Science Literature

The buildup for the 2009 bicentennial of Darwin's birth suggests that there is more here than celebrating the life of this Victorian gentleman scientist. An essay in Nature, marking the 150th anniversary of the short paper Alfred Russel Wallace sent to Darwin unveiling his thoughts on evolution by natural selection, gives some clues about the wider agenda for Darwin's acclaim.

Do we see the real Darwin? or do we get an image constructed by his heirs? (Source here)

Darwin communicated the striking convergence between his own thinking and that of Wallace in a letter to Charles Lyell on 18 June 1858. Lyell and Hooker urged a joint publication of the theory, so the article by Wallace and another from Darwin was read at a meeting of the Linnean Society on 1st July. At the time, it was not perceived as a landmark event in science. Neither Darwin or Wallace was present and their papers made little impact.

Thomas Bell, president of the Linnean Society, guaranteed himself an unfortunate footnote in the history books by writing in his annual review of 1858: "The year which has passed has not, indeed, been marked by any of those striking discoveries which at once revolutionize, so to speak, the department of science on which they bear".

The convergence can be attributed to intelligent design. Both men were thinking along the same lines and proposed essentially the same mechanism to explain evolutionary transformation. They were not alone as pioneers. In 1831, the plant breeder Patrick Matthew had proposed essentially the same theory in the appendix of a book on arboriculture - but he did not develop his ideas further.

"Exploring Wallace's role in the evolutionary story reveals a host of other figures who also deserve to be heard. over the past twenty years, the Darwinian revolution has been shown to be neither a revolution as commonly understood nor solely due to Darwin. Many people proposed developmental schemes, some as famous as Jean-Baptiste Lamark and Herbert Spencer, others relatively unknown but just as interesting. To remember Wallace is therefore to recognise that "evolution was in the air", and prompts one to wonder how Darwin's name rose so smoothly to the top."

Berry and Browne (the authors of the essay) refer to several factors explaining why Darwin became so dominant. The first concerns the honour placed on those who advance science: "precedence is everything; posterity ignores the second place". This is not particularly convincing, as Matthew has a justifiable claim for precedence, and both Darwin and Wallace agreed with joint publication of their ideas in 1858. Secondly, "major changes in scientific theory are not just about the formulation of new ideas, but also depend on circulation and discussion." Whilst there is no doubt that Darwin's work did trigger discussion, we should note that many of the responses were critical. His proposals were not received as the key to unlock the mystery of life, but many felt that his theory, where it could be tested, was not confirmed by the evidence. Thirdly, the authors point to Wallace's contribution to his own eclipse by adopting the term Darwinism and undermining his credibility as a scientist by becoming "a spiritualist". I have referred to these aspects of Wallace in a previous blog.

If we take Wallace on his own merits, he had many commendable strengths. "In fact, he was a superb scientist, whose contributions to many aspects of evolutionary biology and biogeography remain influential. His conduct in the evolution business is exemplary." So why was he eclipsed by Darwin? This comment deserves further thought:

"[T]he making of a new theory rarely occurs in isolation. Rather, it depends on the support of colleagues, social networks and interactions within the scientific community, as well as the power of the theory itself."

The key to understand this situation is that Darwinism is not just a scientific theory. Those who think this (and I am referring primarily to theistic evolutionists) appear to be blind to this analysis of history. Darwinism succeeded because it fitted into the next phase of Enlightenment rationalism. Up until Darwin, Enlightenment science was content to coexist with a modified Deism, where God was the First Cause and then left Creation to run as a giant machine apart from occasional interventions of destruction and recreation. Darwin's approach allowed these interventions to be excluded and God was restricted to acting as the First Cause and science became autonomous. Of course, there were a growing number of science leaders, including Darwin, who were prepared to contemplate agnosticism about God and wanted to promote the secularisation of science. Wallace was not part of this ideological shift, so he remained an outsider. Darwin was a prominent node in the network of Victorian science, and it suited his colleagues for him to be the front-man for their ideological revolution.

Why are these things important? It is because there continue to be many who think that ID advocates have invented the concept of a culture war. They think that Darwinism should always be considered as a "pure" scientific theory. The flaw with this is that it never was and it cannot today be defended purely on science grounds. There have always been significant doubts as to what variations (mutations) and natural selection can accomplish. However, to acknowledge this should not be isolated from the ideology underpinning Darwinism - which is where the real drivers are in these debates. That is why Wallace, with his teleological world-view, did not find a place in the emerging secularised scientific culture.

The other beetle-hunter
Andrew Berry and Janet Browne
Nature 453, 1188-1190 (26 June 2008) | doi:10.1038/4531188a

Abstract: Thanks to a fateful letter, the theory of evolution by natural selection was unveiled 150 years ago this week. Andrew Berry and Janet Browne celebrate the letter's writer, Alfred Russel Wallace.

There are many species of bacteria with two modes of life: one is motile with swimming propelled by rotating flagella, and the other is sessile as part of a biofilm. What happens when they change from free swimming mode to attached mode?

"Two things typically happen next. Cells stop expressing genes that encode components of the flagellum, and they secrete a sticky matrix of polysaccharides that holds them together on the surface. Once at a surface, swimming may be a hindrance rather than a help, and an inverse relationship between swimming and attachment has been seen in many diverse species. However, the molecular details underlying this arrest in motility have not been fleshed out. Are flagella ejected or dismantled? If not, do they keep rotating until they are jammed by the newly formed matrix?"

A nanotechnology clutch disengages the flagellum's tail from the engine that powers its rotation (source here)

It turns out that neither of these possibilities apply. Recent research by Blair et al. has shown that there is an "off-switch for rotation". This device utilises a special protein, EpsE.

"To determine whether EpsE acts as a brake that locks the motor, or a clutch that leaves the rotor freely spinning, Blair et al. tethered bacteria to a substrate by their filaments and observed rotation of the cell bodies around single flagellar motors. Under the influence of EpsE, cells stopped spinning but continued to undergo free rotational Brownian motion, indicating a clutch mechanism."

This finding has been a surprise:

It had been thought that bacteria slowed down by switching off the genes that make flagella, says Richard Berry, a physicist at the University of Oxford, UK, who studies molecular motors.
"This is a completely unknown thing," he says. "The previous wisdom was that flagella would spin for ever."

With hindsight, the clutch mechanism makes a lot of sense:

"The direct inhibition of motor rotation by EpsE represents a newly discovered control mechanism for bacterial swimming. Bacterial flagella are large protein complexes that require about 40 to 50 genes to assemble. Thus, the most obvious advantage of the EpsE mechanism over transcriptional control of flagellar genes is speed. In B. subtilis, only one protein, EpsE, needs to be expressed to stop the motor. Presumably, this is important if cells are to stay put in the early stages of biofilm formation. However, the advantages of a clutch over a brake mechanism are not so clear. Perhaps free rotation of flagella - or, alternatively, reduced motility during the transition to the EpsE-inhibited state - is important for the formation of well-structured biofilms. Or maybe a clutch is simply easier to make than a brake."

The researchers contrast the strategy of turning off flagellum synthesis with the clutch alternative, and supply one additional consideration - the possible need for reactivation of the flagellar motor:

"The flagellum is an elaborate, durable, energetically expensive, molecular machine and simply turning off de novo flagellum synthesis does not necessarily arrest motility. Once flagellar gene expression is inactivated, multiple rounds of cell division may be required to segregate preexisting flagella to extinction in daughter cells. In contrast, the clutch requires the synthesis of only a single protein to inhibit motility. Furthermore, if biofilm formation is prematurely aborted, flagella once disabled by the clutch might be reactivated, allowing cells to bypass fresh investment in flagellar synthesis. Whereas flagellum expression and assembly are complex and slow, clutch control is simple, rapid, and potentially reversible."

The clutch "solution" is therefore a neat, effective and potentially reversible mechanism. The authors describe it as "simple", which is OK if the meaning is that just one component is needed to disengage the flagellar motor. However, this conceptual simplicity in no way conflicts with understanding this system in terms of complex specified information. The researchers have identified a gene epsE responsible for making the EpsE protein which engages with the critical protein transmitting torque to the flagellum and removing the link to the source of power. The measure of complexity is in the unique shape of the EpsE protein and its ability to engage with the torque-transmitting protein so that power is no longer transmitted. The team is now "looking for a protein that disengages the clutch and reconnects the motor". This would help to disaggregate biofilms and could lead to significant medical applications. One measure of "simplicity" is the ease of finding such a protein. My prediction is that the researchers will not be using the word "simple" to describe this phase of the research. The science community is well aware that nanotechnology successes are achieved only by the application of sophisticated science and intelligent engineering design.

