Science Literature

The mollusc, known as the scaly-foot gastropod, has been known for about a decade. It was discovered living in the deep sea near the Kairei Indian hydrothermal vent field on the Central Indian Ridge. The natural environment for the animal is harsh. There are extremes of temperatures, high pressures and high acidity levels that can easily damage shells of calcium carbonate. Brachyuran crabs live in the vicinity and these "are known to compress gastropod mollusc shells between their chela" with loads of up to 60N.

"To understand how the valiant gastropod holds up to these trials, Christine Ortiz of MIT and her colleagues used nanoscale experiments and computer simulations to dig in to the shell's structure. Many other species' shells exhibit what Ortiz calls "mechanical property amplification," in which the whole material is hundreds of times stronger than the sum of its parts."

The scaly-foot gastropod uses a unique trilayered shell to protect itself from hazards. (Image credit: Anders Waren, Swedish Museum of Natural History. Source here)

Most exoskeletal structures are technically known as multilayered composites. The parameters are the layer thicknesses, the nano- and microstructure of each layer, the number of layers, the sequence of layers, etc. Each species appears to have its own resultant profile.

"Design, inspired by nature, of engineering materials with robust and multifunctional mechanical properties [i.e., those which sustain a variety of loading conditions] is a topic of major technological interest in a variety of civilian and defense applications. Here, we identify the design principles of the shell of a gastropod mollusc from a deep-sea hydrothermal vent [order Neomphalina, family Peltospiridae, species Crysomallon squamiferum]. This system has a trilayered structure unlike any other known mollusc or any other known natural armor, with a relatively thick compliant organic layer embedded between two stiffer mineralized layers, an outer iron sulfide-based layer and an inner calcified shell."

The outer layer is about 30 micrometres thick and is mineralised: it contains iron sulphide particles (greigite, Fe2S4). This gastropod is the only metazoan known to employ iron sulphide as a skeletal material. The middle layer is about 150 micrometres thick and is thought to be the periostracum (the template for shell mineralization, providing protection against corrosive and dissolutive marine environments, and also chemical protection from boring organisms). The inner layer is composed of aragonite that is itself layered:

"[It] possesses a gradient layer [. . .] with a typical crossed lamellar layer (CLL) microstructure (approximately 50 [micro]m thick), followed by a relatively thick layer also with a CLL microstructure (approximately 200 [micro]m thick, followed by a thin prismatic layer (PL) on the inner surface of the shell (approximately 1.5 [micro]m thick)."

This structure has been studied empirically and modelled. Simulations were performed to understand how the shell responds to impacts and applied loads. There are too many details to document here.

"It is interesting to see how C. squamiferum has created these additional different protection mechanism compared to other gastropod molluscs by using materials plentiful and specific to the deep-sea hydrothermal vent environment, i.e., vent fluids rich in dissolved sulfides and metals.
The design principles of the trilayered shell of C. squamiferum exhibit many aspects that are different from the highly calcified shells of typical gastropod molluscs or any other natural armor. Each material layer serves distinct and multifunctional roles leading to many advantages."

Design principles have emerged from this research. The authors have found new design features leading to enhanced functional performance. "Each material layer serves distinct and multifunctional roles leading to many advantages". They point out that design principles are extremely important because there are so many variables: "The design space for synthetic multilayered structural composites for protective applications is enormous". The great merit of biological systems is that they provide a chart to steer through this space. However, the authors attribute design in biological systems to an "evolutionary process".

"Biological systems, such as the one described here, greatly reduce the engineering design space since efficient threat-protection design concepts have emerged through the lengthy evolutionary process that fulfill the necessary functions and constraints."

The problem with this evolutionary framework is that it has no empirical validity. We have no warrant for explaining design principles via evolutionary processes. The authors explain that they do not know whether the observed design "represents an advanced functional adaptation as an antipredatory response or an exaptation (i.e., a trait that evolved to serve one function, but subsequently and simultaneously may serve other functions)". This comment is, unfortunately, entirely typical of the culture prevailing in science produced by philosophical materialism. Evolutionists have supreme confidence in their theoretical framework, but do not seem to see the need to constrain theory by reference to empirical data. Observed adaptations do not demonstrate the emergence of design concepts. The only sources of design concepts that we know of are intelligent agents. Replacing the culture of materialism by one that integrates information inputs with physics and chemistry is long overdue.

With this alternative culture, paragraphs like the following take on a new richness of meaning:

"In particular, the efficient natural armor structural system described here sustains both mechanical loading, as well as thermal fluctuations with inherent mechanisms to prevent catastrophic failure. The multimaterial, trilayer design and advantageous curved geometry enables structural stiffening, reduction of radial displacements, penetration resistance, and stability during thermal impulses even with the presence of large mismatches between constituent materials. Trilayered sandwich composite designs have had limited use in military applications, and the concepts reported here could lead to bioinspired improvements and broader applicability and improved performance for human, vehicle, and structural armor."

Protection mechanisms of the iron-plated armor of a deep-sea hydrothermal vent gastropod
Haimin Yao, Ming Dao, Timothy Imholt, Jamie Huang, Kevin Wheeler, Alejandro Bonilla, Subra Suresh, and Christine Ortiz
Proceedings of the National Academy of Sciences, January 19, 2010, vol. 107, no. 3, 987-992 | doi:10.1073/pnas.0912988107

Abstract: Biological exoskeletons, in particular those with unusually robust and multifunctional properties, hold enormous potential for the development of improved load-bearing and protective engineering materials. Here, we report new materials and mechanical design principles of the iron-plated multilayered structure of the natural armor of Crysomallon squamiferum, a recently discovered gastropod mollusc from the Kairei Indian hydrothermal vent field, which is unlike any other known natural or synthetic engineered armor. We have determined through nanoscale experiments and computational simulations of a predatory attack that the specific combination of different materials, microstructures, interfacial geometries, gradation, and layering are advantageous for penetration resistance, energy dissipation, mitigation of fracture and crack arrest, reduction of back deflections, and resistance to bending and tensile loads. The structure-property-performance relationships described are expected to be of technological interest for a variety of civilian and defense applications.

See also:

Grossman, L. Snail In Shining Armor, Science News, February 13th, 2010; Vol.177 #4 (p. 13)

Spider silk has been an active area for biomimetics research for several years. Spinoff companies have been launched in anticipation of commercial gains. However, despite the enthusiasm and commitment of research staff, the prizes are still elusive. Whilst the main goal is to produce fibres that are as strong and as flexible as spider silk, there are other aspects of the natural material that have attracted the interest of researchers. One of these concerns the ability of webs to be a site for dew collection.

"When Lei Jiang first observed the phenomenon, he was intrigued. "How does that happen?" he wondered. After all, he says, "if you took a human hair, water would not stick to it like that". His initial curiosity led to an almost five-year-long study. The findings could have implications for the design of materials for water collection and for the efficiency of chemical reactions."

