Science Literature

The blogosphere seems to have realised that there is more hype than substance about the alleged status of Darwinius masillae. In itself, this is reassuring. Providing critical thought about the claims is not just the province of Darwin-doubters. For a selection of relevant links, try ScienceNOW, The Times, Livescience and Ergo Sum Daniel. An overview of the hype is elsewhere on the ARN site, Nature published some quotes that illustrate the "frenzy", and an Editorial in Nature refers to the media communicating a "drastic misrepresentation" of the significance of Ida and what the research team actually claim in their research paper. My interest in adding some thoughts is to tease out some of the scientific issues stimulated by the fossil find.

Ida under the spotlight (Credit: Tyler Lang, Source here)

Today, lemurs are found only on Madagascar and the neighbouring Comores Islands. Fossil lemurs are known: although Madagascar is the dominant source. A significant find in the year 2001, dated at 30 Ma (which makes it earlier than all the African lemurs), comes from Pakistan. This raised questions about whether lemurs originated in Asia rather than Africa. The Messel Pit in Germany has yielded eight fragmentary specimens of primates. A lemur-like species named Godinotia is one of these. Ida is recognisably a fossil lemur and she also comes from the Messel Pit. This confirms that questions need to be asked about the past geographical spread of these animals and also suggests that the model of the lemur ancestors being marooned on Madagascar with subsequent diversification is over-simplistic.

The term "missing link" has been used to publicise the fossil find. The term has fallen out of favour because Darwinists are committed to gradualism, and it follows that every fossil represents a link in the chain from an ancestral form to descendants. For them, it is misleading to refer to one particular fossil as a transitional form because every fosil is transitional in some sense. Advocates of Punctuated Equilibria reject this. They consider species to have a distinct identity: they are born, they live, they die (extinctions). Within their paradigm, it is reasonable to talk about forms that are transitional between one distinct species and another.

To get an evolutionary perspective on human ancestors, we can turn to Richard Dawkins' book The Ancestor's Tale. In a pilgrimage back in time, Dawkins leads his readers to rendezvous with human ancestors. He traces the phylogeny back through the apes and, at Rendezvous 5 about 25 Ma ago, we meet the common ancestor of apes and Old World monkeys. Going back further, at Rendezvous 6 about 40 Ma ago, the apes/Old World monkeys branch meets the New World monkeys branch. Going back further, at Rendezvous 7 which Dawkins puts at 58 Ma ago, the apes/monkeys (anthropoid) branch meets the tarsiers branch. It is only at Rendezvous 8 (associated with a date of 63 Ma) that we reach the ancestor of all primates. The two branches here are the haplorhine primates (apes/monkeys/tarsiers) and strepsirhine primates (mostly lemurs). It is this ancestral "link" that the researchers are claiming to have found: the common ancestor of all primates, including humans. (Note the mismatch on time - Ida is dated as 47 Ma).

The media hype passed lightly over these technical details: the headlines say the missing link is ancestral to humans! When asked about the mismatch between the technical paper and the media headlines, lead author Hurum said:

"I don't think a discussion of Haplorhines [tarsiers, apes, monkeys and humans] and Strepsirhines [the suborder of primates comprising lemurs and lorises] would be easy in popular science. You need to simplify it down to more understandable words. Of course in that you lose a little bit of the scientific terms, but really I think the message is very, very much the same in what we are doing popularly and scientifically."

The claim of the researchers is that the newly described fossil is not just another fossil lemur, but an animal that is ancestral to both lemurs and haplorhines. This requires a redrawing of the family tree and it conflicts with the thinking of numerous other researchers in the field. Norman MacLeod and Angela Milner make some interesting comments about the structure needed for a convincing argument:

"So is Ida another of these great "missing links"? Perhaps - but there is a problem. In order to be recognised as a true ancestor, a fossil must have no truly unique aspects: it must have passed all of its characteristics on to its daughter species, albeit in an altered form. [. . .] On this qualification, the Tiktaalik and Archaeopteryx both fall down as true missing links: both have unique features that have not been passed on to any living creatures. In other words, despite their enormous importance, they are not true ancestors, but belong to small branches of the tree of life whose form is close to that of the true ancestor.
Is the same true of Ida? Well, her fossil's status as a missing link is controversial in a slightly different way. Ida lacks some of the features common to modern lemurs, but does not appear to possess any features unique to our own lineage of anthropoid primates. This renders Ida's evolutionary status ambiguous, at best."