A Molecular Clutch Disables Flagella in the Bacillus subtilis Biofilm
Kris M. Blair, Linda Turner, Jared T. Winkelman, Howard C. Berg, and Daniel B. Kearns
Science 320, 20 June 2008: 1636-1638.

Abstract: Biofilms are multicellular aggregates of sessile bacteria encased by an extracellular matrix and are important medically as a source of drug-resistant microbes. In Bacillus subtilis, we found that an operon required for biofilm matrix biosynthesis also encoded an inhibitor of motility, EpsE. EpsE arrested flagellar rotation in a manner similar to that of a clutch, by disengaging motor force-generating elements in cells embedded in the biofilm matrix. The clutch is a simple, rapid, and potentially reversible form of motility control.

See also:

Berry R.M. and Armitage, J.P., How Bacteria Change Gear, Science 320, 20 June 2008: 1599-1600.

Whitfield, J. Bacterial engines have their own clutch, news@nature.com, 19 June 2008 | doi:10.1038/news.2008.903

The instinctive reaction of most people to this question is "Of course not! Without critical thinking, science is dead!" So when one of the leading science journals carries a report on the Louisiana bill promoting the development of "critical thinking skills" describing it as an "attack [. . .] on the teaching of evolution and mainstream scientific thought on global warming and other topics" - it is time to reflect on the reasons why.

One of the many caricatures of "academic freedom" initiatives (Source here)

The report puts great weight on the scientific consensus about evolution. It refers to "mainstream scientific thought", the "overwhelming support from our science teacher members", and to "agreed-upon standards". The implication is that all talk of "critical thinking" to challenge the consensus must be motivated by factors outside science. Consequently, we read comments like: "Science educators say the new wording is intended simply to circumvent rulings by U.S. courts that creationism and intelligent design are unconstitutional religious intrusions into a public school science curriculum."

This dismissive perception fails to acknowledge the intense debates and fundamental differences about evolution that exist within the scientific community (for a current example, go here). Can any issue relating to evolutionary theory be found that is free from controversy? I cannot think of one. The emphasis on 'consensus', with the implication that dissent comes from outside science, is actually alien to the spirit if science. It can (and should) be argued that this emphasis is a threat to the health and vigour of all disciplines of science. Sociologists of science have come to recognise that the 'consensus' argument is part of a struggle for power and influence. In his recent book, Professor Steve Fuller suggests that "public professions of faith in evolution by scientists are best interpreted as simply marking solidarity with the reigning orthodoxy" (p.32). He refers to one of the major recent 'consensus' statements on evolution:

"The first case is the InterAcademy Panel of 67 national academies of science, which in June 2006 issued a joint statement calling for the promotion of evolutionary theory in schools against an alleged worldwide creationist threat. Yet, the statement failed to identify any specific evolutionary mechanisms for mandatory instruction, resorting instead to an anodyne characterisation of evolution as somehow responsible for the diversity of life on Earth, and an easy dismissal of young-Earth creationism. One suspects that to manufacture the appearance of widespread scientific consensus, the statement's drafters were forced to edit out any specifically Darwinian references, especially to natural selection, that might prove divisive to some of the signatories." (p.32-33)

The inclusion of Global Warming issue is very interesting. This is another topic where 'the scientific consensus' has been thrust down the throats of the public, political leaders and funding bodies. The issue, of course, is not primarily about global warming per se, but whether the human activity of burning fossil fuels (and releasing extra carbon dioxide) has had a significant influence on atmospheric temperatures. (For a useful overview of issues, go here). It will be a surprise to many that there is a significant community of dissenting scientists who feel that the consensus is contrived and are very concerned about the pressures they face to conform. They vigorously object to the ad hominem claim that their dissent is sponsored by oil companies. Their responses in the media reveal titles and counter-arguments that have much common ground with the experiences of ID scientists. There is a general problem here for the science community to address: consensus arguments are being constructed which are undermining scholarly activity by treating dissent as anti-science and driven by vested interests. It appears to me that the real problem is with the champions of consensus, for they are selectively reporting the science issues and have an agenda that includes power, influence and access to research funds.

The consensus arguments about evolution are somewhat more complex than this. Why is it that "academic freedom" issues and the promotion of "critical thinking skills" are linked so easily to "creationism and intelligent design"? Those who do this are either advocates of philosophical materialism ('matter is all there is' so living things must be explained by material processes only and any dissent about this must be religious) or people who have adopted sphere sovereignty in their thinking about science. This is Gould's NOMA thesis, which requires an absolute line to be drawn between science/facts and religion/values. Anything to do with design (they say) is located within the religion/values sphere and is completely outside science. By embracing one of these philosophical stances, the opponents of the Louisiana bill have driven into a cul-de-sac which results in their flat, stereotyped responses. They are unable to conceive that their might be any philosophy of science other than their own, and they cannot recognise scientific arguments against evolution even when they are spelled out. As evidence of this, the cover of Explore Evolution is reproduced in the Science report with the comment "Political science?" Sad! It looks as though the author would benefit from education that develops "critical thinking skills".

This graphic is given the title: "Political Science?" in Science

Louisiana Opens School Door for Opponents of Evolution
Fayana Richards
Science 320, 20 June 2008: 1572.

A bill passed overwhelmingly by the Louisiana state legislature and expected to become law as early as next week marks the latest attack in the United States on the teaching of evolution and mainstream scientific thought on global warming and other topics.

See also:

Fuller, S. Dissent over Descent, Icon Books Ltd, Cambridge, 2008 (Chapter 1).

Crowther, R. Explore Evolution Textbook Featured in Science Magazine, Evolution News & Views, 22 June 2008

Crowther, R. Victory in Louisiana: Governor Jindal Signs Historic Science Education Act On Evolution and Education, Evolution News & Views, 27 June 2008

West, J.G. Louisiana Confounds the Science Thought Police (National Review Online, July 08, 2008)

Robert Deyes
ARN Correspondent

If Darwin was right then we would be just sophisticated monkeys, there would be no right or wrong, just 'make-em-up' ethics and there would be no God. This was the assessment of one local of Kanawha County in West Virginia as journalist Lee Strobel arrived to capture the story of Anti-Darwinian protests in 1974. Strobel at the time was a self-confessed atheist, believing that much of what the anti-Darwinian movement was promulgating reflected nothing more than blind ignorance. He considered the biblical creation story as simply fictitious, surpassed and discredited as it was by the knowledge gleaned by modern science. That year, as the protests against the teaching of Darwin in West Virginia's schools heated up, Strobel found himself alienated by the residents of a town that had already banished several hundred different textbooks from school circulation- books that, according to the local school board, taught the "wrong kind of ethic". In all truth Strobel was very much a convert of the scientific story of evolution, convinced as he was by the 'facts' and apparently clear-cut examples in support of evolutionary theory. As Strobel saw things, the random and undirected nature of Darwinism could not be reconciled with the purposeful nature of the biblical account. The very least that could be said was that, if Darwinism were as unshakable as its proponents claimed, God would not be needed for life to emerge. The Case For A Creator is an account of Strobel's journey to test the veracity of the apparent 'facts' of evolution and the materialistic world view- a journey that takes him across the United States as he interviews several key experts in various fields of science.

The first stop over for Strobel is with Jonathan Wells- a Berkeley graduate whose outspoken criticism of some of the icons of evolution is well known. During the interview Wells dismantles the evidences that Strobel had himself learnt as a graduate by showing how much of what we supposedly know about evolution is unsupported by the evidence. It is now widely accepted for example that Stanley Miller's laboratory experiments showing how amino acids could be generated under reducing atmospheric conditions did not accurately mimic the environment of the early earth. And yet today these experiments continue to feature prominently in biology text books as does Darwin's tree of life. As Wells points out, rather than revealing an unbroken chain of intermediates linking all of life to a few early forms as Darwin's tree required, the fossil record shows a sudden 'explosion' of life approximately 550 million years ago during which most of the major animal taxa appeared in a five million year time frame without any preceding intermediates. Equally troubling is the finding that embryologist Ernst Haeckel modified his now famous drawings of vertebrate embryos so that they would fit within preconceived ideas of an evolutionary continuum. Wells' criticism of the disjunction that exists between apparently homologous structures in vertebrates- that is, those structures that are considered to reveal common ancestry- and the genes responsible for their formation, different as they are in different animal species, shows just how much of what we know today contradicts the basic tenets of Darwinism.

