Literature

When Jurassic Park was written, I don't think any scientist seriously thought that genetic material from dinosaurs would ever be recovered. However, that is exactly what was reported in Science a few days ago. The genetic sequences are derived from collagen protein recovered from the fossilised leg bone of a T. rex. The main authors have been publishing for some time about their find of dinosaur soft tissue, and this new paper is the latest step of a remarkable journey of exploration. If amino acid sequences are preserved in other fossilised bones, many new avenues for research will open up.

The bone yielding the collagen used in the research (Source: here)

The paper would have been memorable if that were the only point made by the authors. However, the authors wanted to show that their data could be useful to molecular phylogenetics. They used 21 extant organisms and protein sequence data from an Ice Age mastodon. They used four methods to reconstruct an evolutionary tree. According to the New Scientist report:

"To build the family tree, Asara and colleague Chris Organ compared the T. rex sequence with collagen from other animals. Those with similar collagen sequences were grouped closely together on the tree, while differences in the sequences suggested the animals had long diverged. For the most part, the collagen tree captured relationships palaeontologists and evolutionary biologists had little reason to doubt, including T. rex's kinship to birds and the mastodon's ancestry to elephants."

The relationship between the dinosaur and birds caught the interest of the media. "T. rex confirmed as great granddaddy of all birds" said New Scientist. The Daily Mail had the headline: "Terrifying Tyrannosaurus rex had close links to the humble chicken". One of the more ingenious was the Washington Post: "T. Rex Closer to Gizzards Than Lizards". However, the New Scientist, particularly, over-reached itself with its portrayal of the find. The word "confirmed" is a gross overstatement (see below) and the word "granddaddy" is simply wrong, as birds were contemporaneous with T.rex.

What few have realised is that the T. rex sequence is mainly missing. In their supplementary information, the authors document their data for the dinosaur collagen. It looks like this (where the dashes represent missing data - visible in IE but there is a problem with Firefox. If you are using the latter, copy and paste into a text file to see the data):

----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GATGAPGIAGAPGFPGARGAPGPQGPSGAPGPK---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GVQGPPGPQGPR------------------------------------------------------------------------------------------------------------------------------------------------------------------------GSAGPPGATGFPGAAGR----------------------------------------------------------------------------GVVGLPGQR---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GLPGESGAVGPAGPPGSR------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Since molecular phylogenies are somewhat controversial even with full data, it seems completely wild to claim "confirmed" results at this stage of research. Furthermore, surprising outcome was obtained for the green anole (Anolis carolinensis, a lizard). This was expected to be grouped with alligators as a sister taxon. However, the phylogeny reported puts it at the base of the amniotes. This puts it as close to mammals as to alligators. "Such errors are common when working with limited sequences, Asara says." But if the data re T. rex and birds is accepted, why not the Anolis-mammal data? There are indications here that the researchers are letting "generally-agreed relationships" guide their analysis. Even more worrying, they suggest that the phylogeny emerging from their study validates the genuineness of the collagen extracted from the fossil bones. This is dangerously close to a circular argument.

"These results support the endogenous origin of the preserved collagen molecules and confirm the prediction based on morphology that, if biomolecules could be retrieved from a nonavian dinosaur, they would share a higher degree of similarity with birds than with other extant vertebrates."

Some have looked at this analysis and find it too speculative. For example, the Washington Post report has this:

"Pavel Pevzner, director of the Center for Algorithmic and Systems Biology at the University of California at San Diego, said his own research, soon to be published, refutes Asara's work. He said he cannot describe details until they are published, but he was blunt in his response to the new study, which appears in today's issue of the journal Science. The findings are "a joke," Pevzner wrote in an e-mail. "Serious evolutionary biologists will laugh reading this piece.""

Molecular Phylogenetics of Mastodon and Tyrannosaurus rex
Chris L. Organ, Mary H. Schweitzer, Wenxia Zheng, Lisa M. Freimark, Lewis C. Cantley, and John M. Asara
Science 320, 25 April 2008: 499.

Abstract: We report a molecular phylogeny for a nonavian dinosaur, extending our knowledge of trait evolution within nonavian dinosaurs into the macromolecular level of biological organization. Fragments of collagen [alpha]1(I) and [alpha]2(I) proteins extracted from fossil bones of Tyrannosaurus rex and Mammut americanum (mastodon) were analyzed with a variety of phylogenetic methods. Despite missing sequence data, the mastodon groups with elephant and the T. rex groups with birds, consistent with predictions based on genetic and morphological data for mastodon and on morphological data for T. rex. Our findings suggest that molecular data from long-extinct organisms may have the potential for resolving relationships at critical areas in the vertebrate evolutionary tree that have, so far, been phylogenetically intractable.

See also:

Callaway, E. T. rex confirmed as great granddaddy of all birds, NewScientist.com, 24 April 2008

Weiss, R. T. rex closer to Gizzards Than Lizards, The Washington Post, April 25, 2008; A02

Earlier this year, an interesting survey of first-year science students was conducted in the University of Cape Town, South Africa. A questionnaire was distributed to test their "knowledge and opinions of what they thought about evolution". Then came a course of 16 lectures on evolution, covering "the concept of evolution, the mechanisms of evolution, and dealt with hypotheses to test whether evolution occurred". After the course, the students were re-tesed with the same questions. The authors report that they "discovered no statistically significant change in the views of students before the evolution course and thereafter, for questions that challenged religious ideologies about creation, biodiversity, and intelligent design."

The authors frequently compare their findings with other studies, mainly to point out that the pattern is much the same wherever you go.

"Interestingly, the smallest change in Before/After responses to any question was the response to an ID argument, namely that "Organisms are incredibly well designed. This is proof that they must have been created by God." An impasse on this point mirrors the findings of others around the world."

There is a notable tension in their thinking about the relationship between evolutionary theory and Theism. On the one hand, they say that evolutionary theory does bring challenges:

"[D]espite scientific advances in evolutionary biology, evolution is often seen as contentious and "troubling". This is because evolutionary biology intersects and often challenges religious beliefs and values, which lead to an intellectual and spiritual dilemma. Thus, diplomacy and discussion become key in smoothing the interface between science and society."

On the other hand, towards the end, they fall back on sphere sovereignty (Gould's NOMA approach).

"[T]he biggest challenges evolutionary biology faces is that evolution is often equated with atheism, and students often feel that they need to choose between religious convictions and the credibility of evolution [. . .]. It is therefore important that students recognize that science and faith have separate domains, and that there are many scientists who are theists, and accept evolutionary theory as an explanation of the natural world."

Nevertheless, the authors do not appear to be completely convinced about these separate domains, as the write in their conclusions to say:

"We concur with Demastes et al. (1995) that because evolution often challenges preexisting conceptual ideas, a supportive classroom atmosphere is essential to ensure an understanding of evolution, even if this conflicts with cultural belief systems."

This vascillation between "separate domains" and "challenges [to] preexisting conceptual ideas" is a significant problem for educators. What is needed is an open debate about such matters, where evolutionary biologists interact with others advocating either Intelligent Design or Creationism to explore these issues in depth. The problem we face at present is that the science forums that are organised on this topic select their panels very carefully and dialogue and/or exposure to counter arguments is totally missing.

A further insight emerging from the survey is found in this paragraph:

"We further suggest that because students seem amenable to changing their views when presented with "facts", lecturers should ensure that they give examples of experimental evolutionary studies, and there should be strong emphasis on the scientific method of inquiry. [. . .] It may be equally important to simultaneously focus discussion on what constitutes a scientific theory and an empirical test, thereby equipping learners with the necessary tools and understanding to appreciate where ID fails and evolutionary theory holds from a scientific standpoint."

