Science Literature

The transition from fish to land animal is regarded by many as well documented: it is number two in Nature's presentation of "15 evolutionary gems". Some of the names given to members of the tetrapod lineage are quite well known: Panderichthys and Tiktaalik, Ichthyostega and Acanthostega, for example.

"Open any paleontology text or children's book on prehistoric animals, and you will find something between fish and tetrapod, forelimbs or fins planted on the land, tail receding into the water, eyes cast hopefully forward. These images encapsulate an episode of vertebrate history spanning the latter half (390 to 360 million years ago) of the Devonian, the waning days of the "Age of Fishes.""

The first animals deemed to be tetrapods (rather than fish) are called Ichthyostega and Acanthostega. They both come from rocks from Greenland. Until recently, Acanthostega was considered to be the most primitive tetrapod, and Ichthyostega was considered to have more derived characters. New research has placed Ichthyostega before Acanthostega in evolutionary development. Whilst this appears a very minor tweaking of the story, there are more important issues raised by the change. Before discussing these, it is worth reminding ourselves that the tetrapod evolution story has morphed dramatically with time. The quotation above represents the 'conquest of the land' model, with fish-like animals crawling out of the water. However, more recent work has exploded this hypothesis. All the Devonian tetrapods have characteristics that suggest they were aquatic and that fin-limbs evolved for negotiating their way through underwater obstacles. Somehow, the hypothesis goes, these structures were co-opted for terrestrial use.

Painting of Acanthostaga at home in the water (Credit Janice McCafferty, Source here)

The researchers examined the humeri of Ichthyostega and Acanthostega. They could not do this by extracting the fossil bones and examining them visually. To avoid damaging them, they utilised computed tomography (CT) scanning to sense the shape of the fossils remotely. Then the animals were "reconstructed" using imaging software, The first significant discovery was that some of the rocks contained juvenile forms of Ichthyostega - previously known only as adults. Interest then focussed on the upper arm bones, or humeri. In his commentary article, Friedman writes:

"Found in both the forelimbs of tetrapods and the lobed fins of their "fish" relatives, the humerus is the single bone that links the appendage to the body. It is a complicated, festooned with bumps and ridges marking muscle origins and insertions. Because humeri are integral to the pectoral appendages, they record the biomechanical signature of the shift from fins to weight-bearing limbs."

The researchers obtained four sets of data: juvenile and adult Ichthyostega humeri, and juvenile and adult Acanthostega humeri. This allowed them to assess developmental differences between the two animals as they matured. An overview of the findings is provided in the press release (which cites Callier as first author):

"Anatomies can morph as animals move towards adulthood, Callier said. And such shifts can help scientists deduce when in development the animal acquired the terrestrial habit. The fossils suggest that Ichthyostega juveniles were aquatically adapted, and that the terrestrial habit was acquired relatively late in development. The fossils bore evidence that the muscle arrangement in adults was better suited to weight-bearing, terrestrial locomotion than the juvenile morphology. It is possible that Ichthyostega came out of the water only as a fully mature adult.
In contrast, in Acanthostega "there is less change from the juvenile to the adult. Although Acanthostega appears to be aquatically adapted throughout the recorded developmental span, its humerus exhibits subtle traits that make it more similar to the later, fully terrestrial tetrapods," Callier said."

This creates an unexpected situation: subtle traits in the humerus of Acanthostega place it nearer the fully terrestrial tetrapods, but other characters point to an aquatic existence. Resolving this tension results in some surprising speculations:

"Ironically, the shape of Acanthostega's limb's, in both adult and the newly-discovered juvenile forms, is more "paddle-like" than Ichthyostega's, Callier said. "They would have been really good swimmers. So, although Acanthostega had limbs with digits, we don't think it was really terrestrial. We think even the adults were aquatic."
"If Ichthyostega is actually more primitive than Acanthostega, then maybe animals evolved towards a terrestrial existence a lot earlier than originally believed," she said. "Maybe Acanthostega was actually derived from a terrestrial ancestor, and then, went back to an aquatic lifestyle.""

Some may consider this situation unconvincing, with rather too much speculation about subtle morphological traits. Nevertheless, since there is a presumption of evolutionary transformation, these data have to be fitted into a coherent framework. Earlier in the fossil record, there are fish and no tetrapods; later in the fossil record, there are clear signs of terrestrial tetrapods - so, it is inferred, there has to be a transition between them. The more we now of the fossil record, however, the more difficult it is to identify an evolutionary branch. Instead of a tree, we see a bush. But this means that the quest for missing links will be elusive. We cannot identify ancestors and descendants in the data accessible to us. This changes the nature of the debate. As Friedman says:

"After 150 years of paleontological research dedicated to filling the gap between fishes and tetrapods, it is time to move past the simple formula of "the next missing link" and confront broader questions about tetrapod origins. The field has come far from its pre-Darwinian roots and ancestor-descendant daisy-chains, and now yields a profusely branching tree and correspondingly nuanced scenarios of terrestrialization, including that proposed by Callier et al: in a very real sense, a tangled bank."

According to Viviane Callier: "If there is one take-home message, it is that the evolutionary relationship between these early tetrapods is not well resolved". To that we can add the need to abandon talk of "ancestor-descendant daisy-chains" and to recognise the role of evolutionary presuppositions in the analysis of data.