During Strobel's journey, philosopher Stephen Meyer makes his case for an intelligently-designed universe on the grounds that the information-rich instruction code of DNA that comprises life directly parallels information-rich code that we know has been generated by intelligent agents. Meyer asserts how it is the irreducibly complexity of many of the 'machines' of the cellular world, with their requirement for all their components to be present before their function can be achieved, that most clearly defies the expectations of the Darwinian framework. As Meyer argues, since natural selection can only begin to select systems that have reached a minimal level of functionality and since this functionality is only attained when all the components of these systems are present, their initial assembly must have been directed by some guiding process. That is, they must have been intelligently designed. Biochemistry Professor Michael Behe, also on Strobel's long list of visits, was the initial proponent of irreducible complexity in biology. Behe has provided several examples of irreducibly complex biological systems notably the blood clotting cascade, the structure of the bacterial flagellum and the makeup of tiny hairs called cilia citing them as evidence for an intelligently-designed biological world.

A vast body of data is accumulating outside of the realm of biology in support of the design inference and many scientists are now realizing how uniquely fit for the existence of life our own earth appears to be. We now know that not only is our earth ideally positioned in our solar system so as to meet the survival needs of animals and plants but that it is also very well placed for humans to make important scientific discoveries about our cosmos. Strobel's interview with philosopher Jay Richards and astronomer Guillermo Gonzalez provides a catalog of such 'biocentricities'. Everything from the protective influence of the larger planets in our solar system to the consistent warmth and energy from our sun, from the effect of the moon on the tilt of the earth's axis to the overall mass of the earth, from the influence of the earth's own internal heat on the earth's environment to the orbit of our solar system within the strict confines of a 'habitability zone' around our galaxy draws us to the inevitable conclusion that ours is in every sense a unique world, designed as it is for our own enjoyment. As Strobel's discussions with physicist Robin Collins make all too clear, the physical characteristics of the elements that make up matter throughout the cosmos fall precisely within the narrow range of values that are permissible if life is to exist. The magnitude of the gravitational force, the size of the cosmological constant in Einstein's equations of general relativity, the difference in size between the protons and neutrons of atomic nuclei and the size of the strong and weak atomic forces that hold atoms together are so exactly placed in this permissible range that we can only conclude that an intelligence has been at work in the design of our cosmos. Theologian William Lane Craig likewise presents his arguments for a single, finely-tuned and controlled cosmic origin approximately 14 billion years ago from which our universe has subsequently expanded.

One of Strobel's final interviews is with philosopher J.P Moreland to discuss the subject of human and animal consciousness. While many contend that consciousness in humans is nothing more than the by-product of accumulating brain power, others such as Moreland conclude that it reveals something much deeper. Indeed observations on human behavior point to what psychologists call 'dualism'- a state in which consciousness and the mind exist separate from the rest of the brain. Our awareness of our selves- own thoughts, our own emotions, our desires and our own decisions- points to an entity one might call the 'soul' that exists outside of the electrical firings of the brain mass inside our heads. This 'inner and private mind' of man, asserts philosopher Alvin Platinga, is that one part of man that appears inaccessible to a naturalistic explanation. What we know about the mind of man, Moreland argues, directly agrees with the Christian world view of an omnipresent God who exists everywhere and manifests his presence in humanity through the soul. In the end Strobel's case also leads him to the identification of the God of Christianity as the designer whose works have fashioned all that we see around us. But metaphysical assertions aside, the scientific evidence that Strobel accumulates in his book provide a strong case against the purely naturalistic assertions of modern day Darwinism. Indeed one can only imagine how things would have turned out for the inhabitants of Kanawha County and the rest of West Virginia if they had been aware of this evidence back in 1974. They would have had a case to defend that was based on a very compelling scientific story.

After cellulose, lignin is a major constituent of plant material, comprising 25-33% of the dry mass and imparting mechanical strength and conducting water. There are three major types of lignin, depending on the monomers involved in the formation of this material. "Lignins are derived mainly from the phenylpropanoid monomers p-coumaryl, coniferyl, and sinapyl alcohol, which give rise to p-hydroxyphenyl, guaiacyl, and syringyl subunits when incorporated into the lignin polymer." These different types are significant for the research being considered here. "Generally, ferns and gymnosperms deposit lignins that are derived primarily from guaiacyl monomers together with a small proportion of p-hydroxyphenyl units, whereas angiosperm lignins are guaiacyl/syringyl copolymers that also can contain some p-hydroxyphenyl monomers." Since angiosperms appear in the Late Cretaceous, and the other types of vascular plant are found from the Silurian, some have thought that syringyl lignin is a late arrival in the evolutionary story of plants.

Selaginella moellendorffii (Source here)

The plant studied is a lycophyte - Selaginella moellendorffii - popularly known as spike moss. It can be considered a living fossil, and is described by the researchers as "a relict of an ancient vascular plant lineage". Its genome has been sequenced and it is the subject of numerous studies relating to lycophytes.

In their discussion, the researchers summarise their findings in this way:

"The distribution of syringyl lignin in the plant kingdom suggested two possible models for the evolution of F5H [an essential component in the formation of syringyl lignin]. First, the enzyme could have arisen early in plant evolution, was lost in ferns and gymnosperms, but was not lost in angiosperms or Selaginella. Alternatively, F5H could have evolved independently in lycophyte and angiosperm lineages after they had diverged. Our results suggest that the second model is correct and that F5H from Selaginella is functionally equivalent to, but phylogenetically independent from, angiosperm F5Hs. This conclusion is further supported by the observation that syringyl lignin derivatives are not detected in extant members of the Lycopodiaceae and have not been found in fossils of the extinct lycophyte Sigillaria ovata (order Lepidodendrales)."

The press release for the research paper summarises the achievement in these words:

"Biologists have discovered that a fundamental building block in the cells of flowering plants evolved independently, yet almost identically, on a separate branch of the evolutionary tree - in an ancient plant group called lycophytes that originated at least 420 million years ago. Researchers believe that flowering plants evolved from gymnosperms, the group that includes conifers, ginkgos and related plants. This group split from lycophytes hundreds of millions of years before flowering plants appeared. The building block, called syringyl lignin, is a critical part of the plants' scaffolding and water-transport systems. It apparently emerged separately in the two plant groups, much like flight arose separately in both bats and birds."

The conclusion, that this complex material "evolved independently" deserves careful scrutiny. We are dealing here with some very complex chemistry that does not exist in isolation from other aspects of the plant. The idea that almost identical innovations occurred independently may be the best of the explanations considered above, but there is at least one other option that needs to be considered: and that emerges from a design inference. Complex chemistry like this does not just happen: it suggests the presence of intelligence. This is confirmed by the potential this research offers for engineering plants for easier lignin breakdown in the manufacture of biofuels:

"Findings from studies such as this really have implications regarding the potential for designing plants to better make use of cellulose in cell walls," said Gerald Berkowitz [. . .] "Different forms of lignin are present in crop plant cell walls; engineering plants to express specifically syringyl lignin could allow for easier break down of cellulose. Overcoming this obstacle is an important next step for advancing second generation biofuel production."

These researchers are proposing to use their expertise in biotechnology and design engineering to bring about changes to plants that bear comparison with changes evolutionists attribute to mindless tinkering processes. This particular plant provides a remarkable example of convergence that argues against contingency in evolution and for intelligent agency in the way plant materials are constructed.

Independent origins of syringyl lignin in vascular plants
Jing-Ke Weng, Xu Li, Jake Stout, and Clint Chapple
Proceedings of the National Academy of Sciences USA, June 3, 2008, vol. 105, no. 22, 7887-7892.

Lycophytes arose in the early Silurian (~400 Mya) and represent a major lineage of vascular plants that has evolved in parallel with the ferns, gymnosperms, and angiosperms. A hallmark of vascular plants is the presence of the phenolic lignin heteropolymer in xylem and other sclerified cell types. Although syringyl lignin is often considered to be restricted in angiosperms, it has been detected in lycophytes as well. Here we report the characterization of a cytochrome P450-dependent monooxygenase from the lycophyte Selaginella moellendorffii. Gene expression data, cross-species complementation experiments, and in vitro enzyme assays indicate that this P450 is a ferulic acid/coniferaldehyde/coniferyl alcohol 5-hydroxylase (F5H), and is capable of diverting guaiacyl-substituted intermediates into syringyl lignin biosynthesis. Phylogenetic analysis indicates that the Selaginella F5H represents a new family of plant P450s and suggests that it has evolved independently of angiosperm F5Hs.

