Science Literature

Hot on the heels of an arthropod with complex compound eyes from the Emu Bay Shale (in Australia) has come an even more dramatic discovery! The same lagerstatten has yielded some fossil eyes, attributed to Anomalocaris, that show just how much 'modernity' can be traced back to the Cambrian fauna.

"The number of ommatidia in the Anomalocaris eyes would almost certainly have greatly exceeded the count based on the exposed surface of the eye alone. [. . .] the total count could be substantially greater than the observed 16,000+ lenses. If this is indeed the case, few living arthropods have as many ommatidia, and these eyes would certainly have functioned with a high degree of acuity. [. . .] Throughout the geological history of Arthropoda, compound eyes have rarely exceeded this size; very large Siluro-Devonian pterygotid eurypterids and some Jurassic thylacocephalans represent some of the rare examples with eyes larger than those of Anomalocaris."

Anomalocaris and its compound eyes (source here)

Inevitably, this raises questions about the way the evolution of compound eyes has been presented in the past. Plots of ommatidia density vs geological time have been used to defend gradualism. However, most of the data was related to trilobites, which are dominated by benthic forms in the Lower Cambrian, diversifying to include nektonic species in the Late Cambrian and subsequent Periods. Now that the eyes of nektonic animals are being discovered and documented, the picture looks rather different. A whole range of eye designs were present during the Early-Middle Cambrian.

"The eyes of Anomalocaris expand the known diversity of visual adaptations in the early Cambrian: low-resolution organs with >100 ommatidia (eodiscoid trilobites), higher-resolution eyes with a distinct bright zone that might have functioned in low light, and very large eyes with a uniformly dense visual field adapted to bright environments."

It should always be remembered that eye complexity means nothing without neuronal processing capability. Light signals have to be transmitted, analysed and decoded as visual images. Modernity in these aspects must be inferred also.

"The very large size of anomalocaridid compound eyes and the visual acuity inferred from the elevated lensnumber and low interommatidial angles suggest that processing of visual information would have required the optic neuropils and brain to be of comparable complexity to crown-group (that is, modern) arthropods. In the crown group, two optic neuropils are reconstructed in the most recent commonancestor, transmitting to a protocerebrum with a median unpaired neuropil, the central body."

Discoveries like this create major challenges for advocates of Darwinian gradualism. Again and again, the source of novelty is pushed earlier into the undocumented past. Gradualism as a working concept is sustained, not by data, but by inference - but the gaps available for gradualist change are ever shrinking!

"Dense, hexagonal packing of ommatidia in compound eyes has been demonstrated to have been unequivocally present in Schinderhannes bartelsi, a Devonian species resolved as the immediate sister group to the arthropod crown group. The eyes of Schinderhannes resemble those of Anomalocaris in being large, stalked, having an ovoid outline of the visual surface, and a highly elevated number of lenses. The finding that Anomalocaris, resolved more basally than Schinderhannes in the arthropod stem group, possesses the same kind of ommatidial packing as in Schinderhannes and crown-group arthropods pushes the origin of compound eyes further down the arthropod stem group. As such, compound eyes evolved earlier than the origin of a hardened tergal exoskeleton and biramous trunk limbs (the latter characters being present in Schinderhannes but not anomalocaridids). We infer that the stalked eyes of all Radiodonta (that is, anomalocaridids) are arthropod-type compound eyes."

The same general analysis applies to all the evolutionary stories that are developed around the fossil record. As in so many research papers, the evolutionary comments are tacked on and are little more than table-talk. The last sentence of the abstract and the last sentence of the paper make the same point: the sophisticated visual system of Anomalocaris would have the consequence of enhancing selection pressures and "probably helped to accelerate the escalatory 'arms race' that began" with the Cambrian fauna.

However, justification of the 'arms race' and the way it is supposed to affect the course of evolution is left to the imagination. As an alternative scenario, consider an ecological perspective. The more we know of Cambrian faunas, the more we are finding evidence of ecosystems adapting to environmental change over time. The changes documented in the fossil record are better explained by reference to ecological concepts combined with the phenomenon of phenotypic plasticity.

Acute vision in the giant Cambrian predatorAnomalocaris and the origin of compound eyes
John R. Paterson, Diego C. Garcia-Bellido, Michael S. Y. Lee, Glenn A. Brock, James B. Jago & Gregory D. Edgecombe
Nature, 480, 237-240 (08 December 2011) | doi:10.1038/nature10689

Until recently, intricate details of the optical design of non-biomineralized arthropod eyes remained elusive in Cambrian Burgess-Shale-type deposits, despite exceptional preservation of soft-part anatomy in such Konservat-Lagerstatten. The structure and development of ommatidia in arthropod compound eyes support a single origin some time before the latest common ancestor of crown-group arthropods, but the appearance of compound eyes in the arthropod stem group has been poorly constrained in the absence of adequate fossils. Here we report 2-3-cm paired eyes from the early Cambrian (approximately 515 million years old) Emu Bay Shale of South Australia, assigned to the Cambrian apex predator Anomalocaris. Their preserved visual surfaces are composed of at least 16,000 hexagonally packed ommatidial lenses (in a single eye), rivalling the most acute compound eyes in modern arthropods. The specimens show two distinct taphonomic modes, preserved as iron oxide (after pyrite) and calcium phosphate, demonstrating that disparate styles of early diagenetic mineralization can replicate the same type of extracellular tissue (that is, cuticle) within a single Burgess-Shale-type deposit. These fossils also provide compelling evidence for the arthropod affinities of anomalocaridids, push the origin of compound eyes deeper down the arthropod stem lineage, and indicate that the compound eye evolved before such features as a hardened exoskeleton. The inferred acuity of the anomalocaridid eye is consistent with other evidence that these animals were highly mobile visual predators in the water column. The existence of large, macrophagous nektonic predators possessing sharp vision - such as Anomalocaris - within the early Cambrian ecosystem probably helped to accelerate the escalatory 'arms race' that began over half a billion years ago

See also:

Marshall, M. First top predator was giant shrimp with amazing eyes, New Scientist (7 December 2011)

The earliest example of a domestic dwelling built from bone has been discovered in the Ukraine. The structure is considered to be 44,000 years old and the builders were Neanderthals. The significance of this is that Neanderthals are supposed to be lacking in creativity and aesthetics, so they are usually portrayed as pragmatists dwelling in caves and rock shelters, largely devoid of characteristics we associate with humanity. Yet again, the evidence base shows the iconic Neanderthal to be a figment of the imagination.

"Neandertals are stumping for bragging rights as the first builders of mammoth-bone structures, an accomplishment usually attributed to Stone Age people. Humanity's extinct cousins constructed a large, ring-shaped enclosure out of 116 mammoth bones and tusks at least 44,000 years ago in West Asia, say archaeologist Laetitia Demay of the National Museum of Natural History in Paris and her colleagues. The bone edifice, which encircles a 40-square-meter area in which mammoths and other animals were butchered, cooked and eaten, served either to keep out cold winds or as a base for a wooden building." (source here)

Caves are portrayed as dwelling places and burial locations for Homo neanderthalensis. This scene is from Hannover Zoo. (Source here)

Finding a building made of mammoth bones is suggestive of a lifestyle that involved creativity, forward planning, cooperation and language. To build a dwelling is suggestive of them living in one place for extended periods of time. In addition, many of the bones had been decorated with carvings and ochre pigments, revealing an aesthetic sense in Neanderthals. Here is a selection of comments from Laetitia Demay, who led the research:

"It appears that Neanderthals were the oldest known humans who used mammoth bones to build a dwelling structure.
"This mammoth bone structure could be described as the basement of a wooden cover or as a windscreen.
"Neanderthals purposely chose large bones of the largest available mammal, the woolly mammoth, to build a structure.
"The mammoth bones have been deliberately selected - long and flat bones, tusks and connected vertebrae - and were circularly arranged.
"The use of bones as building elements can be appreciated as anticipation of climatic variations. Under a cold climate in an open environment, the lack of wood led humans to use bones to build protections against the wind."

People have been talking about revising our assessment of Neanderthals for some time now, but we still find them portrayed as brutish; still as sub-human; still as making noises to communicate rather than using speech. In a report on the research, Richard Gray says that the new finds "add to the growing view that Neanderthals were in fact quite advanced humans who had their own culture and may have even used language to communicate". Another comment is provided by Simon Underdown, an academic who researches Neanderthals at Oxford Brookes University, who said:

"It's another piece in the newly emerging Neanderthal jigsaw puzzle. Far from being the stupid cavemen of popular image it's becoming increasingly clear the Neanderthals were a highly sophisticated species of human. We can now add shelter building to the list of advanced behaviours that includes burying the dead, spoken language, cooking and wearing jewellery."

What is it that stops us thinking that Neanderthals were humans like us? For more on this, and an answer, go here.

Mammoths used as food and building resources by Neanderthals: Zooarchaeological study applied to layer 4, Molodova I (Ukraine)
Laetitia Demay, Stephane Pean, Marylene Patou-Mathis
Quaternary International, In Press, Available online 26 November 2011

Abstract: Considering Neanderthal subsistence, the use of mammoth resources has been particularly discussed. Apart from procurement for food, the use of mammoth bones as building material has been proposed. The hypothesis was based on the discovery made in Molodova I, Ukraine (Dniester valley). In this large multistratified open-air site, a rich Mousterian layer was excavated. Dated to the Inter-Pleniglacial (MIS 3), it has yielded 40 000 lithic remains associated with ca. 3000 mammal bones, mostly from mammoth. Several areas have been excavated: a pit filled with bones, different areas of activities (butchering, tool production), twenty-five hearths and a circular accumulation made of mammoth bones, described as a dwelling structure set up by Neanderthals. Attested dwelling structures made of mammoth bones are known in Upper Paleolithic sites, from Ukraine and Russia, attributed to the Epigravettian tradition. [. . .] Based on anthropogenic marks, mammoth meat has been eaten. The presence of series of striations and ochre on mammoth bones are associated with a technical or symbolic use. Furthermore, mammoth bones have been deliberately selected (long and flat bones, tusks, connected vertebrae) and circularly arranged. This mammoth bone structure could be described as the basement of a wooden cover or as a wind-screen. The inner presence of fifteen hearths, lithic artifacts and waste of mammal butchery and cooking is characteristic of a domestic area, which was probably the centre of a residential camp recurrently settled. It appears that Neanderthals were the oldest known humans who used mammoth bones to build a dwelling structure.

Most biological students think that adaptive radiations and Darwinism go together, and that the mechanisms of genetic mutation and natural selection explain all the data. However, in most cases, this explanation is assumed and not supported by evidence. It is assumed because of the dominance of neodarwinism in evolutionary biology and because students are very impressed with the "mountains of evidence" claimed to support the consensus. Happily, there are some biologists prepared to step outside the paradigm, and one of them is Austin Hughes from the University of South Carolina. In preparing the ground for his iconoclastic analysis, he writes:

"I will refer to this mechanism as the Neo-Darwinian mechanism; and, following general usage, I will refer to an allele that has been fixed by this process as one that has been fixed by positive Darwinian selection. The Neo-Darwinian mechanism is often assumed by biologists to be the only source of adaptive traits of organisms, to the point where 'adaptive evolution' and 'positive (Darwinian) selection' are treated as interchangeable terms in the literature."

Cichlids are a textbook example of rapid speciation - but not of Darwinian evolution! (For more, go here. Image source here)

Also, by way of preparation, he refers to the significant theoretical and evidential base for neutral evolution (Kimura, 1976). There is a phenomenon known as genetic drift involving neutral or nearly neutral mutations. There are mechanisms for fixing these genetic changes - all invisible to natural selection. These are considered to be more important than we realise, evidenced by the continuing scarcity of advantageous mutations. This was recognised in 1976 and it continues to this day.

"In the ensuing decades, a vast amount of molecular sequence data, including complete genome sequences of many organisms, has become available to test for the evidence of positive selection at the molecular level. However, the number of well-established cases has not increased greatly in comparison with those known in the mid-1970s. It is true that a very large number of papers have been published in recent years purporting to show evidence of positive selection on the basis of various statistical methods. However, the vast majority of these cases cannot be considered well established. [. . .] Moreover, in almost all of the putative cases of positive selection identified by statistical analysis of sequence data alone, the biological basis of the supposed selection and even the phenotypic effects, if any, of the supposedly selected nucleotide substitutions have not been addressed."

Hughes has previously pointed out difficulties in identifying evidence for positive selection, yet there appears to be plenty of evidence for purifying selection (the elimination of deleterious variants).

"The predominance of purifying selection was predicted by Kimura and Ohta (1974), and the fact that their prediction has been proved to be correct is the cornerstone of many routine methods of modern bioinformatics, whereby evolutionary conservation of a sequence element (the consequence of purifying selection) is taken as evidence of that element's functional importance."

So, in view of the meagre evidential support for "the Neo-Darwinian mechanism", Hughes turns his attention to the thought that adaptive phenotypes might arise by alternative routes. This has been considered by a few other authors, but the field is wide open. Consequently, Hughes proposes one such mechanism: the plasticity - relaxation - mutation (PRM) mechanism. He argues that the evidential base for this concept is already in existence in the biological literature.

"I examine some predictions of this theory and summarize evidence relating to those predictions. The present hypothesis does not deny that the Neo-Darwinian mechanism operates in certain cases. Rather, based on what we can learn from the known cases of positive selection, I conclude that the phenomenon of positive selection may be of relatively minor importance in phenotypic evolution. Instead, phenotypic plasticity and changes in the direction and nature of purifying selection, combined with the chance fixation of neutral or nearly neutral mutations, are proposed to be the major factors in the evolution of adaptive phenotypes."

Much of the paper provides clarification of the PRM mechanism and justifies the claim that the concept has a track record in the literature. The emerging scenario is that organisms typically have an ability to adapt to environmental inputs in ways that change and fix the phenotype. This is a variability that does not depend on mutations for new genetic information, although mutations may be involved in the fixing of the phenotype. The genomic architecture is already present that supports adaptation in a variety of directions. Influences may come from neutral mutations and genetic drift, and they may involve epigenetic mechanisms. After reviewing a variety of evidences, Hughes concludes:

"The PRM mechanism provides unification to the biological sciences by uniting observations at the genomic level (where purifying selection and genetic drift predominate) with those at the phenotypic level (where adaptive characters are well known). As mentioned above, some known examples are suggestive of the action of the PRM mechanism, but it is not yet known how widespread this mechanism is. However, I would predict that the PRM mechanism is likely to be a major mechanism for the origin of evolved adaptations, and perhaps more common than the Neo-Darwinian mechanism."

Let's look at some of the applications of the PRM concept.
First, a comment on the general picture. Adaptive radiations in the fossil record appear to have been rapid, followed by stasis. This pattern is quite unlike the branching illustration found in On the Origin of Species.

"In some cases, the time frame seems rather short for a Darwinian process to have occurred, and in other cases, the effective population sizes of the species in question are small, suggesting that there is unlikely to have been extensive genetic variation in the population prior to selection. However, none of these factors are problematic if these cases of apparent rapid evolution in fact represent cases of phenotypic plasticity, perhaps in some cases rendered heritable through germline DNA methylation. Thus, rather than the paradoxical observation of Darwinian evolution over ecological time, we may be merely seeing incipient evolution by the PRM mechanism, which is expected to operate over ecological time."

Second, the specific case of cichlid fishes is of interest, because these radiations do not have the luxury of extensive time.

"The PRM mechanism provides a simple explanation of such comparatively recent adaptive radiations as that of the cichlids of the East African Great Lakes. The oldest of these lakes, Lake Victoria, is no more than 200,000 years old, and others are still more recent. The diversity of species in these lakes is problematic for Neo-Darwinism, but is easily explained by the PRM mechanism if prior to the divergence of ecotypes the ancestral species showed a phenotypic plasticity similar to that described in sticklebacks."

Third, consider that classic example of adaptive radiation: the Galapagos finches.

"Perhaps ironically, the PRM mechanism can likewise account readily for the radiation of Darwin's finches in the Galapagos Islands. The natural history of Darwin's finches provides many examples where it is plausible that phenotypic plasticity preceded morphological change; a striking example involves the sharper bill shape of a population of the ground finch Geospiza diffilis that feeds on the blood of boobies."

Fourth, the topic of artificial selection is of interest - not least because Darwin (and modern textbooks) portrayed artificial selection as directly relevant to natural selection, whereas Wallace thought it was irrelevant. There is no doubt that artificial selection produces rapid phenotypic change, but we already know that most of this does not involve mutations.

"The same process [incipient evolution by the PRM mechanism] might also be involved in rapid responses to artificial selection, for instance in accelerated domestication."

The significance of this research for the study of biological variation surely deserves our attention. We are not here considering a theory that claims to explain the concept of common descent from a single cell, but it has the more modest aim of explaining adaptive radiations from ancestral populations. However, the main critique that has been advanced is that the PRM hypothesis "does not explain why the ancestral state should be phenotypically plastic, or why this plasticity should be adaptive in the first place." The critique is not a fair one, because the new theory is proposed to explain observations of biological variation, rather than to explain the origin of all species.

The perspective provided by Hughes is one that is based on both theory and empirical data, and it stands up to testing very well. This model of variation provides an understanding that differs markedly from the Darwinism and the Neo-Darwinism of most textbooks. It is time for evolutionists to cease claiming all examples of variation and adaptation as evidence for Darwinian mechanisms of evolution. This is bad science and it is the perpetuation of a consensus by repetition rather than by hypothesis testing and validation. Hughes concludes thus:
"The hypothesis proposed here has the advantage of explaining the available data regarding adaptive evolution on the levels of genomics, ecology and paleontology, without invoking any mechanisms other than the commonly observed phenomena of phenotypic plasticity, purifying selection, mutation and genetic drift. Although it may represent a new perspective to biologists schooled in Neo-Darwinism, this view of life in its own way is not without 'a certain grandeur.'"

Evolution of adaptive phenotypic traits without positive Darwinian selection
A L Hughes
Heredity, advance online publication 2 November 2011 | doi: 10.1038/hdy.2011.97

Recent evidence suggests the frequent occurrence of a simple non-Darwinian (but non-Lamarckian) model for the evolution of adaptive phenotypic traits, here entitled the plasticity-relaxation-mutation (PRM) mechanism. This mechanism involves ancestral phenotypic plasticity followed by specialization in one alternative environment and thus the permanent expression of one alternative phenotype. Once this specialization occurs, purifying selection on the molecular basis of other phenotypes is relaxed. Finally, mutations that permanently eliminate the pathways leading to alternative phenotypes can be fixed by genetic drift. Although the generality of the PRM mechanism is at present unknown, I discuss evidence for its widespread occurrence, including the prevalence of exaptations in evolution, evidence that phenotypic plasticity has preceded adaptation in a number of taxa and evidence that adaptive traits have resulted from loss of alternative developmental pathways. The PRM mechanism can easily explain cases of explosive adaptive radiation, as well as recently reported cases of apparent adaptive evolution over ecological time.

See also:

Levi, P.J. No Positive Selection, No Darwin: A New Non-Darwinian Mechanism for the Origin of Adaptive Phenotypes, Evolution News & Views (November 14, 2011)

Tyler, D. Rodents evolve - but does the evidence suggest phenotypic plasticity? ARN Literature Blog (18 November 2011)

Tyler, D. A call for an end to Pseudo-Darwinian hype, ARN Literature Blog (11 September 2008)

It is universally claimed that the early Earth had a reducing atmosphere. Models have been proposed for the gases to have accumulated after outgassing of volatiles from volcanism. This reducing atmosphere was originally thought to have been dominant throughout the Precambrian, but signs of oxygenation have pushed it back earlier than the earliest rocks that researchers have discovered. The earlier claims for a reducing atmosphere have other explanations, such as resulting from the action of hydrodynamic fluids. This has put severe constraints on theories of abiogenesis, because the proposed mechanisms typically presuppose a reducing atmosphere. By the earliest Archaean, the atmosphere was at least neutral - so abiogenesis is inferred to have occurred even earlier. But moving back earlier brings us to the Late Heavy Bombardment which is generally deemed to have obliterated all traces of any life that may have been present. So there is a little window in the Hadean that is deemed to have offered a reducing atmosphere free from the destructive bombardment.

"For decades, scientists believed that the atmosphere of early Earth was highly reduced, meaning that oxygen was greatly limited. Such oxygen-poor conditions would have resulted in an atmosphere filled with noxious methane, carbon monoxide, hydrogen sulfide, and ammonia. To date, there remain widely held theories and studies of how life on Earth may have been built out of this deadly atmosphere cocktail." (Source here)

Artist's impression of the Hadean Earth (source here)

The evidence for a Hadean reducing atmosphere has been entirely theoretical. It does not rest on empirical evidence because there has been so little to work with. However, a new study of zircon crystals has reported some fascinating results that allow speculation about the Hadean black box to be replaced by empirical evidence. Zircons have been identified that carry signatures identifying them with the Hadean - and zircons are remarkably stable once formed. Using zircons dated to almost 4.4 Ga, the researchers have analysed their redox state (a measure of the degree of oxygenation of the mineral). This gives a handle on the type of gases that would have been outgassed by the magmas, and so, according to these models of Earth history, the type of atmosphere that would have been formed.

"Unlike other materials that are destroyed over time by erosion and subduction, certain zircons are nearly as old as Earth itself. As such, zircons can literally tell the entire history of the planet - if you know the right questions to ask. The scientists sought to determine the oxidation levels of the magmas that formed these ancient zircons to quantify, for the first time ever, how oxidized were the gases being released early in Earth's history. Understanding the level of oxidation could spell the difference between nasty swamp gas and the mixture of water vapor and carbon dioxide we are currently so accustomed to, according to study lead author Dustin Trail, a postdoctoral researcher in the Center for Astrobiology. "By determining the oxidation state of the magmas that created zircon, we could then determine the types of gases that would eventually make their way into the atmosphere," said Trail." (Source here)

It is important to realise what was predicted by prevailing theories: the redox state of the magmas with which the zircons were associated was expected to be strongly reducing. This prediction is a necessary part of the Earth having a reducing atmosphere in the Hadean. The research findings did not confirm the prediction. Here is the comment of the authors of a News & Views commentary in Nature:

"[In] this issue, Trail et al. report their analysis of the sole mineral survivors of the Hadean, zircon samples more than 4 billion years old. Their findings allowed them to determine the 'fugacity' of oxygen in Hadean magmatic melts, a quantity that acts as a measure of magmatic redox conditions. Unexpectedly, the zircons record oxygen fugacities identical to those in the present-day mantle, leading the authors to conclude that Hadean volcanic gases were as highly oxidized as those emitted today."

To keep the reducing atmosphere theoretical approach, the timescales must again shrink. The window is now less that 150 Ma - right at the beginning of Earth history - preceding the Late Heavy Bombardment. If life appeared so early, it must have been pulverised before the Archaean provided an environment stable enough for single-celled organisms to survive.

"Their findings extend the mantle's oxidized realm to almost 4.4 billion years ago. Although somewhat tenuous, this is the first direct evidence of the redox state of the earliest Earth. If the zircons analysed by the authors are representative of the Hadean eon, this result shrinks the duration of the reduced era of Earth's mantle to less than 150 million years. It also increases the lag time between the oxidation of the mantle and the subsequent oxidation of the atmosphere [. . .]." (source here)

The authors are well aware of the implications of their research. We need to discard theories that require a reducing atmosphere on Earth - if interest in these theories is to be perpetuated, then locations should be sought outside the Earth.

"The calibrations reveal an atmosphere with an oxidation state closer to present-day conditions. The findings provide an important starting point for future research on the origins of life on Earth. [. . .] Despite being the atmosphere that life currently breathes, lives, and thrives on, our current oxidized atmosphere is not currently understood to be a great starting point for life. Methane and its oxygen-poor counterparts have much more biologic potential to jump from inorganic compounds to life-supporting amino acids and DNA. As such, Watson thinks the discovery of his group may reinvigorate theories that perhaps those building blocks for life were not created on Earth, but delivered from elsewhere in the galaxy." (Source here)

There are two points worth making here. The first concerns the importance of empirical evidence in developing theory. The problem for any historical science is that it is relatively easy for speculation to become dominant because testing hypotheses by reference to empirical data is often a challenge. Abiogenesis is a case in point. The reducing atmosphere scenario and the mechanisms for turning simple chemicals into self-replicating cells have received theoretical development that has gone far beyond the evidential base. So confident have researchers become that they have created the delusion that it is unscientific to even challenge the consensus! Yet they have had to retreat before the evidence. The Archaean atmosphere was realised not to be reducing, so the theorists retreated to the Hadean where data is almost non-existent. They could just about live there - until this week! Now, they must revise their theories to make it all happen in the first 150 Ma of Earth history (and somehow miraculously survive bombardment) or move it "elsewhere in the galaxy". If you are aware of "god of the gaps" reasoning, this case seems to fit the pattern pretty well - the argument is from theory unsupported by evidence and there is a progressive retreat in response to evidence to a place where the theory looks untenable.

The second point is that science has not demonstrated self-correction as it is supposed to do. Evidence has been around for 30 years that the Earth's early atmosphere was not reducing. Jonathan Wells has summarised the research evidence against the reducing atmosphere in Icons of Evolution (2000). He refers to geologists who declared the concept to be mere "dogma" in 1982. Yet the reducing atmosphere has persisted in textbooks, the media, and in the research community to this day! The new research findings bring a renewed challenge to the science community: it is time to revise the textbooks and to follow the evidence wherever it leads.

The oxidation state of Hadean magmas and implications for early Earth's atmosphere
Dustin Trail, E. Bruce Watson & Nicholas D. Tailby
Nature, 480, 79-82, (01 December 2011) | doi:10.1038/nature10655

Magmatic outgassing of volatiles from Earth's interior probably played a critical part in determining the composition of the earliest atmosphere, more than 4,000 million years (Myr) ago. Given an elemental inventory of hydrogen, carbon, nitrogen, oxygen and sulphur, the identity of molecular species in gaseous volcanic emanations depends critically on the pressure (fugacity) of oxygen. Reduced melts having oxygen fugacities close to that defined by the iron-wustite buffer would yield volatile species such as CH4, H2, H2S, NH3 and CO, whereas melts close to the fayalite-magnetite-quartz buffer would be similar to present-day conditions and would be dominated by H2O, CO2, SO2 and N2. Direct constraints on the oxidation state of terrestrial magmas before 3,850 Myr before present (that is, the Hadean eon) are tenuous because the rock record is sparse or absent. Samples from this earliest period of Earth's history are limited to igneous detrital zircons that pre-date the known rock record, with ages approaching ~4,400 Myr. Here we report a redox-sensitive calibration to determine the oxidation state of Hadean magmatic melts that is based on the incorporation of cerium into zircon crystals. We find that the melts have average oxygen fugacities that are consistent with an oxidation state defined by the fayalite-magnetite-quartz buffer, similar to present-day conditions. Moreover, selected Hadean zircons (having chemical characteristics consistent with crystallization specifically from mantle-derived melts) suggest oxygen fugacities similar to those of Archaean and present-day mantle-derived lavas as early as ~4,350 Myr before present. These results suggest that outgassing of Earth's interior later than ~200 Myr into the history of Solar System formation would not have resulted in a reducing atmosphere.

Redox state of early magmas
Bruno Scaillet & Fabrice Gaillard
Nature, 480, 48-49 (01 December 2011) | doi:10.1038/480048a

A study of cerium in zircon minerals has allowed an assessment of the redox conditions that prevailed when Earth's earliest magmas formed. The results suggest that the mantle became oxidized sooner than had been thought.

See also:

Setting the Stage for Life: Scientists Make Key Discovery About the Atmosphere of Early Earth, ScienceDaily (30 November 2011)

Earlier this year, the UK government's chief scientist, John Beddington, delivered a speech in which he urged his audience of 300 government scientists to be "grossly intolerant" of "pernicious" and "fatuous" "pseudoscience". Clearly, Beddington was outraged by people claiming to speak in the name of science but who are promoting views that he regarded as dangerously erroneous. This broadside resulted in two contributions to the correspondence column of Nature. The first was by Professor Andy Stirling, who last year contributed a science policy commentary to Nature. Stirling was not comfortable with the issues highlighted by Beddington as pseudoscience.

"In this he included: scepticism of genetic modification technology; "illegitimate" advocacy of environmental precaution in response to unknowns; and suggestions that science is subject to morality. This approach is a rejection not just of irrational denial but of entirely reasonable social scepticism concerning science itself. [. . .] Open publication, peer review, experimentation and critical respect for evidence help promote reasoned argument. But rational scepticism is as important outside as inside the social practices of science. Hence the motto of Britain's Royal Society, 'Nullius in verba': take nothing solely on authority - even from scientists."

Does the "weight of consensus" trump "rational scepticism"? (image here)

The other correspondence was written by Professor Brian Wynne, who was also alarmed by the use of the term "pseudoscience" to describe those who were challenging government science on certain policy issues. Wynne also contributed to the pages of Nature last year when he reviewed a book that documented ways in which scientific uncertainty has been manipulated to undermine evidence that supported regulation. The review was not altogether favourable. Wynne explains that the book is incomplete: "it does not examine other areas, such as genetically modified organisms, in which grounds for doubt have been downplayed rather than amplified by powerful players to the same deregulatory ends". He would like to see discussion of "how science can be led to overreach itself in arbitrating public facts, meanings and norms". Regarding the Beddington speech, Wynne writes:

"However, none of the growing range of public issues involving important scientific questions can be reduced, as Beddington did, simply to "science" or "pseudoscience". [. . .] What policy advisers anoint as 'science' for intended public authority always embodies unstated policy-related commitments, including presumptions over the defining questions. Such social questions in public science should be recognized and debated openly. Scientific knowledge should inform public issues, not define them."

The following week, Beddington replied. "Andy Stirling and Brian Wynne call respectively for a democratic approach to scepticism and for recognition that scientific evidence often forms only part of complex decisions. I agree with them on both counts". When pressed, scientists will agree on principles, but it is not unusual for substantial differences to persist in their analysis of the issues. This is where the attainment of a "consensus" status is important, for this sways the decisions of policy makers.

"Of course it is true that advancement is attained through criticism, scepticism and debate. But my point was that there can sometimes be a thin line between healthy scepticism and a cynical approach that ignores or distorts inconvenient evidence. Where significant consensus exists on an issue, this has not always been made obvious; also, tokenistic opposing views can be presented in a way that exaggerates their support. Clearly, the role of scientific evidence in decision-making must be considered in the wider political and social context. However, I make no apology for demanding that the fundamental evidence and weight of consensus in such cases is set out in a proper and fair way."

Unfortunately, the matter of "consensus science" was not discussed further, but it is obviously a key issue for policy makers and science advisors. The drive to achieve a "consensus" often becomes a social and political battle, rather than the healthy convergence of thinking within the science community. The way things have developed makes "consensus" a problem for the science community, because dissenting voices are sidelined and debate is squashed (for more, go here).

Consensus science has become a big issue for all concerned with Origins. For many, the debate is over - the consensus has spoken. Some will say: there is no controversy. They regularly ask: where are the peer-reviewed papers supporting your views? These attitudes spill over into the arena for policy-making in education. Words like "pernicious" and "fatuous" and "pseudoscience" are commonplace. But what we are witnessing is the same fundamental problem: an uncompromising rejection of rational scepticism on these issues reinforced by personal worldviews that allow no deviation from the philosophy of naturalism.

This year has seen some high profile cases of bigotry and intolerance in the world of science. The science community in general appears to be in a state of denial about these cases of blatant trampling on academic freedom and liberty of conscience. The first of these cases relates to the astronomer Martin Gaskell who was the leading candidate for the founding director of a new observatory at the University of Kentucky. Although there is evidence that he was judged the best candidate, he was turned down because of his Christian beliefs and willingness to use the word "creation" in discussions. Although he explained he is a theistic evolutionist, this was not enough to turn away suspicions that his scientific judgment could be swayed by irrational factors. In January of this year, the university authorities agreed an out-of-court settlement to avoid the charge of religious discrimination being considered. For further comment see here. This did not stop some scientists thinking that Gaskell should have been turned down because of his Christianity. For an example, see Richard Dawkins' comments here.

A second example concerns the mathematician Granville Sewell, whose paper "A Second Look at the Second Law" was accepted by Applied Mathematics Letters in January 2011. However, as a result of fierce protests from people who cannot bear to see ID scholars publish in refereed journals, the paper was withdrawn at the last moment by the editor. After some exchanges, the journal apologised to Dr Sewell and provided some financial compensation. For further comments on this case, go here and here.

A third case concerns a group of geologists participating in annual meetings of the American Geophysical Union and the Geological Society of America. They have given lectures, presented posters, and even led a field trip. The reason why this has generated much heat is that the group members are Young Earth Creationists. They have chosen to participate in professional activities rather than stand outside like exiles from the geological community. The reactions of mainstream geologists have been mixed. A plea to keep these people out of the meetings appeared in EOS, the magazine of the AGU. The YEC geologists were described as "the enemies of science" and the call was for the professional societies to "enforce objective acceptance guidelines" based on "high scientific merit" (with YEC geology defined as being "devoid of scientific merit"). For a blustering report by someone who was at this Fall's meeting, go here. Steven Newton wrote, in New Scientist, that Creationist "infiltration" of scientific conferences seems outrageous, but banning them would do more harm than good. One wonders whether this counsel will prevail or whether those baying for strenuous efforts to keep them out will be successful.

The most recent case to note is that of David Coppedge who worked at NASA's Jet Propulsion Lab (JPL) as a system administrator. His employer first demoted and then terminated his employment. Apparently, Coppedge's "crime" was to share pro-intelligent design videos with coworkers. He was first forbidden to talk with colleagues about these issues, which he complied with. However, he was then terminated for "pushing religion". For more on this, go here. A legal action is under way because California's Fair Employment and Housing Act forbids employers from taking adverse action against an employee because of the employee's religious expression or affiliation. Since NASA is publicly funded, US citizens are able to influence this situation - for advice, go here and here.

These four recent cases show that all in not well in the science community. The entrenched attitudes captured in the film "Expelled" are still with us. Intolerance, bigotry and posturing is found not only in origins issues, but in many other areas of science. There are many indications that we need to lay again some foundations for science, because instead of following the evidence wherever it leads, far too many scholars are protecting their own patch and portraying as pseudoscience anything that does not fit into their personal agenda.

Intolerance: retain healthy scepticism, by Andy Stirling
Nature, 471, 305 (17 March 2011) | doi:10.1038/471305a

Intolerance: science informs, not defines, by Brian Wynne
Nature, 471, 305 (17 March 2011) | doi:10.1038/471305b

Intolerance: UK chief scientist responds, by John Beddington
Nature, 471, 448, (24 March 2011) | doi:10.1038/471448d

Whose foot in the door? by Paul S. Braterman and John W. Geissman
EOS, Transactions of the American Geophysical Union, 92(18), 153 (3 May 2011)

It is well known that rodents "evolve" fast. Archaeologists have used fossil vole remains as a means of dating because the different morphologies and species link to different time zones: this is the "vole clock". So pervasive are these changes, it has become a matter of note when stasis is observed! A case in point is the birch mouse (genus Sicista). A "living fossil" at the generic level has been found in Inner Mongolia by Yuri Kimura, a doctoral student. It has been identified by its fossilised teeth - the only part of the animal still accessible for study. The teeth can be read like a book, with the cusps, valleys and ridges providing a signature by which the animal is known.

"The new fossils of Sicista primus from the Early Miocene age are also now the earliest known record of Sicista, the birch mouse genus that comprises 13 modern and 7 fossil species, said Kimura. As a result, Sicista now boasts the most ancient ancestry of the 326 genera in the largest rodent suborder to which it belongs, Myomorpha. The suborder includes laboratory mice and rats. "The birch mouse is a rare case of a small mammal genus persisting from the Early Miocene without significant morphological changes," Kimura said in reporting the findings."

