age of the Earth, based on mathematical modeling of Earth cooling and direct measurements of thermal gradients. As a physicist, Kelvin sought to develop quantitative, rather than qualitative, science and he found himself in conflict with geologists who wanted an Earth with "no vestige of a beginning". Kelvin"s estimate of 24-400 million years was a thorn in their side for over 40 years. The story that has been passed down to modern-day students of Earth history is that Kelvin had overlooked the possibility of another heat source - that of radioactive decay - which was not discovered until 1903. Then, Kelvin was proved wrong and the geologists claimed victory!
Describing this aa a modern myth, England et al. have provided a splendid service to the Earth science community in putting the record straight. They rework the calculations of Kelvin and demonstrate their coherence and rational basis. They also repeat the calculations to incorporate a radiogenic heat energy component, showing that Kelvin's conclusions are unaffected. "Thus, the discovery of radioactivity did not invalidate Kelvin's calculation for the age of the Earth."
How then did the myth come about and why did it persist? The authors suggest two reasons. The first is that the myth was a "good story" for the geologists, convenient for reinforcing the idea that geophysics must be the servant, not the master, of geology. (In another context, we have met the "good story" justification before). The second is the personal influence of Lord Rutherford, who had a humorous anecdote to tell of his encounters with Kelvin. The authors have an astute comment on the way established researchers can promote opinion as science: "It is hard to dissuade aging scientists, as they slip into their anecdotage, from repeating stories that they find amusing, but their younger colleagues must not mistake such stories for the history of science."
The main thrust of England et al's excellent article is that Kelvin's argument was addressed in 1895 by John Perry, who suggested a different physical model for the interior of the Earth. "Instead of focusing on Kelvin's calculations, Perry suggested, one should examine his assumptions." Perry's revised model introduced the concept of convection, which was at that time controversial, because the Earth was considered a solid. However, although Perry did have a valid response to Kelvin, which did allow the Earth to have an age of several billion years, it was not received with approval. This is because the geologists of the day, like Kelvin, also held to a solid Earth. "If Perry's analysis had been absorbed by the scientific community of the day, then the first radiometric ages for the Earth would have come as confirmation of the convective explanation for the Earth's surface heat flux, and the "fixist" view of the Earth, which exerted such a brake on geological progress in the first half of the twentieth century, would have been difficult to sustain."
In one sense, Kelvin's challenge to the geological community was successful. Whereas previously they thought they could invoke as much time as they wanted (drawing on Hutton's view of the cycle of time), the geologists were forced to come to terms with time's arrow and a beginning for Earth history. For this achievement, Kelvin ought to be held in esteem by students of geology, and not dismissed. Paradoxically, the geologists and Kelvin now emerge as both victors and losers!
This controversy illustrates very well the importance of paradigms in science. Kelvin and the geologists held to a fixist Earth; eventually, Perry's concept of convection came to be adopted; and radioactive decay brought significant changes to our understanding of the Earth. We all work with mental models or paradigms, and science can easily become an exercise in finding ways of making available data fit the particular model we are working with. Far better to operate with multiple working hypotheses, so that alternative paradigms can be tested and potentially falsified. This strategy applies just as much to biology as it does to geology. This is where ID should be seen as a stimulus to good science, facilitating the methodology of testing and falsifying paradigms. The real dangers we face today are the dogmatists in science who refuse to allow their own paradigms to be critically appraised.

John Perry's neglected critique of Kelvin's age for the Earth: A missed opportunity in geodynamics
Philip England, Peter Molnar, Frank Richter
GSA Today, January 2007, 17(1), 4-9.

Abstract: Many readers know the tale of how William Thomson (later Lord Kelvin) calculated the age of the Earth from physical principles and adhered for over 50 years to an estimate that was far younger than geologists' estimates, despite the virtually unanimous opposition of the geological community of the time. The prevalent version of this tale alleges that the discovery of radioactivity simultaneously provided the demonstration (through radiometric dating) that Kelvin had greatly underestimated the age of the Earth and the explanation of why he was wrong (radioactivity being a source of heat that invalidated Kelvin's calculation). We show this popular story to be incorrect; introducing the known distribution of radioactivity into Kelvin's calculation does not invalidate its conclusion. In 1895, before the discovery of radioactivity, John Perry showed that convection in the Earth's interior would invalidate Kelvin's estimate for the age of the Earth, but Perry's analysis was neglected or forgotten, with the consequence that a powerful argument in favor of mobilism was overlooked during the first few decades of debate about continental drift.

See also:

COMMENT by Anne M. Hofmeister, Robert E. Criss
REPLY by Philip England, Peter Molnar, Frank Richter
GSA Today, July 2007, 17(7), 10-11.

Lord Kelvin's Core Values Defended, by David Coppedge, 2 July 2007.

The quest for a plausible scenario for tetrapod evolution continues. Contrary to much popular (and some technical) literature, we have not yet arrived. A new fossil find promises to stimulate a fresh debate about the contribution the Coelacanth makes to our thinking.
The new fossil reveals, for the first time, the pectoral fin endoskeleton. Significantly, it is not like the modern form. "The most conspicuous feature of Shoshonia is its broad, fanshaped pectoral fin supported by a central lobe [. . . This] differs from the near-symmetrical finweb common to the living coelacanth Latimeria and lungfishes and their closest extinct relatives." One of the co-authors said that the fossil's pattern is similar to the branching arrangement still embedded in the fins of paddlefishes, sturgeons and sharks. "To understand the developmental evolution of the limbs of tetrapods, we shouldn't be looking at the fins of our nearest living fish relatives - lungfishes and coelacanths - because they're far too specialized."
The find is significant for consigning an extensive discussion of coelacanth and lungfish fins to the filing cabinet of history. The main author is quoted as saying: "Our fossil shows that what we've been using to define a primitive state is actually very specialized, which means it might give a deceptive view of what evolution was like for these fins skeletons."
Previous discussion drew attention to significant similarities of coelacanth and lungfish fins, and this was considered to give confidence in the validity of the argument. The new fossil turns that upside down also. "The discovery suggests that the two living groups of close fish relatives of tetrapods (lungfish and coelacanth) are both highly specialized [. . .]. Both groups acquired many of the same specializations, but independently of one another." Convergent evolution of derived characters replaces shared primitive traits. Such is the vulnerability of the account of tetrapod evolution that many have regarded as plausible!
What can be said about the similarities with paddlefins, sturgeons and sharks? "With this fossil, we have a conservative pattern in a close relative of tetrapods that is actually conserved in other fish groups outside of this immediate group." Where this will lead is not at all clear. The words in the title of the paper, that the discovery "fills a major gap" might suggest to some that the evolutionary trajectory has been clarified. But the content of the paper says: 'back to the drawing board'!

First discovery of a primitive coelacanth fin fills a major gap in the evolution of lobed fins and limbs
Matt Friedman, Michael I. Coates, Philip Anderson
Evolution & Development, 9(4), 329-337 | doi:10.1111/j.1525-142X.2007.00169.x

SUMMARY: The fossil record provides unique clues about the primitive pattern of lobed fins, the precursors of digit-bearing limbs. Such information is vital for understanding the evolutionary transition from fish fins to tetrapod limbs, and it guides the choice of model systems for investigating the developmental changes underpinning this event. However, the evolutionary preconditions for tetrapod limbs remain unclear. This uncertainty arises from an outstanding gap in our knowledge of early lobed fins: there are no fossil data that record primitive pectoral fin conditions in coelacanths, one of the three major groups of sarcopterygian (lobe-finned) fishes. A new fossil from the Middle-Late Devonian of Wyoming preserves the first and only example of a primitive coelacanth pectoral fin endoskeleton. The strongly asymmetrical skeleton of this fin corroborates the hypothesis that this is the primitive sarcopterygian pattern, and that this pattern persisted in the closest fish-like relatives of land vertebrates. The new material reveals the specializations of paired fins in the modern coelacanth, as well as in living lungfishes. Consequently, the context in which these might be used to investigate evolutionary and developmental relationships between vertebrate fins and limbs is changed. Our data suggest that primitive actinopterygians, rather than living sarcopterygian fishes and their derived appendages, are the most informative comparators for developmental studies seeking to understand the origin of tetrapod limbs.

See also:

Coelacanth Fossil Sheds Light On Fin-to-limb Evolution, Science Daily, August 1, 2007

Flagged up as an "Opinion" paper, the contribution of Forrest and Gross to Trends in Biochemical Sciences cannot be accused of sailing under false colours. Here is opinion in abundance. There is opinion about Michael Behe (notably, his "evasion of the evidential responsibilities of his profession"), William Dembski ("No Free Lunch was, and is, a failed argument"), the ID Movement (characterised by "scientific sterility" and "propelled by powerful cultural and political currents"). There is also opinion about Behe's critics (identified as "competent hands" that have provided "solid refutations"), the Kitzmiller trial (with ID's "deserved legal defeat") and the 'Teach the Controversy' campaign (a "clever marketing ploy").
Academic content of this paper is provided by citing recent objections that have been made to Behe's irreducible complexity arguments. As might be expected from this "Opinion" paper, these arguments are presented as knockdown and final - as though nothing more needs be said! It might be worth reminding ourselves that this just repeats the story of the past 10 years.
I will pick up just one point made in the following quotation. "The ID movement's antipathy to the Enlightenment is understandable: critical inquiry, the central legacy of the Enlightenment, threatens the pre-modern intellectual and religious authoritarianism that the creationists would reinstate." Let it be said that critical enquiry is not the exclusive legacy of the Enlightenment. That emphasis comes from the founders of science in the 17th Century and it is highly prized by ID advocates. This emphasis is much needed today, because Darwinism and the Modern Synthesis appear to be protected from critical scrutiny in schools and colleges. The distinctive legacy of the Enlightenment is rationalism. It is the elevation of reason to create a secular authoritarianism that has managed to establish a stranglehold on the academic community so that any dissenters are deemed to be betrayers of the cause. This paper, sad to say, epitomises the hegemony of the Enlightenment as the authors try to portray dissent from their rationalist ideology as an attack on science.

Biochemistry by design
Barbara C. Forrest and Paul R. Gross
Trends in Biochemical Sciences, Volume 32, Issue 7, July 2007, Pages 301-310

Abstract: Creationists are attempting to use biochemistry to win acceptance for their doctrine in the public mind and especially in state-funded schools. Biochemist Michael Behe is a major figure in this effort. His contention that certain cellular structures and biochemical processes - bacterial flagella, the blood-clotting cascade and the vertebrate immune system - cannot be the products of evolution has generated vigorous opposition from fellow scientists, many of whom have refuted Behe's claims. Yet, despite these refutations and a decisive defeat in a US federal court case, Behe and his associates at the Discovery Institute continue to cultivate American supporters. They are also stepping up their efforts abroad and, worryingly, have achieved some success. Should biochemists (and other scientists) be concerned? We think they should be.

If proteins and enzymes could not recognise their targets, cellular chemistry would be in chaos. "It was realized early that recognizing molecules should be complementary in shape, akin of matching lock and key". The metaphor of lock and key has served many generations of biology students well - only when the protein key meets the substrate lock do the molecules bind and generate a response. However, "half a century of research has shown, however, that in numerous cases, the molecules need to deform in order to bind, as the key is not an exact fit for the molecular lock." What is to be made of these findings? "Why search for a key that does not match its lock exactly, and then require that the imperfect key warp its shape to fit the lock?" Is this an indication that evolution is a tinkerer and cannot get it right? Is it an example of biology making sense without an intelligent designer?
Actually no. The authors of new study of this phenomenon asked one simple question: "Does molecular recognition gain any advantage by such conformational changes?" They concluded that a definite advantage is present. "Optimal specificity is achieved when the ligand is slightly off target; that is, a conformational mismatch between the ligand and its main target improves the selectivity of the process." In more popular language: "The researchers' model shows that the key's deformation actually helps in discerning the right target. Although the energy required to deform the molecular key slightly lowers the probability of its binding to the right target, it also reduces the probability that it will bind to a wrong one by quite a bit."
"This simple mechanism is coined "conformational proofreading" and may explain the observed deformations in many biological recognition systems. Furthermore, conformational proofreading may turn out be a crucial factor affecting the evolution of biological systems, and it may also be useful in the design of artificial molecular recognition systems." The authors write: "Our analysis suggests that conformational changes upon binding may arise as the outcome of an evolutionary selection for enhancing recognition specificity in a noisy environment."
So, something that could have been interpreted as evidence for tinkering evolution is discovered to have advantages after all. Furthermore, it has potential for the design of human systems operating in noisy environments. By invoking "evolutionary selection", the authors suggest an evolutionary context for their work. However, there is no evidence that evolutionary selection was involved, and the link with evolutionary theory is gratuitous. This is another example where the questioning of imperfect design has led to the discovery of exquisite design. The simple question asked by the researchers emerges routinely from the perspective of Intelligent Design.

Conformational Proofreading: The Impact of Conformational Changes on the Specificity of Molecular Recognition
Yonatan Savir, Tsvi Tlusty
PLoS ONE 2(5) 2007: e468. doi:10.1371/journal.pone.0000468

Abstract: To perform recognition, molecules must locate and specifically bind their targets within a noisy biochemical environment with many look-alikes. Molecular recognition processes, especially the induced-fit mechanism, are known to involve conformational changes. This raises a basic question: Does molecular recognition gain any advantage by such conformational changes? By introducing a simple statistical-mechanics approach, we study the effect of conformation and flexibility on the quality of recognition processes. Our model relates specificity to the conformation of the participant molecules and thus suggests a possible answer: Optimal specificity is achieved when the ligand is slightly off target; that is, a conformational mismatch between the ligand and its main target improves the selectivity of the process. This indicates that deformations upon binding serve as a conformational proofreading mechanism, which may be selected for via evolution.

See also:

When Off-target Is Right On, Newswise,26 July 2007.

The fossil record shows a consistent pattern of rapid (sometimes explosive) variation followed by stasis. This is found in the Early Cambrian with the dramatic appearance of animal phyla and, subsequently, with rapid radiations affecting classes, orders and families. Gould's advice to treat stasis as data has not been taken seriously by neodarwinists, who continue to treat the phenomenon as a quirk of history rather than a pervasive characteristic of living things.
Thinking on this topic deserves to be rekindled by a major study of trilobites by Mark Webster. Trilobites have a fossil record stretching from the Early Cambrian to the Late Permian, and 9 orders, 180 families, about 5000 genera and over 15,000 species of trilobites have been described to date. Many of these species are poorly documented and unsuitable for inclusion in a systematic study of morphological variation.
Webster's work involved coding for different character states and finding ways to document the variability. "Overall, approximately 35 percent of the 982 trilobite species exhibited some variation in some aspect of their appearance that was evolving. But more than 70 percent of early and middle Cambrian species exhibited variation, while only 13 percent of later trilobite species did so." The research documented both rapid morphological variation and subsequent stasis. "There's hardly any variation in the post-Cambrian," Webster said. "Even the presence or absence or the kind of ornamentation on the head shield varies within these Cambrian trilobites and doesn't vary in the post-Cambrian trilobites."
In a commentary on these findings, Hunt writes: "This study, in establishing the reality of increased Cambrian variability for trilobites, implies that evolutionary processes in the distant past may have acted differently, or in a different balance than in more recent periods of time." It is important to put the new research into context, for what Webster has done is to use trilobites to quantify a trend that is far from unique.
Hunt goes on to consider two possible ways of making sense of the findings: "These explanations fall into two broad categories: genetic and ecological. The former suggest that Cambrian genomes were less constrained, or otherwise less apt to generate profoundly novel morphologies, whereas the latter invoke the relative sparseness of early animal ecosystems in allowing large evolutionary jumps to become successfully established." This debate gets really interesting if it is recognised that the trilobite record is representative of the norm. "We need to tease apart what's controlling this pattern of high within-species variation. There's a lot more work to do," says Webster. With more and more and more evidences emerging of initial complexity, methodologies based on ID have much to offer. One hypothesis is that radiations occur because organisms are designed to vary, but the process results in genetic impoverishment that leads to stasis.

A Cambrian Peak in Morphological Variation Within Trilobite Species
Mark Webster
Science, 317, 27 July 2007: 499-502.

Abstract: Morphological variation within species is a raw material subject to natural selection. However, temporal change in morphological diversity has usually been studied in terms of variation among rather than within species. The distribution of polymorphic traits in cladistic character-taxon matrices reveals that the frequency and extent of morphological variation in 982 trilobite species are greatest early in the evolution of the group: Stratigraphically old and/or phylogenetically basal taxa are significantly more variable than younger and/or more derived taxa. Through its influence on evolutionary tempo, high intraspecific variation may have played a major role in the pronounced Cambrian diversification of trilobites.

See also:

Hunt, G. Variation and Early Evolution, Science, 317, 27 July 2007: 459-460.

Fossils Older Than Dinosaurs Reveal Pattern Of Early Animal Evolution On Earth, Science Daily, July 26, 2007

Congratulations to Sean Nee for writing a most readable and informative review of Tim Friend's book on the untold story of the archaea. This features in large measure the research of Carl Woese, who has identified the archaea as the third domain of life (alongside bacteria and eukaryotes). "Woese pulled all the evidence together and made the intellectual leap that is now accepted: there is a third domain of life - the archaea. All of this is told, and much more."
For some of us, it is the "much more" that gives this story a special fascination. Not mentioned in the review, but essential to understanding Woese's contribution, is the claim that horizontal gene transfer was extensive in life's early history. Freeman Dyson draws attention to this in a recent essay: "Evolution was a communal affair, the whole community advancing in metabolic and reproductive efficiency as the genes of the most efficient cells were shared. Evolution could be rapid, as new chemical devices could be evolved simultaneously by cells of different kinds working in parallel and then reassembled in a single cell by horizontal gene transfer."
Consequently, Woese is known as someone who questions the role of Darwinism in the early earth. Here is Dyson again: "He presents evidence that Darwinian evolution does not go back to the beginning of life. When we compare genomes of ancient lineages of living creatures, we find evidence of numerous transfers of genetic information from one lineage to another. In early times, horizontal gene transfer, the sharing of genes between unrelated species, was prevalent. It becomes more prevalent the further back you go in time." Darwinism is perceived as a reductionistic approach which fails to do justice to appreciating and understanding complexity. Dyson writes: "Woese's main theme is the obsolescence of reductionist biology as it has been practiced for the last hundred years, with its assumption that biological processes can be understood by studying genes and molecules. What is needed instead is a new synthetic biology based on emergent patterns of organization."
Perhaps these issues were too controversial to go into a review in Nature. Nevertheless, Nee does slip in this comment: "It is probably no coincidence that Oxford's most famous popular writer on biology, Richard Dawkins, notoriously gave only a single page to the third domain of life in his take on biodiversity, The Ancestor's Tale, apparently more interested in things like cabbages." With his strong stance on the logical imperative of neodarwinism, it is understandable that Dawkins is not aligning himself with Woese's opposition to reductionism in biology, nor his rejection of Darwinism prior to the appearance of bacteria, archaea and eukaryotes.
With the proviso that "new ways of thinking" should include ID, we can let Dyson have the last word: "The reductionist physics and the reductionist molecular biology of the twentieth century will continue to be important in the twenty-first century, but they will not be dominant. The big problems, the evolution of the universe as a whole, the origin of life, the nature of human consciousness, and the evolution of the earth's climate, cannot be understood by reducing them to elementary particles and molecules. New ways of thinking and new ways of organizing large databases will be needed."

Introducing the extremophiles
Sean Nee
Nature, 448, 413-414 (26 July 2007) | doi:10.1038/448413a

BOOK REVIEWED-The Third Domain: The Untold Story of Archaea and the Future of Biotechnology, by Tim Friend, Joseph Henry Press: 2007.

First para: Envy the achievement of Carl Woese, who announced his discovery of the third domain of life on Earth a mere 30 years ago. Marvel at the fact that most people are unaware of this three-domain understanding of biodiversity. Admire the journalist Tim Friend who resigned from the newspaper USA Today to write this superb book introducing the public to the third domain. Buy it and enjoy the personalities, the adventures, the drama and the science too, all presented in an admirable mix that is a terrific read.

See also:

Dyson, F., Our Biotech Future, The New York Review of Books, Volume 54, Number 12, July 19, 2007.

Watching geckos dart with equal ease over walls, floors and ceilings must have engaged the attention of countless travellers. How do these little animals do it? It is only in recent years that the answers have been forthcoming. The adhesion comes from van der Waals forces between nano-sized spatulae located on hairs on the gecko's foot and the substrate. The gecko provides a superb demonstration of how nanofibres can be organised to have a macroscopic impact. Research to reproduce the adhesion effects has taken place in many countries and two significant papers report recent progress.
Lee and colleagues have sought to enhance the wet performance of adhesion by incorporating a "synthetic polymer that mimics the wet adhesive proteins found in mussel holdfasts". They report greatly improved adhesion properties. "The hybrid material, which they call a geckel nanoadhesive, proved in initial testing to be adherent under dry and wet conditions. It also adhered much longer under both extremes than previous gecko-based synthetic adhesives, a major issue in this area of research."
The other paper, by Ge and colleagues, reports on a gecko-inspired adhesive tape. "We have demonstrated for the first time a macroscopic flexible patch that can be used repeatedly with peeling and adhesive properties better than the natural gecko foot. The carbon nanotube-based tape offers an excellent synthetic option as a dry conductive reversible adhesive in microelectronics, robotics, and space applications."
One thing we can learn from this particular exercise in biomimetics is that the gecko does not demonstrate just a single trait with enhanced performance. There are issues of adhesion and delamination, self-cleaning, and achieving a sustained adhesive performance. What we have in the gecko is exquisite design and, for that, biomimetics needs a methodology that can relate well to intelligent engineering design concepts. For more on this, go here.
One report of the adhesive tape research says: "Work is now underway to make the tape self-cleaning as well". Interestingly, in 2005, Hansen and Autumn speculated that the nano-sized setae might be self-cleaning, but this ongoing activity suggests that there are more gecko secrets yet to emerge in this area!

A reversible wet/dry adhesive inspired by mussels and geckos
Haeshin Lee, Bruce P. Lee & Phillip B. Messersmith
Nature, 448, 338-341 (19 July 2007) | doi:10.1038/nature05968

The adhesive strategy of the gecko relies on foot pads composed of specialized keratinous foot-hairs called setae, which are subdivided into terminal spatulae of approximately 200 nm (ref. 1). Contact between the gecko foot and an opposing surface generates adhesive forces that are sufficient to allow the gecko to cling onto vertical and even inverted surfaces. Although strong, the adhesion is temporary, permitting rapid detachment and reattachment of the gecko foot during locomotion. Researchers have attempted to capture these properties of gecko adhesive in synthetic mimics with nanoscale surface features reminiscent of setae2, 3, 4, 5, 6, 7; however, maintenance of adhesive performance over many cycles has been elusive2, 8, and gecko adhesion is greatly diminished upon full immersion in water9, 10. Here we report a hybrid biologically inspired adhesive consisting of an array of nanofabricated polymer pillars coated with a thin layer of a synthetic polymer that mimics the wet adhesive proteins found in mussel holdfasts. Wet adhesion of the nanostructured polymer pillar arrays increased nearly 15-fold when coated with mussel-mimetic polymer. The system maintains its adhesive performance for over a thousand contact cycles in both dry and wet environments. This hybrid adhesive, which combines the salient design elements of both gecko and mussel adhesives, should be useful for reversible attachment to a variety of surfaces in any environment.

Carbon nanotube-based synthetic gecko tapes
Liehui Ge, Sunny Sethi, Lijie Ci, Pulickel M. Ajayan, and Ali Dhinojwala
Proceedings of the National Academy of Sciences USA, June 26, 2007, vol. 104, no. 26, 10792-10795 | 10.1073/pnas.0703505104

We have developed a synthetic gecko tape by transferring micropatterned carbon nanotube arrays onto flexible polymer tape based on the hierarchical structure found on the foot of a gecko lizard. The gecko tape can support a shear stress (36 N/cm2) nearly four times higher than the gecko foot and sticks to a variety of surfaces, including Teflon. Both the micrometer-size setae (replicated by nanotube bundles) and nanometer-size spatulas (individual nanotubes) are necessary to achieve macroscopic shear adhesion and to translate the weak van der Waals interactions into high shear forces. We have demonstrated for the first time a macroscopic flexible patch that can be used repeatedly with peeling and adhesive properties better than the natural gecko foot. The carbon nanotube-based tape offers an excellent synthetic option as a dry conductive reversible adhesive in microelectronics, robotics, and space applications.

See also:

Gould, P. Nanotube tape mimics gecko's sticky feet, NanoToday, Volume 2, Issue 4, August 2007, Page 12.

Hansen, W.R. and Autumn, K., Evidence for self-cleaning in gecko setae, Proceedings of the National Academy of Sciences USA, January 11, 2005, vol. 102, no. 2, 385-389 | 10.1073/pnas.0408304102

Nature's secrets yield new adhesive material, EurekAlert, 18 July 2007.

When I first heard of treadmill studies involving chimps and humans, I wondered if the researchers would be open to design paradigms as well as Darwinian adaptation. Would they get beyond the narrow conceptual window exhibited by another group studying assisted bipedalism in orangutans? The answer to that question would appear to be no.
"The researches collected metabolic, kinematic and kinetic data from five chimpanzees and four adult humans walking on a treadmill. The chimpanzees were trained to walk quadrupedally and bipedally on the treadmill. Humans walking on two legs only used one-quarter of the energy that chimpanzees who knuckle-walked on four legs did. On average, the chimpanzees used the same amount of energy using two legs as they did when they used four legs." This is certainly an interesting result. Those who have declared human upright movement to be associated with numerous bad design features will be given food for thought by this research. Those who already recognise design in the human body will regard the new data as strengthening this understanding.
The researchers, however, pursue an adaptationist agenda. The new study is said to provide support "for the hypothesis that walking on two legs, or bipedalism, evolved because it used less energy than quadrupedal knucklewalking." Also, "it has been hypothesized that the reduced energy cost of walking upright would have provided evolutionary advantages by decreasing the cost of foraging." OK, this is an adaptationist hypothesis, but it needs to be tested. Demonstrating an energy differential does not prove a hypothesis: in this case it just stimulates a hypothesis.
This is a situation where the Adaptive Landscape concept may be helpful. When considered holistically, bipedalism involves a whole raft of characters, all of which are needed to form a workable organism. Bipedalism involves arched feet, strong big toes, long legs, upright knee joints, angled femur bones, upright hip joints, straight back, upright skull, flat face and a very fine sense of balance. Taking all these characters into account means that the adaptive landscape looks like to very sharp peaks separated by a wide plain. We could call the peaks Mount Ape Improbable and Mount Human Improbable. The claim that there is an incremental route for an apelike animal to move from one peak to the other has so far eluded Darwinians. The authors comment: "why our unique two-legged gait evolved remains unknown." We have no evidence that apes have ever climbed a Mount Improbable, and there is a long way to go before an adaptive story based on the "evolutionary advantages [of decreased] cost of foraging" can begin to be convincing. Studying evidences of a "more extended hip and a longer hindlimb" do not get close to a holistic appreciation of the issues.
In 2002, a film was produced with the name Most Vertical Primate. In it, a chimpanzee becomes a competent skateboarder. A trailer can be found here. The task of training the chimpanzee to skateboard was impossible. One foot had to be tied to the board and the other positioned carefully so that the animal could get a grip with its toes. Even then, the chimp could not steer or balance. The film of skateboarding was pierced together from tiny clips of a few seconds each. Stuart Burgess, a design engineer, concluded: "Despite the title of the film, the film actually demonstrated that apes are not designed to be vertical!"

Chimpanzee locomotor energetics and the origin of human bipedalism
Michael D. Sockol, David A. Raichlen, and Herman Pontzer
Proceedings of the National Academy of Sciences US, published July 16, 2007, 10.1073/pnas.0703267104
http://www.pnas.org/cgi/content/abstract/0703267104v1?

Bipedal walking is evident in the earliest hominins [Zollikofer CPE, Ponce de Leon MS, Lieberman DE, Guy F, Pilbeam D, et al. (2005) Nature 434:755-759], but why our unique two-legged gait evolved remains unknown. Here, we analyze walking energetics and biomechanics for adult chimpanzees and humans to investigate the long-standing hypothesis that bipedalism reduced the energy cost of walking compared with our ape-like ancestors [Rodman PS, McHenry HM (1980) Am J Phys Anthropol 52:103-106]. Consistent with previous work on juvenile chimpanzees [Taylor CR, Rowntree VJ (1973) Science 179:186-187], we find that bipedal and quadrupedal walking costs are not significantly different in our sample of adult chimpanzees. However, a more detailed analysis reveals significant differences in bipedal and quadrupedal cost in most individuals, which are masked when subjects are examined as a group. Furthermore, human walking is ~75% less costly than both quadrupedal and bipedal walking in chimpanzees. Variation in cost between bipedal and quadrupedal walking, as well as between chimpanzees and humans, is well explained by biomechanical differences in anatomy and gait, with the decreased cost of human walking attributable to our more extended hip and a longer hindlimb. Analyses of these features in early fossil hominins, coupled with analyses of bipedal walking in chimpanzees, indicate that bipedalism in early, ape-like hominins could indeed have been less costly than quadrupedal knucklewalking.

See also:

Study Identifies Energy Efficiency As Reason For Evolution Of Upright Walking, Science Daily July 17, 2007

Burgess, S. The Origin of Man, Day One Publications, 2004.

The past year has been marked by numerous claims about science disproving God. The terms evidence and reason appear to have been comandeered by some scientists, falsely implying that Christianity has no place for clear thinking or for grappling with data. Studies have been published to show that eminent scientists tend to be atheists, and the conclusion is drawn that science leads people to abandon faith in God.
A new study by social scientists confirms that there is a secularising trend in the beliefs of the science community, but the authors question whether science has anything to do with it. "The first systematic analysis in decades to examine the religious beliefs and practices of elite academics in the sciences supports the notion that science professors at top universities are less religious than the general population, but attributes this to a number of variables that have little to do with their study of science."
The lead researcher is quoted as saying: "Our study data do not strongly support the idea that scientists simply drop their religious identities upon professional training, due to an inherent conflict between science and faith, or to institutional pressure to conform." Furthermore, the researchers found little to distinguish social scientists from scientists, which is another indication that the sciences are not exerting any distinctive influences above those of other academic disciplines.
The authors flag up childhood experience of religion as a major factor in their study. "Academic science has a disproportionately large number of people raised with no religion, potentially producing many more people who do not believe in God." The authors discuss this significant finding in their paper, offering tentative leads, and pointing to further research. I found this comment interesting: "Scientists lament a lack of scientific understanding among the U.S. population (Scientific American 2005; Lakoff 2005). While the general American public may indeed have a less than desirable understanding of science, our findings reveal that academic scientists may have much less experience with religion than many outside the academy." This is worth our attention, not only because there is an important debate here, but also because not a few have noted that the criticisms of Christianity emerging from some vocal scientists do not get beyond the teenager level of sophistication. These opinion-formers have only a rudimentary appreciation of the beliefs they are criticising! This new research could explain why.
For an ID exposition of why academics in general are affected by a cultural secularising tendency, see Phillip Johnson's Reason in the Balance: The Case Against Naturalism in Science, Law and Education (1998).

Religion among Academic Scientists: Distinctions, Disciplines, and Demographics
Elaine Howard Ecklund and Christopher P. Scheitle
Social Problems, May 2007, Vol. 54, No. 2: 289-307.

Abstract: The religiosity of scientists is a persistent topic of interest and debate among both popular and academic commentators. Researchers look to this population as a case study for understanding the intellectual tensions between religion and science and the possible secularizing effects of education. There is little systematic study, however, of religious belief and identity among academic scientists at elite institutions, leaving a lacuna of knowledge in this area. This absence of data exists at a time when the intersection between religion and science is reaching heightened public attention. Especially with increased tensions surrounding teaching evolution in the public schools, understanding what kind of resources scientists have (particularly in terms of their own religious beliefs and practices) to transmit science to a broader religiously-motivated public is crucial. Using data from a recent survey of academic scientists at twenty-one elite U.S. research universities, we compare the religious beliefs and practices of natural and social scientists within seven disciplines as well as academic scientists to the general population. We find that field-specific and interdisciplinary differences are not as significant in predicting religiosity as other research suggests. Instead, demographic factors such as age, marital status, and presence of children in the household are the strongest predictors of religious difference among scientists. In particular, religiosity in the home as a child is the most important predictor of present religiosity among this group of scientists. We discuss the relevance these findings have for understanding issues related to current theory and public debate about the intersection between religion and science.

See also:

Scientists May Not Be Very Religious, but Science May Not Be to Blame, University of Buffalo News, 23 July 2007.

Gene, M. Science Does Not Lead to Atheism (Telic Thoughts, 19 July 2007)

The selectionist/neutralist controversy has continued for nearly 40 years, and a resolution is not in sight. NeoDarwinists like to think that Neutral Evolution is compatible with neoDarwinism, but this is a bit like their attitude to Punctuated Equilibrium: everything worth saying has to be compatible with neoDarwinism! Meanwhile, the controversy goes on. . .
In a recent PNAS review paper, Masatoshi Nei argues that our knowledge of genetics is such that, as far as genes controlling phenotypic characters are concerned, conservation is a more applicable description than evolution. "Phenotypic evolution occurs primarily by mutation of genes that interact with one another in the developmental process. The enormous amount of phenotypic diversity among different phyla or classes of organisms is a product of accumulation of novel mutations and their conservation that have facilitated adaptation to different environments. [. . .] It appears that the driving force of phenotypic evolution is mutation, and natural selection is of secondary importance."
This is, of course, not the message that you get from neoDarwinists, who continue to emphasise adaptive causation. In their view, natural selection is essential to explain the origin of complexity, and they are not impressed by the neutralists diminishing of the role of natural selection.
Whilst this paper can be discussed in various ways, I want to focus on the educational issues. We have here a controversy about the relative significance of mutations and natural selection. It is not a minor matter. NeoDarwinists feel very strongly about it. Take, for example, Richard Dawkins critiquing Michael Behe in The New York Times (July 1 2007):

The crucial passage in The Edge of Evolution is this: "By far the most critical aspect of Darwin's multifaceted theory is the role of random mutation. Almost all of what is novel and important in Darwinian thought is concentrated in this third concept."
What a bizarre thing to say! Leave aside the history: unacquainted with genetics, Darwin set no store by randomness. New variants might arise at random, or they might be acquired characteristics induced by food, for all Darwin knew. Far more important for Darwin was the nonrandom process whereby some survived but others perished. Natural selection is arguably the most momentous idea ever to occur to a human mind, because it - alone as far as we know - explains the elegant illusion of design that pervades the living kingdoms and explains, in passing, us. Whatever else it is, natural selection is not a "modest" idea, nor is descent with modification.

Then compare with Nei, who says this:

Although this type of statement is quite common in the evolutionary literature, it is obvious that any advantageous genotype is produced by mutation including all kinds of genetic changes. Natural selection occurs as a consequence of mutational production of different genotypes, and therefore it is not the fundamental cause of evolution.

This is an issue which is educationally very important, and it also happens to be relevant to ID arguments. It is not in the educational interests of students to prevent such issues being discussed by teachers, and nor should it be deemed a "religious intrusion" into science when neoDarwinism is subjected to critical scrutiny.

The new mutation theory of phenotypic evolution
Masatoshi Nei
Proceedngs of the National Academy of Sciences, USA, July 24, 2007, 104(30), 12235-12242 | doi 10.1073/pnas.0703349104

Recent studies of developmental biology have shown that the genes controlling phenotypic characters expressed in the early stage of development are highly conserved and that recent evolutionary changes have occurred primarily in the characters expressed in later stages of development. Even the genes controlling the latter characters are generally conserved, but there is a large component of neutral or nearly neutral genetic variation within and between closely related species. Phenotypic evolution occurs primarily by mutation of genes that interact with one another in the developmental process. The enormous amount of phenotypic diversity among different phyla or classes of organisms is a product of accumulation of novel mutations and their conservation that have facilitated adaptation to different environments. Novel mutations may be incorporated into the genome by natural selection (elimination of preexisting genotypes) or by random processes such as genetic and genomic drift. However, once the mutations are incorporated into the genome, they may generate developmental constraints that will affect the future direction of phenotypic evolution. It appears that the driving force of phenotypic evolution is mutation, and natural selection is of secondary importance.

