Science Literature

In a Commentary essay, Carl Woese and Nigel Goldenfeld provide an analysis of biological thought that differs profoundly from that presented by those celebrating the Bicentenary of Darwin's birth and, incidentally, the recently published AP Biology Standards.

"This is the story of how biology of the 20th century neglected and otherwise mishandled the study of what is arguably the most important problem in all of science: the nature of the evolutionary process. This problem [ . . ] became the private domain of a quasi-scientific movement, who secreted it away in a morass of petty scholasticism, effectively disguising the fact that their primary concern with it was ideological, not scientific."

Procrustes was slain on his own bed by Theseus: an analogy for the microbial world liberating biology from the "Procrustean bed of dogma" that goes under the name of neo-Darwinism (source here)

The authors want to see biology liberated "from the Procrustean bed of dogma on which it has been cast for so long". A radical overhaul is warranted. The issues are comparable to the "transformation of the physical sciences" in the early 20th Century. This is when the foundations of Newtonian mechanics were undermined and the certainties of that approach were replaced by relativity theory and the statistical uncertainties of quantum mechanics. Just as physics then had to accept that there was much more to learn, so also biology today.

"Although 2009 will be marked by a plethora of celebrations on the subject of evolution, most of the attention is being bestowed on the personalities and historical circumstances surrounding the theory of natural selection, as if this and its synthesis with genetics in the first decades of the 20th century marks the culmination of the theory of evolution. It does not. The MMBR (Microbiology and Molecular Biology Reviews) community has been at the forefront of defying the standard wisdom; and thus it is, in many ways, its story that we now wish to tell."

This blog will refer to some of the themes developed in the essay. The first of these is reductionism. Newtonian physics is described as "deterministic reductionism, and safe in its completeness" and there is a direct link to neo-Darwinism: "the petrified form of evolution that emerged from the modern synthesis". This had adverse consequences for the study of living things: "Organisms, like pinatas, were there to be burst open in order to get at the (biochemical) goodies within - a view of microorganisms that, with justification, persists today among some subfields of microbiology."

"The discipline [of microbiology] clearly had a foundational issue. Biochemistry was simply not sufficient to serve as the basis upon which the study of the microbial world could rest. Neither the organism nor its ecology could be satisfactorily encompassed by this reductionistic perspective - an objection that could also be raised against all the sum-of-the-parts disciplines, such as molecular biology and genetics."

The second theme is the prokaryote hypothesis. In 1962, Stanier and van Niel sought to move microbiology on by declaring all bacteria to be prokaryotes. In their view, all bacteria shared a common cellular organisation and this allowed a common ancestry to be inferred. Woese and Goldenfeld write: "This notion, that all bacteria shared a common cellular organization, was to stand firmly in the path of microbiology's development for the better part of half a century." In their view, the assertion that "all bacteria were prokaryotes was an eminently testable hypothesis", but the microbiology community perceived the hypothesis as "the answer". Indeed, it became an axiom of microbiology. The test of the hypothesis came when Woese looked much more closely at the molecular properties of bacteria and recognised two distinct types: the archaebacteria and the eubacteria. Subsequent research widened the gap when it was realised that there was actually no common cellular organisation.

"[T]here were [. . .] many fundamental molecular properties in which the bacteria (declared to be synonomous with prokaryotes by Stanier and van Niel) differed from one another. The "archaebacteria (Archaea) had finally appeared on the scene, and their molecular properties were as distinct from those of the "eubacteria" (Bacteria) as either one's were from those of the Eukarya. The prokaryote hypothesis had been proven false."

The third theme relates to the concept of the gene. The root problem here is reductionism, but the consequences for genetics have been far-reaching. The mindset of the scientists was highly mechanistic.

"In this Newtonian world, the study of biology becomes a highly derived subdiscipline of the basic science of physics - in effect, an engineering enterprise; there is nothing "fundamental" about it. Biology becomes a study of machines made of assemblages of parts and the interactions among them, an exercise in describing, but not explaining, things as they are. [. . .] A discipline whose perspective is that of classical 19th century physics is inherently incapable of dealings with the problems of a nonlinear world, which is nonreductionist, nondeterministic (acausal), and works in terms of fields and emergent properties, not a static world of particles with linear relationships among them."