Paleontologist Yuri Kimura, Southern Methodist University in Dallas, identified a new species of birch mice, Sicista primus, from 17 tiny teeth. A single molar is about the size of half a grain of rice. The teeth, however, are distinctive among the various genera of rodents known as Dipodidae. Cusps, valleys, ridges and other distinguishing characteristics on the surface of the teeth are identifiable through a microscope. (Credit: Yuri Kimura/Southern Methodist University, source here.)

As far as chronology is concerned, the new fossil is said to be 17 million years old. Previous to this, the earliest fossil of Sicista was considered to be about 9 million years old. Whilst these figures are small compared with those obtained for the coelacanth, or the horse shoe crab, or the Wollemi Pine, they are large for rodents.

"[The observed diversity within this] rodent genus is not unusual, but the long record of the genus Sicista, first recognized at ~17 Ma, is unusual. The discovery of Early Miocene S. primus reveals that Sicista is fundamental to understanding how a long-lived genus persisted among substantially fast-evolving rodent groups."

The above comment concludes the paper, and there is no discussion of how the observation of stasis contributes to a better understanding of stasis. The last sentence says little more than "The fact is fundamental to understanding the fact". Darwinians commonly present everything in terms of adaptive evolution and refer to 'stabilising selection' or to a 'lack of change in the environment'. Whilst this can pass as a reasonable hypothesis with the coelacanth and some other cases, it does not sound at all convincing when the stasis is the exception (as is the case with rodents) rather than an isolated case. This is where multiple working hypotheses are particularly valuable, so that we can weigh alternatives rather than trying to fit everything into a Darwinian framework.

One avenue to explore is whether the rodent radiations could be the result of generating different permutations from the same genetic material. This can occur because the genotype can be expressed in different ways, arising from the phenomenon of phenotypic plasticity. Various triggers, such as from the environment, may be invoked to explain the changes in phenotype followed by the persistence of a specific phenotype for a period of time. A recent analysis of this approach is by Hughes (2011) who points out that phenotypic plasticity provides a ready explanation for abrupt changes in morphology (that cannot be attributed to the gradualistic mechanisms of Darwinism).

"Widespread occurrence of the PRM mechanism [plasticity-relaxation-mutation] would easily explain recently reported cases of apparent phenotypic evolution over ecological time. In most such cases, there has been no genetic evidence demonstrating the operation of the classic Neo-Darwinian mechanism of allelic replacement. In some cases, the time frame seems rather short for a Darwinian process to have occurred, and in other cases, the effective population sizes of the species in question are small, suggesting that there is unlikely to have been extensive genetic variation in the population prior to selection. However, none of these factors are problematic if these cases of apparent rapid evolution in fact represent cases of phenotypic plasticity, perhaps in some cases rendered heritable through germline DNA methylation. Thus, rather than the paradoxical observation of Darwinian evolution over ecological time, we may be merely seeing incipient evolution by the PRM mechanism, which is expected to operate over ecological time."

It is worth saying that Hughes considers that the adaptive evolution mechanism to be poorly supported by data, and he is unimpressed by recent statistical analyses claiming to demonstrate positive adaptation. His non-Darwinian mechanism provides a ready explanation for rapid changes in morphology and he uses as examples adaptive radiations of the cichlid fishes in Africa, and the diversification seen in Darwin's finches in the Galapagos.

"The hypothesis proposed here has the advantage of explaining the available data regarding adaptive evolution on the levels of genomics, ecology and paleontology, without invoking any mechanisms other than the commonly observed phenomena of phenotypic plasticity, purifying selection, mutation and genetic drift. Although it may represent a new perspective to biologists schooled in Neo-Darwinism, this view of life in its own way is not without 'a certain grandeur'."

Kimura is correct that Sicista primus can help us understand better the nature of rapid adaptive radiations. But this is only likely to be realised if scholars are prepared to move out of the comfort zone of neo-Darwinism to test their hypotheses with empirical data.

The earliest record of birch mice from the Early Miocene Nei Mongol, China
Yuri Kimura
Naturwissenschaften, (2011) 98:87-95 | DOI 10.1007/s00114-010-0744-1

Abstract: The earliest species of birch mouse, Sicista primus sp. nov., was recovered from the 17-Ma-old (Early Miocene) Gashunyinadege locality, central Nei Mongol, China. It is ~9 Ma older than the previous first appearance datum of Sicista in Eurasia. This study indicates that North American Macrognathomys is a synonym of Eurasian Sicista, having 12 shared dental characters. As a result, the biogeography of dipodids indicates that Asian Sicista dispersed to North America as opposed to the hypothesis that Sicista originated from the North American clade. Sicista is one of the few extant rodent genera that originated as early as the Early Miocene.

See also:

No Positive Selection, No Darwin: A New Non-Darwinian Mechanism for the Origin of Adaptive Phenotypes, by P.J. Levi (Evolution News & Views, November 14, 2011)

Evolution of adaptive phenotypic traits without positive Darwinian selection, by A L Hughes, Heredity advance online publication, 2 November 2011 | doi: 10.1038/hdy.2011.97

Birch Mouse Ancestor Discovered in Inner Mongolia Is New Species of Rare 'Living Fossil', ScienceDaily (May 25, 2011)

In a cave in a fringing reef, at a depth of 35m, off the Ngemelis Island, Republic of Palau, an amazing fish was discovered in March 2009. Not only was this fish new to science, but the more it was studied, the more unusual it appeared to be.

"Despite some early questions about its affinities, preliminary phylogenetic analysis based on whole mitogenome sequences and numerous osteological features confidently placed this fish within the true eels. Additional morphological and molecular analyses demonstrate that in some features it is more primitive than Recent eels, and in others, even more primitive than the oldest known fossil eels, suggesting that it represents a 'living fossil' without a known fossil record. [. . .] Here, we describe a new family, genus and species for this enigmatic eel. We demonstrate, based on convincing evidence from morphology and whole mitochondrial genomes, that this genus is the most primitive living member of the Anguilliformes, and we accordingly assign it to a new family."

Protanguilla palau alive (Source here). For a video of the fish, go here.

Eels are grouped together in the Order Anguilliformes. There are 19 families, 146 genera and 819 species. One family has the freshwater species, and the others are all marine. These 19 families are fairly well defined, but numerous groupings (at the sub-order level) have been proposed (indicating that the inter-relationships are debatable). Additionally, there are a number of eel species represented only as fossils. These have some differences from modern forms which can be understood within a framework of diversification and adaptation.

"Anguilliforms first appeared as fossils in the Cretaceous about 100 million years ago (Ma) and have lost their pelvic fins, and their dorsal, anal and caudal fins have become confluent. Many eels are adapted for occupying small spaces or burrowing, but they occur in diverse habitats, ranging from benthic shallow-water to deep-shelf, slope and abyssal plain, open-water, meso- and bathypelagic realms."

The research team has carried out a very thorough analysis of similarities and differences between Recent eels (excluding Protanguilla), Protanguilla, and the earliest fossil eels (from the Cretaceous). They wanted to provide an input into the unresolved debate about which Recent eels have the most primitive morphologies. They considered all the characters discussed by previous researchers and have added some additional characters that they deemed relevant. The first outcome was to identify 15 characters that are shared by all eels, whether living or fossilised. These are considered synapomorphic for the order. Then, the authors present their analysis of differences within the order. The summary is as follows:

"The preponderance of morphological evidence indicates that Protanguilla is an anguilliform eel that diverged very early in the evolution of the Anguilliformes and is morphologically more primitive than all living eels. It shares at least 15 characters diagnostic of both Cretaceous and Recent taxa of the order, and seven derived characters of Recent eels lacking in the Cretaceous forms. Most notably, Protanguilla differs from all Recent eels in having a premaxilla, metapterygoid, free symplectic and uppermost two hypurals free from one another, all primitive features that also characterize Cretaceous eels, and is more primitive than the latter in having a fully developed set of gill rakers, fewer than 90 vertebrae and a pterosphenoid that forms part of the posterior margin of the orbit."

Various options are possible with the molecular data, but the authors major on one tree that is a close match to the morphological evidence. There are ways of estimating divergence times using the molecular data, and the authors come up with a figure of 220 Ma for Protanguilla - predating significantly the earliest fossil eels. This is the reason they identify the living animal as a "living fossil" - it is deduced to represent a form that preceded all known fossil eels.

"Its long, independent evolutionary history (estimated to date back to the early Mesozoic era), its retention of primitive morphological features, and its apparently restricted distribution warrant its recognition as a "living fossil" and have generated a level of excitement reminiscent of the discovery of another living fossil fish, the coelacanth, in the late 1930's." (Source here)

There are at least three reasons why this interpretation of Protanguilla is premature.
1. I know of no other case where an animal is declared to be a "living fossil" when it is completely unknown as a fossil. Its evolutionary history has been deduced. In this sense, the find is quite different from the coelacanth, which has a significant fossil record.
2. The analysis of characters is essentially an analysis of three groups of eels: Recent, Protanguilla, and the Cretaceous fossils. There are puzzles as well as patterns. John McCosker, chair of Aquatic Biology at the California Academy of Sciences, commented that: "The analysis they have performed using morphology and genetics is brilliant and invites as many questions about eel evolution as it solves."
The analysis has been underpinned by the presupposition of evolutionary transformation, but it is important to articulate the unresolved issues with this approach.
3. There appears to be no interest in exploring any alternative perspectives on diversification. All is presented in terms of evolutionary transformation. There is no sign of a "multiple working hypotheses" approach. Are other avenues even available to explore? This blog is not the place to do this, but John McCosker may help us to identify at least one alternative. He explains that much of the adaptation and diversification story is characterised by the loss of body parts:

"Eels, to most amateur naturalists, aren't even thought of as fish," McCosker said. "They are, in fact, an excellent case of evolution involving the loss of body parts rather than their exaggeration, and in discovering the basal lineage of true eels, the authors have helped to trace the process of eel evolution further back in its ancestry."

An important example, relevant to the "living fossil" interpretation of Protanguilla, is the full set of bony toothed "rakers", in the gill arches. These are said to be a common feature in most bony fishes, but they are lacking in both fossil and living eels. This is taken as evidence supporting the transitional status of the new eel. However, are there other ways of analysing these data? Can characters be related to adaptations and lifestyle? Does the presence or absence of one trait have a bearing on the presence or absence of another? Is the general loss of body parts an indication of degeneration rather than evolution? We are growing in appreciation of the mosaic structure of many animal forms, and are questioning whether morphologies can carry the load necessary to support evolutionary explanations. It would be interesting to revisit eel morphology with this model of mosaic body forms and see whether the diversification story looks more like a bush than a tree. If it does, the take-home message may not be evolution, but variations based on different permutations of the same biological information.

A 'living fossil' eel (Anguilliformes: Protanguillidae, fam. nov.) from an undersea cave in Palau
G. David Johnson, Hitoshi Ida, Jiro Sakaue, Tetsuya Sado, Takashi Asahida, and Masaki Miya
Proceedings of the Royal Society B, Published online before print August 17, 2011, doi:10.1098/rspb.2011.1289

Abstract: We report the discovery of an enigmatic, small eel-like fish from a 35 m-deep fringing-reef cave in the western Pacific Ocean Republic of Palau that exhibits an unusual suite of morphological characters. Many of these uniquely characterize the Recent members of the 19 families comprising the elopomorph order Anguilliformes, the true eels. Others are found among anguilliforms only in the Cretaceous fossils, and still others are primitive with respect to both Recent and fossil eels. Thus, morphological evidence explicitly places it as the most basal lineage (i.e. the sister group of extant anguilliforms). Phylogenetic analysis and divergence time estimation based on whole mitogenome sequences from various actinopterygians, including representatives of all eel families, demonstrate that this fish represents one of the most basal, independent lineages of the true eels, with a long evolutionary history comparable to that of the entire Anguilliformes (approx. 200 Myr). Such a long, independent evolutionary history dating back to the early Mesozoic and a retention of primitive morphological features (e.g. the presence of a premaxilla, metapterygoid, free symplectic, gill rakers, pseudobranch and distinct caudal fin rays) warrant recognition of this species as a 'living fossil' of the true eels, herein described as Protanguilla palau genus et species nov. in the new family Protanguillidae.

See also:

Most Primitive Living Eel Discovered: Creating a New Species, Genus and Family of Animal, ScienceDaily (17 August 2011)

Viegas, J. 'Living Fossil' Retains Dinosaur-Era Look, (Discovery News, Tue Aug 16, 2011)

Entomologists interested in the Coleoptera (beetles) may find themselves struggling with an information overload because there are said to be about 350,000 species alive today. A previous blog drew attention to Darwinian approaches to explaining these large numbers, and to an evidence-based explanation that is not Darwinian. The presumption seems to have been that speciation has occurred so readily that the life-time of an individual species is short. This has affected studies of Pleistocene sub-fossil specimens, in that the finds were assumed to represent extinct species:

"Originally, the remains from the Pleistocene peat-bog or asphalt deposits were assigned to extinct species by historical authors, supporting the idea of a high evolutionary rate induced by the climate changes during the Pleistocene."

General view of the modern Helophorus sibiricus and its newly discovered Early Miocene fossil counterpart. The close-ups show the species-specific granulation of the pronotum in both the recent specimen (top) and the fossil (bottom), one of the characteristics that allowed a reliable identification of the fossil. (Source here. Credit: Martin Fikacek)

With further research, similarities with modern species were recognised and the previous "finding" was completely overturned!

"Later, more detailed studies of sub-fossil specimens sometimes based even on the study of their well-preserved genitalia revealed that the majority of Pleistocene sub-fossil beetles belong to recent species and resulted in the Pleistocene evolutionary stasis paradigm."

The stasis paradigm has not been applied to pre-Pleistocene specimens. This is largely because the information needed to assign a fossil to a modern species is largely lacking in these fossils - so it is assumed (again) that the finds represent extinct species.

"A large missing piece for the acceptance of long-living insects as a general phenomenon and for understanding the reasons for survival of the particular species is the scarcity of the fossils of such species. The reasons seem to be rather straightforward - the majority of the fossils bear too few details to allow a detailed comparison with living species, whose taxonomy is often based on the shape of male genitalia and other details."

Consequently, the recent find of an early Miocene beetle that can be assigned to an extant species was unexpected. The ScienceDaily report notes: "A study of an Early Miocene fossil from southern Siberia [. . .] led to the surprising find that the fossil belongs to a species of aquatic beetles which is still alive today and widely distributed in Eurasia." We should note that the age assigned to this fossil is 16-23 million years, but the average duration of an insect species (let alone a beetle species) is considered to be much shorter.

"The Siberian fossil provides new data for the long-lasting debate among scientists about the average duration of an insect species. It was originally estimated to be ca. 2-3 million years based on the available fossil record, but slowly accumulating data begin to show that such an estimate is an oversimplification of the problem."

Oversimplification is a problem, but it is not solved by the token concession that acknowledges there are a few long-lived species. The root problems are the assumptions that scholars bring to the study of fossil beetles. Just as reconsideration of the Pleistocene beetles led to the recognition of stasis, coleopterists need to be open to stasis being a pervasive feature of the fossil record. Although diversification has occurred readily in the past, in general speciation is followed by stasis. This is not the Darwinian paradigm! Sad to say, this is point in the argument where we struggle to get a meaningful response from Darwinists. There is plenty of scope for discussion of these issues - for more on this and the relevance to intelligent design, go here.

A long-living species of the hydrophiloid beetles: Helophorus sibiricus from the early Miocene deposits of Kartashevo (Siberia, Russia)
Martin Fikacek, Alexander Prokin, Robert Angus.
ZooKeys, 2011; 130 (0): 239 | DOI: 10.3897/zookeys.130.1378

Abstract: The recent hydrophiloid species Helophorus (Gephelophorus) sibiricus (Motschulsky, 1860) is recorded from the early Miocene deposits of Kartashevo assigned to the Ombinsk Formation. A detailed comparison with recent specimens allowed a confident identification of the fossil specimen, which is therefore the oldest record of a recent species for the Hydrophiloidea. The paleodistribution as well as recent distribution of the species is summarized, and the relevance of the fossil is discussed. In addition, the complex geological settings of the Kartashevo area are briefly summarized.

See also:

Living Species of Aquatic Beetle Found in 20-Million-Year-Old Sediments, ScienceDaily (Oct. 6, 2011)

Steven Pinker wants to challenge the claim that "The twentieth century was the bloodiest in history". Those who advance this idea are said to be numbered among "the romantic, the religious, the nostalgic and the cynical". The reason why they make the claim is "to impugn a range of ideas that flourished in that century, including science, reason, secularism, Darwinism and the ideal of progress". However, according to Pinker, there is no substance to this "historical factoid" because historical records are better as we come closer to the present time, because it is a human trait to overestimate the frequency of wars ("vivid, memorable events") and because we care more about violence today. Against all this, Pinker asserts that there has been a historical decline in violence that deserves our attention.

Pinker in a nutshell: "Our dark side is driven by a evolution-based propensity toward predation and dominance. On the angelic side, we have, or at least can learn, some degree of self-control, which allows us to inhibit dark tendencies." (Quote from Robert Epstein, image credit Viking Adult)

As might be anticipated from the list of impugned ideas, Pinker puts himself on the side of "science, reason, secularism, Darwinism and the ideal of progress". He sees himself as an advocate of Enlightenment Humanism. The article stimulating this blog appears in the Comment section of Nature, signifying that the science community in general is willing to promote such views. It is something of a challenge to scientists and historians who take a different approach to these issues, because their scholarship is already undermined by Pinker's labels for them: "the romantic, the religious, the nostalgic and the cynical".

Those who are accustomed to saying that science deals with "How?" questions and religion deals with "Why?" questions have a real problem with Pinker's article, because it appears in a leading science journal and is all about why humans behave the way they do. The philosophical stance of much modern science treats morality, ethics, social behaviour and much else as a sub-set of phenomena in the natural world.

The essay in Nature is remarkably light on evidence, although references are provided on the web version and Pinker's new book on this theme makes reference to much relevant data. Undoubtedly, we are not short of data, but the challenge is in selecting relevant data and constructing a robust interpretation of these data. History provides a warning. Before the First World War, there were numerous voices making optimistic noises about the world being bathed in peace. The 1911 issue edition of the Encyclopaedia Britannica carried a prediction by Sir Thomas Barclay that "in no distant future, life among nations" would be characterized by "law, order and peace among men". We look back on that and see it as a cultural relic of the Victorian age, when the idea of progress for civilised society seemed compelling. Such idealism appeared to be swept away by the military ambitions of a highly civilised nation. But in more recent years, the same vision is being promoted. Mueller (2009) is cited by Pinker as a source, and this paper sets out to make the case again for the decline of armed conflict:

"It may be time to revisit the visions and optimism of a century ago and to assess the massive intervening literature on war because we may be reaching a point where war - in both its international and civil varieties - ceases, or nearly ceases, to exist, a remarkable development that has attracted little notice."

It is not my purpose in this blog to appraise the evidence used to support Pinker's thesis. However, Some reviewers of Pinker's book have expressed strong disagreements. One of these is John Gray in Prospect Magazine:

"The Korean war, the Chinese invasion of Tibet, British counter-insurgency warfare in Malaya and Kenya, the abortive Franco-British invasion of Suez, the Angolan civil war, decades of civil war in the Congo and Guatemala, the Six Day War, the Soviet invasion of Hungary in 1956 and of Czechoslovakia in 1968, the Iran-Iraq war and the Soviet-Afghan war - these are only some of the armed conflicts through which the great powers pursued their rivalries while avoiding direct war with each other. When the end of the Cold War removed the Soviet Union from the scene, war did not end. It continued in the first Gulf war, the Balkan wars, Chechnya, the Iraq war and in Afghanistan and Kashmir, among other conflicts. Taken together these conflicts add up to a formidable sum of violence. For Pinker they are minor, peripheral and hardly worth mentioning. The real story, for him, is the outbreak of peace in advanced societies, a shift that augurs an unprecedented transformation in human affairs."

My interest is the subtle equating of the "decline of war" with the "decline of violence". Even allowing some substance to the argument for reducing military conflict, is war a good measure of "violence"? For a start, some of us consider that some conflicts have resulted from a sense of justice - to overpower the aggressor. We do not accuse members of the police of violence when they restrain those who have committed crimes; nor should we consider all military conflicts as though both sides are in the wrong. A country's military strength may have been a factor in reaching a settled peace. Violence has its roots in anger and other strong passions within, and we should ask if there are other forms of violence that have flourished in otherwise peaceful societies. It is worth noting that Pinker does not do this.

Consider these two ways of identifying violence on a global scale. The first concerns economic exploitation: using the poor to work long hours to make consumer products that can be transported to developed countries. The exploiters of these vulnerable people are usually of the same nationality and their passion is one of making money for themselves. They find all sorts of ways of concealing exploitation (which extends sometimes to economic slavery) and their customers are assured that the business is ethical. Auditors find they can tick all the boxes. Meanwhile, statistics of average earnings usually show figures far below the minimums determined by organisations concerned about people receiving a living wage. The workers often have to experience hazardous working conditions linked to producing products at the lowest possible cost. Consumers in developed countries have learned to ask no questions about ethical sourcing and enjoy acquiring low-priced products. The second window on violence concerns the practice of abortion. The global total number of abortions is currently estimated to be 1,237,000 per month. The estimated cumulative total is nearly 1 billion. The vast majority of these abortions are of healthy babies, and their deaths always involve some violence to both child and mother. This is a practice that stirs strong passions in people, but most developed societies have learned to live with it and not to ask too many questions. They do not think much about the numbers, but if they did, they might be surprised to learn that in the past 100 years, far more humans have been killed by abortion than the estimated 175 million deaths resulting from armed conflict.

The most sensible sentence in Pinker's essay is the following:

"Reason, by itself, can lay out a road map to peace or to war, to tolerance or to persecution, depending on what the reasoner wants."

A similar sentence can be constructed around science. Reasoning and science are both human activities, and humans can use them in many different ways. However, Pinker does not say this to undermine his stance; he goes on to argue that there are two conditions tending to align reasons with non-violence. The first is "that reasoners care about their own well-being". He sees this not so much as a matter of logic but more as an example of what natural selection will do: "any product of natural selection [. . .] is likely to have [those prejudices]". The second condition is "that a reasoner be part of a community of reasoners who can impinge on their well-being and who can comprehend each other's reasoning". This is how he develops a "morality" of non-violence:

"Self-interest and sociality combine with reason to lay out a morality in which non-violence is a goal. If one agent says, "It's bad for you to hurt me", he has also committed to "It's bad for me to hurt you", because logic cannot tell the difference between 'me' and 'you'. Therefore as soon as you try to persuade someone to avoid harming you by appealing to reasons why he shouldn't, you're sucked into a commitment to the avoidance of harm as a general goal."

This argument is one that has eluded me. I can tell the difference between 'me' and 'you' because we are two distinct individuals and not clones of each other. I can envisage a situation where I could gain an advantage from hurting my benefactor, and logic would not be able to prevent me taking that advantage. I am not the only one who thinks Pinker is out of his depth on the grounds for morality - John Gray can also see gaping holes in the arguments:

"Shaped by imperatives of survival, the human mind will not normally function as an organ for seeking out the truth. If science is the pursuit of truth - an assumption that begs some tricky questions - it doesn't follow that anything similar is possible in other areas of human life. The idea that humans can shape their lives by the use of reason is an inheritance from rationalist philosophy that does not fit easily with what we know of the evolution of our mammalian brain. The end result of scientific inquiry may well be that irrational beliefs are humanly indispensable."

My greatest objection to Pinker's essay is not with the arguments he presents, but with the way he has airbrushed out so many of my heroes from history. It is as though the words "Blessed are the peacemakers" were never spoken! He refers to slavery several times, even asking the question: "Why did human rationality need thousands of years to conclude that something might be a wee bit wrong with slavery?" This is not a matter of reason, but it points to something being wrong with the human condition. This is where William Wilberforce and the converted slave-trader John Newton provide a landmark in history, taking seriously biblical texts like Exodus 21:16 and 1 Timothy 1:10 because they were Christians. Regarding reason, Pinker keeps returning to the Enlightenment scholars - but the consistent champions of reason and logic through history have been Christians. Consider the early colleges of Oxford and Cambridge university; consider the founding of the Royal Society, consider the early setting up of schools for common people - history provides ample testimony to the way Christians have promoted reason and logic. Liberty is to be prized, but it was not always deemed a human right. Kings and leaders have always sought to control people under them - their minds as well as their behaviour. The torch of liberty was carried by Christians who were prepared to suffer for their obedience to God - and we need to honour these men and women, not forget them. Pinker's view of history is entirely secularised. There is no acknowledgement that people of faith have changed the course of history.

I think Gray's concluding paragraph is profound. He realises that the secular humanists are showing all the signs of sectarian religion. They rewrite history, they selectively sift data, they do not critique their own arguments, and they turn science into scientism. They look to their version of science to be the saviour of humanity. But in all this, they are living in denial of the most fundamental principle in science: to follow the evidence wherever it leads.

"Pinker's attempt to ground the hope of peace in science is profoundly instructive, for it testifies to our enduring need for faith. We don't need science to tell us that humans are violent animals. History and contemporary experience provide more than sufficient evidence. For liberal humanists, the role of science is, in effect, to explain away this evidence. They look to science to show that, over the long run, violence will decline - hence the panoply of statistics and graphs and the resolute avoidance of inconvenient facts. The result is no more credible than the efforts of Marxists to show the scientific necessity of socialism, or free-market economists to demonstrate the permanence of what was until quite recently hailed as the Long Boom. The Long Peace is another such delusion, and just as ephemeral."

Decline of violence: Taming the devil within us
Steven Pinker
Nature, 478, 309-311 (20 October 2011) | doi:10.1038/478309a (pdf here)

First paragraph: "The twentieth century was the bloodiest in history." This frequently asserted claim is popular among the romantic, the religious, the nostalgic and the cynical. They use it to impugn a range of ideas that flourished in that century, including science, reason, secularism, Darwinism and the ideal of progress. But this historical factoid is rarely backed up by numbers, and it is almost certainly an illusion. We are prone to think that modern life is more violent because historical records from recent eras are more complete, and because the human mind overestimates the frequency of vivid, memorable events. We also care more about violence today. Ancient histories are filled with glorious conquests that today would be classified as genocide, and the leaders known to history as So-and-So the Great would today be prosecuted as war criminals.

See also:

Gray, J. Delusions of peace, Prospect Magazine (21 September 2011, Issue 187)

Tyler, D. On science as the saviour of humanity, ARN Literature blog (27 June 2011)

It looks like a carnivore, has a digestive tract like a carnivore - but its staple diet is bamboo. Any other member of the ursidae would starve on this cellulose-rich fare. How does the Giant Panda get enough energy to keep itself alive? In January 2010, a study of the panda's genome revealed that it has maintained the genetic requirements for being purely carnivorous, despite being a herbivore. Further, no evidence of genes that encode enzymes for digesting cellulose was found. The hypothesis proposed at that time was that the bamboo diet "may instead be more dependent on its gut microbiome". Now this hypothesis has been tested and validated. This is from a report in Nature News:

"Fuwen Wei, an ecologist at the Institute of Zoology at the Chinese Academy of Sciences in Beijing, and his colleagues took a closer look at the microbes that live in the guts of giant pandas. The team collected stool samples from seven wild pandas in the Qinling and Xiangling mountains in central and western China, as well as from eight captive pandas. By sequencing stool DNA, the researchers determined the different kinds of bacteria present, as well as the identity of thousands of microbial genes. Although wild and captive pandas have different diets and lifestyles - the captive pandas eat a more diverse diet that includes fruit and milk - they tended to harbour similar microbe species in their guts. Wei's team found that samples from both groups contained previously unknown genes produced by Clostridium bacteria, which resembled known genes for enzymes that break cellulose into simpler sugars. The microbial enzymes may help giant pandas to extract extra energy from the small amount of bamboo that they manage to process, says Wei."

How can an animal that has the characteristics of a carnivore eat bamboo? (Source here)

Interestingly enough, most of the gut flora was similar to other carnivores. This is from the Nature News report:

"Most herbivores have developed ways to break down cellulose into sugars; for example, cows and other ruminants have complicated digestive systems - involving multiple stomachs filled with microbes - that process plants many times to extract the maximum nutrition. But pandas are bears, a generally carnivorous family, and neither produce the enzymes necessary to digest cellulose nor harbour the same microbes as ruminants. A broad survey of animal gut microbes found that pandas' microorganisms resembled those of black bears, polar bears and other meat-eaters."

So, although the Panda gut appears to be appropriate for a carnivore, it does not eat meat. As the genome paper (2010) revealed, "The giant panda has lost the capability of sensing umami, which means that meat has become unappetizing." Now, a Chinese team has found evidence for cellulose matabolising microbes that are unique to mammals. This is from their research paper:

"Our metagenomic analysis and 16S rRNA gene data confirm the presence of putative cellulose-metabolizing symbionts in this little-studied microbial environment and clarifies how giant pandas are able to partially digest bamboo fibers despite a genome lacking enzymes that can degrade cellulose."

The mystery is revealed! But what should we make of it all? The Chinese researchers explain it in terms of evolutionary adaptation:

"It is becoming increasingly clear that giant pandas possess a suite of evolutionary adaptations for the highly specialized herbivory. Our findings offer a more in-depth look at the microbiome of a species that occupies an interesting place in the evolutionary tree and has an unusually narrow diet. Thus, the putative harboring of cellulose and hemicellulose-digesting microbes in the gut of the giant panda, along with a suite of other traits, including pseudo-thumbs; well-developed teeth, mandible and skull morphology, and chewing muscles; high-volume food ingestion (12.5 kg/day); brief digestion time; and high mucous levels in the digestive tract, likely have arisen as a result of adapting to a highly fibrous bamboo diet within the constraints imposed by the panda's innate carnivore-like digestive system."

It is this conclusion that prompts some cautionary words in this blog. Adaptions they likely are, but the context for these adaptations is degeneration rather than any increase in biological information. These adaptations fit the pattern of "evolutionary tinkering" so beloved by evolutionists. They do not reveal the "exquisite design" that is so often found when we look in detail at living things. Darwinian mechanisms have not equipped the Panda with the genetic information to digest cellulose. They have not led to changes in the gut to make the process of digesting cellulose more efficient. One report put it this way:

"Wei and his team believe that some of the bacteria they've found in the panda stools help the bears break down that cellulose, if only a little bit. A very little bit. In a study conducted at the Washington National zoo several years ago, it was found that pandas only process something like eight percent of the cellulose in the bamboo they eat. Thus, they have to eat not just a lot, but constantly to get enough nutrition from the bamboo to survive."

So the Giant Panda is not an example of a species that is more fit because of adaptation. Rather, it looks more like a species that has suffered some major degenerative mutations in the past, but has (by a process of "tinkering" with what's still working) managed to survive. The design perspective gives us a story of how a superbly designed carnivore has managed to survive the effects of genetic degradation. Design perspectives are needed, also, if we are to secure a future for the Giant Panda - if we leave it to experience the effects imposed by blind Darwinian mechanisms, it will not be long before the species becomes extinct.

Evidence of cellulose metabolism by the giant panda gut microbiome
Lifeng Zhu, Qi Wu, Jiayin Dai, Shanning Zhang, and Fuwen Wei
Proceedings of the National Academy of Sciences, Published online before print October 17, 2011, doi: 10.1073/pnas.1017956108

Abstract: The giant panda genome codes for all necessary enzymes associated with a carnivorous digestive system but lacks genes for enzymes needed to digest cellulose, the principal component of their bamboo diet. It has been posited that this iconic species must therefore possess microbial symbionts capable of metabolizing cellulose, but these symbionts have remained undetected. Here we examined 5,522 prokaryotic ribosomal RNA gene sequences in wild and captive giant panda fecal samples. We found lower species richness of the panda microbiome than of mammalian microbiomes for herbivores and nonherbivorous carnivores. We detected 13 operational taxonomic units closely related to Clostridium groups I and XIVa, both of which contain taxa known to digest cellulose. Seven of these 13 operational taxonomic units were unique to pandas compared with other mammals. Metagenomic analysis using ~37-Mbp contig sequences from gut microbes recovered putative genes coding two cellulose-digesting enzymes and one hemicellulose-digesting enzyme, cellulase, beta-glucosidase, and xylan 1,4-beta-xylosidase, in Clostridium group I. Comparing glycoside hydrolase profiles of pandas with those of herbivores and omnivores, we found a moderate abundance of oligosaccharide-degrading enzymes for pandas (36%), close to that for humans (37%), and the lowest abundance of cellulases and endohemicellulases (2%), which may reflect low digestibility of cellulose and hemicellulose in the panda's unique bamboo diet. The presence of putative cellulose-digesting microbes, in combination with adaptations related to feeding, physiology, and morphology, show that giant pandas have evolved a number of traits to overcome the anatomical and physiological challenge of digesting a diet high in fibrous matter.

See also:

Callaway, E. Microbes help giant pandas overcome meat-eating heritage, Nature News (17 October 2011) | doi:10.1038/news.2011.596

Tyler, D. Jingjing decoded in part, ARN Literature Blog (28 January 2010)

With headlines like "Caveman from 2m years ago may be missing link", the world's media made a field day of some recent work on Australopithecus sediba. For those with a memory, it has all happened previously in 2010. The announcement was made in the journal Science, that the evolutionary path "From Australopithecus to Homo" had been found. Consequently, the media trumpeted the significance of the bones to their readers (see here). You had to read carefully to realize that hype and science were being confused. Move on to the present and the newly reported research: the journal Science carried three News Focus stories and five scientific papers on the fossils. This was picked up by the popular science journals (New Scientist: South African fossils halfway between ape and human) and the press (as in the Telegraph "caveman" headline quoted above). Just like last year, the hype was the message (see here). After this flurry of excitement, we are starting to get a more nuanced assessment - this blog is based on a News & Views piece in Nature by Fred Spoor. He summarises the data reported as follows:

"Overall, the authors find that A. sediba is australopith-like, with a small brain and long arms, and is most similar to its likely ancestor Australopithecus africanus, remains of which have been found at several South African sites. However, some aspects of the A. sediba skeletons seem to show a closer resemblance to the morphology found in species of the genus Homo. These include aspects of the shape of the pelvis and ankle joint, as well as the long thumb and short fingers that are characteristic of hands capable of precise manipulation. The authors suggest that these features are phylogenetically shared with Homo species, rather than being examples of homoplasy (similar traits that evolved independently in separate lineages), and conclude that A. sediba is a plausible candidate ancestor of Homo."

The cover of Science - announcing the new finds (source here)

Basically, the A. sediba fossils are australopith-like, but with some morphological similarities to the genus Homo. There is talk of it having a mosaic form, with a mixture of "primitive" and "advanced" characters. The question being discussed is whether this justifies placing A. sediba on the lineage leading to Homo. There are many problems with taxonomy, not the least of which is that organisms do not always fit the nice neat boxes we create for them. Probably the best known mosaic forms are Archaeopteryx and the duck-billed platypus. The animals have been classified, of course, but taxonomists have to give emphasis to characters that they think are diagnostic. Then, there is the phenomenon of convergent evolution (which leads to homoplasy, as in the quote from Spoor above). Similar characters do not mean that two organisms have a common ancestor, nor does it mean that the presence of a character set in one organism makes it an ancestor of another with the same set. So why should homo-like characters found in one or more of the australopithecenes be regarded as a proof of ancestry?

Spoor points out that this reasoning creates a methodological conflict with Homo-like fossils that predate A. Sediba.