See also:

Dawkins, R. Inferior Design, The New York Times, July 1, 2007 [for link, go here]

Scordova, Prominent NAS member trashes neo-Darwinism, Uncommon Descent, 18 July 2007

According to Winston Churchill, "History is written by the victors." The losers are variously portrayed as a scourge on society that the world is best rid of. The Warfare Thesis was invented towards the end of the 19th Century to replace the hegemony of the established church with the new hegemony of scientism, and ever since that time, the advocates of naturalism have been reinforcing the warfare myth and claiming victory for science against the forces of darkness (which generally means Christianity). The 1925 Scopes Trial in the US was slotted into this format and it now appears that the Dover trial is getting the same treatment.
In Nature, Kevin Padian has reviewed three books that tell the story of the Dover trial: where the decision of the Education Board in Dover, PA to incorporate Intelligent Design into the science lessons of students was declared to be an act of "breathtaking inanity" by the judge. The judge accepted the documents prepared for the prosecution by the National Center for Science Education. The president of the NCSE is none other than the reviewer, Kevin Padian. According to him, after the trial, "Intelligent-design proponents sputtered and fumed; the usual right-wing commentators fulminated; no one has since taken the Discovery Institute seriously."
Spin is ubiquitous in this review. The DI scholars are likened to "persecuted pilgrims who then turn around and ostracize anyone who doesn't agree with them"; after mentioning the textbook Of Pandas and People, the judge is said to have "proscribed bogus criticisms of evolution in science classes"; apparently, "Behe's notions of 'irreducible complexity' and the status of intelligent design as science were shredded by attorney Eric Rothschild", and Dembski gets "withering criticism from actual mathematicians". Needless to say, these comments (and others like them) are content-free. There is nothing offered that goes beyond opinion. This review is a sop to those who want to be associated with the victors (identified by Padian as those who side with the Enlightenment). For an antidote, read "Setting the Record Straight about Discovery Institute's Role in the Dover School District Case". It is unfortunate that Nature is prepared to treat such a partisan essay as though it were a work of scholarship.
Churchill is also responsible for this thought: "History will be kind to me for I intend to write it". I like to think that he was in a humorous mood at the time. However, Padian and the historical revisionists appear to be deadly serious and so it behoves us all to check things out and take people to task for indulging in spin.

The case of creation
Last year's Dover trial resulted in intelligent design being removed from the science curriculum
Kevin Padian
Nature, 448, 253-254 (19 July 2007) | doi:10.1038/448253a

First para: Three new books use as a centrepiece the court case of Kitzmiller et al. versus Dover Area School District, which played out for six weeks in late 2005 at the state capital of Pennsylvania. This trial was the latest in a series of American 'Scopes trials', named after the 1925 prosecution of Tennessee teacher John Scopes, who was fined $100 for flouting a state law that prohibited the teaching of evolution in state-run schools. Scopes volunteered to be the test case, knowingly breaking the law. Famed attorneys Clarence Darrow and William Jennings Bryan argued the case. Scopes lost, Tennessee was ridiculed, a few other states passed similar legislation, and the divide between fundamentalists and secularists in the United States was irrevocably cleft.

See also:

Dembski, W., Kevin Padian: The Archie Bunker Professor of Paleobiology at Cal Berkeley, Uncommon Descent, 20 July 2007.
[putting the record straight about Dembski receiving "withering criticism from actual mathematicians."]

Biomimetics has rapidly emerged as a route to innovative technology and academic publication. Various indicators show that the growth from 1990 to the present has been exponential. Hesselberg says that the favoured methodology to date has been mechanism-driven biomimetics. This starts with an engineering problem, finds potential solutions in the natural world and uses the best as inspiration to develop an engineered product. Well-known examples are the invention of Velcro and the development of Lotus-Effect (self-cleaning) materials.
Two other biomimetic approaches are explained by the author. Both are organism-driven, where organisms are studied for their potential. One approach is focused, where there is a particular phenomenon that is considered to have commercial potential. A good example is gecko feet. The other approach is integrative, where several aspects of an organism are considered concurrently. A widely cited example of this is cockroach locomotion. The case study Hesselberg presents in his paper concerns integrative organism-driven biomimetics relating to ragworms. Despite most people knowing them only as fish bait, these animals give multi-functional inspiration to novel endoscopes, displacement pumps and multifunctional robots.
The reason for drawing attention to this paper is that biomimetics nearly always involves teams of highly skilled people. "The multidisciplinary aspect of biomimetics is very strong, with many active groups including computer scientists, physicists, chemists, and philosophers working alongside biologists and engineers." The implication is that nature's secrets are not easily revealed, and certainly not easy to mimic.
Hesselberg also notes that "the field is still lacking an analytical framework". This has set me wondering whether this is related to the influence of Darwinism within the academic world. According to Darwinism, design is only apparent. It does not reveal an intelligent agent at work. Incremental natural variations combined with natural selection are deemed to be adequate causal agents. The Darwinists themselves predict that this leads to a "tinkering" style of design, but is this what we observe? The reason why biomimetics has taken off is not because people are uncovering designs of the tinkering variety, but designs that are exquisite and holistic. This is particularly apparent in the integrative organism-driven biomimetics reviewed by Hesselberg. Biomimetics as an interdisciplinary discipline may well find that Intelligent Design is superior to Darwinism for underpinning its analytical framework.

Biomimetics and the case of the remarkable ragworms
Thomas Hesselberg
Naturwissenschaften, Volume 94, Number 8 / August, 2007, 613-621.

Abstract: Biomimetics is a rapidly growing field both as an academic and as an applied discipline. This paper gives a short introduction to the current status of the discipline before it describes three approaches to biomimetics: the mechanism-driven, which is based on the study of a specific mechanism; the focused organism-driven, which is based on the study of one function in a model organism; and the integrative organism-driven approach, where multiple functions of a model organism provide inspiration. The first two are established approaches and include many modern studies and the famous biomimetic discoveries of Velcro and the Lotus-Effect, whereas the last approach is not yet well recognized. The advantages of the integrative organism-driven approach are discussed using the ragworms as a case study. A morphological and locomotory study of these marine polychaetes reveals their biomimetic potential, which includes using their ability to move in slippery substrates as inspiration for novel endoscopes, using their compound setae as models for passive friction structures and using their three gaits, slow crawling, fast crawling, and swimming as well as their rapid burrowing technique to provide inspiration for the design of displacement pumps and multifunctional robots.

Today, we are familiar with the metaphor of the cell as a factory, taking in raw materials and converting them, via elaborate processing equipment and complex chemistry, into usable products. But this metaphor is not the only one. The author of a recent review writes: "The history of cell theory offers a rich lesson in the use of metaphor and analogy in scientific thought. The first account of the cell likened it to an empty room, but it has also been conceptualized through the metaphors of a building stone (Baustein), an elementary organism (Elementarorganismus), a chemical laboratory or factory, a motor and a machine."
Of particular interest for this blog is the situation when Darwinism was in its infancy: "The dominant metaphor in the second half of the nineteenth century described the body as a 'society' or 'state' of cells (Zellenstaat). Cells were 'citizens' arranged into separate classes or professions according to their functions, together making up the 'economy of the organism'." "Using the physiologist Ernst Brucke's (1819-1892) proposal that cells be considered 'elementary organisms' (itself an analogy to the way the chemical elements came together to form complex molecules), evolutionary zoologist Ernst Haeckel (1834-1919) gave the cell-state metaphor a Darwinian spin: higher plants and animals, he argued, were evolved into colonies of these elemental organisms and humans were little more than a complex colony of protozoan-like cells with a highly evolved division of labor." So, the cell was conceived as a simple building block, and organisms were portrayed as assemblages with varying degrees of complexity.
The metaphor changed when the focus became process. "The metaphor of the cell factory or laboratory was employed chiefly when the topic of discussion was physiology, and in particular the problem of metabolism. [. . .] For those interested in metabolic activities, wanting to know how these little things worked rather than where they came from, the factory or laboratory metaphor was far more suggestive than the comparison to an elementary organism. This may explain why the metaphor of the cell factory emerged as a serious competitor to the elementary organism metaphor in the early twentieth century. It was then that biologists began to turn away from the construction of phylogenetic trees of the sort made popular by Haeckel towards more experimental investigations of cell activity guided by the mechanistic principles of chemistry and physics." The author concludes with comments on literal cell factories in the age of biotechnology.
The theme of the paper is worth further consideration by us. Thus, empirically-based biologists discovered that the cell was quite different from the simple ("empty room") concept favoured by Haeckel and many other Darwinists. Those who keep repeating the mantra that nothing in biology makes sense except in the light of evolution would do well to reflect on how Darwinism perpetuated a false metaphor of the cell and it needed a new generation of empiricists to move the subject on.
However, such was the hold of Darwinism that a way of maintaining the myth of simplicity was found. Ultimately, the cell had to be simple (they thought), so that incremental changes (mutations) could occur and be selected naturally. Then Michael Behe came along with his book 'Darwin's Black Box'. The ultimate can now be known: at the level of molecular biology. Researchers were finding complexity right down to the molecular level, and some of these mechanisms allow the recognition of irreducible complexity. 'Simplicity' is a word that should never be used when talking about cells!

The cell's journey: from metaphorical to literal factory
Andrew Reynolds
Endeavour, Volume 31, Issue 2, June 2007, Pages 65-70.

The concept of the cell has been based on metaphor since its inception, and the history of cell theory has continued to rely on metaphor and analogy. In the nineteenth century, cells were most popularly conceived either as building stones or elementary autonomous organisms from which larger organisms are composed. With advances in physiology and the rise of modern biochemistry in the early twentieth century, the chemical factory or laboratory became the dominant metaphor for this biological unit. Today in the twenty-first century, the metaphorical imagery has become a reality, with cells acting as chemical factories for the synthesis of commercially valuable bio-products. The history of the cell shows how metaphors act as conceptual tools, with particular strengths for facilitating different sorts of questions and experimental techniques.

It was in 1967 that W.D. Hamilton published his seminal thoughts on "extraordinary sex ratios", suggesting ways of understanding why "Fisher's principle" for 1:1 being the equilibrium ratio has many exceptions in nature. Records of the butterfly Hypolimnas bolina living on the Samoan islands reveal extreme ratios and also extreme fluctuations of those ratios. Media reports have majored on the thought that this is evolution in action: "Evolution occurs in the blink of an eye" (LiveScience) and "Butterfly shows evolution at work" (BBC). Since the media have rarely heeded Phil Johnson's sound advice to distinguish the different meanings of the word "evolution", it is useful for us to consider the research with this in mind.
Sex ratios are distorted by the presence of a maternally inherited bacterium which has the effect of selectively killing male embryos. The authors report ratios of >99% female to nearly 1:1. These were different on different islands and at different times. The genetics of this shift of sex ratios is summarised in one paragraph with some supporting online data. There is not enough information here for anyone to either confirm or challenge their conclusions. However, more substantial evidence for "suppression genes" had previously been published in 2006, and for the sake of this discussion, we will accept that "the shift in sex ratio was caused by the spread of host suppressor genes."
What we should be aware of is that the source of these genes is unknown. Various options exist. A novel mutation is a possibility (the 2006 study considered the suppression was controlled by a single locus). Another avenue to explore is that the gene had existed previously in the population (or sub-populations) of butterflies.
So the story concerns a genetic trait restoring the sex ratio of a species of butterfly living in the Samoan Islands. This seems to be a straightforward case of natural selection of a gene whose presence is directly related to the survival of male butterflies. The lead author comments: "To my knowledge, this is the fastest evolutionary change that has ever been observed". It is true it is rapid, but we might be forgiven the thought that if it were not rapid, the species would last little longer than its lifecycle!
In terms of its significance for evolutionary theory, this research is on a par with the peppered moth: there is no insight into speciation and there is no change in complexity of the organism. It is an observation that is perfectly compatible with Darwinism, ID and creation-based biology. The lead author is quoted as saying: "We're witnessing an evolutionary arms race between the parasite and the host. This strengthens the view that parasites can be major drivers in evolution". This is much more controversial. There is widespread view in ID circles that these genetic skirmishes actually lead to genetic impoverishment. Parasites may drive change, but it is likely to be towards extinction. To justify the "major driver" claim, the genetics of the process need to be analysed in much greater detail.

Extraordinary Flux in Sex Ratio
Sylvain Charlat, Emily A. Hornett, James H. Fullard, Neil Davies, George K. Roderick, Nina Wedell, Gregory D. D. Hurst.
Science, 13 July 2007: Vol. 317, p. 214, DOI: 10.1126/science.1143369

The ratio of males to females in a species is often considered to be relatively constant, at least over ecological time. Hamilton noted that the spread of "selfish" sex ratio-distorting elements could be rapid and produce a switch to highly biased population sex ratios. Selection against a highly skewed sex ratio should promote the spread of mutations that suppress the sex ratio distortion. We show that in the butterfly Hypolimnas bolina the suppression of sex biases occurs extremely fast, with a switch from a 100:1 population sex ratio to 1:1 occurring in fewer than 10 generations.

See also:

Bryner, J. Evolution Occurs in the Blink of an Eye, LiveScience, 12 July 2007

Butterfly shows evolution at work, BBC News, 12 July 2007

Hornett, E.A., Charlat, S., Duplouy, A.M.R., Davies, N., Roderick, G.K., Wedell, N. and Hurst, G.D., Evolution of Male-Killer Suppression in a Natural Population, PLoS Biology Vol. 4, No. 9, e283 doi:10.1371/journal.pbio.0040283

A simulation model of early biological evolution has been developed which claims to advance our knowledge of how the first gene families developed. Although we know very little about how the genotype relates to phenotype, it was necessary for the architects to build something about this into their model. They postulated that the death rate of an organism is determined by the stability of the least stable of their proteins. Initial conditions were as follows: "Our evolution dynamics runs start from an initial population of 100 organisms, each having the same one primordial gene in their genomes. Initial gene sequence is random."
The simulation was executed using a cycle of 4 steps: "(i) random mutation of a nucleotide in a randomly selected gene with constant rate m per unit time per DNA length; mutations leading to the stop codon are rejected to ensure the constant length of protein sequences; (ii) duplication of a randomly selected gene within an organism's genome with constant rate u; (iii) birth of an organism via duplication of an already existing organism with constant rate b (the genome is copied exactly); and (iv) death of an organism with the rate d per unit time."
After running the model, the number of genes increased, but never exceeded 10. "We found that out of 50 simulation runs starting with different starting sequences, 27 runs successfully resulted in a steady exponential growth of the population, whereas in 23 runs the population has quickly gone extinct." Numerous characteristics of the simulations are reported, with this comment: "Based on these observations, we conjecture that biological evolution, exponential population growth, and existence of stable genomes are possible only after the discovery of a narrow set of specific protein structures."
Their general conclusion: "Together, these results and their analysis suggest a plausible comprehensive scenario of emergence of the protein universe in early biological evolution."
One of the principles of simulation is that models are first verified (they perform as they were designed) and second validated (they provide a realistic model of the real world). Unfortunately, there is nothing in the paper about validation. This does raise concerns. The first relates to the descriptor: "advantageous": "We find that exponential population growth is possible only after the discovery of a very small number of specific advantageous protein structures." The problem is: what gives the protein structure an advantage? In the real world, proteins are advantageous because they do something useful by virtue of the way they fold. In the model, the proteins do not have functions and the only significant differences relate to their stability.
The model starts with organisms possessing 1 gene and, after the simulation of biological evolution, they never have more than 10. Compare this with the real world, where a minimal genome of less than 200 genes has to be regarded as a dream.
The authors correctly state: "Our model of natural selection is minimalistic and is limited in its scope". Also: "This work is in progress." The authors suggest their model relates more closely to viruses: "our model can be directly applicable to (and can be experimentally tested on) the evolution of RNA viruses, which often encode for a handful of proteins, all of which are essential for the virus." This is far more realistic. If the authors had focussed on this rather than making grandiose claims about modelling early biological evolution, their work would deserve more respect.

A First-Principles Model of Early Evolution: Emergence of Gene Families, Species, and Preferred Protein Folds
Konstantin B. Zeldovich, Peiqiu Chen, Boris E. Shakhnovich, Eugene I. Shakhnovich
PloS Computational Biology, 3(7): e139 doi:10.1371/journal.pcbi.0030139

Abstract: In this work we develop a microscopic physical model of early evolution where phenotype - organism life expectancy - is directly related to genotype - the stability of its proteins in their native conformations - which can be determined exactly in the model. Simulating the model on a computer, we consistently observe the "Big Bang" scenario whereby exponential population growth ensues as soon as favorable sequence-structure combinations (precursors of stable proteins) are discovered. Upon that, random diversity of the structural space abruptly collapses into a small set of preferred proteins. We observe that protein folds remain stable and abundant in the population at timescales much greater than mutation or organism lifetime, and the distribution of the lifetimes of dominant folds in a population approximately follows a power law. The separation of evolutionary timescales between discovery of new folds and generation of new sequences gives rise to emergence of protein families and superfamilies whose sizes are power-law distributed, closely matching the same distributions for real proteins. On the population level we observe emergence of species-subpopulations that carry similar genomes. Further, we present a simple theory that relates stability of evolving proteins to the sizes of emerging genomes. Together, these results provide a microscopic first-principles picture of how first-gene families developed in the course of early evolution.

Sea anemones, jellyfish and corals are all cnidarians, a phylum that goes back to the Late Precambrian. Geneticists studying this group of organisms have made much use of the starlet sea anemone Nematostella vectensis. Whilst previously reported research has been concerned with specific genetic elements, a new study reports on a comparative analysis of the whole genome. The sea anemone genome has been found to contain about 18,000 protein-coding genes with many of the same gene families that are found in other sequenced animals. This is where the surprises start.
The authors write: "The sea anemone genome is complex, with a gene repertoire, exon-intron structure, and large-scale gene linkage more similar to vertebrates than to flies or nematodes, implying that the genome of the eumetazoan ancestor was similarly complex." Elizabeth Pennisi observes: "This implies that even very ancient genomes were quite complex and contained most of the genes necessary to build today's most sophisticated multicellular creatures." Eugene Koonin of the National Center for Biotechnology Information was interviewed about the research. He said that it is surprising to find such a "high level of genomic complexity in a supposedly primitive animal such as the sea anemone". It implies that the ancestral animal "was already extremely highly complex, at least in terms of its genomic organization and regulatory and signal transduction circuits, if not necessarily morphologically."
The comparative study had some additional surprises. Writing in The Scientist, Melissa Lee Phillips points out: "The study also found that these similarities were absent from fruit fly and nematode genomes, contradicting the widely held belief that organisms become more complex through evolution. The findings suggest that the ancestral animal genome was quite complex, and fly and worm genomes lost some of that intricacy as they evolved."
Some have inferred that the vertebrate genome must therefore be primitive, but this fails to do justice to the observed sophistication. The implication of this research is that we are not tracking an evolution of complexity with time, but we have identified the sudden emergence of complexity in the Precambrian. It is the genetic equivalent of the 'Cambrian explosion'!
A hint of this was published in 2005 in a study of the Wnt gene family, which encodes secreted signalling molecules that control cell fate in animal development and human diseases. "Cnidarians and bilaterians have at least eleven of the twelve known Wnt gene subfamilies in common; [. . .] This unexpectedly complex inventory of Wnt family signalling factors evolved in early multi-cellular animals about 650 million years (Myr) ago, predating the Cambrian explosion by at least 100 Myr."
Researchers have looked for simplicity but have found complexity. They have selected organisms described as primitive and have proved them to be advanced. One evolutionary developmental biologist is quoted as saying: "The work is truly stunning for its deep evolutionary implications". He's right, but not in the sense he intended: when the data is profoundly at variance with evolutionary expectations, it is time to consider whether a new paradigm is needed.

Sea Anemone Genome Reveals Ancestral Eumetazoan Gene Repertoire and Genomic Organization
Nicholas H. Putnam, Mansi Srivastava, Uffe Hellsten, Bill Dirks, Jarrod Chapman, Asaf Salamov, Astrid Terry, Harris Shapiro, Erika Lindquist, Vladimir V. Kapitonov, Jerzy Jurka, Grigory Genikhovich, Igor V. Grigoriev, Susan M. Lucas, Robert E. Steele, John R. Finnerty, Ulrich Technau, Mark Q. Martindale, and Daniel S. Rokhsar
Science, 316, 6 July 2007: 86-94.

Sea anemones are seemingly primitive animals that, along with corals, jellyfish, and hydras, constitute the oldest eumetazoan phylum, the Cnidaria. Here, we report a comparative analysis of the draft genome of an emerging cnidarian model, the starlet sea anemone Nematostella vectensis. The sea anemone genome is complex, with a gene repertoire, exon-intron structure, and large-scale gene linkage more similar to vertebrates than to flies or nematodes, implying that the genome of the eumetazoan ancestor was similarly complex. Nearly one-fifth of the inferred genes of the ancestor are eumetazoan novelties, which are enriched for animal functions like cell signaling, adhesion, and synaptic transmission. Analysis of diverse pathways suggests that these gene "inventions" along the lineage leading to animals were likely already well integrated with preexisting eukaryotic genes in the eumetazoan progenitor.

See also:

Pennisi, E., Sea Anemone Provides a New View of Animal Evolution, Science, 316, 6 July 2007: 27.
Melissa Lee Phillips, M.L. Surprises in sea anemone genome, The Scientist, 5th July 2007
Kusserow, A., et al., Unexpected complexity of the Wnt gene family in a sea anemone, Nature 433, 156-160, (13 January 2005)

We are indebted to Gould and Lewontin for pointing out so eloquently to adaptationists that biological structures should be explained in context and not as independently constructed adaptations. They wanted to revive the great historic themes of developmental morphology and the bauplan in which some features are, like spandrels, consequences of a larger-scale architecture. David Hartl has chosen to remind readers of this emphasis in his review of a book on the origins of genome architecture.
At the outset, some garbage must be cleared away. Adaptationists have tended to develop lazy ways of thinking and rarely seek out ways to test their offered scenarios. "Glib generalizations [according to the author] come from the assumption shared by many biologists that natural selection is the only mechanism of evolutionary change, and hence every observed feature of organisms must have come about because of natural selection." This mechanism is highly prized because they think it can do anything. They claim it is the great creator of complexity. But the concept is qualitative, not quantitative, and there are inadequate checks to avoid the pathways to fantasy. "This conveniently licenses anyone to concoct any adaptive story about anything biological and put it forward as a serious contribution to the science of evolution."
Michael Lynch, the book's author, has come to the view that many complex structures cannot be explained using adaptation. "The recurring theme is that many of the major molecular features of genes and genomes in multicellular organisms can be explained without invoking natural selection. The list will raise some eyebrows: it includes the transition from the RNA world to DNA, streamlining of microbial genomes, variation in nucleotide composition within and among genomes, centromere expansion, proliferation of transposable elements, growth of untranslated regions in messenger RNAs, origin of spliceosomes and the proliferation of introns, origin of modular gene regulation, variation in the architecture of organelle genomes, mRNA editing in plant organelles and the evolution of sex chromosomes."
"The problem with natural selection is that if it explains everything, it explains nothing, and instead it becomes an exercise in story telling. [. . .] The challenge for those who would invoke natural selection as causing any biological feature is therefore to propose a specific adaptive mechanism, to deduce attributes that would differ according to which hypothesis were correct and then to make the necessary observations or comparisons."
What a welcome airing of these issues! And wouldn't it be good if biology students could be alerted to such thinking before they get brainwashed by neo-Darwinism?

The spandrels of the genome
Daniel Hartl
Nature Genetics, 39, 811 (July 2007) | doi:10.1038/ng0707-811

BOOK REVIEWED - The Origins of Genome Architecture by Michael Lynch, Sinauer Associates: 2007

See also:
Gould, S.J. & Lewontin, R.C. The spandrels of San Marco and the Panglossian paradigm, Proceedings of the Royal Society of London, B. 1979, 205, 581-598.

In his July editorial in The Scientist, Richard Gallagher marks the 35th anniversary of the term "Junk DNA" by asking the question "Is it time to retire provocative descriptors such as "junk DNA"?" His answer is negative, and he proceeds to justify the term on the grounds that: "junk DNA works as a catchy moniker that helps frame the debate for the general public while evoking passionate debate among scientists". This blog has drawn attention previously to the way evolutionary biologists like to frame the debate for the general public: instead of equipping the public with the concepts and resources to make informed judgments, the objective appears to be to safeguard Darwinism to ensure the public do not revolt!
There is no doubt that "Junk DNA" has been a controversial term within the scientific community. However, for many years, the sceptics were in a minority. The general public were presented with overwhelming evidence that our genomes are "filled with the remains of extinct genes" that are of marginal interest until advantageous mutations bring them back again into centre stage. The Framers made sure the public got the message: "...the designer made serious errors, wasting millions of bases of DNA on a blueprint full of junk and scribbles. Evolution, in contrast, can easily explain them as nothing more than failed experiments in a random process . . ." (Kenneth Miller, 1994) and "DNA differs from written language in that islands of sense are separated by a sea of nonsense, never transcribed" (Richard Dawkins, 2004).
The policy of retaining the term to help frame the debate for the general public is actually very misleading. Recent research is uncovering a mass of functionality that suggests the term actually promotes falsehoods in the name of science.
Even more significantly, Gallagher writes: "The latest iniquity to befall junk DNA is the attempted hijack by proponents of Intelligent Design. Some of them would have us believe that their movement has provided the tools to find function in junk DNA. A withering critique by Pim van Meurs can be found on the Web site, The Panda's Thumb, along with an entertaining and educational thread of 150 or so comments."
This comment is also seriously misleading. The key contribution ID scientists have made is to predict functionality for some, if not most, of the supposed junk DNA. This prediction has emerged partly from an appreciation of the exquisite complexity of living things (including its DNA) and partly from a scepticism about the capabilities of Darwinian mechanisms to achieve large-scale transformations. It was also provoked by declarations like this from Phillip Kitcher (philosopher of science at Columbia University) in 2005: "A lot of the DNA in there is not needed -- it's junk. If it's intelligently designed, then God needs to go back to school." A more judicious assessment would be: ID scientists have risen to the "Junk DNA" challenges thrown at them, and have shown that ID thinking does make successful predictions. It may be concluded that any continuing refrain about ID not making predictions is just more "framing" of the debate for the masses.

Junk Worth Keeping (Editorial)
By Richard Gallagher
The Scientist, July 2007

First Para: June 30, 1972, was a high point for the lexicon of biology. That day, Susumu Ohno coined (or at least publicly introduced) the term "junk DNA." In a talk titled "So Much 'Junk DNA' in our Genome," Ohno argued that the frequency of deleterious mutations restricts the number of serviceable genes to around 105 and that the great bulk of our DNA is merely the debris of failed duplication. "The earth is full of extinct species," he said. "Is it a wonder that our genome, too, is filled with the remains of extinct genes?"

See also:

Junk DNA, ResearchID.org (June 2007)

Pearson, A., Why 'junk DNA' may be useful after all, New Scientist, 11 July 2007.

In a bold and incisive paper, philosopher Owen Anderson writes: "In what follows I explain the principle of uniformity as developed by Lyell, consider its philosophical grounding in Humean empiricism and epistemological naturalism, and argue that, although Lyell himself may have believed in the theistic view of God, this principle raises questions about the role of God and natural evil in the world. By identifying the role that uniformitarianism has played in subsequent science and understanding its role as a nonempirical interpretive principle, I show how fideism can be avoided at the level of first principles." Among the many issues raised, I draw attention to just one. This concerns the fundamental importance of interpretive principles (or paradigms) in science.
There is a tendency for scholars in the Lyell tradition to think that empirical evidence can be gathered objectively and that analysis leads to robust knowledge. However, Lyell filtered the data available to him by an unarticulated interpretive principle. Anderson seeks to revise our perceptions of Lyell's contribution by focusing attention on his philosophical roots. "Just as the Aristotelians gathered huge amounts of data and yet because of false interpretive principles drew false conclusions about the world, so any other "science" is only as good as its interpretive principles."
Lyell appeared to have been deeply influenced by the philosopher David Hume. "Lyell's principle requires a radical form of empiricism as developed by David Hume. Hume's invective against anything that appears to be metaphysical or theological has had immeasurable influence on the modern mind. He believed that there were only two sources of knowledge and ruled out the idea of special revelation." The picture that emerges involves two competing philosophical stances: naturalism and theism. Although Lyell professed to be a theist, his thinking was that of a naturalist. "For the naturalist to maintain that he or she is simply working with the evidence while the theist is importing theology is for the naturalist to ignore his or her own interpretive assumptions. The theist will maintain that the material world and its past cannot be entirely explained through secondary causes and that, although God has created these causes and endowed the human mind with the ability to know them, they do not exhaust what humans should know about the formation of the world (there is also the redemptive work of God in history). Neither of these interpretive principles can claim to be neutral or "just following the evidence where it leads"."
The great strength of this paper is the way the author frames the science-faith debate. The differences are not about scientific methodology, nor about the role of reason. The fundamental differences are philosophical, particularly relating to naturalism and theism. Those who think that the term "theistic scientist" is an oxymoron would do well to read what Anderson has to say.

Charles Lyell, uniformitarianism, and interpretive principles
Anderson, Owen
Zygon, 42(2), June 2007, 449-462.

Abstract: I examine the development of Charles Lyell's principle of uniformity and its influence on the development of modern geology and biology and argue that distinguishing between philosophical starting points and empirical findings is essential for clarity in the discussion between science and religion. First, I explore Lyell's arguments against catastrophism and how these were both empirically and religiously motivated. I then consider how David Hume's empiricism, theory of causation, and rejection of miracles influenced Lyell. Using these insights, Lyell formulated his principle of uniformity, which he believed was based on current empirical findings, and rejected explanatory hypotheses that used the biblical Flood or other catastrophist accounts as violations of uniform causation and introductions of theological concepts into empirical science. I next examine the influence of Lyell's principle on Charles Darwin. Although Lyell opposed Darwinism for most of his life, Darwin relied heavily on Lyell, as is evidenced by references throughout The Origin of Species. I contend that the most important aspect of Lyell's principle for Darwin is that it makes natural evil (the struggle for survival) a process that has always been occurring rather than something introduced after the Fall as recorded in Genesis. Finally, I discuss the role that uniformity plays for Lyell, Darwin, and modern science as an interpretive principle rather than as an inference from empirical data, and I conclude by noting that keeping the distinction in mind between interpretive principles and empirical findings will help clarify debates between science and religion.

Earlier this year, Liu and Ochman made some dramatic claims about how the bacterial flagellum evolved: by the simple processes of successive duplications and diversifications. They discounted lateral gene transfer (LGT) as having had any significant influence. This received much applause, one critical blog and it was briefly reviewed here.
In a recent contribution to Current Biology, we read: "there are some caveats we evolutionists should consider before hailing Liu and Ochman as our next champions in the war against unreason." The caveats are to be welcomed. It was surprising to read the uncritical acclaim accompanying the publication of the original paper and a more measured assessment of its bold claims is to be welcomed. However, the reference to "war against unreason" is misguided. The authors are referring to ID, yet ID scientists are strong defenders of reason. Their reason leads them to make design inferences, and design inferences are totally unacceptable to scientists who have adopted the philosophy of naturalism.
After mentioning with approval the blog by Matzke, the authors write: "Equally problematic, we think, is their conclusion that "proteins forming the flagellum, the rod, hook and filament proteins, originated in an order that mirrors the 'inside-out' flagellar assembly process". Common sense might suggest such a scenario, but only rooted trees, which Liu and Ochman do not provide, can prove it."
Regarding the LGT claim, the authors (one of whom is a champion of LGT) write: "Critics of LGT often assume that trees with little resolution, because they do not show statistically significant conflict, must be in agreement and support vertical descent. But most often there is simply insufficient signal. Making vertical descent the null hypothesis is to assume that which was to be proved - and in this case to give false credibility to the claim for a common evolutionary history." This argument is very interesting, because it is closely related to arguments that have often been made by ID scientists. The problem of "little resolution" is widespread and the result is that researchers end up confirming their own assumptions.
It is obviously important that scientific debate be encouraged. There are serious problems linked to researchers apparently proving their presuppositions. We ask: when will this critical thinking be applied to science itself? Many scientists assume naturalism and then go on to 'prove' that naturalism can explain everything. This approach to science is one of the things ID scientists are seeking to change.

Evolution: Reducible Complexity - The Case for Bacterial Flagella
W. Ford Doolittle and Olga Zhaxybayeva
Current Biology, 17(13), 3 July 2007, R510-R512 | doi:10.1016/j.cub.2007.05.003

Abstract: A recent paper, which will surely figure centrally in the debate between evolutionists and Intelligent Design creationists, proposes a (perhaps too simple) scheme for the evolution of bacterial flagella.

See also:
Sequence similarities in the bacterial flagellum: what do they mean? ARN Literature Blog, 04/19/07

For over 30 years, the public have been led to believe that human and chimpanzee genetics differ by mere 1%. This 'fact' of science has been used on innumerable occasions to silence anyone who offered the thought that humans are special among the animal kingdom. "Today we take as a given that the two species are genetically 99% the same." However, this "given" is about to be discarded.
Apparently, it is now OK to openly acknowledge that those who are involved in this research have never been comfortable that the 1% figure was an accurate summary of the scientific information. But more recent studies have made it impossible to sustain the old orthodoxy. They have raised "the question of whether the 1% truism should be retired." One zoologist is quoted as saying: "Now it's totally clear that it's more a hindrance for understanding than a help."
"Researchers are finding that on top of the 1% distinction, chunks of missing DNA, extra genes, altered connections in gene networks, and the very structure of chromosomes confound any quantification of "humanness" versus "chimpness." [. . .] In the December 2006 issue of PLoS ONE, Hahn and co-workers reported that human and chimpanzee gene copy numbers differ by a whopping 6.4%, concluding that "gene duplication and loss may have played a greater role than nucleotide substitution in the evolution of uniquely human phenotypes and certainly a greater role than has been widely appreciated."" The diversity of relevant factors that are mentioned suggest that the problem has been one of oversimplification leading researchers to draw unwarranted conclusions from limited data.
The zoologist quoted above is also quoted as saying: "For many, many years, the 1% difference served us well because it was underappreciated how similar we were." Another researcher is quoted thus: "In the end, it's a political and social and cultural thing about how we see our differences." It is comments like these that can give sociologists of science a field day, for they reveal how social context influences what results are emphasised and what are overlooked. In this particular case, evolutionary biologists need to take full responsibility.
It is good to see a start being made in setting the record straight. Steve Jones, professor of genetics at University College London, writes: "DNA is beside the point. To concede so much to biology risks taking such privileges away from ourselves. [. . .] Chimps may resemble Homo sapiens in a tedious and literal sense, but in everything that makes us what we are H sapiens is unique indeed. Biology, in its proof of our physical similarity to other primates, underlines its own irrelevance."
It should be a "given" that humans are different from animals. If anyone struggles with this intellectually, then it may be appropriate to learn something from history. Let's be mindful that our knowledge of the relevant issues is limited.

Relative Differences: The Myth of 1%
Jon Cohen
Science 316, 29 June 2007: 1836.