Contrasting Developmental Trajectories in the Earliest Known Tetrapod Forelimbs
Viviane Callier, Jennifer A. Clack, and Per E. Ahlberg
Science, 324 17 April 2009: 364-367 | DOI: 10.1126/science.1167542

Ichthyostega and Acanthostega are the earliest tetrapods known from multiple near-complete skeletons, with Acanthostega generally considered the more primitive. New material indicates differing ontogenetic trajectories for their forelimbs: In Ichthyostega, the pattern of muscle attachment processes on small humeri (upper arm bones) resembles that in "fish" members of the tetrapod stem group such as Tiktaalik, whereas large humeri approach (but fail to attain) the tetrapod crown-group condition; in Acanthostega, both small and large humeri exhibit the crown-group pattern. We infer that Ichthyostega underwent greater locomotory terrestrialization during ontogeny. The newly recognized primitive characteristics also suggest that Ichthyostega could be phylogenetically more basal than Acanthostega.

See also:

Friedman, M. Emerging onto a Tangled Bank, Science 324, 17 April 2009: 341-342.

From Fish To Landlubber: Fossils Suggest Earlier Land-water Transition Of Tetrapod, ScienceDaily (Apr. 19, 2009)

The true story of oxygen in the Earth's atmosphere has yet to be told. Most researchers have been brought up to believe the Miller-Urey model of abiogenesis, which required the Earth to have a reducing atmosphere to facilitate the spontaneous generation of life. The atmosphere was then considered to be neutral for over a billion years. The evolution of organisms capable of photosynthesis was the next important step, with rises of oxygen levels triggering the flowering of eukaryotes, the rise of the Ediacaran fauna and then the Cambrian Explosion. The first significant rise is understood to be abrupt and sufficient of a milestone in Earth history to warrant a name of its own. Richard Kerr's comments below lead us to the new research by Ohmoto and colleagues:

The first living things did not require oxygen to "breathe," but early life on Earth never would have gotten much beyond pond scum without free oxygen in the atmosphere. Conventional thinking has oxygen produced by photosynthesis gaining the upper hand 2.4 billion years ago, nearly halfway into Earth history. But new laboratory results reported in tomorrow's issue of Science challenge the late arrival of this "Great Oxidation Event."

Ocean sediments deposited prior to the GOE contain red hematite - fully oxidised iron. (Credit: Hiroshi Ohmoto, source here)

Ohmoto's hypothesis is that significant quantities of free oxygen were present in Earth's atmosphere prior to the GOE. He represents a minority position, but he continues to provide leadership in this area and a regular stream of relevant papers. One of the issues concerns patterns found in sulphur isotopes. Here is Kerr again:

"Then in 2000, geochemist James Farquhar of the University of Maryland, College Park, came up with a nifty technique involving sulfur isotopes. The proportion of one isotope to another of the same element can change during a chemical reaction. Normally, the change depends on the masses of the isotopes. But Farquhar found isotopic shifts among three sulfur isotopes before 2.4 billion years ago that hadn't depended on isotope mass. As far as anyone knew, such "mass-independent fractionation" (MIF) could have happened only under solar ultraviolet radiation in an oxygen-free atmosphere - and MIF sulfur disappeared 2.4 billion years ago."

The new paper, with Farquar as one of the co-authors, proposes an alternative origin for these isotopic signatures that keep the door open for discussion of an early, oxygen-rich atmosphere.

"The significance of this finding is that an abnormal isotope fractionation (of sulfur) may not be linked to the atmosphere at all," says Yumiko Watanabe, research associate [and co-author], Penn State. "The strongest evidence for an oxygen poor atmosphere 2.4 billion years ago is now brought into question."

Several papers have appeared in recent years hinting at atmospheric oxygen prior to the GOE. Direct evidence of photosynthesising organisms goes back to rocks dated to 2.7 Ga, and indirect evidence even earlier. In February this year, supporting evidence comes from the presence of fully oxidised iron (hematite) in rocks from Western Australia:

Then, the minimum pO2 of the pre-2.76-Ga atmosphere can be estimated to be 3 x 10-3 atm or 1.5% of the present atmospheric value. This scenario of oxygenated atmosphere is, however, inconsistent with a current popular model for atmospheric evolution based on the MIF-S record in sedimentary rocks.

Hematite minerals have demonstrated an abundance of oxygen during the time of deposition. In an oxygenated world, it is easy to find places that are reducing or neutral (we have them today). What is not easy is to explain regions rich in oxygen within a reducing or neutral world. This gives a strong case for early oxygenation. "This is at least a possibility that we should be thinking about," Ohmoto says and adds, "I feel the findings we made fit nicely to what I've been saying for years."

Why are these research findings of interest to ID scientists? The main reason concerns the "evolutionary storytelling" mindset that afflicts many researchers. It is important to them that the findings of research fit within the evolutionary paradigm. There is a consensus that the abiogenesis scenario, followed by a step-by-step evolution of the atmosphere, is a given. Within this, another evolutionary story, of fauna and flora, can be constructed. It all fits together beautifully (they think). Ohmoto's research breaks this mould, pushing back the origin of complex photosynthesising organisms into the Early Archaean and reducing the evidential base for abiogenesis from tenuous to zero. This puts extreme constraints on thinking about the origins of biological complexity - as ID scientists have often pointed out. Design, rather than stochastic processes, is therefore indicated.

Anomalous Fractionations of Sulfur Isotopes During Thermochemical Sulfate Reduction
Yumiko Watanabe, James Farquhar, and Hiroshi Ohmoto
Science, 324, 17 April 2009: 370-373.