"The fossil most secure in its affinities and provenance is the approximately 2.35-Myr-old upper jawbone from Hadar, Ethiopia, which is more Homo-like than that of A. sediba and pre-dates the Malapa finds by some 370,000 years. This evidence seems at odds with the idea that A. sediba was involved in the first appearance of Homo."

There is a way of resolving the conundrum. A. sediba could be ancestral to the putative Homo fossils. This scenario was suggested in the 2010 paper and developed in the recent report. This is why the authors are prepared to contest the Homo affinities of all the fossil material older than 2.0 Myr. However, Spoor finds this a speculation that pushes past the limit of credibility:

"It will, however, be difficult to uphold the suggestion that the extensive evolutionary change required could have occurred in the time available (a maximum of 80,000 years) if A. sediba at Malapa gave rise to Homo species. Moreover, the idea that no fossil older than 2.0 Myr is legitimately attributable to Homo is highly debatable - the arguments provided in the paper are insufficiently specific to be conclusive, particularly with respect to the Hadar jawbone."

After discussing several of the morphological analyses made by the research team, Spoor gives his conclusion:

"Taken together, the published evidence indicates that A. sediba is a late australopith that has several intriguing Homo-like features. If these features do indeed associate A. sediba with the emergence of Homo, rather than reflecting homoplasy, then it seems that the scenario in which the Malapa specimens represent a late surviving population is the most plausible explanation for Berger and colleagues' findings."

Thus, the evidence is by no means conclusive. It is perfectly legitimate to advance homoplasy as the explanation of the similarities - and more and more evidence can be advanced to support this interpretation (see here). If (and this is a big if) A. sediba has a place in human ancestry, then it must have been around significantly earlier so as to predate all Homo-like fossils and to have time to experience the "extensive evolutionary change" that was necessary. This scenario requires the Malapa specimens to be a relict population of this species - which can be regarded as a hypothesis needing to be tested before getting too excited.

Before we conclude, it is worth revisiting the headline that introduced this story. The problem with the term "missing link" is not that we get two gaps in the fossil record to replace one. This is not a serious problem for palaeontologists - because if a trajectory exists, it is more clearly displayed when more links are identified. The real problem with the term is that it presupposes Darwinism and small incremental changes. This mindset colours the way people perceive the fossil record - and it hides the fact that most morphological change is punctuated and the main trend is one of stasis. It is Darwinism that is responsible for the term, and until Darwinism is dropped as the conceptual framework for evolutionary theory, we will continue to have the "missing link" issue.

However, the alternative phrase "transitional fossil" is not much better. The danger here is that any morphological character can be interpreted in terms of being transitional. As we have seen above, there are other explanations for similarities because the phenomenon known as "convergent evolution" is ubiquitous. Consequently, claims for transitional status can be devoid of substance. A study by DeWitt has looked closely at these similarities and reached exactly this conclusion:

"In spite of certain human-like characteristics - many of which are consistent with tree dwelling - the overwhelming evidence is that Au. sediba was a type of Australopithecine and thus an extinct ape rather than a human ancestor."

Malapa and the genus Homo
Fred Spoor
Nature, 478, 44-45 (06 October 2011) | doi:10.1038/478044a

Abstract: Two remarkably well-preserved skeletons of the hominin species Australopithecus sediba, found at Malapa, South Africa, show an intriguing combination of features, and open up a debate about the origins of the genus Homo.

See also:

Tyler, D. Learning from the history of human evolution research, ARN Literature Blog (4 March 2011)

The thumbnail portrait of science that most children get in schools is that science is objective and "value-free" knowledge. Science is supposed to reach the same outcomes in whatever culture it is practised and whoever does the research. The simplest response to this is to say that the thumbnail is misleading: science is an activity practised by creative but fallible human beings who bring cultural values into their work, sometimes consciously but mostly unconsciously. A well-written contribution on these issues is by Henry Gee in Nature, reviewing a book by palaeoanthropologist Dean Falk. Her subject is human evolution and the controversies about Australopithecus africanus in 1924 and Homo floresiensis in 2003. Gee begins his review with this iconoclastic paragraph:

"We have all seen the canonical parade of apes, each one becoming more human. We know that, as a depiction of evolution, this line-up is tosh. Yet we cling to it. Ideas of what human evolution ought to have been like still colour our debates."

"This line-up is tosh" - Henry Gee (source here)

The 1924 paper, authored by Raymond Dart, was received with scepticism. Whilst the fossil became known as the "Ape-Man of South Africa", the skull was that of a juvenile. Everyone knows (or should know) that juvenile apes have more human-like characteristics than adult apes. But resistance to Dart's hypothesis came mainly because his peers considered that brain expansion preceded bipedalism and these people defended their thinking by reference to Piltdown Man. Gee sees this as evidence of prejudice affecting the course of science.

"Dart's original paper on A. africanus was, it is true, long on waffle and short on substance. But the reason that this small-brained, possibly erect-walking creature took two decades to be accepted as a hominin was that researchers were in thrall to the idea that the expansion of the human brain came first, before the adoption of a fully erect gait. This preconception was supported by the discovery of the large-brained, ape-jawed Piltdown Man in 1912. The fact that it took 40 years to expose Piltdown as a fraud is a mark of how deeply rooted such prejudices can be."

Falk has unearthed a new angle on this story. It is known that Dart "was critically mauled by the London establishment - notably the 'Piltdown Committee' who believed in the fake fossil" and that "he almost deserted palaeoanthropology". Nevertheless, he did continue to develop his hypothesis and submitted a paper to the Royal Society in 1929. This paper suggested that the cognitive capacity of Australopithecus was belied by its small brain. However, the paper was rejected (as Gee suggests: "presumably on the basis of reports by the Piltdown Committee").

Falk has, of course, a similar story to tell about Homo floresiensis, alias the Hobbit. Her role was to scan the cranium of the LB1 fossil and show its affinities are closest to Homo erectus. Papers are still being published suggesting that the Hobbit is not a separate species but the bones are from deformed humans.

"Almost every time someone claims to have found a new species of hominin, someone else refutes it. The species is said to be either a member of Homo sapiens, but pathological, or an ape. Brickbats of the first kind were levelled recently at H. floresiensis - that it wasn't a genuine species, but a modern human suffering from one of several kinds of microcephaly or from cretinism. But they had also been aimed at Neanderthal Man, discovered back in 1856, and thought by some to be the remains of a Mongolian Cossack from the Napoleonic wars."

Thus, to grasp the meaning of fossils, particularly human fossils, we need not just to have an appreciation of technical issues, but also an understanding of the cultural, social and ideological contexts for the reporting.

Craniums with clout
Henry Gee
Nature, 478, 34 (06 October 2011) | doi:10.1038/478034a

Abstract: A look at two early human fossils reveals the prejudices in ideas about human evolution, finds Henry Gee.

Book reviewed:
The Fossil Chronicles: How Two Controversial Discoveries Changed Our View of Human Evolution, Dean Falk, University of California Press: 2011. 280 pp. ISBN: 9780520266704

The premier computer tool for simulating evolutionary processes has the name Avida. Researchers have reported studies on the evolution of complexity, altruism, changes to genetic architecture, and even the evolution of sex. Avida can be used to illustrate numerous concepts and mechanisms of Darwinian evolution and it has achieved a reputation as a platform for carrying out evolution experiments with digital organisms. As someone who has used simulation as a research tool, the question I have always asked (but to which I have struggled to find a satisfactory answer) concerns validation. It appears that Avida authors have made little or no attempt to cross-validate digital evolution with biological evolution. They have not attempted to move out of their virtual reality world by drawing attention to empirical experiments that give credibility to their conclusions. So how does Avida relate to the real world? At last, a paper has appeared which appears to ask similar questions:

" . . . some may ask whether the results of experiments with digital organisms have any relevance to living systems. We conclude that digital genetics is a valid platform for studying some biological questions, but that the applicability of results will depend critically upon the parameters used." (p.11)

The Avida Digital Life Platform demonstrates Darwinian concepts - but does it relate to the real world? (source here)

Inevitably, all simulation models have simplified the system being investigated. This is not, in itself, a problem as long as validation work is undertaken to establish what features in the simulated system can be mapped against the real-world system. So, for example, "key terms such as nucleotide, gene, heritability, selection, and fertility lack a clear equivalent in the software" (p.8). This can be OK, but users must not imagine an equivalence when none exists. Validation work to establish application areas is therefore both relevant and essential.

One problem with Avida has been the high values assigned to beneficial mutation rates and fitness effects.

"Previous experiments using Avida have studied the evolutionary emergence of complex features resulting from high-impact beneficial mutations. Avida's default settings provide mutational fitness effects of 1.0-31.0 for beneficial mutations that give rise to certain computational operations [. . .]. However, fitness effects this large are extremely rare in nature." (p.3)

Avida is constructed according to the Darwinian paradigm. The software is designed so that variations appear using mechanisms of mutation and natural selection. Avida assigns a high proportion of the digital genome to functionless code. Just as Darwinists imagine happens in the real world, so Avida has a genome much of which can be disturbed without disrupting fitness, but which is also capable of experiencing mutations that result in functionality. We now know that this is not a valid representation of the real world. The authors indicate that 85% of the Avida genome is initially benign, but it has the potential to contrinbute to fitness after certain mutations occur. However, as more and more functions are found for junk DNA, this aspect of Avida's design appears increasingly anachronistic.

"Mutations randomly substitute, insert, or delete single instructions in an Avidian genome, drawing upon 26 available instructions defined in the software. The ancestral genome devotes about 15 instructions to the essential replication code, while the remaining 85 positions are occupied by benign no-operation instructions, analogous to inert "junk DNA" that can be used as raw material for evolutionary tinkering." (p.3)

Although the software has been developed with Darwinian mechanisms in mind, the use of more realistic parameters needs attention - principally fitness effects and the proportion of advantageous mutations. The results reported by the authors do not confirm that Darwinian mechanisms can deliver the transformations that Darwinists claim. The problem with gradual incremental evolution is that small advantages are not selected naturally and do not become dominant in the population. Avida assumes and implements a scheme in which complex features can be built step-wise. Whether this is true for biological organisms is another question entirely.

"We observed that, when fitness effects in Avida are small, all advantageous logic operations are lost. Though digital organisms are peculiar in that they can survive such a loss, these data confirm that the accumulation of slightly deleterious mutations can lead to decreasing biological functionality and potentially eventual extinction. Because deleterious mutations are much more common than advantageous mutations in most systems studied, reduction in the efficacy of selection imposes strong directionality on evolution by favoring the fixation of deleterious mutations. The conditions under which fitness recovery may be possible should be studied more thoroughly using computational approaches." (p.12)

The most far-reaching conclusion relates to adaptation. "Plausible" adaptation accounts are pervasive in the literature of Darwinism (see here and here) but few of them are supported by empirical evidence. The Avida findings imply that "plausible" only means "realistic" when mutational fitness effects are large. With only marginal benefits, it is far more likely that "plausible" scenarios turn into "adaptationist just-so-stories".

"In contrast to Avida's default settings, most mutations in biological organisms are low-impact, and this class of mutations may dominate evolutionary change. When Avida is used with more realistic mutational fitness effects, it demonstrates a clear selection threshold. Mutations that influence fitness by approximately 20% or less come to be dominated by random genetic drift. Mutations that affect fitness by 7.5 - 10.0% or less are entirely invisible to selection in this system. These results provide evidence that low-impact mutations can present a substantial barrier to progressive evolution by natural selection. Understanding mutation is of primary importance, as selection depends on the mutational production of new genotypes. Numerous changes that would be beneficial may nevertheless fail to occur because mutation cannot produce them in the time available. Further, it is important for biologists to realistically appraise what selection can and cannot do under various circumstances. Selection may neither be necessary nor sufficient to explain numerous genomic or cellular features of complex organisms." (p.13)

It is worth considering how this research might affect the way evolutionary theory is presented in schools and universities. Adaptation is typically demonstrated by standard examples: peppered moths, Galapagos finches, antibiotic resistance, and more. The logic then appears to be: adaptive change is a real phenomenon so we can proceed on the basis that Darwinian evolution is validated, i.e. it is a plausible explanation for not just some but all features of life. This Avida research allows teachers and students to evaluate this questionable logic and assess the significance of these evidences.
* Are mutations low-, medium- or high-impact?
* What are the evidences relevant to random genetic drift?
* What data are relevant to assessing the relative proportions of low-, medium- and high-impact mutations?
* How important is the concept of "selection threshold" in evaluating potential evolutionary scenarios?
* Does the accumulation of low-impact mutations constitute a health hazard?

At the very least, students can be alerted to the fact that whilst examples of adaptation are documented in the literature, they occur only when mutational fitness effects are large enough. It follows that barriers to adaptive change may be just as important for understanding ecosystems as adaptation. This will take many out of their comfort zone (see here), but they can be encouraged by the thought that they are studying real science, not a virtual reality world.

The effects of low-impact mutations in digital organisms
Chase W. Nelson and John C. Sanford
Theoretical Biology and Medical Modelling, 2011, 8:9 | doi:10.1186/1742-4682-8-9

Abstract:
Background: Avida is a computer program that performs evolution experiments with digital organisms. Previous work has used the program to study the evolutionary origin of complex features, namely logic operations, but has consistently used extremely large mutational fitness effects. The present study uses Avida to better understand the role of low-impact mutations in evolution.
Results: When mutational fitness effects were approximately 0.075 or less, no new logic operations evolved, and those that had previously evolved were lost. When fitness effects were approximately 0.2, only half of the operations evolved, reflecting a threshold for selection breakdown. In contrast, when Avida's default fitness effects were used, all operations routinely evolved to high frequencies and fitness increased by an average of 20 million in only 10,000 generations.
Conclusions: Avidian organisms evolve new logic operations only when mutations producing them are assigned high-impact fitness effects. Furthermore, purifying selection cannot protect operations with low-impact benefits from mutational deterioration. These results suggest that selection breaks down for low-impact mutations below a certain fitness effect, the selection threshold. Experiments using biologically relevant parameter settings show the tendency for increasing genetic load to lead to loss of biological functionality. An understanding of such genetic deterioration is relevant to human disease, and may be applicable to the control of pathogens by use of lethal mutagenesis.

See also:

Anderson, E. Bits, Bytes and Biology: What Evolutionary Algorithms (Don't) Teach Us About Biology, ISCID Paper, November 2, 2004.

Truman, R. Evaluation of neo-Darwinian Theory with Avida Simulations (Part 1 and Part 2), PCID, 3(1), November 2004.

The essay stimulating this blog emerged from the Darwin Bicentennial year, when surveys of "educated lay people" in Switzerland revealed that only 20% had any clarity of thinking about Darwin's theory of evolution. About half explained it in a circular way, another 20% implied some form of Lamarckism and the remaining 10% talked about evolution being a flow towards complexity. These responses evidence "poor understanding" and two major reasons are suggested to explain the observations. The first is "The theory of evolution is counterintuitive" and the second is "The theory of evolution opposes most people's worldview". The worldview issues are of considerable importance to the issues considered here. It is worth asking: what is a Darwinian worldview? and why do most people have a different worldview? The first paragraph of the essay is significant for its candour:

"Early teaching of the basic principles of science by qualified teachers, together with the creative involvement of scientists, will help the general public to appreciate what the theory of evolution calls for, namely a worldview based on reality rather than on mysticism and dogma."

Worldviews affect the way we perceive and understand the world (source here)

OK, so Jacques Dubochet, the author of the essay, is linking Darwinism to a worldview based on reality and most of the general public, even those that are educated, have worldviews based on mysticism and dogma. At least this tells us where he's coming from. But Dubochet's reality is not self-evident. Indeed, many aspects of it are "shocking" because this reality conflicts with any worldviews that find a place for purpose and meaning transcending the individual level. As an example, Dubochet says that "the idea that our legs are not made for walking or our eyes for seeing is difficult to grasp". He recognises that most educated people do think our legs are made for walking and that our eyes are made for seeing - but considers these views to be delusional. These people need to be informed by Darwinism which shows us that "life evolves without a goal".

"The confrontation between intuitive understanding and reality is nothing new. The Copernican idea that the Earth revolves, not the Sun, also caused serious trouble in the past but nowadays everybody accepts it as obvious. Will this be the case with the theory of evolution? I have my doubts."

These doubts are interesting. Why is education not the answer? This brings us to the importance of worldview thinking. Dubochet does not dwell on the Copernican Revolution, but it is instructive. The intellectual world at that time was dominated by Aristotelianism. This had been integrated within Roman Catholicism by the influence of Thomas Aquinas - and the theologians happily went along with the views of their Aristotelian astronomers and interpreted the Bible accordingly. This became the Medieval worldview. The opposition to Copernicanism was led by the astronomers, who were sure that Aristotelian physics equated with reality. Outside the Catholic Church, it was possible for people to be more free-thinking and many of the early champions of Copernicanism were in the Reformation tradition. This led to a willingness to revisit biblical interpretation and they found that the relevant texts used the language of appearance and were not making scientific statements. For more on this, go here. At that time, if the education strategy had been followed, all that would have emerged would have been more and more complexities in the Ptolemaic system. What was really needed was an atmosphere where there was academic freedom and a willingness to critique alternative explanations of the data. This is what the Reformation facilitated and this is the culture that nurtured the rise of science.

Dubochet develops his worldview argument by saying that science answers "How?" questions and philosophy answers "Why?" questions. How-questions, he says, are concerned with causality and the quest to understand natural phenomena. Why-questions, however, imply goals, meaning and purpose. But Dubochet has already explained that Darwinism declares there is no goal and no "finality". To many of us, this seems as though Darwinism wants to claim the right to answer both "How?" and "Why?" questions!

"Why? What for? For which goal? For these questions, Darwin has an answer: in life, there is no finality, so the question "why" makes no sense, full stop! Here is where the shoe pinches. During discussions with non-specialists, signs of tensions are frequently observed the instant they understand that biological evolution does not lead anywhere."

It is at this point that Dubochet acknowledges that people have goals - but he only acknowledges that these goals are personal to individuals: "Humans have their future in their hands". Not only can we choose to inject meaning and purpose into our lives, we can clothe this desire for finality to include the adoption of religiosity.

"The human desire for finality extends further; it includes transcendance. Religiosity is, in fact, one more trait of our human nature as is made evident by ethnology, evolutionary biology, population genetics, or the science of religion. Where does this come from? It has been suggested that it offers a sufficient advantage to be selected by evolution. Others think it is a necessary corollary to the development of human intelligence when faced with the fear of death. Still others see religion as a by-product of some other naturally selected function. In all cases, the consequence for us is that "Some form of religious thinking seems to be the path of least resistance for our cognitive systems.""

So, not only do Darwinists make claims about "Why?" questions, they also seek to understand religion and human psychology from Darwinian perspective. On these grounds, they will allow religious life to coexist with the Darwinian view of reality. As an example, the "blameless Darwinian" in the following quote is Francis Collins, a leading US theistic evolutionist Christian.

"Even if the theory of evolution describes life without involving divine action, it does not prove the absence of transcendence or the non-existence of God. The blameless Darwinians who declared their indisputable religiosity prove that a peaceful collaboration is possible. In my view, it should be valued."

If anyone is in any doubt, this form of religiosity is far removed from biblical Christianity. Instead of subjective goals, the Christian maintains a cosmic purpose that integrates all history. Instead of an existential choice to secure meaning, the Christian affirms God's plan to be the master plan for all. Eyes are made for seeing and ears are made for hearing (for more, go here). Divine action is everywhere, for "in him we live and move and have our being". This is a different worldview from that described by Dubochet.

The main take-home message from this blog is that there is such a thing as a Darwinian worldview, that those adhering to this view consider themselves to be living in the real world and all others have succumbed to mysticism and/or dogma. This post should be read in parallel with "Creationism and Intelligent Design in science lessons" which argues for treating Darwinism as a worldview at all levels of education. The following quote comes from the conclusion of that blog:

"Darwinism does not exist in isolation from a worldview and the attempt by many to portray it as objective 'pure' science is philosophically naive. Just as the objections of creationists and ID scholars cannot be properly understood without a worldview perspective, so also the commitments of evolutionary biologists to the blind watchmaker model of evolutionary transformation cannot be properly understood without reference to the worldview of these scientists."

As an example of what the Darwinian worldview entails, and why educationalists should be alert to the metaphysical implications of Darwin's theory, Dubochet's essay is necessary reading. Worldviews affect the way all of us perceive the world. The Darwinian view is no exception. It has to deny the truth claims of Christianity. If coexistence with religion is envisaged, it must be based on privatised religious commitments that are ultimately superstition and delusion - nothing to do with ultimate truth. It is not surprising (or shocking) when Darwinists say these things - knowing their worldview, such words are entirely predictable.

Our response should be that of the scientists in the Reformation tradition: let us question dogmas, test hypotheses, perform relevant experiments and follow the evidence wherever it leads. What we seem to be getting from many Darwinians is a hardening attitude that presumes that only they live in the real world. Consequently, humanist champions of evolution are seeking changes to education policy that will deny academic freedom to both students and teachers with a different worldview. Their stance is one that has to be resisted.

Why is it so difficult to accept Darwin's theory of evolution?
Jacques Dubochet
Bioessays, 33: 240-242, April 2011 | DOI 10.1002/bies.201000142

Most educated people do not understand Darwin's theory of evolution. This is because the idea that our legs are not made for walking or our eyes for seeing is difficult to grasp. Adepts of intelligent design have it easier. Furthermore, stating that life evolves without a goal and in the absence of finality is shocking for most people because it clashes with their idea of the meaning of life. In fact, the theory of evolution is intellectually satisfying and it can serve as a solid basis for a responsible worldview in the sense of the Enlightenment. It need not come into conflict with transcendental belief. Early teaching of the basic principles of science by qualified teachers, together with the creative involvement of scientists, will help the general public to appreciate what the theory of evolution calls for, namely a worldview based on reality rather than on mysticism and dogma.

Michael Reiss deserves credit for his persistence in advocating views that are counter to those of many individuals and organisations. The issues are concerned with the way evolutionary theory is taught in schools. There is, and should continue to be, an evaluation of alternative approaches and the arguments presented by Reiss in his recent scholarly paper deserve a fair hearing.

"I am especially interested in the education provided to those for whom education is mandatory. I am also concerned to make suggestions that can be implemented in today's classrooms. [. . .] I concentrate on the UK, though argue that in fact there are fewer differences between countries in this regard than is commonly suspected." (p.401)

Handling controversy in the classroom need not be stressful (source here)

In developing his approach, Reiss considers whether creationism and intelligent design (ID) are "controversial" issues. This has relevance because educationalists have a long tradition of teaching about controversies. They do not fear that the mere exposure of students to a controversial issue will undermine all the foundations that have been previously laid. The inference is that if creationism and ID are deemed controversial issues, then any good science teacher will take this as an opportunity to develop a scientific mind and use the controversies to advantage. However, as Reiss notes, "What is controversial for one group may not be controversial for another." There are evolutionary scientists who do not regard creationism and ID as controversial - for them, this issue is settled. The continuing phenomenon of creationism and ID is regarded by them as a subversive anti-science tendency in society. Similarly, there are creationists who present evolutionary theory "as illogical [. . .] contradicted by the scientific evidence, [. . .] the product of non-scientific reasoning." Since both groups use rational arguments to make their case, Reiss seeks to understand the issues within a broader philosophical framework.

"As is generally accepted, there are two major epistemological families for knowledge that is not a priori: those centred on perceiving the world for ourself, and those centred on the testimony of others. There is obviously not the space here to go into a major discussion of each of these but it is sufficient for my purposes to note that in both cases knowledge, for all that it may be reliable, has an element of provisionality. Of course, some knowledge is more provisional than others. A useful distinction in science is made by Imre Lakatos who argued that scientists work within research programmes. A research programme consists of a set of core beliefs surrounded by layers of less central beliefs. Scientists are willing to accept changes in these more peripheral beliefs so long as the core beliefs can be retained." (p.402)

This brings us to the topic of worldviews, which is increasing in importance in science education. Reiss quotes approvingly a definition by Aerts et al. (1994): "A worldview is a coherent collection of concepts and theorems that must allow us to construct a global image of the world, and in this way to understand as many elements of our experience as possible" (p.405). The question is being asked: 'Is science itself a worldview?'

"The term has recently been explored as a way of helping conceptualise why, despite the best efforts of many science educators, so few students leave their schooling with the sort of scientific understanding and disposition that most science teachers wish they had. The principal conclusion is that school science fails to enable most students to see the world from a scientific perspective." (p.405)

To illustrate the relevance and importance of worldviews, Reiss turns to the film "March of the Penguins". This has been the most successful nature film in America motion picture history and it has received several awards. A contributory factor was the endorsement of the "Christian right". Reviewers in this tradition found the film to be a compelling message of love, perseverance and God's intelligent design. All this was communicated rationally by the reviewers, revealing how the worldview of the Christian "right" found meaning, purpose and intelligent design revealed in the natural world. Perspective is vitally important, so much so that it highlights the "difficulty of using the criterion of 'reason' to decide whether an issue is controversial or not." It also suggests that "standard ways of addressing the diversity of student views in a science classroom may be inadequate." (p.407)

Reiss goes on to articulate what he means by the phrase "standard ways". In the UK, the Department of Children, Schools and Families produced "Guidance on creationism and Intelligent Design" - rejecting the idea that creationism and ID can be considered science. The report suggested that the only context for referring to these issues is to explain why they are not to be "considered to be scientific theories" and why evolution "is considered to be a scientific theory". In the US, the National Academy of Science guidance says much the same.

Why are these approaches inadequate? Reiss cites one analysis that suggests the guidance looks like placing "a gag order on teachers" and fails to engage meaningfully with children and communities of people who find creationism and ID thinking persuasive. Reiss refers also to Thomas Nagel, who finds that the "so-called scientific reasons for excluding ID from science lessons do not stand up to critical scrutiny". (For a related post, go here). Furthermore, the UK guidance for considering these issues in religious education units is quite different in character from the guidance previously mentioned: the RE guidelines encourage teachers to give students opportunities to explore the issues. Additionally, Reiss points out that much of the discourse on creation, ID and evolution overlooks primary school contexts:

"I should note that the distinction between science lessons, religious education lessons and citizenship lessons, while it may hold at secondary level with subject-specific teaching rather breaks down at primary level where a pupil generally has the same teacher for most or all lessons. From an epistemological point of view this is both the strength and potential weakness of primary teaching. Teaching in the primary school has the potential to make links between subjects with greater ease than is generally the case at secondary school, precisely because the one teacher is responsible for such a diversity of subjects." (p.410)

Reiss is advocating a change of stance about the way creationism and ID are handled in science lessons. Instead of going into battle over controversies, Reiss advises a discourse that is sensitive to worldviews.

"An advantage of shifting the discourse from controversy to sensitivity is that one shifts the focus from epistemology to pedagogy. One can be sensitive with someone in respect of an issue without implying that one shares the same perspective (or worldview) as the person to whom one is being respectful and considerate." (p.411)

Most of Reiss' analysis is very helpful and good common sense. Adopting his approach will enhance the educational experience of all pupils. However, there is one major area where I would like to see a further development of the analysis: this is to provide a more thorough analysis of science using a worldview perspective. What should we make of Reiss when he writes: "The scientific worldview is materialistic in the sense that it is neither idealistic nor admits of non-physical explanations" (p.403)? Some of us do not find this summary one that we would use in our scientific work. In fact, the prohibition of non-physical explanations should be regarded as an example of the way many modern scientists are idealistic, bringing to science a precondition about what the natural world ought to be like and how it ought to behave. This is particularly relevant to the origin of information - materialistic science has to interpret information in terms of random variations that are selected and fixed. Consequently, they have no tools to test whether the approach is realistic or can be falsified - as a matter of ideology, it cannot be falsified!

Science is not neutral territory for scholarship. Ideologies, presuppositions, paradigms and worldviews are important for all branches of science, including evolutionary biology. Darwinism does not exist in isolation from a worldview and the attempt by many to portray it as objective 'pure' science is philosophically naive. Just as the objections of creationists and ID scholars cannot be properly understood without a worldview perspective, so also the commitments of evolutionary biologists to the blind watchmaker model of evolutionary transformation cannot be properly understood without reference to the worldview of these scientists. Then it will be clear that many of their key concepts (the Tree of Life emerging from a single cell, common descent, the central role of variation and natural selection) go far beyond what can reasonably be inferred from the data and ultimately are derived from the worldview of the evolutionist.

Using this approach with students will avoid labelling any group as having a "non-scientific worldview". Rather students will be more aware of the role of presuppositions and ideologies in science, will be able to understand better why scientific revolutions occur, and will be better equipped to understand why science thrives in some cultures more than in others. Instead of the controversy about Science & Faith, students will be aware of the way personal belief systems feed into and influence the way science is practiced. This seems to me to be far healthier for science than the present grid-locked polemics.

How should creationism and intelligent design be dealt with in the classroom?
Michael J. Reiss
Journal of Philosophy of Education, 45(3), August 2011, 399-415 | DOI: 10.1111/j.1467-9752.2011.00790.x

Abstract: Until recently, little attention has been paid in the school classroom to creationism and almost none to intelligent design. However, creationism and possibly intelligent design appear to be on the increase and there are indications that there are more countries in which schools are becoming battle-grounds over them. I begin by examining whether creationism and intelligent design are controversial issues, drawing on Robert Dearden's epistemic criterion of the controversial and more recent responses to and defences of this. I then examine whether the notion of 'worldviews' in the context of creationism is a useful one by considering the film March of the Penguins. I conclude that the 'worldviews' perspective on creationism is useful for two reasons: first it indicates the difficulty of using the criterion of reason to decide whether an issue is controversial or not; secondly, it suggests that standard ways of addressing the diversity of student views in a science classroom may be inadequate. I close by examining the implications of this view for teaching in science lessons and elsewhere, for example in religious education lessons and citizenship lessons and at primary level where subject divisions cannot be made in so clear-cut a manner.

See also:

Tyler, D. Science education and the origins issue (ARN Literature blog, 3 June 2011)

Harvestmen are said to be the third most-diverse arachnid order, and few will be unaware of these long-legged creepy-crawlies living somewhere near to our own homes. They belong to the order Opiliones and although the fossil record is understandably sparse (the exoskeleton is poorly mineralised), the fossil record is informative. Some of the earliest insects known are in intimate association with plant material - preserved in the Rhynie Chert. "Devonian (~410 Myr) harvestman fossils from the Rhynie Chert, while incomplete, preserve a three-dimensional internal anatomy suggestive of an essentially modern body plan." The opportunity has come to check out this suggestion, using high-resolution X-ray micro-tomography to examine specimens preserved in siderite nodules. The X-ray scans allow parallel slice images of the fossils to be recorded, from which three-dimensional, virtual models of the organisms are assembled.

"The international team, led by scientists at Imperial College London, took over 3000 X-rays of the harvestmen fossils from France, dating to the Carboniferous Period [. . .]
The scans were edited using computer software to produce highly detailed and accurate 3D models. They reveal 2 new species of ancient harvestmen, Macroglyon cronos and Ameticos scolos, which, unlike most land animals from this time, had bodies very similar to their modern relatives living today."

The probable appearance in life of A. scolos gen. et sp. nov. (above) and M. cronus gen. et sp. nov. (below). Scale bar, 5 mm. (Source here)

The most notable finding is that these insects are essentially modern. They belong to two identifiable suborders. The research paper provides a cladogram with the ancient harvestmen alongside modern forms: "comparable taxa of the modern Eupnoi and Dyspnoi". Dr Russell Garwood, currently based in the computed tomography lab at the Natural History Museum in London, is quoted as saying:

"It is absolutely remarkable how little harvestmen have changed in appearance since before the dinosaurs. If you went out into the garden and found one of these creatures today it would be like holding a little bit of prehistory in your hands. We can't yet be sure why harvestmen appear so modern when most land animals, including their cousins such as scorpions, were in such a primitive form at the time. It may be because they evolved early to be good at what they do, and their bodies did not need to change any further."

There is a problem with much of the terminology being used to describe fossils. I am thinking of words like: "primitive" and "modern" (also "stem" and "crown"). Much of this terminology is driven by a Darwinian perspective - a theoretical model of what the fossil record ought to be like. Cladism has imbibed this mindset, because it infers a lineage of organisms that can be reconstructed by the appearance of novel structures. Unfortunately, the fossil record is proving to be less and less Darwinian as we examine the details. We have modern body plans where there should be primitive body plans. We have primitive 'relict' species living on when they should have become extinct. We have to invoke 'convergence' to explain similar structures that do not fit the linear model. (But convergence is ubiquitous - here). Why should we live with such an unwieldy interpretative framework?

Most significant is the pattern of animal and plant radiation that we find in the fossil record. Darwin predicted a branching bush or tree - but this is not what we find! The Cambrian Explosion is the best rebuttal of this, for it demonstrates an initial burst of diversification and speciation followed by relative stasis (See here, here and here). This pattern of diversification suggests caution about using the word "primitive" or "modern" in an evolutionary sense. Are the characters under investigation part of the early diversification of an order or a Family? If the answer is 'yes', then we should be very cautious about placing an evolutionary interpretation on it - to say something is primitive then becomes little more than saying that it became extinct. This is one reason for documenting cases of stasis in the fossil record - there is far more evidence of modernity in the fossil record than is currently acknowledged by Darwinists. (For some recent blogs, try one, two, three, four and five).

Anatomically modern Carboniferous harvestmen demonstrate early cladogenesis and stasis in Opiliones
Russell J. Garwood, Jason A. Dunlop, Gonzalo Giribet, Mark D. Sutton
Nature Communications, 23 August 2011, 2, Article number: 444 | doi:10.1038/ncomms1458 (pdf here.)

Abstract: Harvestmen, the third most-diverse arachnid order, are an ancient group found on all continental landmasses, except Antarctica. However, a terrestrial mode of life and leathery, poorly mineralized exoskeleton makes preservation unlikely, and their fossil record is limited. The few Palaeozoic species discovered to date appear surprisingly modern, but are too poorly preserved to allow unequivocal taxonomic placement. Here, we use high-resolution X-ray micro-tomography to describe two new harvestmen from the Carboniferous (~305 Myr) of France. The resulting computer models allow the first phylogenetic analysis of any Palaeozoic Opiliones, explicitly resolving both specimens as members of different extant lineages, and providing corroboration for molecular estimates of an early Palaeozoic radiation within the order. Furthermore, remarkable similarities between these fossils and extant harvestmen implies extensive morphological stasis in the order. Compared with other arachnids - and terrestrial arthropods generally - harvestmen are amongst the first groups to evolve fully modern body plans.

See also:

Ancient harvestmen in 3D reveals early evolution, Natural History Museum Press Release (23 August 2011)

Crop circles are patterns formed by the flattening of crops. They have been reported for hundreds of years and are reputed to appear around the world at a rate of one every evening. They only form during the night. Crop circles have always had something extraordinary about them, stimulating "mowing devil" explanations and also the influence of aliens. What are we to make of these phenomena? This is a good opportunity to discuss how a scientific mind approaches the problems and the relevance of design inferences to science. In a recent feature article on crop circles, Richard Taylor writes:

"Speculation over the origin of crop circles has raged since they were first reported in England in the 1600s, with rolling hedgehogs, urinating cattle, romping romantic couples and the actions of a "mowing devil" all offered as early explanations. In 1678 a series of circles in Hertfordshire was attributed to the devil because the manufacture appeared to be beyond human capabilities. According to a report in a 1678 issue of News Out of Hartfordshire, the devil "placed every straw with an exactness that would have taken up above an age for any man to perform what he [the devil] did that one night"."