Abstract: Genomewise, humans and chimpanzees are quite similar, but studies are showing that they are not as similar as many tend to believe

See also:

Jones, S., View from the lab, Daily Telegraph, 26/06/2007

An Editorial in Nature deflects legitimate concerns about the ethics of a specific research project by interpreting these concerns as a luddite attack on science by vitalists who think the research is "an affront on God". The offence has been caused by the Venter Institute which is applying for worldwide patents on what they refer to as Mycoplasma laboratorium. This novel bacterium is claimed to have been made with synthetic DNA in the laboratory.
The attack comes from the ETC Group, which is known as an environmental pressure group. They are not associated with a religious agenda. Although one of the employees is quoted as saying "For the first time, God has competition", this reference to God is the only instance I can find on the ETC site. The person went on to say: "Venter and his colleagues have breached a societal boundary, and the public hasn't even had a chance to debate the far-reaching social, ethical and environmental implications of synthetic life".
The concerns of the ETC Group are as follows: synthetic life takes us into previously unexplored areas, raising questions about the ethics of research and the need for a public debate. Specifically: "How could their accidental release into the environment be prevented or the effects of their intentional release be evaluated? Who will control them, and how? How will research be regulated?" These concerns are heightened by the knowledge that large corporations are financing this research and looking for ways to commercialise the findings. Previous experience reveals a story of ethical concerns and public debate being trampled underfoot in the zeal for financial benefits.
The ETC Group seems to have commendable concerns. However, instead of encouraging a debate on the ethics of research, the Editorial goes on the offensive against those raising accusations against "scientists". Furthermore, it takes the opportunity to attack "chronic vitalism" which is apparently any perception "of a need for a qualitative difference between inert and living matter". The editorial adds: "It would be a service to more than synthetic biology if we might now be permitted to dismiss the idea that life is a precise scientific concept." It goes on: "Synthetic biology's view of life as a molecular process lacking moral thresholds at the level of the cell is a powerful one. And it can and perhaps should be invoked to challenge characterizations of life that are sometimes used to defend religious dogma about the embryo."
The Editorial fails to reveal any ethical framework apart from scientific autonomy. It is as though scientists operate outside any regulative framework, and any discussion of ethics is deemed religious or ideological interference with the legitimate process of science. This is really worrying and it should raise concerns in society at large about how scientists have come to accept spokespersons like this.
From an ID perspective, this situation can be understood in terms of the philosophical materialism that has captured the minds of the scientific intelligentsia. There is no possibility of developing ethics within naturalistic science, and there is a resolute refusal to accept the authority of any ethical claims that are not developed by using the scientific method.
Do ID scientists say that "life is a precise scientific concept"? Yes, we do. We say life has complex specified information and this differentiates life clearly from non-life. We do not deny that life can be made in the lab, but we do predict that it will not be made using natural processes. It will only ever be possible with intelligent design.

Meanings of 'life' (Editorial).
Nature 447, 1031-1032 (28 June 2007) | doi:10.1038/4471031b

Abstract: Synthetic biology provides a welcome antidote to chronic vitalism.

See also:

Patenting Pandora's Bug: Goodbye, Dolly...Hello, Synthia!
J. Craig Venter Institute Seeks Monopoly Patents on the World's First-Ever Human-Made Life Form
ETC Group Will Challenge Patents on "Synthia" - Original Syn Organism Created in Laboratory

First paragraph: Ten years after Dolly the cloned sheep made her stunning debut, the J. Craig Venter Institute is applying for a patent on a new biological bombshell - the world's first-ever human-made species. The novel bacterium is made entirely with synthetic DNA in the laboratory.

Ball, P. Genome transplant makes species switch, news@nature.com: 28 June 2007; | doi:10.1038/news070625-9

Natural proteins are remarkable materials, and immense efforts have been devoted to engineering proteins for use in biotechnology applications. Two methodologies have been used: Darwinian blind searches (inspired by evolutionary theory) and rational design (requiring an understanding of the principles of protein structure and function). In their review paper, Leisola and Turunen point out that "some impressive practical achievements have been done using directed evolution methodologies". The analogy here is not with natural selection, but with the artificial selection of desired traits. It should be noted that "the starting point is always a functional protein". These are not engineered from scratch, but promising materials are chosen in order to improve existing properties. The authors raise questions about this approach. "In view of the very substantial challenges remaining and the considerable effort expended thus far, we should pause to ask what things are most impeding our progress." They identify three significant obstacles: lack of a theory for structure design, lack of a general approach for sequence design, and over-reliance on the Darwinian methodology. The problem is that the directed evolution methodology does not focus on understanding the way proteins work. "Thus, we are still missing general theories that would help us to design novel enzymes without a need to use methods that are based on a random search in the local sequence space." "In spite of the progress, we still do not have a general theory on how a sequence produces a specific structure and how a structure determines a function. Therefore, a blind Darwinian search within a known protein scaffold is often used to modify proteins. Unfortunately, blind searches have hard resource limits whereas insight has not. Therefore, in the long run, blind searches are of limited value in compensating our present ignorance."
This is a very interesting conclusion. It illustrates the central theme of Michael Behe's new book: that there are limits to what Darwinian processes can do. Tweaking existing materials is feasible, but if you want to go further than that, you need a rational design methodology. Darwinian mechanisms can be used to explain the adaptation of proteins, but it is unwarranted extrapolation to think that the same mechanisms explain the origins of those proteins.

Protein engineering: opportunities and challenges
Matti Leisola and Ossi Turunen
Applied Microbiology and Biotechnology, 75(6), July 2007, 1225-1232.

Abstract: The extraordinary properties of natural proteins demonstrate that life-like protein engineering is both achievable and valuable. Rapid progress and impressive results have been made towards this goal using rational design and random techniques or a combination of both. However, we still do not have a general theory on how to specify a structure that is suited to a target function nor can we specify a sequence that folds to a target structure. There is also overreliance on the Darwinian blind search to obtain practical results. In the long run, random methods cannot replace insight in constructing life-like proteins. For the near future, however, in enzyme development, we need to rely on a combination of both.

According to Eugene Koonin, the central problem facing origin of life researchers concerns the emergence of biological evolution (that transitional phase before the time when Darwinian mechanisms were able to operate). The origin(s) of replication and translation (OORT) "is qualitatively different from all other problems in evolutionary biology and might be viewed as the hardest problem in all of biology". The distinction comes about because Darwinists think they have natural mechanisms to account for the origin of complexity, but these only work when replication and translation processes are in place. "The crucial question, then, is how was the minimal complexity attained that is required to achieve the threshold replication fidelity."
Koonin identifies the first paradox of OORT in this way: although we talk about a "minimal" system for enabling Darwinian mechanisms to operate, even this system is a "highly evolved one"! The hurdle that must be jumped is very high indeed. "How such a system could evolve, is a puzzle that defeats conventional evolutionary thinking."
The second paradox of OORT "pertains to the origin of the translation system from within the RNA world via a Darwinian evolutionary process: until the translation system produces functional proteins, there is no obvious selective advantage to the evolution of any parts of this elaborate (even in its most primitive form) molecular machine." Current thinking about the RNA world faces "formidable difficulties".
Basically, Koonin offers no resolution of these paradoxes from within conventional evolutionary thinking. His way out of the impasse is to reposition the debate to take into account recent developments in cosmology. This means adopting the multiverse hypothesis: "The model of eternal inflation implies that all macroscopic histories permitted by the laws of physics are repeated an infinite number of times in the infinite multiverse." This model radically alters our perspectives, such that the "emergence of highly complex systems by chance is inevitable." This is claimed to be the answer to the OORT paradoxes. The multiverse "model not only permits but guarantees that, somewhere in the infinite multiverse [. . .] such a system would emerge." Thus, given the multiverse, chance and the weak anthropic principle are sufficient explanations for the appearance of life as we know it.
This paper is worthy of our attention on several counts: (a) it presents a realistic assessment of the problems of OORT; (b) it explains why the multiverse concept is needed in biology as well as cosmology in order to avoid the need to make design inferences; (c) it provides an appendix on the probabilities of the emergence, by chance, of getting through the OORT impasse (less than 10 to the power -1018).
The paper is accompanied by referees comments and author responses, which enhance its' value. However, two additional critical comments need to be made. The first concerns the author's appeal to the "infinite". Granted that probabilities deemed impossible become possible when multiplied by infinity, it is worth saying that "infinity" is not a concept that belongs to science. It is to be found in pure maths and in philosophy. Koonin does not clearly differentiate science from philosophy here and this detracts from what he has to say. The second critical comment relates to his attitude to the "weak anthropic principle" and the "strong anthropic principle". The latter idea, Koonin asserts, "does not belong in the scientific domain." It must be pointed out that whilst science does not have access to teleology, this does not mean that there is no purpose or goal in the Cosmos. To develop a science that is overtly opposed to the idea of teleology is actually to force-fit science into scientism. Science should never be in the position of declaring what the natural world should be like; its role is to explore what it is like. For more on this interesting paper, go here.

The cosmological model of eternal inflation and the transition from chance to biological evolution in the history of life
Eugene V Koonin
Biology Direct 2007, 2:15 doi:10.1186/1745-6150-2-15 [open access]

Background: Recent developments in cosmology radically change the conception of the universe as well as the very notions of "probable" and "possible". The model of eternal inflation implies that all macroscopic histories permitted by laws of physics are repeated an infinite number of times in the infinite multiverse. In contrast to the traditional cosmological models of a single, finite universe, this worldview provides for the origin of an infinite number of complex systems by chance, even as the probability of complexity emerging in any given region of the multiverse is extremely low. This change in perspective has profound implications for the history of any phenomenon, and life on earth cannot be an exception.
Hypothesis: Origin of life is a chicken and egg problem: for biological evolution that is governed, primarily, by natural selection, to take off, efficient systems for replication and translation are required, but even barebones cores of these systems appear to be products of extensive selection. The currently favored (partial) solution is an RNA world without proteins in which replication is catalyzed by ribozymes and which serves as the cradle for the translation system. However, the RNA world faces its own hard problems as ribozyme-catalyzed RNA replication remains a hypothesis and the selective pressures behind the origin of translation remain mysterious. Eternal inflation offers a viable alternative that is untenable in a finite universe, i.e., that a coupled system of translation and replication emerged by chance, and became the breakthrough stage from which biological evolution, centered around Darwinian selection, took off. A corollary of this hypothesis is that an RNA world, as a diverse population of replicating RNA molecules, might have never existed. In this model, the stage for Darwinian selection is set by anthropic selection of complex systems that rarely but inevitably emerge by chance in the infinite universe (multiverse).
Conclusion: The plausibility of different models for the origin of life on earth directly depends on the adopted cosmological scenario. In an infinite universe (multiverse), emergence of highly complex systems by chance is inevitable. Therefore, under this cosmology, an entity as complex as a coupled translation-replication system should be considered a viable breakthrough stage for the onset of biological evolution.

According to Poole and Penny, there has been far too much speculation about the origin of eukaryotes. "The conflicting hypotheses currently on offer show a curious disregard for mechanism." Up until the mid-1990s, the 'archezoa hypothesis' was dominant. "This maintained that a protoeukaryote (with nucleus) engulfed the mitochondrial ancestor". Support for the theory came from archezoa: anaerobic eukaryotes with no mitochondria, suggesting that "eukaryotes began diversifying before mitochondria entered the picture". The authors point out that this hypothesis has two independent components: "(a) that a protoeukaryote host (PEH) engulfed the mitochondrial ancestor, and (b) that modern archezoa are 'missing links' that never possessed mitochondria."
Hypothesis (b) "is now universally rejected" and the evidence is that the archezoa are derived, not missing links. The authors continue: "Hypothesis (a) was also rejected, and because eukaryotes and archaea share a number of similar genes, the deposed PEH was replaced with archaea. Consequently, incorporation of the mitochondrion - not the origin of the nucleus - was hailed as the defining event in eukaryotic origins. This opened the floodgates of speculation, and numerous new hypotheses emerged. None is supoported by observation: no archaea reside within bacteria, viruses have preposterously few similarities to the nucleus, and no RNA cells exist." The authors go on to develop their critique of these newer hypotheses and to defend the PEH theory. They argue that a nucleus-bearing protoeukaryote was the direct ancestor of modern eukaryotes.
The comments about "floodgates of speculation" in the name of science are undoubtedly correct. They apply generally to the Darwinian story-telling tradition, in which scientists propose speculative scenarios rather than document the real problems that should constrain thinking. Poole and Penny have provided us with a welcome caution about the way science should be done, but have they really gone further than acknowledging the problems? Their ancestral host is a protoeukaryote, not something else! This is the problem of irreducible complexity (noted previously here and here) and it is not going to go away!

Engulfed by speculation
Anthony Poole & David Penny
Nature 447, 913 (21 June 2007) | doi:10.1038/447913a

Abstract: The notion that eukaryotes evolved via a merger of cells from the other two domains - archaea and bacteria - overlooks known processes.

The Human Genome Project was anticipated to have provided us with a blueprint of what makes us human. Very quickly, it became apparent that the published genome was not a blueprint: we had raw data but no information. Although a watershed, it was but a first step in understanding the genetics of human beings.
The follow-on ENCODE Project Consortium focused on a selected 1% of the human genome "to map a variety of sequence elements including genes, promoters, enhancers, repressor or silencer sequences, exons, replication origin and termination sites, transcription factor binding sites, methylation sites, DNase I hypersensitive sites, chromatin modifications, conserved sequences, and RNA transcripts, to name only those considered in the pilot project." One of the major conclusions concerns the organisation of functional elements in the genome. In some cases, this confirmed current models but, the authors of the Nature paper write, "we also uncovered some surprises that challenge the current dogma on biological mechanisms." The surprises all involve unexpected complexity in the genome; complexity that necessitates a revision of the way we think about transcription and genes.
Furthermore, the ENCODE findings should lead to the final demise of the term "Junk DNA". "The ENCODE consortium's major findings include the discovery that the majority of DNA in the human genome is transcribed into functional molecules, called RNA, and that these transcripts extensively overlap one another. This broad pattern of transcription challenges the long-standing view that the human genome consists of a relatively small set of discrete genes, along with a vast amount of so-called junk DNA that is not biologically active." The majority of the genome now appears to have functionality. It must be regarded as a "complex, interwoven network" with genes being just one of many functional elements.
It is worth reminding ourselves that the "long-standing view" of the human genome has been used to argue against Intelligent Design. Evolutionary biologists have regarded the existence of Junk DNA as evidence supporting their Darwinian perspective (having a pool of non-functional genetic material with the potential to mutate into something biologically meaningful). Not only has the supposed reservoir of variability evaporated (by the discovery of functionality for most of the genome), the organisational structure of the functional elements has been found to be breathtakingly complex. No wonder the evolutionary biologists find it difficult to avoid using the word "surprise"! ID biologists, on the other hand, have received the findings with enthusiasm, because the discovery of functionality and extraordinary complexity fits the expectation of design-oriented thinking.

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
The ENCODE Project Consortium
Nature, 447, (14 June 2007), 799-816 | doi:10.1038/nature05874 [Open Access]

Abstract: We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.

See also:

National Human Genome Research Institute (Press Release), New Findings Challenge Established Views on Human Genome, June 13 2007.

Weinstock, G.M., ENCODE: More genomic empowerment, Genome Research, 2007 17: 667-668. [Open Access]

In the minds of large swathes of the intellectual community, there is a line between facts and values, between the objective findings of science and the subjective beliefs of individuals. This line goes back a long way in history and many regard it as the only way to bring harmony to science and faith questions.
In a recent issue of the New York Times, Senator Brownback explained his reservations about the way the theory of evolution is used in contemporary discourse. In particular, he wrote: "It does not strike me as anti-science or anti-reason to question the philosophical presuppositions behind theories offered by scientists who, in excluding the possibility of design or purpose, venture far beyond their realm of empirical science."
This comment, and several others in his article, has stirred strong reactions from the Editor of the journal Nature. "But there are lines that should not be crossed, and in a recent defence of his beliefs and disbeliefs in the matter of evolution, US Senator Sam Brownback (Republican, Kansas) crosses at least one." The particular point at issue concerns the human mind, and the Editorial insists that the conceptual framework for understanding humanity is evolutionary theory. Thinking based upon human minds being "the product of evolution is not atheistic theology. It is unassailable fact." Furthermore, the Editorial goes on, "our feelings, intuitions, the ways in which we love and loathe, are the product of experience, evolution and culture alone." The Editorial concludes: "Scientific theories of human nature may be discomforting or unsatisfying, but they are not illegitimate. And serious attempts to frame them will reflect the origins of the human mind in biological and cultural evolution, without reference to a divine creation." The abstract of the Editorial reads: "With all deference to the sensibilities of religious people, the idea that man was created in the image of God can surely be put aside."
The real problem is a belief that there is a line between facts and values. Senator Brownback pointed to this when he wrote about "philosophical presuppositions behind theories", but the implications of this have eluded the writer of the Editorial. We do not have empirical evidence that the human mind is the product of evolution: the "unassailable fact" is actually a deduction imposed by the a priori adoption of evolutionary premises (that everything about the human mind can be understood in terms of natural causes: "the product of experience, evolution and culture alone"). In denying the reservations of Senator Brownback, the Editorial has to cross the line in the other direction! Apparently, "science" requires Christians to put aside the idea that man was created in the image of God, and evolutionary psychology requires Christians to abandon the idea that feelings, intuitions and emotions are related to the relationship people have with God. The assertion that "science" has these theological implications should surely make us realise that the fact/value demarcation is inappropriate and that it is time to revisit these issues. The "science" of the Editorial is naturalistic and it is inherently impoverished. We need ID inputs to this debate to reclaim science from the tyranny of naturalism.

Evolution and the brain (Editorial)
Nature 447, 753 (14 June 2007) | doi:10.1038/447753a

Abstract: With all deference to the sensibilities of religious people, the idea that man was created in the image of God can surely be put aside.

See also:
Brownback, S. What I Think About Evolution, New York Times, May 31, 2007.

IN our sound-bite political culture, it is unrealistic to expect that every complicated issue will be addressed with the nuance or subtlety it deserves. So I suppose I should not have been surprised earlier this month when, during the first Republican presidential debate, the candidates on stage were asked to raise their hands if they did not "believe" in evolution. As one of those who raised his hand, I think it would be helpful to discuss the issue in a bit more detail and with the seriousness it demands. [snip]

Michael Behe's sequel to Darwin's Black Box appeared this week and the occasion was marked by a scathing review in the journal Science, authored by Sean Carroll. The reviewer starts by saying that his experience of reading the book reminded him of Thomas Huxley's words during his 1860 debate with Samuel Wilberforce: "The Lord hath delivered him into mine hands." He expands on this with this comment: "Behe makes a new set of explicit claims about the limits of Darwinian evolution, claims that are so poorly conceived and readily dispatched that he has unwittingly done his critics a great favor in stating them."
Unfortunately for Carroll, the words attributed to Huxley were unknown for at least 30 years after the event. They were probably a retrospective invention to further the aims of those trying to represent any questioning of Darwinism as anti-science. Sad to say, Carroll continues to affirm the warfare thesis in this review, painting Behe as writing for "various flavors of creationists", drawing attention to legal decisions declaring ID to be a religious concept, and more.
Readers of Carroll will learn very little about what actually is to be found in Behe's book. This excerpt comprises most of what he has to say: "Behe also explores some examples of Darwinian evolution at the molecular level, including an extensive treatment of the evolutionary "trench warfare" fought between humans and malarial parasites over the millennia - all in the context of what Darwinian evolution "can do." So what's the problem? The problem is what Behe asserts Darwinian evolution can't do: produce more "complex" changes than those that have enabled humans to battle malaria or allowed malarial parasites to evade the drugs we throw at them. Behe's main argument rests on the assertion that two or more simultaneous mutations are required for increases in biochemical complexity and that such changes are, except in rare circumstances, beyond the limit of evolution. He concludes that "most mutations that built the great structures of life must have been nonrandom." In short, God is a genetic engineer, somehow designing changes in DNA to make biochemical machines and higher taxa."
Although Behe's book is packed with arguments from evidence, Carroll has only broad brush rejections of his thesis. He declares "an immense body of experimental data directly refutes this claim". Also, that Behe has "again gone "public" with assertions without the benefit (or wisdom) of first testing their strength before qualified experts." This type of reasoning has often been heard before. Instead of engaging with ID scholarship, there is an appeal to mountains of contrary evidence and to qualified experts who know best.
What Carroll does not acknowledge is that Behe's thesis is recognised as significant among many professional biologists: they have been talking for years about what Darwinism can and can not do! Carroll's selection of literature should not be read as a fait accompli, but as a rear-guard defence of the Darwinian paradigm. There should be an academic debate about the significance of these data.
The real issue is: will a debate within science be allowed? If Behe is not allowed the right of reply, this review should be treated as an exercise in polemics, designed to protect the world of science from ever having to face up to evidences of ID. If there is the opportunity to reply, readers will enjoy a genuine scientific debate. This review must backfire, because science has shown that there are limits to Darwinism and it is perfectly legitimate to ask what Darwinism can and cannot do.

God as Genetic Engineer
Sean B. Carroll
Science 316, 8 June 2007, 1427 – 1428 | DOI: 10.1126/science.1145104

Review of The Edge of Evolution: The Search for the Limits of Darwinism by Michael J. Behe, Free Press, New York, 2007. 331 pp. ISBN 9780743296205.

"The Lord hath delivered him into mine hands."
Those are the words that Thomas Huxley, Darwin's confidant and staunchest ally, purportedly murmured to a colleague as he rose to turn Bishop Samuel Wilberforce's own words to his advantage and rebut the bishop's critique of Darwin's theory at their legendary 1860 Oxford debate. They are also the first words that popped into my head as I read Michael J. Behe's The Edge of Evolution: The Search for the Limits of Darwinism. In it, Behe makes a new set of explicit claims about the limits of Darwinian evolution, claims that are so poorly conceived and readily dispatched that he has unwittingly done his critics a great favor in stating them. [snip]

See also:
John Hedley Brooke, The Wilberforce-Huxley Debate: Why Did It Happen? Science & Christian Belief, (2001), 13(2), 127-141
Excerpt: "Far from any lasting significance, the event almost completely disappeared from public awareness until it was resurrected in the 1890s as an appropriate tribute to a recently deceased hero of scientific education. That delicious remark, "the Lord hath delivered him into mine hands", was probably a retrospective invention of that decade. There is, to my knowledge, no reference to it in the few contemporary reports."(p.129)

Behe, M. Response to Critics, Part 2: Sean Carroll,
AmazonConnect Blog, June 26, 2007

Luskin, C. Sean Carroll Fails to Scale The Edge of Evolution (Part IV): Mistaking Protein Sequence Similarity for Natural Selection
Evolution News & Views, July 2, 2007 [This essay has links to the other three parts of this response to Carroll]

In a major review paper, Jacquelyn Thomas and Fazale Rana argue the critical importance of cell membranes: "Few would question if life, or at least life as we know it today, could exist without boundaries. Should the cell membrane be compromised, key processes of the cell are disrupted. Membrane formation is an essential step in the emergence of life."
Research has tended deliver "proof-of-principle" results designed to show that feasibility of membranes forming by natural processes, but there have been two omissions. The first is an integrated approach, because there are many steps involved in forming a workable membrane. The second concerns the "exacting relationship between environmental conditions and amphiphile composition and phase behaviour": "we have discovered that virtually every step in the process of membrane origins and evolution appears to be crucially influenced by environmental conditions, and lipid composition and polymorphic phase behavior. While researchers have noted the influence of these factors on the emergence of cell membranes, their pervasiveness has largely gone unrecognized."
When an overview of the research is assembled in this way, the landscape can only be described as totally fragmented: "It is almost like having 50 pieces to a puzzle and finding no two pieces fit together because they are from 50 different puzzles." When environmental factors are brought into the analysis, it is found that factors permitting some outcomes prevent others: "Proof-of-principle experiments indicate that physicochemical processes could conceivably lead to the origin and birth of cell membranes, but environmental and lipid compositional fluctuations on early Earth could hinder the emergence of cell membrane systems and the transition to contemporary cell membranes."
The conclusion of the paper is that the focus needs to be shifted towards understanding the role of environmental conditions.
Elsewhere, Rana has this to say about the research outcomes to date: "The exacting conditions needed to self-assemble and maintain biological membranes make the conclusion that these structures could emerge by natural processes improbable. At the same time, the fine-tuning and singularity of conditions needed for cell membrane structure and function stand as hallmark characteristics of Intelligent Design - reasonable expectations if God is responsible for life."

The influence of environmental conditions, lipid composition, and phase behavior on the origin of cell membranes
Jacquelyn A. Thomas and F. R. Rana
Origins of Life and Evolution of Biospheres, 2007 Jun, 37(3), 267-85 | doi 10.1007/s11084-007-9065-6

At some point in life's development, membranes formed, providing barriers between the environment and the interior of the 'cell.' This paper evaluates the research to date on the prebiotic origin of cell membranes and highlights possible areas of continuing study. A careful review of the literature uncovered unexpected factors that influence membrane evolution. The major stages in primitive membrane formation and the transition to contemporary cell membranes appear to require an exacting relationship between environmental conditions and amphiphile composition and phase behavior. Also, environmental and compositional requirements for individual stages are in some instances incompatible with one another, potentially stultifying the pathway to contemporary membranes. Previous studies in membrane evolution have noted the effects composition and environment have on membrane formation but the crucial dependence and interdependence on these two factors has not been emphasized. This review makes clear the need to focus future investigations away from proof-of-principle studies towards developing a better understanding of the roles that environmental factors and lipid composition and polymorphic phase behavior played in the origin and evolution of cell membranes.

From the conclusion: While precise membrane composition and environmental factors may be regulated in individual steps, major difficulties arise when trying to integrate the conditions essential for each step into a cohesive stepwise evolution. It is almost like having 50 pieces to a puzzle and finding no two pieces fit together because they are from 50 different puzzles. Likewise, the conditions necessary for each step of the transition from free saturated fatty acids to modern cell membranes does not "fit" together to form the completed puzzle. [snip] Proof-of-principle experiments indicate that physicochemical processes could conceivably lead to the origin and birth of cell membranes, but environmental and lipid compositional fluctuations on early Earth could hinder the emergence of cell membrane systems and the transition to contemporary cell membranes. Future investigations need to concentrate on developing a better understanding of the role that environmental conditions, and lipid composition and phase structure play in membrane origins.

We've had the "Junk DNA" debacle; now it is the turn of the brain to be analysed as endowed with "anachronistic junk". According to David Linden, the brain is a product of the tinkering blind watchmaker espoused by Darwinist biologists. Unfortunately, few readers will realise that this "central thesis" is a deduction from dogma and not empirical evidence. The data that is discussed is perfectly capable of being understood within a design perspective, including the tendency for our minds to distort reality and to act foolishly.
The reviewer, although sympathetic, baulks at the crassness of the thesis: "More difficult to show is that the use of pre-existing parts imposes functional constraints or 'bad design'." Also: "Linden is right to stress that brains evolved, but hasty to conclude that they are flawed in their design. We still know too little about the brain's inner workings to judge how well it does its job. What we do know, and what The Accidental Mind helps us to realize, is that the human brain is not designed as many have imagined."
Some of us look at the biology of the brain and find exquisite design, not an organ full of flaws. It is true to say that the science of understanding the brain is in its infancy: without hesitation, a prediction can be offered that, as research develops, exquisite design will replace "an imperfect amalgam of shoddy components" in the minds of researchers. This book tells us more about the ideology of its writer than it does about the human mind.
Books like this, and reviews like this, demonstrate yet again how unlevel the playing field is in contemporary science journals. Contributions that deny design, meaning and intelligent agency are given space, whereas proponents of design, meaning and intelligent agency are excluded (and told they have abandoned the scientific method). This is a good example of the tendency for "our minds to distort reality and to act foolishly"!

Brain botch
Georg Striedter
Nature 447, 640 (7 June 2007) | doi:10.1038/447640a

A review of The Accidental Mind: How Brain Evolution Has Given Us Love, Memory, Dreams, and God by David Linden, Harvard University Press: 2007. 288pp.

The human brain, and hence the human mind, is not an optimal, designed-from-scratch apparatus. Rather, it is an imperfect amalgam of shoddy components. That is the central thesis of David Linden's new book The Accidental Mind. Neurons are slow, leaky, and unreliable - hardly ideal computing elements. The whole brain, too, is not designed to the plan of some omnipotent engineer. Instead, evolution has endowed it with plenty of 'anachronistic junk': Which is why, according to Linden, our minds often distort reality and can lead us to act foolishly. [snip]

See also:
http://accidentalmind.org

UK researchers have contributed a fascinating study of assisted bipedalism in orangutans. These animals can keep their legs straight as they move through trees with support provided by the arms. This mode of locomotion occurs when the animals are feeding from small, flexible branches or moving between trees. "Our results are consistent with the prediction that bipedalism allows orangutans to move along multiple supports that are more slender, and hence more deformable, than does quadrupedalism or even orthograde suspension." This confirms the hypothesis that hand-assisted bipedalism confers selective advantages on arboreal apes.
However, the empirical research is not the reason why this paper was the cover story in Science. The authors use their study to argue that bipedalism is a trait that evolved in an arboreal context. One media story describes the significance thus: "The new theory marks a U-turn in scientific thinking. Previously it was assumed humans only began to stand upright after moving out of the forests on to the wide open savannahs of East Africa." The authors claim: "Hand-assisted locomotor bipedality, adopted under these strong selective pressures, seems the most likely evolutionary precursor of straight-limbed human walking."
Although the paper has created a stir, what has been totally lacking is a design perspective. This, I think, is to the detriment of the scientific debate. In particular, the differences between "hand-assisted locomotor bipedality" and the bipedality evidenced by humans are not explored. Yet a fundamental aspect of design thinking is that a whole raft of characters must be in place to enable humans to balance and move on two feet! These include: arched feet, strong big toes, long legs, upright knee joints, angled femur bones, upright hip joints, straight back, upright skull, flat face and a very fine sense of balance. To develop a coherent account of the origin of bipedalism from a "hypothetical common ancestor of the great apes", observations of orangutans moving through trees with straight legs must be supplemented by an extensive analysis of other relevant information. In this analysis, design perspectives have a significant contribution to make.
Another conclusion of interest is that knuckle-walking is inferred to be a derived (rather than a primitive) feature. They suggest that early bipedalism was retained, not gained, in humans but lost by apes and chimps. One is tempted to observe that many widely-held scenarios about human evolution have had to be abandoned like this. Adopting a cautionary stance does seem the wisest long-term strategy.
One last point: the debate over bipedality has artificially restricted boundaries. The participants are all presuming that there is a "hypothetical common ancestor of the great apes". There is no hypothesis that there may not be such an ancestor. This is because the evolutionary framework is accepted as a 'given', deemed to have been proved long ago and not worth revisiting. Consequently, this whole exercise is an example of Kuhnian 'normal' science. The researchers are working within a closed paradigm and trying to put the jigsaw together. Some of us want to change the boundaries of the debate, to revisit the claims of evolutionary theory and to test hypotheses that others are not testing. This, we think, should be deemed essential for the health of science.

Origin of Human Bipedalism As an Adaptation for Locomotion on Flexible Branches
S. K. S. Thorpe, R. L. Holder, and R. H. Crompton
Science, 316, 1 June 2007: 1328-1331.

Abstract: Human bipedalism is commonly thought to have evolved from a quadrupedal terrestrial precursor, yet some recent paleontological evidence suggests that adaptations for bipedalism arose in an arboreal context. However, the adaptive benefit of arboreal bipedalism has been unknown. Here we show that it allows the most arboreal great ape, the orangutan, to access supports too flexible to be negotiated otherwise. Orangutans react to branch flexibility like humans running on springy tracks, by increasing knee and hip extension, whereas all other primates do the reverse. Human bipedalism is thus less an innovation than an exploitation of a locomotor behavior retained from the common great ape ancestor.

See also:

O'Higgins, P. and Elton, S., Walking on Trees, Science, 316, 1 June 2007: 1292-1294.

Gibbons, A., Walk Like an Orangutan, ScienceNOW Daily News, 31 May 2007.

Breitbart.com, May 31 2007, Humans 'learned to walk in trees'

Lungfish are interesting animals, "dependent on their watery environment for food but dying if they can't breathe air with their lungs." It is not unusual for them to be mentioned in accounts of the evolution of fish to land-dwelling tetrapods because they demonstrate an ability to bridge the gap between water and air. (Outside this, they are not good candidates for being transitional).
Water-breathers have a distinctly different biology when compared to air breathers. "All air breathing land dwellers deal with acid - an excess of protons - by reacting protons with bicarbonate ions to create water and CO2, which is breathed out. To deal with too much base, breathing slows down, keeping CO2 and therefore protons in the body. Water breathing fish take a different approach, relying on metabolic processes at their gills and kidneys to restore a normal blood pH." So it is an interesting research question - how do lungfish deal with the problems?
"The lungfish have the best of both worlds" says Gilmour, one of the co-authors. Blackburn's summary is: "Like land dwellers, they rely more on air breathing to redress a more acidic blood pH, but their gills and kidneys deal with an excess of base to return blood pH back to normal, just like water breathing fish."
The research findings are interesting for students of origins. Lungfish do not demonstrate a transitional physiological system, but employ two developed systems side-by-side. They have an air-breathing system for controlling acidity (respiratory compensation) and they use their gills and kidneys to reduce excess base (metabolic compensation). In other words, the ability to operate in both watery and land environments requires two complex systems to be in place: one for living in water and the other for living in air. The case of lungfish shows that biological information precedes and permits biological function.

Mechanisms of acid-base regulation in the African lungfish Protopterus annectens
K. M. Gilmour, R. M. Euverman, A. J. Esbaugh, L. Kenney, S. F. Chew, Y. K. Ip and S. F. Perry
Journal of Experimental Biology 210, 1944-1959 (2007) | doi: 10.1242/jeb.02776

Abstract: African lungfish Protopterus annectens utilized both respiratory and metabolic compensation to restore arterial pH to control levels following the imposition of a metabolic acidosis or alkalosis. [. . .] These findings suggest that lungfish, like tetrapods, alter ventilation to compensate for metabolic acid-base disturbances, a mechanism that is not employed by water-breathing fish. Like fish and amphibians, however, extra-renal routes play a key role in metabolic compensation

See also:
Blackburn, L., Lungfishes' balancing act, Journal of Experimental Biology 210, 0ii (2007), doi: 10.1242/jeb.007419

Douglas Hofstadter is professor of cognitive science at Indiana University and his recent book, I Am a Strange Loop is yet another attempt to explain consciousness from within a "decidedly materialistic" paradigm. "He seeks an explanation of the phenomenon of consciousness using physical law only." According to this approach, "our feeling of a conscious "I" is but an illusion created by our neuronal circuitry".
So, what is it to be a person? Who am "I"? "If we posit that our consciousness is an illusion created by our thoughts "watching ourselves think" [as the philosopher of mind Daniel Dennett had previously suggested], we might ask "Who watches the watcher?"" Does me asking the question demonstrate that I am a person and that my consciousness is not an illusion? The offered response is 'no!' "The impression of having a mind is just another pattern of [neuronal] firings". This approach considers it entirely reasonable to expect that humans will, one day, construct machines with their own personalities.
Any alternative perspectives are traced back to Descartes and his dualist view of the world. This is unfortunate, because I doubt that most non-materialists see themselves as exponents of Cartesian philosophy. Some, for example, would want to identify information as a fundamental aspect of reality (an avenue of research that is excluded within the materialistic paradigm). Adoni (the reviewer) notes that a "surprising (to me) number of philosophers of the mind" are not materialists, but the review does not attempt to interact with any of their ideas. It is effectively declaring that non-materialists have nothing useful to say about consciousness.
Reading reviews like this is quite depressing. The materialist mind-set is a universal acid that eats away at everything, including itself. Consequently, the mind has to be a product of hierarchical levels of neuronal firings, and personality has to be an illusion. We are ultimately conscious machines. Why anyone with these views should think that our neuronal activity can have anything to do with truth and reality is a mystery to me!
But even more important, the materialist approach to consciousness is commonly dignified by the name "science". Other approaches, which are likely to be linked to Theism, are labelled "religion" and are excluded, on demarcation grounds, from science. This is an unacceptable situation, for as metaphysics, materialism has a philosophical standing that is entirely equivalent to Theism. It is simply that people choose to build their thoughts on different foundations. The paradox is that materialistic science wants to be realist and to have truth as a goal, but its approach to human consciousness can only support a post-modern philosophy which emphasises the socially constructed nature of reality and substitutes relativism for truth. And, for materialists, individuals have to seek for meaning and self-worth in existential experiences (an escape from reason) because the universal acid of rationalism has completely corroded realism and truth in human psychology.

Who Watches the Watcher?
Christoph C. Adami
Science 316, 25 May 2007: 1125-1126.

A review of I am a Strange Loop by Douglas Hofstadter
Basic Books, New York, 2007. | ISBN 9780465030781

According to Paul Rees "textbooks for GCE Advanced Level Biology have provided over-simplified and inaccurate accounts of Charles Darwin's contribution to the study of evolution over a period of many decades." The author has 20 years of teaching the subject and is now an academic in a British university. The paper reminded me of Jonathan Wells' book-length critique of the way US textbooks portray the classic 'evidences' advanced to support Darwinism. Rees' contribution is much more modest in what it attempts to do, but he is rightly concerned about the way the textbooks "have perpetuated myths about Darwin and his work". It would have been an interesting exercise for him to offer some analysis of the phenomenon, but maybe this would create a hostile reception, similar to that experienced by Wells.
An interesting addendum is his observation about "a worrying absence of references to Darwin in current A-level Biology specifications and some texts." This trend is also found in the US, where evolutionary biologists tend to point the finger at creationists and ID activists, inferring that the textbook authors are swayed by sales potential. This is quite unjust, as creationists and ID educators consistently call for more accurate information (rather than content that is cherry-picked to advance the case for Darwinism). But what can be said when the same trend of diminishing the significance of Darwin is observed in the UK? There is no parallel with the US case: this is not a trend linked to the market for textbooks. Maybe Darwinism is actually not as significant for biology as many would like to make it? Maybe the textbook authors have a problem showing its relevance to the curriculum? This may be a revolutionary thought to those who keep telling us that nothing in biology makes sense except in the light of evolution, but more and more people are coming to realise that Darwinism explains everything but predicts nothing. This is not something that fits well into the ethos of science.

