Literature

According to the authors of a research paper in Science, "Although strong and stiff human-made composites have long been developed, the microstructure of today's most advanced composites has yet to achieve the order and sophisticated hierarchy of hybrid materials built up by living organisms in nature." Steel and metal alloys have high strength and flaw tolerance, but are heavy; ceramics have strength but poor flaw tolerance; polymers are flaw-tolerant but they deform under applied loads.

"Nature has found its way around this dilemma by combining plateletlike ceramic building blocks with polymeric matrices to render hybrid materials that are both strong and flaw-tolerant. Examples include mineralized tissues of vertebrates, such as bone, teeth, and calcified tendons, as well as the outer skeleton of invertebrates, such as the nacreous layer of mollusk shells.
The exquisite structure of these biological materials and the underlying concepts leading to their mechanical behavior have been extensively studied. Although substantial progress has been made on understanding the mechanical response of such structures, the manufacture of artificial composites that copy nature's designs remains a challenging goal."

Mother-of-pearl is 97% lime, but its microstructure gives it a breaking strength a thousand times higher. (Source: go here)

The authors go on to report on their interesting work with layered hybrid films. This research has stimulated a commentary article by Ortiz and Boyce, which is really the focus of this blog. My purpose here is to draw attention to three of the many excellent points made in their article.

1. The natural world does not just provide examples of materials that are interesting to scientists and engineers - they demonstrate "mechanical design principles". There is an underpinning rationale which, when we have grasped it, is of both theoretical and practical importance. It is not just a case of finding a feature in the natural world that works, but of recognising holistic, information-rich designs in living things.

"Using materials available in the environment that typically exhibit poor macro-scale mechanical properties (brittle biological ceramics and compliant macromolecules), they [living things] can achieve orders-of-magnitude increases in strength and toughness; in many cases, this "mechanical property amplification" occurs in a nonadditive manner that goes beyond the simple composite rule of mixture formulations. Synthetic structural materials that take advantage of the mechanical design principles found in nature could transform many fields; e.g., materials science, mechanical and civil engineering, and aeronautics and astronautics."

2. The design principles are applied to systems. There are many different components and structural variants in biological materials.

"Biological composites make use of local chemistry, compositional gradients, macromolecular supramolecular structure, length scale effects, geometry, and other factors to design robust interfaces and inter-phases that bond together different material phases, even in the presence of water."

3. Biological materials have inherent specificity. We like generic materials, but the natural world works on the basis that although design principles are generic, the applications are specific. Materials in nature are customised to be fit for purpose:

"We have yet to fully understand and take advantage of the inherent specificity of natural mechanical design principles. For example, multilayered armored fish scales serve as protection from predatory penetrating impacts, mussel byssal threads are hysteretic yet resilient to large strain deformation in order to maintain adhesion to rocks in the face of the pounding surf, and graded layer junctions in teeth resist catastrophic fracture during mastication. Each of these systems experiences, and has been designed to endure, very different loading conditions in their environment and during their function."

Biomimetic research is based on the premise that the natural world is information-rich and reverse engineering methodologies are likely to be fruitful. The significance of the two articles discussed here is that both recognise that the information concerns design principles embedded in specific applications. There is a conceptual gulf between this and the "evolutionary tinkering" mechanism of Darwinism, which has no depth and knows only pragmatism as a rationale. Design-based methodologies in biomimetics are yielding tangible results - and evolutionary tinkering is revealed as irrelevant.

Bioinspired Design and Assembly of Platelet Reinforced Polymer Films
Lorenz J. Bonderer, Andre R. Studart, and Ludwig J. Gauckler
Science, 319, 22 February 2008: 1069-1073.

Although strong and stiff human-made composites have long been developed, the microstructure of today's most advanced composites has yet to achieve the order and sophisticated hierarchy of hybrid materials built up by living organisms in nature. Clay-based nanocomposites with layered structure can reach notable stiffness and strength, but these properties are usually not accompanied by the ductility and flaw tolerance found in the structures generated by natural hybrid materials. By using principles found in natural composites, we showed that layered hybrid films combining high tensile strength and ductile behavior can be obtained through the bottom-up colloidal assembly of strong submicrometer-thick ceramic platelets within a ductile polymer matrix.

Bioinspired Structural Materials
Christine Ortiz and Mary C. Boyce
Science, 319, 22 February 2008: 1053-1054.

Materials scientists are seeking to create synthetic materials based on the mechanical design principles found in biological materials such as seashell nacre.

The quest for a plausible story about the evolution of feathers from scales has exercised many minds. A major problem has been to find evidence for primitive feathers - for these are said to be "desperately missing in the fossil record". The feathers of Archaeopteryx, located in the Jurassic, were not primitive but modern in all aspects. There are (later) Cretaceous feathers preserved in amber, but these are also modern, "featuring barbs and barbules organised in asymmetrical vanes". Evolutionary biologists have therefore been relatively unconstrained by data, and this is recognised to be an unsatisfactory situation. Previously, one particular stage was highlighted by the theoreticians, and a new research paper claims to have documented this transition: "We recently discovered several isolated feathers fossilized in an Early Cretaceous amber of France, which display a primitive structure that illustrates the early formation of this critical stage."

These images are claimed to capture a step towards the shape of modern feathers (Source: go here).

To give an idea of the thinking of the authors, here are comments from Didier Neraudeau:

"What is very important in our discovery is that we have found a new clear example of the gradual trend of the evolution in general and in particular in the case of the transition between a primitive filamentous down and a modern feather. Moreover, it shows that in many cases, when an evolutionary stage is predicted by the theory, it can often be found in the fossil record. It is a question of time. Thus, it does not really change our picture of evolution but it gives for the first time a proof of the gradual evolution of feathers from the primitive filaments of some theropod dinosaurs to the modern feathers of Archaeopteryx and Cretaceous birds."

Here is a part of the description. Note how small these feathers are. This description is followed by a discussion comprising three points.

