Science Literature

The world of human phylogeny has been hit by a bombshell. Although scholars and textbooks are presenting chimpanzees as man's closest relatives, Grehan and Schwartz have revived the case for orangutans. They consider hominoids to be comprised of two sister clades: the human-orangutan clade (dental hominoids) and the chimpanzee-gorilla clade (African apes). They claim that humans and orangutans "share a common ancestor that excludes the extant African apes". Since it is received wisdom that chimps are the nearest relative to humans because we share over 98% of their genes and since humans are referred to as the "third chimpanzee", the ramifications of the new paper are immense!

Mr. Jiggs, a six-year-old orangutan at London Zoo, is capable of mopping his own quarters (credit B. A. Stewart and D. S. Boyer, source here)

Conceptual upheavals of this magnitude are unlikely to happen without major methodological modifications. This is the main concern of this blog. The authors do not start with DNA similarities but with morphological data. They note that, originally, the DNA comparisons were interpreted in the light of morphological analyses, but:

"Neither of two oft-cited morphological studies claiming to corroborate the interpretation of molecular data as supporting a close relationship between chimpanzees and humans took into consideration or provided justification for excluding most of the morphological features that have been documented as being shared uniquely by humans and orangutans."

The authors proceed to critique previous studies for the way they selected characters for cladistic analysis. They point out that these approaches incorporated characters considered to be derived within the ingroup "in spite of the fact that the feature is also common in the outgroup".

"Although a range of morphological studies have claimed to support a closer relationship between humans and chimpanzees or African apes, these studies have relied on many of the characters that we found to be problematic, and thus demonstrate how entrenched error becomes as it is unquestioningly passed on from and incorporated into one study after another."

Those familiar with the Kuhnian analysis of the practice of science will discern features here of 'working within the paradigm', with presuppositions unintentionally closing off avenues of enquiry. Conscious of the limitations of other work, Grehan and Schwartz explain and justify their selection of characters. One of their additional objectives was to include numerous fossil apes within their study.

"Our analysis of relationships between living and fossil taxa is based on a character matrix limited to hard-tissue characters that have been sufficiently well described in the literature to permit verification, and whose claimed character states as well as unique occurrence within a large-bodied hominoid clade we could corroborate via a broad outgroup comparison."

It is worth noting that their conclusion has deep roots. Schwartz was making points like this in 1984. His book The Red Ape appeared in 1987 and in a revised form in 2005. The paper has not come from authors who have suddenly hit on a quirky idea but it represents the mature judgment of two respected scholars.

What then shall be said of the DNA similarity data? The analysis of the authors is scathing. The key points are, in their own words:

"But the widely accepted notion that the 'greatest overall molecular similarity' is synonymous with 'most closely related' derives not from any empirical evidence but merely from the acceptance without question of the 'molecular assumption': namely, most recently divergent taxa will be most similar in their proteins and DNA because they will have shared a longer lineage of molecular change prior to their divergence and that the pace of molecular change was clocklike in nature. Nevertheless, despite claims to the contrary, the demonstration of molecular similarity does not a priori equate with a demonstration of homology, which must precede any hypothesis of phylogenetic relationship because a demonstration of similarity alone is only phenetic and must be subject to rigorous phylogenetic enquiry."

They cite previous work by Schwartz & Maresca that was the subject of a blog here. They argue that the published studies lack objectivity and have embedded tautologies. The New Scientist report summarises the argument against chimp/human genetic similarities by quoting one of the authors:

"Grehan, however, argues that this is not scientifically justified. He points out that traditional taxonomy makes a distinction between two types of similarity - "derived novelties" and "primitive retentions". Derived novelties are traits shared by two closely related species and are taken to have evolved in a recent common ancestor. Primitive retentions are older traits with a deeper evolutionary past shared by a larger group of species.
The problem with molecular systematics, says Grehan, is it fails to distinguish between the two. "It does not matter that more DNA similarities may be found between humans and chimpanzees if these similarities are really primitive retentions," he says."

A third element of the new paper is to set the argument for the human/orangutan relationship in a biogeographical context. Whereas the consensus view understands an emergence of humanity "out of Africa", there is a need for these issues to be addressed for the dental hominoid clade. The authors do this utilising data relating to the fossil species included in their analysis.

The significance of the paper is that the arguments relate to cladism (which is very widely used for assigning probabilities to evolutionary relationships) and phylogenomics (which is a standard tool for establishing evolutionary relationships). The authors have challenged the scientific consensus with some cogent and penetrating arguments. It is not just a dispute about the meaning of data, but how that data is selected and what presuppositions the researchers bring to their work. As such, the new paper provides us with a very important case study and sets the agenda for potentially very interesting discussions about methodology. If this is properly done, it will be to the health of the science community. Scientists with an openness to ID will welcome this debate, because many of critiques made by Grehan and Schwartz link directly to issues that concern us.

Evolution of the second orangutan: phylogeny and biogeography of hominid origins
Grehan, J.R. and Schwartz, J. H.
Journal of Biogeography, advance online 22 June 2009 | doi 10.1111/j.1365-2699.2009.02141.x (abstract)

Main conclusions: Humans and orangutans share a common ancestor that excludes the extant African apes. Molecular analyses are compromised by phenetic procedures such as alignment and are probably based on primitive retentions. We infer that the human-orangutan common ancestor had established a widespread distribution by at least 13 Ma. Vicariant differentiation resulted in the ancestors of hominids in East Africa and various primarily Miocene apes distributed between Spain and Southeast Asia (and possibly also parts of East Africa). The geographical disjunction between early hominids and Asian Pongo is attributed to local extinctions between Europe and Central Asia. [. . .]

See also:

Lawton, G. Could the orang-utan be our closest relative? New Scientist, 17 June 2009

Humans and Orangutan, Buffalo Museum of Science web resource.