Further technical discussion is provided by Brian Switek, and his points are picked up and endorsed by many others.

"The bottom line is that the hypothesis that Darwinius is closer to anthropoids than tarsiers or omomyids does not have strong support. Even though the authors of the paper constructed a very simple cladogram they did not undertake a full, rigorous cladistic analysis to support their claims. I am baffled as to how they could stress the significance of this fossil without undertaking the requisite research to support their hypothesis.
Is Darwinius important to understanding primate evolution? Of course! It is an exceptionally preserved specimen that could do much to aid our understanding of adapid evolution and paleobiology. The grand claims about it being our ancestor, though, cannot be upheld as true. The researchers simply did not do the work to support their case."

Hurum was asked about what it would take to persuade other palaeontologists that he is right, and Hurum commented that work is in progress that will convince them. This illustrates the problem with creating a media frenzy. The editorial in Nature suggests that a "hyped-up fossil find highlights the potential dangers of publicity machines". Darwin sceptics are accustomed to such media manipulation. The headlines proclaim the advance in evolutionary understanding, but with the passing of time, the significance of the find decreases exponentially. We may yet find that this superbly preserved fossil lemur is within the range of variation observed in living and fossil lemurs and is more suited to provide evidence of stasis within the lemur basic type.

Complete Primate Skeleton from the Middle Eocene of Messel in Germany: Morphology and Paleobiology.
Franzen JL, Gingerich PD, Habersetzer J, Hurum JH, von Koenigswald W, Smith, B.H.
PLoS ONE, 2009, 4(5): e5723 | doi:10.1371/journal.pone.0005723

From the Abstract: Darwinius masillae represents the most complete fossil primate ever found, including both skeleton, soft body outline and contents of the digestive tract. Study of all these features allows a fairly complete reconstruction of life history, locomotion, and diet. Any future study of Eocene-Oligocene primates should benefit from information preserved in the Darwinius holotype. Of particular importance to phylogenetic studies, the absence of a toilet claw and a toothcomb demonstrates that Darwinius masillae is not simply a fossil lemur, but part of a larger group of primates, Adapoidea, representative of the early haplorhine diversification.

See also:

Media frenzy, Editorial, Nature 459, 484 (28 May 2009) | doi:10.1038/459484a

So could Ida be the true missing link? By Norman MacLeod and Angela Milner, The Daily Telegraph, 26 May 2009

Poor, poor Ida, Or: "Overselling an Adapid", by Brian Switek, Laelaps (blog), May 19, 2009

In an essay in Science's series in honour of the Year of Darwin, John Travis explored the evolution of the immune system. He hits the ground running by recounting the Dover trial and the encounter between biochemist Michael Behe as witness and lawyer Eric Rothschild. A dramatic moment was recalled. Behe had claimed that "The scientific literature has no answers to the question of the origin of the immune system." Rothschild came prepared: he started to bring out journal articles, books, and book chapters, which he said demonstrated research on the evolutionary origins of immunity. Behe was unimpressed. "They're wonderful articles. [. . .] They simply just don't address the question that I pose," he responded. Travis reports that the judge believed Rothschild and rejected Behe's testimony:

The judge, John E. Jones, found Behe's responses revealing. Behe "was presented with 58 peer-reviewed publications, nine books, and several immunology textbook chapters about the evolution of the immune system; however, he simply insisted that this was still not sufficient evidence of evolution," the judge wrote in his decision. Jones concluded that ID proponents set "a scientifically unreasonable burden of proof for the theory of evolution." Score one for evolution, which is now taught without competition from ID in Dover schools.

Exhibit A. This stack of evolutionary immune research literature was used in the Dover trial. (Credit: Nick Matzke/National Center For Science Education, Source Science)

One only has to read Travis' essay to realise that answers have been proposed but are still being evaluated. Some perceive a sudden and dramatic assembly of the immune system and others look for gradual change. Here is a taste of the tensions:

"The basic idea of an immune 'big bang' in the vertebrates has led to a variety of oversimplifications and conceptual problems," says Rast. "Whatever the actual evolutionary pathway that led to the very complex vertebrate adaptive system, it was surely a gradual progression that co-opted many preexisting immune mechanisms."