The evolution of textbook misconceptions about Darwin
Paul A. Rees
Journal of Biological Education, 41(2), Spring 2007, 53-55.

Abstract: Textbooks for GCE Advanced Level Biology have provided over-simplified and inaccurate accounts of Charles Darwin's contribution to the study of evolution over a period of many decades. They have credited him with field skills and insight that he did not possess, and repeated several historical inaccuracies. Darwin's strength was as a synthesiser of information but, at least in his early life, he was not a particularly observant or careful field biologist. The specimens collected on his voyage on HMS Beagle were largely identified and analysed by others, but this is rarely acknowledged. This article criticises the historical accuracy of the treatment of Darwin and his ideas in a range of A-level textbooks, and notes a worrying absence of references to Darwin in current A-level Biology specifications and some texts.

"He's a young astronomer with dozens of articles in top journals; he has made an important discovery in the field of extrasolar planets; and he is a proponent of intelligent design, the idea that an intelligent force has shaped the Universe." His academic credentials are impressive; Guillermo Gonzalez has an international reputation. David Lambert, director of the MacDonald Observatory, has an assessment that should carry some weight: "I would have said he was a serious tenure candidate."
However, others think differently. "I would have voted to deny him tenure," says Robert Park, a physicist at the University of Maryland in College Park. "He has established that he does not understand the scientific process." Also, "in 2005, Gonzalez's rising profile led a group of 131 faculty members to sign a petition disavowing intelligent design."
Others, looking on, have real concerns about academic freedom. "There is a pattern happening to everybody who's pro intelligent design," says one pro-design biologist, who declined to be named because his own tenure process has just begun. "The same thing could happen to me," he says. "I don't want to get into trouble."
There are deep and significant differences here about the philosophy of science, and the hostile deniers are convinced that ID is incompatible with science. This is a battle that has to be fought, because this "academic hostility" is fundamentally wrong. These people conveniently forget that the pioneers of science were all advocates of ID. There are numerous philosophers of science who recognise the legitimacy of ID within science - the recent high profile case involving Professor Anthony Flew is witness to that. Those who claim that ID advocates do "not understand the scientific process" are nearly always advocates of the philosophy of naturalism: nature is all there is. They are using their version of the scientific process to ram atheistic philosophy into our minds. We must ensure that science does not become an ideological weapon, and this is why we need university leaders and other opinion formers to defend academic freedom and allow the issues to be explored openly and honestly.

Darwin sceptic says views cost tenure
Geoff Brumfiel
Nature 447, 364 (24 May 2007) | doi:10.1038/447364a

Abstract: Astronomer blames setback on his support of intelligent design.

See also:
Crowther, R. World's Premiere Scientific Journal Reports on Iowa State's Denial of Tenure to Guillermo Gonzalez, Evolution News & Views. May 23 2007.
Excerpt: "I am not appealing the tenure decision on the grounds of religious discrimination" (Guillermo Gonzalez).

The Darwin Exhibition constructed for the American Museum of Natural History has received many accolades. However, are people getting the Darwin of history, or are they being presented with a cardboard Darwin, constructed by people who have a particular agenda? It is worth asking this question, because it has happened many times before. For example, the "warfare thesis" between science and Christianity was the invention of Thomas Huxley and his allies. Theirs was not a fair view of history and they had the agenda of shifting the power base in society from 'the Church' to the scientific elite.
Unfortunately, Darwin has become an iconic figure for many people. This has emerged in recent discussions regarding the teaching of evolution in schools: any criticism of Darwin's theory has been interpreted as an assault on science. This is a deplorable state of affairs. Any serious educationalist ought to be encouraging students to think critically, and it is good scholarship to examine arguments for and against any theory. Hiram Caton has contributed a worthy critique of the new exhibition. Particularly welcome is his recognition that there was serious scientific criticism of Darwin's theory. "The Exhibition promotes an extreme version the triumphalist legend. Viewers are told that the Origin of Species caused a sensation, not only in Britain but around the world [. . .]. It is well established that while evolution was widely accepted by 1870, natural selection was not widely accepted among scientists; [. . .] Darwin's scientific apologists made serious criticisms."
We are fast approaching the bicentennial of Darwin's birth. The indications are that the hype will increase and peak in 2009. What we must not do is allow the myth-makers an easy ride.

Getting Our History Right: Six Errors about Darwin and His Influence
Hiram Caton
Evolutionary Psychology, 2007. 5(1): 52-69

Abstract: The Darwin Exhibition created by the American Museum of Natural History is the centerpiece of the bicentennial of Darwin's birth. It opened in November 2005 and will circulate to a number of museums before terminating at the London Natural History Museum in February 2009. The Exhibition is also a major contributor to online instruction about evolution for schools. The quality of the Exhibition's narrative is accordingly of some significance. This paper argues that the narrative is the legendary history that dominates public opinion. The legend has been thoroughly disassembled by historical research over recent decades. My criticism is organized as six theses. (1) Publication of the Origin was not a sudden ("revolutionary") interruption of Victorian society's confident belief in the traditional theological world-view. (2) The Origin did not "revolutionize" the biological sciences by removing the creationist premise or introducing new principles. (3) The Origin did not revolutionize Victorian public opinion. The public considered Darwin and Spencer to be teaching the same lesson, known today as "Social Darwinism", which, though fashionable, never achieved dominance. (4) Many biologists expressed significant disagreements with Darwin's principles. (5) Darwin made little or no contribution to the renovation of theology. His public statements on Providence were inconsistent and the liberal reform of theology was well advanced by 1850. (6) The so-called "Darwinian revolution" was, at the public opinion level, the fashion of laissez-faire economic beliefs backed by Darwin and Spencer's inclusion of the living world in the economic paradigm.

Two psychologists have argued that "resistance to science" in adults has its origins in the experiences of childhood. In particular, they claim, there are two adult traits that can be traced back to childlike characteristics. These are a reliance on "common-sense intuitions" about the world around us, and a sensitivity to the "trustworthiness of the source" when information is provided by trusted teachers/parents.
First, I am not taking issue with the idea that the experiences of childhood affect our adult lives. I am sure a paper could equally be written on 'attraction to science' being traced back to childhood (which happens to be my own experience).
Second, there is a tension between the authors' primary example of resistance to science (denying evolution) and the other examples (alternative medicine, spirits, astrology, ESP, divination). I do not think these can be lumped together in this way. By and large, in the US, evolution-doubting is widespread among the Christian community, but these same people do not indulge in the other cases of "resistance". Indeed, the Christian community tends to regard them as 'New Age' practices which are linked to an evolutionary world view that has no place for a Sovereign Creator God. In this spiritual vacuum, New Age practices flourish. Rationalism in the physical world spawns irrational existentialism in the religious world. Significantly, there is no interaction with thoughts like this by the authors of the paper.
Thirdly, and this is the most important point, the authors have a very narrow understanding of 'science' and 'scientific ideas'. This is best illustrated by the way they handle the mind/brain issue. "The strong intuitive pull of dualism makes it difficult for people to accept what Francis Crick called "the astonishing hypothesis". Dualism is mistaken - mental life emerges from physical processes." This statement is false because the authors are not presenting the conclusions of science, but the presuppositions of many neuroscience scholars. The authors are presenting an input as an output! The presupposition (that the human mind and consciousness "emerges from physical processes") has never been demonstrated empirically. Indeed, some of us predict that consciousness will never be understood by working within this naturalistic paradigm. These authors are confusing scientism with science. Any departure from the tenets of scientism are interpreted as "resistance to science" - which, in the case of evolutionary theory and understanding consciousness + the human mind is a travesty of the issue. Anyone one who reads Darwin on Trial by Phillip Johnson (for example) and thinks this is an example of "resistance to science" is sadly under a delusion.

Childhood Origins of Adult Resistance to Science
Paul Bloom and Deena Skolnick Weisberg
Science, 18 May 2007: 316, 996-997 | DOI: 10.1126/science.1133398

Abstract: Resistance to certain scientific ideas derives in large part from assumptions and biases that can be demonstrated experimentally in young children and that may persist into adulthood. In particular, both adults and children resist acquiring scientific information that clashes with common-sense intuitions about the physical and psychological domains. Additionally, when learning information from other people, both adults and children are sensitive to the trustworthiness of the source of that information. Resistance to science, then, is particularly exaggerated in societies where nonscientific ideologies have the advantages of being both grounded in common sense and transmitted by trustworthy sources.

See also:
Why do some people resist science? By Paul Bloom and Deena Skolnick Weisberg

In a recent blog, I described some introductory words in a paper by Eugenie Scott and Nicholas Matzke as Darwinian spin. They declared evolutionary theory to be "replete with explanations for complex biological structures" and that it "continues to make progress in explaining such fascinating structures". To prove my point, just look at the current issue of Nature, where Wallace Arthur reviews the book: From Embryology to Evo-Devo. He asks: "How do novelties arise? We can't yet agree on a definition for them, let alone answer this fundamental question. But we can see the nature of the challenge ahead." Arthur describes a research agenda in its infancy, at the stage of sorting out research objectives. He is right, and Scott + Matzke are wrong.
This is a serious point to make, because it affects what we teach students about the subject and what message goes out to the general public. Scott + Matzke claim to be acting in the interests of science education; but their message is not an accurate portrayal of what the research community have achieved. The reality is that the community have a prospect ahead of them. "As Wagner [the author of one of the chapters] says: "One of the main sources of intellectual excitement in devo-evo (sic) is the prospect of understanding major evolutionary transformations.""
Implicit in the comments of Arthur and of Wagner is the recognition that Darwinism does not have the answers, and that the ID insistence on addressing the issue of novelty is on target.

The search for novelty
Wallace Arthur reviews From Embryology to Evo-Devo: A History of Developmental Evolution
Nature 447, 261-262 (17 May 2007) | doi:10.1038/447261a

Excerpt: Third, and most important in my view, the origin of novelty is becoming one of the major themes of evo-devo. Attention is shifting from the retention of the old (as in recapitulation) to the creation of the new (be it an eye, a leg, a feather or even a whole body plan). Both the historical and the current importance of novelty emerge repeatedly in the book. How do novelties arise? We can't yet agree on a definition for them, let alone answer this fundamental question. But we can see the nature of the challenge ahead.

Paper from the colloquium: In the light of Evolution

John Gerhart and Marc Kirschner offer a radical theory of variation: one that majors on the regulatory elements rather than on the genes themselves. Coming from the Evo-Devo school, this theory offers numerous novel avenues of thought.
First, there are real problems with many traditional models of phenotypic variation. The models work in a limited way with single traits, but they do not handle complex variations at all well. In such cases, selection has to act on several traits concurrently and mutations (the source of variation) just may not be forthcoming. Consequently, "evolution may be impeded".
Second, it is not widely realised that there is a remarkable "metazoan toolkit of conserved functional components and processes". These were all in place by the end of the Precambrian. These are referred to as "conserved core processes". "They comprise an enormous toolkit, and the genes encoding them comprise the majority of the genetic repertoire of the animal. They have changed very little in the course of animal evolution since the Cambrian, even though animal anatomy and physiology have changed."
Third, if the toolkit and the genes encoding them have not changed since the Precambrian, what has? The answer offered is the regulatory system. The metazoan toolkit was so powerful and versatile "that post-Cambrian animals could largely omit further functional innovation at the gene product level (protein and functional RNA evolution) and instead exploit regulatory innovation to diversify anatomy, physiology, and development." As an example, the authors point out (from genome analysis) that 79% of mouse genes retain Precambrian sequences.
Whilst the authors go on to discuss many aspects of this theory and point out some empirical data that appears to provide validation (but see comments from Wells on this), it is pointed out here (and by Wells) that this theory does not address the origin of complex specified information. All the essential genetic information existed in the Precambrian and is accepted by the authors almost as a gift bequeathed to Phanerozoic animals and plants. The Cambrian organisms possessed the innate capacity to vary. "If the capacity to develop large phenotypic differences already exists in the organism as self-inhibited alternate states, and these can be elicited by simple signals (weak linkage), then large evolutionary steps can be made with a modicum of genetic change. In such cases, the distinction blurs between evolutionary gradualism and saltation (the generation of significant traits by single mutations)."
Curiously, this paper can be read as a vindication of concepts developed by ID scholars: if you want to develop models of variation involving complex specified information, you must start out with complex specified information. For more on this, go here and here.

The theory of facilitated variation
John Gerhart and Marc Kirschner
Proceedings of the National Academy of Sciences USA, published May 9, 2007, 10.1073/pnas.0701035104

This theory concerns the means by which animals generate phenotypic variation from genetic change. Most anatomical and physiological traits that have evolved since the Cambrian are, we propose, the result of regulatory changes in the usage of various members of a large set of conserved core components that function in development and physiology. Genetic change of the DNA sequences for regulatory elements of DNA, RNAs, and proteins leads to heritable regulatory change, which specifies new combinations of core components, operating in new amounts and states at new times and places in the animal. These new configurations of components comprise new traits. The number and kinds of regulatory changes needed for viable phenotypic variation are determined by the properties of the developmental and physiological processes in which core components serve, in particular by the processes' modularity, robustness, adaptability, capacity to engage in weak regulatory linkage, and exploratory behavior. These properties reduce the number of regulatory changes needed to generate viable selectable phenotypic variation, increase the variety of regulatory targets, reduce the lethality of genetic change, and increase the amount of genetic variation retained by a population. By such reductions and increases, the conserved core processes facilitate the generation of phenotypic variation, which selection thereafter converts to evolutionary and genetic change in the population. Thus, we call it a theory of facilitated phenotypic variation.

See also:

Wells, J. What's New? Books & Culture, September/October 2006, Vol. 12, No. 5, Page 45

Paper from the colloquium: In the light of Evolution

Eugenie Scott and Nicholas Matzke, from the National Center for Science Education, offer their analysis of how ID is making "a serious challenge not in the world of science, but in the world of public educational policy." It is a paper that reworks the NCSE position without contributing any new ideas to the debate.
These authors reveal an unqualified confidence that evolutionary theory has the answers. It is "replete with explanations for complex biological structures." It "continues to make progress in explaining such fascinating structures". They assert that there is "no serious scientific challenge to evolution." Underpinning theory are "fertile and unifying evolutionary principles". Anyone challenging such robust scholarly accomplishments must be deemed lacking in academic credibility, inevitably with a political or religious agenda! (If you don't recognise this as Darwinian spin, or if you want more input on this, go here).
Unfortunately the paper is very weak in its handling of complexity. Although the authors recognise the terms "irreducible complexity" and "specified complexity", they very quickly discard them in favour of mere "complexity". Thus, we read, "complexity is not a reliable marker of intelligent agency." Yes, exactly - that is why the terms irreducible complexity and complex specified information are needed! Failure to engage with ID arguments leads to a paper that completely misses the mark.
The authors do make a good point when they write: "complex biological 'machines' are always, upon investigation, found to be cobbled together from preexisting modules with other functions. Biological designs are not really 'purposeful arrangements of parts,' they are really adaptations of parts originally used for some other purpose." But this is a contrived assertion! What we find in the biological world, in most cases, is exquisite design and not the tinkering design of Darwinism. If we consistently found "cobbled together" design, the ID community would be much smaller than it is. Also, biomimetics, as a mushrooming interdisciplinary research activity, would not exist. Similarly, Systems Biology would have great difficulty developing a coherent methodology for research.
The authors go to great lengths to derive ID from creation science. No one will deny that connections can be made. However, Scott and Matzke overlook the fact that the ID community is capable of learning, of modifying its thinking, of maturing in its approach to science, philosophy and to education. What is needed is not an inferred 'guilt by association' exercise, but an engagement with the arguments. Unfortunately, there is very little of the latter for those who take the trouble to read the paper.

Biological design in science classrooms
Eugenie C. Scott and Nicholas J. Matzke
Published online before print May 9, 2007
Proceedings of the National Academy of Sciences USA, 10.1073/pnas.0701505104

Abstract: Although evolutionary biology is replete with explanations for complex biological structures, scientists concerned about evolution education have been forced to confront "intelligent design" (ID), which rejects a natural origin for biological complexity. The content of ID is a subset of the claims made by the older "creation science" movement. Both creationist views contend that highly complex biological adaptations and even organisms categorically cannot result from natural causes but require a supernatural creative agent. Historically, ID arose from efforts to produce a form of creationism that would be less vulnerable to legal challenges and that would not overtly rely upon biblical literalism. Scientists do not use ID to explain nature, but because it has support from outside the scientific community, ID is nonetheless contributing substantially to a long-standing assault on the integrity of science education.

Paper from the colloquium: In the light of Evolution

According to Michael Lynch, "the myth that all of evolution can be explained by adaptation continues to be perpetuated by our continued homage to Darwin's treatise in the popular literature. For example, Dawkins' agenda to spread the word on the awesome power of natural selection has been quite successful, but it has come at the expense of reference to any other mechanisms, a view that is in some ways profoundly misleading." Despite all the textbooks and most popular literature giving the impression that adaptive forces are the key to understanding evolutionary transformation, there are very real questions as to "whether natural selection is a necessary or sufficient force to explain the emergence of the genomic and cellular features central to the building of complex organisms."
Lynch describes evolution as "a population-genetic process governed by four fundamental forces." These are: natural selection (which is adaptive), mutation, recombination and genetic drift (which are non-adaptive). "Given the century of work devoted to the study of evolution, it is reasonable to conclude that these four broad classes encompass all of the fundamental forces of evolution."
The body of Lynch's paper is really a manifesto for non-adaptive forces being central to our understanding of organismal complexity, so that the features of interest "may be nothing more than indirect by-products of processes operating at lower levels of organization."
This is probably the most significant paper in the colloquium. It demonstrates the vulnerability of the adaptationist paradigm to critical scrutiny. "If complexity, modularity, evolvability, and/or robustness are entirely products of adaptive processes, then where is the evidence?" Significantly, it is questioning like this that has been ruled inadmissible in the education of biology students in several US states!
But what happens when the non-adaptive 'forces' (with the addition of migration) are critiqued and found to be inadequate for creating complex specified information? What if we come to the conclusion that biological information demands intelligent causation? What is needed is a rational exploration of these issues, not a "religious adherence to the adaptationist paradigm" nor a demarkationist blocking of ID concepts from the domain of science.

The frailty of adaptive hypotheses for the origins of organismal complexity
Michael Lynch
Published online before print May 9, 2007
Proceedings of the National Academy of Sciences USA, May 15, 2007, vol. 104, suppl. 1, 8597-8604 | doi 10.1073/pnas.0702207104

Abstract: The vast majority of biologists engaged in evolutionary studies interpret virtually every aspect of biodiversity in adaptive terms. This narrow view of evolution has become untenable in light of recent observations from genomic sequencing and population-genetic theory. Numerous aspects of genomic architecture, gene structure, and developmental pathways are difficult to explain without invoking the nonadaptive forces of genetic drift and mutation. In addition, emergent biological features such as complexity, modularity, and evolvability, all of which are current targets of considerable speculation, may be nothing more than indirect by-products of processes operating at lower levels of organization. These issues are examined in the context of the view that the origins of many aspects of biological diversity, from gene-structural embellishments to novelties at the phenotypic level, have roots in nonadaptive processes, with the population-genetic environment imposing strong directionality on the paths that are open to evolutionary exploitation.

Paper from the colloquium: In the light of Evolution

One presumes that Francisco Ayala intended this paper to set the scene for the colloquium. He argues that Darwin's main contribution was to find natural mechanisms that accounted for the apparent design of living things. This, he claims, links Darwin with Copernicus as the two architects of the Scientific Revolution: with Darwin addressing the biological world and Copernicus the workings of the universe. This is highly contentious history, but even more troubling is the philosophy of science emanating from Ayala. His view of science is that all explanations of natural phenomena must necessarily be in terms of "chance and necessity" (a phrase included in the keywords). Thus, "The theory of evolution conveys chance and necessity jointly enmeshed in the stuff of life; randomness and determinism interlocked in a natural process that has spurted the most complex, diverse, and beautiful entities that we know of in the universe. [. . .] And this is the conceptual revolution that Darwin completed: the idea that the design of living organisms can be accounted for as the result of natural processes governed by natural laws."
It is this vision of science that excludes intelligent causation as a matter of principle and pre-empts all discussion of design and information linked to intelligent agency by declaring it 'out of bounds'. This is a demarcationist agenda, which ends up concluding that which was assumed at the outset. With Ayala's philosophy of science, if the cosmos and living things were intelligently designed, no one could ever know!
The paper is full of unqualified compliments to Darwin's genius. It is a market promotion exercise rather than an academic paper. Again, historians of science would want to take issue with many of the points made. However, my concern here is with the presentation of natural selection (and Darwin's references to "my theory"). "Natural selection accounts for the "design" of organisms because adaptive variations tend to increase the probability of survival and reproduction of their carriers at the expense of maladaptive, or less adaptive, variations." Also, "Mutation and selection have jointly driven the marvelous process that, starting from microscopic organisms, has yielded orchids, birds, and humans." When ID scholars focus their attention on the inability of mutations and natural selection to deliver specified complexity and novel structures, they are informed that they are being simplistic and Darwinism has several other mechanisms in its portfolio. Nevertheless, not a hint of this is manifest in Ayala's paper. "The number of mutations that can be tested, and those eventually selected, in millions of individual animals over millions of generations is difficult for a human mind to fathom, but we can readily understand that the accumulation of millions of small, functionally advantageous changes could yield remarkably complex and adaptive organs, such as the eye."
This is traditional Darwinism, alive and well, robustly critiqued by both ID scholars and by Ayala's peers - yet presented in this colloquium as the essence of evolutionary theory!

Darwin's greatest discovery: Design without designer
Francisco J. Ayala
Proceedings of the National Academy of Sciences USA, published May 9, 2007, 10.1073/pnas.0701072104

Darwin's greatest contribution to science is that he completed the Copernican Revolution by drawing out for biology the notion of nature as a system of matter in motion governed by natural laws. With Darwin's discovery of natural selection, the origin and adaptations of organisms were brought into the realm of science. The adaptive features of organisms could now be explained, like the phenomena of the inanimate world, as the result of natural processes, without recourse to an Intelligent Designer. The Copernican and the Darwinian Revolutions may be seen as the two stages of the one Scientific Revolution. They jointly ushered in the beginning of science in the modern sense of the word: explanation through natural laws. Darwin's theory of natural selection accounts for the "design" of organisms, and for their wondrous diversity, as the result of natural processes, the gradual accumulation of spontaneously arisen variations (mutations) sorted out by natural selection. Which characteristics will be selected depends on which variations happen to be present at a given time in a given place. This in turn depends on the random process of mutation as well as on the previous history of the organisms. Mutation and selection have jointly driven the marvelous process that, starting from microscopic organisms, has yielded orchids, birds, and humans. The theory of evolution conveys chance and necessity, randomness and determinism, jointly enmeshed in the stuff of life. This was Darwin's fundamental discovery, that there is a process that is creative, although not conscious.

Last December, a colloquium was held in Irvine, CA, with the general title "In the light of evolution". This choice of words is an allusion to Dobzhansky's oft-quoted statement that "nothing in biology makes sense except in the light of evolution". A series of colloquia are planned, all seeking to "interpret phenomena in various areas of biology through the lens of evolution". The December event was the first and it took as its theme "Adaptation and Complexity".
The organisers were very aware that this is "a time of resurgent societal interest in supernatural explanations for biological complexity. Especially in the United States, proponents of intelligent design (ID)-the latest reincarnation of religious creationism - argue that biotic complexity can only be the product of a supreme intelligence (i.e., God)." Of course, this is not how the ID community sees the issue. ID arguments major on the rationale for making design inferences. The options for causal explanations are extended from 'Law + Chance' to 'Law + Chance + Design'. This approach is perceived as important for truth and for the integrity of science, because otherwise science gets moulded by the philosophy of naturalism (nature is all there is). This threat to science is neither perceived nor addressed by the organisers.
There is an easy way to show that design inferences are inappropriate - and that is to show the superiority of the explanations based on Law and Chance. However, the failure of the evolutionary community to deliver on this is one of the most important factors behind the sustained interest in ID. The authors of the introductory essay recognise that they do not bring strong, mature arguments to support their claims: "150 years after Darwin the challenge of understanding nature's complexity remains in many regards in its infancy." They go on to refer to new tools to help understand this complexity, but do not acknowledge that the data uncovered by these tools have influenced many in the direction of ID.
The papers are currently in the Early Edition of the PNAS website, all open access. Selected papers will be the subject of further comment on this blog.

In the light of evolution I: Adaptation and complex design
John C. Avise and Francisco J. Ayala
Published online before print May 9, 2007
Proc. Natl. Acad. Sci. USA, 10.1073/pnas.0702066104

Abstract: This paper serves as an introduction to this PNAS supplement, which resulted from the Arthur M. Sackler Colloquium of the National Academy of Sciences, "In the Light of Evolution I: Adaptation and Complex Design," held December 1-2, 2006, at the Arnold and Mabel Beckman Center of the National Academies of Sciences and Engineering in Irvine, CA. It is the first in a planned series of colloquia under the umbrella title "In the Light of Evolution" (see Box 1). The complete program is available on the NAS web site at www.nasonline.org/adaptation_and_complex_design.

Now that the opossum genome has been sequenced, both winners and losers have emerged. The main loser is the 'Genes-R-Us' school, who have argued that genes are the only really interesting components of the genome. This group is a loser because the "vast majority of the opossum's genes are identical to other placental mammals". Genes do not distinguish marsupials from placentals, but the non-coding elements (previously referred to as 'Junk DNA' are distinctly different. Thus, "most of the genetic difference between marsupials and placental mammals comes from non-coding sequences, not proteins."
The Evo-Devo community appears to consider itself a winner. The new research "is bound to make the [evolutionary developmental biology] community very happy, because they've been saying all along that it's the regulation of genes that is what's driving the changes that we see in the evolution of animals." Some of this confidence is, however, misplaced: it is one thing to say that gene regulation is the key to understanding the difference between placentals and marsupials, but linking this to origins is theory-laden. The data does not speak for itself but is interpreted, often through an evolutionary filter.
The ID community is also a winner. ID scholars have long been sceptical of the genetic reductionism displayed by most evolutionary biologists, and have also been quick to recognise the functionality of much of the so-called Junk DNA. These scholars have much in common with evo-devo, but see the regulation system as an extraordinarily complex system that invites design inferences when considering origins.
ID scholars will also welcome the recognition that marsupials are not primitive mammals: "The study helps to erode a common misconception that marsupials are somehow an archaic or second-rate category of mammal. One scientist comments on the discovery of a gene that encodes for a unique form of T-cell receptor not found in placental mammals: this "knocks that assumption on its head [. . .] It shows that they have a very sophisticated immune system, but one that's very different."

Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences
Tarjei S. Mikkelsen, et al.
Nature 447, 167-177 (10 May 2007) | doi:10.1038/nature05805

We report a high-quality draft of the genome sequence of the grey, short-tailed opossum (Monodelphis domestica). As the first metatherian ('marsupial') species to be sequenced, the opossum provides a unique perspective on the organization and evolution of mammalian genomes. Distinctive features of the opossum chromosomes provide support for recent theories about genome evolution and function, including a strong influence of biased gene conversion on nucleotide sequence composition, and a relationship between chromosomal characteristics and X chromosome inactivation. Comparison of opossum and eutherian genomes also reveals a sharp difference in evolutionary innovation between protein-coding and non-coding functional elements. True innovation in protein-coding genes seems to be relatively rare, with lineage-specific differences being largely due to diversification and rapid turnover in gene families involved in environmental interactions. In contrast, about 20% of eutherian conserved non-coding elements (CNEs) are recent inventions that postdate the divergence of Eutheria and Metatheria. A substantial proportion of these eutherian-specific CNEs arose from sequence inserted by transposable elements, pointing to transposons as a major creative force in the evolution of mammalian gene regulation.

See also:

Fairless, D., The awesome opossum gets sequenced, News@nature.com, 9 May 2007; | doi:10.1038/news070508-8

Lee Phillips, M., First marsupial genome released, The Scientist, 9th May 2007.

Glial cells have been known to neuroscientists for over a century and they perform numerous essential functions. Now we can add another. In the vertebrate eye, there are "radial glial cells spanning the entire retinal thickness" known as Muller cells. Shaped like an extended funnel, they are "oriented along the direction of light propagation". These cells "provide a low-scattering passage for light from the retinal surface to the photoreceptor cells", thus acting as optical fibres. Their function is to "mediate the image transfer through the vertebrate retina with minimal distortion and low loss".

For years, we have been told by "blind watchmaker" Darwinians that the eye is an example of bad design because light has to pass through the retina to reach the photoreceptor cells. These folk insist that a good Designer wouldn't have wired our retinas the "wrong" way. The response from those who advocate design has been to show that the eye is an example of optimum design: there are good reasons that can be advanced for having an inverted retina. This approach has satisfied many but certainly not all. The "bad design" claim is still widespread.

This new paper has finally nailed the argument: by revealing yet another level of exquisite design. The authors modestly say: "This finding elucidates a fundamental feature of the inverted retina as an optical system". They describe the Muller cells as "ingeniously designed light collectors". ScienceNow says: "For an organ that delivers such crystal-clear images, the eye is curiously designed. Its light-sensing rods and cones lie hidden behind a blanket of nerve cells that carry visual information to the brain. So what prevents those neurons from obscuring our vision? The answer may be surprisingly high-tech." So, in addition to optimal design arguments, we can now appreciate how these distinctive cells address completely the main perception of compromised design. One of the authors is quoted as saying: "Nature is so clever". Surely, it has to be myopic not to discern here the hallmarks of an intelligent designer. This is argument from evidence par excellence!

Muller cells are living optical fibers in the vertebrate retina
Kristian Franze, Jens Grosche, Serguei N. Skatchkov, Stefan Schinkinger, Christian Foja, Detlev Schild, Ortrud Uckermann, Kort Travis, Andreas Reichenbach, and Jochen Guck.
Proceedings of the National Academy of Sciences USA, May 15, 2007, vol. 104, no. 20, 8287-8292. | 10.1073/pnas.0611180104

Abstract: Although biological cells are mostly transparent, they are phase objects that differ in shape and refractive index. Any image that is projected through layers of randomly oriented cells will normally be distorted by refraction, reflection, and scattering. Counterintuitively, the retina of the vertebrate eye is inverted with respect to its optical function and light must pass through several tissue layers before reaching the light-detecting photoreceptor cells. Here we report on the specific optical properties of glial cells present in the retina, which might contribute to optimize this apparently unfavorable situation. We investigated intact retinal tissue and individual Muller cells, which are radial glial cells spanning the entire retinal thickness. Muller cells have an extended funnel shape, a higher refractive index than their surrounding tissue, and are oriented along the direction of light propagation. Transmission and reflection confocal microscopy of retinal tissue in vitro and in vivo showed that these cells provide a low-scattering passage for light from the retinal surface to the photoreceptor cells. Using a modified dual-beam laser trap we could also demonstrate that individual Muller cells act as optical fibers. Furthermore, their parallel array in the retina is reminiscent of fiberoptic plates used for low-distortion image transfer. Thus, Muller cells seem to mediate the image transfer through the vertebrate retina with minimal distortion and low loss. This finding elucidates a fundamental feature of the inverted retina as an optical system and ascribes a new function to glial cells.

See also:

Living fibre optics light up our eyes (Science Museum, 4 May 2007)

Sherriff, L. Living optical fibres found in the eye, The Register, Tuesday 1st May 2007

Ayoub, G. On the Design of the Vertebrate Retina, Origins & Design 17:1

Denton, M., The Inverted Retina: Maladaption or Pre Adaption? Origins & Design 19:2, Winter, 1999

The origins of language has long been discussed with little sign of any resolution. Now, "a team of researchers has rekindled an old hypothesis: that human language evolved from gesturing, rather than from vocal calls." Captive bonobos and chimpanzees were studied, to document manual gestures, facial signals and vocalisations. "The study distinguished 31 manual gestures and 18 facial/vocal signals. It was found that homologous facial/vocal displays were used very similarly by both ape species, yet the same did not apply to gestures. Both within and between species gesture usage varied enormously." One neuroscientist has commented: The greater variety of hand gestures "supports the idea that language evolved from manual gestures rather than animal calls".
This research has not been met with universal appreciation. Take this comment, for example: "Although all primates use vocal and facial expressions to communicate, only the great apes - chimpanzees, bonobos, orangutan and gorillas - use gestures as well, an ability they share with humans." Many people think that other animals do use gestures! Whilst manual gestures are only possible with animals having hands, gestures are possible with paws, tails, ears, fur and body posture. Maybe the reason why other animals are claimed not to use gestures is that their body language has not been formally studied. If gesturing is widespread as a means of communication, can there be any special significance of apes making gestures with limbs and hands? Human language remains a distinctive human trait.

Ape gestures and language evolution
Amy S. Pollick and Frans B. M. de Waal
Proceedings of the National Academy of Sciences USA, published April 30, 2007, 10.1073/pnas.0702624104

The natural communication of apes may hold clues about language origins, especially because apes frequently gesture with limbs and hands, a mode of communication thought to have been the starting point of human language evolution. The present study aimed to contrast brachiomanual gestures with orofacial movements and vocalizations in the natural communication of our closest primate relatives, bonobos (Pan paniscus) and chimpanzees (Pan troglodytes). We tested whether gesture is the more flexible form of communication by measuring the strength of association between signals and specific behavioral contexts, comparing groups of both the same and different ape species. Subjects were two captive bonobo groups, a total of 13 individuals, and two captive chimpanzee groups, a total of 34 individuals. The study distinguished 31 manual gestures and 18 facial/vocal signals. It was found that homologous facial/vocal displays were used very similarly by both ape species, yet the same did not apply to gestures. Both within and between species gesture usage varied enormously. Moreover, bonobos showed greater flexibility in this regard than chimpanzees and were also the only species in which multimodal communication (i.e., combinations of gestures and facial/vocal signals) added to behavioral impact on the recipient.

See also:

Morell, V. The Handy Way of Speaking, ScienceNOW Daily News, 30 April 2007

Ape gestures 'show human links', BBC News, 1 May 2007.

Two criticisms of ID are commonly heard: (1) it is unfalsifiable; and (2) it is falsified by observations of imperfect adaptations. Taking the second objection first, philosopher Elliott Sober acknowledges that there is a valid response: 'How can anyone know what an intelligent designer wanted to achieve unless the designer tells us?' Those who continue to use this style of criticism would do well to digest Sober's comments.
However, the first criticism is, in Sober's judgment, more substantial. Nevertheless, Popper's criterion of falsifiability should not be invoked if the grounds are that design inferences are probabilistic. If Popper's criterion is used in this way, not only would ID be deemed unfalsifiable, but also much evolutionary theory! Consequently, Sober invokes the necessity of considering "auxiliary propositions" in evaluating ID's scientific claims. These propositions, in other contexts, allow theories to make specific predictions. In the context of ID, "we have no independent evidence concerning which auxiliary propositions about the putative designer's goals and abilities are true". Thus, the robust response to the second criticism (noted above) is actually a demonstration that the first criticism is valid.
Sober's paper certainly needs to be discussed within ID circles. Suffice to say here that his reformulated criticism interacts only with a small subset of possible ID enquiries that purport to explain why an observed design was selected from the range of options. This is not a substantial criticism because ID scholars are concerned with making design inferences, not identifying design goals.
Sober's criticism needs to focus more on the mainstream ID arguments relating to objective evidences of design and the recognition of irreducible complexity. The probabilistic recognition of design is an integral part of archaeological science and forensic science, and any philosophy of science that does not find a place for design inferences must be defective. Furthermore, it is not a convincing argument against irreducible complexity to talk about genetic drift or crossing valleys in the fitness landscape. What we need, on the part of critics of ID, is a more penetrating analysis of actual ID arguments.

