Science Literature

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.