Spider silk manipulates water with skill (source here)

Not only do webs attract dew, the droplets are able to hang stably on the silk fibres. This suggests the presence of a microstructural mechanism. All polymeric fibres have a microstructure and spider silk is no exception. SEM images reveal a series of amorphous regions (called puffs) and crystalline regions (called joints). The nanofibrils are highly hydrophilic: enhancing wettability and favourable for condensing dew. The puffs have a very open structure and are semi-transparent in images. However, when water starts to condense, the puffs shrink - first to "opaque bumps" and then to "spindle-knots". As they shrink, tiny water droplets coalesce to form larger drops with movement from joints to spindle-knots.

"Further work revealed that movement of the droplets towards the knots is directed by two forces acting together: the force generated by a gradient of surface energy on the fibrils and the one produced by the spindle shape of the knots. "This is quite different from other reported surfaces, on which drops are driven just by individual forces," says Jiang."

These findings are stimulating human invention. The research paper reports success with nylon filaments that are coated with a hydrophilic material that dries in tiny knots similar to those found in spider silk. The goal now is to produce something of commercial value.

"These observations clearly show that our artificial spider silk not only mimics the structure of wet-rebuilt spider silk but also its directional water collection capability. We therefore anticipate that the design principles uncovered and implemented in this study will aid the development of functional fibres for use in water collection and in liquid aerosols filtering in manufacturing processes."

Why does the spider produce a web with dew-gathering potential? "The researchers are unsure of why the spider has evolved to possess this ability. "It could be for its drinking activities, or it could be to refresh the web structure to make it stronger and stickier for prey," Jiang told physicsworld.com." Magdalena Helmer wrote a short News & Views piece on "Dew catchers", saying: "spiders don't need to look for water because the silk fibres that they spin are highly efficient at collecting it from moist air". However, direct evidence of functionality is lacking. There is considerable scepticism that spiders make any use of dew-gathering.

"But Fritz Vollrath, who studies spider silk at Oxford University in the UK, disagrees with Jiang's theory. He thinks spider silk has to be dry to function. 'If I am correct, then the authors are studying an artefact, which is still interesting, although it has no biological function,' says Vollrath. [. . .] Brent Opell, a spider expert at Virginia Tech in Virginia, US, is equally cautious about the results, although he says the experimental work is sound. 'The implication that [capture] threads have evolved to harvest moisture is not the view of most arachnologists,' he says."

Is there an ID perspective on this? Wherever researchers recognise "design principles" in the natural world, the answer is, of course, 'yes'. The presumption with ID is that design features imply functionality, whether or not we know the details. Dew gathering is a unique and remarkable feature of spider silk simply because other fibres do not display such behaviour. The authors comment:

"We observed such directional water collection behaviour only with wetted silk fibres (that is, wet-rebuilt silk) from the cribellate spider Uloborus walckenaerius; in contrast, silkworm silk and nylon fibres with a uniform structure did not exhibit the directional water collection phenomenon."

Whether evolutionists can explain 'how the spider came to gather dew' is more uncertain. Even with functionality identified, perfecting this highly engineered system makes it most reasonable to infer intelligent, rather than natural, causation.

Directional water collection on wetted spider silk
Yongmei Zheng, Hao Bai, Zhongbing Huang, Xuelin Tian, Fu-Qiang Nie, Yong Zhao, Jin Zhai & Lei Jiang
Nature, 463, 640-643 (4 February 2010) | doi:10.1038/nature08729

First paragraph: Many biological surfaces in both the plant and animal kingdom possess unusual structural features at the micro- and nanometre-scale that control their interaction with water and hence wettability. An intriguing example is provided by desert beetles, which use micrometre-sized patterns of hydrophobic and hydrophilic regions on their backs to capture water from humid air. As anyone who has admired spider webs adorned with dew drops will appreciate, spider silk is also capable of efficiently collecting water from air. Here we show that the water-collecting ability of the capture silk of the cribellate spider Uloborus walckenaerius is the result of a unique fibre structure that forms after wetting, with the 'wet-rebuilt' fibres characterized by periodic spindle-knots made of random nanofibrils and separated by joints made of aligned nanofibrils. These structural features result in a surface energy gradient between the spindle-knots and the joints and also in a difference in Laplace pressure, with both factors acting together to achieve continuous condensation and directional collection of water drops around spindle-knots. Submillimetre-sized liquid drops have been driven by surface energy gradients or a difference in Laplace pressure, but until now neither force on its own has been used to overcome the larger hysteresis effects that make the movement of micrometre-sized drops more difficult. By tapping into both driving forces, spider silk achieves this task. Inspired by this finding, we designed artificial fibres that mimic the structural features of silk and exhibit its directional water-collecting ability.

Making the paper: Lei Jiang
Nature, 463, 586 (4 February 2010) | doi:10.1038/7281586a

Abstract: Spider silk structure holds secret to catching water as well as flies.

See also:

Birch, H. How spider silk soaks up water, Chemistry World (3 February 2010)

Dacey, J. Spider web inspires fibres for industry, physicsworld.com (3 February 2010)

Helmer, M. Dew catchers, Nature, 463, 618 (4 February 2010) | doi:10.1038/463618a

Two research psychologists have contributed an Opinion paper based on the empirical finding "that individuals presented with unfamiliar moral dilemmas show no difference in their responses if they have a religious background or not". The data used was obtained from an online web questionnaire which is open to any volunteer participants (including myself). Findings are reported elsewhere and in their Opinion paper the authors provide only a summary:

"These studies, carried out using the web-based Moral Sense Test (http://moral.wjh.harvard.edu/), recruit thousands of male and female subjects, with educational levels that range from elementary school to graduate degrees, with political affiliations that range from liberal to conservative, and religious backgrounds that range from devout to atheist. In each of these studies, subjects read and judged the moral permissibility of an action on a 7pt-Likert scale [. . .]. Each scenario presented a contrast between a harmful action and a significant benefit in terms of lives saved."

Moral dilemmas come in all shapes and sizes (source here)

The hypothetical scenarios in the test present dilemmas where actions that are evidently harmful to human life considered in isolation result in significant benefits to other humans (whose lives are saved). The generalized results are as follows:

"More specifically, in dozens of dilemmas, and with thousands of subjects, the pattern of moral judgments delivered by subjects with a religious background do not differ from those who are atheists, and even in cases where we find statistically significant differences, the effect sizes are trivial."

This conclusion is the anchor-point for the author's wide-ranging discussion of the origin of morality and, as indicated in their title, the origin of religion. In evaluating their paper, we need to consider whether their empirical starting point is robust enough to carry such far-reaching conclusions.

Some caution is needed in the way "religious background" is understood. There is no systematic probing of the concept in the web-based questionnaire. Participants have to select a label that best fits their current religion, the religion of their upbringing, and locate themselves on the spectrum of "not-at-all" religious to "very" religious. This is all pretty superficial and subjective, given the diversity of religious experience around the world. There is no attempt to use Likert scales to assess the degree to which respondents understood God to be a creator, transcendent, immanent, able to answer prayer or, even more relevant, the reference point for our sense of right and wrong. Consequently, the term "religious" is 1-dimensional and almost devoid of content. Yet, the authors place considerable weight on their analysis of responses gathered.