A field of fractals. On 29 July 1996 this crop circle appeared on Windmill Hill near Avebury, UK. Its design is based on an equation formulated by Gaston Julia in 1918. A similar "Triple Julia" fractal design was also used in a crop circle in Switzerland last year. (Courtesy: Steve Alexander. Source here)

Apparently, the first scientific analysis of crop circles invoked "Law" as an explanation. This was in 1686, by a British scientist called Robert Plot. Linear wind surges and circular eddies were considered to account for the observations. Natural phenomena continue to be considered. More recently, a prominent advocate has been Terence Meaden, a Canadian meteorologist and physicist.

"In 1980 Meaden [. . .] propos[ed] that the curvature of hillsides in southern England affected the local airflow, allowing whirlwinds to stabilize their positions long enough to define circles in the crop fields."

Even Professor Stephen Hawking has given some credence to weather-related causation:

"When a spate of circles appeared in the countryside near his Cambridge home in 1991, Hawking told a local newspaper that "crop circles are either hoaxes or formed by vortex movement of air"."

"Chance" has not been favoured as an explanation of the data. Rolling hedgehogs and urinating cattle leave their marks, but nothing like crop circles! Analysts have been impressed by the specified complexity of the flattened crops. The choice for them has always been either "Law" or "Design".

Whilst many suspected human activity, people did not own-up to making crop circles. If this is the explanation, the perpetrators have kept remarkably silent about their accomplishments! There were two schools of thought: one group concentrated on humans, whereas the other group looked for aliens and UFOs.

"In the waning decades of the 20th century, this conclusion ignited a heated aliens-versus-humans debate, with "UFOlogists" looking to outer space for the circles' artistic creators, while "cereologists" concentrated on hunting for terrestrial hoaxers. This debate was complicated by the fact that the creators (whoever they were) were clearly science-savvy. In particular, one formation that appeared next to Chilbolton Observatory in Hampshire appeared to be a reply to a "search for extraterrestrial intelligence" signal beamed into space 30 years earlier."

However, this discourse changed in 1991, when "two unassuming men in their sixties declared that they had been creating crop circles for more than 25 years." At last, the silence had been broken! These two could not be responsible for all the crop circles made in this period, but they did confess to making 250 of them (20% of the total in England).

"Their hobby had begun one summer evening in the mid-1970s, when artist Douglas Bower recounted a story to his friend David Chorley about an Australian farmer who had reported a UFO rising into the sky and leaving behind a circular "saucer nest". As Bower and Chorley strolled home from the pub through the English countryside, they created their first imitation nest."

According to Taylor, the Bower & Chorley announcement triggered a revival in construction of crop circles. The practice went international, and was characterised by sophistication. Although England still boasts 50% of each year's crop circles, they occur in Europe, North and South America, Russia, Australia, Japan and India.

"Artists who readily admit to having made crop circles in the past say they do not know who is responsible for all of today's masterworks. This is partly because many crop-circle artists have followed the conventions established by their predecessors: creating their pictographs anonymously, under cover of darkness, and leaving the scene free of human traces. But although the new artists are traditionalists in this sense, in other respects their craft has moved on considerably. Today's artists, for example, have access to computers, GPS equipment and lasers to help map out their patterns."

The rise of high technology crop circle creation has been noted in the media, and an example is an article by Nick Collins in the Daily Telegraph. What some regard as unexpected mathematical sophistication in human hoaxers, others continue to regard as the signatures of alien minds.

"Today's crop-circle designs are more complex than ever, featuring up to 2000 individual shapes arranged using intricate construction lines that are invisible to the casual observer. The increase in available computing power has also meant that iterative equations are now frequently used to generate fractal shapes such as the Triple Julia design, which reappeared in Switzerland last year. Other famous fractal icons such as the Mandelbrot set, the Julia set and the Koch snowflake have also popped up regularly in crop fields since 1991."

There are still mysteries about how these patterns are made, how secrecy is maintained, and how so much is done in the available time. These puzzles continue to engage the interest of enthusiasts. Taylor writes: "Crop-circle artists are not going to give up their secrets easily." Interest in the alien explanation continues. Are we dealing here with "The most science-oriented art movement in history"? - as Taylor suggests. Or are we witnessing tangible signs of the presence of aliens? As has been pointed out many times before, design inferences allow us to infer intelligent causation, but the identity of an intelligent agent is a separate issue which may or may not be easy to resolve. As this summer period is a time for rest and relaxation for many of us, we have an opportunity to reflect further on these questions - and hopefully reach some answers.

Coming soon to a field near you
Richard Taylor
Physics World, August 2011, 26-31. (pdf here)

Serious studies of crop circles have long been hampered by conspiracy theories and the secretive nature of circle-makers - plus scientists' reluctance to engage with a "fringe" topic. But, as Richard Taylor argues, discovering how circle artists create their most complex patterns could have implications for biophysics

In June 2005, biophysicist David Deamer and colleagues visited a pool of water heated by volcanic activity on Russia's Kamchatka Peninsula. The scientists were under the impression that the water was sterile and that volcanism had erased all signs of life. "Darwin proposed that life started in 'a warm little pond'. . . . We are testing his theory in 'a hot little puddle'," Deamer related at a meeting of the Royal Society in London in February 2006. The group poured a "primordial soup" of proteins, DNA, and cell membranes into the pool and waited to see what would happen.

"When the scientists sampled the water after a few hours, they were surprised to find that most of the added material had disappeared. Tests revealed that the missing ingredients were bound to the clay that lined the tiny pond. The molecules "are nailed down, so they can't interact," Deamer says. As a result, hot volcanic pools may be unlikely spots for the first assembly of life's little bits, says Deamer." (source here)

David Deamer pours a "prebiotic soup" of chemicals into a volcanic pool in Kamchatka, Russia, to test a hypothesis about the origins of life. (Photo by Tony Hoffman, source here)

With this anecdote, Robert Shapiro commences his review of Deamer's latest book: First Life: Discovering the Connections between Stars, Cells, and How Life Began. Actually, Deamer refers also to the incident in the book and describes it as a "reality check". It taught him that natural systems are quite different from the laboratory and although numerous papers have been published on abiogenesis in the lab, the authors have failed to grapple with the principle that "we cannot translate lab results to natural settings".

"Because we can get reactions to work in the controlled conditions of a laboratory, he cautions, it does not follow that similar ones occurred on prebiotic Earth. We might overlook something that becomes apparent when we try to reproduce the reactions in a natural setting. This provocative insight explains why the origin-of-life field has been short on progress over the past half century, whereas molecular biology has flourished."

The dominant contemporary theoretical approach to abiogenesis is known as the RNA World. The basic idea is that an RNA strand appeared spontaneously in the Archaean era of the early Earth. This RNA molecule had the ability to replicate itself. Shapiro says: "The advantage of this idea is that the formation of just one polymer would be all that was needed to get life started. The disadvantage is that such an event would be staggeringly improbable." There are chemical problems just getting the RNA strand, but added to this are the problems of achieving replication. This is why some scientists have chosen to opt out of the RNA World paradigm and attempt to develop a rather different approach.

"Nucleotides, for example, are not encountered in nature beyond organisms or laboratory synthesis. To construct RNA, high concentrations of four select nucleotides would be needed in the same location, with others being excluded. If this is the prerequisite for life, then it is an unusual phenomenon, rare in the Universe. As an alternative, other scientists (myself included) have suggested that life started without the presence of polymers; that instead, heredity and catalysis began with monomers."

So, Deamer's book plows a new furrow. He considers the cell has to come first, so looks for ways of constructing a cell-like compartment. He does not like the deep-oceanic vent approach to doing this, because he considers hot seawater to be a liability, not an asset. Inside this cell-like structure, he seeks to form a self-replicating polymer.

"Deamer's thesis diverges from the standard RNA-world concept. He focuses not on the generation of a naked RNA-like polymer, but on the formation of a simple cell-like compartment, or vesicle. Modern cells are enclosed by a complex fatty membrane, which prevents leakage. Vesicles with similar properties have been formed in the lab from certain fatty acids. Deamer holds that the spontaneous formation of vesicles, into which RNA could be incorporated, was a crucial step in life's origin. Unfortunately, his theory retains the improbable generation of self-replicating polymers such as RNA."

That last comment from Shapiro reveals that he is not very impressed with Deamer's alternative proposal. But he also knows that a review is not the best platform to promote one's own approach. So the conclusion majors on a plea for more realism about the demerits of the RNA World and less deductive thinking about the nature of Archaean geochemistry.

"Nevertheless, Deamer's insight deflates the synthetic proofs put forward in numerous papers supporting the RNA world. He ends First Life by calling for the construction of a new set of biochemical simulators that match more closely the conditions on the early Earth. Unfortunately, the chemicals that he suggests for inclusion are drawn from modern biology, not from ancient geochemistry. We should let nature inform us, rather than pasting our ideas onto her."

This is good advice for all students of Earth history. There may be a consensus about the RNA World, but it is not a consensus based on evidence. The approach is supported by synthetic proofs drawn from unrealistic laboratory experiments, showing all the signs of a dogmatism that pastes its ideas on to nature. At our present state of understanding the issues, it is realistic only to acknowledge the tentativeness of all current theories of abiogenesis.

Astrobiology: Life's beginnings
Robert Shapiro
Nature, 476, 30-31, (04 August 2011) | doi:10.1038/476030a

Abstract: Robert Shapiro on a reminder that laboratory experiments don't always translate to nature.

Book reviewed: First Life: Discovering the Connections between Stars, Cells, and How Life Began, David Deamer, University of California Press: 2011. 288 pp. ISBN: 9780520258327

See also:

Luskin, C. Presto! The Origin of Life in Four Surprisingly Easy Steps, Evolution News & Views, August 8, 2011

The first specimen of Archaeopteryx was discovered in 1861 in Bavaria, Germany, and it quickly made its way into Darwin's Origin of Species as an example of a transitional form. The German name of the fossil was Urvogel ("original bird" or "first bird"), but the English speaking world adopted Archaeopteryx - from the Greek archaios meaning 'ancient' and pteryx meaning 'feather' or 'wing'. The sense of the German name, however, was universally received: this was the first known bird and it displayed sufficient reptilian features to encourage hypotheses about an evolutionary past. This summary is from the University of California Museum of Paleontology: "It has long been accepted that Archaeopteryx was a transitional form between birds and reptiles, and that it is the earliest known bird." The history of evolutionary theory could not be written without the name Archaeopteryx appearing prominently - this is from the National Center for Science Education:

"Archaeopteryx is frequently used for pedagogical purposes because it is easy to recognize its mixture of "bird" and "reptile" features and because it played an historical role in helping to cement Darwin's theory (it was discovered 2 years after publication of the Origin). Textbook authors like Archaeopteryx for these reasons and often illustrate their discussions with pictures of the Berlin specimen, one of the most beautiful fossils ever discovered, and remarkably complete. Textbooks also use Archaeopteryx as an example of how fossils are important for showing transitional features of evolution, and how the fossil record is good evidence that evolution has occurred."

An artist's impression of Xiaotingia zhengi, (credit: Copyright Xing Lida and Liu Yi, source: here)

In recent years, however, the story has become much more complicated, with the finding of the so-called 'feathered dinosaurs' in China, and several Archaeopteryx-like fossils. Lead researcher Xing Xu has reported recently a fossil with the name Xiaotingia zhengi, and published a new phylogenetic analysis which knocks Archaeopteryx off its perch and relocates the animal among a sub-group of dinosaurs. Nature has a news report here, and Discover Magazine here. The latter source has this summary of developments:

"By comparing Xiaotingia's features with those of Archaeopteryx and other related birds and dinosaurs, Xu has drawn up a new family tree. In it, Archaeopteryx sits with Xiaotingia among the deinonychosaurs, a celebrity-filled group of small, predatory dinosaurs that includes Deinonychus and Velociraptor. The lineage that led to modern birds perches on a different branch of the tree."

In view of the iconic status of Archaeopteryx, commentators have been anxious that "creationists" do not gain an advantage from this particular rewriting of the textbooks. When evidence used to prove evolution turns out to be incorrect, there is a danger that people will become disillusioned. Xing Xu knows this: "Because it has held the position as the most primitive bird for such a long time, I am kind of nervous about presenting this result" he said. Consequently, there has been a great deal of damage-limitation activity, pointing out that 'this is the way science works'. This activity is reviewed here, with much of it drawn from Witmer (here):

"In truth, this chapter of the scientific story is just beginning. Just as Xiaotingia moved Archaeopteryx out of the birds, the next find could move it back in - or to somewhere else within this fuzzy tangled knot that makes up the origins of birds and bird-like dinosaurs. That said, during this sesquicentennial anniversary of Archaeopteryx, which is being honoured with exhibits and commemorative coins, the bitter irony may be that it may not have been the bird we've always thought it was. But Archaeopteryx will remain an icon of evolution, perhaps even more so now, providing compelling evidence that, as we should expect, evolutionary origins are rather messy affairs."

One is tempted to say - if the next find could move Archaeopteryx back in, why are people getting so excited about it now? Why can't we treat Xu's approach as a hypothesis that needs to be tested by further analysis and forthcoming discoveries? The answer is that Xu et al. have not presented it like this. Although giving lip-service to tentativeness, they claim that their analysis makes far more sense of the fossil data and that, as Nature News says: "we are about to enter a new era in which Archaeopteryx is considered as distant from the ancestry of modern birds as dinosaurs such as Deinonychus."

The cladistic analysis is recognized as provisional in the abstract: the conclusion has only "tentative statistical support". Animals that deserve to be in the analysis, but are not, are Early Cretaceous birds: Dalianraptor, Jixiangornis, Zhongjianornis; late Jurassic or Early Cretaceous dinosaurs: Pedopenna, Shanag, Sinusonasus, Tianyuraptor, and the enigmatic Jinfengopteryx. Is it possible that the selection of species for inclusion in the cladistic analysis has influenced the outcome? The basal bird species chosen have a stubby snout morphology, and this may have led to those species with a more pointed snout to be shifted over to the deinonychosaurs: namely Archaeopteryx, Anchiornis and Xiaotingia. With additional clear Avialae species, the analysis may come out differently. Witmer writes:

"According to Xu and colleagues' analysis, the most basal fossil birds are forms such as Epidexipteryx, Jeholornis and Sapeornis, all of which were named in the past decade and so comprise new territory even for specialists. Clearly, without the safety net of good old Archaeopteryx at the base of the birds, we've got some fresh work to do."

There is scope also for a discussion of the parameters used within the analysis, although this will have to be pursued by the specialists. Unfortunately, cladistic analyses tend to produce 'black box' outcomes, and there is relatively little attention given to parameter trends within the cladogram and whether these are biologically meaningful. There is also scope for critiquing cladism itself, and whether the underpinning assumptions restrict the scope of the analysis. For more, go here.

According to many commentators, the evolutionary story of the origin of birds is going to be fuzzy:

"The researchers acknowledged that their reclassification was "only weakly supported by the available data," but they said this kind of fuzziness was to be expected when the fossils being analyzed are close to the common ancestor of now-extinct dinosaurs and modern birds. "This phenomenon is also seen in some other major transitions, including the origins of major mammalian groups," they wrote.
Witmer agreed: "We're looking at an origin, and consequently it's going to be messy." [also, he added] "It just shows what evolution is all about. A prediction of evolutionary theory is that it should be really hard for us to figure out what's going on in an origin.""

Interesting. In the past, evolutionists looked for an identifiable trajectory that documented evolution. Now, it is a confused mess which is hard to decipher. Perhaps the most realistic conclusion for the present is that the Late Jurassic-Early Creataceous fossil record shows many features that we do not properly understand, and the most appropriate response is to withhold judgment and await further discoveries and analysis. This applies to the whole of the Birds Are Dinosaurs (BAD) thesis, as is evident here, here, here, here and here.

An Archaeopteryx-like theropod from China and the origin of Avialae
Xing Xu, Hailu You, Kai Du & Fenglu Han
Nature, 475: 465-470 (28 July 2011) | doi:10.1038/nature10288

Abstract: Archaeopteryx is widely accepted as being the most basal bird, and accordingly it is regarded as central to understanding avialan origins; however, recent discoveries of derived maniraptorans have weakened the avialan status of Archaeopteryx. Here we report a new Archaeopteryx-like theropod from China. This find further demonstrates that many features formerly regarded as being diagnostic of Avialae, including long and robust forelimbs, actually characterize the more inclusive group Paraves (composed of the avialans and the deinonychosaurs). Notably, adding the new taxon into a comprehensive phylogenetic analysis shifts Archaeopteryx to the Deinonychosauria. Despite only tentative statistical support, this result challenges the centrality of Archaeopteryx in the transition to birds. If this new phylogenetic hypothesis can be confirmed by further investigation, current assumptions regarding the avialan ancestral condition will need to be re-evaluated.

See also:

Kaplan, M., Archaeopteryx no longer first bird, Nature News (27 July 2011) | doi:10.1038/news.2011.443

Witmer, L.M. An icon knocked from its perch, Nature, 475: 458-459 (28 July 2011) | doi:10.1038/475458a

For 20 years, the National Science Foundation (NSF) has undertaken surveys of science literacy that incorporate these two true-false statements: "Human beings, as we know them today, developed from earlier species of animals", and "The universe began with a huge explosion". Happily, changes have been recommended, but not all have welcomed their suggested replacement wording. The critics say that the revised statements are "surrendering ground to religion". I will suggest below that both the engineers of change and their critics have something to learn about science surveys.

"Two expert panels assembled last year by NSF have suggested qualifying those statements with the phrases "According to evolutionary theory" and "According to astronomers." The board has decided to ask NSF to give the new versions of the questions to half the respondents on its next survey and to analyze the results.
[. . .]
[The second panel advised that] Respondents should also be asked whether they "personally shared this belief.""

The goal: developing a love for science and discovery (source here)

First, what is wrong with the statements as they stand? The first of these concerns the evolution of humans from earlier species of animal. Is this true or false? Is it a statement that will be understood in the same way by the participants? In my view, the statement is problematic. Are we talking about principles here or evidence? If participants are supposed to relate their true/false verdict to evidence, then there are real problems. As Wood and Harrison wrote earlier this year: "Sorting fossil taxa into those that belong on the branch of the tree of life that leads to modern humans from those that belong on other closely related branches is a considerable challenge." Basically, we do not have a clear lineage for human evolution. The reason why many people answer "yes" to the statement is not that they have found the evidence compelling, but that they know that the history of life is framed by evolutionary theory. Ultimately, affirmative responses do not measure scientific literacy, but say something about the worldview of the respondents. (There are other points to make here - linked to whether or not humans are more than animals - but in the interests of conciseness, we move on).

What about the second statement: "The universe began with a huge explosion"? There is a problem with these words - the Big Bang is about the expansion of space as well as the expansion of primordial matter. The word "explosion" is potentially misleading because all familiar explosions are of matter being propelled through existing space. Furthermore, the Big Bang model requires that matter was in a very low-entropy state when it started - consequently it is a misnomer to call the event a "Bang" or an "explosion", because these are words that suggest disorder. The statement, therefore, is OK at a popular level, but the more scientifically-minded participants might find it inadequate. Those who have sympathy with "Big Bang" model dissenters (here and here) may well give the response "false" - and yet this would not be necessarily a sign of poor scientific literacy.

So, the wording of surveys is very important. The researcher writing the questions or statements can unconsciously influence the outcome of the findings. Often, the approach is structured around empirical science (where the problems are much reduced) but then questions or statements about the historical sciences are slipped in as though there is no qualitative difference. The proposed revised wording does improve things significantly. Participants are being asked about their knowledge of what scientists are saying about the past. But what should be more important is whether these scientific ideas are understood and whether the supporting evidence is recognised.

There is a potential problem if respondents are to be asked whether they "personally shared this belief". The advice is sound if participants all recognise that all science is built on presuppositions, many of which cannot be proved scientifically. (It is like having axioms in mathematics). These presuppositions are critically important to the historical sciences. Naturalism is the prime example: the application of naturalism to the history of life leads inevitably to something like Darwinism - as a matter of logic. That humans evolved from apes does not need evidence, because according to the presupposition it must be true - evidence is welcomed as confirming something that is already known. Similarly, on thermodynamic grounds, the universe in its present form must have had a beginning, and the presupposition of naturalism requires that it happened without any specific causation. As New Scientist has expressed it: "Perhaps the big bang was just nothingness doing what comes naturally". Ultimately, naturalism is at the root of a belief system that is expressed in numerous ways. The current "Existence" theme in New Scientist shows where it leads: chance and the multiverse provide the underpinning concepts, leaving humans as zombies existing in a holographic universe, with an illusion of consciousness.

The advocates of naturalism do not accept that their worldview is founded on beliefs. They reserve the word "belief" for superstition and "religion". It is very important to them that a line is drawn between fact/science/knowledge and beliefs. This comes out in Bhattacharjee's report of the proposed modifications to the NSF survey:

"The change infuriates Jon Miller, a science literacy expert at the University of Michigan, Ann Arbor, and architect of the original questionnaire, which is now used by several countries. "If you are altering the questions in that way, you are doing it for religious reasons," he says. "We don't make statements like, 'According to some economists, we had a recession' or 'According to the weatherman, we had a tsunami.'"

Notice that Miller's examples do not relate to the historical sciences. He uses phenomena that can be studied empirically, that relate to contemporary life, and that are defined objectively. From this, conclusions are drawn that go far beyond the point being made. Miller needs to revisit his "religious reasons" claim and start looking at the philosophy of science. Beliefs are of many different types. Yes, there are superstitious beliefs, but there are also beliefs based on evidence and axiomatic beliefs like 2+2=4. For more discussion of these issues, go here.

In defending the recommendation to ask participants whether they "personally shared this belief", Lewenstein appears to put himself on a collision course with the advocates of naturalism. He does not put acceptance of human evolution or the Big Bang in a box marked 'knowledge' but in another marked 'beliefs about knowledge'.

"Bruce Lewenstein, a sociologist at Cornell University who was on the Toumey panel, thinks critics are overreacting. He says the distinction between knowledge and belief is important and must be understood to get a clearer picture of the public's knowledge of science. "Knowledge and belief are not the same," he says. "It might be politically useful for the scientific community to pretend that they are the same, but it would not be intellectually honest.""

This is a debate worthy of our attention. Science needs to be rescued from people who cannot recognise the role presuppositions are playing in their own thinking and from educationalists who think that acceptance of human evolution and the big bang is more important than knowing the evidences on which theories of human evolution and the Big Bang are based. We need to be rescued from people who cannot understand that some beliefs are based on evidence. Most of all, we need to be rescued from people who cannot comprehend that science can be practised without presuming naturalism. Rather, we need a science that is capable, in principle, of falsifying naturalism and which avoids scientists bringing to their work a predetermined vision of what the universe is really like.

New NSF Survey Tries to Separate Knowledge and Belief
Yudhijit Bhattacharjee
Science, 333, (22 July 2011) 394 | DOI: 10.1126/science.333.6041.394

Can a person be scientifically literate without accepting the concepts of evolution and the big bang? To many scientists and educators, the answer to that question is an unqualified "no".

Starting in 1973, Herbert Terrace led an ambitious project to examine the capability of chimps to develop sign language. The chimp participant was born at the Institute for Primate Studies in Oklahoma and was taken from his mother after about a week and handed to Stephanie LaFarge who acted as a surrogate parent. The chimp was effectively adopted. In a recent piece in Nature, Terrace explains why he initiated the project:

"After serving as a graduate assistant at Harvard University with behavioural psychologist B. F. Skinner, I heard that Allen and Beatrix Gardner at the University of Nevada, Reno, were teaching sign language to a chimpanzee named Washoe. But when I looked at their data, I wasn't sure that the chimp's sequences of hand signs were grammatical. I decided to do a study to collect everything a chimp signed, and document the circumstances. We wanted to have full records of the discourse between the infant chimp and the caretaker."

Nim Chimpsky (source here)

The experiment design was based on some important theoretical considerations about the development of language. Influenced by his background in behavioural psychology, Terrace set out to challenge the ideas of the linguist Noam Chomsky - in particular his claim that grammatical speech is uniquely human. Behaviourists tend to the view that animals can be taught to do almost anything, and the Los Angeles Times report says that the "Skinner-Chomsky rivalry framed the Nim project". The new name for Chimp No 37 was Nim Chimpsky, sufficiently distinctive to draw my attention to the project during the 1970s.

To cut a long and fascinating story short, the project ended up supporting the theoretical perspective of Chomsky and underlined the differences between chimp communication and human language. The most influential paper emerging from the project team was published in Science in 1979, with the title: "Can an ape create a sentence?" The answer was no - at every level. Long utterances were not semantic or syntactic elaborations of short utterances - this is quite different from the communications of human children. As the length of utterances of children increase, so also does the complexity of those utterances. This increase in complexity was not observed with Nim. The researchers concluded that all the evidences accumulated in support of apes creating sentences could be explained by reference to simpler non-linguistic processes. They found that animals can learn symbols and signs, but do not show any capability to master the conversational, semantic, or syntactic organisation of language. In answer to the question "Did the experiment meet your expectations?" Terrace replied:

"The language didn't materialize. A human baby starts out mostly imitating, then begins to string words together. Nim didn't learn. His three-sign combinations - such as 'eat me eat' or 'play me Nim' - were redundant. He imitated signs to get rewards. I published the negative results in 1979 in the journal Science, which had a chilling effect on the field."

An interesting follow-up question is: "Why couldn't Nim put a sentence together?" This is particularly important to Darwinists and many other evolutionary thinkers, who go along with Darwin's claim, in The Descent of Man, that there is "no fundamental difference between man and the higher mammals in their mental faculties". Terrace's answer points us to a major difference between humans and animals: only humans have a theory of mind.

"I haven't seen any evidence that a chimp has a theory of mind. It can predict behaviour, but the concept of another individual's thinking is foreign to it. So it is pointless for a chimp to start a conversation: why talk unless you expect a reply?"

After the project, Terrace returned Nim initially to the Institute for Primate Studies. However, after they ran out of funding, he did not want Nim sold as an animal for medical research. Terrace found him a home in a giant cage at a ranch for celebrity animals in Texas where he lived until the year 2000 when he died of a heart attack. But the story does not end there. There are many people who still think of Nim as an adopted human, a chimp who thought he was a boy, an animal that acquired language skills. One of them is Elizabeth Hess, who published a book in 2008 to tell a different story:

"He [Terrace]concluded that Nim and the other chimps who appeared to be communicating were merely mimicking, making fools of the scientists chatting with them. In effect, Terrace had written an obituary for ape-language research. After years of crowing about his achievements with Nim, he leapt into bed with his adversaries and battered other practitioners.
His opponents argued that his failure had been his own. He had been unable to handle his own chimp or provide Nim with consistent teachers. Worst of all, he had ended the study too early to get significant results; at the very least, Terrace's about-face was premature. Then there was the inconvenient fact that once Nim had learnt to sign, he often initiated conversation with humans. Didn't that count?"

The book is now a film. It would appear that the book's agenda resurfaces in the film. Although the science issues are not prominent, viewers are given an emotional roller-coaster as they follow the life of Nim Chimpsky - who is presented as having a theory of mind. Terrace is not happy:

"I'm upset because the film creates the impression the project was a failure because it didn't turn out the way I'd hoped it would when I started," Terrace declared recently in his office at Columbia, where he still runs the Primate Cognition Laboratory. "The only line between success and failure for scientists is really whether they honestly report their results, and I did that."
But that's not all Terrace is displeased about. "The film also suggests I was not affectionately involved with Nim. And that's not true." Marsh, he added, has "made a technically good film, but he's misrepresented me, and he misrepresented the science."

One thing that impresses me about the 1979 paper is the thoroughness with which the data is reported and discussed. The writers are people who started out to challenge Chomsky's theoretical approach, but ended up falsifying their own hypothesis. This is the way science is supposed to work. They impacted the whole field of ape-language studies - but there are other agendas operating. There are people who "know" that there can't be a discontinuity between apes and humans, because that is inconsistent with their understanding of evolutionary theory. So they find ways of undermining the research and promoting their own views. This is ultimately the same problem that we face elsewhere with evolutionary theorists - people confuse theory with fact and see overwhelming evidence where there is plenty of scope for divergent interpretations of the data. Will we ever learn?

Q&A: The interpreter
Jascha Hoffman
Nature, 475, 173 (14 July 2011) | doi:10.1038/475173a

In 1973, Herbert Terrace, a psychologist at Columbia University in New York, embarked on an experiment to teach sign language to an infant chimpanzee named Nim Chimpsky, after linguist Noam Chomsky. On the release of the documentary Project Nim, Terrace talks about research ethics, chimp cognition and the origins of language.

Can an ape create a sentence?
H.S. Terrace, L.A. Petitto, R.J. Sanders and T.G. Bever
Science, 23 November 1979, 206, 891-902 | DOI: 10.1126/science.504995

Abstract: More than 19,000 multisign utterances of an infant chimpanzee (Nim) were analyzed for syntactic and semantic regularities. Lexical regularities were observed in the case of two-sign combinations: particular signs (for example, more) tended to occur in a particular position. These regularities could not be attributed to memorization or to position habits, suggesting that they were structurally constrained. That conclusion, however, was invalidated by videotape analyses, which showed that most of Nim's utterances were prompted by his teacher's prior utterance, and that Nim interrupted his teachers to a much larger extent than a child interrupts an adult's speech. Signed utterances of other apes (as shown on films) revealed similar non-human patterns of discourse.

See also:

Tyler, D. Was Darwin's thinking about continuity of mind well grounded? (ARN Literature blog, 17 April 2009).

For many of us, an important characteristic of science is self-correction. We are proud of the way new findings catalyse re-evaluation and, if corrections are needed, the development of new knowledge. If you are like this, be prepared to be shocked when you read Jonathan Wells' latest book. The concept of Junk DNA was widely held by evolutionary biologists during the 1990s, but only a few were prepared to expose the hypothesis to tests of its validity. Yet this is when publications started to accumulate that reported functionality in genetic material widely regarded as "nonsense". Instead of alerting popularisers of science to be cautious, these writers treated the new data as unrepresentative exceptions. They pressed on with their claim that the bulk of the genome is useless. The trickle of challenging research findings became a stream, but the 'consensus' about junk DNA was not corrected. The stream became a river, but still the much-needed correction was lacking. Here is Richard Dawkins' comment from The Ancestor's Tale (2004, page 22):

"DNA differs from written language in that islands of sense are separated by a sea of nonsense, never transcribed. 'Whole' genes are assembled, during transcription, from meaningful 'exons' separated by meaningless 'introns' whose texts are simply skipped by the reading apparatus. And even meaningful stretches of DNA are in many cases never read -presumably they are superseded copies of once useful genes that hang around like early drafts of a chapter on a cluttered hard disk. Indeed, the image of the genome as an old hard disk, badly in need of a spring clean, is one that will serve us from time to time during the book."

(Source here)

Wells' approach is one of analysing and presenting the evidence for functionality. There are two broad categories to consider. The first concerns the transcription of non-protein coding DNA into various RNAs. The research literature suggests that most of this DNA is transcribed and in many cases, functionality has been confirmed. The second category concerns widespread conserved sequences of non-coding DNA. The very fact of it being conserved in different types of organism is supportive of functionality, even when we do not (yet) know the function.

Wells refers to a hierarchy of three levels for genome functionality. The argument is an interesting one, because it points to genetic information being present in both digital and analogue forms. In some examples discussed, the DNA sequence is in itself not important, but the length of the sequence is critical for successful functioning.

"The genome is hierarchical, and it functions at three levels: the DNA molecule itself; the DNA-RNA-protein complex that makes up chromatin; and the three-dimensional arrangement of chromosomes in the nucleus. At all three of these levels, DNA can function in ways that are independent of its exact nucleotide sequence." (p.93) [. . .]
"At the third level, the position of the chromosome inside the nucleus is important for gene regulation. In most cells, the gene-rich portions of chromosomes tend to be concentrated near the center of the nucleus, and a gene can be inactivated by artificially moving it to the periphery. In some cases, however, the pattern is inverted: rod cells in the retinas of nocturnal mammals contain nuclei in which the non-protein-coding pats of chromosomes are concentrated near the center of the nucleus, where hey form a liquid crystal that serves to focus dim rays of light." (p.94-5)

Junk DNA defenders have argued that junk DNA is supportive of Darwinism and that it refutes ID. This is why design advocates have felt it necessary to engage with these arguments. Well's book is compelling - it demolishes the thesis of junk DNA. If the original argument was logical, then the empirical data that we now have in profusion counts against Darwinism and confirms ID. Wells hastens to say that ID advocates have never suggested that all non-coding DNA is functional, only that it is unlikely that most DNA is non-functional. The design inference leads to the research goal of looking for functionality. This refutes the claim that ID is a science-stopper and does not lead to interesting avenues of research. This case shows that it is the Darwinists who have been guilty of science-stopping by their dogmatic claim that non-coding DNA is "nonsense" and not worth investigating.

Despite the onslaught of new data, with new functionalities being reported each week, there are still die-hards who cannot relinquish the junk DNA thesis. As an example of the intellectual gymnastics that are needed to sustain the myth, Wells refers to the "Onion test" proposed by Ryan Gregory in 2007. He claimed to have a "reality test" for those questioning the junk DNA thesis. "Ask yourself this question: Can I explain why an onion needs about five times more non-coding DNA for this function than a human?" (p.85) Wells' discussion of this test is worth reading in full, but his conclusion points to a logical flaw:

"So the onion test is a red herring. Why onion cells have five times as much DNA as human cells is an interesting question, but it poses no challenge to the growing evidence against the myth of junk DNA." (p.87)

Wells points out that the champions of junk DNA should be held accountable for keeping the myth alive and failing to demonstrate the self-correcting character of science. By quoting their arguments, he shows how they all demonstrate a vested interest in a Darwinian approach to evolution (i.e. demonstrating past tinkering that has accumulated nonsense DNA in the genome) and a hostility to ID. The individuals who need to retract erroneous arguments and conclusions are primarily John Avise, Francis Collins, Jerry Coyne, Richard Dawkins, Douglas Futuyma, Philip Kitcher, Kenneth Miller and PZ Myers. Science writers Richard Robinson, Michael Shermer and Carl Zimmer are also named for failing to demonstrate critical thinking skills when writing on this subject. Only Francis Collins has shown signs of revising his thinking - Wells puts it quite strongly: "he subsequently recanted his belief in the myth of junk DNA" (p.98). In an interview for Wired Magazine, he said: "I've stopped using the term" junk DNA (p.99) However, Collins gets only a partial reprieve, because his own baby The Biologos Foundation still promotes the junk DNA myth to argue against ID. (p.100)

Wells communicates very effectively in 114 pages of text plus 54 pages of references. The book could easily have been much larger if there was more background to the research findings and more discussion of the key implications brought out in the last chapter. Wells writes in a very restrained way, sparing us rhetorical flourishes that are often found in books and articles that deal with controversial issues. The writing style is concise, clear and compelling. Wells has chosen to communicate as a scientist and not as a polemicist. Consequently, the book is an invaluable resource as a state-of-the-art review of the issues. It provides a convincing rebuttal to anyone seeking to perpetuate the myth of junk DNA and anyone who suggests that the genome is a product of Darwinian tinkering rather than intelligent design.

Strongly recommended.

See also:

Tyler, D. Does the human genome have "serious molecular shortcomings"? (ARN Literature Blog, 7 May 2010)

Tyler, D. The Molecular Revolution's unfulfilled promises of simplicity (ARN Literature Blog, 11 April 2010)

Tyler. D. Hidden biological information via antisense transcription (ARN Literature Blog, 17 December 2008)

One of the more unusual research papers to be published recently is Phil Senter's use of the baraminological method to analyse morphological continuity within Dinosauria. The paper explicitly refers to "creation science" in the title and makes extensive use of terms familiar only to baraminologists. Senter's main motive, however, is to demonstrate that evolutionary theory is supported by empirical evidence that is recognised as evidence by creation scientists. By publishing his study, Senter hopes to influence the "huge number of voters who believe that the creationist world view has scientific validity and empirical support".