See also:

Fundamental Building Block In Flowering Plants Evolved Independently, Yet Almost Identically In Ancient Plants, ScienceDaily (May 28, 2008)

In 1969, a large meteorite fell to the ground about 100 miles north of Melbourne, Australia. It broke apart before impact, and the science community has been left with numerous fragments. It is a carbonaceous chondrite, which is commonly thought to be closest in composition to the source materials that formed the terrestrial planets. There has been extensive research into the organic contents of this meteorite, and some of this has concerned contamination. There are some evidences for contamination and some evidences supporting an extraterrestrial origin for the organic molecules. The latest research claims that there are "extraterrestrial nucleobases in the Murchison meteorite".

The Murchison Meteorite continues to attract interest from scientists and the media (source here)

What has been found? The researchers report "many biologically relevant organic molecules" and highlight uracil and xanthine for attention. These are the nucleobases referred to in the title of their paper. They are described as "precursors to the molecules that make up DNA and RNA". Uracil is used to store information contained in RNA, and xanthine is a metabolic intermediate in the breakdown of purine nucleotides (which only works in conjunction with suitable enzymes). What they are not are "genetic material" (as announced by the Imperial College Press Release and repeated by several other forums: ScienceDaily, PhysOrg.com, popsci.com).

Having reported the presence of these molecules, the authors go on to speculate about their significance. Since these molecules represent primordial material, they can be inferred to have been transported to the Earth's surface in the Hadean Period of Earth history. They "may have played a key role in life's origin." Their presence allows a more critical appraisal of theories about the endogenous production of amino acids (which no longer look viable as a source of these building blocks).

"Our data advance proposals that life's raw materials were delivered to the early Earth and other planetary bodies by exogenous sources, including carbonaceous meteorites. In contrast, the endogenous synthesis of prebiotic organic compounds may have been constrained by the conditions on the young Earth, perhaps most importantly by the oxidation state of the atmosphere. For example, only low yields of amino acids were produced under non-reducing conditions in the Miller-Urey-type experiment. Yet, whatever the inventory of endogenous organic compounds on the ancient Earth, it would have been augmented by extraterrestrial material. It is estimated that these sources delivered ~10^9 kg of carbon per year to the Earth during the heavy bombardment phase 4.5-3.9 billion years ago."

The researchers are very excited about their find and its potential for helping theories of abiogenesis:

"We believe early life may have adopted nucleobases from meteoritic fragments for use in genetic coding which enabled them to pass on their successful features to subsequent generations." (Zita Martins)
"Because meteorites represent left over materials from the formation of the solar system, the key components for life - including nucleobases - could be widespread in the cosmos. As more and more of life's raw materials are discovered in objects from space, the possibility of life springing forth wherever the right chemistry is present becomes more likely." (Mark Sephton)

This message is echoed in the media reports. For example, popsci.com says: "If the basic ingredients are zipping around throughout the cosmos, the likelihood of life taking shape wherever the chemistry is right is most certainly increased." Comments like this do not provide a service to anyone, for they confuse rather than clarify. The same point applies to the search for liquid water on other astronomical bodies - as though finding water is the key to life springing forth wherever the right chemistry is present. Research has shown over and over again that life does not self-assemble. Put all the ingredients of life together in a soup and you do not get life! Those who present the issue as one for chemists to solve are seriously astray. It is crucially important to focus on biological information and where it comes from. Law and chance do not deliver. Abiogenesis research that considers only these options has confirmed repeatedly that life does not emerge from a chemistry set. What is needed is a reorientation to the role of information, and for this, we need design perspectives in science.

"In my opinion, there is no basis in known chemistry for the belief that long sequences of reactions can organize spontaneously - and every reason to believe that they cannot. The problem of achieving sufficient specificity, whether in aqueous solution or on the surface of a mineral, is so severe that the chance of closing a cycle of reactions as complex as the reverse citric acid cycle, for example, is negligible." Orgel, Leslie, (Dec 1998) "The origin of life - a review of facts and speculations," Trends in Biochemical Sciences, 23: 491-495.

Extraterrestrial nucleobases in the Murchison meteorite
Zita Martins, Oliver Botta, Marilyn L. Fogel, Mark A. Sephton, Daniel P. Glavin, Jonathan S. Watson, Jason P. Dworkin, Alan W. Schwartz and Pascale Ehrenfreund
Earth and Planetary Science Letters, 270(1-2), 15 June 2008, 130-136

Abstract: Carbon-rich meteorites, carbonaceous chondrites, contain many biologically relevant organic molecules and delivered prebiotic material to the young Earth. We present compound-specific carbon isotope data indicating that measured purine and pyrimidine compounds are indigenous components of the Murchison meteorite. Carbon isotope ratios for uracil and xanthine of [delta]13C [. . .] indicate a non-terrestrial origin for these compounds. These new results demonstrate that organic compounds, which are components of the genetic code in modern biochemistry, were already present in the early solar system and may have played a key role in life's origin.

Robert Deyes
ARN Correspondent

Historically the field of evolutionary biology has been plagued with a fundamental move to fit or adapt scientific data into the picture of organic continuity that Darwin painted in The Origin Of Species (Ref 1). So strong has been this move that on occasions scientific objectivity has been lost and replaced by, what could only be described as a 'force of fit' to ensure that the validity of Darwinian theory was maintained (Ref 1). The unity of form observed during embryonic development was according to Darwin indicative of "the progenitor [. . .] of all the members of the same great class" (Ref 2, p. 600). Darwin's conviction over the importance of the embryological picture to his theory was made plainly clear in his autobiography where he wrote that,

"hardly any point gave me so much satisfaction when I was at work on The Origin, as the explanation of the wide difference in many classes between the embryo and the adult animal, and of the close resemblance of the embryos within each class" (Ref 3, p.125)

Darwin was not an embryologist and so relied very heavily on the viewpoints of his contemporaries. One of these was Professor Ernst Haeckel who, famous for his comparative drawings of embryos including those of fish and amphibians, brought seemingly strong confirmatory evidence to the Darwinian thesis. Darwin had a high regard for Haeckel's perspective and saw Haeckel's study of embryonic characters as "a great beginning" that showed us "how classification will in the future be treated" (Ref 2, p. 579). And yet Haeckel was overzealous and in making his embryo drawings, depicted a number of important details incorrectly (Ref 4). As Michael Richardson and his colleagues pointed out in a letter to Science, significant variations in embryonic size and form were missed (Ref 4). What Haeckel's inaccuracies demonstrated was a zeal to make the data 'fit' the theory. After all, these inaccuracies tended towards supporting the idea of a common progenitor rather than negating it. Richardson and his colleagues revealed the degree of 'supportive approximation' that Haeckel employed in his drawings when they published photographic evidence of progressive stages of development amongst different vertebrate species (Ref 4). Their results showed that, while there was a close correlation between embryonic developmental sequences between humans and other mammals, there was a very weak correlation between humans and other classes of vertebrates. (For Richardson's photos, go here).

Today Haeckel is remembered for his biogenetic law in which he proposed that "ontogeny recapitulated phylogeny" (Ref 5, p. 353). Haeckel theorized that animals climbed up their own family tree during embryonic development and as such presented us with a vision of how things had once been. Armed with his inaccurate representations of embryonic development and the convincing arguments of his biogenetic law, Haeckel created the phylogenist's 'dream' (Ref 6, pp. 246-247). However, by the beginning of the twentieth century, the shine of recapitulation had lost its luster. Gould recounts the disappointment that ensued with a quote from E.B Wilson's description of the "exact" experimental method:

It is a ground of reproach to morphologists that their science should be burdened with such a mass of phylogenetic speculations and hypotheses, many of them mutually exclusive, in the absence of any well-defined standard of value by which to estimate their relative probability. The truth is that the search [. . .] has too often led to a wild speculation unworthy of the name of science; and it would be small wonder if the modern student, especially after a training in the methods of more exact sciences, should regard the whole phylogenetic aspect of morphology as a kind of speculative pedantry unworthy of serious attention." (Ref 6, p. 247)

Paleontologists David Raup and Steven Stanley were equally emphatic about the inaccuracies of Haeckel's claims:

"During the eighteenth and early nineteenth centuries, many students of Mesozoic ammonites attempted to apply Haeckel's recapitulation theory to all ammonite species, believing that the course of ammonite evolution could thus be read from ontogenetic changes in shell ornamentation and suture patterns. In 1901, Pavlow invalidated the strict recapitulation concept by showing that in certain Jurassic lineages of ammonites new evolutionary features arose in the early stages of ontogeny; not until later in the evolutionary history of their respective lineages were these changes retained in the adult stages [. . .] ontogenetic development of the new features was retarded, relative to time of reproductive maturation." (Ref 7, p.275)

In other words, changes in the adult form arose after changes in the embryo, not before. It could no longer be convincingly argued that ontogenetic changes were a reflection of some evolutionary past. In light of such findings, it is paradoxical that prominent zoologists such as Richard Dawkins still maintain the importance of the so called 'embryological continuum'. Dawkins wrote, for example, that science, "can point out that the (embryological) continuum that seamlessly joins a non-sentient foetus to a sentient adult is analogous to the (evolutionary) continuum that joins humans to other species" (Ref 8, p.34). Likewise science writer David Quammen emphasized the classical Darwinian perception of the embryo not only as "the animal in its less modified state" but also the embryo as revealing, "the structure of its progenitor" (Ref 9, p. 13). Obviously, Dawkins and Quammen are at odds with the alternative, more persuasive assessment that was built on empirical evidence.