"Seven identical feathers are lying side by side in the amber piece and very probably originate from a single individual. [. . .] The tangle of these feathers, their three-dimensional disposition in amber, and numerous dust grains hinder the observation of some of them. The following description is mainly based on the three best visible. These are 2.3, 1.6 and 1.1 mm long as measured along the rachis. Filamentous, long and free barbs lacking barbules are inserted opposite to each other on each side of a rather flattened rachis and form two vanes." [. . .] "These feathers are morphologically close to the down, ornamental or afterfeathers, and not to the contour, remiges or rectrices. However, they have a thick and long rachis, unlike classical down feathers whose barbs generally diverge from the very short apex of the rachis."

1. The authors are over-quick in declaring that these fossils are primitive. They are not utilising a methodology of multiple hypotheses. There are at least two other hypotheses worth considering. The first is that the fossils are of down from a chick. This must be considered because the fossils are "morphologically close" to down. Since the fossils are so small, the comparison needed is with down feathers from a newly hatched chick, not a mature bird. There is no indication that the work has been done to make any valid comparisons. The second alternative is that the fossils are degenerate feathers that have lost functionality and taken on a simplified structure. The present lack of suitable derived bird fossils should not prevent this hypothesis being explored. The approach adopted by the authors illustrates Kuhnian "normal science", where data are fitted into the paradigm. This is theory-led science.

2. The Late Albian age assigned to these fossil feathers post-dates the appearance of modern feathers in the Jurassic. Furthermore, they are contemporaneous with other fossil feathers that are modern in appearance. This is an example of the "temporal paradox" that has been also recognised with theories of 'theropod to bird' evolution. The supposed transitional forms are far too late to be transitional!

3. Theoretical discussions of the evolution of any characters generally point out some selective advantage of a developing trait. This discussion is absent from this paper. These feathers have barbs but no barbules. Further exploration of this takes us back to the two alternative hypotheses above and reminds us that "normal science" is not about following the evidence wherever it leads but fitting it into a predetermined theoretical framework.

The early evolution of feathers: fossil evidence from Cretaceous amber of France
Vincent Perrichot, Loic Marion, Didier Neraudeau, Romain Vullo, Paul Tafforeau.
Proceedings of the Royal Society, Biological Sciences, FirstCite, 19 February 2008 | doi 10.1098/rspb.2008.0003

Abstract: The developmental stages of feathers are of major importance in the evolution of body covering and the origin of avian flight. Until now, there were significant gaps in knowledge of early morphologies in theoretical stages of feathers as well as in palaeontological material. Here we report fossil evidence of an intermediate and critical stage in the incremental evolution of feathers which has been predicted by developmental theories but hitherto undocumented by evidence from both the recent and the fossil records. Seven feathers have been found in an Early Cretaceous (Late Albian, ca 100Myr) amber of western France, which display a flattened shaft composed by the still distinct and incompletely fused bases of the barbs forming two irregular vanes. Considering their remarkably primitive features, and since recent discoveries have yielded feathers of modern type in some derived theropod dinosaurs, the Albian feathers from France might have been derived either from an early bird or from a non-avian dinosaur.

See also:

Highfield, R. Missing link feather fossils found in France, The Daily Telegraph, 20/02/2008

Astrobiology is a scientific enigma, because there are no examples of extraterrestrial life on which to build a body of knowledge. It has life on Earth as a clear reference point, but beyond Earth, everything examined has proved barren. In The Living Cosmos, author Chris Impey provides an overview of current thinking in astrobiology, but it consists essentially of discussing how and where we should be looking for extraterrestrial life.
A positive review of the book is by Bruce Jakosky, who presents astrobiology as "firmly science-based rather than speculative". Planet Earth provides the foundation for the science: "We know how life functions, how it may have originated and some types of environment that support its existence." Many things are packaged up together here, and this is a danger. In particular, the claim that we know how life "may have originated" is way off the mark. There have been many hypotheses and much testing of hypotheses, but none of it encourages us to think that we know how life may have originated on Earth. The field is full of controversy and over-optimistic claims. For examples, go here and here.

Beyond the Earth, the most promising planet for hosting life in our Solar System is Mars, and this is where there has been intensive effort by astrobiologists. "Mars is arguably the best place to look for present or past life, given the evidence for liquid water there and the planet's proximity to Earth." However, in his review, Jakosky majors on the need for future missions rather than reflect on what has been learned so far. This is the major problem that we have with astrobiology: it is unable to consider the possibility that the sought-after life is not there! According to the adherents, life beyond Earth must exist, and our task is to keep searching until we find it!

"Even the toughest micro-organisms would have been unable to survive in the harsh environment, say scientists" (Source - go here)

Our understanding of Mars is rapidly developing. Signs of water in the Martian past are plentiful, and this has raised expectations. But today, a report has been published about sand flume studies of delta formation. These have shown that a stepped delta structure found on Mars can best be modelled by a "sudden release of water from subsurface storage". "The distinct morphology of martian stepped (terraced) deltas could only have originated from a single basin-filling event on a timescale of tens of years." This report raises questions about how long water bodies occupied the Martian surface.

Also this week, comments have been made about the extreme salinities of water bodies when they existed on Mars. Researchers have effectively thrown up their hands in despair: "That's not a very good place to live, and it's a worse place for the kind of chemistry that we think gave rise to life on Earth". "At first, we focused on acidity, because the environment would have been very acidic. Now, we also appreciate the high salinity. This tightens the noose on the possibility of life." But they are not giving up. There is always something more to explore: "The best hopes for a story of life on Mars are at environments we haven't studied yet".

Astrobiologists want access to every conceivable habitat.

"Beyond Mars, several moons in the outer Solar System are worth exploring. Jupiter's satellites Europa, Ganymede and Callisto are good targets because they may have recently hosted liquid water. Saturn's moons Titan and Enceladus, targets of the ongoing Cassini mission, are of great interest because of the abundance of organic molecules (especially on Titan) and the potential for near-surface liquid water (Enceladus). NASA is studying possible missions to these objects as a prelude to a major push mission into the outer Solar System."