"Because of this onslaught, it is imperative to demonstrate that evolutionary theory is supported by empirical evidence. Towards this end, it is important to use methodology that is endorsed by creation science, so that creation scientists cannot reject the results of such studies without rejecting their own research. Towards that end, here I present a study using methodology endorsed and used in baraminology, the branch of creation science in which organisms are classified into separately created 'kinds' (baramins)."

Creationists point out that the lighter lines are data and the darker lines are inferred from evolutionary theory. (source here)

Although Senter has published before on these issues, he realised that he needed to refine the method of analysis to engage better with baraminologists, and also enhance his data set. The opportunity to do the latter came in 2010 when he visited the Institute of Vertebrate Paleontology and Paleoanthropology in Beijing. The data matrix used in the new paper includes 392 characters and 102 taxa, and Senter claims it is "the most comprehensive phylogenetic data matrix for Coelurosauria yet published". In this blog, we pass over the details of the data and go straight to the discussion. First, Senter has the "good news for the creationist world view":

"First, seven major dinosaurian groups (birdlike coelurosaurs, Tazoudasaurus + Eusauropoda, Stegosauria, Ankylosauridae, Neoceratopsia, Hadrosauridae and basal Hadrosauriformes) are separated from the rest of Dinosauria by morphological gaps. Creationist inferences that [these groups] represent diversification within separately created kinds are congruent with these results. Second, each morphologically continuous group found by taxon correlation includes at least some herbivores. This is congruent with the creationist assertion that all carnivorous animals are descendants of originally herbivorous ancestors. Third, although creationists have answered the problem of room on Noah's ark for multiple pairs of gigantic dinosaurs by asserting that only about 50 'created kinds' of dinosaurs existed, the problem is solved even better by the results of this study, in which only eight dinosaur 'kinds' are found."

However, Senter is not regarding this research as good news for creationists! He points out that the diversity within each group is "enormous". We should recognise that evolutionists also accept this diversity, but they say it happened in millions rather than hundreds of years.

"Acceptance that such diversity arose by natural means in only a few thousand years therefore stretches the imagination. The largest dinosaurian baramin recovered by this study includes Euparkeria, basal ornithodirans (Silesaurus and Marasuchus), basal saurischians, basal ornithischians, basal sauropodomorphs, basal thyreophorans, nodosaurid ankylosaurs, pachycephalosaurs, basal ceratopsians, basal ornithopods and all but the most birdlike theropods in an unbroken spectrum of morphological continuity. The creationist viewpoint allows for diversification within baramins, but the diversity within this morphologically continuous group is extreme."

Senter has other points to make. Arguably, there are taxon correlations between basal members of these groups, so a case can be made for bridging between the groups. More recent finds are helping to fill morphological gaps.

"Therefore, although results of this study identify seven potential morphological gaps that persist within Dinosauria, any creationist celebration of the persistence of such gaps is premature because of the general trend for such gaps to be filled by continued discovery."

The purpose of this blog is to welcome discussion of these issues in the science literature. From the acknowledgements, it is clear that Senter is already finding it possible to have meaningful communications with baraminologists. It will be a good thing if there is a two-way communication in the journals.

"Todd Wood and David Cavanaugh deserve thanks for much useful communication regarding baraminology. Both are congenial and collegial despite occupying the other side of the ideological fence, and I almost feel that I must apologize to both gentlemen that the results of this study are as they are."

It is my view that there are some methodological issues to be addressed even before engaging with fossil data. The significance of the research is that the issue of morphological discontinuities between groups of species is "on the table" for discussion by evolution-orientated scientists. This is important because systematic tools for studying discontinuity have previously not been given a high priority because the focus has been on establishing relationships (for example, using techniques of cladistic analysis). (For further thoughts on addressing discontinuities, go here). From an evolutionary perspective, we already know the answer: all these dinosaur groups are connected by common descent and must demonstrate a continuous morphological spectrum - any apparent discontinuities are a consequence of an imperfect fossil record. It appears that only a design perspective is capable of the data wherever it leads: there are actually two hypotheses to test: one is monophyletic common descent and the other is the diversification of many basic types.

Regarding tools, it is important for methods to allow competing hypotheses to be explored. Cladism needs to be challenged, because evolutionary branching is part of the underpinning philosophy. It should be called "Evolutionary Cladism" and be treated as a suspect tool because all data is viewed from an evolutionary perspective. It cannot avoid coming up with an evolutionary outcome. There was a time when "Transformed Cladism" was proposed to avoid this methodological flaw - but so embedded is evolutionary thinking in the minds of cladists that they cannot see the problem (for more on cladism, go here). The problem for Baraminology is it has the same fundamental problem - although in this case the creation of distinct baramins is the underlying philosophy. We need to develop tools that are our servants, not our guides, in understanding the data. We need tools that allow patterns in the data to emerge independently of the interpretation. Then the modelling work can start.

Using creation science to demonstrate evolution 2: morphological continuity within Dinosauria
P. Senter
Journal of Evolutionary Biology, Article first published online: 4 JUL 2011 | DOI: 10.1111/j.1420-9101.2011.02349.x

Abstract: Creationist literature claims that sufficient gaps in morphological continuity exist to classify dinosaurs into several distinct baramins ('created kinds'). Here, I apply the baraminological method called taxon correlation to test for morphological continuity within and between dinosaurian taxa. The results show enough morphological continuity within Dinosauria to consider most dinosaurs genetically related, even by this creationist standard. A continuous morphological spectrum unites the basal members of Saurischia, Theropoda, Sauropodomorpha, Ornithischia, Thyreophora, Marginocephalia, and Ornithopoda with Nodosauridae and Pachycephalosauria and with the basal ornithodirans Silesaurus and Marasuchus. Morphological gaps in the known fossil record separate only seven groups from the rest of Dinosauria. Those groups are Therizinosauroidea + Oviraptorosauria + Paraves, Tazoudasaurus + Eusauropoda, Ankylosauridae, Stegosauria, Neoceratopsia, basal Hadrosauriformes and Hadrosauridae. Each of these seven groups exhibits within-group morphological continuity, indicating common descent for all the group's members, even according to this creationist standard.

See also:

Walker, M. Can religious teachings prove evolution to be true? BBC Wondermonkey blog (5 July 2011)

Wood, T. Phil Senter does it again, Todd's Blog (7 July 2011)

We have known for many years that the eyes of trilobites, going back to the Early Cambrian, have highly sophisticated optics. Although vision has been invoked as a probable characteristic of many other types of animal, there have been few examples of preserved eyes in the fossil record, even in the Burgess Shale and Chengjiang lagerstatte. However, the Emu Bay Shale, which provides exquisite preservation of Early Cambrian animals, has now supplied us with the earliest example of an non-trilobite arthropod eye. Of the seven specimens recovered to date, three are spectacular for the detail revealed and stunning because they document eyes that "are as advanced as those of many living forms". One of the authors of the research paper, Dr Jim Jago, is quoted in the press release:

"These are by far the most complicated eyes known from this period of earth's history. Each eye is seven to nine millimetres across and comprises over 3000 tiny lenses. As yet, the animal to which these eyes belonged is unknown, but they may have belonged to a large shrimp like animal. However, the rock layers in which the eyes are preserved include a dazzling array of fossil marine animals, many being new to science. They include primitive trilobite-like creatures, bizarre armoured worms and large swimming predators."

One of the newly reported complex eyes from the Emu Bay Shale (source here)

The abrupt appearance of complexity in the fossil record has often been documented in this blog, primarily to raise questions about the relevance of Darwinism for understanding the origins of complexity. Time and time again, Darwinists fill the gaps in knowledge with their theoretical models, but sooner or later, the next generation of scholars will realise that Darwinists have constructed a virtual world that does not match the real world revealed by research. The features that appear abruptly are as follows:
1. Compound eyes with lenses that are larger than any others previously documented in the Cambrian Period. The largest have an elevational diameter of 150 micrometres and the smallest are about half this size.
2. The arrangement of the lenses shows a regional specialisation otherwise unknown in the Early Cambrian. The larger lenses create a "bright zone" and in living animals this generates binocular vision whilst retaining wide peripheral fields. These features are very useful to fast-moving predators.
Here is Jim Jago again:

"The fossil compound eyes have over 3000 lenses, giving them much sharper vision than anything previously found from rocks this old. The eyes are much more complex than anything found previously in rocks of similar age. The newly discovered eyes are as advanced as the eyes in many living insects such as robberflies. The arrangement and size of the lenses indicates that these eyes belonged to an active predator that was capable of seeing in low light."

The significance of the find is that there are no earlier intermediate forms from which to construct an evolutionary scenario, and that the structure of these eyes is essentially modern. The authors of the research paper anticipate this problem for evolutionary theory in their first sentence: "theory suggests that complex eyes can evolve very rapidly" and they cite the well-known 1994 paper by Nilsson and Pelger. They are right to say "theory suggests" because the Nilsson and Pelger paper has no links with empirical data. It is a conceptual model of morphological change - it completely by-passes issues of how light is sensed, transmitted to the brain and decoded. Parameters are introduced that are guesstimates; there is no link to Darwinian mechanisms of mutation and natural selection; assumptions are introduced throughout, with the minimum of justification. The weight that is put on this paper is justifiably called "A Scientific Scandal" by David Berlinski (for his essay, go here). The paper is really a dressed-up "just-so" story - with no link to the real world. Theory is fine as long as it is tested and validated - the problem with Nilsson and Pelger's theory is that it is an exercise in vivid imagination, has not been tested and cannot be regarded in any sense as authoritative.

There is no doubt that the Cambrian Explosion is a puzzle to Darwinists (for the reason why, see here). Many of them still refuse to concede that there was an non-Darwinian explosion of animal forms and they keep looking for ways of stretching out the timescales. However, others look for some strong selection pressures that could drive rapid evolution. The authors of the research paper align themselves with the latter group: "[The eyes] provide further evidence that the Cambrian explosion involved rapid innovation in fine-scale anatomy as well as gross morphology, and are consistent with the concept that the development of advanced vision helped to drive this great evolutionary event." Their reference for this points to Andrew Parker, who has championed this interpretation. The problem is that there are no transitional eyes to give this argument a connection to evidence. In fact, numerous "explanations" have been proposed, but none of them are compelling. It is far better to admit we do not know, as Shu did in 2008:

"Although we remain as blind men interpreting elephants when we search for the origin of metazoans, more and more accumulating data and hypotheses certainly help us with a better understanding the classic can of worms in both biology and geology."

The hypothesis to which I return repeatedly in these blogs is that the fossil record is not so much a record of evolutionary transformation, as a record of ecological transformation. Whilst I cannot claim the new fossil eyes are a proof of the hypothesis, they can certainly be understood in this way. As the Cambrian seas became richer ecosystems, the fauna became more diverse and the food webs more complex. As part of this picture, the arthropods with "modern" eyes do not look out of place at all.

For further reading on this paper, please refer to Darwin's God and Creation-Evolution Headlines.

Modern optics in exceptionally preserved eyes of Early Cambrian arthropods from Australia
Michael S. Y. Lee, James B. Jago, Diego C. Garcia-Bellido, Gregory D. Edgecombe, James G. Gehling & John R. Paterson
Nature, 474, (30 June 2011), 631-634 | doi:10.1038/nature10097

Despite the status of the eye as an "organ of extreme perfection", theory suggests that complex eyes can evolve very rapidly. The fossil record has, until now, been inadequate in providing insight into the early evolution of eyes during the initial radiation of many animal groups known as the Cambrian explosion. This is surprising because Cambrian Burgess-Shale-type deposits are replete with exquisitely preserved animals, especially arthropods, that possess eyes. However, with the exception of biomineralized trilobite eyes, virtually nothing is known about the details of their optical design. Here we report exceptionally preserved fossil eyes from the Early Cambrian (~515 million years ago) Emu Bay Shale of South Australia, revealing that some of the earliest arthropods possessed highly advanced compound eyes, each with over 3,000 large ommatidial lenses and a specialized 'bright zone'. These are the oldest non-biomineralized eyes known in such detail, with preservation quality exceeding that found in the Burgess Shale and Chengjiang deposits. Non-biomineralized eyes of similar complexity are otherwise unknown until about 85 million years later. The arrangement and size of the lenses indicate that these eyes belonged to an active predator that was capable of seeing in low light. The eyes are more complex than those known from contemporaneous trilobites and are as advanced as those of many living forms. They provide further evidence that the Cambrian explosion involved rapid innovation in fine-scale anatomy as well as gross morphology, and are consistent with the concept that the development of advanced vision helped to drive this great evolutionary event.

See also:

Primitive creatures had powerful eyes, University of South Australia, Press Release (30 June 2011).

Secularists repeatedly tell us that all beliefs are constructed by the human brain as a response to social and historical environments. They are responding to observations of humanity's apparently endless stream of beliefs in supernatural causation. Some of these examples are recognised as religious beliefs; others (such as astrology and ESP) are labelled superstitions and still others (such as belief in UFOs and the importance of coincidences) are often linked to New Ageism. Michael Shermer has a scholarly interest in explaining all of them as manifestations of human cognitive behaviour. He suggests these beliefs can be explained in two basic ways:

"One is the brain's readiness to perceive patterns over random behaviour. The other is its readiness to nominate agency - intentional action - as the cause of natural events. [. . .] The important point, Shermer says, is that we form our beliefs first and then look for evidence in support of them afterwards. He gives the names 'patternicity' and 'agenticity' to the brain's pattern-seeking and agency-attributing propensities, respectively. These underlie the diverse reasons why we form particular beliefs from subjective, personal and emotional promptings, in social and historical environments that influence their content."

Can science preserve us from being superstitious? (source here)

The general explanatory framework involves the brain creating meaning from stochastic data by a process of self-deluded induction. Whether the brain infers that patterns in "noise" are purposeful, or whether chance events are interpreted as intentional, the outcomes are the same: irrational beliefs about the world involving non-natural agents.

"As a 'belief engine', the brain is always seeking to find meaning in the information that pours into it. Once it has constructed a belief, it rationalizes it with explanations, almost always after the event. The brain thus becomes invested in the beliefs, and reinforces them by looking for supporting evidence while blinding itself to anything contrary. Shermer describes this process as "belief-dependent realism" - what we believe determines our reality, not the other way round."

As is usual in such studies, evolutionary theories provide context and plausible scenarios to reinforce the argument:

"He offers an evolution-based analysis of why people are forming supernatural beliefs based on patternicity and agenticity. Our ancestors did well to wonder whether rustling in the grass indicated a predator, even if it was just the breeze. Spotting a significant pattern in the data may have meant an intentional agent was about to pounce."

This is a depressing picture: humanity is embroiled in irrational beliefs from which we need rescuing. How can we be delivered from the fantasies secreted by our own brains? The saviour, according to Shermer, is amongst us - help is at hand!

"How did we ever arrive at a more objective and organised knowledge of the world? How do we tell the difference between noise and data? His answer is science. "Despite the subjectivity of our psychologies, relatively objective knowledge is available," Shermer writes. [. . .] Knowledge is power: the corrective of the scientific method, one hopes, can rescue us from ourselves in this respect."

A distinguishing feature of science is the testing of hypotheses by reference to empirical data. Shermer (and Grayling) claim some evidence to justify the hypothesis of belief-dependent realism.
1. The phenomenon of religious scientists (e.g. Francis Collins). This is said to be "interesting" because they exhibit "the impermeability of the internal barrier that allows simultaneous commitments to science and faith". The barrier is (writes Grayling) demonstrable because "scarcely any of them would accept the challenge to mount a controlled experiment to test the major claims of their faith, such as asking the deity to regrow a severed limb for an accident victim."
2. The existence of atheism. Atheism is considered "partial evidence" against the idea that theistic belief is a hard-wired phenomenon.
3. God-believing religions are said to be "very young in historical terms". Grayling interprets this in terms of the evolution of beliefs: theistic religions seem to have developed after mankind adopted agricultural and non-nomadic lifestyles, "and are therefore less than 10,000 years old".

In the interests of conciseness, and for the benefit of those who find these justifications underwhelming, I do not intend to detail these supposed tests of the hypothesis. All I am going to say here is that these tests serve to convince only those who already believe in the creeds of atheism.

The above comment is intended to stimulate the questions: "What are beliefs?" and "Is a commitment to science to be contrasted with a commitment to faith?" It is here that Shermer (and Grayling) evidence a superficiality of analysis that is inexcusable. Whilst some beliefs are a substitute for knowledge (and in many cases are in conflict with knowledge), it is patently obvious that some beliefs harmonise with knowledge. The contemporary fad of asking "Do you believe in evolution?" (even to Miss USA contestants!) illustrates the point. If the answer is "yes", some questioners may conclude that the respondent is a rational, truth-seeking promoter of science! Also, the questioner may infer that the non-believer is an obscurantist hiding from reality. I use this example just to point out that even in common language, "belief" does not imply irrational patternicity or agenticity. Shermer (and Grayling) owe it to their readers to ask whether some beliefs fall into the knowledge-based category. It appears that Shermer wants to redefine the word "belief" so that it is never applied to science, but this leads to a circular reasoning process where he concludes what he has already defined.

Shermer is described as being "once an evangelical Christian", but who "lost his faith largely as a result of his college studies of psychology and cognitive neuroscience". If he really understood evangelical Christianity, Shermer should know that the Christian meaning of "faith" is not believing something without evidence, but is trust in a person on the basis of evidence. For Christians, faith incorporates cognitive elements but is fundamentally a relationship. Christianity is based on evidence, because Christians recognise the acts of God in history. To suggest that these objective characteristics can be explained by patternicity and agenticity is to offer a weak argument that fails to engage with the challenging responses that Christianity provides.

Shermer should be aware of Christian contributions to epistemology (the study of the nature of knowledge). Christians have answers to questions like "How do we develop beliefs?" and "How do we know that a belief is true?" Unfortunately, these discussions do not inform Shermer's approach. In any other sphere of scholarship, neglect of the contributions of other scholars would be deemed unprofessional, or even shoddy. The net result is that Shermer ends up reinforcing the prejudices of fellow-atheists, but this should not be confused with contributing to knowledge.

Grayling thinks Shermer's analysis is correct: "This stimulating book summarizes what is likely to prove the right view of how our brains secrete religious and superstitious belief." Both Shermer and Grayling consider that science can help us escape irrational beliefs. But is science able to do this? Can it dispel ignorance and superstition? What we would expect here is an appeal to evidence. We should be presented with data that demonstrates a causal link between the adoption of science as a worldview and the erosion of irrational beliefs in society. What we get are assertions. Shermer and Grayling think science ought to have this effect, but we are not supplied with any evidence that it actually achieves the outcome.

Here are some data of relevance to these questions. We have a trend of increasing secularism in the UK and in the US. are there discernible trends elating to superstitions? In the UK, during the National Science Week in 2003, a survey was undertaken of superstitious behaviour. The first two findings are as follows:

"* The current levels of superstitious behaviour and beliefs in the UK are surprisingly high, even among those with a scientific background. Touching wood is the most popular UK superstition, followed by crossing fingers, avoiding ladders, not smashing mirrors, carrying a lucky charm and having superstitious beliefs about the number 13."
"* Superstitious people tend to worry about life, have a strong need for control, and have a low tolerance for ambiguity."
Also, from later in the report, "People become less superstitious as they age - 59% of people aged 11-15 said they were superstitious, compared to 44% of people aged between 31-40 and just 35% of the over 50s.
These findings do not suggest that superstitious behaviour and beliefs will be consigned to the past. Instead, they are strongly held by the younger members of society."

In 2009, via a ComRes poll, the situation was worse. Here is a comment from Tony Watkins:

"That's roughly a four-fold increase in belief in ghosts and astrology, and a doubling of belief in tarot. Interesting, given that Richard Dawkins and other atheists think they are driving superstition away along with religious belief (they see the two as the same category, of course, which they are not)."

In the US, during 2007-08, a detailed survey was undertaken in the Unites States on the state of religion in the country by Baylor University. The outcomes do not fit Shermer's analysis at all: traditional Christianity greatly decreases credulity, as measured by beliefs in such things as dreams, Bigfoot, UFOs, haunted houses, communicating with the dead and astrology. The Press Release has this comment:

"It remains widely believed that religious people are especially credulous, particularly those who identify themselves as Evangelicals, born again, Bible believers and fundamentalists. However, the ISR researchers found that conservative religious Americans are far less likely to believe in the occult and paranormal than are other Americans, with self-identified theological liberals and the irreligious far more likely than other Americans to believe. The researchers say this shows that it is not religion in general that suppresses such beliefs, but conservative religion."

We have seen recently that cultural bias is a real issue for contemporary scholars. We are witnessing atheist scholars promoting ideas that reinforce their personal worldview, but we need to be asking how far their research is affected by bias. They (like all researchers) need to be challenging their own favoured perspectives, and engaging with the best arguments coming from those who differ from them. All the signs are that they are not doing this. Shermer lumps all beliefs together and shows no interest in interacting with those whose beliefs are based on evidence. Grayling reviews Shermer to congratulate him on his insights. The message is passed down to popularisers who regurgitate this false analysis.

A Christian perspective on these matters was provided by Melvin Tinker earlier this year. The article is worthy of reading in full. However, the concluding paragraph is as follows:

"C.S. Lewis observed a number of years ago that, when Christianity is strong, superstition is weak, and vice versa. The 21st century was meant to be the scientific century and the triumph of reason. But what we find is an abundance of superstition which projects us back in time, resulting in a lack of security and hope. And yet these are the very things which come with the Christian gospel."

How we form beliefs
A. C. Grayling
Nature, 474, 446-447 (23 June 2011) | doi:10.1038/474446a

Review of The Believing Brain: From Ghosts and Gods to Politics and Conspiracies - How We Construct Beliefs and Reinforce Them as Truths by Michael Shermer.

One of the few books of Stephen Jay Gould I never read was his Mismeasure of Man. I suppose it was a low priority - as I have never considered cranial capacity a measure of intelligence or state of advancement. This is partly because of an awareness that women tend to have smaller skulls than men and yet this has no bearing on their cognitive skills. I knew that Gould was taking Samuel George Morton to task because Morton had considered cranial capacity to be significant for ranking human races in some sort of hierarchical order. Gould considered that Morton provided a case study of someone who had "finangled" his data and his analysis to reach unwarranted conclusions. His 1978 paper concluded in this way:

"Yet, through all this juggling, I find no indication of fraud or conscious manipulation. Morton made no attempt to cover his tracks, and I must assume that he remained unaware of their existence. He explained everything he did, and published all his raw data. All I discern is an a priori conviction of racial ranking so powerful that it directed his tabulations along pre-established lines. Yet Morton was widely hailed as the objectivist of his age, the man who would rescue American science from the mire of unsupported speculation."

Biological determinism is a minefield for the unwary - and for the mature (source here)

Gould carried the day with his analysis of Morton's work. There were some who questioned his conclusions, but most regarded Gould's paper and book as definitive. It took on an iconic status.

"Gould used Morton as a case study to argue that "unconscious or dimly perceived finagling, doctoring, and massaging are rampant, endemic, and unavoidable in a profession that awards status and power for clean and unambiguous discovery". Gould's analysis of Morton is widely read, frequently cited, and still commonly assigned in university courses. Morton has become a canonical example of scientific misconduct and an oft-told cautionary tale of how human variation is inevitably mismeasured."

The icon has been demolished by Jason Lewis and colleagues, who have remeasured Morton's skulls and revisited the data analysis issues. Their findings have surprised everyone. First, consider the database. Gould did not measure any of the skulls and concentrated his fire on the analysis. However, he did claim that Morton had mismeasured his specimens. To test this, Lewis et al. remeasured 308 of the 670 skulls in Morton's collection. Using their measurements as the standard for comparison, they found that seven of the racial groups were mismeasured by more than 5%. However, they found no correlation of these mismeasurements with Moreton's a priori biases. Therefore, they have concluded that Gould was wrong to make the claims he did about measurement bias. Note these comments from their paper and remember that Gould made no measurements himself to check:

"Gould famously suggested that Morton's measurements may have been subject to bias: "Plausible scenarios are easy to construct. Morton, measuring by seed, picks up a threateningly large black skull, fills it lightly and gives it a few desultory shakes. Next, he takes a distressingly small Caucasian skull, shakes hard, and pushes mightily at the foramen magnum with his thumb. It is easily done, without conscious motivation; expectation is a powerful guide to action"."

Next, Lewis et al. address the analysis of the data. Gould came to the conclusion that there were no differences to speak of among Morton's races and the claimed differences were explained as the misuse of various statistical strategies. The details need not concern us here. Lewis et al. summarise this part of their research as follows: "Our analysis of Gould's claims reveals that most of Gould's criticisms are poorly supported or falsified." Furthermore, they note: "It is doubtful that Morton equated cranial capacity and intelligence, calling into question his motivation for manipulating capacity averages." They conclude that Gould himself provides the better example of developing research to match a personal bias.
"Of the substantive criticisms Gould made of Morton's work, only two are supported here. First, Morton indeed believed in the concept of race and assigned a plethora of different attributes to various groups, often in highly racist fashion. This, however, is readily apparent to anyone reading the opening pages of Morton's Crania Americana. Second, the summary table of Morton's final 1849 catalog has multiple errors. However, had Morton not made those errors his results would have more closely matched his presumed a priori bias. Ironically, Gould's own analysis of Morton is likely the stronger example of a bias influencing results."

Such radical outcomes of this work has raised ripples of astonishment among interested scientists and educators. There are strong words coming from the anthropologist John Hawks' blog:

"Anyway, you can see why I find this outrageous. Gould used the well-documented work of a long-dead man to make an argument that unconscious bias is widespread in science. He posed as a concerned critic, but thereby cast doubt on the validity of the scientific enterprise. He picked volume measurement and tabulation of averages as his target, making it seem as if the simplest and most objective observations - the Junior High-level science methods - were themselves subject to all-encompassing cultural biases. His paper and book are very widely read and cited by people who will never examine the primary evidence. Gould owed us a responsible reading and trustworthy reporting on that evidence. In its place, he made up fictional stories, never directly examined the evidence himself, and misreported Morton's numbers."

The paradox for me is that I regard Gould as having exposed the superficiality of Darwinian "just so" adaptationist stories, yet here he is guilty of the same deed - constructing a just-so story about Morton measuring his skulls. I regarded Gould as injecting some interesting statistical ideas to historical science, and yet here he is, manipulating data to make it conform to an expected outcome. The basic lesson about cultural bias intruding into science is undiminished - but the case study subject is now Stephen Jay Gould, not Samuel George Morton. And if Gould illustrates the problem, questions about the cultural bias of any contemporary scientific writerwriter is legitimate and should be encouraged. John Hawks concludes thus:

"The new paper is open access, and I think that everyone should read it. The text is easy to follow, and the authors include clear answers to common questions about Morton's work and beliefs. It is a very suitable article for assignment in classes. They note that the basic issue here (endocranial volume of different groups) is largely explained by ecogeography - the authors mention climate explicitly, but I would add body size and life history as parameters that covary with climate. Measurement of endocranial volume was cutting edge science in 1840, but I repeat, this is simple stuff."

The Mismeasure of Science: Stephen Jay Gould versus Samuel George Morton on Skulls and Bias
Jason E. Lewis, David DeGusta, Marc R. Meyer, Janet M. Monge, Alan E. Mann, Ralph L. Holloway
PLoS Biology, 9(6): e1001071 | doi:10.1371/journal.pbio.1001071

First paragraph: Stephen Jay Gould, the prominent evolutionary biologist and science historian, argued that "unconscious manipulation of data may be a scientific norm" because "scientists are human beings rooted in cultural contexts, not automatons directed toward external truth", a view now popular in social studies of science. In support of his argument Gould presented the case of Samuel George Morton, a 19th-century physician and physical anthropologist famous for his measurements of human skulls. Morton was considered the objectivist of his era, but Gould reanalyzed Morton's data and in his prize-winning book The Mismeasure of Man argued that Morton skewed his data to fit his preconceptions about human variation. Morton is now viewed as a canonical example of scientific misconduct. But did Morton really fudge his data? Are studies of human variation inevitably biased, as per Gould, or are objective accounts attainable, as Morton attempted? We investigated these questions by remeasuring Morton's skulls and reexamining both Morton's and Gould's analyses. Our results resolve this historical controversy, demonstrating that Morton did not manipulate data to support his preconceptions, contra Gould. In fact, the Morton case provides an example of how the scientific method can shield results from cultural biases.

See also:

Gould, S.J. Morton's Ranking of Races by Cranial Capacity, Science, 5 May 1978, 200, 503-509.

Hawks, J. Gould's "Unconscious Manipulation of Data", John Hawks Weblog (8 June 2011)

Post-script: an Editorial in Nature comments on the research paper and concludes with the paragraph below. Here is another indication that the peer review process as presently practiced is making it more difficult to publish unorthodox or potentially controversial ideas. Can this be good for science?
"Just as important is the readiness of the scientific community to undertake such studies, and to see them through the sometimes difficult publication process. The criticism of Gould was rejected by the journal Current Anthropology, and spent eight months in the review process at PLoS Biology. And although an undergraduate did publish a more modest study scrutinizing Gould in 1988, it is remarkable that it has taken more than 30 years for a research group to check Gould's claims thoroughly. Did Gould's compelling writing and admirable anti-racist motivations help to delay scrutiny of his facts? Quite possibly, and this is regrettable. Although future historians will be happy to scrutinize our most persuasive and celebrated luminaries, today's scientists should not leave the job to them." (Mismeasure for mismeasure, Nature, 474, 419 (23 June 2011)

Two interesting papers contribute significantly to our understanding of science education debates. The first, by Joachim Allgaier, considers newspaper accounts of a UK school (Emmanuel College) that was accused of teaching creationism in science classes. The goal of the study was to find out what sources journalists used, and how the sources of education journalists compares with the sources used by science journalists. The issue is important because of the potential for media accounts of issues like this to mould public opinion and shape responses. The two types of journalists can be distinguished in a broad-brush way:

"Science journalists, for instance, visit scientific conferences, talks and presentations, read and follow scientific journals and receive 'embargoed' press releases from scientific institutions and pre-published articles from science journals. Journalists specialising in stories about education follow the news coverage on education on various media channels, keep in touch with teachers, head teachers and other professionals from the education world, and follow the moves of teaching unions, representatives of the government and education authorities."

Science journalism has its challenges (source here)

The Emmanuel College case study was selected because it was given considerable media coverage and a total of 111 news reports were analysed. This was supplemented by qualitative interviews with a sub-set of reporters covering the story. Very quickly, differences started to emerge. Education reporters sought out informants close to the action: the head-teacher, staff - particularly science teachers, local teaching union, local education committees, pupils and their parents. On the national scale, the views of OFSTEAD were relevant (their assessment of the school was positive), the fact that the Prime Minister supported the school, and representatives of the relevant government department were consulted. The greatest credibility was associated with teachers and educators with long teaching experience. By contrast, the science correspondent in the sample majored on secondary sources: scientists and education policy makers. According to this journalist, most were hostile to the idea of teaching creationism.

"The science correspondent's approach therefore appears less proactive than that of the education correspondents, who directly searched out their contacts at the school. The science correspondent only indirectly referenced the school, when he quoted from the Emmanuel College prospectus (available online), suggesting that creationism is taught in science classes. To justify this indirect approach, he stated, 'the school itself wasn't talking'. This account is in stark contrast to the experience of three education correspondents all of whom commented that representatives and the staff at Emmanuel College were very open towards journalists and also employed PR experts to get their view across. They reported that access to the school was granted to all education correspondents that wanted to visit it."

These findings raise questions about balanced reporting - what is balanced? What is objective? The research has shown that different journalists have different views on objectivity. In particular, the science journalist made a value judgment that prioritised the consensus from the science community that creationism in any form was bad for education.

"The journalistic norm of balanced reporting can have consequences not only for controversies amongst scientists but also when there is consensus amongst the scientific community (e.g., that the theory of evolution is a scientific theory and creationist explanations are not scientific ones) and scientific knowledge is attacked from outside the scientific community. However, there were different notions of legitimacy held by correspondents with regard to the Emmanuel College case that informed them about what was objective or not. Put another way, correspondents with different professional and personal ideals assess the representation of sources and the coverage of the debate in different ways."

Whilst this is a single case study, it does raise issues that warrant further research and reflection. To promote reflective thought on the findings, Michael Reiss contributed a paper with the title "Teachers as Journalists?". There is an analogy to be made:

"In this commentary I would like to use Joachim Allgaier's paper as a springboard that allows me to examine some of the similarities and differences between the work of the journalists he studied and that of science teachers who have, day in and day out, like journalists, though to a lesser extent, to make decisions about how to react to and deal with new issues of topic interest. Like journalists, teachers operate under considerable time pressures and have preferred sources. They are also accountable, though to different bodies."

Reiss points out that teachers in the UK have always been used to a degree of freedom in the way they select and present issues. They have also been encouraged to make links between their classroom teaching and developments in society that will increase the relevance of the content matter and catch the imagination of students. Just as journalists cover the creation-evolution issue because they think there is a interest from their readers, so also teachers might wish to incorporate science-religion questions into their lessons. There appear to be four possible options for science teachers:

* There is a requirement in a particular science course to address the issue
* Science teachers are free to decide whether or not to raise the issue with their students
* Science teachers only choose whether or not to address the issue if it is brought up by their students
* Science teachers do not address the issue under any circumstances.

The first must be ruled out because some science teachers will not want to do this and constraining teachers to do something they are not committed to is not the way education works. The fourth option also constrains teachers - this time not to address the issue. Reiss says this "seems unduly restrictive". His reason? -

"After all creationists make empirical claims about the world (notably that not all organisms share common ancestors and, in creationist Christianity and Judaism, though not in creationist Islam, that the world is much younger than deduced by science). Are we really saying that such claims lay outwith the compass of science?"

So this leaves the second and third possibilities, giving teachers the choice as to how these issues will be addressed, if at all. This brings Reiss to the topic of how teachers should deal with the issue. Should they be like education reporters, who make an attempt to be balanced by talking to people on all sides and producing a report where their sources can recognise their positions being portrayed fairly? Or should teachers be like the science reporter, who wanted to bring out the scientific consensus position. Reiss refers to the "Teach the controversy" approach in the US and explains why some teachers do not want to go down that pathway.

Finally, Reiss considers outcomes. What are the deliverables? - the learning outcomes? From practical experience, Reiss thinks it is more important to have outcomes that promote use of the scientific method and critical reasoning than it is to have students signing up to a consensus position.

"It is, I hold, the job of science teachers to strive to communicate this scientific understanding to their students, not for the students necessarily to accept it but for them to understand it. [. . .] The job of a science teacher is therefore to present a very particular way of understanding the world."

These thoughts are highly relevant to contemporary developments in the UK and in the US. There are many very vocal people wanting to require teachers to handle these issues in a particular way - enforcing the consensus. For some of us, this is very worrying and it should be worrying to the teaching profession. This is a move towards totalitarian control, and that always ends up damaging real education, because the focus is not on critical thought but on conformance to an externally imposed norm. This is an issue where the students should come first, and this is an issue where Michael Reiss has some really valuable advice for us all. (For more on Reiss' approach, go here).