There is no doubt that many immunologists have written about the origin of the immune system. Judge Jones was impressed by that. But academics do not weigh student essays to award marks - they look at the arguments presented. This principle must also apply to research papers. Speculation does not count as evidence! Furthermore, when the presuppositions of the research exclude design, these do not count either when evaluating alternatives that include design. As an example, consider Marchalonis et al (2006): these words are taken from the Introduction.

"At the onset, we emphasize that evolution is a stochastic or accidental process building upon the spontaneous generation of mutations followed by natural selection based upon survival to reproduce under external/environmental conditions. Our conceptual approach, thus, differs fundamentally from the theoretical approach presented by Cohn, because we adhere to the principle that 'in evolutionary systems there is no design'."

Dr Behe submitted a letter of response to Science, but has been informed that his letter was not of sufficient interest to publish. The Darwinians are quick to claim a victory over these issues but are simply not able to get beyond speculations about the origin of the immune system. Here is Behe's last paragraph.

In my court testimony I cited the then-new article by Klein and Nikolaidis, "The descent of the antibody-based immune system by gradual evolution" (Proc. Natl. Acad. Sci. USA 102:169-174, 2005), which first disputed the big bang hypothesis. In it the authors candidly remark, "Here, we sketch out some of the changes that the emergence of the AIS entailed and speculate how they may have come about." Valuable as it might be to science, however, speculation is not data, let alone an experimental result. Students are poorly served when they are not taught to distinguish among them.

On the Origin of The Immune System
John Travis
Science, 324, 1 May 2009: 580-582.
Did the immune system evolve to keep out harmful organisms, or is it like a bouncer at a nightclub, trained to allow the right microbes in and kick the less desirable ones out? In the fifth essay in Science's series in honor of the Year of Darwin, John Travis explores the evolution of the immune system.

See also:

Behe, M.J. Letter to Science (unpublished), Amazon Blog, 21 May 2009

Marchalonis, J.J. et al. The antibody repertoire in evolution: Chance, selection, and continuity, Developmental & Comparative Immunology, 30(1-2), 2006, 223-247 | doi: 10.1016/j.dci.2005.06.011

It is good advice to be wary of anyone purporting to represent the consensus in science. Those who speak the loudest about scientific consensus are often advancing other agendas. A good example can be derived from what people say about the 'scientific method'. Anyone practising science needs to know what it is, but in the real world, the progress of science often departs from the norm. Paul Dirac was a case in point. He was a theoretical physicist at Cambridge University who, in 1928, developed the maths that described the quantum behaviour of electrons. This led to the conclusion that it must be possible for an electron to have a positive charge. Later, Dirac described it as an "anti-electron" and when it was discovered in 1932 it was named the positron. The following year, Dirac received the Nobel Prize for his work. The first biography of this genius has been published recently and an informative review appears in the current Nature.

The unconventional Paul Dirac (Credit: Bettmann/Corbis, Source here)

Several characteristics of Dirac's work do not fit well with the consensus way of doing science. First, Dirac was a pure theoretician. He was not an experimentalist (although, later in life, this changed). He did not show any interest in stimulating a quest to find the positron.

"Although he commented that it could be made transiently in experiments, he was surprisingly circumspect, more concerned with the difficulties of detection than the inevitability of its existence. He made no suggestion as to how experimentalists might make it, or recognize it. He was away in the United States later that year when Robert Millikan gave a talk at the University of Cambridge, UK, showing Anderson's images of particle tracks from cosmic rays - including some that looked like those of electrons but which curved the wrong way in a magnetic field. No one associated these tracks with Dirac's holes."

Second, not brought out in the Nature review, but nicely described in other essays, Dirac was a theoretician who thought that elegant theory, beautiful maths and good science go together. Dirac was confident in his theoretical work, not because it had been confirmed empirically, but because it satisfied his aesthetic sense of the relationship between physics and the real world.

[Waldegrave]: "And yet Dirac's brand of theoretical physics, and the way he saw the world, was so close to philosophy. He was convinced that the more beautiful an equation, the more likely it was to be accurate - in other words, he saw a picture of the world that was of such beauty that it had to be true."
[and]
[Carey] "Even his fellow physicists complained that he worked in a deliberately mystifying private language. For his part, he insisted that the quantum world could not be expressed in words or imagined. To draw its picture would be "like a blind man sensing a snowflake. One touch and it's gone". Its beauty revealed itself only in mathematical formulae."