The question needs to be asked: what makes this science? There are no hypotheses being tested. There is no hint that astrobiologists are willing to consider that their basic assumption (about extraterrestrial life existing) can ever be falsified. There is no acknowledgement that all the research to date emphasises the uniqueness of Earth as an environment supporting life. The insatiable appetite for the next probe is not grounded in reality, but in aspiration. The hype surrounding the quest for extraterrestrial life springs from an ideology that appears to use science as a tool to achieve its goals.

Quest for extraterrestrial life
Bruce Jakosky
Nature, 451, 890 (21 February 2008) | doi:10.1038/451890a

BOOK REVIEWED - The Living Cosmos: Our Search for Life in the Universe by Chris Impey, Random House: 2007.
First paragraph: From only one example, that of life on Earth, we have learned a lot about what makes a planet habitable. We know how life functions, how it may have originated and some types of environment that support its existence. Yet we do not know how widespread life might be. To do so we must extend our knowledge past Earth, into the Solar System and beyond.

Since vertebrates have a spine, they are regarded as having a higher complexity. "Nonetheless, demonstrating this difference in morphological complexity is difficult, and determining its causal basis has proven even less tractable. Typically, causality has been sought in the phenomenon of genome duplication." There is a problem with this, as the authors explain: "However, the absence of any obvious increase in morphological complexity associated with other known genome duplication events (GDEs), especially within the actinopterygian fishes, suggests that the causal link between morphological complexity and GDEs is tenuous at best." Towards the end of their paper, they reject GDE completely as a plausible mechanism:

"Indeed, in contrast to the rhetoric, no good evidence has been marshaled in support of the much-vaunted hypothesis that GDEs can confer increasing organismal complexity."

To understand the argument of the research paper, it should be noted that the original model of protein formation within the cell was that DNA was first transcribed to RNA, and RNA was then translated to protein. Subsequently, there have been many modifications, all associated with control mechanisms. Many RNAs are non-coding and they do not make protein. These RNAs can be thought of as switch-like controls that regulate the formation of gene products.

"An alternative explanation for increasing morphological complexity has been increasing the complexity of gene regulatory networks. Although usually considered from the perspective of protein-coding genes, vertebrates are also distinguished from invertebrates by the transcribed, noncoding complements of their genome, with mammalian genomes transcribing over an order of magnitude more noncodingRNAas compared with either worm or fly. Importantly, it is among this noncoding sequence that a variety of new classes of regulatory factors has been discovered, including microRNAs (miRNAs), which has been postulated as developmental and evolutionary determinants of organismal complexity. Indeed, vertebrates possess many more miRNAs than any invertebrate sampled to date, and >50 new miRNA families are thought to have evolved in the vertebrate lineage sometime after its split from the invertebrate chordates and before the divergence of osteichthyan fishes."

miRNA processing. [1] Transcription from miRNA gene. [2] Cleavage by Drosha. [3] Transport of pre-miRNA by Exportin 5. [4] Processing in to the mature miRNA by Dicer. [5] Complexing with the RNA-induced silencing complex (RISC). [6] Targeting of the complex guided by the miRNA sequence, followed by translation inhibition or degradation of the messenger RNA. For expansion, go here.

The paper does establish a link between the emergence of many new miRNA families and vertebrate morphological complexity, and the authors ask whether this is a coincidence or whether there is causality. In their view, causality must be the answer.

"Of course, it could be argued that the correlation between miRNA acquisition and morphological complexity is exactly that, a simple correlation. However, we suggest otherwise given that many of these 41 miRNA families are expressed in vertebrate-specific cell types or tissues [. . .]. Given the role miRNAs play in the specification of cell and tissue types, we suggest that the origin of these cellular novelties was predicated on the origin and fixation of these novel miRNAs."

Alysha Heimberg summarises the situation thus: "There was an explosive increase in the number of new microRNAs added to the genome of vertebrates and this is unparalleled in evolutionary history." Co-author, Philip Donoghue adds: "Most of these new genes are required for the growth of organs that are unique to vertebrates, such as the liver, pancreas and brain. Therefore, the origin of vertebrates and the origin of these genes is no coincidence." The press release refers to the authors claiming "to have solved this scientific riddle".

The authors have established an association, but causation is a much stronger word. There are numerous gaps in the causal explanation as it stands.

"Such rapid rates of miRNA innovation, and the correlation with the dramatic increase in morphological complexity, beg the question of how and why this burst of miRNA family innovation occurred. The basis of miRNA innovation in animals is controversial as there are a number of competing, but weakly supported, hypotheses."

It is an understatement to say that how and why questions abound! We do not just have to consider miRNA innovation, but the introduction of miRNAs that deliver functionality. With the proposed rapid burst of changes, there are important questions about the viability of animals experiencing concurrent transformation of numerous regulatory networks. In the present state of knowledge, design-based explananations of causation cannot be dismissed except on ideological grounds. We have here a striking case of complex specified information, and that is the hallmark of designed systems.

It is worth noting, before concluding, that the initial reaction of many evolutionary biologists was to regard all non-coding DNA (including the sequences now known as miRNA) as junk. This is the context for understanding the headline of the EurekAlert report. This blog has drawn attention previously (here, here and here) to this cul-de-sac in the history of evolutionary thought.

MicroRNAs and the advent of vertebrate morphological complexity
Alysha M. Heimberg, Lorenzo F. Sempere, Vanessa N. Moy, Philip C. J. Donoghue and Kevin J. Peterson
Proceedings of the National Academy of Sciences, USA, February 11-15 2008.

Abstract: The causal basis of vertebrate complexity has been sought in genome duplication events (GDEs) that occurred during the emergence of vertebrates, but evidence beyond coincidence is wanting. MicroRNAs (miRNAs) have recently been identified as a viable causal factor in increasing organismal complexity through the action of these ~22-nt noncoding RNAs in regulating gene expression. Because miRNAs are continuously being added to animalian genomes, and, once integrated into a gene regulatory network, are strongly conserved in primary sequence and rarely secondarily lost, their evolutionary history can be accurately reconstructed. Here, using a combination of Northern analyses and genomic searches, we show that 41 miRNA families evolved at the base of Vertebrata, as they are found and/or detected in lamprey, but not in either ascidians or amphioxus (or any other nonchordate taxon). When placed into temporal context, the rate of miRNA acquisition and the extent of phenotypic evolution are anomalously high early in vertebrate history, far outstripping any other episode in chordate evolution. The genomic position of miRNA paralogues in humans, together with gene trees incorporating lamprey orthologues, indicates that although GDEs can account for an increase in the diversity of miRNA family members, which occurred before the last common ancestor of all living vertebrates, GDEs cannot account for the origin of these novel families themselves. We hypothesize that lying behind the origin of vertebrate complexity is the dramatic expansion of the noncoding RNA inventory including miRNAs, rather than an increase in the protein-encoding inventory caused by GDEs.