This is very interesting, because this emphasis on presenting "facts" is exactly in line with ID thinking (although the word "evidence" would probably be used to make the point). ID biologists welcome the opportunity to critically scrutinise the evidence, to find out what Darwinian mechanisms can and cannot do, to discuss the potential contribution of evo-devo to explain the diversification of living things and whether there is a route here to build complexity. We seek more evidence-based teaching, and less flag-waving statements like: "It is well recognized by scientists that evolution is the unifying theme that underlies the biological sciences" (which happens to be the first sentence of the paper). ID advocates are similarly keen to promote dialogue on what "constitutes a scientific theory and an empirical test", and the quotation above shows that this is clearly needed!

ACCEPTING EVOLUTION
Anusuya Chinsamy and Eva Plaganyi
Evolution, 62(1), 2008, 248-254 | doi:10.1111/j.1558-5646.2007.00276.x

Poor public perceptions and understanding of evolution are not unique to the developed and more industrialized nations of the world. International resistance to the science of evolutionary biology appears to be driven by both proponents of intelligent design and perceived incompatibilities between evolution and a diversity of religious faiths. We assessed the success of a first-year evolution course at the University of Cape Town and discovered no statistically significant change in the views of students before the evolution course and thereafter, for questions that challenged religious ideologies about creation, biodiversity, and intelligent design. Given that students only appreciably changed their views when presented with "facts," we suggest that teaching approaches that focus on providing examples of experimental evolutionary studies, and a strong emphasis on the scientific method of inquiry, are likely to achieve greater success. This study also reiterates the importance of engaging with students' prior conceptions, and makes suggestions for improving an understanding and appreciation of evolutionary biology in countries such as South Africa with an inadequate secondary science education system, and a dire lack of public engagement with issues in science.

See also:

Educators guide to dealing with "intelligent design", Internal Memorandum, Ivory Tower University, Department of Natural Sciences, no date.

The malaria parasite continues to plague humanity and the death toll is enormous. Much effort has been devoted to studying its life cycle and all identifiable natural mechanisms giving resistance. The best known trait conferring resistance is sickle cell anaemia: this affects red blood cells so that the malaria parasite (Plasmodium falciparum) does not gain a foothold in the body, but at the same time it adversely affects the functionality of the blood so that the human is regarded as having a genetic disease.

Mosquitoes can transmit malaria

It has been found recently that red blood cells from patients with pyruvate kinase deficiency are resistant to invasion by the malaria parasite. Furthermore, those cells that do succumb to infection are more rapidly cleared by macrophages than are infected cells from control subjects. Kevin Kain, one of the lead researchers on the project is quoted as saying: "Our research shows that people who have an enzyme deficiency or those who carry the gene trait for this deficiency may be protected from severe and fatal malaria." It is hoped that the findings will lead to the design of novel therapies by enhancing the body's protective pathways instead of inundating the body with drugs.

This research brings to mind Michael Behe's analysis of malaria research findings for understanding what Darwinian mechanisms can and cannot do. To explain his conclusions, he rejected the analogy of an arms race (often used by Darwinians to describe the outcome of the struggle for survival). In the struggle against the malaria parasite, we do not see an arms race (with the incremental refinement of weapons). Rather, according to Behe, we see trench warfare. In wartime, a bridge could be blown up to prevent the enemy from crossing; a tree could be felled across a railway track to create disruption. The trench warfare analogy fits malaria well (sickle cell anaemia involves damage to the red blood cells, and in this case, resistance is conferred by pyruvate kinase deficiency). The same lessons are learned from antibiotic resistance, which might arise as a loss of a transporter or the alteration of a ribosome.

Darwinians say that we can obtain new functions by mutation and selection, but the evidence is that loss of function is the explanation for both resistance against malaria and antibiotic resistance.

Pyruvate Kinase Deficiency and Malaria
Kodjo Ayi, Gundula Min-Oo, Lena Serghides, Maryanne Crockett, Melanie Kirby-Allen, Ian Quirt, Philippe Gros, and Kevin C. Kain.
The New England Journal of Medicine, 358(17), April 24 2008, 1805-1810.

SUMMARY: Malaria that is caused by Plasmodium falciparum is a significant global health problem. Genetic characteristics of the host influence the severity of disease and the ultimate outcome of infection, and there is evidence of coevolution of the plasmodium parasite with its host. In humans, pyruvate kinase deficiency is the second most common erythrocyte enzyme disorder. Here, we show that pyruvate kinase deficiency provides protection against infection and replication of P. falciparum in human erythrocytes, raising the possibility that mutant pyruvate kinase alleles may confer a protective advantage against malaria in human populations in areas where the disease is endemic.

See also:

Mutation In Human Gene Helps Protect Against Fatal Malaria, ScienceDaily (Apr. 22, 2008)

According to National Geographic News, a remarkable evolutionary change has occurred in a population of lizards:

"Italian wall lizards introduced to a tiny island off the coast of Croatia are evolving in ways that would normally take millions of years to play out, new research shows. In just a few decades the 5-inch-long (13-centimeter-long) lizards have developed a completely new gut structure, larger heads, and a harder bite, researchers say."

The experiment started in 1971, when 5 adult pairs of Podarcis sicula were introduced to the tiny island of Pod Mrcaru. Then came the Croatian War of Independence which lasted until the mid-1990s. Tourism did not start again, however, until about 2004, and this is when researchers returned to the island to see what had happened in the intervening years.

"Lizards Evolve "Overnight" on Island" says National Geographic News (to enlarge, click here)

What had happened to the introduced species? What impact had this had on the native lizards? "What they found, however, was shocking." No trace was found of the lizard species Podarcis milisellensis, which had previously inhabited the island. The introduced species were everywhere, at higher densities than their homeland. Furthermore, they had developed an appetite for eating plant food (34% in the Spring and 61% in the summer) whereas plant consumption in the source population was low (4%-7%). Their social structure was different and the lizards no longer defended territories.

Detailed analysis revealed three apparently related morphological changes: "head morphology, bite strength, and digestive tract structure". They appear to be adaptive, as all are related to the increased diet of plant materials.

"Physically, however, the lizards were not built to digest a vegetarian diet. Researchers found that the lizards developed cecal valves - muscles between the large and small intestine - that slowed down food digestion in fermenting chambers, which allowed their bodies to process the vegetation's cellulose into volatile fatty acids. "They evolved an expanded gut to allow them to process these leaves," Irschick said, adding it was something that had not been documented before. "This was a brand-new structure.""

In the paper, the authors note that <1% of all currently known species of squamates have cecal valves, and that: "These valves are similar in overall appearance and structure to those found in herbivorous lacertid, agamid, and iguanid lizards and are not found in other populations of P. sicula or in P. melisellensis." Herbivory explains why cecal valves are useful to these lizards. Also, "along with the ability to digest plants came the ability to bite harder, powered by a head that had grown longer and wider." All these changes came in a 36 year time window.

So, the question must be asked: how are we to understand the observations? The harder bite and the larger head are two aspects of the same phenomenon. Observations like this can be related to trends observed in artificial selection and they are not surprising. We have no reason to think that natural selection acting on natural variations over 30 generations cannot deliver this outcome.

The cecal valve finding is, however, dramatic. This is the finding that drew the comment that the animals "are evolving in ways that would normally take millions of years to play out". There can be no rationale for a Darwinian mechanism here - involving incremental assembly of the cecal valve. There is no time for this, even if a gradualist route could be found. No, the relevant genetic information must be present in the ancestors and epigenetic factors can be inferred to have activated the relevant mechanisms to make the structure. This research is revealing that organisms have a capacity for variability that goes significantly beyond their current phenotype. This implication has not escaped the attention of creationist biologists, who find this research a vindication of their view that animal radiations are rapid and the expression of innate variability embedded in the genome. It would be an interesting and educational activity for students to evaluate this theoretical model alongside others - although we can already be confident that Darwinism would not fare well in the exercise.