Abstract: Anomalously fractionated sulfur isotopes in many sedimentary rocks older than 2.4 billion years have been widely believed to be the products of ultraviolet photolysis of volcanic sulfur dioxide in an anoxic atmosphere. Our laboratory experiments have revealed that reduced-sulfur species produced by reactions between powders of amino acids and sulfate at 150 to 200 degrees C possess anomalously fractionated sulfur isotopes: [. . .]. These results suggest that reactions between organic matter in sediments and sulfate-rich hydrothermal solutions may have produced anomalous sulfur isotope signatures in some sedimentary rocks. If so, the sulfur isotope record of sedimentary rocks may be linked to the biological and thermal evolution of Earth in ways different than previously thought.

Primary haematite formation in an oxygenated sea 3.46 billion years ago
Masamichi Hoashi, David C. Bevacqua, Tsubasa Otake, Yumiko Watanabe, Arthur H. Hickman, Satoshi Utsunomiya & Hiroshi Ohmoto
Nature Geoscience, Published online: 15 March 2009 | doi:10.1038/ngeo465

Abstract: The timing of the origin of photosynthesis on the early Earth is greatly debated. It is generally agreed, on the basis of the presence of biological molecules found in shales from the Hamersley Basin, Australia, that oxygenic photosynthesis had evolved 2.7 billion years (Gyr) ago. However, whether photosynthesis occurred before this time remains controversial. Here we report primary haematite crystals and associated minerals within the marine sedimentary rocks preserved in a jasper formation of the Pilbara Craton, Australia, which we interpret as evidence for the formation of these rocks in an oxygenated water body 3.46 Gyr ago. We suggest that these haematite crystals formed at temperatures greater than 60 degrees C from locally discharged hydrothermal fluids rich in ferrous iron. The crystals precipitated when the fluids rapidly mixed with overlying oxygenated sea water, at depths greater than 200 m. As our findings imply the existence of noticeable quantities of molecular oxygen, we propose that organisms capable of oxygenic photosynthesis evolved more than 700 million years earlier than previously recognized, resulting in the oxygenation of at least some intermediate and deep ocean regions.

See also:

Berardelli, P. Oxygenated Oceans Go Way, Way Back, ScienceNOW Daily News, 16 March 2009

Kato, Y., Suzuki, K., Nakamura, K., Hickman, A.H., Nedachi, M., Kusakabe, M., Bevacqua, D.C. and Ohmoto, H. Hematite formation by oxygenated groundwater more than 2.76 billion years ago, Earth and Planetary Science Letters, Volume 278, Issues 1-2, 15 February 2009, Pages 40-49 | doi:10.1016/j.epsl.2008.11.021

Kerr, R. Great Oxidation Event Dethroned? Science, 324, 17 April 2009: 321.

For years, the public has been bombarded with grandiose claims about the future benefits of genetic research for human health. Patients at risk could be diagnosed and treated before symptoms appeared, and the potential for devising cures was mooted. The story-line for this goes back to the discovery of the double helix and the recognition that genes were encoded in DNA sequences. Genes were considered to make mankind - or, as some would have it, mankind was considered to be the vehicle for making genes. This 'Genes-R-Us' mentality led to the idea that genetic causes were primarily responsible for illnesses and afflictions that could not be linked to bacteria or viruses. Geneticist Steve Jones writes:

"The hope was (and five years ago, it was a reasonable one) that such conditions could be blamed on a small set of common genetic variants. Track them down and we would begin to understand what had gone wrong [. . .]. The logic was to search the double helix for about half a million variants that could be used to set up a grid of diversity, scattered across the whole genome. This could then be scanned using a magic "chip", which could identify thousands of changes at once to see whether one, or a few, of the molecular milestones might predispose a given individual to a particular disease."

Those who think that advances in genetics will define the future of medicine are mistaken (Source here).

The tide has now turned. Sufficient results are now in to show that a change of direction is needed. Lessons need to be learned by academic, by funding agencies and by the general public. Over 100 large-scale projects have now been completed, looking for associations between genes and human diseases. On the way, statistical methodologies for finding associations have been refined so that researchers can now be sure that reported results reflect real biologic causation. In a Perspective piece, Goldstein asks the question: "But do they matter?"

"Unfortunately, most common gene variants that are implicated by such studies are responsible for only a small fraction of the genetic variation that we know exists. This observation is particularly troubling because the studies are largely comprehensive in terms of common single-nucleotide polymorphisms (SNPs), the genomic markers that are genotyped and with which disease associations are tested. We're finding the biggest effects that exist for this class of genetic variant, and common variation is packing much less of a phenotypic punch than expected."

Some examples are given: type 2 diabetes and height. Whilst similar conclusions are for both, the height trait is more substantial, because the robustness of the database. 20 polymorphisms have emerged from research, but collectively, they explain less than 3% of the population variation in height. Goldstein explains the basis of an equation to predict how many polymorphisms would be needed to explain 80% of the variation in height, and the answer comes out as 93,000. Whilst this figure could be reduced if there were significant numbers of undiscovered genes, the number is still in the thousands. This finding illustrates the general case and this means the original driver for this research (that we have genes for specific traits) was misconceived. Goldstein comments:

"If common variants are responsible for most genetic components of type 2 diabetes, height, and similar traits, then genetics will provide relatively little guidance about the biology of these conditions, because most genes are "height genes" or "type 2 diabetes genes." [. . .] But even though genomewide association studies have worked better and faster than expected, they have not explained as much of the genetic component of many diseases and conditions as was anticipated."