See also:

Evolving complexity out of 'junk DNA', EurekAlert, 11 February 2008

One of the lessons we can learn from Richard Dawkins is that science is a very human activity. This, of course, comes from looking at what he does and not by listening to what he has to say! Scientists are not the objective analysts that they are often portrayed to be. Like you and I, they are people with passions, hopes and fears, and products of the society which nurtured them. Some scientists claim that science leads us to adopt atheism and Dawkins is providing leadership for this stance. Michael Ruse's review of The God Delusion in the current issue of ISIS reveals deep concerns about the direction in which Dawkins is heading. These are of wider interest and are highlighted below.

"The God Delusion" under the microscope

Ruse recognises that Dawkins is a "brilliant science writer" and refers to his first book as "a work of genius". But in The God Delusion, Dawkins moves into areas where Ruse has particular expertise. And Ruse is not impressed by Dawkins or any of the other scientific atheists who have caught the headlines recently.

"It is not that the atheists are having a field day because of the brilliance and novelty of their thinking. Frankly - and I speak here as a nonbeliever myself, pretty atheistic about Christianity and skeptical about all theological claims - the material being churned out is second rate. And that is a euphemism for "downright awful." [. . .] It is simply that it (and the other works, some of which I have gone after elsewhere) is not very good. For a start, Dawkins is brazen in his ignorance of philosophy and theology (not to mention the history of science). [. . .] Dawkins misunderstands the place of the proofs, but this is nothing to his treatment of the proofs themselves. This is a man truly out of his depth."

Dawkins has confidence in the findings of science, and he communicates the same sense of certainty in his rejection of theism. Ruse realises that there is a fundamental problem here: how can we be so sure of the robustness of our reasoning? If Darwinism is true, then we cannot get beyond pragmatism - 'this approach works for me'. It is rather presumptuous for genetic survival machines to discourse about ultimate realities.

"The paradox is that Dawkins should be more modest. He stresses that we are the product of Darwinian evolution, and hence there is no good reason to think we have the power to penetrate into the mysteries of the universe. Our abilities are to get out of the jungle and live on the plains. In a way, the Darwinian is back-to-back with Saint Paul: we peer through a glass darkly."

This is worth further comment here. How did realism become embedded in the scientific mind? It goes back to the pioneers of science, who were Christian theists with a worldview that considered the creation objective, real and rationally understood. Realism has solid Christian roots. The second phase of science came at the Enlightenment, when Theism gave way to Deism and the adoption of methodological empiricism. God's providential control of his creation was replaced by the mechanistic worldview, with God as the original, but now distant, Creator. Realism was carried over from Theism. Then came the rise of naturalism and positivism. This swept away Deism and secularised science completely. Naturalism and the mechanistic universe went together well, but the rationale for both realism and rationality was lacking. Apart from the few philosophers of science who realised there was a problem, the scientific naturalists just grabbed what they wanted from their scientific heritage and avoided the challenge of thinking through their epistemology. We are today in a fourth phase: postmodernism. Many try to portray this intellectual movement as anti-science, but it is actually the inevitable consequence of scientific naturalism. Postmodernists realise that there is no rationale for realism - and all our perceptions are socially constructed. They realise that the scientific enterprise is no exception to their relativistic worldview, and science must be studied as a social phenomenon. If this four-phase analysis is valid, the only route back to realism is via a revival of theistic science.

Ruse's last point is of great interest to educationalists.

"A major part of the atheist attack is that science has shown that the God hypothesis is silly. Suppose this is true - that if you are a Darwinian, then you cannot be a Christian. How then does one answer the creationist who objects to the teaching of Darwinism in schools? Sauce for the goose is sauce for the gander. If theism cannot be taught in schools (in America) because it violates the separation of church and state, why then should Darwinism be permitted? If Darwinism leads to atheism, does this not also violate the separation of church and state? At the very least, Dawkins and company should be showing more responsibility. If they are right, then so be it. I would not want to conceal the fact. But let us face the consequences of the arguments. Explain to us on what grounds one can now legitimately teach evolution in schools. I think one can because I don't see the link between Darwinism and atheism. Those who do see such a link should tell us why Darwinism can be taught or accept that perhaps, given the U.S. Constitution, the creationists are right and Darwinism should be excluded."

If Dawkins replies that Darwinism and atheism should be taught because these things are true, then this is no different to creationists wanting creation taught because it is true. Ruse's point is not about truth, but about the legal implications of linking atheism to Darwinism in education - this violates the principle of church-state separation enshrined in the U.S. Constitution. This is not a new point, but it is the first time it has expressed within a scholarly forum. Perhaps now the scientific atheists will realise that they need to address the challenge.

Book Review: Richard Dawkins - The God Delusion
Michael Ruse
Isis, December 2007, 98(4), 814-816 | DOI: 10.1086/529280

First paragraph: God is getting a bit of a bashing these days. First there was the graduate student Sam Harris, with his powerful polemics against the deity (The End of Faith: Religion, Terror, and the Future of Reason [Norton, 2004]; Letter to a Christian Nation [Knopf, 2006]). Then there was the philosopher Daniel Dennett, telling us all that religion is like the liver fluke, a dreadful parasite that should be sought out and eradicated (Breaking the Spell: Religion as a Natural Phenomenon [Viking, 2005]). The journalist Christopher Hitchens has taken time out from bashing the Clintons and supporting the Iraq war to tell us that God's time is up (God Is Not Great: How Religion Poisons Everything [Twelve/Warner, 2007]). And above all, there is the smash-hit best seller The God Delusion, by the brilliant science writer Richard Dawkins.