Rapid large-scale evolutionary divergence in morphology and performance associated with exploitation of a different dietary resource
Anthony Herrel, Katleen Huyghe, Bieke Vanhooydonck, Thierry Backeljau, Karin Breugelmans, Irena Grbac, Raoul Van Damme, and Duncan J. Irschick
Proceedings of the National Academy of Sciences, 25 March 2008 105: 4792-4795 | doi 10.1073/pnas.0711998105

Abstract: Although rapid adaptive changes in morphology on ecological time scales are now well documented in natural populations, the effects of such changes on whole-organism performance capacity and the consequences on ecological dynamics at the population level are often unclear. Here we show how lizards have rapidly evolved differences in head morphology, bite strength, and digestive tract structure after experimental introduction into a novel environment. Despite the short time scale (~36 years) since this introduction, these changes in morphology and performance parallel those typically documented among species and even families of lizards in both the type and extent of their specialization. Moreover, these changes have occurred side-by-side with dramatic changes in population density and social structure, providing a compelling example of how the invasion of a novel habitat can evolutionarily drive multiple aspects of the phenotype.

See also:

Johnson, K., Lizards Rapidly Evolve After Introduction to Island National Geographic News (April 21, 2008)

Lizards Undergo Rapid Evolution After Introduction To A New Home, ScienceDaily (Apr. 18, 2008)

The first known lungless frog has been found in the Indonesian region of Borneo. It lives in fast-flowing water and breathes entirely through its skin.

"As the researchers were doing initial dissections of the frogs as they caught them in the field, they were surprised to discover these amphibians lacked lungs. "At first I did not believe that the frogs had no lungs, but then, we just kept on seeing the evidence pile up. I was flabbergasted," Bickford said."

Barbourula kalimantanensis (Photo: David Bickford, Current Biology. Larger image here.)

Although the words "evolution" and "evolutionary history" are noticeable in the paper and media reports, it is worth reminding ourselves that lunglessness involves the loss of a complex organ. The find reveals degenerative change, rather like blindness in cave fish. Such traits are all derived features, indicative of extreme specialisation.

"Of all tetrapods (animals with four limbs), lunglessness is only known to occur in amphibians. There are many lungless salamanders and a single species of caecilian, a limbless amphibian resembling an earthworm, known to science. Nevertheless, Bickford said, the complete loss of lungs is a particularly rare evolutionary event that has probably only occurred three times. The discovery of lunglessness in a secretive Bornean frog supports the idea that lungs are a malleable trait in amphibians, which represent the evolutionary sister group to all other tetrapods, according to the researchers."

As a general rule, as knowledge develops, so does the language we use. Researchers find it necessary to define their terminology and even invent new words to ensure clarity. Significantly, this has not happened with one particular word in evolutionary biology. There are numerous meanings of the word "evolution" and yet its usage within the research community is much the same as usage by the man in the street. Sometimes it refers to allele changes in a population (e.g. the peppered moth), sometimes to the development of barriers to breeding (e.g. ring species), and there are several other usages that reach deeper into Darwin's "Tree of Life" concept. In addition, there is the philosophical meaning of the word: drawing together gradualism, materialism and the rejection of ultimate purpose. Many years ago, Phillip Johnson drew attention to this problem in his lectures and books, but the evolutionary community seems to prefer retaining the E-word with a fuzzy meaning.

These thoughts are relevant to the lungless frog because this is not an example illustrating the evolution of complexity, but the reverse. It is also relevant because, for research to progress, it is important to clarify mechanisms. The tendency within evolutionary biology is to explore a variety of mechanisms but to fall back on Darwinism when the going gets tough. Darwinism is the baseline that is deemed secure (especially as 2009 approaches). The problem is that Darwinism can explain only minor changes and extrapolation of observed small variations to explain major transitions has never been justified scientifically. Fuzzy meanings to "Evolution" are inhibitors: they do nothing to move research forward.

To develop an analogy, this frog has some similarities with evolutionary biology research. As long as there is plenty of aerated water, the research team has a sense that progress is being made. However, when the water becomes stagnant (as it often does!), the team finds it cannot breathe properly. The tools they are using do not deliver convincing answers. What is needed is a breath of fresh air - and this can be provided by people who are prepared to look outside the philosophical naturalism of their peers and recognise pervasive design features in the natural world. By grappling with design in living things, the capabilities and limitations of each proposed mechanism can be explored without it being force-fitted into a particular paradigm.

A lungless frog discovered on Borneo
David Bickford, Djoko Iskandar, and Anggraini Barlian
Current Biology, online 17 April 2008, 18(9), | doi 10.1016/j.cub.2008.03.010

Summary: The evolution of lunglessness in tetrapods (amphibians, reptiles, birds, and mammals) is an exceedingly rare event. So far lunglessness is known to occur only in amphibians, in particular two families of salamanders [1, 2] and a single species of caecilian [3]. Here, we report the first case of complete lunglessness in a frog, Barbourula kalimantanensis, from the Indonesian portion of Borneo. Previously only known from two specimens [4, 5], a recent expedition to central Kalimantan on Borneo rediscovered two new populations of this enigmatic aquatic frog. This allowed for a more comprehensive assessment of the species' ecology and anatomy that led to the discovery of its lack of lungs. Loss of lungs in Amphibia is most likely due to their evolutionary history at the interface between aquatic and terrestrial habitats and their ancient ability to respire through the skin [5].

See also:

First Lungless Frog Discovered, ScienceDaily (Apr. 8, 2008)

Choi, C.Q. Bizarre Frog Has No Lungs, Livescience (7 April 2008)

The human Genome Project has stimulated numerous new avenues for research, not the least of which relates to the functionality of the genome that does not code for proteins. Often referred to as "Junk DNA", this genetic material has previously had a tough time getting taken seriously. But not now. There are many signs of functionality. This is one aspect of the background to some newly published research.

"How much of the rest performs other biological functions, and how much is merely residue of prior genetic events? Scientists from Cold Spring Harbor Laboratory (CSHL) and the University of Chicago now report that one of the steps in turning genetic information into proteins leaves genetic fingerprints, even on regions of the DNA that are not involved in coding for the final protein. They estimate that such fingerprints affect at least a third of the genome, suggesting that while most DNA does not code for proteins, much of it is nonetheless biologically important - important enough, that is, to persist during evolution."

Genetic fingerprints reveal functionality in a large part of the human genome.

"Previous researchers assumed that mutations in the middle of introns do not affect the final protein, so they simply accumulate." To assess the evidence for selection, the researchers looked in the genomes of humans and mice for symmetry and repeat patterns in specific code sequences.

"To test for conservation, researchers need to find matching stretches in the two species. This is relatively easy for stretches that "code" for proteins, where scientists long ago learned the meaning of the sequence. For "noncoding" regions, however, the comparison is often ambiguous. Even within a gene, stretches of DNA that code for pieces of the target protein are usually interspersed with much larger noncoding stretches, called introns, that are removed from the RNA working copy of the DNA before the protein is made."
[. . .]
"The scientists found a preference for some "letters" across intron regions, and the opposite preference in coding regions. Together, these regions make up at least a third of the genome, which is thus under selective pressure during evolution. The result supports other recent studies that suggest that, although most DNA does not code for proteins, much of it is nonetheless biologically important."

Without getting into details, this finding is potentially of great importance. Introns comprise about 30% of the genome, and the fingerprint of functionality is pervasive. The rest of the genome awaits further research, and we may find that most of that has some functionality also. We still have a lot to find out about how the splicing-regulatory elements work, and we can predict some interesting tests of contrasting hypotheses. The evolutionary hypothesis appears to be that Junk DNA has been coopted for the purposes of regulation, and can be described in terms of "tinkering evolution". The design hypothsis says nothing directly about the way the DNA code was assembled, but the prediction is of "exquisite design" features.