Who is having a voice? Journalists' selection of sources in a creationism controversy in the UK press
Joachim Allgaier
Cultural Studies of Science Education, 2011, 6(2), 445-467 | DOI: 10.1007/s11422-011-9319-5

Abstract: Media accounts of reality have the potential to influence public opinion and decision making processes. Therefore who has and who does not have access to the media and can make their voice heard is a crucial question with serious political consequences. In this article it is investigated whether the speciality of journalists influences their source selection procedures. The coverage of science in schools is an interesting example, since it can be covered by specialized science or education correspondents, but also by general news reporters. A public controversy in the UK about the inclusion of creationism in a school is used to identify which types of sources were selected by various journalists. The focus is upon the selection of sources and whether journalists with different specialties consider various sources relevant and credible. A content analysis of articles, featuring this controversy, is combined with an analysis of correspondent's strategies for selecting sources based on interviews with them. The findings suggest that compared to journalists that specialize in education issues, science correspondents employ a narrower scope when seeking sources. This might have important consequences for the representation of views on science education in the media.

Teachers as journalists?
Michael J. Reiss
Cultural Studies in Science Education,2011, 6(2), 469-473 | DOI: 10.1007/s11422-011-9322-x

Abstract: I start by considering some of the similarities between journalists and science teachers in their work and then go on to examine three questions that are of importance in dealing with creationism in schools: Is the issue one that is worth dealing with? How might one deal with it? What does one hope to achieve by dealing with it? I conclude that (i) it is worth science teachers dealing with the issue of creationism in schools but only if they wish to; (ii) science teachers should not give the impression that the theory of evolution is scientifically controversial; (iii) while one is very unlikely to change the mind, as a result of school teaching, of someone who does not, on religious grounds, accept the theory of evolution, it is very worth presenting the scientific account of the theory and enabling students to review the evidence for it.

Although it did not appear to hit the popular media, a recent paper on the Earth's earliest non-marine eukaryotes is worthy of note here. Like many discoveries, the researchers were not expecting to find what they did. Conventional wisdom is that the Precambrian land surface was barren, and that the important developments were to be found in the sea. So Torridonian rocks from NW Scotland, having all the marks of non-marine sediments, were not expected to yield much of interest. The story is continued by Cristina Luiggi in The Scientist:

"In 2007, Strother and a colleague came across a dusty museum collection of microfossil slides recovered from an outcrop of the oldest sedimentary rocks in the British Isles: the Torridonian sequence. Sections of these rocks date between 1 to 1.2 billion years, and have preserved sediments that were once part of freshwater lakes formed in the depressions of an ancient land surface. To Strother's amazement, the collection contained what appeared to be fossils of multicellular organisms. "We were finding clusters of cells as well things that looked like little pieces of tissue," he said. This came as a surprise given that multicellular organisms of that time period were believed to exclusively inhabit the oceans."

Artist reconstruction of specimens from the Applecross Formation, Loch Diabaig. (Credit: Oxford University/Martin Brasier, source here)

The find triggered an extensive search using samples gathered from all groups of strata comprising the Torridonian - and evidences of eukaryotes were found at all horizons. This means that from the beginning of the Neoproterozoic era, non-marine eukaryotes have been preserved. The researchers have found complexity, as is shown by the following quote from their paper:

"The Torridonian assemblages contain some striking examples of microfossils that show complexity that goes considerably beyond that of simple leiospheres. Figure 1h illustrates a multicellular sphere from a phosphatic nodule with a clearly differentiated outer wall [. . .] Some of these interior cells retain a dense 'spot', probably the plasmolysed remnants of original cell contents. Figure 2b illustrates a large fusiform vesicle (475 mm wide) with a pitted interior wall structure. Figure 2d shows a dark, heterogeneous central body enclosed within a large cyst with a peripheral asymmetrical structure, which itself appears to consist of several cylindrical cells or membranous outgrowths of the vesicle wall."

They were also impressed by the diversity of what they have documented (possibly 50 species):

"Sample to sample heterogeneity seen throughout the Torridonian clearly indicates a significant degree of biotic diversity, reflecting adaptation to freshwater aquatic and subaerially exposed habitats by earliest Neoproterozoic time. Early eukaryotes were clearly capable of diversifying within non-marine habitats, not just in marine settings as has been generally assumed."

What do these findings mean for our understanding of life on the Precambrian Earth? Dr Charles Wellman, an author of the paper, is quoted by ScienceDaily as saying:

"It is generally considered that life originated in the ocean and that the important developments in the early evolution of life took place in the marine environment: the origin of prokaryotes, eukaryotes, sex and multicellularity. During this time the continents are often considered to have been essentially barren of life -- or at the most with an insignificant microbial biota dominated by cyanobacteria. We have discovered evidence for complex life on land from 1 billion year old deposits from Scotland. This suggests that life on land at this time was more abundant and complex than anticipated. It also opens the intriguing possibility that some of the major events in the early history of life may have taken place on land and not entirely within the marine realm."

We should note that marine organisms are isotonic with seawater: this means the same salt concentration exists inside as well as outside the cell membrane and there are no osmotic pressures. However, fresh-water and land organisms are all hypertonic, which means that the internal salinity exceeds that of the fresh-water outside the cell, and unless there are mechanisms to counter osmosis, the cell will die. In addition, non-marine life may have to face the problem of desiccation. This appears to be a real issue for some of the Torridonian eukaryotes, because some of the samples were obtained from desiccation cracks in the Diabaig Formation at Loch Diabaig (this is of personal interest, having obtained samples of these desiccation cracks some years ago from this same locality). The researchers comment:

"Freshwater habitats are ecologically more variable than marine habitats, providing temporal and physiochemical heterogeneity, including wet-drying cycles and direct atmosphere-organism gas exchange. Such habitat heterogeneity translates directly into increased speciation potential. Some of the microfossils illustrated here must have experienced subaerial exposure because they occur in situ in microbially induced sedimentary structures with desiccation cracks, but the extent to which they lived subaerially cannot be ascertained with certainty."

Speciation potential is fair enough as a concept, but the hard work then starts - to identify viable routes for generating the relevant biological mechanisms and associated information. This is where big questions have to be raised about the viability of mutation and natural selection to deliver significant changes (see here). When confronted by the realities of the changes that are needed, it is very easy for evolutionists to put out what they call a plausible narrative - otherwise known as "Darwinian storytelling".

One of the themes developed in this blog has been an ecological perspective on the fossil record. This suggests that the key issues to grasp when seeking to understand past life relate to ecology and the environment. Here we have another example. In the Neoproterozoic, seawaters were not yet able to support multicellular animals - for these, the Earth had to wait until the Ediacaran (for an advance party) and then the Cambrian (for the explosion of animal life).
Nevertheless, the Neoproterozoic could support some eukaryote species (as well as prokaryotes). And that's what we find, not only in the seas but also on land. The word "surprising" appears alongside this discovery, but this draws its rationale from Darwinian gradualism - but from a design perspective, the Earth was ready for freshwater life.

"We've been thinking about the evolution of life in the Precambrian as primarily happening in the oceans," Strother said, "but 1 billion years ago, fresh water environments were really teeming with life."

Earth's earliest non-marine eukaryotes
Paul K. Strother, Leila Battison, Martin D. Brasier & Charles H. Wellman
Nature, 473, 505-509, (26 May 2011) | doi:10.1038/nature09943

The existence of a terrestrial Precambrian (more than 542 Myr ago) biota has been largely inferred from indirect chemical and geological evidence associated with palaeosols, the weathering of clay minerals and microbially induced sedimentary structures in siliciclastic sediments. Direct evidence of fossils within rocks of non-marine origin in the Precambrian is exceedingly rare. The most widely cited example comprises a single report of morphologically simple mineralized tubes and spheres interpreted as cyanobacteria, obtained from 1,200-Myr-old palaeokarst in Arizona. Organic-walled microfossils were first described from the non-marine Torridonian (1.2-1.0 Gyr ago) sequence of northwest Scotland in 1907. Subsequent studies found few distinctive taxa - a century later, the Torridonian microflora is still being characterized as primarily nondescript "leiospheres". We have comprehensively sampled grey shales and phosphatic nodules throughout the Torridonian sequence. Here we report the recovery of large populations of diverse organic-walled microfossils extracted by acid maceration, complemented by studies using thin sections of phosphatic nodules that yield exceptionally detailed three-dimensional preservation. These assemblages contain multicellular structures, complex-walled cysts, asymmetric organic structures, and dorsiventral, compressed organic thalli, some approaching one millimetre in diameter. They offer direct evidence of eukaryotes living in freshwater aquatic and subaerially exposed habitats during the Proterozoic era. The apparent dominance of eukaryotes in non-marine settings by 1 Gyr ago indicates that eukaryotic evolution on land may have commenced far earlier than previously thought.

See also:

Supplementary information here.

Loch Fossils Show Life Harnessed Sun and Sex Early on, ScienceDaily (14 April 2011)

Luiggi, C. Old open air voyagers, The Scientist (13th April 2011)

The editors-in-chief of Synthese, a leading philosophy journal, published an unusual disclaimer in the print-version of a guest edited special release of the journal. Basically, they apologised that some of the papers in the "Evolution and Its Rivals" issue fell short of the standards of professional discourse that would be expected by readers.

"We believe that vigorous debate is clearly of the essence in intellectual communities, and that even strong disagreements can be an engine of progress. However, tone and prose should follow the usual academic standards of politeness and respect in phrasing. We recognize that these are not consistently met in this particular issue. These standards, especially toward people we deeply disagree with, are a common benefit to us all. We regret any deviation from our usual standards."

Demarcation lines and warfare warfare often go together - but do we need one to define science? (Image source here)

The guest editors took this badly, and a heated discussion has followed (see here and here). One philosopher, Brian Leiter produced a blog post "Synthese Editors Cave in to Pressure from the Intelligent Design Lobby: Philosophers Should Boycott Synthese." The special issue was concerned with intelligent design and creationism, and all the papers were contributed by critics - some outspokenly hostile. The most extreme example of unprofessionalism came from the philosopher Barbara Forrest, whose hatchet-job on another philosopher Francis J. Beckwith, was triggered by his claim that the teaching of intelligent design in public schools is constitutionally permissible. The Synthese Editors-in-Chief have offered Beckwith the opportunity to respond in a future issue of the journal. The Forrest paper has been the subject of comment here and here.

This blog considers another case of bully-boy behaviour masquerading as scholarship - the paper on demarcation by Robert T. Pennock. Those most opposed to intelligent design (ID) and creationism have typically maintained that a clear line can be drawn between science and non-science, and ID and creationism are declared to be outside the boundary of science. In this essay, Pennock choses to talk down to one of his peers in the world of philosophy. An example is as follows:

"When we look empirically at what scientists and science educators themselves say science is, then we see immediately that they all ignore Laudan and clearly operate on the idea that there is a real distinction between science and non-science. Indeed, the evidence for this view is so pervasive that it is hard to see how one can take Laudan's incredible pronouncements as anything but indicating a cavilier [sic] disregard for the balance of evidence and a foolhardy disengagement from what should be the subject matter of philosophy of science. I can here only give an outline of some of some of what Laudan had to ignore in his anti-demarcationist screed."

A bit of background may help those not familiar with the demarcation debates between philosophers of science. Some have argued strongly that science can be distinguished from non-science by a number of criteria (these are the demarcation criteria). Examples of some of these criteria are falsifiability (science involves testing hypotheses to establish whether they are consistent or falsified), and the ability to make predictions (with hypotheses being a form of prediction). After claiming that ID and creationism fail against these criteria, the conclusion is drawn that ID and creationism should be excluded from science and treated as sectarian religion or as political activist movements. However, the giant fly in this ointment is that some other philosophers of science find that all the proposed criteria fail under close scrutiny because disciplines that are widely regarded as legitimate science would also have to be excluded. These philosophers regard the demarcation issue as dead. Pennock defends the demarcation approach and Laudan has championed the other side.

Before looking at these issues more closely, it is worth noting that Pennock appeals repeatedly to the scientific consensus. This is apparent in the quotation given above and it is pervasive in his paper. This strikes me as surprising for a philosopher to be so impressed by the majority view - philosophers are supposed to reach conclusions by the use of reason, without giving weight to how many people support a particular position. Here is another example, this time relating to methodological naturalism (MN) - the view that the methodology of science should assume that all causes are natural (i.e. excluding intelligent causation):

"there is good reason to think that MN is accepted by a large majority of philosophers of science and is probably as close to a settled consensus as is possible in our profession. In any case, as will be discussed in detail in the next section, there is excellent evidence that it is all-but-universally accepted as a tacit ground rule of science among scientists, which is the more relevant standard."

The controversy surrounding the disclaimer was the subject of a philosophy blog here, inviting comments. One of the respondents was Larry Laudan, who has long arguing that the 'demarcation problem' cannot be solved. Laudan refrains from commenting on whether the editors were pressurised to issue the disclaimer, but declares that their statement "was not only in order but essential as a matter of professional ethics." He goes on to identify himself as the target of Pennock's vitriol:

"I will limit my comments to a single paper by Robert Pennock from the issue in question. In the course of some twenty pages, he alleges that the work of a fellow philosopher is "almost willfully naive and misguided", that it "can only be described as histrionic and ill-considered" and that it "continue[s] to muddy the waters to the detriment of both science and philosophy of science". He goes on to endorse the proposal that the philosopher in question should be excluded from 'the conversation of mankind' because said author "ha[s] lost touch with reality in a profound and perverse way". Those of you who have read Pennock's paper will know that I am not a wholly disinterested party here, since all his barbs are directed specifically at yours truly. But I think I can lay aside self interest long enough to say that discourse of this sort has no legitimate place in any serious journal of philosophy (most especially the suggestion that those who disagree with Pennock should be excluded from 'the conversation of mankind')."

We need to recognise that Laudan is writing as a philosopher of science, and the stance he takes does not imply he is an ID supporter. Nevertheless, he presents demarcation arguments as a slovenly contrivance that leads to a cardboard front for the enterprise of science. He offended many of his colleagues by commenting negatively on the testimony of Michael Ruse at the 1981-1982 McLean v. Arkansas legal case:

"The victory in the Arkansas case was hollow, for it was achieved only at the expense of perpetuating and canonizing a false stereotype of what science is and how it works. If it goes unchallenged by the scientific community, it will raise grave doubts about that community's intellectual integrity."

This blog does not attempt to address Pennock's 30-page defense of demarcation. However, it is worth pointing out that methodological naturalism and demarcation are inextricably linked in the minds of Pennock and many others. If science is defined as a discipline that considers only natural explanations of phenomena, then ID and creationism are excluded from science by definition (as are archaeology and forensic science!). Here is Pennock again, commenting on a (2000) statement by the National Science Teachers Association on the nature of science:

"Although no single universal step-by-step scientific method captures the complexity of doing science, a number of shared values and perspectives characterize a scientific approach to understanding nature. Among these are a demand for naturalistic explanations supported by empirical evidence that are, at least in principle, testable against the natural world. Other shared elements include observations, rational argument, inference, skepticism, peer review and replicability of work. [. . .] Science, by definition, is limited to naturalistic methods and explanations and, as such, is precluded from using supernatural elements in the production of scientific knowledge."
Pennock comments:
"In another statement on the teaching of evolution, NSTA explicitly rejects creation science and ID on the grounds that they are not science for just such reasons. One can find dozens of similar statements from both scientific and science education organizations that in more or less direct ways articulate a presumption of natural regularity and the requirement that science appeal only to naturalistic explanations."

The absurdity of this position is that this mutant version of science is methodologically incapable of detecting intelligent design even if it were "in your face" design. This is the ultimate circular argument, carrying no more authority than a novel. If there is to be any meaningful discourse about design in nature, we have to have tools and methodologies for detecting design - and that is what ID has offered as a way forward.

Can't philosophers tell the difference between science and religion?: Demarcation revisited
Robert T. Pennock
Synthese, Volume 178, Number 2, 177-206 | DOI: 10.1007/s11229-009-9547-3

Abstract: In the 2005 Kitzmiller v Dover Area School Board case, a federal district court ruled that Intelligent Design creationism was not science, but a disguised religious view and that teaching it in public schools is unconstitutional. But creationists contend that it is illegitimate to distinguish science and religion, citing philosophers Quinn and especially Laudan, who had criticized a similar ruling in the 1981 McLean v. Arkansas creation-science case on the grounds that no necessary and sufficient demarcation criterion was possible and that demarcation was a dead pseudo-problem. This article discusses problems with those conclusions and their application to the quite different reasoning between these two cases. Laudan focused too narrowly on the problem of demarcation as Popper defined it. Distinguishing science from religion was and remains an important conceptual issue with significant practical import, and philosophers who say there is no difference have lost touch with reality in a profound and perverse way. The Kitzmiller case did not rely on a strict demarcation criterion, but appealed only to a "ballpark" demarcation that identifies methodological naturalism (MN) as a "ground rule" of science. MN is shown to be a distinguishing feature of science both in explicit statements from scientific organizations and in actual practice. There is good reason to think that MN is shared as a tacit assumption among philosophers who emphasize other demarcation criteria and even by Laudan himself.

See also:

Luskin, C. Synthese Opposed the Disrespectful Methods of Intelligent Design Critics, Evolution News & Views (May 20, 2011)

It has been recognised for some time that the uniformitarianism of Charles Lyell has hindered the development of geological science. It is perhaps less widely known that Charles Darwin perceived himself initially as a geologist and he drew heavily on Lyell's uniformitarian agenda (for an example, go here). Later, as Darwin's focus moved to biology, he retained his commitment to a uniformitarian methodology: evolutionary gradualism was Darwin's attempt to apply uniformitarianism to biology. (For an example of it leading him astray in understanding inheritance, go here). Scholarly criticism of gradualism, however, has been muted because alternatives to Neo-Darwinism lack maturity and there are many hypotheses that await testing. Notwithstanding this, the data derived from a study of fossils has consistently pointed to discontinuity rather than gradualism.

"The ubiquity of morphological discontinuities between clades of organisms has troubled evolutionary biologists since Cuvier and Darwin and remains one of most important questions in evolutionary biology. Why is it that the distribution of morphologies is clumpy at virtually all scales? Although both Darwin and the proponents of the Modern Synthesis expected an 'insensible' gradation of form from one species to the next, this is only sometimes found among extant species (for example, among cryptic species) and is rare in the fossil record."

The pervasive pattern of natural history: disparity precedes diversity (source here)

Despite these problems, many Darwinists have found ways of turning evidence against their theory into something they can be positive about. Notably, they portray the fossil record as compelling evidence that evolution has occurred. Hard-line Darwinists explain morphological disparity by the non-preservation of intermediate forms, allowing them to insist that macroevolution is achieved by extrapolating microevolution. There are a growing number of scholars who recognise the need to develop theory beyond the Modern Synthesis and two approaches are summarised by Erwin thus:

"a hierarchical view of macroevolution where species sorting or selection drives evolutionary trends (although it is not clear how this produces a non-uniform distribution of morphologies); and various formalist or structuralist schools where major evolutionary transitions reflect structural or physical requirements, with selection entering only as a secondary sorting mechanism. Generally absent from each of these approaches is consideration of the possibility that the nature of the evolutionary process, as distinct from the organisms on which evolution acts, has itself evolved over time."

The "Cambrian Explosion" refers to the abrupt appearance of animal phyla and classes in the fossil record. It has been much discussed by both critics and defenders of Darwinism. Apart from pleading the impoverishment of the fossil record, the defenders have sought to 'spread out' the Explosion, to make it appear that gradualism can still be discerned. An example of this approach was blogged here, where I noted that critics have never insised on an instantaneous explosion, but have merely drawn attention to the numerous characteristics of the Explosion that are inconsistent with Darwinism. Stimulated by the iconoclastic approach of Stephen Jay Gould, the critics have shown themselves to be the true empiricists.

"These studies quantitatively substantiated Gould's intuitive conclusion: morphologies really are unevenly distributed at the origin of a clade. In the majority of cases studied, morphologic disparity greatly exceeds taxonomic diversity in the early history of a clade. This result could only be the result of sampling artifacts if one were to posit that unusual morphologies were more likely to be preserved and recovered than morphologies similar to one another, which is hard to credit. Such studies have demonstrated that the apparent gaps between morphologies are not simply due to extinction of once-intermediate forms."

In an important contribution to this debate, Douglas Erwin revisits the task of analysing data relevant to the first appearance of phyla and classes.

"Here I explore growing evidence that a significant factor in the clumpy nature of morphology is systematic, time-inhomogeneous patterns in types of variation upon which natural selection and other evolutionary processes could act. I present a new compilation of the first occurrences of marine invertebrate phyla, classes and equivalent stem groups during the Ediacaran, Cambrian and Ordovician, focusing on the Ediacaran-Cambrian (579-490 Ma) diversification of animals."

The summary of results for phyla is as follows. The pattern reinforces earlier research that concluded the Explosion is not an artefact of sampling. Much the same finding applies to the appearance of classes. These data are presented in Figures 1 and 2 in the paper.

"Ediacaran originations are relatively few, reflecting the uncertainties about the phylogenetic placement of most Ediacaran fossils. A major pulse of origination is evident in Cambrian Stage 1, largely of small skeletonized fossils known as the 'small shelly fossils', followed by the first appearances of many clades in Cambrian Stage 3, corresponding to the exquisite soft-bodied preservation of the Chengjiang biota in southern China. A later, smaller pulse is associated with first appearances in the Burgess Shale fauna of British Columbia, Canada. The only later occurrence of a durably skeletonized phylum is the Bryozoa in Cambrian stage 9. Twelve phyla are known only from the Recent and four phyla first occur in the fossil record after the late Cambrian: one each in the Carboniferous, Jurassic, Cretaceous and Eocene."

Having documented a non-uniformitarian pattern in the empirical data, Erwin turns to analysis and interpretation. He points to work on developmental gene regulatory networks (GRNs), termed kernels, that appear to be highly conserved and "remarkably refractory to subsequent evolutionary change" (previously discussed here). This research has concluded that developmental GRNs formed during the Ediacaran-Cambrian and that their stability corresponds to both the early disparity of the phyla and classes and also their subsequent stasis. This is why uniformitarianism fails as an explanatory framework:

"the establishment of these kernels early in the history of metazoan evolution suggests a temporal change in the type of developmental variation exposed to selection and drift, indicating that aspects of evolutionary change are not uniformitarian."

Erwin's paper helps to structure debate about these important issues. Questions about the origin of phyla and classes can now be represented in terms of the origin of biological information, notably developmental GRNs. Erwin's study shows that gradualistic, incremental approaches to the origin of biological information are in tension with empirical data. This is where debate, if it is to be meaningful, must be focussed.

"The pattern of origination of metazoan phyla and classes is highly non-uniform through the Phanerozoic, with an overwhelming bias towards the Cambrian and Ordovician. In the past non-paleontologists have attempted to rescue uniformitarian explanations by 'explaining away' this empirical pattern as a result of various biases. Both taxic and quantitative morphometric approaches have established that the pattern is accurate reflection of the appearance of morphological novelties. By combining this information on the pattern of morphologic evolution with mechanistic information from comparative studies of modern developmental GRNs, a new, non-uniformitarian view of evolution emerges. From this perspective, the growth of developmental networks has progressively structured the nature of accessible developmental innovations overtime."

There is a 'standard' explanation of the origin of biological information that has been developed by Darwinists (but not by Darwin - who was more interested in diversification than complexity increases). An example of this is given as an addendum - if Darwinists could take this seriously, it would help avoid the distractions of finch beaks and industrial melanism! Erwin's study shows that the Darwinian paradigm, whether or not it can explain the origin of information, is irrelevant to the origin of phyla and classes. We need a debate that takes biological information seriously, including its non-uniformitarian pattern. Causation can be found in Law, Chance and Design, but neither Law nor Chance can deliver complex specified information (here and here). This is why a debate that does not exclude design considerations on ideological grounds is long overdue.

Evolutionary uniformitarianism
Douglas H. Erwin
Developmental Biology, In Press, Available online 27 January 2011

Abstract: I present a new compilation of the distribution of the temporal distribution of new morphologies of marine invertebrates associated with the Ediacaran-Cambrian (578-510 Ma) diversification of Metazoa. Combining this data with previous work on the hierarchical structure of gene regulatory networks, I argue that the distribution of morphologies may be, in part, a record of the time-asymmetric generation of variation. Evolution has been implicitly viewed as a uniformitarian process where the rates may vary but the underlying processes, including the types of variation, are essentially invariant through time. Recent studies demonstrate that this uniformitarian assumption is false, suggesting that the types of variation may vary through time.

Addendum: On the origin of complexity by natural selection
The text below is taken from: Arthur, W. Creatures of accident, New York: Hill and Wang, 2006, pages 118-9.

Like so much about evolution, the production of complexity by natural selection is an accident, or, if you prefer, a by-product. Selection is never trying to achieve anything - it just happens. Because of the nature of the selective process, it inevitably produces adaptation. That is, it causes organisms to have forms and functions that are appropriate to their environment. It does not optimize such forms or functions; rather, it makes the best of a bad job in that it increases the frequency of fitter variants and decreases the frequency of less fit ones. [. . .]
Most selection, most of the time, is probably of this general kind: making limbs more appropriate to the nature of the environment; making beaks more appropriate to the nature of the food supply; and so on. We might call these changes complexity-neutral. But in some small proportion of cases, the thing that is fitter is also more or less complex than the thing it replaces. These, especially the "mores", are the cases on which we must focus our attention.

When first reported, this hominin was given the name Zinjanthropus boisei. He was considered to be a human ancestor and was portrayed as an upright hairy apeman. Later, he was renamed Australopithecus boisei, but then was moved to a separate genus, receiving the name Paranthropus boisei. He still appears in some presentations of human ancestry. What makes him memorable are his magnificent teeth:

"For decades, scientists thought that the large, heavy teeth the primates had were used in cracking open hard foods such as nuts. The common name for Paranthropus was "Nutcracker Man" for this very reason."

This photo of casts of two palates demonstrates the large size of the teeth of Paranthropus boisei (left) known as Nutcracker Man. Much smaller teeth from a human skull are shown on the right. (Credit: University of Arkansas, Melissa Lutz Blouin, source here)

Three years ago, this blog commented on a microwear texture analysis of the molars of seven specimens of P. boisei. The teeth had light wear, suggesting that none of the individuals ate extremely hard or tough foods. In other words, they did not eat nuts! The researchers suggested that the wear pattern was more consistent with modern-day fruit-eating animals.

More recent work has reached a surprising conclusion. P. boisei did not eat fruit but had a diet majoring on grass! This has been discovered by an analysis of carbon-isotope ratios.

"Carbon isotope ratios in tooth enamel can reveal whether ancient animals ate plants that used what is called C3 photosynthesis - trees (and the leaves, nuts and fruits they produce), shrubs, cool-season grasses, herbs and forbs - or plants such as warm-season or tropical grasses and sedges that use what is known as C4 photosynthesis. [. . .] The study found that not only did the Nutcracker Man Paranthropus boisei not eat nuts or other C3 plant products, but dined more heavily on C4 plants like grasses than any other early human, human ancestor or human relative studied to date. Only an extinct species of grass-eating baboon had a diet so dominated by C4 plants. Carbon isotopes showed the 22 individuals had diets averaging 77 percent C4 plants such as grasses, ranging from a low of 61 percent to a high of 91 percent. That's statistically indistinguishable from grass diets of grazing animals that lived at the same time: the ancestors of zebras, pigs and warthogs, and hippos, Cerling says."

How are the enormous teeth to be explained? The researchers have suggested that the high degree of wear observed comes from frequent chewing on foods containing small hard particles - which are, of course, found in C4 grasses. These are known as phytoliths. Although this has not featured in the analysis, this is in tension with the thought that P. boisei was an upright hominin. Grass eaters need to get down to eat - and herbivores generally consume large quantities of food each day. It is significant that the only known primate with a comparable diet was an extinct species of grass-eating baboon.

Furthermore, this discovery "upsets conventional wisdom about early humanity's diet". P. boisei is likely to be a catalyst for fresh thinking about the Australopithecenes - from whom it is considered to have evolved. What interpretation should be placed on the dental features of Australopithecenes?

"Specifically, scientists have believed human ancestors in the genus Australopithecus - which gave rise to now-extinct Paranthropus and to Homo or early humans - also had head and tooth features suggesting they ate hard objects like nuts. Cerling says carbon isotope ratios in australopiths' teeth now should be studied, since the Paranthropus findings bring in to question interpretations that are made without isotopic information on diets."
And from the paper:
"The similarity in dental microwear fabrics among the eastern African australopiths, all of which lack any evidence for hard-object food consumption, is consistent with the notion that their craniodental morphology could reflect "repetitive loading" rather than hard-object consumption."

This research provides another angle on the problems reviewed by Bernard Wood & Terry Harrison (blogged here). It is true that "shared morphology need not mean shared history" but it is also true that shared morphology need not mean shared functionality. Nutcracker Man is a notable example of how morphology was wrongly interpreted for decades and only recently overturned. The problem with "conventional wisdom" is that it has been led by a dogma about the nature of evolutionary transformation from ape-like ancestor to humanity and it is long overdue that this "wisdom" be subjected to some systematic and rational critical scrutiny.

Maybe it will help if this particular fossil hominin gets a new popular name. It was not a nutcracker nor was it a man! It was a specialised (derived) ape that fed primarily on grass and is now extinct. It has nothing to do with human ancestry. Any thoughts on a suitable popular name?

Diet of Paranthropus boisei in the early Pleistocene of East Africa
Thure E. Cerling, Emma Mbua, Francis M. Kirera, Fredrick Kyalo Manthi, Frederick E. Grine, Meave G. Leakey, Matt Sponheimere, and Kevin T. Uno
Proceedings of the National Academy of Sciences, Published online before print May 2, 2011 | doi: 10.1073/pnas.1104627108

Abstract: The East African hominin Paranthropus boisei was characterized by a suite of craniodental features that have been widely interpreted as adaptations to a diet that consisted of hard objects that required powerful peak masticatory loads. These morphological adaptations represent the culmination of an evolutionary trend that began in earlier taxa such as Australopithecus afarensis, and presumably facilitated utilization of open habitats in the Plio-Pleistocene. Here, we use stable isotopes to show that P. boisei had a diet that was dominated by C4 biomass such as grasses or sedges. Its diet included more C4 biomass than any other hominin studied to date, including its congener Paranthropus robustus from South Africa. These results, coupled with recent evidence from dental microwear, may indicate that the remarkable craniodental morphology of this taxon represents an adaptation for processing large quantities of low-quality vegetation rather than hard objects.

See also:

No Nuts for 'Nutcracker Man': Early Human Relative Apparently Chewed Grass Instead, ScienceDaily (May 3, 2011)

Digital codes can be protected against failure. A variety of options have been explored by computer programmers because it is important to catch malfunctions early and alert the user to a problem.

"In digital codes, the bits are usually packed into sets of eight bits called bytes. Normally, seven bits are used to record information and one bit - called the 'parity bit' - is used for mutation protection, usually denoted as error protection. The seven-bit string 1000001, for example, codes the letter A and 0110011 codes the number 3. If the number of 1's in the seven-bit string is even, the parity bit is given the value 1, else the value 0. If one of the seven information bits changes, for instance, by radiation, heat, or mechanical influences, they no longer correspond with the parity bit value; this is detected, an error message is generated, and the program stops, is aborted, or a switch is made towards a back-up."

The word that comes most readily to mind when considering DNA repair mechanisms is sophisticated (source here)

DNA codes are far more sophisticated than their human counterparts, and they also have a variety of repair mechanisms. A recent report of a microbe's "extraordinary maintenance and repair system" drew attention to the striking similarities between the DNA repair systems of bacteria and humans.

"Like council crews repairing damaged roads these DNA repair mechanisms employ individuals with different specialities: sometimes all that is needed is a small patch on the DNA, like filling in a pothole, other times large sections of the DNA need to be removed entirely and replaced. The repair systems need molecular machines that can detect the DNA damage in the first place, machines that can cut away the damaged DNA, and machines that can finish the repair by building new undamaged DNA. All of these molecular machines must work together in an organised fashion to carry out these very intricate repairs, and so they also require machines that take the part of foreman and co-ordinate the work of the others. When DNA is heavily damaged, cells from humans to bacteria ensure the sections that are being read at that moment (in a process called transcription) are repaired before sections that aren't being read. (Source here)"

In a new paper, William DeJong and Hans Degens discuss the implications of DNA repair mechanisms for evolutionary theory. They accompany the discussion with a simulation of a population of digital amoebae experiencing mutation and repair.

"To illustrate the difference between random change of digital and nucleotide codes within the boundaries of mutation protection and unbounded random change, we present a computer simulation of the evolutionary dynamics of a population of digital amoebae."

The findings are of considerable interest. They show that any evolutionary theory which ignores mutation protection is missing out a factor of great importance. The consequence of protection is that limitations of the evolutionary dynamics of digital and nucleotide codes are highly probable.

"Our mutation protection perspective advances the understanding of the evolutionary dynamics of both digital and nucleotide codes. It reveals that random change of digital codes is limited to the variation, recombination, and selection of predefined parameters, operators, or program modules, as a consequence of the normal mutation protection of digital codes that is present at the bit-level and the higher levels of a digital code."

They identify an ambiguity between 'mutational robustness' - that is the persistence of an organismal trait under genetic perturbations - and evolvability. The mutational robustness characteristic is often given the name 'microevolution' whereas evolvability is known as 'macroevolution'. These terms have received attention in the literature of evolutionary biology, but DeYong and Degens have brought the distinction to prominence by showing that only 'mutational robustness' scenarios are consistent with repair mechanisms.

"Unbounded random change of nucleotide codes through the accumulation of irreparable, advantageous, code-expanding, inheritable mutations at the level of individual nucleotides, as proposed by evolutionary theory, requires the mutation protection at the level of the individual nucleotides and at the higher levels of the code to be switched off or at least to dysfunction. Dysfunctioning mutation protection, however, is the origin of cancer and hereditary diseases, which reduce the capacity to live and to reproduce. Our mutation protection perspective of the evolutionary dynamics of digital and nucleotide codes thus reveals the presence of a paradox in evolutionary theory between the necessity and the disadvantage of dysfunctioning mutation protection. This mutation protection paradox, which is closely related with the paradox between evolvability and mutational robustness, needs further investigation."

A video presentation of the article can be found here. The authors have made a significant contribution to thinking about origins. The novelty of the argument is the way they have used simulation to illustrate cogent differences between evolvability and mutational robustness, something that appears to have been lacking in other models of evolutionary processes. Simulation depends, of course, on the validity of the underlying logic and associated parameters. Without the link with the empirical world, simulation models are just games to entertain. The paper shows that all the empirical evidences for evolutionary processes (Darwin's finches, lizard legs, etc) fit into the mutational robustness type of change. We do not have empirical data for evolvability. This is why Darwinists insist that the present is the key to the past and that the small scale changes can be extrapolated to produce novel life forms. The DNA repair argument needs to be answered before they can be allowed to continue with such wishful thinking.

A note to educators and policy makers: is this information that students should consider in their education? Should the Darwinists have the freedom to promote their dogmas without being challenged?

The Evolutionary Dynamics of Digital and Nucleotide Codes: A Mutation Protection Perspective
William DeJong and Hans Degens
Open Evolution Journal, February 2011, 5(1), 1-4 | DOI: 10.2174/1874404401105010001

Abstract: Both digital codes in computers and nucleotide codes in cells are protected against mutations. Here we explore how mutation protection affects the random change and selection of digital and nucleotide codes. We illustrate our findings with a computer simulation of the evolution of a population of self replicating digital amoebae. We show that evolutionary programming of digital codes is a valid model for the evolution of nucleotide codes by random change within the boundaries of mutation protection, not for evolution by unbounded random change. Our mutation protection perspective enhances the understanding of the evolutionary dynamics of digital and nucleotide codes and its limitations, and reveals a paradox between the necessity of dysfunctioning mutation protection for evolution and its disadvantage for survival. Our mutation protection perspective suggests new directions for research into mutational robustness.