More caution is needed when we read in the above quote about "trivial" effect sizes. In another study the authors mention, radical altruism was the focus of interest: does religious background affect thinking about whether to sacrifice ones own life "in order to save the lives of a greater number of anonymous others". Significant differences were found. But these could be predicted, say the authors, "given the fact that many religions praise martyrdom". They go on to offer this analysis:

"[A]lthough there are significant evolutionary pressures against such acts of radical altruism, religious pressures might lead people to offer this judgment because they believe it is the morally appropriate answer. What religion can do, and what political and legal institutions can do as well, is alter local and highly specific cases. And yet, they appear to have no influence at all on the intuitive system that operates more generally, and for unfamiliar cases."

These comments about the need for caution are intended to show that the authors have a very inadequate view of the concept of "religion". To them, the various religions can all be lumped together and there are no distinctions worth making. They do not see the need to explain why they think that radical altruism can somehow be linked to the praise of martyrdom. Even when differences are discernable between the moral judgments of the religious and those of atheists, they are considered trivial apparently because there are (untested) evolutionary explanations of why the religious are so minded. All this raises questions about the adopted methodology and the analysis of the authors.

Before making further comments on the arguments built on the empirical findings, it is useful to note some comments by Philip Ball, writing a column for Nature. He draws attention to the conceptual framework underpinning the research: "By taking it as a given that religion is an evolved social behaviour rather than a matter of divine revelation, [the authors' paper] tacitly adopts an atheistic framework." Ball is absolutely right, and we can add the thought that tacit atheism is a pervasive problem in many areas of scholarly activity. Given their presuppositions, no one should expect the authors to reach a conclusion that challenges atheism. However, this does not mean such conclusions cannot be drawn by others who approach the same data with a different conceptual framework.

The first thesis developed in the paper is that "moral intuitions operate independently of religious background" and are therefore not explained by religion. The authors develop an analogy with linguistics, where the concept of innate ability for language acquisition is widely held, and this innate ability is independent of the cultural background. Ball describes this thesis in this way:

"The paper [ . . ] challenges the assertion commonly made in defence of religion: that it inculcates a moral awareness. If we follow the authors' line of thinking, religious people are no more likely to be moral than atheists."

Whenever there is only one hypothesis on the table, there should be concern! Scholars should be cultivating multiple working hypotheses and looking for ways of testing them. To show the significance of an alternative conceptual framework, consider a perspective that understands mankind as made in the image of its Designer. Innate abilities are imparted by this Designer: we speak because the Designer speaks; we have a moral awareness because the Designer is the reference point for what is right and what is wrong. These innate abilities affect all people - whether they are atheists or religious, whether they are pantheists or theists, whether they are male or female, young or old. This is a hypothesis that explains the data and scholars who "tacitly adopt[] an atheistic framework" are excluding this alternative purely on ideological grounds.

The second thesis is concerned with the origin of religion. The authors think their work on moral intuitions leads naturally to the hypothesis that religion is a by-product of pre-existing capabilities.

"Specifically, recent work in moral psychology supports the view that religion evolved as a cognitive by-product of pre-existing capacities that evolved for non-religious functions."
[. . .]
"Religion is a set of ideas that survives in cultural transmission because it effectively parasitizes other evolved cognitive structures."
[. . .]
"Here again, religion stands on the shoulders of cognitive giants, psychological mechanisms that evolved for solving more general problems of social interactions in large, genetically unrelated groups."

For the purposes of this blog, we shall defer comment and let Philip Ball speak: "Whether it [i.e. the research] 'explains' religion is another matter."

"It's debatable, however, whether these moral tests are probing religion or culture as a moral-forming agency, because non-believers in a predominantly religious culture are likely to acquire the moral predispositions of the majority. Western culture, say, has long been shaped by Christian morality. [. . .] But to uncover religion's roots, is morality necessarily the best place to look? It seems hard to credit the idea that the immense cultural investment in religion was made merely to strengthen and fine-tune existing neural circuits related to morality. [. . .] Yet attempting to explain the origins of such a rich cultural phenomenon as religion is doomed to some extent to be a thankless task. For to 'explain' Chartres Cathedral or Bach's Mass in B Minor in terms of non-kin cooperation is obviously to have explained nothing."

The origins of religion: evolved adaptation or by-product?
Ilkka Pyysiainen and Marc Hauser
Trends in Cognitive Sciences, 14(3), 104-109, March 2010 | doi:10.1016/j.tics.2009.12.007

Abstract: Considerable debate has surrounded the question of the origins and evolution of religion. One proposal views religion as an adaptation for cooperation, whereas an alternative proposal views religion as a by-product of evolved, non-religious, cognitive functions. We critically evaluate each approach, explore the link between religion and morality in particular, and argue that recent empirical work in moral psychology provides stronger support for the by-product approach. Specifically, despite differences in religious background, individuals show no difference in the pattern of their moral judgments for unfamiliar moral scenarios. These findings suggest that religion evolved from pre-existing cognitive functions, but that it may then have been subject to selection, creating an adaptively designed system for solving the problem of cooperation.

Morals don't come from God
Philip Ball
Nature, 8 February 2010 | doi:10.1038/news.2010.55

Abstract: The finding that religion scarcely influences moral intuition undermines the idea that a godless society will be immoral, says Philip Ball. Whether it 'explains' religion is another matter.

See also:

Morality Research Sheds Light on the Origins of Religion, ScienceDaily (9 February 2010)

Hunter, C. Important New Paper on Evolutionary Explanation, Darwin's God (8 February 2010)

It is well known that Darwin speculated on what might happen in "some warm little pond" (previously discussed here). But it was not until 1929 that J.B.S. Haldane developed a testable hypothesis involving a "prebiotic broth, or primordial soup". He proposed that organic compounds were made when methane, ammonia and water reacted as a result of energy supplied by ultraviolet radiation. The reaction products were suggested to have accumulated in a "hot dilute soup" in the primeval earth. In this scenario, further reactions led to macromolecules, protocells and then life.

"Backed up by Stanley Miller's (1953) inorganic synthesis of organic molecules in the laboratory, it seemed to generations of scientists that Haldane's narrative was basically right, and all that was left was to sort out the details."

It is time to move on from this unproductive research (source here)

Miller's experiments became an icon of naturalistic evolution and entered the textbooks with very little critical analysis of the findings. Even recently, Miller's work was acclaimed in the journal Science. Happily, there are opportunities to get beyond the hype but, as Jonathan Wells showed in his Icons of Evolution, these contributions rarely get beyond the technical literature. William Martin and colleagues have presented a strong case for retiring the primordial soup concept from active service. It has reached the grand old age of 81 and, as a hypothesis, it has not been confirmed. Normally, when hypotheses are tested and found wanting, they are discarded - but we are now overdue for this to happen with the primordial soup. It is "well past its sell-by date".

Two reasons are provided in the paper. The first is that a soup of organic chemicals will be in thermodynamic equilibrium. The reaction products are already present and there is no obvious source of energy to drive polymerisation or any other significant change. "Ionizing UV radiation inherently destroys as much as it creates."