"The assumption that ancestral reminiscences could always be distinguished from recent embryonic adaptations had not been sustained. Too many stages were missing, too many others discombobulated. The application of Haeckel's law produced endless, unresolvable, fruitless argument, not an unambiguous tree of life." (Ref 6, p. 246)

These findings are in themselves preliminary indicators that the different classes of vertebrate are discontinuous. The data does not fit Darwin's premise of a few common progenitors from which all of life had originated.

REFERENCES

1. Gareth Nelson (1998), Colin Patterson (1933-98): Paleontologist-reformer of the fossil record, Nature, Volume 394 p626

2. Charles Darwin (1859), The Origin of Species By Means of Natural Selection Or The Preservation of Favored Races In the Struggle For Survival, Modern Library Paperbacks Edition (1998), New York

3. Charles Darwin, The autobiography of Charles Darwin, Copyright held by Nora Barlow in 1958, W.W. Norton and Company Inc, New York

4. Michael K. Richardson, James Hanken, Lynne Selwood, Glenda M. Wright, Robert J. Richards, Claude Pieau, Albert Raynaud (1998), Haeckel, Embryos, and Evolution, Science Vol 280 p293

5. Stephen Jay Gould (2002), The Structure of Evolutionary Theory, Belknap Press of Harvard University Press, Cambridge, Massachusetts

6. Stephen Jay Gould (1992), The Panda's Thumb- More Reflections In Natural History W.W Norton and Company, New York

7. David Raup and Steven Stanley (1971), Principles of Paleontology, W. H. Freeman and Company, San Francisco

8. Richard Dawkins (2003), A Devil's Chaplain, Published by Weidenfeld and Nicolson, London

9. David Quammen (2004), Was Darwin Wrong? National Geographic Magazine, November 2004 pp4-31

Robert Deyes

In his book The Crucible of Creation Conway Morris brought the Cambrian era of the earth's history to life with a pseudo-real journey into the past (Ref 1, pp. 63-115). Formidable amongst the examples of animals that he discussed was the Anomalocaris - a creature that David Gee would describe as, "a fearsome-looking metre-long predator" with "a circular mouth like a kitchen garbage-disposal unit" (Ref 2) What we also learn from the Cambrian explosion is that many of the animals that made their first appearance during that sudden moment of time would continue to exist for millions of years later albeit in different forms and in varying degrees of ecological 'domination' (Ref 3). The hand of a film director moving actors around the stage of life's theater is the picture that emerges. As paleontologist Niles Eldredge emphasized it is difficult to get away from the idea that someone was at the root of this theatrical jiggering:

"There really is something strange about the Cambrian. It is very much as if [. . .] life got going and somehow, somewhere, someone decided that it wasn't quite right. But rather than starting all over again, a simple, radical, reorganization was effected: new players were recruited, to be sure, and old ones dropped, but there was also a matter of emphasis - an expanded role for some, a diminished role for others - all rather reminiscent of cabinet changes at the beginning of a second presidential term" (Ref 3 p83)

The Cambrian Explosion is in tension with the fossil data (Source here)

Eldredge described the Cambrian explosion as a global event in which, "very suddenly, and at about the same horizon the world over, life showed up in the rocks with a bang" (Ref 3. p24). Gregory Wray, Russell Doolittle and colleagues dismissed the suddenness of this event presupposing a much earlier, unrecorded divergence of animal life (Ref 4,5). Interestingly this sudden appearance was not confined solely to invertebrate phyla. In 1999 a team from the Northwest University in China found fossil specimens in the Chinese Chengjiang region that suggested that vertebrates had also experienced a sudden origin in the lower Cambrian (Ref 6). It was the sudden appearance of so many animal phyla or body plans in a period of only several million years that led Stephen Meyer and his colleagues to infer that a concurrent quantum leap must have occurred in the molecular and cellular components of these organisms (Ref 7, pp. 31-37). These observations led Stephen Meyer and colleagues to the conclusion that intelligent design, rather than natural, undirected processes, provided the best causal explanation for the origin of the Cambrian fauna (Ref 7). Likewise the subsequent maintenance of phyletic disparity from the Cambrian to the present day constituted a phenomenon that, based on what we know from our everyday experiences, implied intelligent causation (Ref 7). Concluding their arguments Meyer and colleagues wrote:

"As a result of this observed "stasis" and the absence of "directional change," the morphological disparity or isolation between distinct animal body plans has remained un-bridged. Moreover [. . .] developmental mechanisms constrain the degree to which organisms may vary without deleterious consequences. Intelligent design also helps to explain these phenomena. Human experience suggests that designed objects have a functional integrity that makes the modification of some parts of their basic architecture difficult or even impossible" (Ref 7, p39).

We only have to look at modern forms of technology to realize just how right such an assessment is. Many cases can be cited where technology exhibits the same functional form now as it did at its inception. The car is a classical example of this. While having changed in detail over the last 100 years (introduction of automatic gear shifts, aerodynamic shaping, turbo engines, etc.), the car exhibits the same functional form that it always has (axles, wheels, drive shafts and chassis) (Refs 7, 8). Conversely there are examples of technological form that exhibit a marked discontinuity. The CD ROM, for example, represents a functional unit that does not directly follow on from the technology employed in the earlier LP record. In short, LPs and the CD ROM demonstrate a functional and structural disparity that parallels that which we see in the Cambrian fauna. Our technological world is rife with such examples of systems that mirror the maintenance of functional integrity that we see in biology (Refs 7, 8).

The maintenance of the basic Cambrian body plans throughout their subsequent history is best demonstrated through what Meyer and colleagues call 'the inverted cone of diversity' (Refs 7, 8). To understand what we mean by this, consider the basis of the Darwinian model of natural selection - a model that predicts the gradual increase in diversity from a few common ancestors at the beginning of the evolutionary process. This model is precisely the reverse of what we see in reality since, as already demonstrated, the Cambrian displays phyletic-level disparity preceding species-level diversity (Refs 7, 8). This inverted cone is once again precisely what we see in the blueprints or prototypes of everyday technological designs. Such prototypes are conceived first and only then are parts assembled, changes made and slight modifications executed. The Cambrian reproduces this order of construction very well- animals are first materially instantiated in their disparate, phyletic groups forming the fundamental body plans upon which subsequent modifications are made (Refs 7,8). The Cambrian explosion thus represents the epitome of what the modern Intelligent Design (ID) movement is all about.