It is worth drawing attention to a blog by Cornelius Hunter which points out the gratuitous link with evolutionary theory in the various reports of this research:

"The paper's title alone ("RNA landscape of evolution for optimal exon and intron discrimination") suggests a new finding about evolution, and the paper concludes that human genes seem to have been optimized "during evolution." But the "during evolution" part is gratuitous. The key findings are about how the genetic signals work, not that they evolved. There is, in fact, nothing in the findings to indicate evolution. The science writer concluded that "the researchers found signs that evolution rejects some types of mutations," but there simply was no such finding. What the researchers actually found was the presence of certain subtle signals in the genome. They found no evidence that the signals were produced by evolution."

RNA landscape of evolution for optimal exon and intron discrimination
Chaolin Zhang, Wen-Hsiung Li, Adrian R. Krainer, and Michael Q. Zhang
Proc. Natl. Acad. Sci. USA, April 15 2008, 105(15, 5797-5802 | doi 10.1073/pnas.0801692105

Abstract: Accurate pre-mRNA splicing requires primary splicing signals, including the splice sites, a polypyrimidine tract, and a branch site, other splicing-regulatory elements (SREs). The SREs include exonic splicing enhancers (ESEs), exonic splicing silencers (ESSs), intronic splicing enhancers (ISEs), and intronic splicing silencers (ISSs), which are typically located near the splice sites. However, it is unclear to what extent splicing-driven selective pressure constrains exonic and intronic sequences, especially those distant from the splice sites. Here, we studied the distribution of SREs in human genes in terms of DNA strand-asymmetry patterns. Under a neutral evolution model, each mononucleotide or oligonucleotide should have a symmetric (Chargaff's second parity rule), or weakly asymmetric yet uniform, distribution throughout a pre-mRNA transcript. However, we found that large sets of unbiased, experimentally determined SREs show a distinct strand-asymmetry pattern that is inconsistent with the neutral evolution model, and reflects their functional roles in splicing. ESEs are selected in exons and depleted in introns and vice versa for ESSs. Surprisingly, this trend extends into deep intronic sequences, accounting for one third of the genome. Selection is detectable even at the mononucleotide level, so that the asymmetric base compositions of exons and introns are predictive of ESEs and ESSs. We developed a method that effectively predicts SREs based on strand asymmetry, expanding the current catalog of SREs. Our results suggest that human genes have been optimized for exon and intron discrimination through an RNA landscape shaped during evolution.

See also:

Scientists Find a Fingerprint of Evolution Across the Human Genome, Cold Spring Harbor, NY. Press Release, 8 April 2008

Hunter, C. Raising the Bar on the Evolution Debate, Evolution News & Views, 15 April 2008

"Is there anybody out there?" is a question that drives media interest in astrobiology and probably all science fiction. Enthusiasts routinely rehearse their arguments that persuade them that the universe is teeming with life, some of which is intelligent. However, these arguments are not very robust. The answer to the question, according to a recent paper is "Probably not".

"Structurally complex and intelligent life evolved late on Earth and it has already been suggested that this process might be governed by a small number of very difficult evolutionary steps.
Prof Watson, from the School of Environmental Sciences, takes this idea further by looking at the probability of each of these critical steps occurring in relation to the life span of Earth, giving an improved mathematical model for the evolution of intelligent life."

A wishful wave of friendship to some passing aliens

There are constraints on the timescales for the evolution of life, according to the author. The sun has been the primary source of heat and light for the Earth for 4.5 Ga and models of solar activity give it another billion years.

"The Earth's biosphere is now in its old age and this has implications for our understanding of the likelihood of complex life and intelligence arising on any given planet," said Prof Watson. At present, Earth is the only example we have of a planet with life. If we learned the planet would be habitable for a set period and that we had evolved early in this period, then even with a sample of one, we'd suspect that evolution from simple to complex and intelligent life was quite likely to occur. By contrast, we now believe that we evolved late in the habitable period, and this suggests that our evolution is rather unlikely. In fact, the timing of events is consistent with it being very rare indeed."

Starting with some classic work by Maynard Smith and Szathmary, Watson lists 7 major transitions and uses a probability density function to allocate probabilities to each transition.

"These steps included the emergence of single celled life about half a billion years after the Earth was formed, multicellular life about a billion and a half years later, specialized cells allowing complex life forms with functional organs a billion years after that, and human language a billion years later still."

Crucial to the model are the probabilities assigned. Watson uses very generous figures, constrained by the thought that evolution will occur, given enough time. If any aspect of the transitions involve design inputs, the probabilities will inevitably be much, much lower. The paper gives an optimistic scenario:

"In his model, the probability of each evolutionary step occurring in any given epoch is 10 percent or less, so the total probability that intelligent life will emerge is quite low (less than 0.01 percent over 4 billion years). Even if intelligent life eventually emerges, the model suggests its persistence will be relatively short by comparison to the lifespan of the planet on which it developed."

Seth Shostak, Senior Astronomer at the SETI Institute, summarised Watson's argument thus: "intelligent life will be dismayingly rare". Watson, himself, sees his work as lending "some theoretical support to the Rare Earth hypothesis of Ward and Brownlee." It also lends support to the design-orientated arguments of Gonzalez & Richards in The Privileged Planet. To those who see an evolutionary path to intelligent life as an inevitability, Watson has this to say:

"From the perspective adopted here, this appearance of evolution as a monotonic "progress" toward ourselves results from "anthropic self-selection bias". In this case, there is no need to postulate any directionality to evolution; and, in general, the kind of outcome seen on Earth may be vanishingly unlikely."

Implications of an Anthropic Model of Evolution for Emergence of Complex Life and Intelligence
Andrew J. Watson
Astrobiology. February 1, 2008, 8(1): 175-185 | doi:10.1089/ast.2006.0115

Abstract: Structurally complex life and intelligence evolved late on Earth; models for the evolution of global temperature suggest that, due to the increasing solar luminosity, the future life span of the (eukaryote) biosphere will be "only" about another billion years, a short time compared to the ~ 4 Ga since life began. A simple stochastic model (Carter, 1983) suggests that this timing might be governed by the necessity to pass a small number, n, of very difficult evolutionary steps, with n less than 10 and a best guess of n equals 4, in order for intelligent observers like ourselves to evolve. Here I extend the model analysis to derive probability distributions for each step. Past steps should tend to be evenly spaced through Earth's history, and this is consistent with identification of the steps with some of the major transitions in the evolution of life on Earth. A complementary approach, identifying the critical steps with major reorganizations in Earth's biogeochemical cycles, suggests that the Archean-Proterozoic and Proterozoic-Phanerozoic transitions might be identified with critical steps. The success of the model lends support to a "Rare Earth" hypothesis (Ward and Brownlee, 2000): structurally complex life is separated from prokaryotes by several very unlikely steps and, hence, will be much less common than prokaryotes. Intelligence is one further unlikely step, so it is much less common still.

See also:

Is there anybody out there? University of East Anglia Communications Office, April 2008

Ruley, J.D. Intelligence: A Rare Cosmic Commodity, Astrobiology Magazine, 14 April 2008.

Bostrom, N., Where Are They? Why I hope the search for extraterrestrial life finds nothing. Technology Review, May/June 2008

Although the forth-coming film EXPELLED: No Intelligence Allowed has been featured in many blogs, popular science magazines have only started to make their comments. Michael Shermer's piece for Scientific American sets the tone in establishing at the outset that the film is "a Science-free Attack on Darwin" and that it advances "the pseudoscience of intelligent design". The lack of clarity about the real issues in this debate is apparent from the comment: "Intelligent design creationists, by contrast, have no interest in doing science at all." This is so blatantly untrue that most readers will realise that that something deeper is going on here.