See also:

Contradiction in evolutionary theory [video], by INIResearch (19 Apr 2011)

The golden orb-weaver spider features in newly reported research and provides an exciting insight into past ecosystems. Today, these animals adorn tropical rainforests, with giant females of Nephila maculate (legs spanning up to 20 cm), and small males (just a few centimetres across). However, the fossil record of the Nephilidae family is meagre. The earliest example of the genus Nephila comes from the Eocene (considered to be about 34 Ma) and the earliest example of the family Nephilidae is a male from the Cretaceous (considered to be 130 Ma). The newly reported fossil golden orb-weaver spider is a giant female with a leg span of about 15 cm.

"Here, we report the largest known fossil spider, Nephila jurassica sp. nov., from Middle Jurassic (approx. 165 Ma) strata of Daohugou, Inner Mongolia, China. The new species extends the fossil record of the family by approximately 35 Ma and of the genus Nephila by approximately 130 Ma, making it the longest ranging spider genus known."

Nephila jurassica (Credit: Royal Society Biology Letters, P. Selden et al. Source here)

Since all known male fossil nephilids are of normal small size, the large size of the female indicates that sexual dimorphism characterised the Middle Jurassic population (although, as the authors say, confirmation of this awaits the discovery of a male). Of particular interest are some of the fine details preserved in the tuffaceous sedimentary source rock. These include the pedipalps, spinnerets, setal brushes and trichobothria.

"You see not just the hairs on the legs but little things like the trichobothria which are very, very fine. They're used to detect air vibrations. There's a very distinct group of them and they're a very distinct size which is typical of this genus, Nephila," Professor Selden explained.

So this particular living fossil exhibits stasis at the genus level and raises again the issue of what can be learned from the phenomenon of stasis. A previous blog expressed some frustration at Neodarwinian evolutionists who file stasis in a box that says: no environmental change, no selection pressures, no evolution. The problem with this is that so many potentially interesting questions are never asked - and the result is an impoverished science. However, there are evolutionary biologists who think differently, and it is worth considering what an alternative perspective on stasis might look like.

For over a decade, Eric Davidson has been championing the concept of developmental gene regulatory networks (dGRNs) which control ontogeny of the body plan. More than most biologists, he is aware of the significance of different paradigms and how they affect the way we approach the phenomenon of stasis since the Cambrian Explosion. He introduces his latest paper in this way:

"Never in the modern history of evolutionary bioscience have such essentially different ideas about how to understand evolution of the animal body plan been simultaneously current. Of the many different aspects of evolution, we are here to be concerned with how the developmental mechanisms generating the body plan architectures recognized in Linnaen systematics at the level of phylum and class evolve, and how these mechanisms have been maintained, often since the Cambrian or Ordovician. Ideas about the nature of the underlying evolutionary mechanisms, and what to do to study them, generally associate with one of several paradigmatic views."

Davidson considers that the neo-Darwinian paradigm has failed to deliver on its promises and has pursued unjustified assumptions that are in tension with the real world.

"[I]ts fundamental concepts are largely irrelevant to the process by which the body plan is formed in ontogeny. In addition it gives rise to lethal errors in respect to evolutionary process. Neo-Darwinian evolution is uniformitarian in that it assumes that all process works the same way, so that evolution of enzymes or flower colors can be used as current proxies for study of evolution of the body plan. It erroneously assumes that change in protein coding sequence is the basic cause of change in developmental program; and it erroneously assumes that evolutionary change in body plan morphology occurs by a continuous process. All of these assumptions are basically counterfactual."

The phenomenon of stasis is not a quirk of history (i.e. no drivers for transformation) but rather, it requires a genetic explanation. For that, we need to look beyond neoDarwinism to develop a regulatory systems biology.

"The answers lie in the architecture of dGRNs and the developmental logic they generate at the system level, far from micro-evolutionary mechanism. While adaptive evolutionary variation occurs constantly in modern animals at the periphery of dGRNs, the stability over geological epochs of the developmental properties that define the major attributes of their body plans requires special explanations rooted deep in the structure/function relations of dGRNs."

More, of course, needs to be said. The point I am making here is that if stasis is data, we need to take body plans seriously, and also those distinctives associated with Class, Order and Family levels of taxonomy. Some scholars approach these issues open to the thought that body plans really are planned and that intelligent design is the underpinning concept providing integration and coherence. Others do not advocate intelligent design, but are nevertheless committed to working with body plans, developmental logic and regulatory systems. Regarding the science, there is common ground. More comment on Davidson's paper will appear in a future blog.

A golden orb-weaver spider (Araneae: Nephilidae: Nephila) from the Middle Jurassic of China
Paul A. Selden, ChungKun Shih and Dong Ren
Biology Letters, October 23 2011, 7:775-778 | doi:10.1098/rsbl.2011.0228 [Open access]

Abstract: Nephila are large, conspicuous weavers of orb webs composed of golden silk, in tropical and subtropical regions. Nephilids have a sparse fossil record, the oldest described hitherto being Cretaraneus vilaltae from the Cretaceous of Spain. Five species from Neogene Dominican amber and one from the Eocene of Florissant, CO, USA, have been referred to the extant genus Nephila. Here, we report the largest known fossil spider, Nephila jurassica sp. nov., from Middle Jurassic (approx. 165 Ma) strata of Daohugou, Inner Mongolia, China. The new species extends the fossil record of the family by approximately 35 Ma and of the genus Nephila by approximately 130 Ma, making it the longest ranging spider genus known. Nephilidae originated somewhere on Pangaea, possibly the North China block, followed by dispersal almost worldwide before the break-up of the supercontinent later in the Mesozoic. The find suggests that the palaeoclimate was warm and humid at this time. This giant fossil orb-weaver provides evidence of predation on medium to large insects, well known from the Daohugou beds, and would have played an important role in the evolution of these insects.

Evolutionary bioscience as regulatory systems biology
Eric H. Davidson
Developmental Biology, 2011, in press | doi:10.1016/j.ydbio.2011.02.004

Abstract: At present several entirely different explanatory approaches compete to illuminate the mechanisms by which animal body plans have evolved. Their respective relevance is briefly considered here in the light of modern knowledge of genomes and the regulatory processes by which development is controlled. Just as development is a system property of the regulatory genome, causal explanation of evolutionary change in developmental process must be considered at a system level. Here I enumerate some mechanistic consequences that follow from the conclusion that evolution of the body plan has occurred by alteration of the structure of developmental gene regulatory networks. The hierarchy and multiple additional design features of these networks act to produce Boolean regulatory state specification functions at upstream phases of development of the body plan. These are created by the logic outputs of network subcircuits, and in modern animals these outputs are impervious to continuous adaptive variation unlike genes operating more peripherally in the network.

See also:

Fossilised spider 'biggest on record' By Jonathan Amos, BBC News (20 April 2011)

A few years ago, a new fossil cricket species was discovered and named. This year, after the discovery of a second fossil, the specimen was renamed and assigned to the extant genus Schizodactylus of the family Schizodactylidae. It should be noted that no other fossils of this modern family are known.

"Schizodactylidae, or splay-footed crickets, are an unusual group of large, fearsome-looking predatory insects related to the true crickets, katydids and grasshoppers, in the order Orthoptera," said University of Illinois entomologist and lead author Sam Heads, of the Illinois Natural History Survey. "They get their common name from the large, paddle-like projections on their feet, which help support their large bodies as they move around their sandy habitats, hunting down prey."

The new fossil (source here)

We should remind ourselves that the details of classifying genera and species is a matter of human judgment, but the tendency is to consider all differences as significant. There was enough in common to assign the fossil to an extant genus, but it was given a distinct species name.

"The Schizodactylus specimen had features that were different enough from other members of the genus to warrant its own species (Schizodactylus groeningae). For instance, its legs and the lobe-shaped structures on its feet had slightly different shapes than species living today. Even so, its general features differ very little, Heads said, revealing that the genus has been in a period of "evolutionary stasis" for at least the last 100 million years. "It's obviously doing something right," Heads said of the new species and its body plan."

It is of interest to note how living fossils are described. Sometimes, they are "some of evolution's greatest survivors", and the splay-footed cricket is "obviously doing something right". The Economist reporter says that the insect illustrates the "first rule of natural selection": "If it ain't broke, don't fix it." LiveScience took a different view, making the point that the animal has been "stuck in time for the past 100 million years or so". Evolutionary theory wins all ways: if the animals document stasis, then they are fit for their environment and the environment has not changed with time. If they document change, then natural selection is at work, acting on natural variations. Images of the modern cricket are here and here.

The problem with evolutionary theory today is that it finds nothing significant to learn from these examples of stasis. "If it ain't broke, don't fix it" seems to exhaust their mental powers. However, there are a host of issues waiting to be explored: What do these organisms tell us about limits to variation? What can be learned about biological innovation? Can microevolution be extrapolated to macroevolution? Is it realistic to expect environments to show the same stasis as these animals and plants? Living fossils are not just quirky - they are telling us something significant about the biological world. For more, go here.

On the placement of the Cretaceous orthopteran Brauckmannia groeningae from Brazil, with notes on the relationships of Schizodactylidae (Orthoptera, Ensifera)
Sam W. Heads, Lea Leuzinger
ZooKeys, 2011, 77, 17-30 | doi: 10.3897/zookeys.77.769

Abstract: The fossil orthopteran Brauckmannia groeningae Martins-Neto (Orthoptera, Ensifera) from the Early Cretaceous Crato Formation of Brazil, currently misplaced at both the genus and family level, is transferred to the family Schizodactylidae and assigned to the extant genus Schizodactylus Brulle; ergo, Brauckmannia enters synonymy under Schizodactylus and Brauckmanniidae enters synonymy under Schizodactylidae. Schizodactylus groeningae (Martins-Neto), comb. n. agrees in size and general habitus with extant members of the genus, but can be readily separated by the robust, subovoid form of the metatibiae and the distinctive morphology of the lateral metabasitarsal processes. This species represents the first fossil occurrence of Schizodactylidae and the only New World record of this ancient lineage. Phylogenetic relationships of the schizodactylids are reviewed and a sister-group relationship with Grylloidea advocated based on a reappraisal of morphological and molecular evidence.

See also:

Rare Insect Fossil Reveals 100 Million Years of Evolutionary Stasis, ScienceDaily (Feb. 4, 2011)

After trilobites, the most characteristic fossils of the Palaeozoic are known as graptolites. Whereas trilobites lasted throughout that era, the graptolites have been documented (until now) from the Middle Cambrian to the Lower Devonian. They are described as colonial hemichordates, with both benthic and planktonic forms. Although graptolites as a class are extinct, a related group within the phylum hemichordata are extant, with fossil ancestors also going back to the Cambrian Explosion. These animals belong to the class Pterobranchia, and can be described as living fossils. There are about 30 species alive today. Newly published is a report of the earliest and largest hemichordate zooid ever found. It is a pterobranch with the name Galeaplumosus abilus and it is preserved in exquisite detail.

"The 525-million-year-old fossil belongs to a group of tentacle-bearing creatures which lived inside hard tubes. Previously only the tubes have been seen in detail but this new specimen clearly shows the soft parts of the body including tentacles for feeding."

Galeaplumosus abilus (source here)

A modern-day pterobranch genus is Rhabdopleura. An informative description is provided here. Comparing the new fossil and Rhabdopleura leads to the exclamation: "You don't look a day over 500 million years. You and Rhabdopleura could be sisters". The detail has led to comments such as this from co-author Professor David Siveter: "Amazingly, it has exceptionally preserved soft tissues -- including arms and tentacles used for feeding -- giving unrivalled insight into the ancient biology of the group." The significant finding is that the earliest fossil hemichordate zooid looks remarkably similar to Rhabdopleura.

"Galeaplumosus abilus demonstrates stasis in pterobranch morphology, mode of coenecium construction, and probable feeding mechanism over 525 million years."

The phenomenon of stasis is something Darwinists and neo-Darwinists have struggled with. Their theory predicts gradualism, but gradualism is not what the fossil record delivers. Darwinists have sought to evade the evidence by appealing to an impoverished fossil record, but we have reached the stage where this retort must be interpreted as a form of denialism. Stephen Jay Gould declared in 1991 that "Stasis is data" and any theory of Earth history that fails to face up to this data must be abandoned. The conclusion was apparent several decades ago - the following quotations are taken from this source.

Eldredge and Tattersall (1982) wrote: "Darwin's prediction of rampant, albeit gradual, change affecting all lineages through time is refuted. The record is there, and the record speaks for tremendous anatomical conservatism. Change in the manner Darwin expected is just not found in the fossil record."
Gould (1993) wrote: "[S]tasis, or nonchange, of most fossil species during their lengthy geological lifespans was tacitly acknowledged by all paleontologists, but almost never studied explicitly because prevailing theory treated stasis as uninteresting nonevidence for nonevolution. [T]he overwhelming prevalence of stasis became an embarrassing feature of the fossil record, best left ignored as a manifestation of nothing (that is, nonevolution)."

Having said this, it should be pointed out that stasis does not mean absolute fixity. Organisms vary as alleles are shuffled, as was demonstrated by Mendel. More recent work has documented significant epigenetic variability and other causal factors that may or may not be generic. Most examples of "living fossils" are not at the species level, but more often at the genus level of classification. Most, if not all, living fossils can be understood in terms of Mendelian genetics and epigenetics. But Darwinists have approached "stasis" in defensive mode, as though the honour of their hero is at stake. It would appear that the only scientists who can think clearly about the implications of stasis are scientists with reservations about Darwinism! A recent example is Lynn Margulis, the author of the theory of endosymbiosis (some discussion is here). Margulis has been speaking about some of her radical views and the interview appears in Discover for April 2011. This is what she says about Mendelian genetics:

"In the first half of the 20th century, neo-Darwinism became the name for the people who reconciled the type of gradual evolutionary change described by Charles Darwin with Gregor Mendel's rules of heredity (which first gained widespread recognition around 1900), in which fixed traits are passed from one generation to the next. The problem was that the laws of genetics showed stasis, not change. If you have pure breeding red flowers and pure breeding white flowers, like carnations, you cross them and you get pink flowers. You back-cross them to the red parent and you could get three-quarters red, one-quarter white. Mendel showed that the grandparent flowers and the offspring flowers could be identical to each other. There was no change through time. There's no doubt that Mendel was correct."

The changes that we find in the fossil record reveal that something other than Darwinian gradualism is involved. This is what turned Margulis against neo-Darwinism:

"What you'd like to see is a good case for gradual change from one species to another in the field, in the laboratory, or in the fossil record - and preferably in all three. Darwin's big mystery was why there was no record at all before a specific point [dated to 542 million years ago by modern researchers], and then all of the sudden in the fossil record you get nearly all the major types of animals. The paleontologists Niles Eldredge and Stephen Jay Gould studied lakes in East Africa and on Caribbean islands looking for Darwin's gradual change from one species of trilobite or snail to another. What they found was lots of back-and-forth variation in the population and then - whoop - a whole new species. There is no gradualism in the fossil record."

Back to Galeaplumosus abilus which is a Lower Cambrian life form. The research paper declares that it "demonstrates stasis in pterobranch morphology, mode of coenecium construction, and probable feeding mechanism over 525 million years." This organism is found among the pioneers of the Cambrian Explosion. As soon as seawater became calcitic, they could thrive. Although there has been diversification, this has not contributed new biological information, for ancient forms are recognisably the same as their modern counterparts. For more on the Cambrian Explosion, go here.

There are major implications here for education and the importance of doing justice to evidence. Those who want to conceal the problems facing Darwinism must face the charge that they are acting more to defend their adopted paradigm than they are prepared to follow the evidence wherever it leads.

An Early Cambrian Hemichordate Zooid
Xian-guang Hou, Richard J. Aldridge, David J. Siveter, Derek J. Siveter, Mark Williams, Jan Zalasiewicz, Xiao-ya Ma
Current Biology, Volume 21, Issue 7, 612-616, 24 March 2011 | 10.1016/j.cub.2011.03.005

Summary: Hemichordates are known as fossils from at least the earliest mid-Cambrian Period (ca. 510 Ma) and are well represented in the fossil record by the graptolithinid pterobranchs ("graptolites"), which include the most abundantly preserved component of Paleozoic macroplankton. However, records of the soft tissues of fossil hemichordates are exceedingly rare and lack clear anatomical details. Galeaplumosus abilus gen. et sp. nov. from the lower Cambrian of China, an exceptionally preserved fossil with soft parts, represents by far the best-preserved, the earliest, and the largest hemichordate zooid from the fossil record; it provides new insight into the evolution of the group. The fossil is assigned to the pterobranch hemichordates on the basis of its morphological similarity to extant representatives. It has a zooidal tube (coenecium) with banding throughout comparable to that in the extant pterobranchs and a zooid with paired annulated arms bearing paired rows of annulated tentacles; it also displays a putative contractile stalk. G. abilus demonstrates stasis in pterobranch morphology, mode of coenecium construction, and probable feeding mechanism over 525 million years.

See also:

Remarkable Fossil Sea Creature - 525 Million Years Old - Shows Soft Parts of Body Including Tentacles, ScienceDaily (Mar. 28, 2011)

Many portrayals of habitats purporting to represent the Age of Dinosaurs have conifer trees and ferns, but very little ground cover. As palaeontologists continue their research, they are coming to recognise that the ecosystems were much more diverse. The earliest flowering plants are represented by pollen grains and considered to be about 130 Ma years old. However, diversity after this was rapid (see here). Recently, a strikingly beautiful fossil has been reported from China, in the Lower Cretaceous Yixian Formation.

"The fossil shows the above-ground portion of a mature plant. A single stem leads to five leaves, and one leads to a fully developed flower. The entire fossil is about 16 cm (6.3 in) tall. Leaves are innervated by branching veins, and the small, cup-shaped flower has five petals."

"Amazing. It just 'feels' like a modern plant, the whole gestalt is reminiscent of something you'd find in a meadow today." Comment from Per Ahlberg (Image source here).

The fossil remains are of a mature eudicot, a type of flowering plant. A taxonomic analysis of the plant's form has led to the fossil being placed among the Ranunculaceae, a family within the eudicots that includes buttercups and crowroot plants. By all assessments, the description in the journal Nature reveals a "remarkably developed species" rather than a primitive ancestral form. The sedimentary rock preserving this fossil has also yielded several other significant angiosperm species with an age considered to be about 124 Ma.

"This fossil opens up a new way of thinking about the evolution of some of the first flowering plants," said Indiana University Bloomington biologist David Dilcher, the Nature paper's American coauthor. "We are also beginning to understand that the explosive radiation of all flowering plants about 111 million years ago has had a long history that began with the slower diversification of many families of eudicots over 10, perhaps 15 million years earlier."

Some questions deserve to be asked about the phrase "slower diversification of many families of eudicots": if the evolution of the angiosperms was an "abominable mystery" to Darwin, the abrupt appearance of a "remarkably developed" member of the Ranunculaceae, with no earlier fossilised ancestors apart from pollen, deserves to be described as doubly abominable for Darwinism! The buttercup cousin is nothing like an intermediate form, but it has lots of features that are present in extant genera of the Ranunculaceae.

"When we look at the branching relationships of the tree for this group, the Ranunculaceae is at the end of several branches going to the other families, such as the poppies," Dilcher said. "As a result, we believe that prior to 122 to 124 million years ago, several families of flowering plants had already begun to diverge. How much older the eudicots are we do not know yet, but this fossil suggests their origin certainly goes further back in the Cretaceous, perhaps even into the Jurassic."

The earliest record of eudicots comes from fossil pollen dated at 125 Ma. The search is on for earlier body fossils and also for pollen. The problem for Darwinists is that they have no other avenues for interpreting the data. There is no alternative but to adopt the hypothesis of earlier incremental transformations to account for the evolution of angiosperms with subsequent diversification. To maintain credibility, they have to do what Darwin did and invoke the imperfection of the fossil record. But maybe they are pursuing a dream, and the data is actually calling them to wake up!

A eudicot from the Early Cretaceous of China
Ge Sun, David L. Dilcher, Hongshan Wang & Zhiduan Chen
Nature, 471, 625-628. (31 March 2011) | doi:10.1038/nature09811

Abstract: The current molecular systematics of angiosperms recognizes the basal angiosperms and five major angiosperm lineages: the Chloranthaceae, the magnoliids, the monocots, Ceratophyllum and the eudicots, which consist of the basal eudicots and the core eudicots. The eudicots form the majority of the angiosperms in the world today. The flowering plants are of exceptional evolutionary interest because of their diversity of over 250,000 species and their abundance as the dominant vegetation in most terrestrial ecosystems, but little is known of their very early history. In this report we document an early presence of eudicots during the Early Cretaceous Period. Diagnostic characters of the eudicot fossil Leefructus gen. nov. include simple and deeply trilobate leaves clustered at the nodes in threes or fours, basal palinactinodromous primary venation, pinnate secondary venation, and a long axillary reproductive axis terminating in a flattened receptacle bearing five long, narrow pseudo-syncarpous carpels. These morphological characters suggest that its affinities are with the Ranunculaceae, a basal eudicot family. The fossil co-occurs with Archaefructus sinensis and Hyrcantha decussata whereas Archaefructus liaoningensis comes from more ancient sediments. Multiple radiometric dates of the Lower Cretaceous Yixian Formation place the bed yielding this fossil at 122.6 - 125.8 million years old. The earliest fossil records of eudicots are 127 to 125 million years old, on the basis of pollen. Thus, Leefructus gen. nov. suggests that the basal eudicots were already present and diverse by the latest Barremian and earliest Aptian.

See also:

Fossil Is Best Look Yet at an Ancestor of Buttercups, ScienceDaily (Mar. 31, 2011)

We have been told for years that evolutionary biology is pure science and has no religious implications. Theistic evolutionists emphasise the concept of complementarity, pointing out that evolutionary theory seeks to explain how? questions whereas theism is concerned with why? questions. There appear to be many non-theists, including most organisations representing scientists, who say something very similar. These people have adopted the NOMA approach popularised by Stephen Jay Gould. For more on this, go here. However, you do not have to read far in the intelligent design literature (or in the creationist literature) to realise that this approach is controversial. These sources claim that all science has metaphysical presuppositions that are of a religious nature. There is a consistent message coming through - whereas science was first nurtured by scholars with Christian presuppositions, the situation has significantly changed. Since the Enlightenment, science has come to be dominated by the philosophy of naturalism. Happily, some opinion-formers also recognise the validity of this analysis: John Gray has some penetrating comments on this and an excerpt is below.

"As we know it, the secular world-view is simply the Christian take on the world with God left out. Liberal humanism is the contemporary version of an eccentric 19th-century cult - less colourful than its positivist precursor, no doubt, but just as clearly modelled on Christianity. Religious thinkers grasp this and look forward to a post-secular age. Befogged missionaries for a dull Victorian heresy, secular thinkers remain stuck in the past."

Some evolutionists with the mantra "no design, no purpose, no evil and no good, nothing but blind pitiless indifference" find "existential comfort" in rejecting intelligent design. (source here)

The debates about origins have been engineered to present advocates of design as religiously motivated and evolutionary biologists as the champions of facts and evidence. A recent paper authored by psychologists adopts this contrived delineation of the debate as self-evident. Here is the way they introduce the paper:

"Despite overwhelming evidence for Darwin's theory of evolution (ET) and scientific consensus that intelligent design theory (IDT) is inherently unscientific, IDT has received considerable support from the general public, educators, and elected officials. Many schools include IDT in science curricula; 25% of U.S. high-school biology teachers devote at least some class time to the topic, and nearly half of those view IDT as a "valid scientific alternative to Darwinian explanations for the origin of species" [for more on these stats, go here]. Although a Dover, PA, court ruled in 2005 that schools could not include IDT in Pennsylvania science curricula, the debate is far from over."

Since the researchers deduce that the arguments for design can have nothing to do with genuine science, they have sought psychological reasons for the widespread adoption of ID perspectives. This is how they present their hypothesis:

"In the present research, we examined whether implicit concerns stemming from individuals' awareness of their own mortality might be a cause of the widespread support for IDT and corresponding skepticism of ET seen among a wide range of individuals in North America. We tested the hypothesis that heightened mortality awareness would lead individuals to embrace IDT and reject ET; in other words, that shifting one's opinion on these theories is a "terror management" strategy - stimulated by the basic need to maintain psychological security."

So, they constructed a series of experiments that were designed to remind participants of their own mortality, inducing "mortality salience" (MS). Then, the subjects were presented with a passage authored by Richard Dawkins arguing for ET and/or a compilation of comments arguing for IDT linked to the name of Michael Behe. Consequently, an assessment was made of participant views toward the author of each passage and the corresponding theory.

"The researchers carried out five studies with 1,674 U.S. and Canadian participants of different ages and a broad range of educational, socioeconomic and religious backgrounds.
In each study, participants were asked to imagine their own death and write about their subsequent thoughts and feelings, or they were assigned to a control condition: imagining dental pain and writing about that.
The participants were then asked to read two similarly styled, 174-word excerpts from the writings of Behe and Dawkins, which make no mention of religion or belief, but describe the scientific and empirical support for their respective positions.
After going through these steps, participants who imagined their own death showed greater support for intelligent design and greater liking for Behe, or a rejection of evolution theory coupled with disliking for Dawkins, compared to participants in the control condition."

There is much more to the paper than can be captured with a few brief quotations. However, we need to note the conclusions:

From the paper: "In sum, although religious ideology plays a large role in public support for IDT and antagonism toward ET, these attitudes, held by both religious and non-religious individuals, can be partly explained by IDT's potential for assuaging existential anxiety, and ET's apparent lack of an existentially compelling solution to life's origins."
From Science Daily: "Our results suggest that when confronted with existential concerns, people respond by searching for a sense of meaning and purpose in life," says Tracy. "For many, it appears that evolutionary theory doesn't offer enough of a compelling answer to deal with these big questions."

Given their acceptance of "overwhelming evidence" for evolutionary theory, the psychologists go on to consider ways of overcoming the psychological barriers to acceptance of ET. Since this will probably be the focus of wider discussion, this blog points to other implications of the research. Remember that ID scholars are developing scientific responses to the claims of naturalistic science that all phenomena can be explained by a combination of Law and Chance. These scholars are not convinced by the arguments for ET and, in many cases, claim that numerous aspects of ET have already been falsified. What, then, explains the intransigence of evolutionists and their failure to follow through the scientific method they claim to espouse? Why is it that there are so many vocal atheists championing ET? Is there a link between atheism and ET? Returning to John Gray for a moment, does this cast light on his opening comment?

"Religion is a natural human impulse, which our society tries to repress just as the Victorians did sex. That is why atheists are so rancorous and intolerant."

There is great potential for psychologists to turn their telescopes on vocal evolutionists. What made them become vocal? Where do they position themselves in the spectrum of religious views? (Research along these lines will regard atheism as a religious position). Do they use evolutionary science to support their worldview? The reported research confirms that these questions are worth asking, for the authors find that "rejecting IDT can be a source of existential comfort for a limited population of individuals". How might ET advocates react to these statements by Dawkins?

"[A]lthough atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist." (The Blind Watchmaker (1986), page 6)

"Religion teaches the dangerous nonsense that death is not the end." (Religion's Misguided Missiles, September 15, 2001)

"The universe we observe has precisely the properties we should expect if there is, at bottom, no design, no purpose, no evil and no good, nothing but blind pitiless indifference." (River Out of Eden: A Darwinian View of Life, 1995)

If it is true that "evolutionary theory doesn't offer enough of a compelling answer to deal with these big questions", then what might be the reactions of ET's advocates? The answer appears to be that they will dress up their "no design, no purpose, no evil and no good, nothing but blind pitiless indifference" in rather more attractive attire. They will quote more frequently the concluding words of Charles Darwin's magnum opus (but not from the 6th edition!):

"There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved."

We have a growing number of atheistic ET's talking about wonder, mystery and awe at the amazing universe we inhabit. Richard Dawkins set the tone with Unweaving the Rainbow and in various attempts to influence the public understanding of science (see here). Many popularisers of science are following this lead. In the UK we have Professor Brian Cox presenting several series of programmes for the BBC, all characterised by talk of wonder and the thrill of understanding how the universe works. Answers to ultimate questions are hinted at, but take away the hype and we are left with scientism covered by a veneer of existentialism (i.e. we choose to find personal meaning in understanding the science). The psychologists should have plenty of material to work with - but will they apply their skills to deconstruct establishment figures?

Death and Science: The Existential Underpinnings of Belief in Intelligent Design and Discomfort with Evolution
Jessica L. Tracy, Joshua Hart, Jason P. Martens.
PLoS ONE, 2011, 6(3): e17349 | DOI: 10.1371/journal.pone.0017349

Abstract: The present research examined the psychological motives underlying widespread support for intelligent design theory (IDT), a purportedly scientific theory that lacks any scientific evidence; and antagonism toward evolutionary theory (ET), a theory supported by a large body of scientific evidence. We tested whether these attitudes are influenced by IDT's provision of an explanation of life's origins that better addresses existential concerns than ET. In four studies, existential threat (induced via reminders of participants' own mortality) increased acceptance of IDT and/or rejection of ET, regardless of participants' religion, religiosity, educational background, or preexisting attitude toward evolution. Effects were reversed by teaching participants that naturalism can be a source of existential meaning (Study 4), and among natural-science students for whom ET may already provide existential meaning (Study 5). These reversals suggest that the effect of heightened mortality awareness on attitudes toward ET and IDT is due to a desire to find greater meaning and purpose in science when existential threats are activated.

See also:

Death Anxiety Prompts People to Believe in Intelligent Design, Reject Evolution, Study Suggests, ScienceDaily (March 30, 2011)

Predation in the Early Cambrian is demonstrated by the occurrence of borings or drill holes in shelly fauna. Confirmatory evidence has been adduced from gut content analyses, although these evidences could also be attributed to scavenging. However, predation involving shell breakage or crushing has been documented previously only from the late Ordovician. This situation has changed with the published research on Lower Cambrian lingulate brachiopods.

"Here we present the first report of repaired damage to linguliform brachiopod shells caused by durophagous shell-crushing, which is exquisitely recorded from exceptionally preserved specimens in the early Cambrian Wulongqing Formation (Guanshan fauna), Kunming, China. The healed fractures on specimens with preserved thin pedicles unambiguously suggest failed predation attempts. Although they cannot be linked to any specific predators, this record shows that early Cambrian brachiopods experienced predation pressure by unspecified durophagous predators, probably anomalocariids."

Slab containing fossils of Diandongia pista (Source here)

The organism being studied is Diandongia pista, one of the most common species of its type in the Lower Cambrian of South China. It was first studied as a member of the Chengjiang fauna (which is assigned to Stage 3 of the Lower Cambrian). A total of 1150 specimens have been collected for research purposes, none of which have been damaged by predation. The newly reported research is based on a study of fossils of Diandongia pista from the overlying Guanshan fauna (assigned to Stage 4 of the Lower Cambrian). 273 specimens have been collected, 13 of which have non-lethal predatory shell damage and subsequent shell repair. The hypothesis that these features do not signify predation has been examined and rejected.

"However, the possibility of non-predatory causes can be directly rejected with certainty in the specimens described here; the shell damages illustrated from Diandongia cannot have been formed by marginal abrasion of the shell, and the damaged areas are not restricted to anterolateral marginal edge of shell. Evidently, the healed injuries are steeply U or V-shaped, cutting vertically across multiple concentric growth lines, contradicting to the proposed marginal gashes."

These evidences show that the earliest-known record of repaired predatory attack on brachiopods can be assigned to Stage 3 of the Lower Cambrian. The authors infer that predation levels were comparatively very low in the earliest phases of Cambrian brachiopods. Adaptive changes associated with predation are suggested to increase with time, but it is only in the Great Ordovician Biodiversification that it becomes important.

"[T]he emergence and subsequent diversification of smashing/crushing attacks throughout the Cambrian may be the precursor to an Early Palaeozoic marine revolution. Such marine revolutions, attributed to durophage radiations, have been recognized in the Early Cretaceous, and in the Middle Devonian. By the Early Ordovician, brachiopod communities were very different from their Late Cambrian counterparts, and increasing predation pressure from durophages may have been a contributing factor to the proliferation of calcitic-shelled brachiopods in the Ordovician, and possibly to the subsequent infaunal habit of some linguliform taxa, as phosphatic shells were likely insufficient to protect against attacks."

Whilst agreeing with this conclusion of the authors, a design perspective does allow some additional conclusions to be reached. Three of these are outlined below.

1. Drivers of change in the Lower Cambrian. This point is concerned with the Cambrian Explosion and possible drivers of diversification. Darwinian concepts of the struggle for survival have featured strongly in attempts to explain the Cambrian Explosion. However, although predator-prey roles are to be found, the evidence linking these with adaptive change is lacking. Last December, an alternative ecological framework for interpreting this part of the fossil record was discussed (go here for the 4th in the series). The authors introduce their paper by pointing out the importance of this issue in the minds of evolutionary biologists, but then they go on to show evidence that for shell-crushing predation, this selection force was non-existent before Stage 4 of the Lower Cambrian. Some re-evaluation of drivers affecting the Cambrian Explosion is therefore needed.

"Predation has been considered as one of the driving and selective forces in evolution, and thus plays an important macroevolutionary role in marine environments. Coevolution between organisms and their predators had led to an intensification of the struggle for existence and increased complexity of organisms during the Cambrian explosion interval."

2. Evidence of repair mechanisms co-exist with the first appearance of durophagous shell damage. The process of growing a mollusc shell is a remarkable phenomenon in itself, but mechanisms for repairing damaged shells should be regarded as an additional level of complexity. The fossil record does not provide us with a 3-stage story (i.e. no predation by shell breaking - predation without repair - predation accompanied by repair). The Chengjiang fauna document 'no predation by shell breaking'. The "slightly younger" Guanshan fauna documents 'predation accompanied by repair'. This leaves open the issue of the origin of the repair mechanism - did it evolve rapidly under the influence of natural selection? - is this a pointer to design?

"[T]he healed fractures show sets of distinctive drape-like arches of shell repairs, which markedly differs from the marginal concentric secretion of shell complements on scars in the mollusk Marocella described by Skovsted et al. (2007) from the Mernmerna Formation and Oraparinna Shale of South Australia, thus implying that a wider range of shell repair mechanisms evolved in different Cambrian shelly organisms of concentric accretionary growth."

3. When lingulids experienced selection forces associated with predation, they did respond, but remained lingulids. The exquisite preservation of the fossils has allowed soft tissue preservation: the pedicle used to anchor the animal in sediment. Lingulids subsequent to the Cambrian have a muscular pedicle and thick shells, as is appropriate for a burrowing infaunal lifestyle. However, the Lower Cambrian lingulids are different. The pedicles are more delicate and are suggestive of a semi-infaunal lifestyle "with only the pedicle buried in deep sediments for its anchorage and the anterior marginal shell margin tilted upwards". Thus, the Lower Cambrian lingulids were vulnerable to predation and selection pressures favoured animals that buried deeper into the sediments. By the Ordovician, this change was complete, and it never changes again in the fossil record. The stasis in Lingula was noted by Charles Darwin in Chapter XI of On the Origin of Species. He wrote: "The Silurian Lingula differs but little from the living species of this genus; whereas most of the other Silurian Molluscs and all the Crustaceans have changed greatly." (Source here) The case of Lingula is therefore a fascinating one: an abrupt appearance in the Lower Cambrian with a semi-infaunal lifestyle; durophagous-style predation by Stage 4 of the Lower Cambrian; adaptive change to a burrowing infaunal lifestyle followed by stasis (earning the extant Lingula the right to be called a living fossil). This case study illustrates well the empirical evidence relating to the capabilities of natural selection acting on natural variations. There is no sign of the evolution of complexity, but only the fine-tuning of existing complexity.