WHAT IS WRONG WITH INTELLIGENT DESIGN?
Elliott Sober
The Quarterly Review of Biology, March 2007, vol. 82, pp. 3-8.

ABSTRACT: This article reviews two standard criticisms of creationism/intelligent design (ID): it is unfalsifiable, and it is refuted by the many imperfect adaptations found in nature. Problems with both criticisms are discussed. A conception of testability is described that avoids the defects in Karl Popper's falsifiability criterion. Although ID comes in multiple forms, which call for different criticisms, it emerges that ID fails to constitute a serious alternative to evolutionary theory.

See also:

What is Wrong with Sober's Attack on ID? Evolution News, Posted by Casey Luskin
(Part I): Defining ID and its Historical Origins (March 21, 2007)
(Part II): Comparing ID and Darwinism while Ignoring Darwinism's Epicycles (March 28, 2007)
(Part III): Ignoring the Widely Discussed Positive Predictions of Intelligent Design (March 30, 2007)
(Part IV): Sober's Regressive Arguments (March 31, 2007)

Junk DNA must be the most misleading phrase in the vocabulary of evolutionary biologists. Now that researchers have realised that "non-coding" does not mean "useless", discoveries of functionality are commonplace. The latest contribution concerns mobile genetic elements - transposons. "Large swaths of garbled human DNA once dismissed as junk appear to contain some valuable sections, according to a new study". It has been recognised that many of these elements have an association with genes that are significant for early development. According to one of the researchers, "We used to think they were mostly messing things up. Here is a case where they are actually useful".
Next time you hear someone saying that humans share useless genetic information with chimpanzees, it is worth remembering the comment (in the abstract) that conserved sequences are, by extension, functional sequences. We are likely to share elements because we have similar functional needs, not because the sequences are vestigial. Whilst design inferences do not exclude the concept of degradation, they do help to avoid the pitfall of thinking that non-coding sequences are junk and not worth researching. That has been shown to be an argument from ignorance.

Thousands of human mobile element fragments undergo strong purifying selection near developmental genes
Craig B. Lowe, Gill Bejerano, and David Haussler
Proceedings of the National Academy of Sciences USA, published April 26, 2007, 10.1073/pnas.0611223104

Abstract: At least 5% of the human genome predating the mammalian radiation is thought to have evolved under purifying selection, yet protein-coding and related untranslated exons occupy at most 2% of the genome. Thus, the majority of conserved and, by extension, functional sequence in the human genome seems to be nonexonic. Recent work has highlighted a handful of cases where mobile element insertions have resulted in the introduction of novel conserved nonexonic elements. Here, we present a genome-wide survey of 10,402 constrained nonexonic elements in the human genome that have all been deposited by characterized mobile elements. These repeat instances have been under strong purifying selection since at least the boreoeutherian ancestor (100 Mya). They are most often located in gene deserts and show a strong preference for residing closest to genes involved in development and transcription regulation. In particular, constrained nonexonic elements with clear repetitive origins are located near genes involved in cell adhesion, including all characterized cellular members of the reelin-signaling pathway. Overall, we find that mobile elements have contributed at least 5.5% of all constrained nonexonic elements unique to mammals, suggesting that mobile elements may have played a larger role than previously recognized in shaping and specializing the landscape of gene regulation during mammalian evolution.

See also:

'Junk' DNA Now Looks Like Powerful Regulator, Scientists Find
Science Daily, April 24, 2007

The announcement of an Earth-like planet in the "habitable zone" of the star Gliese 581 has stirred immense interest in the media and blogs around the world. This appears to be the news many have been waiting for. The Daily Mail announced: It "forced bookies to slash odds on the existence of alien beings", and "This remarkable discovery appears to confirm the suspicions of most astronomers that the universe is swarming with Earth-like worlds."
The planet is thought to have a mass 5 times that of the Earth and a diameter 50% larger. The host star is a red dwarf with a small diameter and a surface temperature of about 3300 K. The planet is 14 times closer to the star than Earth is to the sun, and a full orbit is completed every 13 days. Taking into account the reduced radiation from the star and the closeness of the planet, the surface temperature of the planet is estimated in the range 0-40 C. This is sufficient to say that it lies in the "habitable zone" or (more evocatively) the "Goldilocks zone" where temperatures are just right for life.
However, the situation is not as comfortable as it might seem. A planet so close to the sun will become tidally locked with one side constantly in light and he other in darkness. Since it has an elliptical orbit, the case of Mercury might be a useful analogy. The discoverers of the planet say: "A detailed study will also need to consider the possible tidal locking of the planetary rotation to the orbital period". The implication is that liquid water (if water actually exists) is highly unlikely: most will be either in water vapour form or locked up as ice. The only real "Goldilocks zone" is at the terminator, which is sunset for unbridled excitement about the discovery.
Another problem concerns the light falling on the planet. Since the star is quite cool, the radiation peaks in the infrared. The radiation energy is relatively low compared with white light, insufficient to break chemical bonds necessary for plant-based photosynthesis. Whilst bacteria on earth appear to be able to exploit energy from hydrothermal vents , they inhabit a world that is far from our experience. So, even if the new planet's atmosphere was "just right" (which is also doubtful), Earth-like plant life would be impossible.
So, although some have spoken of an "oasis in space" and a "treasure", we ought to consider this new planet as very hostile to life and focus our excitement and energies on the "Goldilocks zone" represented by our own Earth.

The HARPS search for southern extra-solar planets
XI. Super-Earths (5&8M) in a 3-planet system
S. Udry, X. Bonfils, X. Delfosse, T. Forveille, M. Mayor, C. Perrier, F. Bouchy, C. Lovis, F. Pepe, D. Queloz, and J.-L. Bertaux.
Astronomy & Astrophysics, accepted for publication

Abstract. This Letter reports on the detection of two super-Earth planets in the Gl 581 system, already known to harbour a hot Neptune. One of the planets has a mass of 5M_ and resides at the "warm" edge of the habitable zone of the star. It is thus the known exoplanet which most resembles our own Earth. The other planet has a 7.7M_ mass and orbits at 0.25AU from the star, close to the "cold" edge of the habitable zone. These two new light planets around an M3 dwarf further confirm the formerly tentative statistical trend for i) many more very low-mass planets being found around M dwarfs than around solar-type stars and ii) low-mass planets outnumbering Jovian planets around M dwarfs.

See also:

Schilling, G. Exoplanets: Habitable, But Not Much Like Home, Science 316, 27 April 2007: 528.
For the first time, astronomers have found an Earth-like planet that could be habitable. Like an oasis in space, the rocky world, possibly covered with oceans, orbits a puny red dwarf star just over 20 light-years away in the constellation Libra. "On the treasure map of the universe, one would be tempted to mark this planet with an X," says team member Xavier Delfosse of Grenoble University in France. [snip]

Found 20 light years away: the New Earth
Daily Mail, 25th April 2007

The day after James Lake's interesting essay appeared in Nature, acknowledging that the origin of eukaryotes is one of the greatest enigmas in biology, he appeared as a co-signatory to some correspondence, attacking a paper published last year in Science. The paper maintained that hypotheses invoking genome fusion to explain the characteristic features of the eukaryote cell have failed. The authors reviewed recent data from proteomics and genome sequences and suggested that "eukaryotes are a unique primordial lineage".
The critics declared that this paper "delivered only biased opinions" and that the authors "arbitrarily pick and choose among available observations relating to sequence similarity". The end of their critique has this punchline: "Finally, and most disturbing, if contemporary eukaryotic cells are truly of "irreducible nature," as Kurland et al.'s title declares, then no stepwise evolutionary process could have possibly brought about their origin, and processes other than evolution must be invoked. Is there a hidden message in their paper?"
The authors of the paper have responded in a non-inflammatory way. They stand their ground. "Our view is that cellular and molecular biology, especially genomics, reveals signs of an ancient complexity of the eukaryotic cell." They conclude: "our primary conclusion is that there is good progress on understanding the complexity of the ancestral eukaryote cell".
The reason for drawing attention to this critique is that it provides a good example of how 'norms' are sustained within the scientific community. The critics cannot even consider the possibility of "stepwise evolutionary processes" failing to account for eukaryotes, and they have reacted with alarm. Thinking they have detected a hint of intelligent design (by the use the word "irreducible"), they declare this as "most disturbing" and talk about a "hidden message". This reaction moves the critique beyond the realm of scientific discourse into the world of ideological materialism. Those seeking to learn more about ID will do well to recognise the role played by worldviews held by those involved in the debates.

The Evolution of Eukaryotes (Letter )
William Martin, Tal Dagan, Eugene V. Koonin, Jonathan L. Dipippo, J. Peter Gogarten, James A. Lake.
Response by C. G. Kurland, Lesley J. Collins, and David Penny
Science 316, 27 April 2007: 542-543.

What can be said about the origin of the eukaryotic cell? "Until recently, everyone assumed, based on a single ribosomal RNA gene, that eukaryotes descended from archaebacteria - extremophilic prokaryotes distinct from 'true' bacteria, or eubacteria. Now we know that's not the case.' Genome studies reveal links with eubacteria as well as archaebacteria. There are also numerous losses of genes that are puzzling: "But how did evolution come up with the strange distribution of eubacterial and archaebacterial genes we see in eukaryotes today?"
In passing, we must note that an explanation in terms of evolutionary theory is assumed as a 'given'. It is as though no other avenues need be explored.
A remarkable paradox is introduced thus: "Because eukaryotes are derived from archaebacteria and eubacteria, one might expect to find an archaebacterial and a eubacterial copy of each nuclear gene. But strangely, archaebacterial operational and eubacterial informational genes are almost completely absent from eukaryotes, even though the first eukaryote contained two sets of informational and operational genes."
The author, James Lake, uses the analogy of the Roman god Janus. "Like the two faces of the Roman god Janus, thought to represent the Moon and the Sun, the phylogenetic origins of informational and operational genes in eukaryotes are as different as night and day. Finding a gene distribution such as this is the statistical equivalent of finding that a coin tossed at night (Janus's archaebacterial face) always comes up heads (informational genes), and tossed during the day (Janus's eubacterial face) always comes up tails (operational genes)."
Lake then discusses possible explanations of the Janus paradox. He offers a possible explanation as to why the eubacterial informational genes disappeared, but that's as far as he goes. "Unfortunately, I have no good suggestion for why the archaebacterial operational genes were eliminated." He concludes: "How the eukaryotic cell came to be is one of the greatest enigmas in biology. It is a story so complex that no single gene can tell it. Only entire genomes can."
The more we look at eukaryotes, the more obvious it becomes that an evolutionary story of simple to complex is woefully inadequate. But will genome studies help? Last year, the authors of a research paper wrote: "we review recent data from proteomics and genome sequences suggesting that eukaryotes are a unique primordial lineage". Some paradoxes can only be solved by changing the paradigm: maybe the avenue to be explored is signposted "intelligent design".

Disappearing act
James A. Lake
Nature 446, 983, (26 April 2007) | doi:10.1038/446983a
The bizarre absence of certain gene classes in eukaryotes is key to understanding their evolution and complex links with prokaryotes.

See also:
Kurland, C.G., Collins, L.J. and Penny, D. Genomics and the Irreducible Nature of Eukaryote Cells, Science 312, 19 May 2006: 1011-1014.

Wing morphology has a profound effect on aerodynamic performance. Gliding birds such as swifts exploit their ability to morph their wings: "Extended wings are superior for slow glides and turns; swept wings are superior for fast glides and turns. This superiority is due to better aerodynamic performance - with the exception of fast turns. Swept wings are less effective at generating lift while turning at high speeds, but can bear the extreme loads."
New research has led to a more refined aerodynamicmodel, enhancing understanding and stimulating ideas for future developments in aircraft design. "Lentink says that these aircraft designs are crude compared with what the swifts can do, thanks to the engineering challenges involved. "The swifts are just better at it," he says, "The amount of feathers and muscle involved is challenging for us [to imitate].""
One might anticipate that research like this might stimulate thoughts about intelligent design. That is certainly the way engineers have to approach their work. The glide speeds at which the birds minimize energy expenditure have been determined. But one of the co-authors is quoted as saying: "They [swifts] have evolved an aerodynamic design for cheap flight". However, there is nothing in this research that suggests that these capabilities are evolved rather than intelligently designed. This comment linking design to an evolutionary origin is theory-laden and is actually a pointer to a socially-constructed 'reality' adopted by the researcher.

How swifts control their glide performance with morphing wings
D. Lentink, U. K. Muller, E. J. Stamhuis, R. de Kat, W. van Gestel, L. L. M. Veldhuis, P. Henningsson, A. Hedenstrom, J. J. Videler and J. L. van Leeuwen.
Nature 446, 1082-1085 (26 April 2007) | doi:10.1038/nature05733

Gliding birds continually change the shape and size of their wings1, 2, 3, 4, 5, 6, presumably to exploit the profound effect of wing morphology on aerodynamic performance7, 8, 9. That birds should adjust wing sweep to suit glide speed has been predicted qualitatively by analytical glide models2, 10, which extrapolated the wing's performance envelope from aerodynamic theory. Here we describe the aerodynamic and structural performance of actual swift wings, as measured in a wind tunnel, and on this basis build a semi-empirical glide model. By measuring inside and outside swifts' behavioural envelope, we show that choosing the most suitable sweep can halve sink speed or triple turning rate. Extended wings are superior for slow glides and turns; swept wings are superior for fast glides and turns. This superiority is due to better aerodynamic performance - with the exception of fast turns. Swept wings are less effective at generating lift while turning at high speeds, but can bear the extreme loads. Finally, our glide model predicts that cost-effective gliding occurs at speeds of 8-10 m s-1, whereas agility-related figures of merit peak at 15-25 m s-1. In fact, swifts spend the night ('roost') in flight at 8-10 m s-1 (ref. 11), thus our model can explain this choice for a resting behaviour11, 12. Morphing not only adjusts birds' wing performance to the task at hand, but could also control the flight of future aircraft7.

See also:
Ledford, H. Wings in a wind tunnel show secrets of flight. Study of swifts could improve airplane designs.
news@nature.com, 25 April 2007 | doi:10.1038/news070423-7

For as long as many of us can remember, Lucy has been an iconic fossil in the story of human evolution. The discussions about walking erect have been extensive. Many regard the evidence as definitive. However, "Rak and colleagues studied 146 mature primate bone specimens, including those from modern humans, gorillas, chimpanzees and orangutans and found that the "ramus element" of the mandible connecting the lower jaw to the skull is like that of the robust forms". The presence of this morphology in both Australopithecus robustus and Australopithecus afarensis and its absence in modern humans has "cast doubt on the role of [Lucy] as a common ancestor." Like a baton passed from runner to runner, the distinctive bone does the job of "eliminating the possibility that Lucy and her kind are Man's direct ancestors."
So what can be said about Lucy? "The specimen was only 1.1 meters tall, estimated to weigh 29 kilograms and look somewhat like a common chimpanzee." Also, "the structure of Lucy's mandibular ramus closely matches that of gorillas", which was an unexpected find, because this does not fit the previous cladistic analyses of chimps, gorillas and humans.
It looks like this is an appropriate time to reappraise the way museums and textbooks present the story of human evolution.

Gorilla-like anatomy on Australopithecus afarensis mandibles suggests Au. afarensis link to robust australopiths
Yoel Rak, Avishag Ginzburg, and Eli Geffen
Proceedings of the National Academy of Sciences USA, April 17 2007, 104: 6568-6572, doi 10.1073/pnas.0606454104

Abstract: Mandibular ramus morphology on a recently discovered specimen of Australopithecus afarensis closely matches that of gorillas. This finding was unexpected given that chimpanzees are the closest living relatives of humans. Because modern humans, chimpanzees, orangutans, and many other primates share a ramal morphology that differs from that of gorillas, the gorilla anatomy must represent a unique condition, and its appearance in fossil hominins must represent an independently derived morphology. This particular morphology appears also in Australopithecus robustus. The presence of the morphology in both the latter and Au. afarensis and its absence in modern humans cast doubt on the role of Au. afarensis as a modern human ancestor. The ramal anatomy of the earlier Ardipithecus ramidus is virtually that of a chimpanzee, corroborating the proposed phylogenetic scenario.

See also:
Siegel-Itzkovich, J. Israeli researchers: 'Lucy' is not direct ancestor of humans, THE JERUSALEM POST, Apr. 16, 2007

Whilst some scholars recognise boundaries for scientific research, others strongly resist the thought that science has limits. One of the sensitive areas involves human consciousness and free agency. The authors of an essay on law and human behaviour write that "many contemporary neuroscientists assume that the essential ingredients of the human condition, including free will, empathy, and morality, are the calculable consequences of an immense assembly of neurons firing." This view "assumes that violence and antisocial behaviour emanate from a mechanistically determined brain". This effectively means that our sense of free agency is an illusion.
Whilst this stance man have legal implications (because of laws about diminished responsibility and even freedom from liability if declared legally insane), suffice to note here that our approach to the science of human behaviour has important ramifications.
What difference does this approach make to our thinking about humanity and society? "Clearly free will is a prerequisite for moral agency, and for society to run smoothly, we all need to believe that we are in full control of our actions." This sounds very much like living an illusion! To paraphrase: we cannot do without a sense of personal responsibility in order to have a society that works, but the neuroscientists know better (i.e. our behaviour is governed by neurons firing in our brains).
When we ask: 'how do we know?', we find out that the evidence is equivocal. No one has proved that the firings of neurons lead to "free-will, empathy and morality". The authors of the essay are right to use the word "assume". It is a major assumption that everything has a natural expanation: chance and necessity explains all (after Monod).
If these authors (and mechanistic neuroscientists) are right, then it is not only society that has to live an illusion. We ourselves have to live a delusion. We think we choose (but really it is only the firing of our neurons); we think we love (but this is just another form of brain signalling); and we think we know right from wrong (and this too is the product of neuron activity). Furthermore, our claims to be truth seekers are empty, because our response to truth is also an illusionary experience.
The authors write: "New studies of the criminal brain are likely to shape moral views on responsibility and free will, with possible impacts on how legal systems punish and treat criminals". If we are concerned about these issues, we need to look very carefully at the assumptions we bring to the science underpinning these studies.

Law, Responsibility, and the Brain
Dean Mobbs, Hakwan C. Lau, Owen D. Jones, Christopher D. Frith
PLoS Biol 5(4): e103 doi:10.1371/journal.pbio.0050103

Archaeological discoveries of traumatic injuries in primitive hominid skulls strongly hint that our species has a long history of violence. Despite repeated attempts throughout history, including efforts to eliminate violence through the imposition of criminal sanctions, we have yet to dispel our violent nature. Consequently, criminal violence remains a common feature of most societies. As policy-makers seek deeper understandings of criminally violent and anti-social behaviour, many contemporary neuroscientists assume that the essential ingredients of the human condition, including free will, empathy, and morality, are the calculable consequences of an immense assembly of neurons firing. Intuitively, this view opposes Cartesian dualism (i.e., the brain and mind are separate, but interacting, entities) and assumes that violence and antisocial behaviour emanate from a mechanistically determined brain.

"The rise of the central nervous system [CNS] in animal evolution has puzzled scientists for centuries." According to evolutionary theory, "Vertebrates, insects and worms evolved from the same ancestor, but their CNSs are different and were thought to have evolved only after their lineages had split during evolution." To gain an insight into what CNS of the last common ancestor of these groups might have been like, researchers selected for study the nervous system of a marine annelid worm called Platynereis dumerilii. "Platynereis can be considered a living fossil," says Arendt (who led the team), "it still lives in the same environment as the last common ancestors used to and has preserved many ancestral features, including a prototype invertebrate CNS."
"Our findings were overwhelming," says Alexandru Denes (who carried out the research in Arendt's lab). "The molecular anatomy of the developing CNS turned out to be virtually the same in vertebrates and Platynereis." The research paper expresses it thus: "Our comparative study of mediolateral neural patterning and neuron-type distribution in the developing trunk CNS of the annelid Platynereis revealed an unexpected degree of similarity to the mediolateral architecture of the developing vertebrate neural tube."
The implication is that something very like the vertebrate CNS existed in the putative common ancestor: "Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS, as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria."
So, the implication is that a highly complex nervous system existed in Precambrian organisms. "Such a complex arrangement could not have been invented twice throughout evolution, it must be the same system," adds Gaspar Jekely. "It looks like Platynereis and vertebrates have inherited the organisation of their CNS from their remote common ancestors."
This is interesting logic, because it links complexity with improbability. The greater the complexity, the less likely it is for processes governed by law or chance to produce it. Science built on naturalism has no other options available: complexity has to be the result of improbable interactions in nature. Design inferences are not permitted alongside inferences of law or chance. It is not acceptable to think that if it is too complex to have been 'invented' twice by evolution, it is also reasonable to conclude that it could not have been 'invented by evolution' even once.
Based on the research, the authors acknowledge that their findings "would imply that it was initially present also in the evolutionary lines leading to Drosophila, the nematode Caenorhabditis, and the enteropneust Saccoglossus. Yet it is clear from the available data that these animals are missing or have modified at least part of this pattern." Loss of complexity is a part of their story, which is a surprising result.
One cannot help notice that studies of this type keep pushing back the origin of complexity into the Precambrian, dominated until the Ediacaran by single-celled animals. Arguing that all this complexity is the product of mutation and natural selection becomes less and less convincing as we learn more about the data needing an explanation.

Molecular Architecture of Annelid Nerve Cord Supports Common Origin of Nervous System Centralization in Bilateria
Alexandru S. Denes, Gaspar Jekely, Patrick R.H. Steinmetz, Florian Raible, Heidi Snyman, Benjamin Prud'homme, David E.K. Ferrier, Guillaume Balavoine, and Detlev Arendt
Cell, Vol 129, 277-288, 20 April 2007

Summary: To elucidate the evolutionary origin of nervous system centralization, we investigated the molecular architecture of the trunk nervous system in the annelid Platynereis dumerilii. Annelids belong to Bilateria, an evolutionary lineage of bilateral animals that also includes vertebrates and insects. Comparing nervous system development in annelids to that of other bilaterians could provide valuable information about the common ancestor of all Bilateria. We find that the Platynereis neuroectoderm is subdivided into longitudinal progenitor domains by partially overlapping expression regions of nk and pax genes. These domains match corresponding domains in the vertebrate neural tube and give rise to conserved neural cell types. As in vertebrates, neural patterning genes are sensitive to Bmp signaling. Our data indicate that this mediolateral architecture was present in the last common bilaterian ancestor and thus support a common origin of nervous system centralization in Bilateria.

See also:
The origin of the brain lies in a worm
Researchers discover that the centralised nervous system of vertebrates is much older than expected
EMBL Press Release 20 April 2007

The iconic status of the bacterial flagellum as an irreducibly complex structure has stimulated interest among evolutionary biologists and an extensive literature. The latest is by Liu and Ochman who claim not only that the bacterial flagellum has originated in a stepwise manner from simple precursors, but also that "a single gene that underwent successive duplications and subsequent diversification during the early evolution of Bacteria."
ScienceNow has a report on this paper, with quotes drawn from the science community: "Complexity builds out of simplicity, and this is a well-documented argument for how that can happen," and "By testing the hypothesis of common ancestry of the flagellum in so many different species, the researchers clearly show these genes were derived from one another through gene duplication."
The major claim of the authors is to have traced the history of a set of core flagellum genes. "Our results show that flagellum originated very early, before the diversification of contemporary bacterial phyla, and evolved in a stepwise fashion through a series of gene duplication, loss and transfer events." They have adopted a methodology based on gene sequencing: "Comparisons of the complete genome sequences of flagellated bacteria revealed that the flagellum is based on an ancestral set of 24 core genes for which homologs are present in genomes of all bacterial phyla. The most striking finding from our analysis is that these core genes originated from one another through a series of duplications, an inference based on the fact that they still retain significant sequence homology."
So, have ID scientists got it wrong? The first point to be made is that the problem of actually forming the flagellum has not been addressed in the paper at all! There is no engagement with the challenge of irreducible complexity. Instead, this paper simply compares sequences of proteins, looking for similarities and differences in amino acid order. The analysis is concerned with sequence data, and the interpretation is dependent on the conceptual framework adopted by the researchers. In this case, the conceptual framework is Darwinism. The researchers have assumed that sequence similarity is related to ancestry, even though they cannot show that Darwinian processes produced the flagellum using their data set. This is a basic methodological point, and ID scholars have been making it for at least a decade. Consequently: 'Darwinism in - Darwinism out' sums up the findings.
There are many other detailed criticisms that can be made. Happily, a good start has been made here by Nick Matzke, who refers to "canine qualities" of the paper. By this he means that "there is nothing for it but to suck it up and declare this paper a dog." Of the claim that all flagellar proteins come from one gene, Matzke writes: "Frankly it is a flabbergasting thing to say, and I can't understand how it got published." Also: "There is just no way that the flagellum evolved by diversification of a single gene." However, Matzke misses the main methodological flaw in the research, which concerns their interpretation of sequence homologies in terms of descent with stepwise modification.
Jennifer Cutraro wrote that the study "not only answers an important question about the evolution of complex structures but also provides additional ammunition to counter arguments from evolution's foes." ID scientists are opposed to the 'just-so' stories and unwarranted extrapolations which are often found associated with evolutionary biology. By overstepping the mark so badly, perhaps this new paper will help people to understand the importance of paradigms in science and why critical issues are continually being overlooked.

Stepwise formation of the bacterial flagellar system
Renyi Liu and Howard Ochman
Proc. Natl. Acad. Sci. USA, 10.1073/pnas.0700266104, Published online before print April 16, 2007 [OPEN ACCESS ARTICLE]

Abstract: Elucidating the origins of complex biological structures has been one of the major challenges of evolutionary studies. The bacterial flagellum is a primary example of a complex apparatus whose origins and evolutionary history have proven difficult to reconstruct. The gene clusters encoding the components of the flagellum can include >50 genes, but these clusters vary greatly in their numbers and contents among bacterial phyla. To investigate how this diversity arose, we identified all homologs of all flagellar proteins encoded in the complete genome sequences of 41 flagellated species from 11 bacterial phyla. Based on the phylogenetic occurrence and histories of each of these proteins, we could distinguish an ancient core set of 24 structural genes that were present in the common ancestor to all Bacteria. Within a genome, many of these core genes show sequence similarity only to other flagellar core genes, indicating that they were derived from one another, and the relationships among these genes suggest the probable order in which the structural components of the bacterial flagellum arose. These results show that core components of the bacterial flagellum originated through the successive duplication and modification of a few, or perhaps even a single, precursor gene.

See also:

Cutraro, J., A Complex Tail, Simply Told, ScienceNOW Daily News, 17 April 2007

Matzke, N., Flagellum evolution paper exhibits canine qualities, Panda's Thumb, April 16, 2007

Behe, M. DARWINISM GONE WILD: Neither sequence similarity nor common descent address a claim of Intelligent Design, Evolution News & Views, 19 April 2007.

Reconstructions of ancient hominids are typically presented with no explanation of the principles on which the various bones are reassembled. Dr. Timothy Bromage is a paleoanthropologist who works on the biological principle "that the eyes, ears, and mouth must be in precise relationship to one another in all mammals." He claims to have found a rule that applies to all primates: "The angle created by drawing a line from the eye socket to the ear and then to the top back molar is always 45 degrees". Applying this to Homo rudolfensis (1470 Man) has challenged the previously accepted work. "Shifting the skull bones to conform to the rule pushes out the lower face and leads to a much smaller brain: about 575 cubic centimetres" instead of 750-775 cc. "Dr. Leakey produced a biased reconstruction based on erroneous preconceived expectations of early human appearance that violated principles of craniofacial development," said Dr. Bromage. His new reconstruction "shows a sharply protruding jaw and a brain less than half the size of a modern human". The first human-like skulls come with Homo ergaster and Homo erectus. This is exactly where many put the ape/homo line, and this new work reinforces the view that the gradualist model of human evolution is artificial and an imposition on the data.

New face for Kenya hominid?
Constance Holden
Science 316, 6 April 2007, 27.

See also:
Man's earliest direct ancestors looked more apelike than previously believed
EurekAlert, 24 March 2007.

"Photosynthetic complexes are exquisitely tuned to capture solar light efficiently, and then transmit the excitation energy to reaction centres, where long term energy storage is initiated." The problem has been one of understanding how 95%+ efficiencies are possible in a natural system.
The photosynthetic apparatus is constructed so that adjacent chlorophyll molecules have different energy levels. "When light shines on one of these molecules, an electron is momentarily excited before passing its energy over to a nearby molecule with a slightly lower energy level. In this way energy can flow "downhill" from energy level to energy level until it reaches the crucial "reaction centre" where the actual photosynthesis occurs. Scientists had assumed that the energy moves downhill in a "random walk", which is essentially an incoherent "hopping" between energy levels." But this mechanism does not yield the "extreme efficiency" of photosynthesis.
Researchers in the US have "discovered regular variations of signal that sustained for hundreds of femtoseconds, which the physicists interpreted as "quantum beats" coherently linking all the energy levels together." This "quantum trickery" has an analogy in "Grover's algorithm" (proposed in 1997) which determines "the fastest possible search of an unsorted database in quantum computation." With this mechanism, "vast areas of phase space can be sampled effectively to find the most efficient path for energy transfer."
Those involved in a quest for simplicity in the machinery of molecular biology are not having a very happy time. The story being uncovered is one of complexity in the details, as Michael Behe demonstrated in Darwin's Black Box. Knowing that quantum paths have been used in photosynthesis, the "primary energy source for almost all life on Earth", provides yet more grounds for making design inferences.

Evidence for wavelike energy transfer through quantum coherence in photosynthetic systems
Gregory S. Engel, Tessa R. Calhoun, Elizabeth L. Read, Tae-Kyu Ahn, Tomas Mancal, Yuan-Chung Cheng, Robert E. Blankenship and Graham R. Fleming.
Nature 446, 782-786 (12 April 2007) | doi:10.1038/nature05678

Abstract: Photosynthetic complexes are exquisitely tuned to capture solar light efficiently, and then transmit the excitation energy to reaction centres, where long term energy storage is initiated. The energy transfer mechanism is often described by semiclassical models that invoke 'hopping' of excited-state populations along discrete energy levels1, 2. Two-dimensional Fourier transform electronic spectroscopy3, 4, 5 has mapped6 these energy levels and their coupling in the Fenna-Matthews-Olson (FMO) bacteriochlorophyll complex, which is found in green sulphur bacteria and acts as an energy 'wire' connecting a large peripheral light-harvesting antenna, the chlorosome, to the reaction centre7, 8, 9. The spectroscopic data clearly document the dependence of the dominant energy transport pathways on the spatial properties of the excited-state wavefunctions of the whole bacteriochlorophyll complex6, 10. But the intricate dynamics of quantum coherence, which has no classical analogue, was largely neglected in the analyses-even though electronic energy transfer involving oscillatory populations of donors and acceptors was first discussed more than 70 years ago11, and electronic quantum beats arising from quantum coherence in photosynthetic complexes have been predicted12, 13 and indirectly observed14. Here we extend previous two-dimensional electronic spectroscopy investigations of the FMO bacteriochlorophyll complex, and obtain direct evidence for remarkably long-lived electronic quantum coherence playing an important part in energy transfer processes within this system. The quantum coherence manifests itself in characteristic, directly observable quantum beating signals among the excitons within the Chlorobium tepidum FMO complex at 77 K. This wavelike characteristic of the energy transfer within the photosynthetic complex can explain its extreme efficiency, in that it allows the complexes to sample vast areas of phase space to find the most efficient path.

See also:

Making photosynthesis tick (Editor's summary, Nature 446,(12 April 2007).

Sension, R.J. Quantum path to photosynthesis, Nature 446, 782-786 (12 April 2007) | doi:10.1038/446740a
Knowing how plants and bacteria harvest light for photosynthesis so efficiently could provide a clean solution to mankind's energy requirements. The secret, it seems, may be the coherent application of quantum principles.

Cartwright, J. Photosynthesis takes a leaf out of the quantum book, PhysicsWeb, April 13 2007.
Quantum computers and blades of grass have more in common than you might think. Physicists in the US have shown that electrons involved in photosynthesis reactions "sample" different energy-level routes in much the same way quantum-computer algorithms can - at least in theory - quickly search through unsorted databases. The researchers claim that the discovery could explain how photosynthesis can proceed at efficiencies unparalleled in manmade solar cells.

Two outspoken defenders of Darwinism and critics of ID have contributed a Policy Forum piece to Science on how scientists should contribute to "highly contested issues". They identify three cases for consideration: human-induced global warming, evolution and ID, and embryonic stem cells. In each case, they suggest that the thinking of scientists has converged towards an unambiguous position. But, they write: "Research shows that people are rarely well enough informed or motivated to weigh competing ideas and arguments." We live in societies where political and religious ideologies act as screens to distort the messages they hear. So we need to develop skills of communicating: "scientists must learn to actively "frame" information to make it relevant to different audiences". "Frames organize central ideas, defining a controversy to resonate with core values and assumptions".
These two communicators realise that they are advancing ideas that could be seen as manipulation of the media to keep the masses submissive. They conclude: "Some readers may consider our proposals too Orwellian, preferring to safely stick to the facts. Yet scientists must realize that facts will be repeatedly misapplied and twisted in direct proportion to their relevance to the political debate and decision-making. In short, as unnatural as it might feel, in many cases, scientists should strategically avoid emphasizing the technical details of science when trying to defend it."
The fundamental problem evident here is that the authors have failed to grasp that all three of their illustrative cases relate to contested issues within science, as well as having major ramifications for society. There is a significant debate as to whether global warming is human-induced; there is a community of scientists who dissent from Darwinism, many of whom are ID advocates; and there are good scientific reasons for focussing research on adult stem cells rather than embryonic stem cells. The authors are seeing these controversies through their personal ideological "frame".
They qualify their advice on strategy using these words: "without misrepresenting scientific information". However, their analysis of the controversial issues reveals that they have already misrepresented scientific information - by failing to acknowledge the reality of scientific debate and by linking dissent only to political and religious agendas. This is a sure sign of Orwellian control police and a sad day for science.

Framing Science
Matthew C. Nisbet and Chris Mooney
Science 315, 6 April 2007: 56

Issues at the intersection of science and politics, such as climate change, evolution, and embryonic stem cell research, receive considerable public attention, which is likely to grow, especially in the United States as the 2008 presidential election heats up.

Although hagfish have no jaws and no vertebrae, they do have other characters that identify them as fish. These traits make them an interesting candidate for being in some way transitional between chordates and vertebrates. Research has not been helped by the extreme difficulty of breeding these animals in captivity. A recent study has, however, succeeded in analyzing hagfish embryos and late-stage specimens have revealed the presence of a neural crest, a distinctive characteristic of vertebrates. The neural crest is a remarkable tissue that differentiates into a great variety of specialist cells, and is consequently very important for developmental biologists.
From an evolutionary perspective, this implies that the common ancestor of vertebrates would have possessed a neural crest. The authors suggest that "the neural crest probably existed as a population of delaminating and migrating cells in the common ancestor of the entire vertebrate clade, and thus its origin should be sought in non-vertebrate chordates."
Where do these animals fit into our understanding of living things? Are they (as many like to think) primitive vertebrates? This question has not been answered by palaeontology, because the earliest hagfishes are very similar to living forms. Two possibilities have been suggested: they could be primitive vertebrates (lacking vertebrae and jaws), or they could be degenerate organisms after losing several vertebrate characters (an option which also gets support from DNA and RNA sequencing). These possibilities are discussed by Janvier in a useful "News & Views" essay. In his judgment, "with this discovery, hagfishes become more 'conventional' vertebrates". The issues now are clearer than they were. But the big question remains unresolved. "Further analyses of the developmental genetics of hagfish embryos might enable us to discover whether hagfish anatomy is primitive or degenerate, and may help in reconstructing the theoretical common ancestor to all vertebrates."
At present, it is necessary to acknowledge that this theoretical "common ancestor to all vertebrates" is highly elusive. The search itself is theory-driven: based on the conviction that there must be a common ancestor. The authors say that their work "opens up new approaches to clarifying the evolutionary history of vertebrates", and this is true. However, should we adopt the restrictive approach that insists on a common ancestor in a Darwinian sense? Is there not scope here for an information-perspective on the basic types of life?