Research into the skeletal remains of Stone Age Man has been undertaken in parallel with work to clarify the cultural and cognitive skills of these people. The dominant paradigm has been gradualism linked to the slow transformation of ape-like creatures into Modern Man. Darwinism has influenced the way people have approached the data and the interpretations they have placed on findings.

Papers are regularly published which point out the earliest example of a cultural trait: use of fire, hunting using spears, artefacts (like jewellery) indicating the presence of aesthetic values, Venus figurines, and so on. Two recent examples are noted in this blog.

Musical instruments like these allow inferences to be made about the cognitive skills of the users (Source here)

The first example concerns hafted spears, which are said to date back to 200,000 years ago. These are compound tools, where a sharp, hard point is hafted to a shaft. Archaeologists recognise that this invention has implications for our understanding of the minds of the spear-makers. The newly reported discovery is of spears where the hafting was found to be associated with a number of naturally occurring materials. Why were these materials located at the join? By an extensive programme of experimentation, the researchers came to the view that the artisans were using the materials as adhesives, and that the manufacturing process demonstrated a high level of abstract thinking.

"Wadley et al. identified naturally available materials (acacia gums and beeswax) that could be combined with ochre (found as residue on the tools), after which they experimented with various combinations to find the most effective mixture. They also tried different techniques for producing the actual haft, including the use of fire for rapid drying of the adhesives. With the most effective procedure in hand they could then ask themselves what an artisan needed to understand in order to conceive of and execute this task. "We propose that these artisans were exceedingly skilled; they understood the properties of their adhesive ingredients and they were able to manipulate them knowingly". In particular the artisans needed to understand the properties of their ingredients (e.g., cohesiveness), to be able to judge the effects of temperature, to be able to switch attention back and forth between separate rapidly changing variables, and to be flexible enough to adjust to the variability inherent in naturally occurring ingredients."

In a Commentary on the paper, Wynn points out that the reasoning that leads to such a conclusion must be "based on a sequence of inferences, each of which must be explicit and persuasive if the argument as a whole is to be credible." He spells out the details of that reasoning process, "borrowed loosely from Botha's detailed critique of an archaeological argument for the use of syntactical language by people at Blombos Cave 77,000 years ago." The merit of this approach is that observations and inferences can be clearly identified and each step can be scrutinised carefully. Archaeologists have new avenues to explore, which is very exciting.

"Most of the focus in this debate has been on the role language and symbolism but, as Wadley et al. make clear, there is more to modern cognition than language and the use of symbols. Indeed, language has proven to be a particularly intractable topic for archaeologists, a point made cogently by Botha. By focusing on activities that tax reasoning ability and are also visible archaeologically, such as hafting, archaeologists are in a better position to contribute to an understanding of the evolution of the modern mind."

The second paper concerns the finding of musical instruments. "Researchers universally accept the existence of complex musical instruments as an indication of fully modern behaviour and advanced symbolic communication." Previously, the oldest instriument was about 30,000 years ago, but the new finds come from a site dated at about 35,000 years. Some of the reported comments are as follows:

"It's becoming increasingly clear that music was part of day-to-day life," he said.
"Music was used in many kinds of social contexts: possibly religious, possibly recreational - much like we use music today in many kinds of settings."
The researchers also suggest that not only was music widespread much earlier than previously thought, but so was humanity's creative spirit.
"The modern humans that came into our area already had a whole range of symbolic artifacts, figurative art, depictions of mythological creatures, many kinds of personal ornaments and also a well-developed musical tradition," Professor Conard explained.

The first general point I want to make is that the procedures described (for making inferences from archaeological data) are not dissimilar from the procedures used by Intelligent Design scholars for making inferences about design in nature. These procedures are not arbitrary or poorly conceived, but rigorous and evidence-based (and exciting!). This is why the objections most often heard are based on demarcation arguments: 'Design is not part of Science'. Clearly, in archaeology, design is part of science!

The second general point concerns the creeping awareness that Stone Age men were far more "modern" than we have given them credit for. The problem is that most scholars understand consciousness, capacity for abstract thought and aesthetics as emergent properties of evolving animals. They do not allow the thought that these capabilities might be present by design. So, the data is moulded to fit a slow evolutionary transformation and other ways of interpreting the data are neglected. To show that design perspectives can propose hypotheses that can be tested, here is possible scenario. All these Stone Age men are human and have essentially modern cognitive skills. However, they lived in environments where they needed to adopt survival strategies and this prevented the flowering of sedentary communities and limited evidences of creativity. The prediction is that evidences of modernity will continue to be found, pushing the appearance of cultural artefacts earlier and earlier in time.

Implications for complex cognition from the hafting of tools with compound adhesives in the Middle Stone Age, South Africa
Lyn Wadley, Tamaryn Hodgskiss and Michael Grant
Proceedings of the National Academy of Science USA, Published online May 11, 2009 | doi: 10.1073/pnas.0900957106

Abstract: Compound adhesives made from red ochre mixed with plant gum were used in the Middle Stone Age (MSA), South Africa. Replications reported here suggest that early artisans did not merely color their glues red; they deliberately effected physical transformations involving chemical changes from acidic to less acidic pH, dehydration of the adhesive near wood fires, and changes to mechanical workability and electrostatic forces. Some of the steps required for making compound adhesive seem impossible without multitasking and abstract thought. This ability suggests overlap between the cognitive abilities of modern people and people in the MSA. Our multidisciplinary analysis provides a new way to recognize complex cognition in the MSA without necessarily invoking the concept of symbolism.