Goldstein's article accompanies three others in the current New England Journal of Medicine, and these provide a landmark for evaluating the extensive research of recent years. The story was picked up by The New York Times in an article by Nicholas Wade. It became front page news in the UK when Steve Jones, Professor of Genetics, entered the fray. Writing in The Daily Telegraph, he comments:

"In other words, our chances of being born with a predisposition to a common illness such as diabetes or heart disease are not represented by the roll of a single die, but a gamble involving huge numbers of cards. Some people are dealt a poor mix and suffer as a result. Rather than drawing one fatal error, they lose life's poker game in complicated and unpredictable ways. So many small cards can be shuffled that everyone fails in their own private fashion. Most individual genes say very little about the real risk of illness. As a result, the thousands of people who are paying for tests for susceptibility to particular diseases are wasting their money."

The problems troubling this research field are not a surprise to some. Those who are critical of genetic reductionism have long argued that the research community was going down the wrong track. The idea that genes have one function was disproved long ago, but the fallout of that thinking continues to this day. Still, the media gets excited when researchers claim to have found a gene for this or that trait. Genes are not everything: they are but part of a complex unity. The whole field needs to move on: so-called Junk DNA is not junk, but most of it has functionality; epigenetics is being recognised as a significant issue for understanding development,; the cell, not the nucleus, is an integrated whole and need to be considered as such; there are health, diet, exercise and lifestyle issues to address and also psychological factors to consider. This is where there is a link with ID: we need to shift our focus away from humans as an aggregation of molecular machines and towards humans as designed beings exhibiting an abundance of complex specified information.

Common Genetic Variation and Human Traits
David B. Goldstein
The New England Journal of Medicine, April 15, 2009 (10.1056/NEJMp0806284)

First para: The human genome has been cracked wide open in recent years and is spilling many of its secrets. More than 100 genomewide association studies have been conducted for scores of human diseases, identifying hundreds of polymorphisms that are widely seen to influence disease risk. After many years in which the study of complex human traits was mired in false claims and methodologic inconsistencies, genomics has brought not only comprehensive representation of common variation but also welcome rigor in the interpretation of statistical evidence. Researchers now know how to properly account for most of the multiple hypothesis testing involved in mining the genome for associations, and most reported associations reflect real biologic causation. But do they matter?

See also:

Alleyne, R. and Devlin, K. Genetic 'magic bullet' cures have proven a 'false dawn', The Daily Telegraph (21 April 2009)

Jones, S. One gene will not reveal all life's secrets, The Daily Telegraph (21 Apr 2009)

Koenig, R. Genome Scans: Impatient for the Payoff, Science, 324, 24 April 2009: 448.
Excerpt: [Francis] Collins says, "it is clear that most of the heritability for common disease has not yet been discovered - this is now generally referred to as 'the dark matter of the genome'". That dark matter is at the center of the current genomics debate.

Wade, N. Genes Show Limited Value in Predicting Diseases, The New York Times (April 15, 2009)

In The Descent of Man, Charles Darwin argued that there is "no fundamental difference between man and the higher mammals in their mental faculties". To support this claim, he drew attention to cases where precursors of human intelligence could be found in animals, including "similar passions, affections, and emotions, . . . [such as] jealousy, suspicion, emulation, gratitude and magnanimity". This approach has spawned numerous research projects to further Darwin's agenda.

"Over the past two decades, researchers have reported that chimpanzees can empathize with other members of their species, and that they reconcile and even console each other after conflicts. Monkeys and apes have been credited with a sense of fairness and aversion to inequity and, in the case of apes, an awareness of the mental states of others - in other words, a theory of mind."

This chimp has something to smile about (Source here)

There has been a major problem, however, with establishing suitable control conditions. Furthermore, many researchers have not been objective analysts, but have indulged in "a flurry of anthropomorphic overinterpretation". In an excellent essay on these matters, Bolhuis and Wynne provide a healthy check on these enthusiasms.

"For instance, capuchin monkeys were thought to have a sense of fairness because they reject a slice of cucumber if they see another monkey in an adjacent cage, performing the same task, rewarded with a more sought-after grape. Researchers interpreted a monkey's refusal to eat the cucumber as evidence of 'inequity aversion' prompted by seeing another monkey being more generously rewarded. Yet, closer analysis has revealed that a monkey will still refuse cucumber when a grape is placed in a nearby empty cage. This suggests that the monkeys simply reject lesser rewards when better ones are available."

Bolhuis and Wynne point out several behaviours and skills displayed by birds which have been interpreted in anthropomorphic ways when seen in apes and monkeys. They suggest that evolutionary convergence may be more important than ancestral relationships. They point out that many researchers have laboured hard at teaching apes some form of language, but "linguists generally agree that the resulting efforts made by chimps and bonobos don't qualify as language". When it comes to copying sounds, birds are often "striking vocal mimics". This allows them to give their first summary statement:

"The appearance of similar abilities in distantly related species, but not necessarily in closely related ones, illustrates that cognitive traits cannot be neatly arranged on an evolutionary scale of relatedness."

The second issue addressed concerns the factors that drove the "emergence of contemporary animal and human traits". These drivers are not amenable to leaving traces in the fossil record. Consequently, this whole field is wide open to the import of assumptions. They give an example: the idea that "our modern skulls house a Stone Age mind". They stress that this is an assumption, not a conclusion.

Thirdly, they point out a methodological problem in the way evolutionary analyses have been employed. If researchers want to find the cause of a particular behavioural trait, why use a methodology that traces the course of history? Failure to appreciate this mismatch has led to countless cases of Darwinian storytelling based on speculations about adaptation.

"Questions about the causal underpinnings of behavioural differences can be elucidated only with a causal analysis, not through reconstructing evolutionary history."

The essay closes with an appeal for more empirical research and less "naive evolutionary presuppositions". Any evolutionary interpretation must be "verified using controlled experiments". Those who claim that nothing in biology makes sense except in the light of evolution need to bite their tongues and realise this approach has promoted unhealthy science. If Darwinism at any level is to survive, it must be underpinned by empirical research, not imported as theoretical baggage or added on as an intellectual gloss.