References
1. Simon Conway Morris (1998), The Crucible of Creation; The Burgess Shale And The Rise Of Animals, 1st Ed, Oxford University Press

2. David Gee (1999), Relics: Squashy fossil in the bag, Nature Science Update

3. Niles Eldredge (1987), Life Pulse: Episodes From The Story of The Fossil Record, Facts On File Publications, New York

4. Gregory Wray, Jeffrey Levinton and Leo. H. Shapiro (1996), Molecular Evidence for Deep Precambrian Divergences Among Metazoan Phyla, Science Vol 274 pp 568-573

5. Russell F. Doolittle, Da-Fei Feng, Simon Tsang, Glen Cho, Elizabeth Little (1996), Determining Divergence Times of the Major Kingdoms of Living Organisms with a Protein Clock, Science Vol 271 pp 470-477

6. D-G. Shu, H-L. Luo, S. Conway Morris, X-L. Zhang, S-X. Hu, L. Chen, J. Han, M. Zhu, Y. Li and L-Z. Chen (1999), Lower Cambrian vertebrates from south China, Nature 402, 42 – 46

7. Stephen Meyer, Paul Nelson and Paul Chien (2001) The Cambrian Explosion: Biology's Big Bang, http://www.discovery.org/articleFiles/PDFs/Cambrian.pdf

8. Stephen Meyer (2004), The Origin of Biological Information and the Higher Taxonomic Categories, Proceedings of the Biological Society of Washington, Volume 117, pp. 213-239

The most trenchant and effective critiques of evolutionary biology have tended to come from scholars who are themselves advocates of evolutionary biology. Two books have appeared in recent years, both reviewed by Johan Bolhuis in the pages of Science. "In the end", says Bolhuis, "the two books are complementary, and together they constitute a formidable critique of evolutionary psychology." The theory of evolution is

"generally considered one of the most important intellectual achievements of the modern age. It therefore seems logical to extend the theory to cognition, as Darwin himself did in The Descent of Man when he considered human characteristics such as morality or emotions to have been evolved. Evolutionary psychology aims to do just that: applying evolutionary theory to the human mind. Specifically, it proposes that the mind consists of cognitive modules that evolved in response to selection pressures faced by our Stone Age ancestors. The approach has a wide popular appeal, perhaps because it often addresses such exciting topics as human desire, sex, and passion."

The archetypal evolutionary psychology perspective of human nature (Image source here)

The first book is Adapting Minds by David J. Buller. Since this was published in 2005, comment here will be brief.

Buller eventually concludes that the paradigm is not particularly well founded theoretically. One of its key claims is that "our modern skulls house stone-age minds" - that the human mind has not evolved significantly since the Pleistocene. Buller offers overwhelming evidence for the contrary conclusion. As he puts it, "There is no reason to think that contemporary humans are, like Fred and Wilma Flintstone, just Pleistocene hunter-gatherers struggling to survive and reproduce in evolutionarily novel suburban habitats."

The review offers a specific example, drawn from Buller's own analysis of child abuse data in the US.

"Buller devotes three chapters to the paradigm's interpretations of mate preferences, marriage and infidelity, and parenthood. In one, he focuses on Martin Daly and Margo Wilson's evidence for what they have called "discriminative parental solicitude." They provided data suggesting that children are much more likely to suffer abuse from stepparents than from their biological parents. Their findings are consistent with an evolutionary interpretation whereby parental investment is directed at increasing the chances of survival of one's own genes. Buller argues that Daly and Wilson's analysis is influenced by a reporting bias. He and Elliott Smith have analyzed a large dataset on child abuse in the United States, and they conclude that the evidence does not support the evolutionary psychology hypothesis."

The second book, by Robert C. Richardson, has the provocative title: Evolutionary Psychology as Maladapted Psychology. Despite this, Bolhuis writes: "The merit of his critique is that it is not polemic in the way those of some of his fellow critics (such as Jerry Fodor or Stephen Jay Gould) have been." The approach is to consider the methodology of evolutionary psychology: "he criticizes mainly the methods used by evolutionary psychologists".

"Richardson evaluates in some detail whether particular human cognitive traits, such as language or human reasoning, can be seen as adaptations. He concludes that although it should be possible to find evidence to support such claims, evolutionary psychologists have generally failed to do so. [. . .] The main problem with evolutionary psychology is that it usually does not consider alternative explanations but takes the assumption of adaptation through natural selection as given."

This point is very important. A characteristic of Kuhn's "normal science" is that people work within the paradigm. They are typically blind to alternatives that can only be considered rigorously by moving outside the paradigm. Evolutionary psychologists have given priority to dogma by emphasising adaptation and presuming an evolutionary trajectory. But this approach leads to force-fitting data to theory and because the dogma reigns supreme, the system cannot be falsified.

A major problem is that critical data is typically lacking. Theory reigns unconstrained by data! Often, it is very difficult to contest the conclusions of the evolutionary psychologists. Thus far, the onus of proof has tended to rest on the sceptics, but this is methodologically very weak. It allows theory to dominate with the guise of empirical science.

"At various places in Evolutionary Psychology as Maladaptive Psychology, Richardson concludes that we simply lack the historical evidence for a reconstruction of the evolution of human cognition. For human language, an "explanation" favored by evolutionary psychology is that it evolved for use in complex social groups, that is, there was a functional demand for language. Richardson rightly suggests that paleontologists are unlikely to unearth the evidence that can inform us about the social structure of our ancestral communities."

Bolhuis reveals something of his own concern when elaborating on this point:

The study of evolution is concerned with a historical reconstruction of traits. It does not, and cannot, address the mechanisms that are involved in the human brain. Those fall within the domains of neuroscience and cognitive psychology. In that sense, evolutionary psychology will never succeed, because it attempts to explain mechanisms by appealing to the history of these mechanisms. To use the author's words, "We might as well explain the structure of orchids in terms of their beauty." In this excellent book, Richardson shows very clearly that attempts at reconstruction of our cognitive history amount to little more than "speculation disguised as results."

Piling On the Selection Pressure
Johan J. Bolhuis
Science 320, 6 June 2008: 1293 | DOI: 10.1126/science.1157403

A review of Evolutionary Psychology as Maladapted Psychology by Robert C. Richardson, MIT Press, Cambridge, MA, 2007. 225 pp. ISBN 9780262182607.

We're Not Fred or Wilma
Johan J. Bolhuis
Science 309, 29 July 2005: 706 | DOI: 10.1126/science.1115209

A review of Adapting Minds by David J. Buller, MIT Press, Cambridge, MA, 2005. 564 pp. ISBN 0-262-02579-5.

Robert Deyes

Astronomer and mathematician Chandra Wickramasinghe, has been a notable figure in the ongoing scientific debates on evolution, promulgating the unlikelihood that natural selection could explain the origin of something as complicated as the cell [1]. Wickramasinghe is better known for his conviction that life is a "cosmic phenomenon" - that it is through cosmic dust that life has been seeded on earth [1]. Yet he is also known for his criticism of what he calls Darwinist indoctrination as witnessed in his appearance at the 1981 Creation Science trial in Arkansas. In his testimony he severely attacked Darwinian theory on the basis that the accumulation of mutations upon which natural selection supposedly acted would, if anything, lead to the gradual degradation and not accumulation of the genetic information that we see in organisms today [1]. He thus relegated Darwinian Theory to its more conservative form in which, "the processes of mutation and natural selection can only produce very minor effects in life as a kind of fine tuning of the whole evolutionary process" [1].

The low probabilities of obtaining functional enzymes in a primordial soup rule out explanations appealing to law and chance (image source here)

Wickramasinghe argued that gaps in the fossil record as well as the absence of transitional forms linking up the different phyletic groupings of fossils make the broader application of Darwinism across biology untenable [1]. Nevertheless, what really convinced Wickramasinghe of the insufficiency of Darwinism was that specific enzymes are needed within the cell for life to even exist. According to Wickramasinghe, if one were to envisage the random assembly of all these enzymes from some concoction of amino acids in a hypothetical primordial soup, the odds of obtaining these enzymes with the specific functions they have in the cell would be a staggeringly low 1 in 10exp40,000. As he subsequently concluded, "the number of shufflings needed to find life exceeds by many powers of 10 the number of all the atoms in the entire observable Universe". [1]

The above observations themselves provide a source of awe and contravene the rather dismissive trivialization often used to oppose the inference of design- that the very fact that we are here to look back on the history of the universe is testimony that this very small probability must have been fulfilled without recourse to a designer's 'hand'. In reviewing Harold Morowitz work, for example, physicist and Nobel laureate Murray Gell-Mann defined prebiotic evolution as a 'gateway event' in which the synthesis of nucleotides permitted genomes to simply, "come into existence" [2]. But the inference that big things like genomes come out of small changes like the synthesis of nucleotides carries with it a complete lack of causal specificity [3]. We have no naturalistic causal chain that takes us from a primordial soup to a living cell. From the origin of the bacterial cell to the advent of the first single-celled eukaryotes and the eventual evolution of higher animals, we find crevasse-size gaps and discontinuities that do not lend themselves easily to simple 'gateway event'-type explanations. True, there is a clearly observable increase in the level of complexity throughout our natural history and certainly we observe the emergence of higher levels of organization in the 'aggrandizement' of human societies and animal communities. Nevertheless, while theorists such as Stuart Kauffman believe that chemicals can arrange themselves into stable cycles 'for free', without any purpose or forethought [4], design theorists see the complexity of living form as a hallmark of an intelligence behind the design. I would concur.