DEBATING DARWIN: Ben Stein stands in front of a statue of Darwin at The Natural History Museum in London. (Photo by Kelly Engstrom)

It seems that nothing in the documentary gains Shermer's approval. He does not like Darwin's ideas being used as justification for any social action, whether it is Nazi attempts to weed out the weak and unfit, or greedy exploiters of others within the capitalist economic system. He says: "Scientific theorists cannot be held responsible for how their ideas are employed in the service of non-scientific agendas." The problem here is that of naivety. People do use Darwinism to justify their actions. They claim this is the way nature works, so it must be OK. There are books being published on a regular basis that are trying to make Darwinism the key to unlock ethics and to say what is "natural" (see comments in a previous blog).

The root problem with Shermer's understanding of science is that he wants to demarcate scientific knowledge from thinking that is not science. This is a hopeless task, and those who set out to do this always miss out some significant areas of scientific research. What he does is to compartmentalise knowledge - yet knowledge should not be compartmentalised! Ultimately, knowledge needs to be unified and we should make sure that knowledge is always related to truth. If we do not have this vision, scholarship will forever be impoverished. In his concluding paragraphs, Shermer writes:

"When will people learn that Darwinian naturalism has nothing whatsoever to do with religious supernaturalism? By the very definitions of the words it is not possible for supernatural processes to be understood by a method designed strictly for analyzing natural causes. Unless God reaches into our world through natural and detectable means, he remains wholly outside the realm of science.
So, yes Mr. Stein, sometimes walls are bad (Berlin), but other times good walls make good neighbors. Let's build up that wall separating church and state, along with science and religion, and let freedom ring for all people to believe or disbelieve what they will."

Here, Shermer's compartmentalised approach is vividly displayed. Science is a method "designed strictly for analyzing natural causes", but does this mean archaeologists and forensic scientists are banished from science? This must be wrong - but Shermer can only concede this by admitting design inferences into science. Then he would have to modify his comment about God - to allow for intelligent design to be detected by rational means.

Instead of this, Shermer wants to erect a wall: one separating science and religion. He wants knowledge to be compartmentalised. He thinks that science and religion should be good neighbours who never talk to each other! There is no acknowledgement in the piece that many atheistic scientists will have nothing to do with these walls. For them, the only knowledge worth having is scientific knowledge - and all else is superstition and delusion. They do not want to be good neighbours to "religion" but are working tirelessly to replace delusions with scientific atheism. These are the people who have captured the wills of the intelligentsia in the US and many parts of Europe and who make it clear that if others will not join them, they will not find a home within the scientific community.

Others can see this message in the film. Here is Kate Wright in American Thinker:

"Via onscreen interviews with Neo-Darwinists such as Professor Richard ("The God Delusion") Dawkins, Ben typifies the pervasive practice of authoritarian attitudes in academic elites, particularly toward God-fearing people. As such, this is not a film about believers vs. non-believers. This is a first-rate expose about the consequences of suppressing freedom of expression, based on the questionable assumption that atheistic secularism is the state religion of the United States of America. [. . .]
This film states that Neo-Darwinism is about world view, not scientific exploration."

Another who has felt the pulse of the documentary is Joseph Farrar:

"It turns out some of the most hardened, doctrinaire anti-design zealots in the scientific establishment - people like Richard Dawkins, author of "The God Delusion" and, coincidentally, the de facto leader of the worldwide atheist movement - aren't really opposed to the notion of design at all. They just can't accept God as the designer.
You will hear some of the world's most celebrated evolutionists admit design is possible - just not by the hand of God.
They will attribute the possibility of design to visitors from other planets and even to crystals. The two things they cannot tolerate are consideration of God's role and any of their colleagues deviating from their own ideas about origins."

Finally, here is Ben Stein himself, talking to Megan Basham in World Magazine:

"I would want it to open freedom of speech at schools and universities so that people could express their concerns and reservations about Darwinism and any subject in science related to macroevolution so that one small group wouldn't have a lock on what's discussed on campuses. And there's already some progress on that front. In Florida there's a law making its way through the House of Representatives that helps ensure academic freedom by mandating that you cannot be punished for questioning Darwinism. And there's a similar law that's about to be introduced in Missouri to the same effect. And I think it's unfortunate that we even need such laws, but apparently we do.
Besides that, I want people to walk away remembering that there is a great deal that Darwinism cannot explain and that there is a great deal that can be explained by intelligent design. If you have a book in front of you that has hundreds of millions of words written in it, it was probably written by an author rather than by rain dripping on a page."

Expelled: No Intelligence Allowed--Ben Stein Launches a Science-free Attack on Darwin
Michael Shermer
Scientific American, 9 April 2008

In a new documentary film, actor, game show host and financial columnist Ben Stein falls for the pseudoscience of intelligent design

See also:

Wright, K. Ben Stein's Intelligent Adventure, American Thinker, 13 April 2008

Basham, M. Mocked and belittled, World Magazine, April 2008 (restricted access)

Farah, J. I can't wait to be 'Expelled', World Net Daily, March 04, 2008

Luskin, C. Michael Shermer's Fact-Free Attack on Expelled Exposes Intolerance of Darwinists towards Pro-Intelligent Design Scientists (Part 1) (Part 2), (Part 3), Evolution News & Views, April 2008.

Quotation: "Expelled, by contrast, points up the unhealthy state of contemporary science regarding biological origins. Our intellectual elite have insulated Darwinian evolution from scientific scrutiny. Moreover, they have institutionalized intolerance to any criticism of it. Expelled documents this institutionalized intolerance and thereby unmasks the hypocrisy of an intellectual class that pretends to value freedom of thought and expression, but undercuts it whenever it conflicts with their deeply held secular ideals." (Bill Dembski, The Difference 'Expelled' Will Make, Baptist Press News, Apr 18, 2008).

An editorial in Nature this week considers our thinking about what is "natural" and suggests it often bypasses reason.

"From an evolutionary perspective, we humans have good reason to be wary of things that seem to be 'unnatural'. Anything out of the ordinary can be dangerous. But the evolutionary origin of that response also guarantees that it will be guided more by emotion than by reason."

Two examples are supplied. The first concerns a transgendered woman who, as a man, married another woman. The wife could not bear children, so the transgendered woman ceased taking the hormone treatment and was given artificial insemination. This person is now pregnant and expecting a baby girl. The Editorial contrasts the "natural" longing for a baby with the "visceral responses [that] were common on message boards and blogs on the Internet, where the situation was often held to be disgusting and unnatural." Attention was then drawn to a news feature about bdelloid rotifers in the same issue of Nature: "Biologists have found that gender-straddling and gender-switching behaviours are not at all uncommon in the 'natural' world, either for humans or non-human animals". The inference is that there is a lesson here for us: for these rotifers, apparently unnatural behaviour is natural!

The second example concerns neuroenhancing drugs. In an online poll, "respondents were asked to report on their non-medical use of drugs such as modafinil and methylphenidate to improve their concentration."

"The claim, repeated in many responses to our survey is that using such drugs, or any performance-enhancing drug, makes accomplishments somehow less worthy because they aren't natural. But again, what is 'natural'? Devices such as glasses, hearing aids, pacemakers and artificial hips are unnatural. Yet they are widely accepted as legitimate ways to enhance the human experience. By the same token, if drugs enhance performance on a standardized test, what is so 'natural' about prep courses designed to improve scores?"

All this led up to the conclusion that our sense of "natural" is developed in a social and cultural context and owes more to emotion than to reason. Furthermore, we should get used to the idea that our sense of "natural" is evolving.

"Ultimately, our visceral concept of what is 'natural' depends on what we are used to, and will continue to evolve as technology does. But in the meantime, we should not allow it to distract us from the rational consideration of deeper and more important ethical issues."