"We are not suggesting an abandonment of Darwin's insights. Rather, we call for care in their application. When reconstructing the evolutionary history of cognitive traits, there is no a priori reason to assume that convergence will be more important than common descent or vice versa. In addition, evolutionary theory may suggest hypotheses about the mechanisms of cognition, but it cannot be used to actually study these mechanisms."

This essay is a useful contribution to thinking about the cognitive abilities of animals and humans. Very refreshing! For more blogs on human traits, go here and here.

Can evolution explain how minds work?
Johan J. Bolhuis & Clive D. L. Wynne
Nature, 458, 832-833 (16 April 2009) | doi:10.1038/458832a [restricted access link]

Abstract: Biologists have tended to assume that closely related species will have similar cognitive abilities. Johan J. Bolhuis and Clive D. L. Wynne put this evolutionarily inspired idea through its paces.

A fascinating book review draws attention to the way images were used to promote evolutionary theories during the 1920s. According to the book's author, images were "central to the public communication of evolutionary biology, and its enemies have prominently exploited their ambiguity". Two case studies appear in the review: the Scopes Trial in 1925 and the influence of Henry Osborn, President of New York's American Museum of Natural History.

The Scopes trial charged John Scopes with teaching that "man has descended from a lower order of animals". The prosecutor William Jennings Bryan gave an address which "peaked in his denunciation of a diagram". This, presumably, fits the 'exploiting their ambiguity' description of those opposing evolutionary transformation.

The picture, in a state-prescribed biology text, represented the relations of animal groups by circles of size corresponding to number of species: huge for insects and tiny for mammals. That "little ring" appalled Bryan, who later objected that "no circle is reserved for man alone". "What," he demanded to know, "shall we say of the intelligence, not to say religion, of those who . . . put man with an immortal soul in the same circle with the wolf, the hyena, and the skunk?"

"The Neanderthal Flint Workers" by Charles Knight (Credit: American Mus. Nat. Hist. Library #618, Source here)

The mural depicted above was commissioned by Henry Osborn and created by Charles Knight. It shows a family group of Neanderthals making tools, using spears, and portrays them as innovative and alert. This was unlike contemporary portrayals of 'apemen' which made them more brutish and animal-like. This mural is significant because it provides a reminder that different scientists interpret the same data in different ways. In the context of origins, these interpretations are heavily dependent on the presuppositions brought to the research by scientists. Thus, the "secular scientists" portrayed Neanderthals as brutish apemen, emphasising their continuity with ape-like ancestors. Osborn, however, described as a theistic evolutionist, thought that the evolutionary process gave "a sublime conception of God". He wanted to emphasise the humanity of the Neanderthals and "put so much distance between humans and apes that many saw him as selling out".

There is a puzzling error in Hopwood's review. The image annotation correctly identifies the family group as Neanderthals, but the text of the review refers to Osborn commissioning "murals and book covers that ennobled cave-painting Cro-Magnon man (as pictured, left)". To my knowledge, Cro-Magnon man has always been perceived as mainstream humanity, and the picture referred to (reproduced above) depicts Neanderthals.

The message of the book is that images had a significant role in the way American scientists responded to evolution-doubters in the 1920s. The author "reconstructs the attempts of influential evolutionists to get their messages across in a world of unruly images, competing voices and fragile authority". Hopwood adds:

"The 1920s shaped pictures of evolution, and of evolutionary debate, that are still in our heads."

The power of images to shape the way people think is a timely and important subject. The two examples provided in the review raise questions that go far beyond "promot[ing the] public understanding of evolution". The image from the biology textbook used in the Scopes trial clearly offended Bryan, who thought it undermined the uniqueness of humanity. The mural commissioned by Osborn consciously moved away from presenting Neanderthals as apemen. Scientists will inevitably differ in their judgments depending on whether they are secular evolutionists, theistic evolutionists or some form of creationist.

Illustrations may be used to present the anticipated findings of science (as has occurred with feathered dinosaurs - but see here), or to fit data into a predetermined mould (as often occurs with the cladistic analysis of characters), or to convey the concept of progression (as in the classic portrayals of horse evolution). Darwin, himself, can be framed as the model scientist, building theory from empirical data - for further comment on this, go here. This is a potentially fruitful area for educationalists to explore. Students can be helped to understand some of the agendas in origins science by considering the images used by scientists (and science popularisers) to communicate with others.

A clash of visual cultures
Nick Hopwood
Nature 458, 704-705 (9 April 2009) | doi:10.1038/458704a

Abstract: Nick Hopwood applauds an account of how US scientists used images to counter creationism and promote public understanding of evolution in the 1920s.

BOOK REVIEWED- God - or Gorilla: Images of Evolution in the Jazz Age, by Constance Areson Clark, Johns Hopkins University Press: 2008.

See also:

Martin, L.D. An Iconoclast for Evolution? World and I, February 1, 2001

Tyler, D. Evolution, Museums and Society, ARN Literature blog (15 November 2008)

Whilst our understanding of coloured objects is dominated by the role of pigments and dyes, the natural world makes extensive use of nanotechnology to yield vivid hues, often with added iridescence. The mechanisms involve constructive and destructive interference of light - this is referred to as structural colour. This is the best way to get a brilliant white or an ultrablack. Structural colours can be produced by highly periodic photonic crystals (as in butterfly wings), and also by "amorphous, or quasi-ordered, dielectric nanostructures where there are local correlations but little long-range order" (as in the feathers of some birds).