New flutes document the earliest musical tradition in southwestern Germany
Nicholas J. Conard, Maria Malina, Susanne C. Munzel
Nature (online 24 June 2009) | doi:10.1038/nature08169 (Abstract)

Considerable debate surrounds claims for early evidence of music in the archaeological record. Researchers universally accept the existence of complex musical instruments as an indication of fully modern behaviour and advanced symbolic communication but, owing to the scarcity of finds, the archaeological record of the evolution and spread of music remains incomplete. Although arguments have been made for Neanderthal musical traditions and the presence of musical instruments in Middle Palaeolithic assemblages, concrete evidence to support these claims is lacking. Here we report the discovery of bone and ivory flutes from the early Aurignacian period of southwestern Germany. These finds demonstrate the presence of a well-established musical tradition at the time when modern humans colonized Europe, more than 35,000 calendar years ago. Other than the caves of the Swabian Jura, the earliest secure archaeological evidence for music comes from sites in France and Austria and post-date 30,000 years ago.

See also:

Ghosh, P. 'Oldest musical instrument' found, BBC News, 25 June 2009.

Wynn, T. Hafted spears and the archaeology of mind, Proceedings of the National Academy of Science USA, 2009 | doi: 106:9544-9545 (Extract)

By Robert Deyes
ARN Correspondent

The summer of 2000 promised to be very exciting for ornithologists and paleontologists alike as they flew into Beijing for the fifth quadrennial meeting of the Society of Avian Paleontology and Evolution (Ref 1). The setting was most appropriate given the richness of fossils that have been unearthed in Chinese soil. The central theme of the meeting lay in trying to resolve the question of whether birds had really evolved from dinosaurs (Ref 1). However, rather than a harmonious discussion with the constructive disagreement that one might expect from any scientific 'get-together' aimed at resolving discrepancies in data, the meeting did nothing but expose an underlying discord (Ref 1).

While some scientists such as Berkeley's John Hutchinson and Yale ornithologist Richard Prum were frustrated over issues that they considered long resolved, others were much more skeptical about the certainty of the facts. Storrs Olson, head of ornithology at the National Museum of Natural History, weighed in by accusing Prum of engaging in "ideological mumbo-jumbo" when Prum claimed that feathers had the same evolutionary origin as "hair like integuments found on dinosaur fossils" (Ref 1). So strong was Olson's feeling against the evolutionary link drawn between birds and dinosaurs that throughout the meeting he and others wore badges stating their case: "BIRDS ARE NOT DINOSAURS" (or B.A.N.D for short; Ref 1). University Of North Carolina paleontologist Alan Feduccia, well known for his discussions on temporal discrepancies between bird and dinosaur fossils, was similarly uncertain about the dinosaur-bird link. Feduccia made his uncertainty public to the sound of accusations claiming a creationist undertone (Ref 1).

With the latest evidence Olson and his 'BAND of merry men' appear to have been vindicated. New data on how birds breathe makes the dinosaur-bird link untenable. According to a recent study, the unique thigh bone and muscle structure in birds' legs play a key role in preventing lung collapse (Ref 2). For birds, that need about twenty times more oxygen than say reptiles, such structural support is crucial to survival (Ref 2). Theropod dinosaurs from which birds are thought to have descended, did not sport such a fixed thigh bone structure and are therefore not viable candidates for a hypothetical bird ancestor (Ref 2).

Of course the impasse over how birds evolved extends well beyond thigh bones and muscles. In fact, the origin of feathers continues to be a formidable stumbling block for 'evo-philes'. To further understand the difficulty that the feather poses to the assumed evolutionary transition from dinosaurs to birds, consider the feather's structural foundations. What we know is that the central rachis (or shaft) of the feather branches off into smaller barbs and barbules. The barbules are equipped with tiny hooklets at their ends that interlock with ridges in the posterior barbules to form an impervious, tightly-held vane (Ref 3).

From an aerodynamic standpoint, the arrangement of the feathers in the overall shape of the wing makes for an aerofoil that displays minimal levels of turbulence (Ref 3). The ability to change the geometry and shape of such an aerofoil makes it ideally suited for the various tasks that the bird has to perform such as landing, soaring and flapping. From a molecular and cellular perspective, the story is no less fascinating. The feather follicle, from which the central rachis projects, contains specific zones of epithelial cells specialized in the formation of each of the components of the feather (Ref 4). The molecular mechanisms by which such cell specialization is achieved have also been elucidated in recent years (Ref 4). Through concentration gradients and a highly-regulated activation of specific genes, the morphogenesis and development of a feather is a very tightly-controlled affair (Ref 4).

With such a realization, we begin to get a sense of why it was that twenty three years ago biologist Michael Denton so emphatically decried the step-by-step, unguided evolutionary origin of wings (Ref 3). As Oregon State University Professor John Ruben humorously quipped, "a velociraptor did not just sprout feathers and fly off into the sunset" (Ref 2). The wing- the perfect aerofoil- must meet rigorous criteria before it can provide the necessary lift (Ref 4). No slight fraying of dinosaur scales would have done the job.

Seemingly oblivious of these intractable challenges, some scientists have gone all out to prop up their evolutionary meanderings by focusing on the three-fingered limbs of theropod dinosaurs and modern day birds (Refs 5,6). Paleontologists Xing Xu and James Clark for example recently published on two specimens of a 156 million-old, toothless-beaked, herbivorous theropod called Limusaurus inextricabilis that, they maintain, is a Darwinian-style 'missing link' (Refs 5,6).

One factor that has long been a source of consternation is that the finger digits of theropods and birds do not appear to match. While theropods seemingly carried digits 1,2 and 3 of the pentadactyl arrangement, birds display what scientists believe to be digits 2,3 and 4 (Refs 5,6). Xu and Clark have ruffled feathers by claiming that theropod digits have historically been misidentified. Based on their study of L. inextricabilis, they contend that just like in birds early theropods would have had digits 2,3 and 4 (Refs 5,6).