The great divide: materialistic science reduces ethics to an evolving, utilitarian, postmodernist code

This message, that ethics is utilitarian and evolving as society changes, is shared by many with responsible positions within the science community. Last year, Colin Blakemore, chief executive of the Medical Research Council in the UK, wrote: "Because morality is, for all but the most stubbornly impervious to practical evidence, a matter of utilitarian dialectic. Yesterday's moral outrage has a way of becoming today's necessary evil and tomorrow's common good."

We have a curious situation developing within science: everyone is agreed that ethical frameworks are needed and conformance to ethical guidelines is a requirement of funding bodies, but those ethical guidelines are not a product of scientific research. Consequently, many scientists adopt a postmodernist stance when they refer to ethics, as was pointed out and discussed in an earlier blog.

Still in the same issue of Nature, Eugenie Scott reviewed the book Life as it is by William Loomis. This book "is a tour of the brave new biology relevant to such social issues as abortion, euthanasia, the use of embryonic stem cells, cloning, overpopulation and global warming. Loomis holds that scientific evidence should be taken into account when making socially important decisions." This approach has been tried many times before, but it always fails to convince, because it is possible to find examples of almost every conceivable practice in the natural world. As an example, Scott points out what the author says about embryos (to inform practices relating to embryo research):

"Loomis emphasizes that at the cellular level life is cheap: at any given moment, billions of bacteria in our body are dying. A human zygote is merely a single cell, so shouldn't we think of it as such rather than the multicellular, functioning, conscious and precious baby into which it might develop? If a zygote is just a cell, and cells die regularly, then the answer to whether it is ethically permissible to destroy it is yes."

The good thing about Scott's review is that she realises Loomis is expecting too much from his chosen methodology. "But [Loomis's] argument comes after the ethical question of whether a zygote is just a cell, which is one that science cannot answer. The ethical status of a human zygote or early-stage embryo turns on the issue of personhood." Furthermore:

"The idea that a realistic understanding of biology will usher in a paradise of ethical correctness is naive: the panoply of extra-scientific considerations that influence ethical decision-makings cannot be ignored or minimized. A weakness of Loomis's book is his comparative neglect of such considerations. But if his intention is less ambitious, namely that a realistic appreciation of biology ought to inform ethical decision-making, then that is incontrovertible."

Unfortunately, his intention is not "less ambitious". Consequently, this book reveals, yet again, the bankruptcy of materialistic science when it comes to issues of ethics and morality. As Scott says: "Ethics is about the oughts and the shoulds" - but this implies a realm of truth about human behaviour that scientists holding to a materialistic philosophy cannot handle. This is what pushes them into postmodernism and away from understanding ethics rationally. The "oughts and the shoulds" come from outside science. They can only be understood rationally in the context of a purposeful universe, where human beings gain their dignity, not from something intrinsic to our material bodies, but from the will and purpose of an intelligent Designer.

Editorial: Defining 'natural'
Nature 452, 665-666 (10 April 2008) | doi:10.1038/452665b

Abstract: Visceral reactions to an act should not distract from the real ethical issues.

Brave new bioethics
Eugenie Scott
Nature 452, 690-691 (10 April 2008) | doi:10.1038/452690a

BOOK REVIEWED - Life As It Is: Biology for the Public Sphere
by William F. Loomis
University of California Press: 2008. 272 pp.

First paragraph: Science's task is to explain the natural world: what it is, how it works and why it is the way it is. Ethics is about the oughts and the shoulds. Most ethicists - religious and secular - agree that knowledge of the natural world helps us make better, or at least better-informed, ethical decisions. But, as David Hume, Thomas Henry Huxley and G. E. Moore have noted, a particular understanding of nature does not dictate a unique moral stance. For every Alexander Pope declaring "Whatever is, is right," there is a Rose Sayer (from the film The African Queen) retorting, "Nature ... is what we are put in this world to rise above!"

Evolutionary theory is considered by many to provide integration and coherence to biology. 'Nothing makes sense without it', they say. Some have pointed to fish farming as an area where evolutionary thinking has practical applications and commercial relevance. This was the premise of a policy forum paper in November 2007 that addressed this topic:

"Darwinian evolution is the driving process of innovation and adaptation across the world's biota. Acting on top of natural selection, human-induced selection pressures can also cause rapid evolution. [. . .] studies based on fisheries data and controlled experiments have provided strong empirical evidence for fisheries-induced evolution over a range of species and regions. These evolutionary changes are unfolding on decadal time scales-much faster than previously thought."

Overfishing is a real problem in many parts of the world leading to rapid phenotypic changes.

Evolutionists have championed life-history theory, which "predicts that increased mortality generally favors evolution toward earlier sexual maturation at smaller size and elevated reproductive effort." The authors claim:

"Although alternative causal hypotheses can be difficult to rule out, fisheries-induced evolution consistently arises as the most parsimonious explanation after environmental factors have been accounted for. The question is not whether such evolution will occur, but how fast fishing practices bring about evolutionary changes and what the consequences will be.
Life-history traits are among the primary determinants of population dynamics, and their evolution has repercussions for stock biomass, demography, and economic yield."

The authors propose a tool for the management of evolving resources: Evolutionary Impact Assessment (EvoIA). Their enthusiasm for an evolutionary perspective is captured by the following quotes:

"An evolutionarily enlightened management approach is needed."
"This perspective emphasizes that evolution underlies ecology and influences economies."
"Successful management, therefore, will require the ecological and evolutionary consequences of fishing to be evaluated and mitigated. Adopting EvoIAs will enable fisheries managers to rise to this challenge."

It is worth distinguishing between the genetic changes occurring within contemporary ecosystems (often identified using the term microevolution) and the unobserved transformations that evolutionists need to explain the differences between organisms representing the higher taxonomic levels. The microevolutionary changes are not controversial, and those who would not identify themselves as Darwinians/evolutionary biologists are happy to work with life-history concepts in the context of ecological change.

However, two recent letters in Science have flagged up some additional interesting issues relating to the policy forum paper. Both challenged the view that fisheries-induced evolution (FIE) is the "most important driver of changes in life-history characteristics of heavily exploited marine fishes. Although Jorgensen et al. give the impression that this is well established, the evidence supporting FIE unfortunately remains circumstantial and is often open to alternative interpretations." The first letter questioned the evidence the authors provided to justify their proposed strategy:

"To make the case for EvoIAs, Jorgensen et al. present a selective set of studies - those concluding that FIE was a likely cause of the observed changes, after considering some environmental effects (see their table S2). In doing this, they excluded results that do not support their case. Furthermore, because FIE is often a matter of interpretation and the authors of the Policy Forum are strong advocates of FIE, the majority of the studies on life-history traits included in table S2 were their own. Their analysis does not represent a consensus opinion developed from critical scrutiny of the studies currently available."

The second letter made the point that observed changes do not equate with genetic changes. Consequently the EvolIA tool must be considered critically.

"This is a well-motivated idea in principle, but their reasoning relies entirely on the assumptions that fisheries-induced evolution (FIE) occurs commonly and that it is an undisputable fact. Neither of these assumptions is true. None of the studies of exploited fish populations in their article have provided genetic evidence for the observed phenotypic changes. Because evolution is by definition a change in the genetic constitution of a population, an evolutionary change cannot be postulated without demonstrating a genetic basis for the observed phenotypic shift. In fact, phenotypic changes in mean trait values due to simple environmental inductions are common, as are cases where populations are not evolving despite strong directional selection acting on heritable traits. Furthermore, several studies have shown that observed phenotypic shifts in exploited fish populations are fully consistent with simple environmentally induced changes."

More significantly, the second letter raises the important issue of Darwinians 'seeing the world' through coloured glasses. They acknowledge that some of the case studies listed in the Jorgensen et al. Policy Forum might genuine examples of FIE - but genetic confirmation is needed!