But the greatest contrast between the consensus scientific method and Dirac's research experience is found in the route to reach radical or revolutionary conclusions. Dirac was working on the frontiers of relativistic quantum theory and he was pioneering in his foresight of the "mirror world of antimatter". His colleagues were rather sceptical.

By 1932, the holes had become a joke. At a meeting in Copenhagen, when Bohr lost his patience and confronted Dirac with: "Do you believe all that stuff?", he simply replied, "I don't think anyone has put a conclusive argument against it."
[and]
[Waldegrave]: His great equation for the electron - an improbable marriage of relativity and quantum theory - only worked if you assumed that there was such a thing as an "anti-electron". His colleagues mocked the idea, but Dirac stuck to his guns: the maths was so harmonious that reality had to reflect it.

The hallmark of any revolutionary idea in science is that, before the transformation, the community of scientists are sceptical about the new ideas, with some expressing outright disagreement. After the change, the community applauds the new research - which becomes the new orthodoxy. The 'scientific method' knows nothing of this punctuated change, for it portrays an incremental step-by-step approach towards increasing knowledge. To explain scientific revolutions, we need something more. The analysis of Thomas Kuhn provides such an explanation, forcing us to think through the meaning of scientific paradigms. According to Kuhn, any community of researchers share a set of assumptions, concepts, values, and practices. This is their way of viewing the world and, generally, is exempt from being questioned or changed. Much can be done from within this conceptual framework, but observations will be found that create tensions or understanding. These tensions are the drivers for a paradigm shift, and the process of change can be traumatic.

Paul Dirac's pioneering work in quantum physics led to him sharing with Erwin Schrodinger the 1933 Nobel Prize for physics. This was awarded "for the discovery of new productive forms of atomic theory". He was Lucasian professor of mathematics at Cambridge from 1932 to 1969. His appreciation of beauty in the mathematics of the physical world is reminiscent of one of his predecessors in the Lucasian Chair. Isaac Newton had great confidence in the inverse square law of gravity. This confidence came because of his commitment to design in nature. Dirac is said to have been an atheist, but he is also reported to have said: "God used beautiful mathematics in creating the world".

These thoughts on the scientific method are being contributed because there are many strident voices insisting on what science is and what it is not. The claim that 'ID is not science' crops up repeatedly. Books and articles are published regularly making grandiose claims about the crisis facing science if students are even exposed to design-based thinking. What characterises them all is that they fail to engage with what ID scholars are actually saying. ID scientists are interested in truth. They operate within a different paradigm than scientists starting out with a materialistic philosophy. If there is a commitment to truth-seeking on all sides, then there has to be some way for scientists with different paradigms to interact meaningfully. Isaac Newton and Paul Dirac held the same professorial chair at Cambridge University - perhaps that provides a lesson for us all.

Paul Dirac: a physicist of few words
Frank Close
Nature 459, 326-327 (21 May 2009) | doi:10.1038/459326a

A detailed biography argues that the Nobel prizewinner's notorious reticence delayed experimentalists from discovering the antimatter that would confirm his elegant theory.

According to one commentator, the newly published research provides "one of the great advances in prebiotic chemistry". The media have captured the excitement with headlines like "Chemist Shows How RNA Can Be the Starting Point for Life" (New York Times), "Molecule of life emerges from laboratory slime" (New Scientist) and "How RNA got started" (Science News). These are strong statements and they deserve closer attention. What is going on in the field of OOL research?

Artistic portrayal of the 'RNA World' dream (Credit: Nicolle Rager Fuller & National Science Foundation, Source here)

The first point worth making is that new advances are often shown to be significant by referring to the lack of progress that had earlier characterised the field. This is often a surprise to the general public, who are typically fed a story that the problems are largely cracked and abiogenesis researchers are confident of tying up the loose ends in the near future. Wade's report refers to the solution of "a problem that for 20 years has thwarted researchers trying to understand the origin of life - how the building blocks of RNA, called nucleotides, could have spontaneously assembled themselves in the conditions of the primitive earth." Van Noorden explains the problem like this:

"An RNA polymer is a string of ribonucleotides, each made up of three distinct parts: a ribose sugar, a phosphate group and a base - either cytosine or uracil, known as pyrimidines, or the purines guanine or adenine. Imagining how such a polymer might have formed spontaneously, chemists had thought the subunits would probably assemble themselves first, then join to form a ribonucleotide. But even in the controlled atmosphere of a laboratory, efforts to connect ribose and base together have met with frustrating failure."