"[T]he homogeneous soup has no internal free energy that would allow them to react further. Life is not just about replication; it is also a coupling of chemical reactions - exergonic ones that release energy and endergonic ones that utilise it, preventing the dissipation of energy as heat. It is commonplace to say that life requires energy, but the conception of a primordial soup fails to recognise or incorporate the importance of energy flux. On the congruence principle, what life needed was not some harsh and problematic source of energy like UV radiation (or lightning), but a continuous and replenishing source of chemical energy."

The second reason concerns fermentation as the primordial mechanism of energy generation in a world without oxygen. Haldane promoted this idea, and De Duve supported it as the mechanism for sustaining anaerobic life. "If there can be said to be a textbook view, this is it."

"But there are profound difficulties - both chemical and biological - in viewing fermentation as primitive rather than derived. Fermentation is chemically a disproportionation - not a simple redox reaction, in which electrons are stripped from a donor and passed onto an acceptor, driven by strong thermodynamics. In contrast with respiration, the amount of energy released by fermentation is tiny, reflecting its lack of thermodynamic driving force. To tap such an insignificant source of energy requires more rather than less sophistication, and indeed about 12 enzymes are needed to catalyse a complex succession of steps in glycolytic-type fermentations based around the Embden-Meyerhoff pathway. These enzymes are proteins encoded by genes, which would have had to evolve as a functional unit without any other source of energy in the primordial oceans - close to an impossibility in an RNA world, let alone the only way to evolve one."

The authors go on to defend their view that fermentation is a sophisticated, rather than a primordial, derivation. This brings them to the crunch question:

"But if there was no soup, and no energy from UV radiation or fermentation, then where was the energy that powered the emergence of life?"

They go on to propose alkaline hydrothermal vents as the primordial source of energy for life. They develop their idea that the origin of life can be considered distintly from the origin of replication. They support Russell et al's (1993) proposal that chemiosmosis is "an inherent property of life, one inherited from the very place and space where it arose". Their paper is exploratory, not plotting out any details of what the Last Universal Common Ancestor (LUCA) looked like, but considering how chemiosmosis might have worked in the setting of alkaline hydrothermal vents. Further discussion of this is needed, of course, but this blog is to draw attention to the challenge these authors present to OOL researchers generally and to textbook authors/educators.

"It is time to cast off the shackles of fermentation in some primordial soup as 'life without oxygen' - an idea that dates back to a time before anybody had any understanding of how ATP is made - and to embrace the most revolutionary idea in biology since Darwin as the key not only to the bioenergetics of all life on Earth today, but to its very origin.(80) Thus it seems to us likely that LUCA grew on the H2/CO2 couple, and that she was naturally chemiosmotic."

How did LUCA make a living? Chemiosmosis in the origin of life
Nick Lane, John F. Allen, William Martin
Bioessays, Published Online: Jan 27 2010 | DOI: 10.1002/bies.200900131

Despite thermodynamic, bioenergetic and phylogenetic failings, the 81-year-old concept of primordial soup remains central to mainstream thinking on the origin of life. But soup is homogeneous in pH and redox potential, and so has no capacity for energy coupling by chemiosmosis. Thermodynamic constraints make chemiosmosis strictly necessary for carbon and energy metabolism in all free-living chemotrophs, and presumably the first free-living cells too. Proton gradients form naturally at alkaline hydrothermal vents and are viewed as central to the origin of life. Here we consider how the earliest cells might have harnessed a geochemically created proton-motive force and then learned to make their own, a transition that was necessary for their escape from the vents. Synthesis of ATP by chemiosmosis today involves generation of an ion gradient by means of vectorial electron transfer from a donor to an acceptor. We argue that the first donor was hydrogen and the first acceptor CO2.

See also:

New Research Rejects 80-Year Theory of 'Primordial Soup' as the Origin of Life, ScienceDaily (3 February 2010)

Warren, D. Back to the beginning, The Ottawa Citizen (6 February 2010)

Two years ago, "the most primitive bat known" was reported in Nature. It was not primitive in its wings and body, but "the morphology of the ear region suggests that it could not echolocate, making it a possible intermediate link between bats and their non-flying, non-echolocating mammalian ancestors". At the time, the find was suggested to settle the question as to which came first: flight or echolocation? The answer was a definite flight first.

"The problem of understanding bat evolution dates back at least to Charles Darwin, who in The Origin of Species enumerated a list of difficulties he saw with the theory of evolution by natural selection. The example often discussed is the origin of the eye. But Darwin also mentioned the vexed issue of how bats had arisen from terrestrial ancestors." Speakman 2008).

Onychonycteris finneyi was featured on the cover of Nature in February 2008 (Source here)

This assessment of the fossil must now be reappraised. New work on modern-day bats has revealed another mechanism of echolocation. One of the authors described the work thus:

"We borrowed 35 specimens from the Royal Ontario Museum in Toronto and performed micro-computed tomography on them. This imaging technique allowed us to see the fine details of the bats' ear and throat regions: the larynges, stylohyals and tympanic bones. Previous work had relied on dissecting these bones, a challenge in animals as small as bats. We found that the fusion or connection of two bone structures - the stylohyal bone in a bat's throat and the tympanic bone in the ear region of its skull - was a feature of all laryngeally echolocating bat species we studied."

This finding is new and unexpected. It means that previous conclusions need to be reappraised. This is exactly what is happening with the "most primitive fossil bat".

"The relatively small cochleae and lack of paddle-like expansions on the cranial tips of the stylohyal bones have been interpreted as evidence that O. finneyi lacked laryngeal echolocation, which supports the hypothesis that flight evolved before echolocation. However, we find that articulation between the stylohyal and tympanic bones is a better predictor of laryngeal echolocation ability than the shape of the stylohyal bone, at least among extant bats. If the stylohyal bones articulated with the tympanic bones in O. finneyi, then we propose that this species had the capacity for laryngeal echolocation. Our results thus reopen basic questions about the timing of the appearance of echolocation and flight in the evolution of bats."

There are several lessons to be learned here - and one of these is to always be prepared to hold judgment on the word "primitive" - even if it is said to be the "most primitive"!

A bony connection signals laryngeal echolocation in bats
Nina Veselka, David D. McErlain, David W. Holdsworth, Judith L. Eger, Rethy K. Chhem, Matthew J. Mason, Kirsty L. Brain, Paul A. Faure & M. Brock Fenton
Nature 463, 939-942 (18 February 2010) | doi:10.1038/nature08737

Echolocation is usually associated with bats. Many echolocating bats produce signals in the larynx, but a few species produce tongue clicks. Here, studies show that in all bats that use larynx-generated clicks, the stylohyal bone is connected to the tympanic bone. Study of the stylohyal and tympanic bones of a primitive fossil bat indicates that this species may have been able to echolocate, despite previous evidence to the contrary, raising the question of when and how echolocation evolved in bats.