"However, until that proof is provided, the claims about FIE are nothing but "adaptive storytelling". As pointed out by S. J. Gould and R. C. Lewontin three decades ago, unwillingness to consider alternatives to adaptive stories, reliance on plausibility as a criterion for accepting speculative tales, and failure to consider adequately competing themes are characteristics of an "adaptationist program" that seems to have become revitalized in the context of fisheries-induced "evolution.""

Of course, Jorgensen et al. provided a response to these letters. What is of interest to this blog is the way Darwinism acts as a constraint on the thinking of scientists. They did not like being challenged on the lack of genetic evidence for FIE.

"This claim questions the fundamental assumption that scientists can make inferences about genotypes by studying phenotypes. It is worth remembering that Darwin formulated his theory of evolution with a similar assumption - that traits are heritable - nearly a century before DNA was found to carry hereditary information. Without such assumptions, evolutionary ecology could not operate."

It is worth remembering that Darwin thought all variations were evidence for his theory, allowing him to claim that natural selection was analogous to artificial selection. Mendel changed all that: most of the phenotypic variations we see are innate and they occur without any changes to the genotype.
There is no controversy that some Darwinian concepts are useful to ecology, but we must not allow the situation to develop where ecology is equated with Darwinism.

Correspondence: The Role of Fisheries-Induced Evolution
Howard I. Browman, Richard Law, C. Tara Marshall;
Anna Kuparinen, Juha Merila ;
Response by Christian Jorgensen et al.
Science 320, 4 April 2008: 47-50.

Managing Evolving Fish Stocks
Christian Jorgensen, Katja Enberg, Erin S. Dunlop, Robert Arlinghaus, David S. Boukal, Keith Brander, Bruno Ernande, Anna Gardmark, Fiona Johnston, Shuichi Matsumura, Heidi Pardoe, Kristina Raab, Alexandra Silva, Anssi Vainikka, Ulf Dieckmann, Mikko Heino, and Adriaan D. Rijnsdorp
Science 318, 23 November 2007: 1247-1248.

First paragraph: Darwinian evolution is the driving process of innovation and adaptation across the world's biota. Acting on top of natural selection, human-induced selection pressures can also cause rapid evolution. Sometimes such evolution has undesirable consequences, one example being the spreading resistance to antibiotics and pesticides, which causes suffering and billion-dollar losses annually (1). A comparable anthropogenic selection pressure originates from fishing, which has become the main source of mortality in many fish stocks, and may exceed natural mortality by more than 400% (2). This has, however, been largely ignored, even though studies based on fisheries data and controlled experiments have provided strong empirical evidence for fisheries-induced evolution over a range of species and regions (see table). These evolutionary changes are unfolding on decadal time scales-much faster than previously thought.

It is an unusual experience to read a paper where Elliott Sober, Larry Laudan, George Williams and Richard Dawkins are all taken to task for daring to put in a good word for William Paley.

"Unfortunately the philosophers make some serious philosophical mistakes and join these to a good portion of irredeemably bad history. The biologists on the other hand are historically mistaken about what Paley was actually up to and philosophically forgetful about what they themselves are up to."

Some of William Paley's foes are willing to approve some of his arguments

What alarms Peter McLaughlin, philosopher of science, is that

"William Paley has been enjoying a rather strong revival of late and has acquired admirers from a quarter that would have surprised him greatly. [. . .] The fact that philosophical naturalists at the turn of the twenty-first century should find value in his arguments is something Paley would have found too good to be true."

The heart of McLaughlin's paper is a critical appraisal of Sober's analysis of creationism. There are no principled reasons, according to Sober, for excluding creationism from science, and the ground for excluding creationism from education is that it is 'bad science' that has been falsified. In developing this position, Sober has acknowledged that, when Paley was writing, the creation explanation was "scientifically acceptable as the best explanation available before Darwin". McLaughlin systematically demolishes this position:

"The problem with this elegant argument is that many of the crucial facts about the history of science and the history of philosophy are wrong and the systematic philosophical argumentation is flawed. [. . .] It is straightforward, clear and appealing - but ultimately untenable."

The quotation below gives an insight into McLaughlin's disagreement with the two biologists:

"Two of the most prominent proponents of adaptationism in recent biology, George Williams and Richard Dawkins, have gone out of their way to praise Paley. [. . .] Dawkins even goes out on a limb with the assertion that 'Paley's argument . . . is informed by the best biological scholarship of his day'. Paley, he believes, 'had a proper reverence for the complexity of the living world, and he saw that it demands a very special kind of explanation'. Neither of Dawkins's assertions is true."

It is not my purpose in this blog to unpack these points of controversy (the paper needs to be read before doing that), but there is merit in drawing attention to McLaughlin's understanding of science itself. He writes: "Modern science explains natural (material) processes and events by adducing natural (material) processes and events." Presumably, we have to add, 'except when the processes and events are not natural (as is the case with archaeological science and forensic science)'. Then, it is perfectly legitimate to invoke intelligent agency alongside natural processes and events.

Should science be open to intelligent agency when it comes to origins? The answer has to be 'yes' - otherwise science becomes a tool to ensure philosophical naturalism dominates our thinking. Falsification of intelligent agency is then pre-empted by dogma rather than being a matter of science. Most people have a perception of science that researchers are open to truth and are not working within the constraints of a particular ideology. Perhaps McLaughlin is conscious of this problem in his own thinking when he notes: "It is often considered mere dogmatism to insist that naturalism is a presupposition of science." Let there be no doubt that he is advocating this dogma: according to McLaughlin, "secular science" is authentic science.

Regarding science education, McLaughlin has strong views:

"Most of us who are strongly against having creationism taught in biology class are against it because we value science and don't want our children to acquire a debased view of science or to conflate it with religious sectarianism."

Substitute "secular science" or "philosophical naturalism" for "creationism" in this quote, and you have a good idea why there is an ongoing tension. Ultimately, the differences are not about the data of science, but about epistemology and philosophical foundations.

Reverend Paley's naturalist revival
Peter McLaughlin
Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences, 39(1), March 2008, 25-37.

Abstract: This paper analyzes the remarkable popularity of William Paley's argument from design among contemporary naturalists in biology and the philosophy of science. In philosophy of science Elliott Sober has argued that creationism should be excluded from the schools not because it is not science but because it is 'less likely' than evolution according to fairly standard confirmation theory. Creationism is said to have been a plausible scientific option as presented by Paley but no longer to be acceptable according to the same standards that once approved it. In biology C. G. Williams and Richard Dawkins have seen in Paley a proto-adaptationist. This paper shows that the historical assumptions of Sober's arguments are wrong and that the philosophical arguments themselves take alternatives to science to be alternatives in science and conflate the null hypothesis, chance, with a competing explanatory hypothesis. It is also shown that the similarity of Paley's adaptationism to that of contemporary biology is not what it is made out to be.

For a long time it has been known that many highly coloured surfaces of living organisms are not the result of pigments or dyes, but are the effects of highly ordered structural mechanisms. These structures are only apparent at nanometre scales (comparable to visible light), and colours are generated by interference. Recent interest in these photonic structures is

"mainly because these media happened to be very interesting examples of optical metamaterials, that draw their optical properties from highly-tunable submicron geometric shapes, rather than from the nature of the materials used to make them. These complex structures, found on many living species: birds, insects, snakes, fish and even mammals, could be a very effective and inspirative track to new visual effects or even new optical devices. The structure described in the present study is very special, because its optical response can be drastically changed by its exposure to humidity. This phenomenon is one of the astonishing characteristics of a tropical beetle, Dynastes hercules."

The Hercules Beetle, one of the largest Coleopterans reaching up to 170 mm in length. It is reputed to be the strongest creature on Earth, carrying loads that are 850 times its own body weight. (The smaller beetle is Eudicella gralli).