Hagfish embryology with reference to the evolution of the neural crest
Kinya G. Ota, Shigehiro Kuraku & Shigeru Kuratani
Nature 446, 672-675 (5 April 2007) | doi:10.1038/nature05633

Hagfish, which lack both jaws and vertebrae, have long been the subject of intense interest owing to their position at a crucial point in the evolutionary transition to a truly vertebrate body plan1, 2, 3, 4. However, unlike the comparatively well characterized vertebrate agnathan lamprey, little is known about hagfish development. The inability to analyse hagfish at early embryonic stages has frustrated attempts to resolve questions with important phylogenetic implications, including fundamental ones relating to the emergence of the neural crest1, 5, 6. Here we report the obtainment of multiple pharyngula-stage embryos of the hagfish species Eptatretus burgeri and our preliminary analyses of their early development. We present histological evidence of putative neural crest cells, which appear as delaminated cells that migrate along pathways corresponding to neural crest cells in fish and amphibians2, 7, 8, 9, 10, 11. Molecular cloning studies further revealed the expression of several regulatory genes, including cognates of Pax6, Pax3/7, SoxEa and Sox9, suggesting that the hagfish neural crest is specified by molecular mechanisms that are general to vertebrates. We propose that the neural crest emerged as a population of de-epithelialized migratory cells in a common vertebrate ancestor, and suggest that the possibility of classical and molecular embryology in hagfish opens up new approaches to clarifying the evolutionary history of vertebrates.

See also:
Janvier, P. Born-again hagfishes, Nature 446, 622-623 (5 April 2007) | doi:10.1038/nature05712
Abstract: The strange, slimy creatures called hagfishes are of abiding interest to students of vertebrate evolution: just where do they fit in? Investigations of hagfish development take the story forward.

Comb jellies are some of the most evocative marine animals, with transparent tissues enclosing blue combs in constant motion. Their fossil record goes back to the Cambrian, where they appear with essentially modern forms. A new research paper documents "an exquisitely preserved late-stage embryo of a ctenophore ("comb jelly")" in sediments that are right at the base of the Cambrian. "This specimen represents the earliest firm evidence of the Ctenophora now known".
"The ctenophoran affinities of this embryo are firmly supported by the presence of eight sets of comb rows and comb plates, and of meridional and aboral canals, all having the same relative positions as those in modern ctenophores. The presence of an adult body plan and of adult-like structures, even in its prehatching embryonic condition, suggests that this ancient ctenophore embryo would have likely directly matured into a planktonic juvenile like that of most modern ctenophores.[. . .] Its lack of tentacles and the presence of branched meridional canals, however, are characters shared by the embryos of extant beroidian ctenophores, with which this fossil therefore seems more closely allied."
The authors consider the common ancestor of these organisms. Their discovery rules out several previously proposed candidates. Links with Precambrian faunas are also rejected: "the suggestion by Shu et al. that the Ctenophora occupies an intermediate evolutionary position between sponges and cnidarians is inconsistent with numerous lines of evidence, both anatomical and molecular."
So we are left with the thought that the earliest ctenophore was rather like "extant beroidian ctenophores" and some of us might question whether there ever was a branch linking ctenophores to the elusive Darwinian Tree of Life.

Raman spectra of a Lower Cambrian ctenophore embryo from southwestern Shaanxi, China
Jun-Yuan Chen, J. William Schopf, David J. Bottjer, Chen-Yu Zhang, Anatoliy B. Kudryavtsev, Abhishek B. Tripathi, Xiu-Qiang Wang, Yong-Hua Yang, Xiang Gao, and Ying Yang.
Proc. Natl. Acad. Sci. USA, (10 April, 2007), 104(15), 6289-6292. DOI: 10.1073/pnas.0701246104 (OPEN ACCESS ARTICLE)

The Early Cambrian (~540 million years old) Meishucun fossil assemblage of Ningqiang County (Shaanxi Province), China, contains the oldest complex skeletonized organisms known in the geological record. We here report the finding in this assemblage of an exquisitely preserved late-stage embryo of a ctenophore ("comb jelly"), its fine structure documented by confocal laser scanning microscopy and shown by Raman spectroscopy to be composed of carbonaceous kerogen permineralized in apatite. In its spheroidal morphology, the presence of eight comb rows and the absence of tentacles, this embryo resembles an adult ctenophore (Maotianoascus octonarius) known from the immediately younger Chengjiang fauna of Yunnan, China. The oldest ctenophore and the only embryonic comb jelly known from the fossil record, this exceptionally well preserved specimen provides important clues about the early evolution of the phylum Ctenophora and of metazoans in general.

Despite the tremendous range of size and shape, terrestrial animals engaged in straight-line running can be modelled successfully. "Using simple mathematical models such as the SLIP model to describe movement allows for design and function to be understood in terms of overall mechanical task constraints." Add to this manoeuvring, and the story gets much more complicated. Stops, starts and changes in direction are much more of a challenge.
Past work in this area has involved cockroaches and humans. Newly reported research concerns ostriches. At first glance, these large birds might seem unlikely runners, but they are actually capable of taking on racehorses and certainly outmanoeuvring predators. Compared with humans, the centre of mass is higher, they have long spindly legs and long necks, and their heads are small. Not only can they run much faster than humans, they look remarkably graceful, even when changing direction. They do run turn differently: "When humans execute 30 degreees sidestep and crossover cuts, braking forces are 26% of Fpmax compared to 6-11% for ostriches executing 15-20 degree turns. Moreover, whereas humans generated almost exclusively braking forces during sidesteps and crossovers, 40% of the net forces observed during turns for ostriches were acceleratory." How do they achieve this remarkable performance?
"Most of the differences between ostriches and humans were explained by differences in body morphology. Ostrich morphology is appropriate for effective maneuvers that require minimal acceleratory or braking forces." "These results suggest that, with an appropriately designed morphological system, maneuvers can be executed with minimal changes to running dynamics." "In summary, ostrich morphology is appropriate for maneuvering without requiring large braking or acceleratory forces."
What stands out in these studies is the effectiveness of design thinking. Some will attribute this design to the powers of natural selection acting on genetic variations, with little or no direct evidence to support this hypothesis. However, there is another alternative, which is to be open to the possibility of this design being real, involving intelligent (rather than natural) agency. Ostriches have traditionally been considered the epitome of foolish behaviour, supposedly burying their heads in the sand. However, their running skills are outstanding and demonstrate superb design. One wonders whether heads are being buried in the sand when design inferences are excluded on ideological grounds from science.

Mechanics of cutting maneuvers by ostriches (Struthio camelus)
Devin L. Jindrich, Nicola C. Smith, Karin Jespers, and Alan M. Wilson
Journal of Experimental Biology, 2007 210: 1378-1390.

Abstract: We studied the strategies used by cursorial bipeds (ostriches) to maneuver during running. Eight ostriches were induced to run along a trackway and execute turns. Ground reaction forces and three-dimensional kinematics of the body and leg joints were simultaneously recorded, allowing calculation of joint angles and quasi-static net joint torques. Sidesteps, where the leg on the outside of the turn changes the movement direction, and crossovers using the inside leg, occurred with nearly equal frequency. Ostriches executed maneuvers using a simple control strategy that required minimal changes to leg kinematics or net torque production at individual joints. Although ostriches did use acceleration or braking forces to control body rotation, their morphology allowed for both crossovers and sidesteps to be accomplished with minimal net acceleratory/braking force production. Moreover, body roll and ab/adduction of the leg shifted the foot position away from the turn direction, reducing the acceleratory/braking forces required to prevent under- or over-rotation and aligning the leg with the ground reaction force.

See also:
Clare, S. BUILT TO RUN, Journal of Experimental Biology, 210, 0i (March 31, 2007)

Here is a paper that significantly shifts the focus of the debate about Neanderthal Man. What happened to the Neanderthals during the last glaciation? Did anatomically modern humans (AMH) slaughter them? Did they talk with them? Did they interbreed with them? To what extend did they exchange technologies and ideas? Finlayson and Carrion describe much of this debate as the expression of a "simplistic Neanderthal-AMH dichotomy".
After reviewing much data, they point out an interesting pattern: "An examination of the distribution of Aurignacian and transitional industries across Europe during the crucial time frame between 45 and 30 kya reveals a striking correspondence between location and the presence of sharp physiographical boundaries. This suggests that these industries, some made by Neanderthals (Chatelperronian) and others perhaps by AMHs (Aurignacian?), were independent regional responses to rapidly fluctuating ecological conditions. Their absence from more stable regions, such as south-western Iberia, supports this view. The changing circumstances and stresses experienced by human populations across the Palaearctic, most notably between the MLB and the plains, created a template for innovation."
Thus, instead of the emphasis being on culture associated with evolutionary change, the real issue is analysing the responses people made to their environment. "Technological innovations of the so-called Upper Palaeolithic can be understood as responses to living in vast open spaces rather than to the consequence of a cognitive revolution associated with an evolutionary change."
Of course, this presupposes that the Neanderthals were not much different from the other human groups around at the time. The authors claim that "Neanderthals were capable of behaviour that is regarded as modern". This may come as a surprise to those who have been brought up to think of Neanderthals as hairy brutes that could make little more than grunting noises to each other. Have we been misled by an evolutionary mindset? Is the key to understanding Neanderthals "ecology" rather than "brain wiring"?

Rapid ecological turnover and its impact on Neanderthal and other human populations
Clive Finlayson and Jose S. Carrion
Trends in Ecology & Evolution, Volume 22, Issue 4 , April 2007, Pages 213-222

Abstract: The latter part of the last glaciation, 50,000 - 12,000 years ago (kya), was characterized by a rapidly changing climate, cold conditions and corresponding vegetation and faunal turnover. It also coincided with the extinction of the Neanderthals and the expansion of modern human populations. Established views of modern human superiority over Neanderthals as the cause of their extinction are under attack as recent work shows that Neanderthals were capable of behaviour that is regarded as modern. As we discuss here, the exact nature of biological and cultural interactions between Neanderthals and other human groups between 50 kya and 30 kya is currently hotly contested. The extinction of the Neanderthals, and other modern human lineages, now appears to have been a drawn-out, climate-related affair.

Most of us know that aspirin derives from a naturally occurring chemical, salicylic acid, found in the bark of willow trees. Many of us know that the inhabitants of tropical rainforests are aware of the medicinal properties of a great number of leaves, roots, bark and other natural materials. What few of us realise is just how many of the drugs on pharmacy shelves derive from the natural world. In a review covering the past 60 years, two chemists have concluded that 70% of new drugs (never previously available as commercial products) are either derived from plants and animals or synthesised to mimic the natural product. This statistic is entirely in line with two previous reviews these authors had undertaken.
They write: "the continuing and overwhelming contribution of natural products to the expansion of the chemotherapeutic armamentarium is clearly evident, and as we stated in our earlier papers, much of Nature's "treasure trove of small molecules" remains to be explored, particularly from the marine and microbial environments." They make a particular point about microbially-produced substances: "We wish to draw the attention of readers to the rapidly evolving recognition that a significant number of natural product drugs/leads are actually produced by microbes and/or microbial interactions with the "host from whence it was isolated", and therefore we consider that this area of natural product research should be expanded significantly."
In a recent entry to this literature blog, a link was made between "systems biology" and design theory. Both lead to the same scientific methodologies. Both emphasise the multidisciplinary character of research, and the importance of holistic (rather than reductionistic) thinking. The review authors have the same approach: "To us, a multidisciplinary approach to drug discovery, involving the generation of truly novel molecular diversity from natural product sources, combined with total and combinatorial synthetic methodologies, and including the manipulation of biosynthetic pathways (so-called combinatorial biosynthesis), provides the best solution to the current productivity crisis facing the scientific community engaged in drug discovery and development."
If the natural world is designed, and if mankind has a legitimate place within this designed world, the finding that natural medicinal products actually work is not surprising. Indeed, positive thoughts about design naturally follow.

Natural Products as Sources of New Drugs over the Last 25 Years
David J. Newman and Gordon M. Cragg
Journal of Natural Products, 70(3), 461-477, 2007. 10.1021/np068054v S0163-3864(06)08054-2

Abstract: This review is an updated and expanded version of two prior reviews that were published in this journal in 1997 and 2003. In the case of all approved agents the time frame has been extended to include the 251/2 years from 01/1981 to 06/2006 for all diseases worldwide and from 1950 (earliest so far identified) to 06/2006 for all approved antitumor drugs worldwide. We have continued to utilize our secondary subdivision of a "natural product mimic" or "NM" to join the original primary divisions. From the data presented, the utility of natural products as sources of novel structures, but not necessarily the final drug entity, is still alive and well. Thus, in the area of cancer, over the time frame from around the 1940s to date, of the 155 small molecules, 73% are other than "S" (synthetic), with 47% actually being either natural products or directly derived therefrom. In other areas, the influence of natural product structures is quite marked, with, as expected from prior information, the antiinfective area being dependent on natural products and their structures. Although combinatorial chemistry techniques have succeeded as methods of optimizing structures and have, in fact, been used in the optimization of many recently approved agents, we are able to identify only one de novo combinatorial compound approved as a drug in this 25 plus year time frame. We wish to draw the attention of readers to the rapidly evolving recognition that a significant number of natural product drugs/leads are actually produced by microbes and/or microbial interactions with the "host from whence it was isolated", and therefore we consider that this area of natural product research should be expanded significantly.

See also:
Mother Nature's Medicine Cabinet
Science Daily, March 20, 2007.

Phylogenomics makes use of "large quantities of genetic data (not just entire genomes) to build evolutionary trees, or phylogenies." The new discipline makes great claims, for it aims to "reshape systematics" using the extensive data sets emerging from genome mapping projects. One researcher explains its scope: "Genomes are giving a much better view of the tree of life on Earth" and "The revolution is just starting - every new genome is causing rethinking."
It may surprise some, but Linnaeus did not pioneer systematics with the tree of life in mind. It is not necessary to presuppose a common ancestor for all living things to be a scholar working in this field.
More importantly, waving "the banner of phylogenetics" must not be confused with delivering results. Because some say the revolution is just starting, this does not mean that they are right. "What has also become clear is that many problems cannot simply be battered into submission with more data."
To illustrate one problem: "Perhaps the most high-profile gaffe was the declaration by the Human Genome Project in 2001 that 100-200 genes in humans had come directly from bacteria." Lateral gene transfer (LGT) was invoked to explain the data. It was challenged by several "flabbergasted evolutionary biologists, [who] rapidly shot the claim down, showing that the genes in question were more likely to have been present in the common ancestor of humans and bacteria but then lost in other lineages."
What is surprising is that there has not been a similar response to the new explanation: for it implies that the relevant genes were present in the evolutionary descendants and were systematically lost in every branch and twig of the tree of life except for that leading to humans. This explanation is as contrived as LGT!
According to one expert quoted: "you can't do good genome analysis without evolutionary analysis." Linnaeus would not have agreed with this. He would have warned of the dangers of force-fitting the data into a predetermined mould. If you presuppose the tree of life, how could researchers ever conclude that they were studying a forest, not a tree?

Linnaeus at 300: We are family
John Whitfield
Nature 446, 247-249, (15 March 2007) | doi:10.1038/446247a
Updating the tree of life needs both the skills of evolutionary biologists and the data from genome-crunchers - the two ignore each other at their peril.

Medicinal research is the best funded area in biology, with large inputs of money from pharmaceutical companies as well as from research funding bodies. For longer than anyone can remember, "a reductionist focus has been the Holy Grail" in biological research. This has achieved results: "In medicine, tremendous scientific advancements have been made in understanding diseases from a reductionistic viewpoint." However, it appears that a turning point has arrived. "The success formula built on reductionism seems to have reached its limits and the pharmaceutical industry faces enormous challenges with productivity decreasing and development costs rapidly increasing."
Where next? Do we need a bolt-on to reductionism (so that reductionism is part of the solution), or do we conclude that reductionism is part of the problem and that a different methodology is needed?
The authors of the paper abstracted below have come to the view that Systems Biology is that "new strategic tool in Life Sciences". Systems thinking is a move to holism rather than reductionism. It is thus a complete change of direction, not an add-on.
"Understanding biology requires knowledge of connectivity in systems and their self-organization. [. . .] the need to map patterns of relationship is surfacing, as demonstrated in mammalian systems based on de novo measurements across transcriptomics, proteomics, and metabolomics. To achieve this crucial understanding of complex relationships in an intact system, there is a great need for reliable, high-quality experimental data beyond the cellular level."
"The most important step forward however is the paradigm shift needed to become a system thinking organization. [. . .] Such a paradigm shift will occur when a critical mass of global intelligence has embraced this concept of systems thinking."
All this is very interesting reading for Intelligent Design advocates. The philosophy of reductionism has long been identified as a negative influence when it ceases to be a tool and becomes a statement about the nature of reality. ID scholars have championed the cell, rather than DNA, as the most basic unit of living things. The ID approach is to see the importance of systems, whether they be complex specified systems or irreducibly complex systems. This is a real point of contact with systems biology: there is much common ground and this is to be welcomed. The methodologies being developed within systems biology are methodologies perfectly consistent with those emerging via design inferences.
The authors realise that a paradigm shift is urgently needed. Perhaps this is an area where funding agencies and employers will realise that ID biologists can assist with the development of systems thinking and will come to regard ID as an ally and an asset.

The Art and Practice of Systems Biology in Medicine: Mapping Patterns of Relationships
J. van der Greef, S. Martin, P. Juhasz, A. Adourian, T. Plasterer, E. R. Verheij, and R. N. McBurney
Journal of Proteome Research, ASAP Article 10.1021/pr0606530 S1535-3893(06)00653-1

Abstract: Systems biology has developed in recent years from a technology-driven enterprise to a new strategic tool in Life Sciences, particularly for innovative drug discovery and drug development. Combining the ultimate in systems phenotyping with in-depth investigations of biomolecular mechanisms will enable a revolution in our understanding of disease pathology and will advance translational medicine, combination therapies, integrative medicine, and personalized medicine. A prerequisite for deriving the benefits of such a systems approach is a reliable and well-validated bioanalytical platform across complementary measurement modalities, especially transcriptomics, proteomics, and metabolomics, that operates in concert with a megavariate integrative biostatistical/bioinformatics platform. The applicable bioanalytical methodologies must undergo an intense development trajectory to reach an optimal level of reliable performance and quantitative reproducibility in daily practice. Moreover, to generate such enabling systems information, it is essential to design experiments based on an understanding of the complexity and statistical characteristics of the large data sets created. Novel insights into biology and system science can be obtained by evaluating the molecular connectivity within a system through correlation networks, by monitoring the dynamics of a system, or by measuring the system responses to perturbations such as drug administration or challenge tests. In addition, cross-compartment communication and control/feed-back mechanisms can be studied via correlation network analyses. All these data analyses depend critically upon the generation of high-quality bioanalytical platform data sets. The emphasis of this paper is on the characteristics of a bioanalytical platform that we have developed to generate such data sets. The broad applicability of Systems Biology in pharmaceutical research and development is discussed with examples in disease biomarker research, in pharmacology using system response monitoring, and in cross-compartment system toxicology assessment.

Disillusionment with molecular clocks appears to be quite widespread. This paper draws attention to the great disparities that exist in the dates that emerge from these studies. The authors say that they await further work "with some nervousness, given that we suspect they might reveal that many past studies placed too much confidence in simple molecular clock analyses, and that their conclusions should thus be revisited."
Pessimism about the method is high. The worst case scenario is raised with the question: "is there likely to be so much uncertainty about molecular dating that the estimates are no longer useful? We fear that, for many current studies, the answer is yes."
The root problem is that the method has been built on Darwinian foundations. When legitimate concerns about these are addressed (see here), it may be possible do do something useful with the data.

Dates from the molecular clock: how wrong can we be?
Mario J.F. Pulquerio and Richard A. Nichols
Trends in Ecology & Evolution, Volume 22, Issue 4, April 2007, Pages 180-184

Abstract: Large discrepancies have been found in dates of evolutionary events obtained using the molecular clock. Twofold differences have been reported between the dates estimated from molecular data and those from the fossil record; furthermore, different molecular methods can give dates that differ 20-fold. New software attempts to incorporate appropriate allowances for this uncertainty into the calculation of the accuracy of date estimates. Here, we propose that these innovations represent welcome progress towards obtaining reliable dates from the molecular clock, but warn that they are currently unproven, given that the causes and pattern of the discrepancies are the subject of ongoing research. This research implies that many previous studies, even some of those using recently developed methods, might have placed too much confidence in their date estimates, and their conclusions might need to be revised.

Last sentence: We await the more rigorous type of assessment with some nervousness, given that we suspect they might reveal that many past studies placed too much confidence in simple molecular clock analyses, and that their conclusions should thus be revisited.

Evolutionary biologists have to squarely face the fact that living things look designed. However, is this appearance real (with the implication that there is an intelligent designer) or is it a subjective assessment without substance (with the implication that there are mechanisms for design emerging through natural causes)? The issue is not helped by those who try to trivialise the design argument. And Wedekind notes: "evolutionary biologists can struggle to find their best arguments when challenged by a well-prepared enthusiast of 'intelligent design'".
J. Scott Turner is an associate professor of biology at the State University of New York's College of Environmental Science and Forestry. He has written a book which is uninhibited in describing the harmony of structure and function as 'designedness'. He is aware that this will not please some colleagues, but argues that there is "no better way to open minds than to irritate them a bit".
Keywords for Turner's analysis are: "physiology", "homeostasis", and "self-organisation". He explains the concept of "Bernard machines". These both create and regulate environments, and ultimately are considered to lead to the "marvellous harmony of structure and function we observe in nature".
"But the author argues that life and evolution happen when Darwin machines act in concert with Bernard machines, which are the agents of homeostasis and can be seen, in their own particular way, as goal-seeking and purposeful. These are the 'tinkerer's accomplices' of the title."
People have been talking about self-organisation for many years, but with very little substance. It really is necessary to move from concepts to specifics. The problem is that decay appears to be a stronger trend than self-organisation, and promising starts do not get far. Furthermore, some regard the presence of homeostasis as a consequence of intelligent agency, which presupposes real design at the outset.

The interior designer
Claus Wedekind
Nature 446, 375, (22 March 2007) | doi:10.1038/446375a

Review of: The Tinkerer's Accomplice: How Design Emerges From Life Itself, by J. Scott Turner, Harvard University Press: 2007. 304 pp.

1st para: Sharing a broadly accepted idea or philosophical concept comes with a danger: after a period of indulgence in mutual affirmation, it is easy to forget how to effectively defend the concept against a smart and captious critic. Established politicians sometimes stumble and get lost in clumsy arguments when forced to defend the basic concepts of their politics against a cleverly presented and maybe radically different opinion. And evolutionary biologists can struggle to find their best arguments when challenged by a well-prepared enthusiast of 'intelligent design'. Non-physiologists, for example, might overlook the agents of homeostasis that lead, largely by themselves, to the marvellous harmony of structure and function we observe in nature.

A new eutriconodont mammal species, Yanoconodon, has been reported by a team of Chinese researchers.
The first point to make is that this is not an example of a transitional fossil. The animal has a number of specialised features and is described as "nested within crown mammals". The authors provide a cladogram of dental and skeletal characters of eutriconodonts, and the closest affinity is with Jeholodens. However, Yanoconodon has more thoracic ribs than Jeholodens, and Yanoconodon has lumbar ribs whereas Jeholodens does not. Whilst the authors discuss Hox gene mechanisms to alter the pattern of ribs, they do not attempt to locate Yanoconodon in any particular evolutionary lineage.
Rather, the new fossil has been hailed as illustrating an important evolutionary transition: detachment of the middle ear bones from the mandible. It is therefore better described as a fossil claimed to have a transitional structure associated with ear bones.
It is true that the authors favour the evolutionary transition scenario, but they are forced by the data to consider at least one alternative: that the definitive mammalian inner ear was present in "the common ancestor of monotremes, eutriconodonts and therians; but eutriconodonts re-evolved the middle ear attachment to mandible." (A polyphyletic approach introduces more options). The editors of Nature supplied a summary acknowledging that there is a legitimate debate about the significance of the find: "But the situation is not as clear-cut as it seems. The evolutionary relationships of the fossil suggest that either the 'modern' middle ear evolved twice, independently or that it evolved and was then lost in at least one ancient lineage." (In this comment, they are referring to monotremes and therians. The earbones of the duckbilled platypus emerge during development with a cartilaginous attachment to the jaw - much like Yanoconodon - but this attachment is reabsorbed as the animal grows thereby detaching the earbones).
It should be pointed out that this debate is not one where ID scholars might be expected to have a common view. Are evidences for design in the natural world affected by the earbones of Yanoconodon? The expectation would be that all the features of the animal would have functional significance, and that Darwinian mechanisms are not capable of achieving the specified complexity associated with the mammalian ear. Beyond that, let us explore the data without having to force everything into a Darwinian straitjacket! For those seeking a creationist comment, go here.

A new eutriconodont mammal and evolutionary development in early mammals
Zhe-Xi Luo, Peiji Chen, Gang Li, and Meng Chen
Nature 446, 288-293 (15 March 2007) | doi:10.1038/nature05627

Detachment of the three tiny middle ear bones from the reptilian mandible is an important innovation of modern mammals. Here we describe a Mesozoic eutriconodont nested within crown mammals that clearly illustrates this transition: the middle ear bones are connected to the mandible via an ossified Meckel's cartilage. The connected ear and jaw structure is similar to the embryonic pattern in modern monotremes (egg-laying mammals) and placental mammals, but is a paedomorphic feature retained in the adult, unlike in monotreme and placental adults. This suggests that reversal to (or retention of) this premammalian ancestral condition is correlated with different developmental timing (heterochrony) in eutriconodonts. This new eutriconodont adds to the evidence of homoplasy of vertebral characters in the thoraco-lumbar transition and unfused lumbar ribs among early mammals. This is similar to the effect of homeobox gene patterning of vertebrae in modern mammals, making it plausible to extrapolate the effects of Hox gene patterning to account for homoplastic evolution of vertebral characters in early mammals.

See also:
Editor's summary, An early look at mammals, Nature 446, 15 March 2007, vii.

Who can ever cease to be amazed at the complexity of cells and genetic systems? A Perspective essay in today's Science, concerned with "gene regulatory networks for development", confirms yet again the reality of complexity. The authors bring out the role of subcircuits in the gene regulatory network. These are "often of elegant and sometimes counterintuitive design, even more so, the ways they are combined in the overall network." The authors add: "Among the most fascinating aspects of gene regulatory networks are their design principles, for these are often interestingly different from what would seem the "simplest" solution."
The modular construction of these subcircuits is fascinating because it is at a much deeper level than the feedback circuitry we are more familiar with. "Thus, although subcircuits are indeed the modular functional components of developmental gene regulatory networks, they are to be distinguished from simpler "building blocks" or "motifs" that are used for many diverse developmental functions (e.g., feedforward or feedback elements, per se)."
The complexity goes even deeper: "As we have come to understand developmental gene regulatory networks, there arises an impression of "overlayered" circuit design--or more precisely, deployment of multiple subcircuits--that in different ways support the same end result."
What are we to make of the inter-dependent modular nature of regulatory networks? Is this the 'tinkering' model of Darwinism, or do we have the 'exquisite design' model of ID? "We may interpret this as we like--as overengineering; or as design deluxe, replete with bells and whistles; or as the expected result of an evolutionary process in which individual regulatory modules have been added in and overlain at different times." The authors plump for the 'tinkering' model. But even they appear to concede that what we have before us are irreducibly complex systems: "once integrated into the regulatory system, they are there to stay, barring evolutionary redirection". All I can say is that the hallmarks of 'tinkering' are noticeable by their absence! I'll go for the 'design deluxe' option!

Built to Run, Not Fail
Paola Oliveri and Eric H. Davidson
Science 315, 16 March 2007: 1510-1511.

On first encounter, gene regulatory networks for development often seem so complicated as to defy intuitive understanding. But the overall maze of gene interactions that they represent is actually composed of subcircuits that perform separate functions. The subcircuits are often of elegant and sometimes counterintuitive design, even more so, the ways they are combined in the overall network. As the underlying subcircuit structure is clarified, we see that gene regulatory networks in fact provide a direct and simply organized bridge from the phenomena of development to the detailed genomic programs that encode it. Among the most fascinating aspects of gene regulatory networks are their design principles, for these are often interestingly different from what would seem the "simplest" solution. Gene regulatory networks for development are the direct product of evolution, and the character of their design both illuminates evolution and is illuminated by it.

[snip]

Last para: We may interpret this as we like--as overengineering; or as design deluxe, replete with bells and whistles; or as the expected result of an evolutionary process in which individual regulatory modules have been added in and overlain at different times, so that some are more ancient and others more new (1). However, once integrated into the regulatory system, they are there to stay, barring evolutionary redirection. But the generality of this quality of developmental gene regulatory networks is emerging as a fact of life--it is what we see in modern animals. The consequences of evolutionary history determine the shape of the control apparatus that determines life processes. Perhaps in current system design we are seeing something of the grim pressures that modern lineages survived in past evolutionary bottlenecks--of the absolute necessity for lineage survival of genomic regulatory systems built to run and not to fail.

Carl Linnaeus features large this week in Nature. He is remembered as a towering figure whose impressive shadow looks likely to reach well beyond this 300 year anniversary. The Editorial draws attention to three distinctive contributions: "his systematic spirit, his stress on the concept of species, and the formal but adaptable conventions of nomenclature he introduced". Also, we read: "Nature is glad to celebrate his legacy in this special issue."
There is another aspect of Linnaeus that deserves our attention. The Father of Taxonomy considered that the living world was the product of a creator God: "Linnaeus believed in fixed species of knowable number created by God and observable by men." It should be pointed out that this summary reflects his early view; as he matured and developed in his thinking, he recognised the reality of speciation within distinct groups of organisms. But is his creation-oriented biology part of his legacy? Not in the opinion of the editors of Nature: "He would hopefully come round to evolutionary theory".
What if he failed to "come round"? What if he developed further his polyphyletic approach? What if he were to argue that the Tree of Life were a construct of ideology, not a result of empirical science? Would he then be disowned by the community of scientists who declare their pleasure in celebrating his legacy? Of course, these are all hypothetical questions. However, the deeper issue is this: Linnaeus did not separate his thinking into "public" and "private" compartments. He sought a unified understanding of the natural world. He was a theistic scientist. He was open to the possibility of seeing design in the living world, and he found it. He showed that design inferences were part of the early days of science, and that modern day attempts to banish intelligent design from the vocabulary of science take us away from the historic roots of our discipline. This is an aspect of Linnaeus' legacy that we do well not to overlook.

The legacy of Linnaeus
Editorial
Nature 446, 231-232 (15 March 2007) | doi:10.1038/446231b

Darwinists have never been comfortable with reports of "stasis". They have never been reconciled to Gould's statement that "Stasis is data". Instead, stasis is regarded as a paradox and as a problem to be solved. Estes and Arnold have contributed a significant new paper on the subject. In one paragraph, they review the evidence that stasis might have a genetic explanation and conclude that this refutes "the notion of omnipresent, internal constraints on evolution." However, their perspective is entirely Darwinian, and there is no engagement with structuralist thinking, or bau-plans or basic types. Darwinian theory makes no distinction between adaptations of traits and the development of novel structures, so the fact that "populations are often well equipped genetically to respond to at least short-term ecological challenges" is sufficient to settle the matter. Then "stabilising selection emerges as the leading contender among explanations for stasis."
Estes and Arnold employ the adaptive landscape concept to "evaluate the degree to which six evolutionary models fit the observed data." Three of these models are based on random variation, and these do not fit at all. In a News and Views article in Nature, Hendry comments "This conclusion will be reassuring, or perhaps just obvious, to the innumerable evolutionary biologists who believe that adaptation plays a central role in evolution". The other three models all involve a shift in the fitness peak of the adaptive landscape. In one case, the peak moves continuously in a particular direction. In the second case, there are two peaks separated by a valley. The third case is called the "displaced optimum" model; it has a single peak which jumps in a generation to a new location and stays there. "In the authors' estimation, this last model fits the data quite well."
Approaching a conclusion, Hendry explains the title of his article: "For some, any report of the death of this paradox will probably evoke the same reaction as the death of Elvis, with a large number of fans reluctant to accept its passing. But in the end, evolutionary biologists will probably converge on more pertinent questions, such as 'What generates and maintains adaptive zones in the first place?', and 'How do some lineages ultimately bridge the gap between different adaptive zones?'. In other words, these biologists can get back to the same questions that they have been puzzling over for 60 years!
The analogy with the death of Elvis is most unfortunate, because there is no valid comparison. Stasis is the conclusion of extensive analysis of data by specialists, not the emotive response of bystanders. The adaptive landscape, on the other hand, is a theoretical construct offered to illustrate adaptive change, but never validated by empirical research. The paper by Estes and Arnold provides theoretical modelling of reported data, with no analysis of the environmental factors changing the adaptive landscape, and no attempt to explain the changes in terms of adaptive responses to environmental factors. There are really so many loose ends to this work that the authors should not be allowed to get away with the idea that they have confronted "the predictions of alternative evolutionary models with the reality of data".
The paradox of stasis is not dead, nor is it in its death throes!

Resolving the Paradox of Stasis: Models with Stabilizing Selection Explain Evolutionary Divergence on All Timescales
Suzanne Estes and Stevan J. Arnold
American Naturalist, February 2007. Vol. 169, pp. 227-244.

ABSTRACT: We tested the ability of six quantitative genetic models to explain the evolution of phenotypic means using an extensive database compiled by Gingerich. Our approach differs from past efforts in that we use explicit models of evolutionary process, with parameters estimated from contemporary populations, to analyze a large sample of divergence data on many different timescales. We show that one quantitative genetic model yields a good fit to data on phenotypic divergence across timescales ranging from a few generations to 10 million generations. The key feature of this model is a fitness optimum that moves within fixed limits. Conversely, a model of neutral evolution, models with a stationary optimum that undergoes Brownian or white noise motion, a model with a moving optimum, and a peak shift model all fail to account for the data on most or all timescales. We discuss our results within the framework of Simpson's concept of adaptive landscapes and zones. Our analysis suggests that the underlying process causing phenotypic stasis is adaptation to an optimum that moves within an adaptive zone with stable boundaries. We discuss the implication of our results for comparative studies and phylogeny inference based on phenotypic characters.

See also:
Hendry, A. Evolutionary biology: The Elvis paradox. Nature 446, 147-150, (8 March 2007) | doi:10.1038/446147a
Abstract: Evidence for a universal driver of evolution across all timescales could mean that the venerable paradox of stasis is dead. But even with such evidence, some biologists would be reluctant to accept its passing.

The Ceratopsidae is the name given to a Family of four-legged herbivores from the Upper Cretaceous of Western North America. They are classified in two subfamilies: the Ceratopsinae (which includes the well-known Triceratops) and the Centrosaurinae (which includes Styracosaurus). These are all horned dinosaurs, with a diverse range of protrusions from the frill, from above the eyes and above the nose. The Ceratopsinae are associated with long brow horns whereas in the Centrosaurinae they are short. A new dinosaur find reveals a centrosaurine with long brow horns. Based on the stratigraphical position and a cladistic analysis, the animal has been identified "as the basal member of the Centrosaurinae".
The oldest known horned dinosaur is called Zuniceratops and had large horns. Consequently, "the newly found creature [is] an intermediate between older forms with large horns and later small-horned relatives" suggests Jim Kirkland, State of Utah paleontologist, who co-identified Zuniceratops in 1998. "He predicted then that something like Ryan's find would turn up. "Lo and behold, evolutionary theory actually works," he said."
The extraordinary diversity of the dinosaurs in general is no less apparent in the Ceratopsidae, all of which are documented from a few states of the US and parts of Canada. Variation on a theme is prominent. Evolutionists generally start by trying to trace a linear pathway, with clearly defined intermediates, but more data transforms the picture to a bush, with no obvious tree-like structure. So, although we read a comment like "evolutionary theory actually works", it does not carry much weight. "It is very surprising that a Centrosaur would have long brow horns," said Don Brinkman of the Royal Tyrrell Museum in Drumheller. If the prediction was substantial, one would expect people to say that they were expecting this discovery.
It is worth adding that the real debate over evolutionary theory is not about the positions and sizes of horns. This is just variation affecting existing traits and not controversial at all. Of far greater interest is the origin of novel structures, especially those exhibiting complex specified information. It will be a great day when Darwinists realise that they cannot simply lump together the origin of novelty with observations of variation of existing traits. Then we might witness some really interesting discourse about what evolutionary theory actually is and which aspects actually work!