Such a conclusion is not without its critics. In fact prominent Yale evolutionary geneticist Gunter Wagner has questioned the numbering assignments of bird digits adding that bird wings might be based on digits 1,2 and 3 after all (Ref 5). Wagner cites fundamental aspects of embryonic development in support of his case. University of California paleontologist Kevin Padian has similarly suggested that the digit morphology of L. inextricabilis might represent nothing more than an "oddly reduced hand", commensurate with its herbivorous lifestyle (Ref 5).

Today, nine years after the Beijing meeting, Olson would seemingly be justified in wearing his famous badge. For him and others, the 'B.A.N.D' does indeed play on. To be sure, contemporary evidence shows birds to be a distinct phyletic group not easily integrated into a man made evolutionary scheme. While evolutionists point proudly to the apparent anatomical similarities between birds and dinosaurs, they themselves admit to the pressing need to resolve crucial questions about the origin of flight, the evolution of feathers and the conversion to endothermy (Ref 7).

These are not side questions designed to obfuscate discussions, but rather questions that are central to the matter at hand. In light of such facts, perhaps a more radical message needs to be conveyed that echoes the beat of a different mantra: BIRDS ARE REALLY BIRDS (or B.A.R.B for short). It is perhaps time to re-examine our most treasured notions of bird evolution.

Literature Cited
1. Rex Dalton (2000), Feathers fly in Beijing, Nature, Volume 405, p.992

2. See 'Discovery raises new doubts about dinosaur-bird-links', http://www.eurekalert.org/pub_releases/2009-06/osu-drn060809.php

3. Michael Denton (1986), Evolution: A Theory in Crisis, Adler and Adler Publishers, Bethesda Maryland, 1st Edition, pp. 202-208

4. Mingke Yu, Ping Wu, Randall B. Widelitz, Cheng-Ming Chuong (2002), The morphogenesis of feathers, Nature, Volume 420, pp.308-312

5. Matt Kaplan (2009), Dinosaur's digits show how birds got wings, 17 June 2009, Nature, doi:10.1038/news.2009.577

6. Xing Xu, James M. Clark, Jinyou Mo , Jonah Choiniere, Catherine A. Forster, Gregory M. Erickson, David W. E. Hone, Corwin Sullivan, David A. Eberth, Sterling Nesbitt, Qi Zhao, Rene Hernandez, Cheng-kai Jia, Feng-lu Han, Yu Guo (2009), A Jurassic ceratosaur from China helps clarify avian digital homologies, Nature 459, pp.940-944

7. See 'Are Birds Really Dinosaurs?', http://www.ucmp.berkeley.edu/diapsids/avians.html

In 2002, a team of Argentinian geologists published a paper on what they considered to be the oldest bird tracks. The lead researcher was quoted as saying: "The first and most striking feature of these fossil footprints is the overall resemblance with modern bird footprints". In commenting on the finds, Martin Lockley, a respected palaeontologist, said: "what is commendable here is that the Argentineans have presented their material well and these footprints seem to be distinctly bird-like and different from any known dinosaurs walking around at the time".

a) Footprints are numerous in this slab of the Santa Domingo Formation.
b) The arrows point to a track of footprints. Visible in each print of the track is the hallux, the digit that points backwards in birds. (Credit: Ricardo Melchor, Source here).

During the intervening years, the Argentinians have worked on their find and numerous related themes. For example, they have published "the first comprehensive ichnotaxonomic review of the Triassic tetrapod track record in Argentina, including previous accounts and new material recently discovered, and an analysis of its composition and stratigraphic distribution." They have analysed depositional environments and looked a a whole range of fossil traces. Most recently, they have used a modern-day locality to study trackways left by birds and compared them with previously-found fossil material. Their study is thorough and authoritative. Rather than review the details, we shall go straight to their conclusions:

"The presence of flight trace fossils (Volichnia), i.e. footprints with elongated hallux impressions that are interpreted as representing low angle landing, associated with probing marks and a similar morphology of Gruipeda dominguensis with tracks of modern shorebirds, strongly suggest an avian affinity for the producers of the fossil tracks."

The claim for bird tracks in these rocks is no longer tentative. After rigorous examination, the fossil evidence points clearly to birds feeding and moving about in a "low-gradient fluvio-lacustrine setting under semi-arid climate". The problem this poses is integrating this with other knowledge regarding fossil birds. These deposits are thought to predate Archaeopteryx by 55 Ma. They conflict dramatically with those who claim that birds evolved from theropod dinosaurs. Consequently, these traces are very controversial. The authors back off from confrontation by saying: "in consequence, the Santo Domingo track site would be younger than supposed".

However, the geological Period associated with these rocks may not be dismissed easily. There are three independent pointers to age and the lithology is also typical of rocks known as New Red Sandstone. The authors write:

"The track surface belongs to the Santo Domingo Formation, which is considered of Late Triassic-Early Jurassic age. This age is based on characteristic fossil wood remains, on a 40Ar/39Ar radiometric age from interbedded basalt flows, and palaeomagnetic studies. The formation reaches a minimum thickness of c. 1950 m and is in fault contact with Carboniferous igneous and sedimentary rocks. The Santo Domingo Formation is a red bed succession that displays, from base to top, a transition from alluvial fan, fluvial braided (with calcretes), ephemeral fluvial and shallow lakes, and eolian environments."