There are implications here for the study of evolution. The research community needs to be more aware of the limitations of proposed mechanisms (in particular, the Darwinian mechanisms of mutation and natural selection). It is not good enough to point to industrial melanism or Galapagos finches and claim that here is evolution in action! These examples simply do not address the challenge of building biological complexity. As researchers become more aware of the limitations, it will become apparent that the most appropriate context for analysing natural selection is not evolutionary biology - but ecology.

First record of repaired durophagous shell damages in Early Cambrian lingulate brachiopods with preserved pedicles
Zhifei Zhang, Lars E. Holmer, Sean P. Robson, Shixue Hu, Xiangren Wang and Haizhou Wang.
Palaeogeography, Palaeoclimatology, Palaeoecology, 302, (March 2011) 206-212 | doi:10.1016/j.palaeo.2011.01.010

Durophagy, the macro-predatory consumption of hard-shelled organisms, has been proposed as an important driving and selective force ("arms race") responsible for the explosive advent of Cambrian skeleton-bearing animals. Nevertheless, the direct evidence of durophagous predationis mostly restricted to borings or drill holes in skeletons at around the Ediacaran–Cambrian transition. In contrast, pre-ingestive breakage or crushing of shell, another important type of durophagous predation evidence, is very rarely fossilized. Here we present the first evidence of durophagous shell-breaking in an exceptionally preserved pedunculate lingulate brachiopod from the Lower Cambrian Wulongqing Formation (Series 2, early Stage 4), Yunnan, southern China. The repaired shells of Diandongia pista all have elongate (up to 36 mm) pedicles that demonstrate that they survived the failed predation and remained in situ. The bite embayment shows three sets of distinctive drape-like convex arcs of shell repairs, suggesting that the specific drape-like ornamentation usually seen in lingulate shells could be taken as reparative responses to shell damage and malformation. Discovery of sublethal shell damage demonstrates that durophagous predators may have caused an increasing predation pressure on brachiopods since the Canglangpuian Stage (Series 2, Stage 4). In contrast there are no records of durophagous shell-breaking recognized from thousands of Chengjiang (Series 2, Stage 3) specimens of D. pista with fully developed organization of tissues and organ system. It is therefore assumed that that predation was of little importance to the earliest evolution of Cambrian lingulates.

Daniel Brooks is has been living with controversy ever since 1982, when his ideas first appeared in an academic paper, and then when, in 1986, he co-authored with Ed Wiley a book with the title Evolution as Entropy. As well as promoting the idea that evolutionary diversification is to be understood as inevitable because it represents an increase in entropy, he also argued that the theory proposed was an alternative to Neo-Darwinism (widely known as the New Synthesis). In a commentary in Science, Lewin (1982) explained that:

"Responses to the proposal have been mixed and often quite strong. Some consider the theory to be a brilliant insight that will advance evolutionary biology immeasurably. Others vehemently reject it as an ill-founded attack on neo-Darwinism. Curiously, yet others regard it as nothing but neo-Darwinism translated into incomprehensible form. Still others contend that Brooks and Wiley's use of nonequilibrium thermodynamics is untenable in this context."

Evolutionary theories are said to be in the melting pot - but is there a place for design? (Source here)

The background to the 1982 paper was the burgeoning disquiet with Neo-Darwinism. Gould and Eldredge led the way with their assault on gradualism in the fossil record. Brooks recounts his own involvement with a small band of pioneering rebels:

"By 1982, the centenary of Darwin's death, Niles Eldredge and Steven J. Gould had catalyzed a loosely connected group of evolutionary biologists unhappy with the New Synthesis to unleash a cascade of criticisms and proposals. Emboldened by this display of the scientific community at its meritocratic best, Ed Wiley and I entered the fray. The day we finished proofreading Evolution as Entropy, David Hull presciently warned us the fun was over. Soon, I received an envelope from a friend who had seen a manuscript on a colleague's desk. Such privileged material is rarely copied and forwarded. My friend wrote, "I think you and Ed should know what you're up against." The privately circulated manuscript was authored by three academics at the University of California-Berkeley. Ed and I were stunned by its vicious tone. Why the rhetorical heat?"

Intense hostility to new ideas is often because people feel threatened. There is typically more heat than light. Brooks found this an instructive lesson in both the philosophy of science and the sociology of science.

"Hull (1988) proposed that most scientists, regardless of age, don't like new ideas, even ones that support their own worldview ("I already know that, why do I need this?"). They will fight to keep new ideas from becoming accepted unless they benefit their own careers. Ambitious scientists denounce new ideas, co-opting them once the originators have been frightened into silence or to marginal publication outlets. Eldredge's fundamental findings about the nature of the New Synthesis were equally bold - it had all the trappings of a marriage of convenience and none of the appearances of a consensual union. Thus, the status quo reaction to punctuated equilibrium and the other new ideas was a defense of a sociological arrangement, not of a set of scientific principles."

Yet, with the passing of time, with the retirement of senior figures and the entrance of young blood, the landscape of the debate has come to look rather different. Ideas once considered taboo were co-opted into mainstream thought ("we've always believed this"). A willingness to consider alternatives to Darwinism has arrived.

"Again, there are calls for changes in evolutionary theory. This time, the calls are met with celebration - we almost beg for an Extended Synthesis, some new and fresh framework that allows us to celebrate our legacy and add new findings to it. The lack of negative emotion may reflect the co-opting and rebranding of controversial concepts suggested by Brooks and Wiley, Eldredge and Gould, and many others. But again, I think this is an incomplete explanation because it does not explain the positive emotion, which I believe is linked to 1982, through a second atavistic reaction - new life from old, the continuation of life, the extension of life into the future, even notions of renewal and resurrection."

Brooks' search for a way forward led him to the view that Neo-Darwinism differs from Darwinism "on a number of important issues". He refers to the New Synthesis as the "Hardened Synthesis". Nine statements are presented to show the difference between Darwin's view (as expressed in the sixth edition of the Origin) and views held by neo-Darwinians. Brooks argues strongly that changes in evolutionary theory are overdue.

"The eclipse of Darwinism began to end in the 1980s and hangs in the balance today. We need an Extended Synthesis, using "extension" metaphorically. We must extend back in time to recover important aspects of Darwinism that were set aside, then lost during neo-Darwinism, then move forward beyond neo-Darwinism to encompass new data and concepts."

In many ways, this brings us to the beginning of a debate - one which accepts that the neo-Darwinian hegemony on evolutionary theory has to be overthrown and space created for those who are seeking to encompass new data and develop new concepts. Some of us are less optimistic than Brooks that we have reached this stage. Nevertheless, this is the stage which is needed in order to provide a framework for productive discourse about evolutionary biology. ID biologists have constructive things to say on each of Brooks' proposals about the way forward. The reason why these contributions are not welcome is that ID scholars are not materialists and they have concluded that the hallmarks of intelligent design are to be found in nature. Thus, ultimately, objections to ID are not scientific but metaphysical. Failure to appreciate this point will consign the academic world to an impoverished debate which excludes avenues of thought on ideological grounds.

The Extended Synthesis: Something Old, Something New
Daniel R. Brooks
Evolution: Education and Outreach, (March 2011) 4(1), 3-7 | DOI 10.1007/s12052-010-0304-3

Abstract: The eclipse of Darwinism began to end in the 1980s and hangs in the balance today. We need an Extended Synthesis, using "extension" metaphorically. We must extend back in time to recover important aspects of Darwinism that were set aside, and then lost during neo-Darwinism, then move forward beyond neo-Darwinism to encompass new data and concepts. The most comprehensive framework for the Extended Synthesis is the Major Transitions in Evolution. The Extended Synthesis rests comfortably within a philosophical perspective in which biology does not need to be connected with other areas of science in order to justify itself. I am attracted to an older concept in which biology needs a covering law to connect it with the rest of the natural sciences. Darwin implicated a "higher law," but did not specify it. If we can elucidate that law, the Extended Synthesis will become the Unified Theory of Biology called for by Brooks and Wiley 25 years ago.

See also:

Lewin, R. A Downward Slope to Greater Diversity, Science, 24 September 1982, 217, 1239-1240 | DOI: 10.1126/science.217.4566.1239

Earth systems science is concerned with the relationships between the various components that comprise the Earth as a system, notably environmental and biosphere interactions. Over the years, a wide spectrum of views has been expressed by scholars. At one extreme, the environment is the dominant influence, driving evolution within the biosphere (which is interpreted as being largely moulded by environmental forces). As an example, many have considered that changes in seawater chemistry and atmospheric oxygen levels triggered the Cambrian Explosion. At the other extreme, the Earth's environment can be perceived as the product of the biosphere. This is the position of Nicholas Butterfield, who has written a paradigm-shifting essay saying:

"it is clear that animals figure disproportionately in the maintenance of the modern Earth System, not least because they invented it."

Understanding the complexities of the Earth System is at an early stage (Source here.)

Earth systems thinking has a bearing on our approach to the environment. Is the Earth unstable, easily nudged to 'tipping point' and environmental melt-down? Alternatively, is it resilient, with negative feedback mechanisms operating to restore ecosystems to equilibrium? An inherently unstable Earth appears to be the verdict of Lenton and Watson in their book Revolutions that made the Earth (recently reviewed in Nature). They express concern about the effects of human activity that could destabilise our current planetary state. The reviewer draws attention to three other contributions to Earth System thinking:

"Lenton and Watson's thought-provoking book is the latest in a distinguished line of works that have altered our perception of the planet. Russian-Ukrainian geochemist Vladimir Vernadsky first discussed the deep involvement of life in planetary chemistry in his 1926 book Biosfera (Biosphere). In Gaia (Oxford University Press, 1979), James Lovelock brought the self-stabilizing mechanisms of life into view by seeing the planet as a partially self-regulating, living whole. And Hans Joachim Schellnhuber's book-length chapter in Earth System Analysis (Springer, 1998) laid out a blueprint for a scientific discipline concerned with the interplay of social and environmental dynamics."

Central to Butterfield's analysis is the transition from past environments where animals were absent to past environments where animals were plentiful. Animals were absent in the Proterozoic, and their numbers were much reduced after some of the great mass extinction events documented by the rock and fossil record. This is Butterfield's comment:

"In the absence of relatively large-celled eukaryotic phytoplankton, a positive feedback loop of cyanobacteria-induced turbidity is likely to have excluded higher light-demand eukaryotic algae (both phytoplankton and benthic macrophytes) from all but the most oligotrophic or shallow-water marine settings, thereby inducing widespread oceanic stratification. Stratified, bacterially dominated oceans are a signature of the Proterozoic and have generally been viewed in terms of atmospheric oxygen availability. However, without the water-clearing abilities of suspension-feeding animals, there would have been no mechanism for tipping the system out of this condition, irrespective of ambient oxygen. It is simply the default structure of aquatic ecosystems in an exclusively microbial world."

By contrast, oceans with animals are totally different.

"Organism size lies at the core of aquatic ecology and, in the modern ocean, ranges over 20 orders of magnitude, mostly by virtue of the extended trophic tiering of animals. Without such activity, micrometer-sized phytoplankton are not converted to millimeter-sized zooplankton, centimeter-sized zooplanktivorous fish, decimeter-sized piscivores, and so on. [. . .] Significantly, the body-fossil record of large, ornamented and/or biomineralized phytoplankton is limited exclusively to the Phanerozoic, especially in the highly escalated post-Paleozoic oceans, and fossil biomarker molecules point to a fundamental shift in marine export production accompanying the early radiation of animals: from primarily bacterial during the Proterozoic to primarily algal during the Phanerozoic."

The transition took place in the Ediacaran: that window of time between the end of the Precambrian and the beginning of the Phanerozoic. This was the biggest ecological revolution that has been documented in the rock record. Until recently, we had not realised how dramatic the environmental changes were: Butterfield refers to "some of the most pronounced biogeochemical perturbations in Earth history" and to "unprecedented shifts in C and sulfur cycling, iron geochemistry, phosphate deposition and oceanic oxygenation". Even more significant is the question: what was driving these changes? Why did the stratified, anoxic waters of the Proterozoic not persist? Butterfiled rightly questions the consensus view that incremental changes just happened and they were conducive to animal evolution.

"What is missing from such hypotheses, however, is an appreciation of just how pervasive the role of animals has been in defining the modern Earth system. By facilitating and forcing the diversification of, for example, eukaryotic phytoplankton, large body size, bioturbation and biomineralization, early animals reinvented the chemical interchange between the biosphere and planet. In this light, the biogeochemical perturbations of the Ediacaran-Cambrian interval are more likely to be the top-down consequences of animal evolution than its bottom-up cause. Early animals did not simply fill up previously existing but unoccupied niche space; they created the space itself."

If this radical idea is correct, it transforms our approach to ecology. It provides a different perspective on mass extinction events and global recovery:

"One approach is to examine the effects of Phanerozoic mass extinctions, which preferentially eliminate the largest and most specialized animals (and their associated 'ecosystem services'). Mass extinctions differ in their intensity, causes and evolutionary context, but in the oceans they are commonly accompanied by widespread stratification, bottom-water anoxia and spikes in cyanobacterial export. These intermittent returns to pre-Cambrian conditions point strongly to the top-down control not only of phytoplankton diversity, but also Phanerozoic ocean structure in general."

The implications of this new approach for evolutionary theory are not discussed by Butterfield. However, it seems to me that there are many. Most evolutionary biologists are quick to sign up to the importance of environmental changes as a driver for evolution, but the new approach presents much of this environmental change as an effect, not a cause. Modern Darwinists love the adaptive landscape model of evolutionary transformation, but the new approach considers that the "biosphere 'as we know it' is a space designed by metazoans". Environmental changes are frequently suggested to 'trigger' evolutionary transformation, but the hypotheses never get to the stage where they can be tested. Regular readers of this blog will be aware that I have been promoting the idea that the fossil record is not so much a story of evolutionary transformation as a history of the Earth's colonisation (go here for a recent blog on this theme - with links to earlier blogs). This conceptual model interfaces well with Butterfield's proposed Earth System.

"All organisms alter their physical environment to some degree, but the unique attributes of animals makes them particularly powerful 'ecosystem engineers'. Simply as a consequence of their motility, metazoans mix, ventilate and chemically alter the media though which they move. Such bioturbation is all but ubiquitous in modern soils and soft sediments, and imparts a first-order control over everything from sediment composition to landscape topography and biogeochemical exchange."

Animals and the invention of the Phanerozoic Earth system
Nicholas J. Butterfield
Trends in Ecology & Evolution, 26(2), February 2011, 81-87 | doi:10.1016/j.tree.2010.11.012

Abstract: Animals do not just occupy the modern biosphere, they permeate its structure and define how it works. Their unique combination of organ-grade multicellularity, motility and heterotrophic habit makes them powerful geobiological agents, imposing myriad feedbacks on nutrient cycling, productivity and environment. Most significantly, animals have 'engineered' the biosphere over evolutionary time, forcing the diversification of, for example, phytoplankton, land plants, trophic structure, large body size, bioturbation, biomineralization and indeed the evolutionary process itself. This review surveys how animals contribute to the modern world and provides a basis for reconstructing ancient ecosystems. Earlier, less animal-influenced biospheres worked quite differently from the one currently occupied, with the Ediacaran-Cambrian radiation of organ-grade animals marking a fundamental shift in macroecological and macroevolutionary expression.

See also:

Lucht, W., Earth systems: Shaped by life, Nature, 470, 460-461 (24 February 2011) | doi:10.1038/470460a

The last decade has witnessed three contenders for the title: earliest identifiable human ancestor. These are Ardipithecus, Orrorin and Sahelanthropus. All of them generated great excitement at the time of their discovery and, for many, they were evidence that the lineage of the human genus was being clarified. However, those willing to read research papers (rather than media reports) were more aware that the research community was not of one mind about the significance of these fossil remains. Recently, Wood and Harrison have contributed a major review paper that revisits these arguments and finds that the various claims for human ancestry are not rigorous. They offer alternative explanations for these three fossil hominines.

"In their paper, Wood and Harrison caution that history has shown how uncritical reliance on a few similarities between fossil apes and humans can lead to incorrect assumptions about evolutionary relationships. They point to the case of Ramapithecus, a species of fossil ape from south Asia, which was mistakenly assumed to be an early human ancestor in the 1960s and 1970s, but later found to be a close relative of the orangutan." (source here)

Listed as Breakthrough of the year 2009, but we do need to ask - "is Ardi a man and a brother?" (source here)

The key arguments are presented in a section of their paper entitled: "Shared morphology need not mean shared history". They refer, in particular, to three anatomical characteristics. The first is concerned with canine morphology, the second with the location and orientation of the foramen magnum, and the third with features of the pelvis and other bones that have implications for bipedalism. These character traits have been prominent in discussions of the significance of Ardipithecus, Orrorin and Sahelanthropus. The problem identified by Wood and Harrison is homoplasy, where the same biological trait appears in unrelated lineages. Homoplasy leads to false homologies. The authors express their concerns in this way:

"The important point is that shared similarities can only take one so far in determining phylogenetic relationships, because homoplasy, as well as uncertainties in determining the polarity of character transformation, have the potential to generate substantial noise that serves to confound attempts to generate reliable hypotheses about relationships. These considerations have clear implications for generating hypotheses about the phylogenetic position of Ardipithecus, Sahelanthropus and Orrorin. Even if these taxa share some derived features with later Pliocene hominins, it would be rash simply to assume that those features are immune from homoplasy, especially when other aspects of their respective phenotypes are consistent with a more distant relationship with the hominin clade."

There is also concern expressed about the 'linear' model of human evolution that seems to be promoted by some zealous researchers. There is no reason why a linear trajectory should be expected. A year ago, Harrison published a paper drawing attention to the remarkable diversity of fossil apes from the Miocene with a great variety of character traits. This is the complexity which needs to be recognised by researchers.

"There is no reason why higher primate evolution in Africa in the past ten million years should not mirror the complexity observed in the evolutionary histories of other mammals during the same time period. Nor is there any reason, especially with the lessons from Ramapithecus and Oreopithecus fresh in the minds of researchers, to assume that hominins should not be prone to the same limitations and uncertainties of phylogenetic analysis as other fossil primates."

What about Ardi? The authors views were clearly presented in a blog for Scientific American.

"I think it's equally likely, or perhaps even preferable, that it is an ancestral form or an early representative of the African great ape" group - that "it's not necessarily uniquely linked to humans," Harrison said of Ardipithecus [. . .].
Some of the most solid evidence for Ardi being included in the hominin branch is her small canine teeth. But the researchers are quick to point out that other ancient non-hominin species, including Oreopithecus and Ouranopithecus, also came to have reduced canine teeth, "presumably as a result of parallel shifts in dietary behavior in response to changing ecological conditions," the researchers suggest in their article. "Thus, these changes are in fact, not unique to hominins."
The placement of a hole at the base of the skull, known as the foramen magnum, also might suggest Ardi as an upright walker, and thus perhaps a solid hominin. But in looking to other apes, "this feature is more broadly associated with differences in head carriage and facial length, rather than uniquely with bipedalism," Wood and Harrison note. Some extinct primates, such as Oreopithecus bambolii, evolved outside of the human line but nevertheless possessed similarly hominin-like traits, which, the authors write, "encourage researchers to generate erroneous assumptions about evolutionary relationships."

A helpful overview of the issues is provided by by Brian Switek in his Laelaps blog. Significantly, he uses the title "Ancestor Worship", which captures the reasons for the way these fossil finds are hyped up. Science News succeeded in communicating the strong feelings accompanying this academic debate: "Researchers have to stop publishing papers that say, essentially, 'This fossil is an early hominid, so suck it up and accept it'," Wood says. "Nature and Science could change this practice overnight if they wanted to."
The other side of this controversy is represented by Tim White, champion of Ardi. His comments reveal a stubborn resistance to the message of the paper:

"With no new data, no new ideas, no new methods, no new hypothesis, no new experiments, no new fossils, not even a new classification, this paper will leave everybody wondering what's happened to the peer review process at Nature," White says.

What is to be made of all this? Wood and Harrison are comfortable with the big picture - the pattern of relationships between humans and the great apes as revealed by molecular evidence. Their concern is to inject more caution into the analysis and reporting of new fossil material. Researchers need to be alert to convergent evolution, unrelated to ancestry. A previous blog drew attention to the way the fossil record of human evolution can be likened to a pointillist painting (here) and this analogy still seems relevant. We have lots of data points, but only when we stand back does a picture emerge. However, the picture that emerges reflects very much what we bring as observers. When we expect an evolutionary story, it is possible to see one, but proving that there really is an evolutionary story is quite another matter.

The evolutionary context of the first hominins
Bernard Wood & Terry Harrison
Nature, 17 February 2011; 470, 347-352 | DOI: 10.1038/nature09709

Abstract: The relationships among the living apes and modern humans have effectively been resolved, but it is much more difficult to locate fossil apes on the tree of life because shared skeletal morphology does not always mean shared recent evolutionary history. Sorting fossil taxa into those that belong on the branch of the tree of life that leads to modern humans from those that belong on other closely related branches is a considerable challenge.

See also:
Bower, B. Human Ancestors Have Identity Crisis, Science News (February 17, 2011)

Fossils May Look Like Human Bones: Biological Anthropologists Question Claims for Human Ancestry, ScienceDaily (Feb. 16, 2011)
tm

Harmon, K. Was "Ardi" not a human ancestor after all? New review raises doubts, Scientific American (Observations blog, Feb 16, 2011).

Switek, B. Ancestor Worship, Laelaps (February 22, 2011)

The journal Nature drew attention to concerns about the Templeton Foundation's activities on the occasion of the death of John Templeton in 2008. At that time, the editors indicated that "human moral impulses" have a natural, rather than a spiritual explanation and that their stance is to "turn away from religion in seeking explanations for how the world works". That editorial elicited a blog from me, pointing out that many funding bodies have agendas that can raise suspicions of advocacy rather than following the evidence wherever it leads.

"This publication [i.e. Nature] would turn away from religion in seeking explanations for how the world works, and believes that science is likely to go further in explaining human moral impulses than some religious people will welcome. Thus it shares a degree of suspicion with many in the scientific community at any attempt by religiously driven organizations to fund science. A chief concern is that the influential Templeton Foundation might be seeking to inject religion into the scientific world."

Templeton priorities: then and now (Source here)

Now, Nature has revisited the topic in a news feature authored by Mitchell Waldrop, one of their US editors. The Templeton Foundation logo has the phrase "Supporting science - Investing in the Big Questions". This claim to be the friend of science is not accepted in some quarters - which is why Waldrop asks: "So why does it make so many researchers uneasy?" First witness is Jerry Coyne, evolutionary biologist, who calls the foundation "sneakier than the creationists". Through its grants to researchers, Coyne alleges, the foundation is trying to insinuate religious values into science. "It claims to be on the side of science, but wants to make faith a virtue," he says. This is countered by the testimony of Michael Shermer, editor of Skeptic and recipient of a Templeton grant: "The Templeton Foundation has never in my experience pressured, suggested or hinted at any kind of ideological slant".

Apparently, starting before and continuing since the death of its founder, the Foundation has been "radically reframing its research programme". According to Waldrop, "it is reducing its emphasis on religion to make its programmes more palatable to the broader scientific community." As evidence of this, look at the way the Templeton Prize for Progress in Religion has been used. When first introduced in 1973, the award winners were not scientists. The first time a scientist received this award was in 1985. Now, it is normal to award it to a scientist. The critical witness for this is Harold Kroto:

"The prize has come in for some academic scorn. "There's a distinct feeling in the research community that Templeton just gives the award to the most senior scientist they can find who's willing to say something nice about religion," says Harold Kroto, a chemist at Florida State University in Tallahassee, who was co-recipient of the 1996 Nobel Prize in Chemistry and describes himself as a devout atheist."

The change of emphasis came because of the perception that the word "religion" was alienating too many senior scientists. These people were suspicious and whatever the Foundation did, failed to ease the suspicions. Vocabulary was changed and the Foundation presented itself as supporting science and sponsoring research into the Big Questions of life. (See the word clouds above - larger image here). Waldrop summarises the change in this way:

"This prompted a rethink of the foundation's research programme - a change most clearly seen in the organization's new website, launched last June. Gone were old programme names such as 'science and religion' - or almost any mention of religion at all. Instead, the foundation has embraced the theme of 'science and the big questions' - an open-ended list that includes topics such as 'Does the Universe have a purpose?'"

The Templeton Foundation is interested in meaning and purpose in the Cosmos, but definitely not in intelligent design. Although some ID advocates have received Templeton money in the past, this has proved so embarrassing to the Foundation that the door is now firmly closed. In the FAQ section of the Templeton website, the question is asked: Does the Foundation support "intelligent design"? The answer given is as follows:

"No. We do not support the political movement known as "intelligent design," which denies large areas of well-documented scientific knowledge in evolutionary biology. As a matter of policy and in keeping with our legal status, we do not support or endorse political movements of any kind."

This description is way off the mark. ID scholars are not waging a political battle, but are engaged in these issues as scientists, philosophers or educators. Those who oppose what they are saying do not interact with their arguments but invent strategies to discount them without acknowledging there are issues needing discussion. Unfortunately, the Templeton Foundation has imbibed the falsehoods of ID opponents and have closed down avenues of enquiry "as a matter of policy" instead of being open to the evidence wherever it leads.

The Foundation still faces the wrath of those who oppose ID. Here is Jerry Coyne again:

"Religion is based on dogma and belief, whereas science is based on doubt and questioning," says Coyne, echoing an argument made by many others. "In religion, faith is a virtue. In science, faith is a vice." The purpose of the Templeton Foundation is to break down that wall, he says - to reconcile the irreconcilable and give religion scholarly legitimacy.

The Templeton Foundation is deluded if it thinks it can win over these scientists by taking a stand against ID. The key to the problem is readily found in the writings of ID scholars: science has been hi-jacked by "devout atheists" like Coyne and Kroto. They base their arguments on obsolete positivist views of science that are blind to the metaphysical presuppositions that scientists bring to their work. The secularisation of science has become dominant amongst the leaders of science organisations and journals. Dissent about this issue is not tolerated. Only purely material explanations of the universe are allowed: talk of spirituality, consciousness and morality are acceptable as long as it is understood these characteristics are all products of material forces. One more witness:

"Yet, even scientists who give the foundation high marks for openness often find it hard to shake their unease. Sean Carroll, a physicist at the California Institute of Technology in Pasadena, is willing to participate in Templeton-funded events - but worries about the foundation's emphasis on research into 'spiritual' matters. "The act of doing science means that you accept a purely material explanation of the Universe, that no spiritual dimension is required," he says."

Unless the Templeton Foundation grapples with the secularism that threatens the scientific enterprise, it will slowly retreat from the real issues and end up, as Waldrop notes, as a funding agency with "a certain New Age quality". That will be sad.

Faith in science
M. Mitchell Waldrop
Nature 470, 323-325 (16 February 2011) | doi:10.1038/470323a

First para: At the headquarters of the John Templeton Foundation, a dozen kilometres outside Philadelphia, Pennsylvania, the late billionaire seems to watch over everything. John Templeton's larger-than-life bust stands at one end of the main conference room. His life-sized portrait smiles down from a side wall. His face peers out of framed snapshots propped on bookshelves throughout the many offices.

One of the pleasures of walking through a wood is hearing the distant drumming of woodpeckers. We know they are searching for food, but few of us grasp the extraordinary nature of their achievement. Drumming rates of about 20 impacts per second are normal, with decelerations of 1200 g, and the drumming sessions may be repeated 500-600 times per day. By contrast, humans can lose consciousness when experiencing 4-6 g and are left concussed with a single deceleration of about 100 g. The authors of a recent analysis of the woodpecker's shock-absorbing mechanism describes it as "advanced" and "special". By looking at video material of drumming and CT scans of the bird's head and neck, they found four structures that absorb mechanical shock:

"These are its hard-but-elastic beak; a sinewy, springy tongue-supporting structure that extends behind the skull called the hyoid; an area of spongy bone in its skull; and the way the skull and cerebrospinal fluid interact to suppress vibration." (source)

Golden-fronted Woodpecker (source here)

Informed by these findings, the research sought to mimic these characteristics and construct a system that could protect micromachined devices from high-g impacts.

"To mimic the beak's deformation resistance, they use a cylindrical metal enclosure. The hyoid's ability to distribute mechanical loads is mimicked by a layer of rubber within that cylinder, and the skull/cerebrospinal fluid by an aluminium layer. The spongy bone's vibration resistance is mimicked by closely packed 1-millimetre-diameter glass spheres, in which the fragile circuit sits."

To test out their shock-absorbing material, they used a 60 mm air gun capable of generating scenarios of 60,000 g. For comparison, a hard resin shock absorbing system was used (representing current state-of-the-art technology). They fired micromachined devices and checked them for damage. They found that the hard resin system protected up to 40,000 g but 26.4% were damaged at 60,000 g. By contrast:

"In the bio-inspired shock absorbing system, almost all the micromachined devices survived at a high-g mechanical excitation of 60,000 g. This is because high-frequency mechanical excitations corresponding to the resonance frequencies of the micromachined devices are absorbed by the bio-inspired shock-absorbing system and even the transmitted mechanical excitations are detoured around the micromachined devices."

The researchers are understandably pleased with their new shock-absorbing system, and already the work is creating interest - with many diverse application areas (see Marks). Of particular interest here is the way woodpecker drumming has stimulated this research and has provided the conceptual model for developing the biomimetic system. The authors refer to the conventional Darwinian framework for understanding design in nature:

"Nature causes some traits that aid survival and reproduction to become commoner, and makes other traits that hinder them to become rarer; all creatures in nature are believed to be perfectly equipped with biological features over successive generations through natural selection."

If this is the much-vaunted role of Darwinism underpinning biology, then it is not impressive. When the designs make the organism "perfectly equipped", Darwinism is the explanation; when the designs are 'imperfect' and 'cobbled together', Darwinism is the explanation. Whatever the evidence, Darwinism has the answer! Yet, when the power of natural selection to select characters is studied, it does not appear very effective at all. Whether it is finch beaks or peppered moths, the classic proofs of the power of natural selection do not take us very far. The suggestion that natural selection acting on successive generations of woodpeckers is a convincing explanation of all the adaptations necessary for the birds to engage in drumming must be challenged. What we have here is a complex and sophisticated system of interrelated traits. Natural selection does not begin to address the assembly of such an exquisite design. The only way we know such systems can be assembled is, like the researchers' new shock-absorbing system, by intelligent design.

A mechanical analysis of woodpecker drumming and its application to shock-absorbing systems
Sang-Hee Yoon and Sungmin Park
Bioinspiration & Biomimetics, 6(1), 2011, 016003 | doi: 10.1088/1748-3182/6/1/016003

Abstract: A woodpecker is known to drum the hard woody surface of a tree at a rate of 18 to 22 times per second with a deceleration of 1200 g, yet with no sign of blackout or brain damage. As a model in nature, a woodpecker is studied to find clues to develop a shock-absorbing system for micromachined devices. Its advanced shock-absorbing mechanism, which cannot be explained merely by allometric scaling, is analyzed in terms of endoskeletal structures. In this analysis, the head structures (beak, hyoid, spongy bone, and skull bone with cerebrospinal fluid) of the golden-fronted woodpecker, Melanerpes aurifrons, are explored with x-ray computed tomography images, and their shock-absorbing mechanism is analyzed with a mechanical vibration model and an empirical method. Based on these analyses, a new shock-absorbing system is designed to protect commercial micromachined devices from unwanted high-g and high-frequency mechanical excitations. The new shock-absorbing system consists of close-packed microglasses within two metal enclosures and a viscoelastic layer fastened by steel bolts, which are biologically inspired from a spongy bone contained within a skull bone encompassed with the hyoid of a woodpecker. In the experimental characterizations using a 60 mm smoothbore air-gun, this bio-inspired shock-absorbing system shows a failure rate of 0.7% for the commercial micromachined devices at 60 000 g, whereas a conventional hard-resin method yields a failure rate of 26.4%, thus verifying remarkable improvement in the g-force tolerance of the commercial micromachined devices

See also:

Marks, P. Woodpecker's head inspires shock absorbers, New Scientist (4 February 2011)

As the Urey-Miller model of abiogenesis has grown weaker with time, interest in extra-terrestrial sources of amino acids has increased. The phrase "building blocks of life" is well-used: in 2005, space.com referred to amino acid precursors formed "in the winds of dying stars and spread all over interstellar space"; in 2008, National Geographic used the phrase when reporting on the detection of a precursor of glycine in the galaxy Arp 220. In December 2010, Nasa reported the presence of 19 amino acids in a carbon-rich meteorite and commented: "Finding them in this type of meteorite suggests that there is more than one way to make amino acids in space, which increases the chance for finding life elsewhere in the Universe." Clearly, these sources are promoting the idea that finding amino acids provides a significant part of an abiogenesis solution. This is also the message picked up by the world's media, which dutifully (and uncritically) passes on the hype.

(Source here)

One of the first challenges to be faced when assembling the "building blocks of life" comes from chirality. Of the 20 amino acids found in the biosphere, all except glycine can exist as a left-handed form or a right-handed form. Natural processes generate racemic mixtures, where left-handed and right-handed forms are in equal quantities. In living things, however, only the left-handed forms are found: the L-isomer. This phenomenon (known as an enantiomeric excess) has long been a puzzle to abiogenesis researchers. Some have concluded it was an accident: there is no reasoned explanation of the cause. Those favouring a source of amino acids from space have noted that some meteorites have yielded non-racemic mixtures. Many have not found the argument convincing: Moran provides some reasons. First, the flux of amino acids today is far too small to act as a foundation for a theory of origins. Second, even allowing favourable figures for higher quantities of amino acids in the past, the conclusion is unchanged. Third, racemisation occurs with time, resulting in 50/50 mixtures of left-handed and right-handed forms. Moran cites a paper Bada published in 1991, concluding that chance must be invoked.

"Because of the problem of racemization, it is likely that only after biotic protein synthesis became an efficient process in the evolution of early life could the chirality of amino acids be maintained in proteins. Instead of amino acid chirality preceding the origin of life, it may have developed after life was well established, and possibly in close association with the origin of protein biosynthesis. As to why the protein amino acids consist only of the L-enantiomers, it is probably just a matter of chance."

Notwithstanding all this, papers continue to be published that seek natural causes for producing non-racemic amino acids. The latest reports "the first abiotic cosmic ice simulation experiments that produce species with enantiomeric excesses". For some time, people have anticipated that circularly polarized ultraviolet light might disturb the equilibrium between L- and D-forms. This has now been confirmed. The paper's conclusions are related directly to models of abiogenesis:

"This result, directly comparable with some L excesses measured in meteorites, supports a scenario in which exogenous delivery of organics displaying a slight L excess, produced in an extraterrestrial environment by an asymmetric astrophysical process, is at the origin of biomolecular asymmetry on Earth."

The paper is accompanied by a press release and the media have taken an interest. BBC News carried a report.

"This excess is pretty cool," Dr Glavin [from Nasa] told BBC News. "You've got to break the symmetry somehow, this is critical. But how do you break it? That's one of the most important questions: did life just randomly choose one type over another? It's starting to look like Nature helped a bit."

A welcome critique has come from Larry Moran, who describes their abiogenesis scenario as "nonsense". His first objection to the Primordial Soup model is that amino acid concentrations are far too low (already noted above). Secondly, he asks - what happens next? This is not a trivial question! What processes are going to turn this sterile "broth" into proteins and more? People have spent years working on possible routes and have come up with nothing convincing.

"Instead of trying to prove that asteroids could carry a slight excess of L-amino acids, I wish these workers would apply a bit of healthy skepticism to the subsequent steps of the scenari