As a result, genetics was dominated by concepts of templating and translating that underplayed the "incredible and complex mechanism that can extract information (pattern) from the sequence of one type of macromolecule and "express", i.e., store, most of it as the structure (sequence pattern) of another macromolecule of a different type". Neo-Darwinism cannot deliver answers, because its vision of biology is fundamentally flawed.

"This turn in the road (of applying reductionist metaphysics to the understanding of the biological world) would become a superhighway that dead-ended before it reached molecular biology's ultimate goal, that of understanding the essence of "livingness" and directly answering the question of how molecules come to life."

This sense of biology entering a cul-de-sac is pronounced. Woese and Goldenfeld want to see a different approach to evolutionary thinking: for them, it is the key to moving the discipline forward. Their perception of the Modern Synthesis is that it has led to (a) stagnation (no new ideas) and to (b) safeguarding the consensus (looking after vested interests).

"The basic understanding of evolution, considered as a process, did not advance at all under its tutelage. The presumed fundamental explanation of the evolutionary process, "natural selection", went unchanged and unchallenged from one end of the 20th century to the other. Was this because there was nothing more to understand about the nature of the evolutionary process? Hardly! Instead, the focus was not the study of the evolutionary process so much as the care and tending of the modern synthesis. Safeguarding an old concept, protecting "truths too fragile to bear translation" is scientific anathema."

There is much more in this essay - happily it is open access. The vision of Woese and Goldenfeld warrants further discussion, as do their comments on the significance of horizontal gene transfer. However, this blog has an educational focus. Why are educationalists so keen to make neo-Darwinism the central pillar of evolutionary theory? Why are the AP Biology Standards affirming things that are here so vigorously contested? Why should students be given the impression that evolutionary theory is robust and settled? Woese and Goldenfeld comment:

"What makes the treatment of evolution by biologists of the last century insufferable scientifically is not the modern synthesis per se. Rather, it is the fact that molecular biology accepted the synthesis as a complete theory unquestioningly - thereby giving the impression that evolution was essentially a solved scientific problem with its roots lying only within the molecular paradigm."

Returning to the Procrustean bed of dogma, it is important to realise the significance of this imagery. Biology has been lying on a bed which has led to emasculation. To draw on the other images in the title, biology needs to be delivered from the Scylla of Molecular Biology and the Charybdis of the Modern Synthesis. These theoretical constructs have had serious negative effects on biological science, and yet we still teach them uncritically! In summary:

"Dogmatic thinking has prevailed all too often in our account, with disastrous consequences for the progress of the fields of microbiology, molecular biology, and the study of the evolutionary process. It led to the stagnant and scientifically invalid notion of the prokaryote; it led to the redefinition of the problem of the gene; and through a slavish adherence to the modern evolutionary synthesis, it led to a premature declaration of victory in the struggle to understand the evolutionary process."

How the Microbial World Saved Evolution from the Scylla of Molecular Biology and the Charybdis of the Modern Synthesis
Carl R. Woese and Nigel Goldenfeld
Microbiology And Molecular Biology Reviews, 73(1), March 2009, 14-21 | doi:10.1128/MMBR.00002-09

There must be no barriers for freedom of inquiry. There is no place for dogma in science. The scientist is free, and must be free to ask any question, to doubt any assertion, to seek for any evidence, to correct any errors.
-J. Robert Oppenheimer, The Open Mind, p. 114 (1955)

First sentence: This is the story of how biology of the 20th century neglected and otherwise mishandled the study of what is arguably the most important problem in all of science: the nature of the evolutionary process.

See also:

Tyler, D. Teaching goals for Advanced Placement Biology, ARN Literature Blog (21 September 2009)

Many schools in the US are introducing the Advanced Placement (AP) program which sets out to mirror "an introductory college course". Schools perceive these courses as "a marker for a quality education". Inevitably, teething problems have arisen and have highlighted issues of a pedagogological nature.

"[Reports have found a] flawed approach to teaching science: too much emphasis on facts and memorization and too little attention to the underlying concepts and how science is actually practiced."

With some topics, critical thinking is conflated with knowing the right answers! (source here)

Particular problems arose because AP exam successes give exemption from other introductory courses. Colleges wanted everything covered by those courses to be incorporated in the relevant AP course. One of the organisers said: "AP teachers have had to resort to memorization and factual recall as a way to cover everything that could be on the exam". This is, by most accounts, not the way to design courses. Happily the situation is changing.