Abiogenesis researchers adopt either 'law' or 'chance' as causal explanations. They have rejected 'design' (not because it does not work, but because they insist on all causation being material). The new research is driven by a confidence in 'law'. The researchers are chemists. For them, the origin of life is a matter of chemistry. Thus, Sutherland, the lead author, is quoted as saying:

"My ultimate goal is to get a living system (RNA) emerging from a one-pot experiment. We can pull this off. We just need to know what the constraints on the conditions are first."
[and]
"My assumption is that we are here on this planet as a fundamental consequence of organic chemistry, so it must be chemistry that wants to work."

What, then, has been achieved? The researchers have synthesised both pyrimidine ribonucleotides (but not the purine ribonucleotides). As Van Noorden described it, they have "shown that it is possible to build one part of RNA from small molecules". They have not formed RNA molecules; they have not addressed the chirality problem, they have not generated any biological information and they have not made RNA do anything of biological significance, let alone become clothed with a membrane and undergo replication. Nevertheless, what they have done can be applauded as an elegant example of systems chemistry. A specific bond was needed between the Ribose and the Nucleobase, and a decade of research proved that the bond was not going to form directly. So what the researchers did was to create the bond and then turn the components on each side of the bond into the desired building blocks of the Ribonucleotide. Phosphate, which previously caused problems for OOL researchers, becomes a catalyst. Szostak's News and Views essay draws attention to the elegance of their approach:

"But in a remarkable example of 'systems chemistry', in which reactants from different stages of a pathway are allowed to interact, Powner et al. show that phosphate tames the combinatorial explosion, allowing oxygenous and nitrogenous reactants to interact fruitfully."
[. . .]
"The penultimate reaction of the sequence, in which the phosphate is attached to the nucleoside, is another beautiful example of the influence of systems chemistry in this set of interlinked reactions. The phosphorylation if facilitated by the presence of urea; the urea comes from the phosphate-catalysed hydrolysis of a by-product from an earlier reaction in the sequence."

It is good chemistry, but does it achieve a major advance in abiogenesis research? Questions can certainly be raised. The researchers argue that they are not starting with any unrealistic initial conditions: "We don't use any way-out scenarios - all the conditions are consistent with what we know about early Earth." However, this is disputed.

"The flaw with this kind of research is not in the chemistry. The flaw is in the logic - that this experimental control by researchers in a modern laboratory could have been available on the early Earth," says Robert Shapiro, a chemist at New York University.
[and]
Dr. Robert Shapiro [. . .] said the recipe "definitely does not meet my criteria for a plausible pathway to the RNA world." He said that cyano-acetylene, one of Dr. Sutherland's assumed starting materials, is quickly destroyed by other chemicals and its appearance in pure form on the early earth "could be considered a fantasy."
[and]
"But while this is a step forward, it's not the whole picture," [James] Ferris [of the Rensselaer Polytechnic Institute in Troy, N.Y.] points out. "It's not as simple as putting compounds in a beaker and mixing it up. It's a series of steps. You still have to stop and purify and then do the next step, and that probably didn't happen in the ancient world."

It can be argued that the chemical reactions documented actually yield products that are intelligently designed. The experimental conditions are engineered to selectively accumulate some reaction products (by fractional crystallisation) and selectively destroy others (by the influence of UV radiation). These conditions are considered more plausible in Darwin's hypothetical "little warm pond". Indeed, Wade's report says: "Dr. Sutherland's report supports Darwin". This is significant because the emphasis in abiogenesis research has shifted in recent years to other scenarios - notably at mid-ocean ridge locations. Those who find themselves impressed with the potential of this research would do well to reflect on the way the chemistry is engineered to achieve the outcomes and the associated fine tuning of environmental factors. These are not Darwinian emphases!

Of the other limitations mentioned above, the chirality problem is noted in Wade's report:

"A serious puzzle about the nature of life is that most of its molecules are right-handed or left-handed, whereas in nature mixtures of both forms exist. Dr. Joyce [an expert on the chemical origin of life at the Scripps Research Institute in La Jolla, Calif.] said he had hoped an explanation for the one-handedness of biological molecules would emerge from prebiotic chemistry, but Dr. Sutherland's reactions do not supply any such explanation."