Nanostructures that produce some birds' brightly colored plumage, such as the blue feathers of the male Eastern Bluebird, have a sponge-like structure. (Photo: Ken Thomas, source here)

Some feather colours result from the presence of a spongy material with nano-sized air bubbles. In technical language, the visual effects are created by "light scattering from spongy beta-keratin and air nanostructures within the medullary cells of avian feather barb rami". An interdisciplinary research team have analysed the feathers from different birds and tested out various hypotheses for the formation of colour. They favour a phase-separation model:

"They compared the nanostructures to examples of materials undergoing phase separation, in which mixtures of different substances become unstable and separate from one another, such as the carbon-dioxide bubbles that form when the top is popped off a bubbly drink. They found that the color-producing structures in feathers appear to self-assemble in much the same manner. Bubbles of water form in a protein-rich soup inside the living cell and are replaced with air as the feather grows."

They identified two distinct classes of nanostructure: channel morphologies and sphere morphologies. From previous work, they find that these nanostructures are unrelated to phylogeny and they conclude that the "channel and sphere nanostructures have evolved independently in many lineages of birds".

In order to form recognisable, reproducible plumage patterns, it is necessary for the nanostructure development to be precisely controlled during feather development. This is no mean task. Based on their phase separation model, they are able to spell out the implications for managing the process.

"In this model, birds develop color producing nanostructures by controlling the combined process of phase separation and kinetic arrest with three variables: the rates of beta-keratin expression, beta-keratin polymerization, and filament crosslinking."

There are two points worthy of note here. The first concerns the complexity of the process and the potential for biomimetics. The researchers speak of elegance and intricacy. Self assembly does occur - but only under closely engineered conditions. Thus, the context for self-assembly is intelligent design.

"We have found that nature elegantly self assembles intricate optical structures in bird feathers. We are now mimicking this approach to make a new generation of optical materials in the lab."

The other point relates to Darwinian storytelling regarding bird plumage colours. Many have suggested that feather plumage colours are pointers to fitness - however that is defined. The new research effectively drives a wedge between Darwinian adaptation theory and the empirical data.

"Many biologists think that plumage color can encode information about quality - basically, that a bluer male is a better mate," said Richard Prum, chair of the Department of Ecology and Evolutionary Biology and one of the paper's authors. "Such information would have to be encoded in the feather as the bubbles grow. I think our hypothesis that phase separation is involved provides less opportunity for encoding information about quality than most biologists thought. At the same time, it's exciting to think about other ways birds might be using phase separation."

Self-assembly of amorphous biophotonic nanostructures by phase separation
Eric R. Dufresne, Heeso Noh, Vinodkumar Saranathan, Simon G. J. Mochrie, Hui Cao and Richard O. Prum
Soft Matter, Online 30 March 2009, DOI: 10.1039/b902775k

Some of the most vivid colors in the animal kingdom are created not by pigments, but by wavelength-selective scattering of light from nanostructures. Here we investigate quasi-ordered nanostructures of avian feather barbs which produce vivid non-iridescent colors. These beta-keratin and air nanostructures are found in two basic morphologies: tortuous channels and amorphous packings of spheres. Each class of nanostructure is isotropic and has a pronounced characteristic length scale of variation in composition. These local structural correlations lead to strong backscattering over a narrow range of optical frequencies and little variation with angle of incidence. Such optical properties play important roles in social and sexual communication. To be effective, birds need to precisely control the development of these nanoscale structures, yet little is known about how they grow. We hypothesize that multiple lineages of birds have convergently evolved to exploit phase separation and kinetic arrest to self-assemble spongy color-producing nanostructures in feather barbs. Observed avian nanostructures are strikingly similar to those self-assembled during the phase separation of fluid mixtures; the channel and sphere morphologies are characteristic of phase separation by spinodal decomposition and nucleation and growth, respectively. These unstable structures are locked-in by the kinetic arrest of the beta-keratin matrix, likely through the entanglement or cross-linking of supermolecular beta-keratin fibers. Using the power of self-assembly, birds can robustly realize a diverse range of nanoscopic morphologies with relatively small physical and chemical changes during feather development.

See also:

Bird Feathers Produce Color Through Structure Similar to Beer Foam, Yale University Office of Public Affairs (April 2, 2009)

Tyler, D. Optimal design for brilliant whiteness in a beetle, (ARN Literature blog, 20 January 2007)

As an outside observer of the US educational system, I have to report a sense of incredulity at the stances taken by opponents of change. All scientists and all educators should be able to handle the phrase "strengths and weaknesses" - without it being interpreted as a Trojan Horse for subversive ideas. Strengths and weaknesses are what we are supposed to be doing, whatever our disciplines may be! Yet, according to the report in Science, the new standards for Texas schools are said to "strike a major blow to the teaching of evolution".

What appeared to have happened in the discussions leading up to the vote, is that the S&W phrase was replaced by statements that spelled out the implications for educators. Some of these are cited by the reporter. The first provides the principle behind the changes. There is nothing new here - most people will think that teachers are already doing these things. Educators are expected to:

"analyze, evaluate, and critique scientific explanations in all fields of science by using empirical evidence, logical reasoning, and experimental and observational testing, including examining all sides of scientific evidence of those scientific explanations so as to encourage critical thinking by the student."