The revised approach for science is built on understanding concepts, direct experience of experimentation via laboratory work, and developing an appreciation of how scientists conduct research.

"The new courses will emphasize conceptual knowledge, updated regularly and learned by doing, along with teaching how scientists ask and answer important questions."

A chemistry teacher is quoted to show the differences between rote-learning and the revised approach:

Instead of drilling students on how to apply a particular algorithm, he says, "I'd much rather that students are able to explain the underlying concept to me, in English, and show me they understand something about how nature builds the stuff around us."

It has to be said that such comments echo discussions that have been taking place over many years in colleges of education. These contemporary developments in the US are a reflection on the bureaucratisation of education and the need to tick the right boxes when developing and delivering courses. Another factor may be the way the media presents intellectual prowess: competitions to find the best 'brain' or the person with the most expertise invariably probe knowledge that is memorised. Concepts, and the application of concepts, do not lend themselves to true/false responses needed to sustain the interest of viewers or listeners.

Biology is reported to be the first of the AP Science sources to be revised according to the new emphasis. The big ideas for this discipline have been identified and these set the agenda for structuring the experiences of students.

"[the] big ideas [. . .] include evolution, the storage and transmission of information, and the use of energy to carry out essential functions. That's followed by a series of core principles. One new wrinkle links content knowledge to the actual practice of science. The final layer is a set of performance expectations: what students should know, understand, and be able to do to demonstrate their mastery of the subject."

Of the three big ideas listed, the link between concept and application is straightforward for two of them. Information storage and transmission provides a solid foundation for genetics, developmental biology and systems biology. Similarly, the production of energy and its use provides the conceptual framework for the operation of cellular machines, physiology and metabolism. There is a problem, however, with evolution as a "big idea". This is partly because the word has a fuzzy meaning and is understood in different ways by different people. It is also partly because evolution belongs to the realm of history whereas the other two big ideas are rooted in empiricism. Historical science and empirical science do not have identical methodologies and students grappling with these ideas need to be able to recognise the differences when they link "content knowledge to the actual practice of science". There are serious issues here: why do so many biologists think that observations of peppered moths or deer mice have a bearing on the origin of moths or mice? The answer to this question is: they have not learned the skill of linking the "actual practice of science" with relevant theoretical concepts.

The debate for our consideration is not 'should evolution be taught?' but 'how should evolution be taught?' It is not that evolutionary theory should be dropped (as controversial) but that evolutionary theory should be taught critically - in a way that makes same use of critical faculties as is normal for the empirical sciences. Some of us regard Design as a 'big idea' in biology. Nothing in biology makes sense except in the light of design. We find it strange that whilst design is often mentioned by advocates of evolution, it is only done to reject it summarily. These evolutionists have no intention of finding the best expression of design thinking and subjecting it to critical scrutiny - they are generally content to speak of Rev William Paley or the writings of Charles Darwin. Modern exponents of design thinking are rarely mentioned and their analyses of evidence are typically deemed not worthy of consideration. We consider this situation unhealthy for science. Evolutionists (generally of a Darwinian mindset) are claiming a central role for evolutionary concepts but are resisting all attempts to rigorously scrutinise their claims.

The new standards for AP courses are to be welcomed in principle. The emphasis on concepts and their application to the real world is the right way to go. However, the biology standards have a yielded too much ground to doctrinaire Darwinism. For the details, go here. The AP Biology standards have statements like:

* Natural selection is the major driving mechanism of evolution because the essential features of the mechanism contribute to the change in the genetic makeup of a population over time.
* Although natural selection is usually the major mechanism for evolution, genetic variation in populations can occur through other processes, including mutation, genetic drift, sexual selection and artificial selection.
* Scientific evidence - including emergent diseases, chemical resistance and genomic data - supports the idea that evolution occurs for all organisms and that evolution explains the diversity of life on the planet.
* New species arise when two populations diverge from a common ancestor and become reproductively isolated.