Theory says that "morphological evolution reflects the darwinian process of natural selection, with evidence coming from numerous studies of contemporary populations and from classic interpretations of the fossil record." Selection does operate as an empirical reality, but ecologists have not found it as influential as Darwinians would like. The fossil record is "the fly in this darwininan ointment".

"In particular, statistical analyses of fossil data generally fail to confirm that natural selection strongly influences morphological evolution. Partly for this reason, a cadre of scientists is convinced that natural selection is less prevalent and important than typically assumed."

It is worth pausing to reflect on the word "cadre". Some may think that it signifies a small number of people, which is a valid but inadequate meaning. Other relevant ingredients are 'committed' and 'a nucleus capable of expansion'. There is a recognition here that selectionists do not have the floor to themselves - something previously noted here and discussed by Jerry Fodor here. This is a big concession, because the stance most commonly taken by Darwinists is that evolutionary theory with natural selection playing only a minor role is unthinkable.

The fossil record is the fly in the "darwinian ointment" - but is the problem bigger than this?

The case study chosen by Andrew Hendry in his News & Views essay on this topic concerns the threespine stickleback. The spines have a defensive role against predatory fish. Some exhaustive research has taken place to document how the number of dorsal spines and other related morphological traits varied with time after the last glaciation. The sticklebacks appear to have colonised a lake with few predatory fishes. The hypothesis is that if there is a metabolic cost of maintaining the number and size of these defensive spines, then, in the absence of predation, natural selection will lead to a reduction in the number and size of the spines. The hypothesis needs testing, of course, and this is where the problems surfaced.

"Up to now, few studies have been able to reject randomness; and those that have point to stabilizing selection, rather than directional selection. Taken at face value, these results might suggest that organisms have evolved their distinctive phenotypes without much aid from directional selection. If so, darwinian mechanisms might not be particularly important in generating the diversity of life."

Past statistical analyses concluded that the stickleback spines' hypothesis was not confirmed. Darwininsts are not comfortable with the outcome because they routinely use case studies like this to extrapolate from ecological fine-tuning to "generating the diversity of life". (From an ID perspective, the hypothesis is not unreasonable, but let it be fairly tested. What ID advocates do not do is indulge in large-scale extrapolations like this).

So now we come to the point of Hendry's essay. What he wants to say is that the "evidence has been there all along: we just haven't been looking properly". He refers his readers to several papers by Hunt which have resulted in confirmation of directional selection.

"One of Hunt's refinements was to overturn the usual burden of proof, wherein randomness has been assumed by default and retained as the evolutionary inference unless overwhelmingly rejected in statistical tests. But there is no biological reason for this a priori ascendancy of randomness, and randomness is extremely difficult to reject with the existing methods. [. . .]
First, Hunt et al. start their analysis at exactly the point in time when each armour trait begins to decrease, which favours a model of initially strong directional selection. But this choice does not undermine their general conclusion, because the standard methods could not reject randomness even when started at these same times. Second, the analysis of the stickleback data formally examined only one model of selection - the hybrid directional-stabilizing model they expected beforehand. The authors are here again stacking the deck for success in confirming selection. But then this is the point. Their analysis is akin to a positive control in showing that a new statistical method can infer the correct evolutionary process when that process is almost certain to be acting."

In other words, the analysis is being changed to yield an outcome that reflects the "correct evolutionary process". There is an overt "stacking the deck for success" because the researchers are supremely confident of the outcome. This is a lesson for anyone puzzling over statistical analysis: by changing the starting points and the methodology, a set of figures can yield outcomes which others have not seen! Hendry thinks this is progress:

"This work will almost certainly generate additional support from fossil sequences for the action of natural selection. Perhaps more importantly, it will become easier for biologists to accept randomness when random models still receive the most support. This acceptance, however, needs to be tempered by the realization that selection can certainly generate patterns that look random."

Those of us who have no argument with natural selection as a mechanism operating in nature do not need to adopt Hunt's approach. We are concerned about the introduction of circularity. It is not a robust methodology to select analytical techniques that confirm the theoretical ideas of the researchers. Science needs to be much more objective than that.
But our greatest concern is with Hendry's closing comment: "Ultimately, we might hope for the emergence of general conclusions about the role of natural selection in generating the diversity of life." This is where the potential for circular arguments is high. Darwinism has led many seriously astray by confounding empirical observations of selection with a grand theory to explain the complexity and diversity of life. The numerous sub-hypotheses of Darwinism need to be subjected to critical scrutiny but this is rarely done because this is more than just an irritating fly in the ointment!

Darwin in the fossils
Andrew P. Hendry
Nature, 451, 779-780 (14 February 2008) | doi:10.1038/451779a

Abstract: Adaptation by natural selection is thought to drive evolution. Although it has been difficult to confirm this process in the fossil record, evidence has been there all along: we just haven't been looking properly.

It may seem surprising that the liquid with which we are most familiar is actually the most unusual. It expands as it changes its state from liquid to solid; it has a high thermal capacity which means it can absorb heat energy without large temperature increases; it is an amazing solvent, etc. These properties, and many more, are exploited to the full by life forms - we cannot envisage life without water. Yet there are surprises:

"Water, together with surfaces containing sugar chains, forms the basis of all biological lubrication systems, from the slithering of a snail to the passage of food along the digestive tract. Yet humans have typically lubricated their machines with oils and fats. [. . .] Water on its own is, however, generally a poor lubricant, and unlike oil, its viscosity does not rise substantially with pressure. This property is essential to the mechanism by which oils can form a lubricating film in high-pressure, nonconformal contacts of hard materials such as gears or ball bearings."

Slugs produce a water-based lubricating film to facilitate movement

Biological lubrication then is something worthy of our attention. "Interest in water lubrication is also high in the food, textile, and pharmaceutical industries, where product contamination by oil is a concern". How does water provide lubrication for organisms?