In order to develop critical thinking skills, you have to use them (source here)

The reporter refers to two hot-button topics. The first concerns the complexity of the cell and the way the origin of complexity is handled by evolutionary theories. As is well known, Darwinists are convinced that the action of natural selection to preserve favourable gradational changes in living things is sufficient to explain biological complexity. Not so well known, but nevertheless an important part of the academic community, are scientists who reject the comprehensiveness of Darwinian explanations. They find major shortcomings in the 'Modern Synthesis' and consider that the problems of explaining evolutionary novelties require new theory. It is therefore sad to find NeoDarwinians rejecting all talk of controversy about evolutionary theory and directing their fire, not at the scholars who disagree with them, but at those who are responsible for educating the next generation of scientists. To avoid the dangers of brainwashing young people with one particular theory that is deemed (by some) to have achieved the status of fact, teachers are called upon to help students:

"analyze and evaluate the evidence regarding formation of simple organic molecules and their organization into long complex molecules having information such as the DNA molecule for self-replicating life."

The second controversial area relates to the significance of the fossil record for theories of origins. Students will also be expected to "analyze and evaluate a variety of fossil types such as transitional fossils, proposed transitional fossils, significant fossil deposits with regard to their appearance, completeness, and alignments with scientific explanations in light of this fossil data." What issues are being raised here? In many ways, we have to cover the same ground as for the explanation of biological complexity. Darwinism predicts gradual change. It finds small variations in a breeding population of organisms today, and it extrapolates back in time to explain the origin of species, families, orders, classes and phyla. The problem for Darwinists is that the fossil record has stubbornly resisted this interpretation of the data. This came to a head when Eldredge and Gould famously proposed their theory of Punctuated Equilibrium. It is not difficult to find evidence of the problem in refereed literature: "For instance, with its abrupt transitions, the fossil record provides little evidence for a gradual evolution of new forms." (Theissen, 2008), and "The clamour to revise neo-darwinism is becoming so loud that hopefully most practising evolutionary biologists will begin to pay attention" (Pigliucci, 2005). Students do need to be exposed to this kind of thinking if they are to gain a decent education. 'Teaching the controversy' is an educational practice that enlivens the minds of students, hones critical thinking skills and prepares people for life.

I would expect that all friends of education will welcome the decisions made by the Texas Board of Education and wish them well. However, this response may be muted because most of the media reports are negative - as in this case in Science. Eugenie Scott of the National Center for Science Education is given the last word. She commented on the removal of the phrase "strengths and weaknesses" and its replacement with words about developing critical thinking skills: "It was like you put the stake in the heart of the vampire and it comes back." For anyone with doubts about the seriousness of these issues, that comment should clear them all away.

I give the last word to Don McLeroy, chair of the Texas Board of Education. He wrote in a commentary piece to the Austin American-Statesman as follows:

"If we are to train our students, engage their minds and, frankly, be honest with them, why oppose these standards? If the standards do not promote religion and they are not unscientific and they deal directly with the data, then possibly these standards are being opposed for ideological reasons. This supports the argument that this culture war exists, not because of the religious faith of creationists, but because of the rejection of the empirical demonstration of science by academia's far-left and the secular elite opinionmakers."

New Texas Standards Question Evolution, Fossil Record
Yudhijit Bhattacharjee
Science, 324, 3 April 2009: 25.

Summary: New science standards for Texas schools strike a major blow to the teaching of evolution, say scientists and educators who last week tried unsuccessfully to block the adoption of last-minute amendments aimed at providing an opening for the teaching of creationism.

See also:

Don McLeroy, D., Enlisting in the culture war, Austin American-Statesman, Wednesday, March 25, 2009

Tyler, D. Is critical thinking subversive to science? ARN Literature Blog, (23 June 2008)

Bone joints are remarkable for their physical properties. They are associated with very low coefficients of friction and can work effectively under high pressures. For several years, researchers have tried to emulate biological systems, with advances in understanding coming steadily. Previous blogs related to this topic are here and here. Recent research has, for the first time, matched and exceeded the performance of natural synovial joints, both in terms of the coefficient of friction achieved and in the ability to operate under pressure. The success has come through the use of zwitterionic molecules attached in specific ways to the surfaces. Zwitterions are molecules that are neutral overall but carry both positively and negatively charged groups.

Zwitterionic phosphorylcholine groups on the polymer bristles trap water which lubricates the surfaces (Source here)

Jacob Klein from the Weizmann Institute in Rehovot, Israel, and his group have made polymer 'brushes' by attaching one end of polymer chains to a host surface, leaving the other end sticking out. The polymer chain 'bristles' tend to repel each other and so stand up from the surface to form a brush-like structure. 'When two surfaces coated with polymer brushes compress against each other, they tend to squeeze within themselves rather than intermingling with each other,' explains Klein. 'This allows them to be pressed together quite hard without entangling, so the friction between them is low.' (Source here)

The reason the bristles repel each other is that they have side chains carrying zwitterions and these interact with each other and with water.

'By introducing charges to the brushes you get a hydration layer of water molecules around the charges,' explains Klein. 'These water molecules are tightly bound, in the sense that it's hard to remove them all at once, but individual molecules are able to rapidly exchange with water in the surrounding solvent or the hydration layer of another charge. This gives them the properties of molecular ball-bearings - you can press hard on them and they won't release their water, but when you come to shear them [move the surfaces over each other] they behave in a fluid way, which gives the excellent lubrication properties.'

The researchers say that their system does not have a clear analogue with cartilage surfaces, but they do point to a mechanism (highly hydrated macromolecules) that can achieve the performance of natural systems. A surface chemist and tribologist has commented:

"It's an interesting observation from the point of view of natural lubrication. There are lots of zwitterions in nature, but there are also lots of systems that don't have them and lubricate as well - it's not universal, but it might contribute to our understanding of how natural lubrication systems work."