All these statements can be challenged scientifically - yet the AP document presents them in the sections headed "enduring understanding". This is where the intention to develop the critical skills of students is not matched by the text of the standards. Students taking AP Biology courses will be delivered a non-negotiable package of Neo-Darwinian evolutionary theory. Let's hope the students are alert to these issues: after being encouraged to develop critical skills in the empirical sciences, they learn that these skills must not be used to question the Darwinian framework for understanding the diversity and unity of life!

Revisions to AP Courses Expected to Have Domino Effect
Jeffrey Mervis
Science, 325, 18 September 2009: 1488-1489.

First para: Last month, Jeffrey Lamb began teaching Advanced Placement (AP) chemistry for the first time at Woodmont International Baccalaureate High School in Piedmont, South Carolina. The public school's decision to offer the course reflects the explosive growth of the AP program, a suite of 38 courses intended to mirror an introductory college course.

See also:

Tyler, D., Liberating biology from a Procrustean bed of dogma, ARN Literature blog (25 September 2009)

A cave in the Republic of Georgia has yielded over 1000 fragments of flax that are being interpreted as the oldest example of humans using textile fibres in utilities and garments. The samples come from various dated horizons, the oldest considered to be about 34,000 years before the present. Whereas other archaeological sites of a similar (slightly younger) age have provided impressions of textile materials, the new find pin-points flax and carries the implications of humans gathering the stems, removing the fibres, processing the fibres to make yarns and then using the yarns to either sew skins, to create ropes or even to weave textiles for use in garments.

"This was a critical invention for early humans. They might have used this fiber to create parts of clothing, ropes, or baskets - for items that were mainly used for domestic activities," says Bar-Yosef. "We know that this is wild flax that grew in the vicinity of the cave and was exploited intensively or extensively by modern humans."

A selection of fibres from Dzudzuana Cave, Georgia (Source here)

There are two evidences to support weaving. The first is that a "few of the fibers are colored and appear to have been dyed". "The color range includes yellow, red, blue, violet, black, brown, green, and khaki." The range of colours suggests intentional colouration rather than chance contact with colourants. The second line of evidence relates to organisms that are associated with decaying textiles, as well as the "spores of the Chaetomium fungus, usually growing on clothes and other textiles and unfortunately destroying them". Michael Balter summarises this point as follows:

"The team thinks the flax was used to make garments as well as woven baskets, because it was associated with skin beetles and moth larvae that infest decaying textiles, as well as spores of a fungus known to grow on clothes. The team also found a few twisted and colored fibers of wool from a goat species whose bones were found in the cave."

The significance of the find is that it contributes to the discussion of "when hominins started looking modern and when they began acting modern". In a blog on reports of shells used as jewellery, Michael Balter describes two positions:

"[S]ome scientists [. . .] argue that modern human cognition, including language and other complex symbolic behavior, needed the additional kick-start of a genetic mutation about 50,000 years ago. Yet an increasing number of researchers have come to think that Homo sapiens was capable of modern behavior from the very beginning of its history. Whether those behaviors show up in the archaeological record, these researchers say, depends on a variety of factors unrelated to genetics, such as how big and widespread early human populations were and what environmental challenges they faced."

Ultimately, underlying philosophies influence the way researchers think: some are evolutionary gradualists and predict the slow transformation of culture from animal to human traits. These people are happy to invoke a mutation that switches on self-awareness, or consciousness, or similar. A mutation is, after all, a link in the chain constructed by gradualism. Others go with punctuated equilibrium and abrupt appearance. They typically do not have a mechanism, but they argue they are doing justice to the evidence. It hardly needs to be said, but the history of studies of Palaeolithic culture shows that examples of human traits and human behaviour are being found earlier and earlier in time. The newly reported research is just the latest example of this.

ID thinking has a bearing on these debates. Humanity cannot and should be explained purely in terms of physics and chemistry. Yet Darwin's portrayal of the descent of man was calculated to by-pass design. Evolutionary gradualists are in the Darwinian tradition and they bring this philosophical position to their science. They are not free to follow the evidence wherever it leads, because they 'know' that complexity has to be constructed incrementally. ID does not forcefit design to be the solution to every question researchers ask, but it does allow non-naturalistic avenues to be explored. If Homo sapiens is the product of design, then our species should have been capable of modern behavior from the very beginning of its history. Furthermore, if research confirms modernity, then we do not need to apologise for not invoking a material cause. Those waving a magic wand are those who conjour up a "mutation" or some other simplistic device to transform an ape into a human.