[1]Details of Chandra Wickramasinghe's testimony at the 1981 Arkansas Evolution/Creation trial can be found at http://www.panspermia.org/chandra.htm

[2] Murray Gell-Mann (1994), The Quark and the Jaguar, Adventures in the simple and the complex. W.H. Freeman and Company, New York p.240

[3] William Dembski (2002), No Free Lunch: Why Specified Complexity Cannot Be Purchased Without Intelligence, Rowman & Littlefield Publishers, Inc, Lanham, Maryland pp 239-246

[4] Stuart Kauffman (2000), Investigations, Oxford University Press, New York

Copyright(c), 2008, Robert Deyes

According to the authors of the paper, research has uncovered "the evolution of a key innovation"; the New Scientist report refers to "a major evolutionary innovation" and "a rare and complex new trait"; The Scientist calls it a "big evolutionary jump". They are referring to the "ability to metabolise citrate, a [. . .] nutrient in their culture medium that E. coli normally cannot use."

Escherichia coli (source here)

The experimental work involved keeping 12 strains of the bacterium E. coli in a medium where there was glucose for them to metabolise, but also a plentiful supply of citrate. "Examining E. coli cultures that his lab has maintained since 1988, Lenski found that one population of the bacterium had evolved the ability to metabolize citrate - an unprecedented trait - after more than 30,000 generations, or approximately 15 years." Using samples preserved from earlier stages of this extended experiment, the research team established that one of the 12 populations gained a hidden mutation after about 20,000 generations. Only this population later developed the ability to metabolise citate. Thus, it can be inferred that "this evolutionary novelty grew from the accumulation of unpredictable, chance events."

"It's a very elegant demonstration that major changes may depend on accretion of minor changes before hand," said Albert Bennett, a University of California, Irvine evolutionary physiologist who gave Lenski feedback on the study before it was published in PNAS. "What's really demonstrated here is that the way has to be paved before hand."

This research is being hailed as a vindication of evolutionary theory against the sceptics:

"Lenski's experiment is also yet another poke in the eye for anti-evolutionists, notes Jerry Coyne, an evolutionary biologist at the University of Chicago. "The thing I like most is it says you can get these complex traits evolving by a combination of unlikely events," he says. "That's just what creationists say can't happen."

There are several observation that should be made before reaching general conclusions. The first relates to the machinery needed to metabolise citrate. The system to do this is already largely in place, but one enzyme is lacking. This is the comment from Mike Behe:

"Now, wild E. coli already has a number of enzymes that normally use citrate and can digest it (it's not some exotic chemical the bacterium has never seen before). However, the wild bacterium lacks an enzyme called a "citrate permease" which can transport citrate from outside the cell through the cell's membrane into its interior. So all the bacterium needed to do to use citrate was to find a way to get it into the cell. The rest of the machinery for its metabolism was already there. As Lenski put it, "The only known barrier to aerobic growth on citrate is its inability to transport citrate under oxic conditions."

Consequently, it is at least worth asking the question whether the E.coli bacterium had, in the past, lost the ability to metabolise citrate and what we are now seeing is a restoration of that damaged system. If this were the case, we should not be talking about "a major evolutionary innovation" but rather about the way complex systems can be impaired by mutations.

As yet, it is not known what mutations were involved. But clearly, if there were two, and if the first was needed before the second could complete the job, the experiments demonstrate how difficult it is to achieve orchestrated changes. This was exactly the point of Behe's study of ways of achieving resistance to malaria. In his words:

"I think the results fit a lot more easily into the viewpoint of The Edge of Evolution. One of the major points of the book was that if only one mutation is needed to confer some ability, then Darwinian evolution has little problem finding it. But if more than one is needed, the probability of getting all the right ones grows exponentially worse. "If two mutations have to occur before there is a net beneficial effect - if an intermediate state is harmful, or less fit than the starting state - then there is already a big evolutionary problem." And what if more than two are needed? The task quickly gets out of reach of random mutation."

So, far from this research being "another poke in the eye for anti-evolutionists", it demonstrates a major problem for those evolutionists who want to claim Darwinism can achieve major transformations. These mutations are not only rare, they are also useless without the pre-existence of a biochemical system that can turn the products of mutation into something beneficial. Behe writes:

"If the development of many of the features of the cell required multiple mutations during the course of evolution, then the cell is beyond Darwinian explanation. I show in The Edge of Evolution that it is very reasonable to conclude they did."

Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli
Zachary D. Blount, Christina Z. Borland, and Richard E. Lenski
Proc. Natl. Acad. Sci. USA, 10.1073/pnas.0803151105

Abstract: The role of historical contingency in evolution has been much debated, but rarely tested. Twelve initially identical populations of Escherichia coli were founded in 1988 to investigate this issue. They have since evolved in a glucose-limited medium that also contains citrate, which E. coli cannot use as a carbon source under oxic conditions. No population evolved the capacity to exploit citrate for >30,000 generations, although each population tested billions of mutations. A citrate-using (Cit+) variant finally evolved in one population by 31,500 generations, causing an increase in population size and diversity. The long-delayed and unique evolution of this function might indicate the involvement of some extremely rare mutation. Alternately, it may involve an ordinary mutation, but one whose physical occurrence or phenotypic expression is contingent on prior mutations in that population. We tested these hypotheses in experiments that "replayed" evolution from different points in that population's history. We observed no Cit+ mutants among 8.4 x 1012 ancestral cells, nor among 9 x 1012 cells from 60 clones sampled in the first 15,000 generations. However, we observed a significantly greater tendency for later clones to evolve Cit+, indicating that some potentiating mutation arose by 20,000 generations. This potentiating change increased the mutation rate to Cit+ but did not cause generalized hypermutability. Thus, the evolution of this phenotype was contingent on the particular history of that population. More generally, we suggest that historical contingency is especially important when it facilitates the evolution of key innovations that are not easily evolved by gradual, cumulative selection.

See also:

Behe, M. Multiple mutations needed for E. coli, Amazon Blog, 6 June 2008

Grant, B. Evolution loves history, The Scientist Newsblog, 2 June 2008

Holmes, B. Bacteria make major evolutionary shift in the lab, New Scientist, 09 June 2008

Robert Deyes

The molecular basis of sight is as complex as it is beautiful with interactions between proteins called transducins, phosphodiesterases, ion channels and pumps converting the original photon of light that reaches the eye into a signal that the brain can process (Ref 1). Studies have also revealed an added luxury of sight - self-repair and self-correction of optical aberration (Ref 2). A team of scientists at Cornell heading the study showed how, through neuronal feedback loops linking the eye to the brain, the brain could compensate for at least three different types of visual aberration - a finding that lead the head of the study, Cornell University professor Howard Howland to conclude that, "visual acuity is a result of various component parts 'wanting' to see better [. . .] able to sense aberrations and to change shape and function" (Ref 2). It thus seems rather paradoxical that some should come to the conclusion that complex organs such as the eye are, "not the work of some great composer but of an insensible drudge - an instrument, like all others, built by a tinkerer" (Ref 3).

A variety of feedback mechanisms mean that we see better than we might expect (graphic source here)

Why is it that prominent Darwinists such as Richard Dawkins reject purposeful design in the biological realm even though such a realm, by their own admission, exhibits design and provides every indication having been designed (Ref 4)? A look at Darwin's own reasons for rejecting design provides an important clue. According to Dawkins, Darwin's loss of faith in a purposeful designer came partly from his observation of the 'degoutant' in the natural world (Ref 4). Considering the digger wasp as a prime illustration of the macabre habits of nature, Dawkins recounts how these creatures lay their eggs within the bodies of other insects upon which the emergent larvae consequently feed (Ref 4). The female digger wasps guide their stings so precisely into their prey that their victims become irreversibly paralyzed but do not die (Ref 4). This scenario, according to Dawkins, is the best evidence that nature is not cruel but only pitilessly indifferent to the well being of its members (Ref 4). In Darwin's eyes, it was difficult to admit that an omnipotent and beneficent God could design something so savage and unappealing (Ref 4). Unfortunately for Darwin, in this instance he allowed his judgment to be clouded by his own subjective expectations of what the Judeo-Christian Creator would and would not do. In reference to the Ichneumonidae, distant cousins of the killer wasps, for example, he wrote,

"I cannot persuade myself that a beneficent and omnipotent God would have designedly created the Ichneumonidae with the express intention of their feeding within the living bodies of caterpillars." (Ref 5)

In the process of setting such an expectation, Darwin had unreasonably closed the door on design. Dawkins similarly concluded that the apparent roundabout and seemingly wasteful way through which the recurrent laryngeal nerve loops through the human body presented a perfect illustration of the limitation of evolutionary perfection and evidence for non-design (Ref 6). After all, no one in their right mind would have made a contraption so inefficient and imperfect (Ref 6). Inefficient and imperfect in whose eyes and why is this relevant?