Whilst it is perfectly reasonable to revisit the question about assigned age, it is no less reasonable to revisit the supposed theropod-bird evolutionary transition. In particular, it is worth noting the research of BAND scholars (Birds Are Not Dinosaurs). One of these is John Ruben, who with colleagues (1997), compared the respiratory structures of modern birds, mammals, and crocodiles with those reconstructed from the fossils of early birds and theropod dinosaurs. There are big differences. Theropod dinosaurs appear to have crocodile-like diaphragms. Birds, however, lack a diaphragm and make use of pelvis and chest movements to breathe. The differences are so marked that, it is claimed, there are "fundamental problems" with the proposal that diaphragm-less birds evolved from dinosaurs with diaphragms. For more, go here.

Ruben has co-published another challenging study recently, related to avian respiration.

"It's been known for decades that the femur, or thigh bone in birds is largely fixed and makes birds into "knee runners," unlike virtually all other land animals, the [Oregon State University] experts say. What was just discovered, however, is that it's this fixed position of bird bones and musculature that keeps their air-sac lung from collapsing when the bird inhales. Warm-blooded birds need about 20 times more oxygen than cold-blooded reptiles, and have evolved a unique lung structure that allows for a high rate of gas exchange and high activity level. Their unusual thigh complex is what helps support the lung and prevent its collapse."

Like his analysis of the diaphragm in respiration, Ruben interprets the new findings in terms of a fundamental clash between the designs of birds and the design of dinosaurs. It is unreasonable to postulate an evolutionary transition.

"The implication, the researchers said, is that birds almost certainly did not descend from theropod dinosaurs, such as tyrannosaurus or allosaurus. The findings add to a growing body of evidence in the past two decades that challenge some of the most widely-held beliefs about animal evolution. "For one thing, birds are found earlier in the fossil record than the dinosaurs they are supposed to have descended from," Ruben said. "That's a pretty serious problem, and there are other inconsistencies with the bird-from-dinosaur theories.
"But one of the primary reasons many scientists kept pointing to birds as having descended from dinosaurs was similarities in their lungs," Ruben said. "However, theropod dinosaurs had a moving femur and therefore could not have had a lung that worked like that in birds. Their abdominal air sac, if they had one, would have collapsed. That undercuts a critical piece of supporting evidence for the dinosaur-bird link."

It will be a good day for science when these evidences get featured in educational materials and in media presentations. However, other factors affect this:

"Frankly, there's a lot of museum politics involved in this, a lot of careers committed to a particular point of view even if new scientific evidence raises questions," Ruben said. In some museum displays, he said, the birds-descended-from-dinosaurs evolutionary theory has been portrayed as a largely accepted fact, with an asterisk pointing out in small type that "some scientists disagree."

Application of neoichnological studies to behavioural and taphonomic interpretation of fossil bird-like tracks from lacustrine settings: The Late Triassic–Early Jurassic? Santo Domingo Formation, Argentina
Jorge F. Genise, Ricardo N. Melchor, Miguel Archangelsky, Luis O. Bala, Roberto Straneck and Silvina de Valais
Palaeogeography, Palaeoclimatology, Palaeoecology, 272(3-4), 15 February 2009, 143-161 | doi 10.1016/j.palaeo.2008.08.014

Abstract: The purpose of this study is to apply neoichnological observations to the behavioural and taphonomic interpretation of a Late Triassic-Early Jurassic track surface from the Santo Domingo Formation (Argentina) containing hundreds of bird-like tracks and trackways. [. . .] Field observations allowed to distinguish twenty one behaviours that produced distinct traces and four modern footprint types (1 to 4) related to specific substrate conditions. In particular, the preferential formation of bird tracks parallel to the waterline, also confirmed by studies on droppings and invertebrate fauna of the pond, and other associated sedimentary features (ripple marks, wrinkle marks, mud drape thickness) and trace fossils were important for recognition of the shoreline in the fossil example. [. . .]. Five of the behaviours recognised in the modern pond were inferred from the sixteen trackways distinguished on the fossil track surface, including walking, walking with a zig-zag path, short runs, probing, and landing with legs directed forward (possible trace of flight). The recognition of traces of flight (Volichnia), probing marks, and tracks showing morphology similar to modern shorebirds (G. dominguensis), strongly suggest an avian affinity for the producers of the fossil tracks and, in consequence, the Santo Domingo track site would be younger than supposed.

Cardio-pulmonary anatomy in theropod dinosaurs: Implications from extant archosaurs
Devon E. Quick, John A. Ruben
Journal of Morphology, Early View 20 May 2009 | doi 10.1002/jmor.10752

Abstract: Although crocodilian lung and cardiovascular organs are markedly less specialized than the avian heart and lung air-sac system, all living archosaurs possess four-chambered hearts and heterogeneously vascularized, faveolar lungs. In birds, normal lung function requires extensive, dorsally situated nonvascularized abdominal air-sacs ventilated by an expansive sternum and specially hinged costal ribs. The thin walled and voluminous abdominal air-sacs are supported laterally and caudally to prevent inward (paradoxical) collapse during generation of negative (inhalatory) pressure: the synsacrum, posteriorly directed, laterally open pubes and specialized femoral-thigh complex provide requisite support and largely prevent inhalatory collapse. In comparison, theropod dinosaurs probably lacked similarly enlarged abdominal air-sacs, and skeleto-muscular modifications consistent with their ventilation. In the absence of enlarged, functional abdominal air-sacs, theropods were unlikely to have possessed a specialized bird-like, air-sac lung. The likely absence of bird-like pulmonary function in theropods is inconsistent with suggestions of cardiovascular anatomy more sophisticated than that of modern crocodilians.

See also:

Discovery raises new doubts about dinosaur-bird links, EurekAlert, 9 June 2009.

Towards the end of the 17th Century in England, there was a fascinating debate between philosophers (scientists) and theologians about mountains. The question concerned their significance in our understanding of the natural world. Thomas Burnet triggered the debate by publishing "Sacred Theory of the Earth" in 1681 (in Latin) and in 1684 and 1690 (in English). This book was pioneering in its day in that it proposed a concordance between Biblical history and natural philosophy as well as arguing against Aristotle's eternalism.