30,000-Year-Old Wild Flax Fibers
Eliso Kvavadze, Ofer Bar-Yosef, Anna Belfer-Cohen, Elisabetta Boaretto, Nino Jakeli, Zinovi Matskevich, and Tengiz Meshveliani
Science, 325, 11 September 2009: 1359.

A unique finding of wild flax fibers from a series of Upper Paleolithic layers at Dzudzuana Cave, located in the foothills of the Caucasus, Georgia, indicates that prehistoric hunter-gatherers were making cords for hafting stone tools, weaving baskets, or sewing garments. Radiocarbon dates demonstrate that the cave was inhabited intermittently during several periods dated to 32 to 26 thousand years before the present (kyr B.P.), 23 to 19 kyr B.P., and 13 to 11 kyr B.P. Spun, dyed, and knotted flax fibers are common. Apparently, climatic fluctuations recorded in the cave's deposits did not affect the growth of the plants because a certain level of humidity was sustained.

See also:

Balter, M., Clothes Make the (Hu) Man, Science, 325, 11 September 2009: 1329.

Balter, M., Drawing a Bead on Ancient Symbolic Behavior, Origins Blog, 28 August 2009

Archaeologists discover oldest-known fiber materials used by early humans, EurekAlert (10 September 2009)

The launch of Ida, alias Darwinius masillae, in May this year was unprecedented. It raised eyebrows across the whole range of media-savvy people. Whilst scientists have learned how to capture the interest of the media and promote their work, this particular indulgence was a shock and it was quickly recognised as hype.

"Indeed, Ida has had the public impact of an asteroid. The debut of Darwinius was a media juggernaut: the scientific paper, a public unveiling by New York City's Mayor Bloomberg, a Web site, coverage in People magazine, a television special, and the book all appeared within a week. On the day of the announcement, the traffic at the Web site exceeded that for www.sciencemag.org. But has this fossil rocked our understanding of primate evolution?"

David Attenborough narrated the documentary on Ida, Uncovering Our Earliest Ancestor: The Link (source here)

Thus far, the book has received little attention from the scientific literature. Science has remedied this with an incisive review that leaves readers in no doubt that big mistakes have been made.

"Of the book's nine chapters, the first three and final are written by Young in a sensational style: "Hurum pulled out one final key card and opened the door.... Geffen was stunned." These parts are the most entertaining or, depending on one's point of view, disturbing. Ida is a reprise of the seamier side of paleontology: the exploitation, with the complicity of major museums, of our natural heritage for profit."

The reference to "profit" draws attention to the purchase price of the fossil: reputed to be "a stunning $750,000". The reviewer was one of the signatories to a letter in Nature that expressed "[o]utrage at [the] high price paid for a fossil". When palaeontologists join the ranks of fossil traders, their integrity is suspect. As an Editorial in Nature said: "such arrangements introduce conflicting incentives that can all too easily undermine the process of the assessment and communication of science."

The reviewer is not impressed with the attention to detail that is displayed by coauthor Colin Tudge. This again stimulates comments about the whole process of launching Ida to the world.

"Tudge also offers a tour of primate ecology, behavior, and evolution that is often inaccurate and at times misleading. (For example, he misstates the age of the earliest New World monkey by 6 million years and that of the African anthropoid fossil Apidium by 10 million years.) Why are there so many errors? Perhaps because the book had no scientific editor to check facts or demand reviews that would have uncovered these inaccuracies. The book was rushed out, and the whole project from purchase of the fossil up to the media blitz was cloaked in secrecy."

The palaeontological expertise provided by Philip Gingerich is called into question. This is at the heart of the technical analysis of Ida's significance.

"In short, the interpretation favored by Gingerich and described by Tudge is incompatible with a basal split of anthropoids from lemurs and lorises. Adapoids cannot simultaneously be the source of lemurs, lorises, and anthropoids to the exclusion of tarsiers because tarsiers and anthropoids form a clade. So Darwinius cannot be both an adapoid and a monkey ancestor.
[. . .]
So, Link's premise, that Ida is our ancestor, is fallacious. Ida is a lemur. While the search for anthropoid origins goes on, we shouldn't look for human ancestors in Darwinius or its close relatives."