For those of us more familiar with 'design' as a causal explanation, this work does not dent the arguments already in place to demonstrate the futility of explaining life without design. Notably, the idea that life is just a matter of chemistry simply fails to engage with the information necessary for a cell to function as a biological entity. We are impressed by the systems chemistry reported, but find it such a shame that the hype surrounding the research is driven by the quest to explain life without a designer. Sutherland has ambitions to make a compelling case for chemical evolution: "That is the goal of my career", he says. A more worthy goal, although probably with less hype, would be to apply his undoubted talents to address contemporary conundrums facing the human race.

Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions
Matthew W. Powner, Beatrice Gerland, John D. Sutherland
Nature 459, 239-242 (14 May 2009) | doi:10.1038/nature08013

At some stage in the origin of life, an informational polymer must have arisen by purely chemical means. According to one version of the 'RNA world' hypothesis this polymer was RNA, but attempts to provide experimental support for this have failed. In particular, although there has been some success demonstrating that 'activated' ribonucleotides can polymerize to form RNA, it is far from obvious how such ribonucleotides could have formed from their constituent parts (ribose and nucleobases). Ribose is difficult to form selectively, and the addition of nucleobases to ribose is inefficient in the case of purines and does not occur at all in the case of the canonical pyrimidines. Here we show that activated pyrimidine ribonucleotides can be formed in a short sequence that bypasses free ribose and the nucleobases, and instead proceeds through arabinose amino-oxazoline and anhydronucleoside intermediates. The starting materials for the synthesis - cyanamide, cyanoacetylene, glycolaldehyde, glyceraldehyde and inorganic phosphate - are plausible prebiotic feedstock molecules, and the conditions of the synthesis are consistent with potential early-Earth geochemical models. Although inorganic phosphate is only incorporated into the nucleotides at a late stage of the sequence, its presence from the start is essential as it controls three reactions in the earlier stages by acting as a general acid/base catalyst, a nucleophilic catalyst, a pH buffer and a chemical buffer. For prebiotic reaction sequences, our results highlight the importance of working with mixed chemical systems in which reactants for a particular reaction step can also control other steps.

See also:

Luskin, C. Scientists Say Intelligent Designer Needed for Origin of Life Chemistry, Evolution News & Views, 7 July 2009.

Szostak, J.W., Origins of life: Systems chemistry on early Earth, Nature 459, 171-172 (14 May 2009) | doi:10.1038/459171a

Van Noorden, R., RNA world easier to make, Nature News, 13 May 2009 | doi:10.1038/news.2009.471

Wade, N., Chemist Shows How RNA Can Be the Starting Point for Life, New York Times, 14 May 2009.

The new find "will either be nothing or the biggest revolution in paleontology ever". These words were spoken by a palaeontologist in response to newly published research. He was commenting on a report of well-preserved tissues and primary collagen sequences recovered from the femur of a plant-eating dinosaur identified as a hadrosaur. It followed several years of intense activity by Mary Schweitzer and colleagues, whose previous papers on soft tissues in dinosaur bones were met with great scepticism. Last year, it seemed as if the claim had met its final rebuttal when the soft tissues were suggested by the same palaeontologist quoted above to "have come from bacterial contamination". However, the new research appears to have answered the critics very effectively.

Multiple hadrosaur red blood "cells" surrounded by white, fibrous matrix (Credit Mary H. Schweitzer, Source here)

The authors were well aware that their newly reported work adds fuel to the fire of controversy. They start their abstract by reminding readers about it and they end their paper with comments addressing the "appropriate skepticism" of earlier work. The problem is this: all direct measurements of the degeneration of biomolecules suggest timescales of hundreds or thousands of years (depending on environmental conditions). Indirect measurements, based on detecting biomolecules in artefacts of known age, suggest that the upper limit is less than a million years. Yet, the biomolecules detected in dinosaurs are considered to be 80 million years old. Two orders of magnitude justifies considerable skepticism!