"The book begins with the earth's creation from Chaos and goes on to explain the earth as paradise, the deluge, the destruction of the earth by fire and its eventual restitution at the end of time. What Burnet set out to do was to reconcile the scriptural account of the earth's history with recent sorts of natural philosophical explanations for them. His own preference was for a model of creation and physical causation that owed a great deal to the works of Rene Descartes. The different stages in the earth's history were illustrated in the book's beautiful frontispiece."

The frontispiece of the first volume of Burnet's Theory (Source here)

Burnet was taken to task by numerous scholars: "John Ray [botanist], the Newtonians John Keill and William Whiston, the scholar Richard Bentley and John Woodward [geologist]". They responded at two levels. The first area of concern was theological (which we will not consider further here), and the second was concerned with natural philosophy - particularly related to mountains.

Burnet presented mountains as a consequence of the Deluge, thereby associating them with God's judgment on human sinfulness. After the Deluge, the surface of the Earth was "a broken and confus'd heap of bodies" and mountains presented "the image or picture of a great Ruine".

"Burnet was unequivocal in his claim that mountains 'do not consist of any proportion of parts that is referable to any design, or that hath the least footsteps of Art or Counsel'."

His adversaries did not deny the Biblical narrative of Creation, the Antediluvian Earth, the Deluge and the Modern era - but they did not agree about design! Their writings reveal them demonstrating that mountains have uses (functionality) and that mountains are aesthetically pleasing (not ugly). It appears that the quest to strengthen functionality arguments stimulated scientific enquiry (particularly in understanding the role of mountains in the water cycle).

"Ray, Bentley, Keil and others set about enumerating all the different 'uses' of mountains that they could think of. Their discussions ranged from the role of mountains as alpine habitats, their supposed role in regulating the weather, and they even touted mountains as useful natural frontiers between nations. Perhaps most important to posterity are their inclusion of early explanations of the water cycle. Research carried out by Edmund Halley on St Helena into the possible role of mountains in the water cycle provided Burnet's critics with ammunition to prove that mountains were indeed useful, or perhaps even essential to the very preservation of human life on earth."

Regarding aesthetic arguments, Burnet found it easier to make a case for the ugliness of mountains by comparing them with the mountains of the Moon. If we viewed the Earth from afar, "look'd upon with a good Glass [telescope]",the mountains would appear "rude and ragged". In countering this argument, there was some incredulity with the idea of being elevated to so high a vantage point , but the main objection appealed to the aesthetics of landscape painting and gardening.

"The two key pieces of terminology used by Burnet's opponents to describe the place of mountains in the landscape were 'prospect' and 'variety'. [. . .] In seventeenth-century English discourse the word 'prospect' could be used interchangeably with 'landscape painting' and referred to landscape paintings made through the formal practices of mathematical perspective. [. . .] 'Variety' was the most important aesthetic consideration in contemporary discussions of landscape art. Early English theorists of landscape art praised mountains for their contribution to landscape paintings that would otherwise lack variety and fail to stimulate onlookers. Burnet's critics put this exact argument to use in their criticism of his aesthetic."

Wragge-Morley, the author of this analysis, points out that "the difference between seeing the truth about the design of mountains, and seeing nothing at all, lay in a simple perspectival shift". One person looks at a relief map of the globe and sees lumps and scars; another brings the perspective of landscape art and sees beauty, grandeur and majesty.

"This in turn could lend weight to an argument for or against their utility, which could in turn have ramifications for one's view of their theological meaning."

The history of ideas provides much food for thought, and this "strange and surprising debate" is no exception. There appear to be at least two applications that are relevant to our own day and to contemporary debates about design. First, Wragge-Morley's comments on perspective could be applied to design thinking generally. This is the explanation why some look at the natural world and see design everywhere, whereas others witness the same objects and declare them to be design-free. These perspective differences do not reflect on people's ability to think rationally, but rather point to underlying metaphysical differences affecting both thinking and scientific practice. In his essay, Wragge-Morley does not enlarge on these aspects, but he does draw attention to Burnet's interest in Cartesian philosophy which would be a good launching point for further analysis.

Second, this case-study reveals the way design-based thinking triggered research into functionality. Making a design inference actually stimulated enquiry, because intelligent design suggests purpose and meaning. This is a principle of general application, and it is an effective response to those who claim that ID is a science-stopper. The claim is entirely polemical, unsupported by evidence. A modern-day example is Junk DNA. Darwinian biologists regarded it as garbage and it was not targeted for research. Those brave scientists who were prepared to challenge the paradigm by postulating functionality found that they were stumbling on a treasure-trove of cellular information! (Go here and here).

It is worth pointing out, in conclusion, that design thinking is not lacking in theoretical development. This debate about mountains predated natural theology and William Paley: differences in emphasis can be traced through this period. The modern resurgence of design-thinking is not a return to Paley's watchmaker arguments. Finding complexity and functionality is not enough to confirm design. We recognise that some functionality can be introduced by natural processes: a fallen tree can provide a bridge over a river, but that does not mean the functionality was designed. Today, we talk more about information, and refer to complex specified information when making design inferences.

A strange and surprising debate: mountains, original sin and 'science' in seventeenth-century England
Alexander Wragge-Morley
Endeavour, Volume 33, Issue 2, June 2009, Pages 76-80 | doi:10.1016/j.endeavour.2009.05.001

It could come as a shock to learn that some seventeenth-century men of science and learning thought that mountains were bad. Even more alarmingly, some thought that God had imposed them on the earth to punish man for his sins. By the end of the seventeenth century, surprisingly many English natural philosophers and theologians were engaged in a debate about whether mountains were 'good' or 'bad', useful or useless. At stake in this debate were not just the careers of its participants, but arguments about the best ways of looking at and reckoning with 'nature' itself.