Why is this relevant to a blog addressing issues of Intelligent Design? A previous blog drew attention to some of the reasons for taking an interest in this case. The science community does not like being confronted by a fait accompli: it expects and demands peer review. It does not welcome situations where the judgment of scholars could be influenced by financial commitments. It does not welcome teams who want to control the publicising of their work by publishing their own resources (documentary, book and web site) contemporaneously with publishing their research. The review by Kay is valuable because it articulates very well the human face of science. The big question is whether this represents the tip of an iceberg (and there is much more of this under the surface) or whether it is exceptional. In my assessment, the Ida-team has overstepped the mark but what they have done is not that unusual. Science does not have the objectivity that the textbooks claim. That is why it is essential to have vigorous debate within science. That is why the questions raised by Intelligent Design are important and why it can only be healthy for science to engage in meaningful dialogue.

Much Hype and Many Errors
Richard F. Kay
Science 28 August 2009: 1074-1075.

Summary: This account of Darwinius masillae, its discovery, and its importance was rushed into print as part of the hype surrounding the public announcement of the work.

Book reviewed- The Link: Uncovering Our Earliest Ancestor by Colin Tudge, with Josh Young Little, Brown, New York, 2009. 304 pp. ISBN 9780316070089.

In the past few years, studies of fossil feathers have yielded some surprising and unexpected results. How do graphic artists know what colours to use when illustrating extinct birds? The answer has been: we don't know - we use artistic licence. The new research has not yet provided different answers to this question, but methodologies are in place which should allow more definitive statements to be made in the future.

This Middle Eocene fossil feather had iridescent colours (source here)

Pigment colours are derived from melanin. These are produced within organelles called melanosomes that have a shape not dissimilar to bacteria. Since researchers were expecting to find bacteria rather than melanosomes, bacteria are what they reported - until last year.

"Melanins are synthesized in a special class of pigment cells (melanocytes) and are packaged within organelles (melanosomes) that vary in morphology between tissues, colours and organisms; the chemically inert structure is not fully understood. Wuttke (1983) interpreted the aligned oblate bodies that constitute the fossil feathers of the Messel Oil Shale as lithified bacteria. This interpretation was extrapolated to fossil feathers from other localities. Our recent investigation of a colour-banded feather from the Cretaceous Crato Formation of Brazil led us to interpret the oblate bodies as eumelanosomes, which contain black melanin (Vinther et al. 2008)."

Examples like these demonstrate the importance of multiple working hypotheses in science to avoid the danger of confirmation bias. If there is only one hypothesis on the table, there is a strong temptation to 'fit' the data to the hypothesis (rather than test the hypothesis using data). An example of this phenomenon was pointed out here. These considerations are significant for the application of design thinking within science. At very least, ID provides information-based alternatives to naturalistic hypotheses to account for biological complexity - as is discussed below.

The melanosomes have implications for plumage colouration. Modern-day examples show an association with black, brown, red and buff colours. The new research reports the "laminar nanoscale organization of melanosomes in feather barbules" that is associated in modern birds with iridescence. The melanosome layer lies underneath a very thin covering of keratin.

"These nanostructures produce a structural colour by interference among light waves scattered by the keratin layer and the underlying layer of melanosomes. [. . .] Feathers with this type of colour-producing nanostructure generally appear black with a glossy or oily iridescent sheen. Depending on the thickness of the keratin layer (from approx. 100 to over 300 nm), the iridescent colour varies in reflectance from saturated ultraviolet or blue to an oily appearance. The most distinctive feature of these nanostructures is the highly uniform superficial layer of closely packed melanosomes. The melanosomes may be rod shaped as in some passerines, galliform birds and the fossils described here or flattened as seen in some ducks and swifts."

The "dense external layer of melanosomes" in the fossil feather is now perceived as diagnostic of structural colour. The original hue of the feather cannot be determined because the outer keratin layer has been degraded. However, coauthor Julia Clark says that the reported research is just "proof of concept" and many more insights into colouration lie ahead.

The authors think that "[t]his type of thin-film nanostructure has evolved numerous times in passeriform and non-passeriform birds". The appearance of this phenomenon in diverse groups points, in their minds, to evolutionary convergence. However, it could be argued (as it is here) that structural colour has a high level of complex specified information.