Consequently, the authors have gone to great lengths to address concerns of contamination - particularly by the invasion of bacteria to form biofilms. The femur they have used came from an articulated hindlimb of a hadrosaur. The pes elements, tibia and fibula were collected in 2006, so they knew the femur was still embedded in rock. The following year, the rock containing the femur was removed, taking care that the fossil bone "was not exposed in the field". Every effort was made to prevent contamination so that all the materials examined were representative of the fossil itself. The researchers found a variety of morphological evidences that indicated they were handling fossil material of significance. "The variation in texture, microstructure, and colour of dinosaur material is consistent with extant tissues and not plausibly explained by biofilms". A battery of tests followed, with replication by another lab, leasing to some very convincing findings. Many critics of the earlier work are acknowledging the substantial nature of the new research. Service writes:

"Both groups then independently performed biochemical and antibody-binding studies that showed evidence of collagen as well as laminin and elastin, two proteins found in blood vessels."
[McIntosh, a critic of the earlier work, is quoted as saying:] "I'm not saying it's true. But I cannot right now make a plausible argument that it's not true." He adds: "The door is closing on plausible alternatives."

Yet another aspect of the newly published research is a comparison of the hadrosaur collagen sequences with collagen from birds, reptiles, mammals, amphibians and with the previous sequences obtained for T. rex. The findings from this comparison have captured headlines across the world. The emerging phylogenetic tree first places the two dinosaurs adjacent to the birds - subsequent to the branching point with reptiles. Undoubtedly, both dinosaur sequences are fragmentary. "The eight peptide sequences for collagen alpha1 type I and collagen alpha2 type I represent 7.8 and 2.5% of the full-length sequence for related organiosms, respectively." Nevertheless, whilst acknowledging this, the authors regard their analysis as a significant output.

"The amount of missing data in B. canadensis and T. rex sequences relative to extant samples resulted in relatively low resolution within Dinosauria, but even so, the phylogenetic relationship of recovered B. canadensis sequences supports the species' placement within Archosauria, closer to birds than Alligator."

In view of this, the sequence comparisons can and will be critiqued. Comment at this stage may be premature (although go here for further thoughts on the matter). From a design perspective, there is another angle on sequence comparisons worth considering. Instead of interpreting sequences in terms of evolutionary pathways, with similarities mapping ancestor/descendant relationships, similar sequences may actually correlate with similar functionalities. So, for example, similarities between dinosaur and avian collagen may result from similar design requirements relating to size/weight/strength criteria. These similarities are not evidences for birds and dinosaurs belonging to the same clade, but they are evidences for birds and dinosaurs having common physiological and anatomical design features.

One further point relates to the 'god-of-the-gaps' style of argumentation. ID scientists are unfairly charged with finding a gap in knowledge and filling it with a miracle (whereas design arguments are actually based on evidence - not the lack of it). With dinosaur soft tissue preservation, the shoe is on the other foot. All the knowledge we have points to the impossibility of detecting any protein sequences from dinosaurs. On these grounds, many were intensely sceptical of the T. rex analysis. Now that collagen sequences have been confirmed by replication, the challenge is to explain what was previously considered impossible. The authors conclude their paper with the words: "still unknown is the chemistry behind such preservation". On the basis of what we know, the creationist claim that the dinosaurs are not millions of years old might seem the more parsimonious. The point I am making is that 'god-of-the-gaps' charges are misdirected whenever people argue from evidence, and that most instances of the use of the phrase reveal its role as a rhetorical tool.

Biomolecular Characterization and Protein Sequences of the Campanian Hadrosaur B. canadensis
Mary H. Schweitzer, et al.
Science, 324, 1 May 2009: 626-631.

Abstract: Molecular preservation in non-avian dinosaurs is controversial. We present multiple lines of evidence that endogenous proteinaceous material is preserved in bone fragments and soft tissues from an 80-million-year-old Campanian hadrosaur, Brachylophosaurus canadensis [Museum of the Rockies (MOR) 2598]. Microstructural and immunological data are consistent with preservation of multiple bone matrix and vessel proteins, and phylogenetic analyses of Brachylophosaurus collagen sequenced by mass spectrometry robustly support the bird-dinosaur clade, consistent with an endogenous source for these collagen peptides. These data complement earlier results from Tyrannosaurus rex (MOR 1125) and confirm that molecular preservation in Cretaceous dinosaurs is not a unique event.

See also:

Service, R.F. 'Protein' in 80-Million-Year-Old Fossil Bolsters Controversial T. rex Claim, Science 324, 1 May 2009: 578.

New Data from 80-Million-Year-Old Dinosaur Demonstrates Ancient Protein Is Preserved, Beth Israel Deaconess Medical Center Press Release, 30 April 2009.

Tyler, D. T. rex - spectacular findings - wrong message. ARN Literature Blog (29 April 2008)