In this Bicentennial year of Darwin's birth, there are many who want to drive a wedge between Darwinism as a scientific theory and Darwinism as a philosophical, social or political theory. Here in the UK, we have a Templeton Foundation-funded project called "Rescuing Darwin" which seeks to do exactly this. Darwinism, it is claimed, is essentially a scientific theory and it needs to be rescued from the atheists, the social-engineers and others who are taking it far beyond the domain of science. Here is an excerpt from the report "Rescuing Darwin".

"Social Darwinism did not have the monopoly on interpreting evolution. Indeed, in its time evolution has been used in support of every "ism" imaginable, including socialism, capitalism, racism, eugenics, feminism, theism and atheism. As George Bernard Shaw once remarked, Darwin "had the luck to please everybody who had an axe to grind". The key point is that, from the earliest times, evolution was understood - and sometimes rejected - as a philosophical, social or political theory, rather than simply a biological one." (page 25)

This strategy of presenting Darwinism as science with no philosophical or ideological baggage deserves to be critiqued and challenged. Many of us argue that science necessarily implies a philosophical underpinning, and that metaphysical foundation inevitably affects the way science is practised. This blog, however, is concerned with the evidence from history. What was Darwin's own thinking about laissez-faire social Darwinism? Does he deserve to be rescued from those who have inappropriately applied his science to the workings of human society? Or is he being expelled from his own house?

Will the real Darwin please stand up! (Source here)

In an incisive essay, Richard Weikart contributes to the scholarly answers to these questions. There have been some who say that "social Darwinism was an essential part of Darwin's theory". Others have denied that social Darwinism ever existed, and still others who "blame Herbert Spencer for originating and popularizing social Darwinism". The essay concerns the relationship between Spencer's and Darwin's social views over time.

"That is the task I set for myself, as I explore the following questions: How much influence did Spencer exert on Darwin's social thought and vice-versa? What did Spencer and Darwin think about each others' views of social evolution, especially as it related to laissez-faire economic theory? Was Spencer a social Darwinist? Was Darwin a social Darwinist?"

Both men were influenced by Thomas Malthus's population theory. Both used and developed arguments first made by Malthus. Weikart's analysis is that the views of Spencer and Darwin provide a striking example of convergent evolution.

"Because laissez-faire economic ideals were so prominent in English intellectual and political life in the mid-nineteenth century, it should come as no surprise that Darwin and Spencer imbibed these ideas independently. Their thinking about human society was shaped heavily by mid-Victorian economic values and concepts such as competition, division of labor, and adaptation."

Spencer's thinking was developed earlier than Darwin's, although Spencer's views can be described as Lamarkian. After reading Darwin, he incorporated selection into his thinking.

"Thus long before he read Darwin, Spencer (1851, 324) embraced the position that laissez-faire was necessary to ensure biological progress, not only by stimulating some people to improve themselves (Lamarckism), but also by society "excreting its unhealthy, imbecile, slow, vacillating, faithless members" (Darwinian selection)."

Although there are hints of Darwin's thinking on these matters before 1871, it was not until the publication of "The Descent of Man" that we have something more substantial to refer to.

"But would not the evolution of morality, based on what Darwin called social instincts, ameliorate the struggle for existence among humans? Would it not temper the struggle for existence with moral sentiments that would make humans cooperate? Yes, Darwin explained, when he forthrightly broached the subject in the last half of chapter five, in a section entitled, "Natural Selection as affecting Civilised Nations." In this section Darwin explained his views about how his theory impinged on human society. If one wants to know whether or not Darwin was a social Darwinist, especially in relation to laissez-faire economics, this is the section to examine."

After reviewing the views of different scholars and making his own arguments, Weikart concludes that:

"Though Darwin's advocacy of laissez-faire economic competition was neither as vocal nor as radical as Spencer's, he clearly viewed economic competition as an integral part of the human struggle for existence, and he insisted that governments should foster, not reduce, competition."

So, it is concluded that both men were social Darwinists and that they had come to their views largely independently. Darwin made no attempt to distance himself from Spencer on these matters.

"Despite any differences between them, Darwin and Spencer were both laissez-faire social Darwinists. They both used biological arguments to justify economic policies designed to sharpen human competition. They warned against government involvement or legislation that would significantly reduce economic competition because they thought this would result in biological deterioration. They developed these ideas in a common intellectual and social context where laissez-faire economics was economic orthodoxy. Spencer was certainly the first of the two to publish his social Darwinist ideas, if it is appropriate to use this term before 1859. Spencer's laissez-faire views were also even more radical than Darwin's since his opposition to government intervention was far more radical than most laissez-faire proponents. Darwin's views were more in line with mainstream laissez-faire economics."

The take-home message is this: Darwinism is NOT a purely scientific theory. The science cannot be divorced from the underpinning philosophy. Projects like "Rescuing Darwin" are fundamentally flawed and philosophically naive. Educationalists have a duty to introduce students to these issues in a way that encourages critical thought and analysis.

Was Darwin or Spencer the Father of Laissez-Faire Social Darwinism?
Richard Weikart
Journal of Economic Behavior and Organization, 71, 2009, 20-28 | doi:10.1016/j.jebo.2007.06.011

Abstract: This article explores the way that Darwin and Spencer integrated laissez-faire ideas into their evolutionary biology, and how they then extrapolated from their evolutionary theories to social and economic thought. It argues that Darwin and Spencer developed laissez-faire social Darwinism independently, making both important progenitors of it.