Last year, a workshop was hosted by the International Society of Protistologists at their North American Section Meeting. The workshop was given the title "Horizontal Gene Transfer and Phylogenetic Evolution Debunk Intelligent Design". Some of the presentations have recently been published, and one of these is the focus of attention here. One does not get beyond the first paragraph before finding that the authors regard Neodarwinism as robust and that all challengers have abandoned science:

"Despite the overwhelming body of evidence that supports the basic tenets of evolution (i.e. common descent of organisms with different forms being the result of natural selection acting upon naturally occurring variation), there is a large proportion of the American population that does not accept the validity of what is perhaps the most rigorously tested scientific hypothesis in history."

The "six" kingdom taxonomic scheme (Image from Purves et al., source here)

The second paragraph points the finger at Dr Michael Behe and his influential books Darwin's Black Box and The Edge of Evolution. Although the paper covers much ground, it is one of Behe's arguments that engage their attention.

"In his book "The Edge of Evolution: The Search for the Limits of Darwinism" Behe (2007) draws heavily upon the example of drug resistance in the malarial parasite Plasmodium falciparum as one biochemical pathway that is supposedly too complex to have arisen through natural evolutionary processes. According to Behe (2007), the odds that mutations required to impart chloroquine resistance in Plasmodium could arise naturally are so impossibly long that they lie beyond what he considers "The Edge of Evolution".

Anyone who has read Behe's book and understands his analysis would be alerted at this point to a wearying straw man argument. If you are going to critique someone, you ought to, at least, be able to paraphrase their arguments correctly. One wonders why the workshop participants did not put the authors right. In addition, one wonders why the referees did not point out the need for correction. But further, one wonders why the journal editor did not invite peer review from an ID microbiologist. Certainly, the peer review system failed on this occasion. Happily, the internet does allow misinformation to be corrected, and Behe has posted comments which show that the authors, instead of "dispelling the myths of Intelligent Design" are actually promoting myths about Intelligent Design. Here are Behe's concluding words:

"To recap, several years after The Edge of Evolution was published a scientific society held a workshop to demonstrate the book's errors. Yet they couldn't even get the book's argument straight, and the experimental work they cited against my argument is not even pertinent to it. Apparently the design argument drives some scientists so much to distraction that they lose their normally robust powers of reasoning."

Clearly, there is more to be said about the underlying issues. In the abstract of the paper, ID advocates are said to have the goal of "challenging the philosophy of scientific materialism". This is a good place to start an analysis of the issues: because scientific materialism needs to be challenged. Science has no basis for concluding that matter is all there is and that all causation is natural. Those who claim this are importing an ideology that was absent in the early days of science (when the pioneers were theistic scientists, who were quite comfortable with the thought that the natural world is designed). People with different ideologies look at the same data in different ways, and protagonists who do not recognise this are spreading more heat than light. My fear is that instead of discarding this paper as based on false premises, blind crusaders for philosophical materialism will hail it as "excellent article" and will add it to their list of peer reviewed publications showing that the ID approach is bankrupt.

Using Protistan Examples to Dispel the Myths of Intelligent Design
Mark A. Farmer and Andrea Habura
Journal of Eukaryotic Microbiology, 57(1), 2010, 3-10 | doi 10.1111/j.1550-7408.2009.00460.x

ABSTRACT: In recent years the teaching of the religiously based philosophy of intelligent design (ID) has been proposed as an alternative to modern evolutionary theory. Advocates of ID are largely motivated by their opposition to naturalistic explanations of biological diversity, in accordance with their goal of challenging the philosophy of scientific materialism. Intelligent design has been embraced by a wide variety of creationists who promote highly questionable claims that purport to show the inadequacy of evolutionary theory, which they consider to be a threat to a theistic worldview. We find that examples from protistan biology are well suited for providing evidence of many key evolutionary concepts, and have often been misrepresented or roundly ignored by ID advocates. These include examples of adaptations and radiations that are said to be statistically impossible, as well as examples of speciation both in the laboratory and as documented in the fossil record. Because many biologists may not be familiar with the richness of the protist evolution dataset or with ID-based criticisms of evolution, we provide examples of current ID arguments and specific protistan counter-examples.

Misusing Protistan Examples to Propagate Myths about Intelligent Design
Michael J. Behe
Uncommon Descent, 15 February 2010

Introductory sentences: The Journal of Eukaryotic Microbiology recently published several papers from a workshop sponsored by the International Society of Protistologists entitled "Horizontal Gene Transfer and Phylogenetic Evolution Debunk Intelligent Design." So here we have a respected scientific society, presumably planning a workshop months in advance, and finally laying out their considered case for why intelligent design fails. As you might imagine, I was most anxious to read about it. Unfortunately, rather than scholarly papers, the manuscripts read like press releases from the National Center for (Darwinian) Science Education.

Much to the dismay of the BADs (Birds Are Dinosaurs), there is a group of scientists who are in denial of the thesis that theropod dinosaurs evolved into birds. Furthermore, this BAND of scholars (Birds Are Not Dinosaurs) have published in the esteemed PNAS and not in some obscure low-ranked journal. The research was concerned with the dromaeosaurid Microraptor gui, which was first described in 2002 and has flight feathers on all four limbs. The research team modelled M. gui flight and concluded that gliding was its forte.

"We suggest that Microraptor was an adept glider and would have had little difficulty gliding from tree trunk to tree trunk or climbing trees, but would have been very awkward and vulnerable on the ground. The primary feathers on the tarsometatarsus (foot) of the hindwing of M. gui were too long in relation to the limb bones to have allowed the hindwing to fold compactly as does the modern bird wing. Just as colugos and sloths have their limbs encumbered by patagia, the hindwing feathers on Microraptor would severely hamper any terrestrial locomotion."

John Ruben draws attention to an image drawn in 1915 by naturalist William Beebe. It suggests a hypothetical view of what early birds may have looked like, gliding down from trees - and it bears a striking similarity to a fossil discovered in 2003 that is raising new doubts about whether birds descended from ground-dwelling theropod dinosaurs (Source here)

In an accompanying commentary, John Ruben reviewed the history of the controversy over the origins of bird flight. Much to the disapproval of the BADs, Ruben presents those skeptical of the cursorial, ground-upwards hypothesis as scholars who have championed reasoning from evidence. The new research, Ruben suggests, favours gliding, arboreal proto-birds. But he also suggests that some more radical thinking may be warranted:

"So, is the answer, after all, a hybrid of the two old theories, i.e., avian origins from an arboreal, gliding theropod dinosaur? Perhaps, but then this is paleobiology - very recent data suggest that many clearly cursorial theropods previously thought to have been feathered may not have been so and that dromaeosaurs, the group that birds are assumed to have been derived from, may not even have been dinosaurs. What pops up next is anyone's guess."

The Science Daily report points to these more fundamental divergences of view:

The weight of the evidence is now suggesting that not only did birds not descend from dinosaurs, Ruben said, but that some species now believed to be dinosaurs may have descended from birds.
"We're finally breaking out of the conventional wisdom of the last 20 years, which insisted that birds evolved from dinosaurs and that the debate is all over and done with," Ruben said. "This issue isn't resolved at all. There are just too many inconsistencies with the idea that birds had dinosaur ancestors, and this newest study adds to that."