A new basal centrosaurine ceratopsid from the Oldman Formation, Southeastern Alberta
Michael J. Ryan
Journal of Paleontology, 81(2), March 2007, pp. 376-396

Abstract: A new centrosaurine ceratopsid, Albertaceratops nesmoi, is described from the lower Oldman Formation (Upper Cretaceous) of southern Alberta, and is based on a single, almost complete skull. Referred material is described from equivalent beds in the Judith River Formation of north-central Montana. A limited phylogenetic analysis of the Ceratopsidae places the new taxon as the basal member of the Centrosaurinae and indicates that robust, elongate postorbital horncores that form a synapomorphy of (Ceratopsidae + Zuniceratops) are also present in Centrosaurinae.

See also:

Cleveland Museum of Natural History Scientist Discovers New Horned Dinosaur Genus
Cleveland Museum of Natural History Press Release, February 24, 2007

Dinosaur had yard-long horns over eyebrows
CNN News, March 5 2007.

Paleoanthropologists have always had plenty to debate, and a new genome comparison study is no exception. Whereas the majority view suggests that hominid line can be traced back to between 5 Ma and 7 Ma, the new study gives a more recent figure. "We apply the HMM [a statistical method] to four autosomal contiguous human-chimp-gorilla-orangutan alignments comprising a total of 1.9 million base pairs. We find a very recent speciation time of human-chimp (4.1 ± 0.4 million years)." This is deemed by many as too late. Blair Hedges considers that the figure "is hard to defend because fossils practically reject it". Ian Tattersall says "it's inconceivable that you could have a common ancestor to both at 4 million years ago when you already have evidence in the hominid lineage that there were bipeds already around at that time."
The study raises again the whole question of what the genome comparisons are telling us. It gives particular relevance to the recent critique of Schwartz and Maresca noted here.

It would be a big step forward if the presuppositions and assumptions of every discipline involved in anthropology were more transparent, because there is often considerable difficulty distinguishing between data and interpretations of data.

Genomic Relationships and Speciation Times of Human, Chimpanzee, and Gorilla Inferred from a Coalescent Hidden Markov Model
Asger Hobolth, Ole F. Christensen, Thomas Mailund, Mikkel H. Schierup
PLoS Genetics, 3(2): e7 doi:10.1371/journal.pgen.0030007

Abstract: The genealogical relationship of human, chimpanzee, and gorilla varies along the genome. We develop a hidden Markov model (HMM) that incorporates this variation and relate the model parameters to population genetics quantities such as speciation times and ancestral population sizes. Our HMM is an analytically tractable approximation to the coalescent process with recombination, and in simulations we see no apparent bias in the HMM estimates. We apply the HMM to four autosomal contiguous human-chimp-gorilla-orangutan alignments comprising a total of 1.9 million base pairs. We find a very recent speciation time of human-chimp (4.1 ± 0.4 million years), and fairly large ancestral effective population sizes (65,000 ± 30,000 for the human-chimp ancestor and 45,000 ± 10,000 for the human-chimp-gorilla ancestor). Furthermore, around 50% of the human genome coalesces with chimpanzee after speciation with gorilla. We also consider 250,000 base pairs of X-chromosome alignments and find an effective population size much smaller than 75% of the autosomal effective population sizes. Finally, we find that the rate of transitions between different genealogies correlates well with the region-wide present-day human recombination rate, but does not correlate with the fine-scale recombination rates and recombination hot spots, suggesting that the latter are evolutionarily transient.

See also:

Gibbons, A., A Recent Split of Humans and Chimps? ScienceNOW Daily News, 27 February 2007.

Lloyd, R., First Humans: Time of Origin Pinned Down, LiveScience, 23 February 2007.

The assumptions underlying molecular clocks are all dependent on the "Darwinian model of continual and gradual change". What happens if these assumptions are probed, tested and subjected to critical scrutiny? This is the exercise undertaken by Schwartz and Maresca.
The first part of the paper addresses historical aspects of "molecular systematics" to better understand the "theoretical and methodological underpinnings." The authors are concerned to find out "how belief in the infallibility of molecular data for reconstructing evolutionary relationships emerged, and how this belief became so central, especially to paleoanthropology." This they do with an incisiveness rarely appearing on the printed page of refereed journals. The MA (molecular assumption) is acknowledged to be dominant but to rest on theoretical rather than empirical foundations. "No doubt because it was completely Darwinian, the MA continued to dominate the increasingly influential field of what was now often called molecular systematics."
The authors go on to look at the topic of DNA hybridization, showing that the data may be telling us something about "primitive retention" rather than "closeness of relatedness". They show that although the authors of MA studies use the language of cladism, they are mistaken: "In light of this procedure of hypothesis testing, it is obvious that any molecular analysis based on the MA is not cladistic."
They show that comparisons based on structural genes can be interpreted in ways that are quite different from the MA advocates. "Phylogenetic relationships among metazoans might, therefore, be better revealed through comparing developmentally regulated genes, because changes in their expression can alter phenotypes."
It has been a major problem for Darwinism that its foundations are regarded as inviolable and a 'given'. "Our review [...] reveals that, no matter how sophisticated their mathematical models, molecular systematists have not questioned the basic assumptions upon which they are based. Thus, while refining computer programs to analyze molecular data phylogenetically continues apace [...] with statements of certitude about results following suit, no algorithm is more viable than the assumptions that inform it." The authors offer the hope that their critical review will open the way for a more integrated approach to systematics.
This is a paper that will disturb the Darwinists, but it will offer encouragement to all who want to see less ideology in evolutionary thinking and who want to follow the evidence wherever it leads.

Do Molecular Clocks Run at All? A Critique of Molecular Systematics
Jeffrey H. Schwartz and Bruno Maresca
Biological Theory, Fall, 2006, Vol. 1, No. 4, Pages 357-371 | doi:10.1162/biot.2006.1.4.357 (Open Access)

Abstract: Although molecular systematists may use the terminology of cladism, claiming that the reconstruction of phylogenetic relationships is based on shared derived states (synapomorphies), the latter is not the case. Rather, molecular systematics is (largely) based on the assumption, first clearly articulated by Zuckerkandl and Pauling (1962), that degree of overall similarity reflects degree of relatedness. This assumption derives from interpreting molecular similarity (or dissimilarity) between taxa in the context of a Darwinian model of continual and gradual change. Review of the history of molecular systematics and its claims in the context of molecular biology reveals that there is no basis for the "molecular assumption."

See also:

Prof Questions Darwinian Dogma, Scienceagogo, 12 February 2007

"The genetic code is the mapping of 64 three-letter codons to 20 amino-acids and a stop signal." It stands out among possible competing codes in several ways. "First, the assignment of amino acids to codons appears to be optimal for minimizing the effect of translational misread errors." Errors in misreading a codon tend to have minimal effects on the translated protein. "Second, amino acids with simple chemical structure tend to have more codons assigned to them", as "they are required more often in protein assembly". But the researchers main interest in the paper below was the ability of the genetic code to carry parallel messages. The list is already impressive (and there is no reason why it should not be extended with research) - binding sequences of regulatory proteins that bind within coding regions, splicing signals that include specific 6-8 bp sequences within coding regions and mRNA secondary structure signals - all higher-order codes that ride over the protein forming code. "They found that the real genetic code could accommodate more arbitrary motifs in coding sequence than almost any of the other possibilities - it has a higher information content. One reason for the real genetic code's superiority is the fact that its stop codons, when frame-shifted, tend to form common codons, whereas in other codes frame-shifted stop codons form rarer codons or even other stop codons."
The authors appeal to selection to explain why the genetic code is optimal. The implication of this approach is that the selection had to take place before the Last Common Ancestor emerged on Earth. All this complexity had to be fine tuned in a single celled organism that predated all subsequent diversity. An information-based approach linked to Intelligent Agency deserves a fair hearing when seeking an explanation for optimal design.

The genetic code is nearly optimal for allowing additional information within protein-coding sequences
Shalev Itzkovitz and Uri Alon
Genome Research, 2007 17: 405-412. doi 10.1101/gr.5987307(Open Access)

DNA sequences that code for proteins need to convey, in addition to the protein-coding information, several different signals at the same time. These "parallel codes" include binding sequences for regulatory and structural proteins, signals for splicing, and RNA secondary structure. Here, we show that the universal genetic code can efficiently carry arbitrary parallel codes much better than the vast majority of other possible genetic codes. This property is related to the identity of the stop codons. We find that the ability to support parallel codes is strongly tied to another useful property of the genetic code—minimization of the effects of frame-shift translation errors. Whereas many of the known regulatory codes reside in nontranslated regions of the genome, the present findings suggest that protein-coding regions can readily carry abundant additional information.

See also:
Goymer, P., Evolution: The genetic code sees off rivals, Nature Reviews Genetics 8, 168-169 (March 2007) | doi:10.1038/nrg2076

There are many possible three-letter genetic codes that could adequately encode protein sequences, but what about the need to encode higher-order information on binding and splicing sites? New research shows that the actual genetic code is better than potential alternatives at encoding such information at the same time as encoding protein. [snip]

Evolution and multilevel optimization of the genetic code
Tobias Bollenbach, Kalin Vetsigian, and Roy Kishony
Genome Research, 2007 17: 401-404. doi 10.1101/gr.6144007

Abstract: The discovery of the genetic code was one of the most important advances of modern biology. But there is more to a DNA code than protein sequence; DNA carries signals for splicing, localization, folding, and regulation that are often embedded within the protein-coding sequence. In this issue, Itzkovitz and Alon show that the specific 64-to-20 mapping found in the genetic code may have been optimized for permitting protein-coding regions to carry this extra information and suggest that this property may have evolved as a side benefit of selection to minimize the negative effects of frameshift errors.

Last paragraph: "As we learn more about the functions of the genetic code, it becomes ever clearer that the degeneracy in the genetic code is not exploited in such a way as to optimize one function, but rather to optimize a combination of several different functions simultaneously. Looking deeper into the structure of the code, we wonder what other remarkable properties it may bear. While our understanding of the genetic code has increased substantially over the last decades, it seems that exciting discoveries are waiting to be made."

Although "less than 2% of the human genome is translated into protein, yet more than 40% of the genome is thought to be transcribed into RNA." This non-coding RNA has some "truly remarkable" characteristics: "microRNAs, short interfering (si)RNAs, repeat-associated RNAs and germline-specific RNAs) and of new members of existing classes (for example, small nucleolar (sno)RNAs)".

A recent review paper is concerned with the "biogenesis, trafficking and mechanisms of action of small nuclear and small nucleolar ribonucleoproteins (RNPs)." The authors refer to the "remarkable complexity" of these RNP complexes, pointers to which are as follows:
"ncRNAs have emerged as key trans-acting regulators of diverse cellular activities in all three domains of life."
"Ongoing studies of snRNPs and snoRNPs have revealed unexpectedly elaborate biogenesis pathways."
"ncRNAs often require partner proteins that provide various essential functions in addition to the obvious associated enzymatic activities."
"A common principle in the biogenesis of both snRNPs and snoRNPs is the assembly of stable, but inactive, pre-RNPs that require maturation at locations distinct from the functional sites."

It used to be said that DNA coding for protein was the only thing that mattered in the genome, and all else was lumped under the descriptor "Junk DNA". But not now! Is the term "Junk DNA" best understood as an outdated concept emerging from a very inadequate view of the genome? But even more important, with all this complexity emerging from DNA that does not code for protein, what does this imply for our understanding of living things? A friend writes: "Probability decreases EXPONENTIALLY as complexity increases. When do we reach an increase that makes the Darwinian hypothesis completely incredible? Seems like we must be there now."

Non-coding RNAs: lessons from the small nuclear and small nucleolar RNAs
A. Gregory Matera, Rebecca M. Terns and Michael P. Terns
Nature Reviews Molecular Cell Biology, 8, 209-220 (March 2007) | doi:10.1038/nrm2124

Abstract: Recent advances have fuelled rapid growth in our appreciation of the tremendous number, diversity and biological importance of non-coding (nc)RNAs. Because ncRNAs typically function as ribonucleoprotein (RNP) complexes and not as naked RNAs, understanding their biogenesis is crucial to comprehending their regulation and function. The small nuclear and small nucleolar RNPs are two well studied classes of ncRNPs with elaborate assembly and trafficking pathways that provide paradigms for understanding the biogenesis of other ncRNPs.

Summary of paper here.

Alex Rosenberg is a hardened reductionist who has written a book to persuade biologists that "interactions of macromolecules" are sufficient to explain all biological data. "The only serious challenge that he sees to reductionism comes from the principle of natural selection (PNS), which he believes has a central role in the subject." Rosenberg then attempts to present PNS as a biological law, but "he cannot find an acceptable definition, which is unsurprising given that many others before him have also tried and failed." The reviewer adds: "My own view is that PNS is a tautology, not a law."
Rosenberg writes: "Darwinism includes the claim that natural selection is at least the most significant causal mechanism of evolutionary change instantiated by lineages on Earth's tree of life." In which case, PNS is just declared to have the role that Darwinism assigns to it. It is not something that emerges from empirical science. The reviewer adds: "Darwinism as so defined is not a tautology, but it is more a theory or a paradigm than a law."
So Rosenberg's reductionist crusade founders on not being able to integrate PNS into his philosophical framework. Saunders is not too impressed with the way he handles genetic reductionism either. "Rosenberg has made a serious attempt at an impossible goal. I would like to think that his failure will help convince Darwinians that they should show the same degree of reticence in biology that some are already demonstrating in the study of human behaviour."
This is an interesting review, covering several issues much discussed by scholars associated with the ID Movement. It is encouraging to find common ground with many of the points made by Saunders.

Reductio ad absurdum
Peter T. Saunders
Trends in Ecology & Evolution , Volume 22, Issue 3 , March 2007, Pages 118-119

Book Review: Darwinian Reductionism: Or How to Stop Worrying and Love Molecular Biology, by Alex Rosenberg. University of Chicago Press, 2006.

Most contemporary biologists believe that biological processes are essentially physical. Despite this, most of us do not accept that explanations in biology can be truly satisfactory only if they can be formulated in terms of the laws of physics. In Darwinian Reductionism, Alex Rosenberg dismisses this as illogical. He insists 'that there is a full and complete explanation of every biological fact, state, event, process, trend or generalization, and that this explanation will cite only interactions of macromolecules to provide this explanation.' If this were merely a statement of what is possible in principle, there would be no real disagreement with the majority view. For Rosenberg, however, reductionism is not only a metaphysical thesis, but is also a claim about explanations and a research programme. His aim in Darwinian Reductionism is 'to convince the reader that heaven belongs to the molecular biologist, and to convince non-molecular biologists that there is room for them in the molecular biologist's heaven.'
[snip]

Ever since the first exoplanet was discovered, there has been an insatiable appetite for news of places with environments suitable for life. With over 200 exoplanets documented, none have yet satisfied this hunger. The next phase of research has now commenced, with two reports of planetary atmospheres.
The first is HD 209458b, at a distance of 150 light years from Earth. This gave a flat spectrum "showing nothing apart from a peak (Richardson] attributes to silicates, and possibly a molecule containing carbon-carbon bonds such as those seen in benzene." There was no trace of water, carbon dioxide or methane. The second report concerns HD 189733b, 60 light years from Earth. This also documents "a flat spectrum, with no water, methane or carbon dioxide" and no silicates either.
Richardson et al. comment: "All hot Jupiter spectra are expected to be shaped by water absorption because water is an abundant gas at the high temperatures of hot Jupiters (1,000 - 2,000 K)." Consequently, it is a real puzzle not to detect water in the spectra of these two planets. If water is present, it must be hidden by some means: "Unanticipated sources of opacity may be required to produce a temperature inversion at these altitudes, and thereby mask the effect of water opacity."
Theories of how planetary atmospheres formed will need to be reappraised. The findings create yet more problems for OOL research. In other contexts, finding water outside the Earth has been used to raise expectations of finding life, but at least that does not arise here. However, it is worth contrasting this point with some of the more sensational media reports: "Giant step in search for alien life" and "Nasa closer to discovering life on other planets". Beware of spin!

[Please note: this blog entry is written in the knowledge that some scientists think the earth's water came from comets, and recognises that their hypothesis is unaffected by the new finds. Also, the comments above do not imply that exoplanets containing water will not be found, nor that earth-size planets will not be discovered in the liquid water zone.]

A spectrum of an extrasolar planet
L. Jeremy Richardson, Drake Deming, Karen Horning, Sara Seager and Joseph Harrington
Nature 445, 892-895 (22 February 2007) | doi:10.1038/nature05636

Of the over 200 known extrasolar planets, 14 exhibit transits in front of their parent stars as seen from Earth. Spectroscopic observations of the transiting planets can probe the physical conditions of their atmospheres1, 2. One such technique3, 4 can be used to derive the planetary spectrum by subtracting the stellar spectrum measured during eclipse (planet hidden behind star) from the combined-light spectrum measured outside eclipse (star + planet). Although several attempts have been made from Earth-based observatories, no spectrum has yet been measured for any of the established extrasolar planets. Here we report a measurement of the infrared spectrum (7.5-13.2 [micro]m) of the transiting extrasolar planet HD 209458b. Our observations reveal a hot thermal continuum for the planetary spectrum, with an approximately constant ratio to the stellar flux over this wavelength range. Superposed on this continuum is a broad emission peak centred near 9.65 [micro]m that we attribute to emission by silicate clouds. We also find a narrow, unidentified emission feature at 7.78 m. Models of these 'hot Jupiter'5 planets predict a flux peak6, 7, 8, 9 near 10 m, where thermal emission from the deep atmosphere emerges relatively unimpeded by water absorption, but models dominated by water fit the observed spectrum poorly.

See also:

Sanderson, K. Direct view of a dark and distant world, Nature 445, 803 (22 February 2007)

Minkel, J.R., Water Mysteriously Absent from Extrasolar Planets' Atmospheres, Scientific American News, February 21, 2007
Contrary to predictions, two planets orbiting distant stars show no signs of water and other simple compounds; dark clouds or haze may hide them

Humans are used to the idea that we extract information from our environment, process it and determine an appropriate response. This is OK for those of us with brains that are large enough to do this, but these mental gymnastics are not going to suit creatures of small brain, like insects. Nevertheless, flying insects do not seem phased by this neural problem and they travel with ease over different terrains - rugged or smooth - with headwinds of varying intensities. It has been proposed that, instead of extracting information, insects utilise a visual-feedback loop linking flight with visual cues. "When insects are flying forward, the image of the ground sweeps backward across their ventral viewfield and forms an "optic flow", which depends on both the groundspeed and the groundheight." If a regulation system exists to stabilise the optic flow as perceived by the insect, it provides a means of controlling takeoff and landing, flight against wind, and flight over irregular terrains.
To test this idea, the researchers constructed a micro-helicopter equipped with an optic-flow regulator. The flying robot performed in ways that mirrored the distinctives of insect flight, and the authors, quite rightly, claim that it "sheds light on insect piloting abilities". They also claim numerous advantages for flying robot design, reducing the need for sensors and signal processing.
The authors add that the optic-flow system is "quite simple in terms of its neural implementation". Also that "its neural implementation is not very demanding". These comments do not seem to do justice to the need in flying insects for low weight with corresponding limited neuronal capabilities. Furthermore, the authors have only started to explore the control issues and the underlying neural circuits. They acknowledge themselves that there is some evidence for a second optic-flow regulator that "may be in charge of adjusting the groundspeed by regulating the lateral OF". In a commentary article, Webb identifies another factor: "Ventral optic flow can be easily detected if the animal is flying straight ahead and the sensor is pointing straight down. But if the insect pitches, rolls or rotates, ventral optic flow will be distorted. Can the animal measure and discount these movements, or are other sensorimotor loops, such as the optomotor reflex, deployed simultaneously to minimise them?"
What we have here is an interesting exercise in product development. A design brief could be written for a control system that enables lightweight flyers "to deal single handedly with all maneuvers, such as taking off, flying at a level height, landing, and responding appropriately to wind, without being informed about groundheight, groundspeed, airspeed, windspeed, or ascent or descent speed, and hence without any need for the metric sensors with which conventional aircraft are equipped." To achieve this, we would expect a substantial investment in intelligent design engineering. We recognise that the problem has many complex issues to resolve. Delivering a product that meets the design brief allows us to make inferences about intelligent agency.

A Bio-Inspired Flying Robot Sheds Light on Insect Piloting Abilities
Nicolas Franceschini, Franck Ruffier and Julien Serres
Current Biology, Vol 17, 329-335, 20 February 2007

Summary: When insects are flying forward, the image of the ground sweeps backward across their ventral viewfield and forms an "optic flow", which depends on both the groundspeed and the groundheight. To explain how these animals manage to avoid the ground by using this visual motion cue, we suggest that insect navigation hinges on a visual-feedback loop we have called the optic-flow regulator, which controls the vertical lift. To test this idea, we built a micro-helicopter equipped with an optic-flow regulator and a bio-inspired optic-flow sensor. This fly-by-sight micro-robot can perform exacting tasks such as take-off, level flight, and landing. Our control scheme accounts for many hitherto unexplained findings published during the last 70 years on insects' visually guided performances; for example, it accounts for the fact that honeybees descend in a headwind [1], land with a constant slope [2], and drown when travelling over mirror-smooth water [3]. Our control scheme explains how insects manage to fly safely without any of the instruments used onboard aircraft to measure the groundheight, groundspeed, and descent speed. An optic-flow regulator is quite simple in terms of its neural implementation and just as appropriate for insects as it would be for aircraft [4].

See also:
Insect Behaviour: Controlling Flight Altitude with Optic Flow
Barbara Webb
Current Biology, Vol 17, R124-R125, 20 February 2007

Summary: Insects can smoothly control their height while flying by adjusting lift to maintain a set-point in the ventral optic flow. The efficacy of this simple flight-control mechanism has been demonstrated using a robot helicopter.

The ability of chimpanzees to construct tools has long been an interest of anthropological researchers. The first and only data regarding past tool-making activity has just appeared in the PNAS. The Panin sites from West Africa are the only known prehistoric chimpanzee settlements, and these have "yielded behaviorally modified stones, dated by chronometric means to 4,300 years of age".
The press release explains the rationale for the researchers' conclusion: "The stones they excavated show the hallmarks of use as tools for smashing nuts when compared to ancient human or modern chimpanzee stone tools." In other words, the researchers have made a design inference, based on the data they have gathered. The stones bear the characteristic marks of being used as tools, and starch grains were found on the stones (an indication that the chimps were cracking nuts). It is a good example of a design inference in science, in this case involving non-human subjects. It is a much needed reminder that science should never be defined so as to exclude intelligent causation.
Some analysis of the significance of the finding has been made. The researchers say their work "suggests that percussive material culture could have been inherited from an common human-chimpanzee clade, rather than invented by hominins, or have arisen by imitation, or resulted from independent technological convergence." This does seem to be premature at best. What the data shows is behavioural stasis: chimps today can use tools to crack nuts; chimps 4300 years ago used tools to crack nuts. The data does not constrain explanations of the origins of this trait. One can interpret this in terms of Kuhnian "normal" science, whereby evidence for stasis is interpreted in terms of the prevailing evolutionary paradigm. Of the various options, the authors favour the idea that humans and chimps shared a common ancestor that possessed tool-making abilities. One suspects this hypothesis will not survive critical appraisal by peers.

4300-year-old chimpanzee sites and the origins of percussive stone technology
Mercader, Julio, Huw Barton, Jason Gillespie, Jack Harris, Steven Kuhn, Robert Tyler, and Christophe Boesch
Proceedings of the National Academy of Sciences, published February 20, 2007, 10.1073/pnas.0607909104

Abstract: Archaeological research in the African rainforest reveals unexpected results in the search for the origins of hominoid technology. The ancient Panin sites from Cote d'Ivoire constitute the only evidence of prehistoric ape behavior known to date anywhere in the world. Recent archaeological work has yielded behaviorally modified stones, dated by chronometric means to 4,300 years of age, lodging starch residue suggestive of prehistoric dietary practices by ancient chimpanzees. The "Chimpanzee Stone Age" pre-dates the advent of settled farming villages in this part of the African rainforest and suggests that percussive material culture could have been inherited from an common human-chimpanzee clade, rather than invented by hominins, or have arisen by imitation, or resulted from independent technological convergence.

See also:

The Chimpanzee Stone Age . West African chimpanzees have been cracking nuts with stone tools for thousands of years
Max Planck Society, 13 February 2007.

Ancient chimps 'used stone tools'
Chimpanzees in West Africa used stone tools to crack nuts 4,300 years ago. BBC News, BBC News, 13 February 2007.

Origin Of Life theories all have to engage with the improbability problem. Researchers have to decide whether the low probabilities are telling them NOT to pursue a particular investigation, or whether there is sufficient to justify persevering. There is no escape from this, because natural selection cannot yet be invoked.

The majority of OOL researchers favour a reductionistic approach, via the Miller-Urey model of synthesis of amino acids in a reducing environment followed by the RNA World. Shapiro hows how improbable this option is and comments:

"A highly implausible start for life, as in the RNA-first scenario, implies a universe in which we are alone. In the words of the late Jacques Monod, "The universe was not pregnant with life nor the biosphere with man. Our number came up in the Monte Carlo game.""

As an alternative paradigm, Shapiro favours the "metabolism first" scenario, where small bounded reaction-chambers reach the stage when significant chemical reactions take place but without replication. "Over the years, many theoretical papers have advanced particular metabolism first schemes, but relatively little experimental work has been presented in support of them. In those cases where experiments have been published, they have usually served to demonstrate the plausibility of individual steps in a proposed cycle." In this situation, a variety of events might be possible. "[B]ecause we know that evolution does not anticipate future events, we can presume that nucleotides first appeared in metabolism to serve some other purpose, perhaps as catalysts or as containers for the storage of chemical energy (the nucleotide ATP still serves this function today). Some chance event or circumstance may have led to the connection of nucleotides to form RNA." Perhaps because the experimental work is so limited, Shapiro is willing to entertain the possibility that this route to life is not so improbable, and that what happened on Earth could have happened elsewhere in the Cosmos.

From an Intelligent Design perspective, none of these research paradigms will succeed. This is because none of them address the challenges of biological information. For as long as researchers are content to immerse themselves in the chemistry, they will not progress beyond the empty soup kettle. Is information an accident? Or is information a hallmark of intelligent agency and design? This is why ID needs to be integrated within science and evaluated on its merits (rather than rejected because of the ideology prevailing within the scientific community).

A Simpler Origin for Life
By Robert Shapiro
Scientific American, February 12 2007.

The sudden appearance of a large self-copying molecule such as RNA was exceedingly improbable. Energy-driven networks of small molecules afford better odds as the initiators of life.

The translation of mRNA into protein "occurs on one of nature's most versatile molecular synthesizers: the ribosome." The analogy for this machine in the human world is the factory: the mass production line from which emerges a stream of products. However, the factory is not like a Fordist assembly line, with lots of workstations, but more like an Advanced Manufacturing Technology cell, where all the instructions are digital and where the machinery translates information into a physical product.
"In the past decade or so, the ribosome has gone from being a biomolecule whose very structure was largely a mystery to one whose architecture is known at an atomic level and whose detailed workings are beginning to be better understood." The fruits of this research are to be found in a variety of formats, including some remarkable simulations, such as here. The most favoured model for the working of ribosomes involves the "proton-shuttle mechanism".
"Computation and simulation are likely to be extraordinarily useful for further clarifying the ribosome's mechanism", because nothing else approaches being able to capture the molecular-level motions and chemical reactions. One recent study is described as "the largest simulation performed to date in biology."
One researcher has commented: "at this point, in spite of high-resolution crystal structures and decades of biochemical, genetic, and biophysical studies, I don't think we understand the fundamental mechanisms at all." Another says: "Where one person says we have the answers, the next person says we have the questions."

So how should we approach the next phase of research into this "huge complex of protein and RNA with a practical and life-affirming purpose-catalyzing protein synthesis"? Without ribosomes, DNA and mRNA are destined to degradation. Like a human factory, information by itself is necessary by not sufficient. The ribosome is a super-machine, not a basic tool. The bacterium E. coli has a ribosome made-up of 50 proteins, each of which requires manufacturing prior to assembly. This is the old "which came first: the chicken or the egg?" conundrum. It is a major challenge for abiogenesis, which is still dabbling with organic chemistry and is not within sight of a working cell (the only environment that can be deemed stable for any possible precursor molecules).
The day is coming when biologists will look at the animations of the ribosome and say: "Why did we resist considering the design inference for so long?"

Protein Factory Reveals Its Secrets
Stu Borman
Chemical & Engineering News, 19 February 2007

Last year, the Nobel Prize in Chemistry heralded work on DNA transcription, a cornerstone process in molecular biology in which a cell synthesizes a messenger RNA (mRNA) version of genomic DNA. For some time, many research teams have been studying the other side of molecular biology's central dogma - the translation of mRNA into protein. That translation occurs on one of nature's most versatile molecular synthesizers: the ribosome. [snip]

Translation Movie shows the process of mRNA-to-protein translation, including initiation, protein chain elongation, and termination.

Michael Ruse, in the introduction of his latest book, protests that "well-qualified and articulate evolutionary biologists . . . have been showing so visceral a hatred of Darwinian thinking that one suspects that their objections cannot be grounded purely in theory or evidence." Ruse has Stephen Jay Gould in his sights, and thinks that Marxism is part of the explanation. However, one thing that Ruse and Gould could agree on is the NOMA thesis: that science is a domain of human activity that does not overlap with the religious domain of human experience. The essential Darwinism is science, addressing empirical data and thereby integrating all biology via organic descent. Darwinism does not entail any position on "the reality of free will, the existence of purpose and direction in the universe, the origin of life, the foundations of human ethical behavior, and the moral and political implications of human differences." Consequently, not only is the ID Movement wrong, and not only are creationists wrong, but also many Darwinists are wrong to draw inferences about social, moral and cultural implications. Ruse "seeks "to defend Darwinism from false (or misguided) friends," those who bastardize or misapply Darwin's ideas to advance their own cultural agendas."
The problem for those of us who have not joined "the Darwinian Revolution" is that NOMA only works one way. It provides a barrier to stop creationists and ID people encroaching on science, but it completely fails to inhibit Darwinists from encroaching on issues to do with purpose, meaning, morality and human values. Gould, for example, exemplified this repeatedly: he often wrote about the contingencies of life and the purposeless of history.
What is lacking from Ruse's book appears to be any serious engagement with actual arguments of those who claim that Darwinism is inseparable from its "intellectual baggage". There's lots of stuff about science grinding to a halt if design thinking becomes "an acceptable part of scientists' explanatory tool kit." But there's no evidence! There's no acknowledgement that science emerged in a culture where design thinking was part of the explanatory tool kit! There's no acknowledgement that the ID community is pro-science. One wonders who this book is written for.

Defending Darwinism
Richard Bellon
American Scientist, March-April 2007.

Darwinism and Its Discontents. Michael Ruse. x + 316 pp. Cambridge University Press, 2006. $30.

The historian and philosopher Michael Ruse has spent decades explaining the nature of the Darwinian Revolution. The result has been a constant stream of innovative, provocative, informative, witty and entertaining scholarship. No other contemporary writer has Ruse's knack for seamlessly weaving together history, philosophy, theology and science.
In his latest salvo, Darwinism and Its Discontents, Ruse turns his good-natured pugnacity to a robust and comprehensive defense of the theory of evolution by natural selection as elaborated by Charles Darwin in On the Origin of Species (1859). [snip]

The songs of female birds have attracted very little research interest, with males made the focus of attention because of their plumage and their songs. "Males do the singing and females do the listening" is the preconception of most academic studies. The new research tested the hypothesis that female singing is ancestral and that absence (rather than presence) is the derived trait. The authors write: "To summarize (. . .), we demonstrated that song in females could be an ancestral condition, from which sexual selection may drive females of some species to give up singing." This appears to be an interesting example of evolutionary thinking inhibiting thought processes. "Garamszegi blames Charles Darwin for the oversight. 'He emphasised the importance of male sexual display, and this is what everyone has been looking at.'" Female bird song appears to be yet another case of the ancestral condition being anything but simple.

The evolution of song in female birds in Europe
Laszlo Zsolt Garamszegi, Denitza Zaprianova Pavlova, Marcel Eens, and Anders Pape Moller
Behavioral Ecology, 2007, 18: 86-96; doi:10.1093/beheco/arl047

Abstract: Bird song is usually regarded as an attribute of males. However, in some species, females may also produce songs even with comparable complexity to that of males. It has been suggested that female song may evolve due to similar selection pressures acting on males, but no study has yet investigated the evolution of female vocalization in a phylogenetic context, a gap that we intended to fill with this study. Based on standard descriptions in The Birds of Western Palearctic, we classified 233 European passerine species with respect to whether females are known to produce songs or not. We were more likely to find information on female song for species whose song is more studied than for less intensively studied species. When we traced information on female song on a phylogeny, we found that at least in 2 avian families, female song appeared to be the ancestral state, but such an ancestral state may be expected to be even deeper in the phylogenetic tree with increasing information on female song. In fact, we cannot exclude the possibility that the ancestor of European passerines had females capable of singing. In a preliminary comparative study based on the available data, we found some evidence that female song may have evolved under the influence of sexual selection as carotenoid-based dichromatism was positively related to female song among species. Our findings imply that due to publication bias, the evolutionary importance of female song is generally underestimated.

See also:
Are female songbirds evolution's unsung heroines?
New Scientist, 3 February 2007, page 17.

MALES do the singing and females do the listening. This has been the established, even cherished view of courtship in birds, but now some ornithologists are changing tune.
[snip]Females that sing have been overlooked, the team say, because either their songs are quiet, they are mistaken for males from their similar plumage or they live in less well-studied areas such as the tropics (. . .). Garamszegi blames Charles Darwin for the oversight. "He emphasised the importance of male sexual display, and this is what everyone has been looking at."
[snip]

A News & Views essay in Nature addresses a very significant question. The authors write: "Biologists agree that cyanobacteria invented the art of making oxygen, but when and how this came about remain uncertain." The measure of the problem is here: "Oxygenetic photosynthesis involves about 100 proteins that are highly ordered within the photosynthetic membranes of the cell. The main players are two molecular machines, photosystem I and photosystem II, that act as electrochemical solar cells. With the help of chlorophyll (...), they transform sunlight into electrical current."

Did the precursurs specialise in anoxygenic photosynthesis? There are bacteria that do this, but none have the two photosystems: it is a case of either photosystem I or photosystem II. "No tree of bacterial life can readily account for the observed distributions of the two sets of photosystem genes among the species. This has left biologists with little alternative but to suggest that genes encoding the photosystems have moved across species boundaries during evolution, a process called lateral gene transfer."

With the field apparently wide open for hypotheses, the authors comment approvingly on a recent paper by Mulkidjanian and colleagues suggesting that both photosystems arose in "a precursor of cyanobacteria - a 'protocyanobacterium' - later to be exported to other lineages by lateral transfer." The protocyanobacterium is hypothesised to have a regulatory switch, allowing it to go from photosystem I to photosystem II depending on the environment. The model appears to be one of degeneration: the anoxygenic photosynthesisers were derived by genetic system loss from the precursor.

The cyanobacteria also are associated with genetic loss: in their case the switch. "It would have been only a small step away from the cyanobacterial state of oxygenic photosynthesis provided that it underwent the right mutation - disabling the regulatory switch - and provided that this happened in the right environmental setting and at the right time."

The authors say: "The best evidence for this evolutionary scheme would be the discovery of a modern-day protocyanobacterium." The Editor's summary refers to this hypothetical organism as a "missing link".

However, instead of a gradual increase in complexity (which is most people's perception of a "missing link"), the authors favour a scenario that starts with all the complex machinery and changes thereafter either involve genetic loss or some "fine-tuning" of the existing system. This illustrates the problems of evolving irreducible complexity: if you want to produce an IC system like photosynthesis, you must first start with an IC system! Complexity has to be front loaded. Neo-darwinism cannot deliver this. Intelligent design can.

Out of thin air
John F. Allen and William Martin
Nature 445, 610-612 (8 February 2007) | doi:10.1038/445610a

The invention of oxygenic photosynthesis was a small step for a bacterium, but a giant leap for biology and geochemistry. So when and how did cells first learn to split water to make oxygen gas?