Although this research leaves the nature of cartilage lubrication in need of further clarification, it does point to significant elements of the explanation: complex macromolecules, strong attachment to substrates, ordered side chains with bipolar molecules that interact with each other and with water, together with some distinctive physical properties of water (it is bipolar and incompressible). This is a highly ordered system, but it is not self-assembling. It needs another system to put it together - just as the research team was needed to put together the artificial system. The common element here is Intelligent Design.

Lubrication at Physiological Pressures by Polyzwitterionic Brushes
Meng Chen, Wuge H. Briscoe, Steven P. Armes, and Jacob Klein
Science, 324, 27 March 2009: 1698-1701.

Abstract: The very low sliding friction at natural synovial joints, which have friction coefficients of mu less than 0.002 at pressures up to 5 megapascals or more, has to date not been attained in any human-made joints or between model surfaces in aqueous environments. We found that surfaces in water bearing polyzwitterionic brushes that were polymerized directly from the surface can have mu values as low as 0.0004 at pressures as high as 7.5 megapascals. This extreme lubrication is attributed primarily to the strong hydration of the phosphorylcholine-like monomers that make up the robustly attached brushes, and may have relevance to a wide range of human-made aqueous lubrication situations.

See also:

Broadwith, P. 'Molecular ball-bearings' for artificial joints, Chemistry World, 26 March 2009

It has often been observed that research students gaining a PhD are weaker in philosophy than is implied by their doctorate. Many of the arguments of the New Atheists are proclaimed as though they are unanswerable, but many of us find them to be singularly lacking in substance. In a journal which aims to "expose some of the bad philosophy which often passes as accepted wisdom", philosopher Douglas Groothuis addresses common arguments frequently heard in discussions about Intelligent Design. The editorial policy of the journal is to demonstrate "the relevance of philosophy to everyday life and [to forge] a direct link between contemporary philosophy and the widest possible readership". In keeping with this, Groothius creates a dialogue overheard at a book discussion group. There are three parties: an atheist, a theist and an agnostic. Noted below are three of the topics probed.

"Turtles all the way down" is a specific case of an infinite regress argument - although the illustration is somewhat simplified! (Source here)

Argument 1: Who designed the Designer? The logic goes like this:

"Any supposed designer would be a case of specified complex itself (or herself or himself). Therefore, that designer's existence would need to be explained by a previous designer. And that designer, being complex, would have to be explained by another designer, ad infinitum, ad nauseum. There is a vicious and infinite regress in which nothing at all gets explained." (p.72)

The response is to point out that this is a straw man type of argument, shifting attention from the detection of design to the identity of the Designer. The logic used to detect design is not the logic that can be used to gain understanding of the Designer.

"ID is not operating from the premise that everything that is complex requires an explanation outside itself. Rather, it attempts to explain certain finite and material states of affairs through the design inference. It does not operate on some general philosophical principle that anything at all that is complex requires an explanation outside itself." (p.73)

Argument 2: ID is a science stopper. Those who use this type of argument represent ID scientists as saying "God did it" and no further investigation is needed.

The response is very simple. First, it should be noted that historically, design inferences have not closed up science. Indeed, ID scientists pioneered the time known as the Scientific Revolution. Second, design inferences are claimed to provide -

" - the best scientific explanation for certain empirical facts. It does not rely on any uniquely religious presuppositions nor does it appeal to any sacred texts as premises or conclusions. However, it does challenge any definition of science that limits scientific explanations to only material, or unintelligent, causes."(p.75)

Argument 3: Science is only concerned with natural causes. For atheist scientists, this is absolutely fundamental. With confidence, they assert: "Natural causes explain natural events in biology, chemistry, physics, and so on. Without this idea, science is dead in the water" (p.75). This argument has been remarkably successful and has persuaded many theists that an atheistic definition of science is the only rational option.

The response is to deny the validity of this definition of science. First, it is not true to history:

"The leaders of the Scientific Revolution didn't believe this either, but that didn't exactly retard their discoveries. Should not science better be understood as the giving of good and sufficient rational explanations for empirical objects and events?" (p.76)

Secondly, it is necessary to point out that any definition of science that excludes intelligent causation is inherently blinkered:

"if there is a designer out there, our science would never be allowed to detect it! It puts an epistemological veto on the whole thing. How is that rational or scientific?" (p.76)

This is a crucial argument. Atheists start with the principle that all causation is natural, so all material things must be explained in terms of natural law and chance processes. They want science defined in a way that is consistent with atheism - but this is profoundly an anti-science approach. They have no route for testing out their ideas, because they are defining reality to exclude the operation of an Intelligent Designer. With this "epistemological veto" in place, they declare themselves victors over the forces of superstition and darkness! Not only is this a delusion, it is philosophically naive.

Groothuis has contributed a readable and accessible dialogue that explores these issues (and others) clearly and positively. There is no justification for the New Atheists to continue to present banalities as profound insights. There is an important debate to be had, but until we can get past obsolete and empty arguments, it is difficult to make progress.

Who Designed The Designer?: A Dialogue on Richard Dawkins's The God Delusion
Douglas Groothuis
Think (2009), 8: 71-81 | doi:10.1017/S1477175608000407

Abstract: In The God Delusion, Richard Dawkins argues that any designer capable of creating the universe and the things we find in it would have to be at least as complex as his creation. If complexity requires a designer, then the designer will require a designer, and so on to infinity. Rather than actually providing an explanation for complexity we see around us, those who invoke a cosmic designer merely postpone the problem. Here, Douglas Groothuis challenges Dawkins's argument.

See also:

Groothuis, D., Who Designed the Designer: A Response to Richard Dawkins, The Constructive Curmudgeon (blog), March 28, 2009