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.