Flying insects need to have some feedback mechanisms to aid flight control. Two winged flies have halteres which "detect Coriolis forces and thereby mediate flight stability during maneuvers." Four winged insects do not have halteres but need ways of getting the appropriate sensory inputs. Dragonflies appear to use visual inputs to track their position, but this option is not open to night-flying insects. Until recently, it has been said that the moth's antennae are "primarily known as super-sensitive odor receptors--used to sniff out females and food from miles away--and researchers had hypothesized that they assist in flight only by acting as air flow sensors." But not now! The hawk moth's antennae have been found to perform the same role as the flies' halteres. They also experience Coriolis forces, detect rotational motion and relay this mechanosensory input to neural centers to maintain stability during flight.
As research progresses, the living world appears to be packed with complex specified information. In these cases, it is legitimate to include intelligent design as an option in the causal explanations under consideration. This is because, outside the natural world, complex specified information is always associated with intelligent causation. This point is worth making because the abstract refers to flying insects evolving "sophisticated sensory capabilities", the hind wings having been "modified into club-shaped, mechanosensory halteres" and the editors of Science refer to the halteres as "vestigial". The science of this paper needs to be distinguished from the Darwinian spin.

Antennal Mechanosensors Mediate Flight Control in Moths
Sanjay P. Sane, Alexandre Dieudonne, Mark A. Willis, and Thomas L. Daniel
Science 315, 9 February 2007: 863-866.

Abstract: Flying insects have evolved sophisticated sensory capabilities to achieve rapid course control during aerial maneuvers. Among two-winged insects such as houseflies and their relatives, the hind wings are modified into club-shaped, mechanosensory halteres, which detect Coriolis forces and thereby mediate flight stability during maneuvers. Here, we show that mechanosensory input from the antennae serves a similar role during flight in hawk moths, which are four-winged insects. The antennae of flying moths vibrate and experience Coriolis forces during aerial maneuvers. The antennal vibrations are transduced by individual units of Johnston's organs at the base of their antennae in a frequency range characteristic of the Coriolis input. Reduction of the mechanical input to Johnston's organs by removing the antennal flagellum of these moths severely disrupted their flight stability, but reattachment of the flagellum restored their flight control. The antennae thus play a crucial role in maintaining flight stability of moths.

See also:
Antennae as Gyroscopes by R. McNeill Alexander, Science 315, 9 February 2007: 771-772.

The Moth's Gyroscope by Brendan Borrell, ScienceNOW Daily News, 8 February 2007

Enzymes are really useful organic molecules, speeding up chemical reactions without being consumed. They are essential components of cells, and widely used in industrial processes. Getting the enzyme to work in the precise conditions required by many industrial applications has engaged the attention of many researchers: "there is a strong interest in developing experimental and theoretical methods for changing the pH-dependent characteristics of enzymes."
The authors of the paper abstracted below review these problems and explain that specific mutations in the active site can change the pH-activity profiles, but these mutations are actually very difficult to engineer. "The conclusion from two decade's work is that very specific point mutations in the active sites can change the pH dependence of enzymatic activity, but unless such specific active site point mutations are known (e.g., from comparative studies), there is not much hope of achieving a dramatic pH-activity profile shift with rational engineering methods. This somewhat disheartening conclusion is reached because mutations that give large pH-activity profile shifts normally are close to the active site and therefore likely to give mutant enzymes that are inactive or have dramatically reduced activity."
In ID circles, this would be described as "fine tuning", as a pointer to intelligent design, and an example of why random mutations and natural selection is an inappropriate mechanism to achieve the exquisite properties of the enzymes found in living things.

Redesigning protein pKa values
Barbara Mary Tynan-Connolly and Jens Erik Nielsen
Protein Science (2007), 16:239-249

The ability to re-engineer enzymatic pH-activity profiles is of importance for industrial applications of enzymes. We theoretically explore the feasibility of re-engineering enzymatic pH-activity profiles by changing active site pKa values using point mutations. We calculate the maximum achievable delta pKa values for 141 target titratable groups in seven enzymes by introducing conservative net-charge altering point mutations. We examine the importance of the number of mutations introduced, their distance from the target titratable group, and the characteristics of the target group itself. The results show that multiple mutations at 10Ã… can change pKa values up to two units, but that the introduction of a requirement to keep other pKa values constant reduces the magnitude of the achievable delta pKa. The algorithm presented shows a good correlation with existing experimental data and is available for download and via a web server at http://enzyme.ucd.ie/pKD.

This is from the introduction:
[snip] ... there is a strong interest in developing experimental and theoretical methods for changing the pH-dependent characteristics of enzymes. Advances have been made in the fields of protein engineering and directed evolution, and it is presently possible to routinely optimize the performance of enzymes for a range of conditions using either rational engineering or screening/selection-based approaches (Cherry et al. 1999; Farinas et al. 2001). Unfortunately, not all characteristics of enzymes are equally easy to optimize and successes in rational re-engineering of enzymatic pH-activity profiles remain few despite decades of studies on enzyme structure-function relationships.
[snip]

In this review essay, Ernst Haeckel is presented as the "archetypal German Romantic" who somehow managed to combine his artistic and philosophical interests with his work as Professor of Zoology. His espousal of Darwinism was accompanied by "a search for order, systematization and hierarchy that would reveal far more logic and purpose in life than a mere struggle for survival." His Biogenic Law ("organisms retrace their evolutionary history as they develop from an egg") "was an attempt to extract such a unifying scheme from the natural world." The reviewer finds tensions with science here, for Haeckel had a strong vision of what the world ought to be like. "Haeckel supplies a case study in the collision between Romanticism and science."
The subject of the notorious doctored embryo images is raised. The reviewer says "to my eye the evidence [of doctoring] looks pretty strong". However, the author of the book being reviewed suggests that the illustrations "instructed the reader how to interpret the shapes of nature properly."
Many of us think that generations of students have been cheated by being fed a diet of biogenic law, which is rooted in Haeckel's vision rather than in empirical data. The seriousness of the situation is shown by the way these errors have repeatedly surfaced, even in recent years. It really is time for Haeckel to be reinterpreted as a subversive influence in science. He was a gifted man, but he misused his gifts. He is an example of an ideologically motivated scholar who failed to subject his own ideas to proper critical scrutiny.

Painting the whole picture?
Philip Ball reviews Visions of Nature: The Art and Science of Ernst Haeckel by Olaf Breidbach
Nature 445, 486-487 (1 February 2007) | doi:10.1038/445486a

Darwin's one illustration in "On the Origin of Species" was of a branching "Tree of Life" (TOL). This has entered the mindset of evolutionary biologists and there has been a very real danger of confusing concept with reality. The authors of a discussion paper suggest that this concept has acted like a ladder to climb over an obstacle. "The TOL was thus the ladder that helped the community to climb the wall of acceptance and understanding of evolutionary process. But now that we have climbed it, we do not need this ladder anymore." Not only do we not need it, we are better off without it! "Holding onto this ladder of pattern is an unnecessary hindrance in the understanding of process (which is prior to pattern) both ontologically and in our more down-to-earth conceptualization of how evolution has occurred."
How can this be? Do the authors not know how important the TOL concept is to evolutionary biologists? They do. But they also know that it cannot be justified using empirical data. "The only data sets from which we might construct a universal hierarchy including prokaryotes, the sequences of genes, often disagree and can seldom be proven to agree."
But some argue that the nested hierarchy branching pattern is a proof of Darwinism. These people have something to learn from the authors, who write: "The notion that a tree pattern is the product of induction, obvious to any intelligent observer, is belied by most of the early history of systematics, during which quite different schemes seemed fully defensible." Also, that "hierarchical structure can always be imposed on or extracted from such data sets by algorithms designed to do so." For more on this, go here.
None of this, in the authors view, is to undermine evolutionary theory. The TOL concept "should not be an essential element in our struggle against those who doubt the validity of evolutionary theory, who can take comfort from this challenge to the TOL only by a wilful misunderstanding of its import." If this is a broadside against ID, it is an unfortunate choice of words. ID advocates are fond of the phrase "follow the evidence wherever it leads" and we applaud the authors for their analysis of the TOL concept. However, we want to encourage discussion of the import of this research and reserve the right to come to a different judgment. To describe this as "wilful misunderstanding" is actually opting out of scientific discourse.

Pattern pluralism and the Tree of Life hypothesis
W. Ford Doolittle and Eric Bapteste
Proc. Natl. Acad. Sci. USA, Early Edition 29 Jan 2007 | doi 10.1073/pnas.0610699104

Abstract: Darwin claimed that a unique inclusively hierarchical pattern of relationships between all organisms based on their similarities and differences [the Tree of Life (TOL)] was a fact of nature, for which evolution, and in particular a branching process of descent with modification, was the explanation. However, there is no independent evidence that the natural order is an inclusive hierarchy, and incorporation of prokaryotes into the TOL is especially problematic. The only data sets from which we might construct a universal hierarchy including prokaryotes, the sequences of genes, often disagree and can seldom be proven to agree. Hierarchical structure can always be imposed on or extracted from such data sets by algorithms designed to do so, but at its base the universal TOL rests on an unproven assumption about pattern that, given what we know about process, is unlikely to be broadly true. This is not to say that similarities and differences between organisms are not to be accounted for by evolutionary mechanisms, but descent with modification is only one of these mechanisms, and a single tree-like pattern is not the necessary (or expected) result of their collective operation. Pattern pluralism (the recognition that different evolutionary models and representations of relationships will be appropriate, and true, for different taxa or at different scales or for different purposes) is an attractive alternative to the quixotic pursuit of a single true TOL.

See also:
Cranston, M., Taking an axe to the Tree of Life, Dalhousie News, July 11 2007.

Echolocation calls in bats "have parallels with methods that engineers have adopted in commercial and military uses of sonar and radar." In other words, they appear to be "remarkable examples of 'good design'". The authors of a recent review article start by quoting Richard Dawkins: "In 'The Blind Watchmaker', Dawkins (1986) uses bat echolocation to illustrate features of 'good design' through evolution by natural selection." The whole paper is concerned with "adaptive aspects of call design" and it may be surprising to some that the findings will not be regarded as controversial by ID advocates. Adaptive change does occur in the natural world and there is no reason to think that the calls of bats are exempt.
However, there have always been issues about the origin of complex specified information, and this is to be found in the echolocation apparatus possessed by the bat. There are two completely different questions here: one relates to the design of echolocation calls and the other relates to the origin of the echolocation system. When the authors write: "Bat echolocation calls provide remarkable examples of 'good design' through evolution by natural selection," they are referring to the first question. It can be questioned whether the word "evolution" is appropriate (where it actually means adaptation) and it can be questioned whether natural selection is part of the story (for which no evidence is provided).
Picking up the point about natural selection, it should be noted that bats have brains that process and respond to sensory information. This introduces additional factors to the adaptation story. The significance of what is going on here can perhaps best be grasped by this comment:
"We suggest that engineers can learn from breakthroughs in our understanding of adaptive design in echolocation signals used by bats. For example, autonomously guided vehicles could use speed-dependent sonar signal designs that minimize localization errors, offering advances over the simple signals used in many current robotics applications".

Bat echolocation calls: adaptation and convergent evolution
Gareth Jones and Marc W. Holderied
Proceedings of the Royal Society B - Biological Sciences, Volume 274, Number 1612 / April 07, 2007: 905 - 912 | DOI: 10.1098/rspb.2006.0200

Abstract: Bat echolocation calls provide remarkable examples of 'good design' through evolution by natural selection. Theory developed from acoustics and sonar engineering permits a strong predictive basis for understanding echolocation performance. Call features, such as frequency, bandwidth, duration and pulse interval are all related to ecological niche. Recent technological breakthroughs have aided our understanding of adaptive aspects of call design in free-living bats. Stereo videogrammetry, laser scanning of habitat features and acoustic flight path tracking permit reconstruction of the flight paths of echolocating bats relative to obstacles and prey in nature. These methods show that echolocation calls are among the most intense airborne vocalizations produced by animals. Acoustic tracking has clarified how and why bats vary call structure in relation to flight speed. Bats using broadband echolocation calls adjust call design in a range-dependent manner so that nearby obstacles are localized accurately. Recent phylogenetic analyses based on gene sequences show that particular types of echolocation signals have evolved independently in several lineages of bats. Call design is often influenced more by perceptual challenges imposed by the environment than by phylogeny, and provides excellent examples of convergent evolution. Now that whole genome sequences of bats are imminent, understanding the functional genomics of echolocation will become a major challenge.

1. INTRODUCTION
In 'The Blind Watchmaker', Dawkins (1986) uses bat echolocation to illustrate features of 'good design' through evolution by natural selection. Since the design of the echolocation calls determines the type and quality of information contained in returning echoes, bats have evolved different signals to meet a diversity of sensory demands. Dawkins poses problems that echolocating bats experience, considers solutions that sensible engineers might consider and then arrives at solutions that bats have achieved. Often the solutions adopted by bats, for example, the use of broadband chirps for ranging, and the exploitation of Doppler shifts to calculate relative velocity, have parallels with methods that engineers have adopted in commercial and military uses of sonar and radar. Bat echolocation provides rich examples of good design because echolocation performance can be predicted from theory developed in acoustics and in sonar (and radar) engineering.
[snip]

The nested hierarchies that emerge from taxonomical studies have often been used as evidence supporting the concept of common descent (i.e. all organisms have evolved from an ancestral single cell). Hierarchies emerge from studies of morphology, from genetic similarities and from other data. However, as has recently been pointed out, "to create an evolutionary tree of relationships, one must make assumptions about the evolutionary process that produced the observed data." This highlights one of the major problems we have in the field of evolutionary biology: the assumptions are so deeply embedded that any alternative approach that seeks to stand outside the conventional paradigm is regarded with suspicion. This research paper has the merit of exploring these issues, although it does so without challenging the evolutionary mindset of phylogenetics. To those who doubt the claim that "No phylogeny estimation is assumption free", this paper deserves their close attention. Once it is recognised that "assumptions" are critical for the production of phylogenies, the evidences against common descent, identified by some (but not all) ID advocates, can then be considered on their merits. This is a scientific issue, worthy of wider debate.

Model use in phylogenetics: nine key questions
Scot A. Kelchner and Michael A. Thomas
Trends in Ecology & Evolution, Volume 22, Issue 2 , February 2007, Pages 87-94

Abstract: Models of character evolution underpin all phylogeny estimations, thus model adequacy remains a crucial issue for phylogenetics and its many applications. Although progress has been made in selecting appropriate models for phylogeny estimation, there is still concern about their purpose and proper use. How do we interpret models in a phylogenetic context? What are their effects on phylogeny estimation? How can we improve confidence in the models that we choose? That the phylogenetics community is asking such questions denotes an important stage in the use of explicit models. Here, we examine these and other common questions and draw conclusions about how the community is using and choosing models, and where this process will take us next.

Models in phylogenetics
No phylogeny estimation (see Glossary) is assumption free. To create an evolutionary tree of relationships, one must make assumptions about the evolutionary process that produced the observed data. Taken as a whole, these assumptions form a 'conceptual model' of character evolution with which estimates of evolutionary relationship are made. The conceptual model could include a mathematically explicit 'formal model' of character change, which is parameterized when applied to nucleotide or amino acid sequence data. It is this formal model that is referred to as the 'model' in phylogenetic literature (as it is here).
Phylogenetics cannot escape the use of conceptual models. Even those methods that do not formalize a model, and thus claim to be model-free (e.g. parsimony), make significant and sometimes incorrect assumptions about character evolution when estimating the amount of change between organisms 1, 2, 3 and 4. The growth of formal model use in phylogenetics, however, has created a noticeable level of concern in the community. In particular, we think that confusion about certain model qualities is contributing to controversies about model 'accuracy', complexity and development.
[snip]

Hailed as a "Progress" article by the editors of Nature, a group of evolutionary biologists have responded to "our current ignorance of intermediates" in the trajectories of evolutionary transformation. The key concept is the adaptive landscape, a device developed by Wright in 1932. The difference is that these authors want to use the concept to "explore the step-by-step evolution of molecular functions." They acknowledge implicitly that the adaptive landscape is theory-laden (rather than a fruit of empirical research), because from Darwin onwards, evidence of intermediates as organisms moving around an adaptive landscape is thin. They write: "Although Darwin developed a convincing rationale for their absence, he did realize that the lack of intermediates as proof leaves room for criticism." (It should be noted that not everyone finds Darwins's rationale for their absence convincing).
They also comment: "Indeed, in their opposition to evolution, the proponents of 'intelligent design' have seized on our current ignorance of intermediates." It should be stated that ID proponents do not have a blanket opposition to evolution! Adaptive change does occur and is non-controversial. The real issue is whether adaptive change leads to novel specified complexity and, in particular, to irreducibly complex systems. Furthermore, ID proponents are not arguing from "our current ignorance" but from our current knowledge!
What has this research achieved? "The experimental reconstruction of evolutionary intermediates and putative pathways has provided an exciting first look at molecular adaptive landscapes" and "The molecular systems interrogated so far represent only a start, but one with great potential to spark further exploration." There is no hint that molecular systems suggested to be irreducibly complex have been addressed in this research. It really is a "first look" and "only a start". It is perhaps an indictment of evolutionary biologists that it has taken so long to realise that there are real challenges to the adaptive landscape concept and that serious research is only in the initial stages.

Empirical fitness landscapes reveal accessible evolutionary paths
Frank J. Poelwijk, Daniel J. Kiviet, Daniel M. Weinreich and Sander J. Tans
Nature, 445, 383-386 (25 January 2007) | doi:10.1038/nature05451

Abstract: When attempting to understand evolution, we traditionally rely on analysing evolutionary outcomes, despite the fact that unseen intermediates determine its course. A handful of recent studies has begun to explore these intermediate evolutionary forms, which can be reconstructed in the laboratory. With this first view on empirical evolutionary landscapes, we can now finally start asking why particular evolutionary paths are taken.

"Seeing clearly underwater requires a special spherical lens with a high refractive index in the center but a lower index toward the edge. This gradation is achieved with progressively lower concentrations, from the lens's center outward, of proteins called crystallins." In recent research into the complexity of the squid eye, the variety of crystalline variants has been established, evoking the comment: "It's amazing how finely tuned the squid lens is to do its job." The researcher "is deeply impressed by cephalopod vision." "Indeed, she noted, the shipboard tests showed that the vampire squid's lens, which appeared early in the evolutionary history of cephalopods, "has a visual acuity better than in a state-of-the-art Zeiss dissecting microscope."
The image caption says that "Vampire squid lenses are designed for seeing details, even in virtual darkness." The real issue is whether that design is intelligent or blind.

Loopy Lens Proteins Provide Squid with Excellent Eyesight
Elizabeth Pennisi
Science 315, 26 January 2007: 456.

When Alison Sweeney wanted to learn about eye evolution, she went to sea. While the ship rolled beneath her, she dissected the eyes of squid freshly retrieved from 1000 meters below and tested how well each lens resolved the details of a panel of ever-narrower black and white stripes. Back at Duke University in Durham, North Carolina, as a graduate student in the lab of Sonke Johnsen, she combined those results with biochemical and modeling data on the optical and chemical properties of lens proteins to reconstruct the history of vision in cephalopods--squid, octopi, and their relatives. From just one ancestral lens protein--vertebrates started with several--these marine invertebrates have evolved lens-based eyesight more than once, Sweeney reported at the meeting.
[snip]

In recent years, microbes have emerged as life forms that do not fit easily into the Darwinian mould. "In the wild, microbes form communities, invade biochemical niches and partake in biogeochemical cycles. The available studies strongly indicate that microbes absorb and discard genes as needed, in response to their environment. Rather than discrete genomes, we see a continuum of genomic possibilities, which casts doubt on the validity of the concept of a 'species' when extended into the microbial realm." The research that has stimulated this new thinking concerns "horizontal gene transfer (HGT), the non-genealogical transfer of genetic material from one organism to another - such as from one bacterium to another or from viruses to bacteria." The implication is that neodarwinism is not a very useful model to work with. Also in the melting pot of new thinking is the "clearly documented optimization of the [genetic] code. Its special role in any form of life leads to the striking prediction that early life evolved in a lamarckian way, with vertical descent marginalized by the more powerful early forms of HGT." In their essay, Goldenfeld and Woese provide a challenging and stimulating challege for biologists to get out of the rut made by the "molecular reductionism that dominated twentieth-century biology".

Biology's next revolution
Nigel Goldenfeld and Carl Woese
Nature 445, 369 (25 January 2007) | doi:10.1038/445369a

Abstract: The emerging picture of microbes as gene-swapping collectives demands a revision of such concepts as organism, species and evolution itself.

One of the most fundamental patterns of scientific discovery is the revolution in thought that accompanies a new body of data. Satellite-based astronomy has, during the past decade, overthrown our most cherished ideas of cosmology, especially those relating to the size, dynamics and composition of the Universe.
Similarly, the convergence of fresh theoretical ideas in evolution and the coming avalanche of genomic data will profoundly alter our understanding of the biosphere - and is likely to lead to revision of concepts such as species, organism and evolution. Here we explain why we foresee such a dramatic transformation, and why we believe the molecular reductionism that dominated twentieth-century biology will be superseded by an interdisciplinary approach that embraces collective phenomena.
[snip]

We have known for some years that the energy cost of walking and running is related primarily to the work done by muscles to lift and move the limbs. Furthermore, energy cost is typically independent of running speed. This being so, it is of interest to look at the relative importance of leg length, and it can be predicted that longer legs reduce energy costs because "longer legs [-] reduce the amount of up-and-down movement in a stride, and so also reduce the force needed to push down with each step." A mathematical model for calculating energy costs for bipeds and quadrupeds has been developed by Herman Pontzer and published in The Journal of Experimental Biology. "'All things being equal, leg length is one of the major determinants of cost', says Pontzer, adding that if two animals are identical except for leg length, longer legs are more efficient."
The Nature news report of this paper has the title "These legs were made for walking", which evokes a design recognition response in the reader. However, intelligent design is not being considered. Rather, the emphasis is on adaptation driven by enhanced energy efficiency. "The fossil record shows that two million years ago, there was a big increase in leg length in early humans," says Pontzer. He suggests that a reason for this increase could have been the energy saved by having longer legs."
It should be noted that the link between energy efficiency and leg lengthening is not a very compelling argument because the Darwinian approach to adaptation has to find a link with passing on ones genes (and this requires some dubious just-so stories). More importantly, it is good practice in science to consider multiple hypotheses and to find ways of evaluating them. One often notes arguments by Darwinians making the claim: "an intelligent designer would not do it this way", always leading to rejection of the intelligent design hypothesis. Here is a case where there are good reasons, supported by a mathematical model, why an intelligent designer would do it that way. So, one asks, should the evidence for an ID explanation of why humans have legs that are relatively long be considered for evaluation within science?

Predicting the energy cost of terrestrial locomotion: a test of the LiMb model in humans and quadrupeds.
Pontzer, H.
Journal of Experimental Biology, 2007, 210, 484 -494.

Summary: The energy cost of terrestrial locomotion has been linked to the muscle forces generated to support body weight and swing the limbs. The LiMb model predicts these forces, and hence locomotor cost, as a function of limb length and basic kinematic variables. Here, I test this model in humans, goats and dogs in order to assess the performance of the LiMb model in predicting locomotor cost for bipeds and quadrupeds. Model predictions were compared to observed locomotor cost, measured via oxygen consumption, during treadmill trials performed over a range of speeds for both walking and running gaits. The LiMb model explained more of the variation in locomotor cost than other predictors, including contact time, Froude number and body mass. The LiMb model also accurately predicted the magnitude of vertical ground forces. Results suggest the LiMb model reliably links locomotor anatomy to force production and locomotor cost. Further, these data support the idea that limb length may underlie the scaling of locomotor cost for terrestrial animals.

See also:

Blackburn, L. LONG LIMBS COST LESS, Journal of Experimental Biology, 210, 0ii (2007)

Odling-Smee, L., These legs were made for walking. Model opens up research into efficiency of motion. news@nature.com, 19 January 2007; | doi:10.1038/news070115-9

The two mechanisms of colouration in animals are pigmentation and highly periodic ultrastructure. Whiteness requires an aperiodic ultrastructure so that incident sunlight can be scattered. Material scientists have recognised this need for scattering and have produced surface coatings with the appropriate ultrastructure to yield high whiteness. Recent studies of the unusually brilliant white beetle Cyphochilus reveals that the thickness of the scattering layer is only 5 micrometers, at least two orders of magnitude thinner than man-made coatings with the same degree of whiteness. The scales of the beetle contain a sparse, random network of cuticular filaments that are optimal for the efficient scattering of light. Senior author Peter Vukusic commented that were the filaments crowded more or crowded less, the whiteness would be reduced: "It's a fine line, but this beetle seems to have achieved a good compromise." This research points the way to a new generation of thin optically white materials.
We hear arguments from Darwinists that design in nature is "cobbled together" by the unguided processes of mutation and natural selection. However, whilst a few examples of darwinian design appear convincing, most are definitely not! The discipline of biomimetics is testimony to exquisite design in nature, giving inspiration to scientists and engineers for innovative new materials and products. Intelligent agency is the rationale for exquisite design, just as the "blind watchmaker" is the rationale for "cobbled-together" design.

Brilliant Whiteness in Ultrathin Beetle Scales
Pete Vukusic, Benny Hallam, and Joe Noyes
Science 315, 19 January 2007: 348.

Abstract: The colored appearances of animals are controlled by pigmentation, highly periodic ultrastructure, or a combination of both. Whiteness, however, is less common and is generated by neither of these, because it requires scattering processes appropriate for all visible wavelengths. We report whiteness resulting from a three-dimensional photonic solid in the scales of Cyphochilus spp. beetles. Their scales are characterized by their exceptional whiteness, their perceived brightness, and their optical brilliance, but they are only 5 micrometers thick. This thickness is at least two orders of magnitude thinner than common synthetic systems designed for equivalent-quality whiteness.

See also: Cartwright, J., Tropical beetle has the brightest whites, PhysicsWeb, Jan 18 2007.
This essay has images of the beetle, the internal structure of the scales, and an image of several beetles to demonstrate the unusual whiteness of Cyphochilus.

"A major question in developmental biology is, How do cells know where they are in the body? For example, skin cells on the scalp know to produce hair, and the skin cells on the palms of the hand know not to make hair." Significant progress on this question is published in PloS Genetics. "By comparing cells from 43 unique positions that finely map the entire human body, the authors discovered that cells utilize a ZIP-code system to identify the cell's position in the human body." Just as a zip code has been designed to inform human users of positional information (postal addresses), the developing organism has just such a system to orchestrate its own construction. The authors comment: "A particularly attractive and distinctive feature of the positional identity model is the parsimonious use of molecular entities to construct the system, leading to universality of the coordinate system."
There are some massive challenges here for neodarwinists to offer any coherent thoughts on the origin of such an information-rich system. This is yet another case of research leading to the uncovering of deeper and deeper levels of complex specified information that is best understood by reference to purposeful intelligent design.
Furthermore, there are important questions about where these positional identity markers come from. It is a characteristic of all cells in an organism that they exhibit genomic equivalence. An inference can be made that activating particular "zip codes" requires information external to the DNA of the organism. This suggests a significant epigenetic input during development. In their discussion, the authors write: "the organization of differentiated fibroblasts based on superimposed positional gene expression patterns strongly implicates epigenetic mechanisms that stably specify fibroblast differentiation."
Neodarwinism has locked itself into the dogma that DNA is the key to life. They approach cell biology, developmental biology and evolutionary biology from within this paradigm. However, every time we find indications that information resides outside the DNA of the cell, the neodarwinist model becomes increasingly outdated. Interestingly, ID biologists have identified this as an important area for research, which is yet another indication that ID has much to offer the biological community.

Anatomic Demarcation by Positional Variation in Fibroblast Gene Expression Programs
John L. Rinn, Chanda Bondre, Hayes B. Gladstone, Patrick O. Brown, Howard Y. Chang.
PLoS Genet 2(7): e119 DOI: 10.1371/journal.pgen.0020119

Synopsis: A major question in developmental biology is, How do cells know where they are in the body? For example, skin cells on the scalp know to produce hair, and the skin cells on the palms of the hand know not to make hair. Overall, there are thousands of different cell types and each has a unique job that is important to overall organ function. It is critical that, as we grow and develop, each of these different cells passes on the proper function from generation to generation to maintain organ function. In this study, the authors present a model that explains how cells know where they are in the body. By comparing cells from 43 unique positions that finely map the entire human body, the authors discovered that cells utilize a ZIP-code system to identify the cell's position in the human body. The ZIP code for Stanford is 94305, and each digit hones in on the location of a place in the United States; similarly, cells know their location by using a code of genes. For example, a cell on the hand expresses a set of genes that locate the cell on the top half of the body (anterior) and another set of genes that locates the cell as being far away from the body or distal and a third set of genes that identifies the cell on the outside of the body (not internal). Thus, each set of genes narrows in on the cell's location, just like a ZIP code. These findings have important implications for the etiology of many diseases, wound healing, and tissue engineering.

Leaf insects are a very small percentage of the order Phasmatodea, and are evidently very specialized in their mimicry behaviour and morphology. Rare fossils of leaf insects are found, but a recent report documents an example of a male specimen that is "exquisitely preserved and displays the same foliaceous appearance as extant male leaf insects." This fossil leaf insect "bears considerable resemblance to extant individuals in size and cryptic morphology, indicating minimal change in 47 million years. This absence of evolutionary change is an outstanding example of morphological and, probably, behavioral stasis."

Stasis is one of those characteristics found in the fossil record that gained prominence when punctuated equilibrium was proposed, but has not generally developed theoretically since 1972. The missing emphasis in the discussion is information. An ID perspective at least allows some aspects of stasis to be approached in an original and constructive way.

The first fossil leaf insect: 47 million years of specialized cryptic morphology and behavior
Sonja Wedmann, Sven Bradler, and Jes Rust.
Proceedings of the National Academy of Sciences, January 9, 2007, 104: 565-569. | 10.1073/pnas.0606937104

Abstract: Stick and leaf insects (insect order Phasmatodea) are represented primarily by twig-imitating slender forms. Only a small percentage ( 1%) of extant phasmids belong to the leaf insects (Phylliinae), which exhibit an extreme form of morphological and behavioral leaf mimicry. Fossils of phasmid insects are extremely rare worldwide. Here we report the first fossil leaf insect, Eophyllium messelensis gen. et sp. nov., from 47-million-year-old deposits at Messel in Germany. The new specimen, a male, is exquisitely preserved and displays the same foliaceous appearance as extant male leaf insects. Clearly, an advanced form of extant angiosperm leaf mimicry had already evolved early in the Eocene. We infer that this trait was combined with a special behavior, catalepsy or "adaptive stillness," enabling Eophyllium to deceive visually oriented predators. Potential predators reported from the Eocene are birds, early primates, and bats. The combination of primitive and derived characters revealed by Eophyllium allows the determination of its exact phylogenetic position and illuminates the evolution of leaf mimicry for this insect group. It provides direct evidence that Phylliinae originated at least 47 Mya. Eophyllium enlarges the known geographical range of Phylliinae, currently restricted to southeast Asia, which is apparently a relict distribution. This fossil leaf insect bears considerable resemblance to extant individuals in size and cryptic morphology, indicating minimal change in 47 million years. This absence of evolutionary change is an outstanding example of morphological and, probably, behavioral stasis.

See also:
Scientists discover first fossil of a leaf insect
physorg.com, 8 February 2007

The hawkmoth, Manduca sexta, used CO2 sensors to assess how much nectar it is likely to get from the flowers of Datura wrightii. Honeybees use CO2 sensors to assess the quality of air in their hives: if too high, they show a fanning response. It is not clear why Drosophila flies need CO2 sensors, but they certainly have them and new research has uncovered the architecture of the sensors.
Two genetic receptors are involved: Gr21a and Gr63a. Both are needed for the sensor to work, and they are only sensitive to CO2. “The simplest scenario is that the two receptors form a complex that binds to CO2. It is possible, however, that other molecules are also required.” In a News & Views essay, Rachel Wilson writes: “Considered as tiny chemical sensors, these neurons are wonders of natural engineering.”
There is an important distinction to be made between engineering that is found in the natural world and engineering that is the result of natural processes (law and chance). To have two complex neurons to be present to bind with CO2 and then to have the rest of the circuitry to communicate their signal to the brain of the insect bears all the signs of complex specified information (which in other contexts is associated with intelligent design).
Ths research does appear to have great potential for tackling malaria, because mosquitos are known to use CO2 from animal breath as an arousing stimulus. “If this molecular insight permits the design of novel mosquito deterrents, it could have a major impact on global health.” It is curious that scientific publication allows “design” to be invoked for knocking out one or both of the relevant neurons, but not for the origin of the neurons in the first place!

Two chemosensory receptors together mediate carbon dioxide detection in Drosophila
Walton D. Jones, Pelin Cayirlioglu, Ilona Grunwald Kadow and Leslie B. Vosshall
Nature 445, 86-90 (4 January 2007) | doi:10.1038/nature05466

Blood-feeding insects, including the malaria mosquito Anopheles gambiae, use highly specialized and sensitive olfactory systems to locate their hosts. This is accomplished by detecting and following plumes of volatile host emissions, which include carbon dioxide (CO2)1. CO2 is sensed by a population of olfactory sensory neurons in the maxillary palps of mosquitoes2, 3 and in the antennae of the more genetically tractable fruitfly, Drosophila melanogaster4. The molecular identity of the chemosensory CO2 receptor, however, remains unknown. Here we report that CO2-responsive neurons in Drosophila co-express a pair of chemosensory receptors, Gr21a and Gr63a, at both larval and adult life stages. We identify mosquito homologues of Gr21a and Gr63a, GPRGR22 and GPRGR24, and show that these are co-expressed in A. gambiae maxillary palps. We show that Gr21a and Gr63a together are sufficient for olfactory CO2-chemosensation in Drosophila. Ectopic expression of Gr21a and Gr63a together confers CO2 sensitivity on CO2-insensitive olfactory neurons, but neither gustatory receptor alone has this function. Mutant flies lacking Gr63a lose both electrophysiological and behavioural responses to CO2. Knowledge of the molecular identity of the insect olfactory CO2 receptors may spur the development of novel mosquito control strategies designed to take advantage of this unique and critical olfactory pathway. This in turn could bolster the worldwide fight against malaria and other insect-borne diseases.

See also: Wilson, R.I., Scent secrets of insects, Nature 445, 30-31 (4 January 2007) | doi:10.1038/445030a

Close examination of the bacterial flagellum motor and the ATPsynthase motor reveals many similarities, sufficient (say the authors) to “imply an evolutionary relation between the flagellum and F0F1-ATPsynthase and a similarity in the mechanism between FliI and F1-ATPase despite the apparently different functions of these proteins”.
But is structural similarity a defining mark of an evolutionary relationship? On this basis, the octopus eye has to have an evolutionary relationship with the mammalian eye. Examples described as convergent evolution abound, and in these cases Darwinians invoke natural selection as the driver. Why is this not an option for molecular machines? The authors are so familiar with these complex systems that they know the absurdity of the convergence option: with parallel incremental changes under the influence of selection forces.
So, an “evolutionary relationship” is the only option – or is it? Structural similarities due to intelligent design should also be evaluated as a hypothesis (but is rarely even considered as an option because naturalism is the dominant philosophy in science).

Structural similarity between the flagellar type III ATPase FliI and F1-ATPase subunits
Katsumi Imada, Tohru Minamino, Aiko Tahara, and Keiichi Namba
Proc. Natl. Acad. Sci. USA, Published online before print January 3, 2007, doi: 10.1073/pnas.0608090104

Abstract: Construction of the bacterial flagellum in the cell exterior proceeds at its distal end by highly ordered self-assembly of many different component proteins, which are selectively exported through the central channel of the growing flagellum by the flagellar type III export apparatus. FliI is the ATPase of the export apparatus that drives the export process. Here we report the 2.4 Å resolution crystal structure of FliI in the ADP-bound form. FliI consists of three domains, and the whole structure shows extensive similarities to the α and β subunits of F0F1-ATPsynthase, a rotary motor that drives the chemical reaction of ATP synthesis. A hexamer model of FliI has been constructed based on the F1-ATPase structure composed of the α 3 β 3 γ subunits. Although the regions that differ in conformation between FliI and the F1- α / β subunits are all located on the outer surface of the hexamer ring, the main chain structures at the subunit interface and those surrounding the central channel of the ring are well conserved. These results imply an evolutionary relation between the flagellum and F0F1-ATPsynthase and a similarity in the mechanism between FliI and F1-ATPase despite the apparently different functions of these proteins.