"The low viscosity of water at high pressures can be overcome by biological lubricant additives, usually glycoproteins, in which large numbers of sugar chains are bound along a protein backbone. For example, mucins are found in most parts of the human body that need lubricating, such as eyes and knees. These molecules probably aid lubrication both via their intrinsic viscoelastic properties in solution and via their behavior when adsorbed on the sliding surfaces. The characteristic bottlebrush structure of the molecules is crucial to this mechanism: The hydrophilic sugars immobilize large amounts of water within the contact region, while the backbone interconnects to other bottlebrushes or to a surface."

These brushlike molecules are being actively studied, and the interfaces that develop between them and soft surfaces.

"One biomimetic approach is to decorate the sliding surfaces with a high density of brush-forming polymer chains. Klein et al. have shown that when two mica surfaces bearing polymer brushes are rubbed past each other under compression in "good solvents," the interfacial friction forces lie below the detection limit. The remarkable lubricating effect of such hairy polymer layers is ascribed to interchain repulsion, which leads to the incorporation of large quantities of solvent. The resulting fluid-like cushioning layer on the surface can sustain the externally applied pressure, thereby lowering the friction forces."

We are still a long way from mastering the technology, but progress is being made. "The practical implementation of biomimetic, aqueous lubrication approaches may become a reality in the not-too-distant future". The key thought here is that water-based lubricants are being inspired by biological systems. The problem is far from trivial: engineered solutions are essential. For us, it is a case of designing suitable brush-forming polymer chains. Some would have us believe that these "remarkable" lubricating effects in living things have come about by Darwinian mechanisms of mutation and natural selection. This is not because there is any evidence of natural selection doing anything remotely like this, but because their dogma demands it.

Sweet, Hairy, Soft, and Slippery
Seunghwan Lee and Nicholas D. Spencer
Science, 319, 1 February 2008: 575-576.

First paragraph: Water, together with surfaces containing sugar chains, forms the basis of all biological lubrication systems, from the slithering of a snail to the passage of food along the digestive tract. Yet humans have typically lubricated their machines with oils and fats. Understanding of biological lubrication has now advanced to the point where these principles can be applied to systems of technological importance using synthetic polymers.

No one disputes that Richard Owen was a scientist par excellence. The thumb-nail description of him on the website of London's Natural History Museum says this:

"An outstanding naturalist, with a special gift for interpreting fossils, Richard Owen was a remarkable man. He produced a vast array of scientific work, and famously coined the word 'dinosaur.' One of Owen's greatest achievements was his campaign for the natural specimens in the British Museum to be given a new home. This resulted in the now world-famous Natural History Museum in South Kensington, London. His contribution to science and public learning was enormous."

He was the first to give a clear definition of the term homology: "the same organ in different animals under every variety of form and function." He pointed out that all vertebrate species have a common skeletal plan and explained this in terms of a 'vertebrate archetype'. His classic book on the subject has been reprinted and the publisher has this rationale:

"Just as Darwin's ideas continue to propel the modern study of adaptation, so too will Owen's contributions fuel the new interest in homology, organic form, and evolutionary developmental biology. His theory of the archetype and his views on species origins were first offered to the general public in On the Nature of Limbs, published in 1849. It reemerges here in a facsimile edition with introductory essays by prominent historians, philosophers, and practitioners from the modern evo-devo community."

Richard Owen's classic discourse on homology

It is well known that Owen's thinking brought him into controversy regarding Darwinism. "Nothing," Darwin wrote in On the Origin of Species, "can be more hopeless than to attempt to explain this similarity of pattern in members of the same class, by utility or by the doctrine of final causes." Yet one of these options is exactly what Owen advanced! He explained these "similarities of pattern" in terms of design. He spoke of them as archetypes - abstracted common patterns. (Owen's approach has become more interesting today, not because of the design implications, but because they are relevant to structuralist perspectives in biology).
Although Owen is referred to as a "vitriolic critic of Darwin", there are some grounds for his signs of frustration. Darwin should have known of Owen's work on homology, and of his interpretation of the data in terms of archetypes. But instead of acknowledging that design provides an rational explanation for homology, Darwin persisted in saying that a Creator would not do it that way, and that patterns must be regarded as evidence for common descent. The more Owen looked at Darwin's writing, the more he found mental leaps and the dominance of dogma over data. Owen was the empiricist and Darwin was found wanting:

"But, as we have before been led to remark, most of Mr Darwin's statements elude, by their vagueness and incompleteness, the test of Natural History facts." (Source: go here)

The reviewer alludes to another essay in the same issue of Nature:

"A decade before Darwin's On the Origin of Species, Owen very nearly sketched a theory of evolutionary transformation, fragments of which appear here. However, as Padian describes, such were the sociopolitical and philosophical strains on Owen's position that he stalled at the final intellectual leap. Owen's patrons were of the Oxbridge-educated establishment - adherents to the natural theology of the 'argument from design' (for the existence of God) as advocated most influentially by William Paley (now sadly repackaged with a molecular gloss by the proponents of 'intelligent design')."

The best that can be said of this is that it is historical revisionism. Owen did not stall over the intellectual leap of Darwinism: he found it wanting. He did not like the way Darwin made an unwarranted story out of "Natural History facts". The inference that Owen adjusted his message to please his patrons is completely unsupported by evidence: it is a Darwinian spin on history and a slur on a great scholar. What we can learn from history is that it is certainly possible to be a serious biologist, doing good science, and at the same time be a design theorist. Owen is worth recalling next time you hear someone opining that design thinking is antithetical to science.

In Retrospect: Diagnosing deep similarity in nature
Michael Coates
Nature, 451, 631 (7 February 2008) | doi:10.1038/451631a

BOOK REVIEWED-On the Nature of Limbs: A Discourse
by Richard Owen
University of Chicago Press: 2007. 119 pp.