Some types of colour may point to irreducible complexity. If so, it would seem desirable to adopt a multiple working hypotheses approach and consider design explanations alongside convergence. It is not without significance that the fossil feather documented in this paper is from the Messel Shale (considered to be 40 Ma). It demonstrates the kind of stasis we would expect from a complex specified system. The pattern of abrupt appearance of mature structures is not unusual and the implication is that complexity emerges rapidly (not gradually). The claim for convergence should be understood as an inference from theory, as yet unvalidated by testing.

Inevitably, evolutionary theorists have sought to relate this work to dinosaur 'feathers' and to the 'consensus' view that birds evolved from feathered dinosaurs. Zimmer comments on the ambitions of palaeontologists to extend the methodology to dinosaur feathers. He might have said that such detailed work could reveal fundamental differences between dino-feathers and bird feathers, but he did not. He might have acknowledged the controversial aspects of the dino-bird scenario (see here) but he did not. Rather, he wrote: "It is possible that dinosaurs evolved these colors before they evolved the ability to fly". I see in this an indication that not only the origin of feathers, but also the origin of structural colour, needs to be pushed back earlier and earlier, in order to allow time for such complexity to originate by natural processes.

Structural coloration in a fossil feather
Jakob Vinther, Derek E. G. Briggs, Julia Clarke, Gerald Mayr and Richard O. Prum
Biology Letters, published online before print August 26, 2009, doi:10.1098/rsbl.2009.0524

Abstract: Investigation of feathers from the famous Middle Eocene Messel Oil Shale near Darmstadt, Germany shows that they are preserved as arrays of fossilized melanosomes, the surrounding beta-keratin having degraded. The majority of feathers are preserved as aligned rod-shaped eumelanosomes. In some, however, the barbules of the open pennaceous, distal portion of the feather vane are preserved as a continuous external layer of closely packed melanosomes enclosing loosely aligned melanosomes. This arrangement is similar to the single thin-film nanostructure that generates an iridescent, structurally coloured sheen on the surface of black feathers in many lineages of living birds. This is, to our knowledge, the first evidence of preservation of a colour-producing nanostructure in a fossil feather and confirms the potential for determining colour differences in ancient birds and other dinosaurs.

See also:

Ancient Bird's Feathers Had Iridescent Glow, livescience.com (August 26 2009)

Zimmer, C. First Trace of Color Found in Fossil Bird Feathers, New York Times (August 31, 2009)

The deer mouse is described as one of the "most abundant and widespread mammals in North America" and normally has a dark coloured pelt. The Sand Hills of Nebraska are home to a sub-population of deer mice (Peromyscos maniculatus) with a light-coloured fur that matches the local habitat. The potential for understanding more about adaptive change and the genetics of hair colour has attracted the attention of researchers.

"To unravel evolutionary mechanisms in the wild, we must estimate the fitness advantage of adaptive alleles and infer their source, either as new or pre-existing variation."

Pale-coated deer mouse on a dark soil (Source here)

Based on what is already known about pigment-producing cells at the base of mammalian hair follicles, the gene Agouti was identified as responsible for the different phenotypes. In the house mouse (Mus musculus), it is known that knockouts of Agouti result in dark hairs, whereas overexpression of Agouti leads to light colours. It is also known that "light alleles are generally dominant to dark ones". Significantly, the crosses between dark and light coloured deer mice produced light-coloured offspring. Empirical work pointed unambiguously to Agouti expression as the underlying cause of the two phenotypes (referred to in the paper as wildtype and wideband phenotypes). Sequencing analysis led to the identification of 20 nucleotide differences between the dark and light mice. Of these, two stood out as prime candidates for a genetic mechanism: "a conservative amino acid substitution (Arg37Lys) and a serine deletion (residue 48), both in exon 2". After more detailed investigations, the authors report:

"On the basis of these results, we cannot determine whether the serine deletion, a linked mutation, or both cause wide bands and light coats. [. . .] Nonetheless, the haplotype containing the serine deletion[. . .] explains a substantial amount of ecologically relevant phenotypic variation."

Deer mouse with the darker coat colour. (Source here. For more images, go here)

Further research concluded that "selection is probably acting on the wideband Agouti haplotype". Also, "both population genetic data and predation experiments suggest that selection for light color is strong, and our estimates fall within the range of selection coefficients for other color polymorphisms, including beach mice, pocket mice, ladybirds, and land snails."