The male beetle is normally a greenish colour, but when the humidity rises above 80%, it turns black. Water penetrates the multilayer structure and changes its optical performance. Darwinian adaptationist stories have been proposed. One hypothesis is that the black colour provides camouflage at night when the humidity level is highest and the insect is most active. Then, in the day, the greenish colour returns and the beetle blends in with its environment. Another hypothesis concerns thermoregulation: the insect warms up faster when it is black and then avoids overheating when it is green. Both these proposals are discussed by the researchers and both are rejected. "The reason (if any. . . ) why Dynastes hercules has evolved the ability to change colour with humidity is still a mystery which waits to be unveiled." The authors explain the purpose of their work in this way:

"The aim of the present study is to provide updated data on the morphology of this natural hygrochromic structure, to obtain detailed optical data for various humidity states and to re-examine the colouration mechanism with the help of extensive numerical light-scattering simulations."

These aims have been achieved using a reverse engineering methodology. The hygrochromic structure has been successfully modelled. Theoretical reflectance curves reveal a green colouration for the material under normal humidities and a black colouration when the spaces in the structure are filled with water.

"Hygrochromic behaviour could be an important property of an 'intelligent' material. Such materials could be put to work as humidity sensors, perceptibly changing colour according to the hygrometry level. This could be useful for example in food processing plants to monitor the moisture level. Since optical properties can be transferred to other radiative spectral ranges by scaling the structure lengths up or down, hygrochromic materials could also find thermal uses."

The take-home message for this blog is that design methodologies work and yield outcomes that are practically useful. The authors are explicit on this point: "the present paper addresses the reverse engineering of this complex system in a more complete way and clarifies several aspects of this hygrochromic effect." By contrast, darwinian perspectives appear to have contributed only speculative 'just-so' stories.

Diffractive hygrochromic effect in the cuticle of the hercules beetle Dynastes hercules
M Rassart, J-F Colomer, T Tabarrant and J P Vigneron
New Journal of Physics, 10 (March 2008) 033014 (14pp) | doi:10.1088/1367-2630/10/3/033014

Abstract. The elytra from dry specimens of the hercules beetle, Dynastes hercules appear khaki-green in a dry atmosphere and turn black passively under high humidity levels. New scanning electron images, spectrophotometric measurements and physical modelling are used to unveil the mechanism of this colouration switch. The visible dry-state greenish colouration originates from a widely open porous layer located 3 μm below the cuticle surface. The structure of this layer is three-dimensional, with a network of filamentary strings, arranged in layers parallel to the cuticle surface and stiffening an array of strong cylindrical pillars oriented normal to the surface. Unexpectedly, diffraction plays a significant role in the broadband colouration of the cuticle in the dry state. The backscattering caused by this layer disappears when water infiltrates the structure and weakens the refractive index differences.

Darwinists have a reputation for advancing 'plausible scenarios'. These stories arise because there has to be a gradualist route for forming any biologically interesting structure. Peacock feathers are a case in point, purely because their strikingly beautiful displays cannot be overlooked or ignored. Since elaborate tail feathers do not make peacocks stronger or physically more fit, the mechanism of sexual selection is invoked. The Understanding Evolution for Teachers web resource has this to say on the subject:

"Sexual selection is a "special case" of natural selection. Sexual selection acts on an organism's ability to obtain (often by any means necessary!) or successfully copulate with a mate. Selection makes many organisms go to extreme lengths for sex: peacocks maintain elaborate tails [. . .] Sexual selection is often powerful enough to produce features that are harmful to the individual's survival. For example, extravagant and colorful tail feathers or fins are likely to attract predators as well as interested members of the opposite sex."
Source: go here.

"The sight of a feather in a peacock's tail, whenever I gaze at it, makes me sick!" (Charles Darwin, in a letter to botanist Asa Gray, April 3, 1860)

Unfortunately, for Darwinists, empirical research has failed to sustain this thesis. After spending years studying breeding birds, the researchers came to the conclusion that "peahens do not prefer peacocks with more elaborate trains".

"The feather train on male peacocks is among the most striking and beautiful physical attributes in nature, but it fails to excite, much less interest, females, according to new research. The determination throws a wrench in the long-held belief that male peacock feathers evolved in response to female mate choice. It could also indicate that certain other elaborate features in galliformes, a group that includes turkeys, chickens, grouse, quails and pheasants, as well as peacocks, are not necessarily linked to fitness and mating success."

The researchers have taken note of previous work and the various hypotheses that have been proposed. Their summary reveals that they have been thorough in following up every lead:

"To date, the peacock's train has been proposed not only as a target of current female choice (e.g. Petrie et al. 1991), but also as an indicator of good genes (Petrie 1994). However, there may be at least four problems with these hypotheses.
First, male train morphology seems not to be the universal cue of choice because there is evidence both for and against the effect of male train morphology on male mating success. [. . .] Second, the ways in which females assess male trains (unless females have the ability to count eyespots per se) have been questioned repeatedly but have not been fully investigated. Third, there is no consensus on which traits characterize males with the most elaborate trains. [. . .] Fourth, to our knowledge, mate choice based on a male plumage ornament that is under oestrogen control is very rare."

Their conclusion is effectively 'We do not know the origin or original function of the peacock's tail, but we think it originated a long time ago':

"We propose that the peacock's train is an obsolete signal for which female preference has already been lost or weakened, but which has none the less been maintained up to the present because it is required as a threshold cue to achieve stimulatory levels in females before mating and/or it is maintained as an unreliable cue [. . .]."

The alleged amazing powers of natural selection are much diminished as a result of these findings. The argument that it is "powerful enough" to maintain the feather display against the negative effects of attracting predators must be dropped. Furthermore, it appears not powerful enough to remove the display when it becomes an "obsolete signal". Darwinists need to think very hard about the way they do science. This is a clear example of how a Darwinian hypothesis has become accepted as scientific fact, yet now has been disproved by some rigorous empirical research. This is a falsified prediction. This means that numerous textbooks and web sites need to be revised. More importantly, Darwinists should cease giving the impression that they have the keys to understand the natural world. So much of this 'understanding' is like peacock feathers - lots of show and no substance. Richard Dawkins extols Darwinism as a beautiful theory, but whenever we look closely, it fails to account for the observed data.

Peahens do not prefer peacocks with more elaborate trains
Mariko Takahashi, Hiroyuki Arita, Mariko Hiraiwa-Hasegawa and Toshikazu Hasegawa
Animal Behaviour, 75(4), April 2008, 1209-1219 | doi:10.1016/j.anbehav.2007.10.004

Abstract: The elaborate train of male Indian peafowl, Pavo cristatus, is thought to have evolved in response to female mate choice and may be an indicator of good genes. The aim of this study was to investigate the role of the male train in mate choice using male- and female-centred observations in a feral population of Indian peafowl in Japan over 7 years. We found no evidence that peahens expressed any preference for peacocks with more elaborate trains (i.e. trains having more ocelli, a more symmetrical arrangement or a greater length), similar to other studies of galliforms showing that females disregard male plumage. Combined with previous results, our findings indicate that the peacock's train (1) is not the universal target of female choice, (2) shows small variance among males across populations and (3) based on current physiological knowledge, does not appear to reliably reflect the male condition. We also found that some behavioural characteristics of peacocks during displays were largely affected by female behaviours and were spuriously correlated with male mating success. Although the male train and its direct display towards females seem necessary for successful reproduction, we conclude that peahens in this population are likely to exercise active choice based on cues other than the peacock's train.

See also:

Viegas, J., Female Peacocks Not Impressed by Male Feathers, Discovery News, March 26, 2008

Wiker, B. The Peacock Principle: Beauty, God, and Darwinism, The Discovery Institute, August 2006