Breaking out of the conventional wisdom? Yes - we need some more of that!

Paleobiology and the origins of avian flight
John Ruben
Proceedings of the National Academy of Sciences, published online before print February 9, 2010 | doi:10.1073/pnas.0915099107

First sentence: Interpreting the paleobiology of long extinct taxa, pesky new fossils, and reinterpretations of well-known fossils, sharply at odds with conventional wisdom never seem to cease popping up.

Model tests of gliding with different hindwing configurations in the four-winged dromaeosaurid Microraptor gui
David E. Alexander, Enpu Gong, Larry D. Martin, David A. Burnham, and Amanda R. Falk
Proceedings of the National Academy of Sciences, Published online before print January 25, 2010 | doi: 10.1073/pnas.0911852107

Abstract: Fossils of the remarkable dromaeosaurid Microraptor gui and relatives clearly show well-developed flight feathers on the hind limbs as well as the front limbs. No modern vertebrate has hind limbs functioning as independent, fully developed wings; so, lacking a living example, little agreement exists on the functional morphology or likely flight configuration of the hindwing. Using a detailed reconstruction based on the actual skeleton of one individual, cast in the round, we developed light-weight, three-dimensional physical models and performed glide tests with anatomically reasonable hindwing configurations. Models were tested with hindwings abducted and extended laterally, as well as with a previously described biplane configuration. [. . .] Although the biplane model glided almost as well as the other models, it was structurally deficient and required an unlikely weight distribution (very heavy head) for stable gliding. Our model with laterally abducted hindwings represents a biologically and aerodynamically reasonable configuration for this four-winged gliding animal. M. gui's feathered hindwings, although effective for gliding, would have seriously hampered terrestrial locomotion.

See also:

Bird-from-Dinosaur Theory of Evolution Challenged: Was It the Other Way Around?, ScienceDaily (Feb. 10, 2010)

Deyes, R. B.A.R.B: Birds Are Really.....Birds!, ARN Literature Blog (25 June 2009)

Tyler, D. Did birds fly in the Late Triassic? ARN Literature Blog (16 June 2009)

Professor Steve Fuller is known as a prolific author whose analysis of the scientific enterprise is iconoclastic. He was famously involved as a defense witness in the Kitzmiller v. Dover Area School District (2005) trial, for which he has received a great deal of flak. The essay cited below provides an explanation of his involvement and a challenge for other qualified people to ensure that their voices are heard.

"I believe that tenured historians, philosophers, and sociologists of science - when presented with the opportunity - have a professional obligation to get involved in public controversies over what should count as science. I stress 'tenured' because the involved academics need to be materially protected from the consequences of their involvement, given the amount of misrepresentation and abuse that is likely to follow, whatever position they take."

Why are so few willing to follow this advice? (Source here)

Those who want to read specific comments on the trial should read the essay. My interest here is in the broader issue of what science studies brings to the discussion of origins. Fuller is dissatisfied with the limited scope of the discourse to date because the dominant voices have functioned as "underlaborer[s] to science". He points out "two types of public exemplars" that have been associated with science studies:

"On the one hand, there is the Michael Ruse figure who supplies a historical and philosophical hinterland to the dominant scientific paradigm so as to complement its purely empirical success with a broader cultural and conceptual grounding that will appeal to those unfamiliar with the technical science. On the other hand, there is the Robert Pennock figure, more typical of the younger generation, who outright collaborates with established scientists in their research, providing a running legitimizing narrative in co-authored articles published in technical and popular forums. In both cases, the science studies scholar functions as an underlaborer to science, as opposed to a true metascientist."

Science studies need to rise above partisanship and develop robust contributions to knowledge that do not need the endorsement of the 'scientific consensus' to justify their validity.

"A metascientist evaluates science from a standpoint that does not presuppose the legitimacy of the dominant paradigm. He or she starts by asking why we pursue science in the first place - the question of ends - and then turns to consider the extent to which the normal pursuit of science satisfies those ends. This is the role I have tried to exemplify. [. . .] The approach is 'constructivist' without being 'relativist' in the way these two terms are normally understood in epistemology."

These social epistemological principles are then applied to the origins controversy. Fuller is interested in this debate because it presents so many important and interesting issues needing rational discussion. However, Fuller finds that far too much bigotry has been expressed and has concluded that something needs to be done to raise the level of debate.

"In terms of the evolution-creation controversy, the bottom line for me, then, is not to satisfy the wishes of particular communities by allowing creationism to be taught, but to avoid the opportunity costs to everyone if creationism is not allowed to be taught."

These opportunity costs are worthy of elaboration. Fuller identifies several of these. The first draws attention to the history of science and the fact that many scientists have done good work motivated by the presupposition that the natural world is the handiwork of an Intelligent Designer. Those who say that toleration of ID will be the death of science and the beginning of a new dark age are in denial of history.

"Here I have in mind the overwhelmingly positive role that belief in an intelligent designer has played in motivating religious people to enter and stick with scientific careers, which have resulted in findings that command the assent of even those who lack faith."

The second opportunity cost is academic freedom. Fuller has already made it clear that he thinks tenured academics should be taking the lead in challenging the dominant paradigm. It is simply too risky for others to stick their heads above the parapet - they are easy targets and they get hurt. They are treated as guilty by association and their ideas are deemed unworthy of any further consideration.

"When we start to judge ideas rather than texts, intentions rather than practices, we become complicit in the erosion of academic freedom. Perhaps the most widely publicized recent case to cross that line was the forced resignation of Michael Reiss as director of science education for the Royal Society. Reiss had the temerity to suggest that science teachers should take seriously - albeit critically - creationist queries raised by their students. Reiss, who also holds a chair at the University of London's Institute of Education, based this judgment on his own research on science pedagogy. It is worth noting that he did not propose that teachers should themselves introduce the creationist ideas - yet the Royal Society deemed he still had to go."

The third opportunity cost is concerned with the quality of debate. Academics are supposed to use their minds when defending a position or critiquing others. However, the origins issue reveals people ruled by emotions, prejudices and ideologies.

"The pervasive anti-Christian bigotry surrounding the evolution-creation debate has had other knock-on effects on the conduct of intellectual discourse. It becomes an excuse to lower the tone in both academic and public discussions. Anyone prepared to defend any form of creationism should expect enormous negative attention in the blogosphere, ranging from occasional derision to outright invitations to trash the defender. At first I believed that my own intervention would clarify misunderstandings but it only seemed to intensify them, not least because I addressed my opponents in the spirit they addressed me. They were not prepared to entertain the idea that it was they and not I who misunderstood."

These three opportunity costs deserve the serious attention of all who are engaged in the controversy. However, the dominant response has been to ignore these points and persist in old patterns of thinking and tired polemics. Some have expressed their frustration with Fuller for his bad judgment. One of these is Michael Lynch, Professor of Science & Technology Studies at Cornell University, who has published several articles condemning Fuller's role as an expert witness in the Dover trial. One of these was in the same journal Spontaneous Generations that carried the essay under consideration here, to which Fuller has recently responded. He pointed out that his "game" is not for short-term gain but for long-term success.