Allowing all this, what can be said of this example of adaptive change?
First, selection demonstrably acts on phenotypes that affect the ability of organisms to survive and reproduce. In this case, the phenotype relates to coat colour and its ability to provide camouflage, thus avoiding predation.
Second, the genetic variation involved is linked to a "single amino acid deletion" in the Agouti gene. Deletions are not infrequently found in cases of natural selection. By contrast, additions are rare. Information loss is the norm.
Third, both types of deer mouse interbreed readily. Coat colour is not a factor in mate selection. "Therefore, we hypothesized that light and dark mice interbreed with ample opportunity for recombination between the wideband and wild-type alleles." We are not looking at new species or sub-species here.
Fourth, the adaptive changes are inferred to have been rapid. The authors consider this worthy of comment because they consider the genetic changes to be de novo (i.e. natural selection was not acting on a pre-existing allele).

In the light of these comments, natural selection can be identified as a factor of relevance in ecological studies. Over generations, organisms adapt to their environment and become more optimised to local conditions.

What this research does not do is lend support to Charles Darwin's claim that evolution by natural selection is the key to understanding the development of biological complexity and the origin of species. the genetic changes associated with the modified coat colour are attributed to the deletion of a single amino acid in the Agouti gene - there is no increase in information and no move towards specified complexity. It is necessary to point this out because some (e.g. the BBC report) are suggesting this research is so important for evolutionary theory that it deserves iconic status.

"Rival icon. In some respects, the dune-living deer mice are similar to the famous peppered moths of northern England. For decades, the peppered moths (Biston betularia) have been heralded as one of the best-examples known of a wild animal adapting to its environment due to natural selection. [. . .] "In both species, changes in colour evolve rapidly due to selection by visually-hunting predators," says Prof Hoekstra. But the study by Dr Linnen and Prof Hoekstra's team takes our undertaking of natural selection to a much deeper level. The selection pressure on the moths was technically artificial, caused by pollution produced by people. Whereas the selection causing the pale mice is truly natural. What is more, the scientists have found the gene responsible, and worked out exactly how long it took to evolve and take hold in the population. "Despite the fact that the peppered has been an icon of 'evolution in action', we do not yet know the genetic changes involved," says Prof Hoekstra. "Once researchers find the pigmentation gene responsible for moth colour change, they can do the same types of analyses we have done. It will be really interesting to compare these estimates between mice and men."

Like so many other studies of natural selection, Darwinists think that if they can only demonstrate natural selection in action, their theory is verified. Of course, this is fallacious for the reasons pointed out above. The deer mice example demonstrates ecological adaptation, and does not provide any insight into the origin of complex specified information. To say that the deer mouse example is an icon of evolution is like saying 'if we can only generate amino acids in a reducing atmosphere, we will have shown that the first living cell could have arisen by natural processes'. It is like saying 'if we can show that oxygen levels elevated significantly in the Early Cambrian atmosphere, we will have explained the Cambrian Explosion'. We need these discussions to mature - there is no dispute over natural selection as a driver of adaptive change in ecological systems, but if it is to be presented as a key mechanisms for the creation of biological complexity, the quality of argument needs to be improved by many orders of magnitude!

On the Origin and Spread of an Adaptive Allele in Deer Mice
Catherine R. Linnen, Evan P. Kingsley, Jeffrey D. Jensen, and Hopi E. Hoekstra
Science, 28 August 2009, 325: 1095-1098 | DOI: 10.1126/science.1175826

Adaptation is a central focus of biology, although it can be difficult to identify both the strength and agent of selection and the underlying molecular mechanisms causing change. We studied cryptically colored deer mice living on the Nebraska Sand Hills and show that their light coloration stems from a novel banding pattern on individual hairs produced by an increase in Agouti expression caused by a cis-acting mutation (or mutations), which either is or is closely linked to a single amino acid deletion in Agouti that appears to be under selection. Furthermore, our data suggest that this derived Agouti allele arose de novo after the formation of the Sand Hills. These findings reveal one means by which genetic, developmental, and evolutionary mechanisms can drive rapid adaptation under ecological pressure.

See also:

Walker, M. Mouse set to be 'evolution icon', BBC News (27 August 2009)