On the night of 9 February 1849, Richard Owen, the pre-eminent Victorian anatomist who later founded London's Natural History Museum, delivered a public lecture at the Royal Institution of Great Britain. In a strident discourse that set the stage for Charles Darwin's account of evolution, Owen revealed similarities in biological forms from species to species that suggested some underlying ideal plan or archetype. He sought to debunk the prevailing view that anatomical pattern could be explained as a consequence of biological function. With example after example, Owen hammered home the point that structural correspondences between species, or even between parts of the same individual, cannot be explained simply by adaptation. The echoes of his words still reverberate. [snip]

See also:

Padian, K. Darwin's enduring legacy, Nature, 451, 632-634 (7 February 2008) | doi:10.1038/451632a

We all know that language changes with time: new words, obsolete words, changed meanings, making verbs from nouns, etc. Many are familiar with the old English words "thou" and "thee" and their associated verb endings. Even earlier, English had no standard spellings and many words were used that are strange to our modern ears. Last year, two papers were highlighted here that documented patterns of change that have affected contemporary languages.

The invention of words requires intelligent agency

Those papers were loking at incremental changes with time within languages, and a crude analogy could be drawn with microevolution and Darwinian gradualism. Now, some of these authors have published on the origin of languages. Their study of Bantu, Indo-European, Austronesian, and Polynesian languages shows that "up to one-third of their words arose in rapid evolutionary bursts from the predecessor tongue". Again, the focus has been on vocabulary (there's more to say on this, but it is outside the scope of this blog). The authors write:

"We studied punctuational evolution in phylogenetic trees of language families inferred from vocabulary data. These trees describe the separate paths of evolution leading from a common ancestral language to the set of observed extant languages at the tips of the tree. The lengths of the individual branches of the trees record the amount of lexical divergence (replacement of words) between an ancestral and a descendant language. If lexical divergence is a gradual process that is not affected by the emergence of a new language, then the path length or total distance from the root of the tree to the languages at the tips should be independent of the number of language-splitting events or nodes found along that path. If language-splitting events produce punctuational bursts of evolution, however, we expect to find more total lexical divergence (longer path lengths) along paths through the tree that record more language-splitting events."

They demonstrate that their analysis leads to the conclusion that languages emerged abruptly, in a way that is distinct from the gradualism of subsequent changes.
The New Scientist report quotes one skeptical scholar:

Salikoko Mufwene a linguist at the University of Chicago, however, says it may be misleading to characterise language evolution as "abrupt". "You don't go to bed speaking one way and wake up speaking another way," he says. "Languages may change over centuries, but that is not abrupt, that is gradual."

This looks a bit like the reaction of Darwinists to the theory of Punctuated Equilibria: they just cannot escape from a gradualist mindset. It is significant, of course, that languages are spoken by intelligent agents. Consequently, the theoretical framework for understanding these changes should necessarily include inputs by intelligent agents. This emerges from a comment received last year by a linguist friend:

"One interesting development in the last century was the emergence of Nicaraguan Sign language, an entirely new language developed by deaf children under the age of 11 who were all sent to a new boarding school for deaf children. Older children developed a pigeon form with little grammar but a comprehensive vocabulary. The younger children had a fully formed grammar. It was certainly deemed as complex as American Sign Language. These children had had no contact with any other signing children, so developed the language de novo from their innate abilities."

The root problem appears to be that gradualism is a prevailing philosophy in the historical sciences. It is Lyellian: if it is not something we can study today, it does not count as science. But the data are telling us that things have happened in the past that go beyond our present experience. Perhaps we ought to be listening.

Languages Evolve in Punctuational Bursts
Quentin D. Atkinson, Andrew Meade, Chris Venditti, Simon J. Greenhill, and Mark Pagel.
Science, 319, 1 February 2008: 588.

Abstract: Linguists speculate that human languages often evolve in rapid or punctuational bursts, sometimes associated with their emergence from other languages, but this phenomenon has never been demonstrated. We used vocabulary data from three of the world's major language groups - Bantu, Indo-European, and Austronesian - to show that 10 to 33% of the overall vocabulary differences among these languages arose from rapid bursts of change associated with language-splitting events. Our findings identify a general tendency for increased rates of linguistic evolution in fledgling languages, perhaps arising from a linguistic founder effect or a desire to establish a distinct social identity.

See also:

Holden, C. Punctuation Marks in Language Evolution? ScienceNOW Daily News, 31 January 2008

McKenna, P. Languages evolve in sudden leaps, not creeps, NewScientist.com, 01 February 2008

Ever since it was realised that snowflakes can take "endless forms most beautiful", people have considered whether snowflake formation is in any way analogous to the products of evolutionary processes. For example, here is Mark Isaak on TalkOrigins:

"[. . .] order from disorder is common in nonliving systems, too. Snowflakes, sand dunes, tornadoes, stalactites, graded river beds, and lightning are just a few examples of order coming from disorder in nature; none require an intelligent program to achieve that order."

Snowflakes display a distinctive beauty

Another is David Bailey, writing for the National Center for Science Education, developing an argument around the improbability of getting a snowflake with a specific designated structure:

"[. . .] a snowflake is an exceedingly improbable structure, by any reckoning. In particular, it is extremely unlikely that a random roll-of-the-dice assemblage of water molecules would assemble a single snowflake with a specific designated structure. And yet this phenomenon is repeated trillions of times in a typical snowstorm.
[. . .] Snowflakes just happen - a homogeneous, undifferentiated mass of water molecules cools and becomes a sea of beautiful snowflakes with highly specific and differentiated structures. One could almost convince oneself that snowflakes constitute a demonstration of supernatural power."

With arguments like these, it is worth finding out just why snowflakes have such remarkable structures. A very helpful overview has appeared in Physics World. The author points out that the first problem to address is how crystals grow: "In fact, our understanding of crystal growth in general is remarkably primitive compared with our knowledge of crystal structure." The difficulty is that:

"crystal growth is a complex problem of molecular dynamics. The macroscopic development and morphology of a crystal - i.e. whether it forms facets or not, how fast it grows under different conditions and whether it develops into a single large crystal or many smaller ones - is governed by the precise way that the constituent atoms jostle into place as they solidify."

Scientists have been growing snow crystals in the lab, noting crystal shapes in relation to temperature and humidity. The key findings are illustrated in the graph below.

