Literature

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Compare this with Behe's internet response:

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

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

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

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

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

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

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

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

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

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

See also:

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

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

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

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

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

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

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

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

Biofilms in the large bowel suggest an apparent function of the human vermiform appendix
R. Randal Bollinger, Andrew S. Barbas, Errol L. Bush, Shu S. Lin and William Parker
Journal of Theoretical Biology, In Press, Available online 7 September 2007.

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

See also:

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

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

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

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

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

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

See also:

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

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

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

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

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

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

See also:

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

See also:

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

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

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

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

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

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

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

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

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

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

See also:

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

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

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

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

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

See also:

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