"In that context, I undertake a risky performance in the spirit of a living experiment, the results of which should prove instructive not only to myself but also to others who in the future are similarly well-positioned to bring science studies to bear on public policy. The only mistake would be for others not to repeat the experiment."

Fuller is prepared to criticize Ruse and Pennock for being "traitors to their training" and guilty of "intellectual treason". He is prepared to say that Barbara Forrest's tactic has been to shift the argument from evaluation of ideas to the "intentions of those promoting them", thereby following in the footsteps of John Dewey who used this approach to earn a reputation as "one of the foremost Red-baiters in the US philosophical establishment in the 1940s and '50s". These charges are not ad hominems but are based on analysis of their arguments. The issues are far too important to allow room for complacency - academic freedoms are being eroded, young scientists are fearful of expressing any positive views on design, parental responsibilities for the education of their children are being eroded (with charges of "child abuse" being thrown around), and much more. But Fuller is also prepared to press upon tenured academics the obligation he thinks they have to use their positions of relative security to contribute to public controversies about the nature of science. There is an urgency about the situation. The least that can be said is that Fuller is a trail blazer. No one can criticize him for not acting out what he is encouraging others to do.

Science Studies Goes Public: A Report on an Ongoing Performance
Steve Fuller
Spontaneous Generations, 2(1), (2008), 11-21

First para: I believe that tenured historians, philosophers, and sociologists of science - when presented with the opportunity - have a professional obligation to get involved in public controversies over what should count as science. I stress 'tenured' because the involved academics need to be materially protected from the consequences of their involvement, given the amount of misrepresentation and abuse that is likely to follow, whatever position they take. Indeed, the institution of academic tenure justifies itself most clearly in such heat-seeking situations, where one may appear to offer a reasoned defense for views that many consider indefensible. To be sure, the opportunities for involvement will vary in kind and number, but I believe that we are obliged to embrace them. In the specific case of 'demarcation' questions of what counts as science, the people who possess the sort of general and comparative knowledge most relevant for adducing this matter are historians, philosophers, and sociologists of science - not professional scientists unschooled in these areas.

Response to Lynch
Steve Fuller
Spontaneous Generations, 3(1), (2009), 220-222.

See also:

Lynch, M. Going Public: A Cautionary Tale, Spontaneous Generations, 3(1), (2009), 212-219.

Tyler, D. A "teachable moment" regarding the departure of Michael Reiss, ARN Literature blog (25 September 2008)

Tyler, D. Michael Reiss and the science-religion issue, ARN Literature blog (17 September 2008)

Over the years, there has been much interest in the design of running shoes, with product designers building in protection against impacts and other perceived hazards. However, continuing reports of repetitive strain injuries warrant further research and product re-design. The topic has come to the surface recently with a comparison of the forces experienced by feet of habitually shod versus habitually barefoot runners. It emerges that barefoot runners make contact with the ground in a way that avoids impact-related discomfort and injury.

On the left, a habitually shod Kenyan who is heel-striking; on the right, a Kenyan who has never worn shoes and who is forefoot striking in the way most barefoot runners land. Below are representative force traces (in units of body weight) showing how the two styles of running differ in the force generated when the foot collides with the ground. The barefoot runner lands with no collisional force. (Image: Daniel E. Lieberman, Source here)

As a matter of observation, most habitually shod runners first contact the ground with their heel. This is referred to as heel-striking or rear-foot strike. Modern running shoes have been designed to reduce the impact forces with the help of additional cushioning at the heel. Barefoot runners first contact the ground with the front part of their feet and bend their ankles more as they run. This is referred to as fore-foot or mid-foot strike. This mode of running results in reduced collision forces and enhanced comfort.

"People who don't wear shoes when they run have an astonishingly different strike," says Daniel E. Lieberman, professor of human evolutionary biology at Harvard University and co-author of a paper appearing this week in the journal Nature. "By landing on the middle or front of the foot, barefoot runners have almost no impact collision, much less than most shod runners generate when they heel-strike. Most people today think barefoot running is dangerous and hurts, but actually you can run barefoot on the world's hardest surfaces without the slightest discomfort and pain. All you need is a few calluses to avoid roughing up the skin of the foot. Further, it might be less injurious than the way some people run in shoes."

Since this is a topic where there are numerous agents with commercial interests, the authors of the research paper have felt the need to issue a disclaimer that their reported work is essentially empirical in nature.

"Please note that we present no data on how people should run, whether shoes cause some injuries, or whether barefoot running causes other kinds of injuries. We believe there is a strong need for controlled, prospective studies on these problems." (Source here)

However, the authors go well beyond the empirical data in their analysis when they ground their work in a framework of evolutionary biology. This is also the starting point for Jungers' commentary on the research: "A commitment to walking and running on two legs distinguishes humans from apes, and has long been the defining adaptation of the hominins - the lineages that include both humans and our extinct relatives. This form of locomotion (bipedalism) has been around for millions of years, and we have been unshod for more than 99% of that time." The view, therefore, is that the context for understanding running is that it has evolved as an adaptation under the influence of natural selection.

"Our feet were made in part for running," Lieberman says. But as he and his co-authors write in Nature: "Humans have engaged in endurance running for millions of years, but the modern running shoe was not invented until the 1970s. For most of human evolutionary history, runners were either barefoot or wore minimal footwear such as sandals or moccasins with smaller heels and little cushioning."

There is another perspective on this, which is that of design. Design advocates will affirm: 'Our feet were designed in part for running'. Humans live in many different environments, and the design issues are affected by the need to walk, jump, climb, carry and run in these different environments. A sensitivity to design means that we need to understand how our feet work best in different conditions, so it follows that runners should adopt a biomechanical and physiological approach to developing good running habits. Runners should train to develop the full potential of the design features of their bodies. An evolutionary story of how ape-like animals developed bipedalism is simply a veneer overlying the empirical data.

Foot strike patterns and collision forces in habitually barefoot versus shod runners
Daniel E. Lieberman, Madhusudhan Venkadesan, William A. Werbel, Adam I. Daoud, Susan D'Andrea, Irene S. Davis, Robert Ojiambo Mang'Eni & Yannis Pitsiladis
Nature 463, 531-535 (28 January 2010) | doi:10.1038/nature08723

First para: Humans have engaged in endurance running for millions of years, but the modern running shoe was not invented until the 1970s. For most of human evolutionary history, runners were either barefoot or wore minimal footwear such as sandals or moccasins with smaller heels and little cushioning relative to modern running shoes. We wondered how runners coped with the impact caused by the foot colliding with the ground before the invention of the modern shoe. Here we show that habitually barefoot endurance runners often land on the fore-foot (fore-foot strike) before bringing down the heel, but they sometimes land with a flat foot (mid-foot strike) or, less often, on the heel (rear-foot strike). In contrast, habitually shod runners mostly rear-foot strike, facilitated by the elevated and cushioned heel of the modern running shoe. Kinematic and kinetic analyses show that even on hard surfaces, barefoot runners who fore-foot strike generate smaller collision forces than shod rear-foot strikers. This difference results primarily from a more plantarflexed foot at landing and more ankle compliance during impact, decreasing the effective mass of the body that collides with the ground. Fore-foot- and mid-foot-strike gaits were probably more common when humans ran barefoot or in minimal shoes, and may protect the feet and lower limbs from some of the impact-related injuries now experienced by a high percentage of runners.