Snow-crystal morphology diagram (for larger image, click here. Credit: www.snowcrystals.com)

"Two features in this diagram immediately stand out. First, the crystals become more complex as the humidity increases: simple prisms arise when the humidity is low; while complex, branched forms appear when the humidity is high. Second, the overall morphology behaves peculiarly as a function of temperature, whereby it changes from plate-like to columnar and back again as the temperature is lowered. The latter behaviour has proven particularly difficult to explain, even at a qualitative level. Indeed, after 75 years we still cannot explain why snow crystals grow so differently when the temperature changes by just a few degrees."

Clearly, there are physical processes at work, operating at various levels, from the nano-scale upwards. This allows us to say to Isaak that the "order from disorder" is essentially the same order as any other case of crystallisation from the liquid to the solid state. It is an order that results from cooling, when interatomic forces become dominant over thermal energies. This should not be confused with order in living things, because that order is derived from information. Living things are best described as having "complex specified information", a term which Dembski has championed. Distinguishing "order" from CSI will greatly assist discussions of biological complexity.
Secondly, we can respond to Bailey's "exceedingly improbable structure" by pointing out that the temperature and snowclouds are not homogenous bodies in the sky. There are temperature gradients, humidity gradients, wind fluctuations and much more besides. Put all these together, and it becomes understandable that each snowflake emerges with a separate crystal growth history and a separate morphology. The extreme improbabilities then are inevitable. But how does this relate to evolutionary theory? Here again, CSI is the key. There is no evidence that biological information self-assembles, like snowflakes. So Law is not the explanation. Chance considerations yield numbers that have led some to think a multiverse is necessary to justify a naturalistic origin of life. The other option is Design - which requires a theistic metaphysic for science, but avoids the escapism from empiricism demonstrated by multiverse advocates.

The enigmatic snowflake
Kenneth Libbrecht
Physics World, 21(1), January 2008, 19-23.

Abstract: The beautiful symmetry of snowflakes masks the complex physics that governs how ice crystals grow and develop under different environmental conditions

See also:

Bailey, D.H. Evolution and Probability, Report of National Center for Science Education, vol. 20, no.4, 2001.

Isaak, M. Five Major Misconceptions about Evolution, October 1, 2003, The TalkOrigins Archive.

Quote: The concluding words of the first edition of Darwin's On the Origin of Species:
"There is a 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."

Last November, attention was drawn to a remarkable fossil find in Early Cretaceous rocks from Australia. The researchers discovered structures in the fossil that were just like the canal in a modern platypus that carries nerve fibers from the electrosensory glands in the bill to the brain. Further research has explored the significance of the fossil material coming from Cretaceous rocks, significantly earlier than had previously been thought possible.

The fossils are from the same family as the modern platypus (image credit: AAP & Joe Castro)

The researchers have named the fossil Teinolophos and refer to it as a "crown montreme". It has big implications for thinking about monotreme history:

"The finding that Teinolophos is a platypus indicates that the platypus and echidna clades diverged during or before the Early Cretaceous. This date is more ancient by a factor of 7 than the youngest, and 50% older than the oldest strict molecular clock estimates. The recent characterization of monotreme history as a "long-fuse" clade, whose diversification into platypus and echidna clades postdated the Cretaceous-Tertiary boundary, is difficult to reconcile with our more ancient divergence estimate, nor is there evidence of a diversity "explosion" at any time in monotreme history."
and:
"If the new position of Teinolophos is upheld, crown monotremes had originated and the platypus and echidna clades were established by the Early Cretaceous."

There are important implications for molecular clocks:

"our results suggest that different mammalian clades were subject to evolutionary rate heterogeneities that are incompatible with strict molecular clocks and difficult to accommodate even when relaxed molecular clock models are applied to mammalian history on a deep temporal scale."

This becomes another example of bradytely, akin to the Limulus example discussed recently. It means that many contributions to the literature about stem and crown monotremes have to be discarded in the light of this find. Furthermore, the hypothesis advanced in my Limulus blog - that organisms can be considered as reservoirs of type-specific biological information at the outset, and their subsequent history can result in various permutations of that biological information (e.g. niche specialisation) or to loss (degenerate forms) - appears to fit the platypus data as well.

The oldest platypus and its bearing on divergence timing of the platypus and echidna clades
Timothy Rowe, Thomas H. Rich, Patricia Vickers-Rich, Mark Springer, and Michael O. Woodburne
Proceedings of the National Academy of Sciences USA, January 29, 2008, 105(4), 1238-1242. (OPEN ACCESS ARTICLE)

ABSTRACT. Monotremes have left a poor fossil record, and paleontology has been virtually mute during two decades of discussion about molecular clock estimates of the timing of divergence between the platypus and echidna clades. We describe evidence from high-resolution x-ray computed tomography indicating that Teinolophos, an Early Cretaceous fossil from Australia's Flat Rocks locality (121-112.5 Ma), lies within the crown clade Monotremata, as a basal platypus. Strict molecular clock estimates of the divergence between platypus and echidnas range from 17 to 80 Ma, but Teinolophos suggests that the two monotreme clades were already distinct in the Early Cretaceous, and that their divergence may predate even the oldest strict molecular estimates by at least 50%. We generated relaxed molecular clock models using three different data sets, but only one yielded a date overlapping with the age of Teinolophos. Morphology suggests that Teinolophos is a platypus in both phylogenetic and ecological aspects, and tends to contradict the popular view of rapid Cenozoic monotreme diversification. Whereas the monotreme fossil record is still sparse and open to interpretation, the new data are consistent with much slower ecological, morphological, and taxonomic diversification rates for monotremes than in their sister taxon, the therian mammals. This alternative view of a deep geological history for monotremes suggests that rate heterogeneities may have affected mammalian evolution in such a way as to defeat strict molecular clock models, and to challenge even relaxed molecular clock models when applied to mammalian history at a deep temporal scale.

See also:

Miller, B. Fossil suggests platypus lived in dinosaur times, ABC News, Tue Jan 22, 2008.

Tyler, D. The "implausible" platypus continues to surprise, ARN Literature Blog, 23 November 2007.