The journal Science carries an interview with Eugenie Scott, who is executive director of the National Center for Science Education. She is presented as a tireless warrior, who is to be found "on the frontlines of the contentious battle over teaching evolution in U.S. public schools." She refers to her opponents as "the enemy". They are diverse: "creation science, intelligent design [ID], and antievolution" protagonists. Those of us who follow these issues are well aware of the stance Scott takes and the arguments she brings. This blog is concerned with the way Science presents her thinking as mainstream, with no attempt to provide analysis or to suggest that Scott's thinking deserves to be critiqued.

We have reached a situation today where any criticism of Darwinism is repackaged as an assault on science. To frame the issues in this way is to close down discussion and critical analysis. It is a problem, not only for ID scientists and creation-based scientists, but also for evolutionary biologists who accept that Darwinism does not deliver the mechanisms needed to accomplish biological transformation. For more on this, go here and here. Darwinians like Scott have a blind spot: they have so equated their cherished theory with 'science', that they are unable to appreciate that some of us want a genuine scientific debate about mechanisms: what they can achieve and what their limitations are.

Research has shown that 10% of blind dogs have blurred vision but this appears to make no difference to their day-to-day duties. It is thought that the animals compensate by relying more on smell and hearing. There is a useful analogy here with science leaders. (Source here)

This blind spot spills over into education. "Besides periodic assaults on science standards as we recently saw in Texas, we are concerned about antievolution legislation in different states under the guise of academic freedom bills." Scott does not admit that the principle of academic freedom implies the right to bring criticism of Darwinism into the classroom. Consequently, "academic freedom" advocates are painted as subversive to science. There are ideological agendas behind this opposition to developing the critical minds of students (for more, go here).

A revealing Q&A concerned the relevance of evolutionary theory for practicing scientists. The answer given by Scott is actually very weak. Instead of pointing out examples of relevance, she makes a sweeping statement about seeing the "big picture":

Q: Why is it important to teach evolution? Can't doctors and most life scientists do their jobs without accepting evolution?
E.S.: You can be a mechanic without understanding the niceties of the internal combustion engine. [But] wouldn't you rather go to a mechanic who has the big picture?

This fails to interact with those scientists who are prepared to say that evolutionary theory is more of a surficial veneer than an underpinning framework (go here). Also, it fails to do justice to the place of design in medicine: those who consider the human body to be designed have had a good track record for helping to cure ailments, whereas reductionistic biology tends to focus on symptoms rather than causes and the emerging field of Darwinian medicine is largely untried and untested (go here and here).

One further area where Scott needs to be challenged is in her understanding of the philosophy of science. She appears to think that science transcends philosophy. When talking about what scientists should not do, her argument envisages scientists drawing philosophical ideas from science. Some draw atheism; some draw theism. Here is the relevant part of the interview:

"What university scientists should not do is to force students to choose between religion and science. If a professor were to say that evolution proves there is no God, that's not just bad philosophy of science, it ensures that a significant number of students will stick their fingers in their ears.
When explaining biological questions, such as the evolution of the eye, there is no need to say that God had nothing to do with it. It's an irrelevant comment. I don't think a classroom is an appropriate place to try to create more atheists any more than it is an appropriate place to create more fundamentalist Christians."

A major element of the analysis contributed by ID scholars is that philosophy underpins science. This is not an exclusive emphasis by any means - for this view is common among philosophers of science. The problem is that few ask questions about the ideological underpinnings of science and whether different ideologies matter. Is it fairer to say "evolution proves there is no God" or "atheism leads to a science of origins where there is no purpose, guidance or any role for a Creator"? There is plenty of evidence for "bad philosophy of science", but it is evident at a deeper level than acknowledged by Scott. For more, go here.

What shall we say about Scott's approach to explaining "biological questions, such as the evolution of the eye". Notice that she does not refer to the functioning of the eye (which is a question for empirical science) but rather to the evolution of the eye (which is a question for historical science that presumes the eye has evolved). The philosophical issues needing consideration are affected by the questions asked. Scott says: "there is no need to say that God had nothing to do with it. It's an irrelevant comment." From a scientific perspective, the issue concerns causation. What causes are legitimate to consider within science? We are familiar with the role of natural law within science. We are also aware of chance events which need statistical description rather than physical or chemical laws. The controversial area of causation concerns intelligent agency (design). ID advocates do not think that it is irrelevant to consider the possibility of intelligent causation and have proposed various tests to distinguish law, chance and design. The unwillingness of Scott to acknowledge that design can be even considered within science is a reflection on the philosophy of science she has adopted: a metaphysical presupposition that prohibits design from being discerned. This metaphysical stance creates the blind spot. For more, go here.

The real concern is not that Scott holds these views (for we live in the free world where we protect academic freedom). It is problematical because Science did not think it appropriate to provide a forum for dialogue with scientists who have a different philosophy of science. To pretend that there is no debate over these issues is folly. For a recent contribution relating to the policy adopted by the Texas State Board of Education, go here.

Eugenie Scott Toils in Defense of Evolution
Yudhijit Bhattacharjee
Science 324, 5 June 2009: 1250-1251 | DOI: 10.1126/science.324_1250b

1st para: As executive director of the California-based National Center for Science Education, anthropologist Eugenie Scott has spent the past 2 decades on the frontlines of the contentious battle over teaching evolution in U.S. public schools. [. . .] Last week, Scott won the inaugural Stephen Jay Gould Prize from the Society for the Study of Evolution, only weeks after Scientific American ranked her among the country's top 10 science and technology leaders for her self-described role as "Darwin's golden retriever." Scott spoke to Science last week about where things now stand.

See also:

Hunter, C. Pure Dogma, Darwin's God (blog), 4 June 2009.

Mcleroy, D. State curriculum ensures only science taught in science classes, The Eagle, May 31, 2009

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.