See also:

The Barefoot Professor: by Nature Video

Jungers, W.L., Barefoot running strikes back, Nature 463, 433-434 (28 January 2010) | doi:10.1038/463433a

Tyler, D. The human body is built for running, ARN Literature blog (29 October 2009)

The first species to have its genome decoded by 'next-generation-sequencing' (NGS) machines is the giant panda (Ailuropoda melanoleuca). The individual animal was known previously to the world as the mascot of the 2008 Beijing Olympic Games. Scientists have been excited by the report because the NGS approach is significantly cheaper and faster than other methods. It is not the purpose of this blog to assess the robustness of the method, but it is important to be aware that the reported sequence utilizes previously determined genomes as a reference platform: dog and human genomes in this case.

"Using evidence-based gene prediction, the human and dog genes [. . .] were projected onto the panda genome, and the gene loci were defined by using both sequence similarity and whole-genome synteny information."

The iconic giant panda's genetic makeup reveals degradation (Source here)

The estimated size of the giant panda genome is said to be 2.40 Gb (compared with 2.45 Gb for the dog genome and 3.0 Gb for humans) making up about 21,000 genes (similar to humans). "Overall, we found that the quality of the predicted panda genes was comparable to that of other well-annotated mammalian genes." Although the panda eats only bamboo leaves, genes associated with carnivory are present in the panda:

"Of interest, our analysis of genes potentially involved in the evolution of the panda's reliance on bamboo in its diet showed that the panda seems to have maintained the genetic requirements for being purely carnivorous even though its diet is primarily herbivorous."

There was no trace of genes that encode enzymes for digesting cellulose, raising questions about how the panda can possibly survive on bamboo. The hypothesis proposed is that the bamboo diet "may instead be more dependent on its gut microbiome". Confirmation of this will require further work. A related dietary factor concerns the sense of taste. The authors refer to the five components of taste: sweetness, saltiness, sourness, bitterness and umami. The giant panda has lost the capability of sensing umami, which means that meat has become unappetizing.

"Umami is sensed through the T1R family. In the panda genome, T1R2 and T1R3 are in an intact form, but T1R1 has become a pseudogene - we found that [. . .] two panda T1R1 exons contain transcript errors."
"Two frameshift mutations occurred in the third and sixth exons of the panda T1R1 gene. The third exon contained a 2-bp ('GG') insertion; the sixth exon contained a 4-bp ('GTGT') deletion."

A possible genetic factor affecting the giant panda's low fecundity rate was identified. Nearly all of the mammalian reproduction genes were mapped, and "a putative pseudo follicle-stimulating hormone (FSH) [beta]-subunit gene (giant panda-FSHB2)" was noted. The authors comment:

"At this stage, whether the pseudo FSHB2 gene contributes to the reproduction features of the giant panda remains to be determined."

Some have considered whether the panda genome helps resolve the animal's taxonomic status. Although most place the panda in the bear family (Ursidae), a case has been made that it belongs elsewhere - in the raccoon family (Ailuridae). Since we do not have the genomes for any of these possible relatives, there is little more that can be said on the matter. However, even if other genomes were sequenced, does the "genome" tell us much about what makes a bear differ from a raccoon or a dog or a human? The genome can be described as the repository of housekeeping genes; it provides the materials needed for the organism to function - but something much more than this is needed to inform taxonomy. The ENCODE project (along with many others) has revealed rich functionality in the non-coding DNA (alias 'junk DNA'). Consequently, it is probable that the gene sequencers are just scratching at the surface of genetic information.

If the giant panda is correctly assigned to the Ursidae, the new research contributes significantly to the way we understand the speciation of this animal. Before genome sequencing, we could say that it has diversified significantly from ancestral Ursidae stock. It has a reduced number of chromosomes, 42, whereas most bears have 74. It has a wholly vegetarian diet and it has a modified sesamoid bone which it uses to strip bamboo leaves from stems. The panda genome findings provide the background for understanding herbivory: the panda still retains the genes for carnivory but mutations have destroyed the taste trigger for it to eat meat. Although the panda cannot make enzymes for digesting plant food, communities of gut microbes are the most likely explanation of its continuing survival. The reproduction problems experienced by giant pandas may also be linked to a mutation affecting follicle stimulation.

The overall picture is one of speciation/diversification linked to genetic degradation. Natural selection, which has often been portrayed as all-powerful and capable of building exquisitely complex structures, has failed to provide the giant panda with any enzymes for digesting plant food. We do not know whether the modified sesamoid bone is an evolutionary innovation, a part of the degradation story or information neutral. The News & Views essay that accompanies the research paper calls the panda China's "national treasure" - and so it is. However, from the perspective of genetics, the giant panda is not in a healthy state. Whatever else may be relevant, this case has strong affinities with speciation by gene pool reduction. From the perspective of Darwinism, the giant panda genome testifies to the failure of Darwinian mechanisms to overcome problems caused by mutations. From the perspective of design, we have a story of how a superbly designed carnivore has managed to survive the effects of genetic degradation. From a conservation perspective, without human intervention, the chances of long-term survival are slender.

There is also the finding that Jingjing's genome has a high degree of genetic diversity, but she is unlikely to be representative of the panda population taken as a whole. It is more prudent to assume that the relatively isolated panda enclaves harbour problems of inbreeding and that Jingjing is an example of the benefits of breeding across enclaves - further supporting the case for human intervention.

The sequence and de novo assembly of the giant panda genome
Li, R. et al.
Nature 463, 311-317 (21 January 2010) | doi:10.1038/nature08696

Abstract: Using next-generation sequencing technology alone, we have successfully generated and assembled a draft sequence of the giant panda genome. The assembled contigs (2.25 gigabases (Gb)) cover approximately 94% of the whole genome, and the remaining gaps (0.05 Gb) seem to contain carnivore-specific repeats and tandem repeats. Comparisons with the dog and human showed that the panda genome has a lower divergence rate. The assessment of panda genes potentially underlying some of its unique traits indicated that its bamboo diet might be more dependent on its gut microbiome than its own genetic composition. We also identified more than 2.7 million heterozygous single nucleotide polymorphisms in the diploid genome. Our data and analyses provide a foundation for promoting mammalian genetic research, and demonstrate the feasibility for using next-generation sequencing technologies for accurate, cost-effective and rapid de novo assembly of large eukaryotic genomes.

See also:

Worley, K.C. and Gibbs, R.A. Decoding a national treasure, Nature 463, 303-304 (21 January 2010) | doi:10.1038/463303a

Qiu, J., Genome reveals panda's carnivorous side, 13 December 2009, Nature News | doi:10.1038/news.2009.1141