An inference that a system is not designed simply because its design is not how we would expect it to be is not an inference based on scientific evidence but rather on personal bias. Clearly we have much to learn from nature if we are to reap the benefits of automated, self-correcting systems such as the eye; clearly we have a lot to learn from the designer whose systems we can identify throughout our natural world.

References

1. Michael J Behe (1996) Darwin's Black Box-The Biochemical Challenges to Evolution, 1st Edition, Simon and Schuster, New York; pp. 18-22
2. Better than Hubble, human eye can self-correct some optical faults.
3. Cornelius Hunter (2001) Darwin's God, Evolution and the Problem of Evil, Brazos Press, Grand Rapids, Michigan, p. 83
4. Richard Dawkins (1996), God's Utility Function, Phoenix, Orion Books Ltd, London
5. David Hull (1991), The God of the Galapagos, Nature, Volume 352, pp 485-486
6. Richard Dawkins (2003) A Devil's Chaplain, Weidenfeld and Nicolson London, UK, p.192

Copyright (c), Robert Deyes, 2007

Although parrots are familiar birds today, they are very sparsely represented in the fossil record. This means thinking is largely unconstrained by data. The discovery of two fossil parrots from the Lower Eocene of Denmark has made a significant change to this situation. The new fossils are considered to predate the previous 'oldest parrot' by 40 million years.

Jardine's Parrot (Source: here)

Of the two fossil birds, one is considered a member of the "stem group" and the other (Mopsitta tanta) a representative of "crown group" species. The implication is that stem and crown species co-existed.

"Mopsitta tanta is in many respects, more similar to Recent Psittaciformes than to any other Palaeogene psittaciform. Although it is not absolutely certain on the basis of preserved features (humeral morphology cannot be entirely diagnostic at this level), it is highly likely that Mopsitta tanta is a member of Psittacidae, therefore providing further support to the hypothesis of an early Eocene (or earlier) radiation of Psittaciformes; it is likely that representatives of crown-group Psittaciformes such as Mopsitta, existed in the Early Eocene alongside their stem-group counterparts Pseudasturidae and Quercypsittacidae."

The main focus of this blog concerns the rapidity of the radiation. Although Darwinists like to emphasise gradualism, with a slow pathway linking stem and crown species, here they are found together almost at the beginning of the Tertiary (which is the earliest many palaeontologists would put them). It's another reminder that speciation is not Darwinian, and the mechanisms that explain faunal radiations are currently unknown.

As a postscript, it is worth revisiting Thomas Stidham's 1998 report of a parrot jawbone from the Cretaceous. This raised many eyebrows because it was so early. The consensus seems to be that it was misidentified. "Dyke and Mayr (1999) considered it to be of uncertain taxonomic affinity because of the fragmentary nature of the material and the possibility that it could be from any number of other taxa, such as a caenagnathid-like theropod dinosaur". Whilst caution is justified, there is a possibility that judgments have been influenced by the low credibility of finding a Cretaceous parrot. With the confirmed presence of modern parrots in the Lower Eocene, credibility should no longer be an issue.

Two new parrots (psittaciformes) from the Lower Eocene Fur Formation of Denmark
DAVID M. WATERHOUSE, BENT E. K. LINDOW, NIKITA V. ZELENKOV, GARETH J. DYKE.
Palaeontology, 51(3), May 2008, 575-582 | doi:10.1111/j.1475-4983.2008.00777.x

Abstract: Two new fossil psittaciform birds from the Lower Eocene 'Mo Clay' (Fur Formation) of Denmark (c. 54 Ma) are described. An unnamed specimen is assigned to the extinct avian family of stem-group parrots, Pseudasturidae (genus and species incertae sedis), while a second (Mopsitta tanta gen. et sp. nov.) is the largest fossil parrot yet known. Both specimens are the first fossil records of these birds from Denmark. Although the phylogenetic position of Mopsitta is unclear (it is classified as family incertae sedis), this form is phylogenetically closer to Recent Pstittacidae than to other known Palaeogene psittaciforms and may, therefore, represent the oldest known crown-group parrot.

A lower jaw from a Cretaceous parrot
Thomas A. Stidham
Nature 396, 29-30 (5 November 1998) | doi:10.1038/23841

All known Cretaceous bird fossils representing modern higher taxa are from the aquatic groups Anseriformes, Gaviiformes, Procellariiformes and Charadriiformes. Here I describe a toothless avian dentary symphysis (fused jawbone) from the latest Cretaceous of Wyoming, United States. This symphysis appears to represent the oldest known parrot and is, to my knowledge, the first known fossil of a 'terrestrial' modern bird group from the Cretaceous. The existence of this fossil supports the hypothesis, based on molecular divergence data, that most or all of the major modern bird groups were present in the Cretaceous.

The problem for colour vision can be summarised thus: "The focal length of a simple lens varies as a function of the wavelength of light. Short wavelengths (blue) are focused at shorter distances from the lens, whereas long wavelengths (red) are focused at longer distances from the lens. This longitudinal chromatic aberration (LCA) leads to chromatic blur that degrades image quality." Commercial lenses that are corrected for LCA make use of components made from materials with different refractive indices.

"The biological solution to LCA is the multifocal lens. Such a lens has several distinct zones that focus monochromatic light of a particular wavelength at different distances. Since the refractive power of the multifocal lens is also a function of the wavelength of light, each of the zones of different focal length for monochromatic light focuses a different band of wavelengths on the same plane in the retina. A sharp colour image is created on the background of defocused light. This solution seems at first sight to be inferior to the technical solution, but has the important advantage that the optical system is considerably smaller, which is of energetic benefit to the animal."

The biological solution is utilised in a wide range of animals. "The success of this optical design is reflected in the multifocal systems present in a variety of amphibians, reptiles and mammals (including primates). The evolutionary origins of this lens design, however, are unknown." The research team has set out to cast light on the antiquity of the multifocal lens. Their methodology is very interesting. The key to understanding it is "stasis". Once originated, body plans show little deviation. Similarly, complex structures having come into existence do not change significantly. Genes are conserved rather than modified. As Gould so forcibly argued: "stasis is data" and this principle appears to underpin this research. As we shall note, adopting this principle does not lead to findings that favour Darwinian gradualism.

The southern hemisphere lamprey, Geotria australis, showing its well-developed eye (Source: go here).

The researchers have chosen to work with lampreys, which are extant jawless fish. Recognisable lampreys are also found as fossils in Cambrian rocks, predating bony fish. The argument is: if multifocal optics are found in lampreys, this establishes the design as an early innovation, predating the cartilaginous fish (chondrichthyes) and the bony fish (osteichthyes). Conversely, if multifocal optics are not found, the innovation comes later. Genetic information relevant to this investigation concerns the presence of photopigments, and evidence was known to suggest there was value in an analysis of lamprey colour vision.

"The southern hemisphere lamprey Geotria australis possesses five photopigments [. . .]. At least three of the five visual pigments [. . .] are orthologous to the visual pigments in jawed vertebrates. Although rod opsin-like opsin type A (RhA) and type B (RhB ) of lampreys share similarities with the rod opsin (Rh1) and Rh1-like cone opsin (Rh2) of jawed vertebrates, respectively, the functional identity of the receptors housing these visual pigments remains elusive. It has, however, been suggested that all five photoreceptors in G. australis have close affinities to those of cones in gnathostomes."

The findings relate to all lamprey species studied, selected to be representative of the group:

"All four species of lamprey were found to have multifocal lenses, optically similar to those of bony fishes."
"This is the first study to show that the eyes of lampreys (Agnatha), extant representatives of the earliest vertebrates, possess multifocal lenses and therefore the optical apparatus for well-focused colour vision."

The implications are (1) that colour vision via multifocal optics is a Cambrian-Recent phenomenon; and (2) that multifocal optics is suggestive of a monophyletic origin.

"The presence of multifocal lenses in the eyes of lampreys confirms the early origins of colour vision in vertebrates, and suggests that other aquatic vertebrates and tetrapods have retained this optical feature, the latter despite the transition from an aquatic environment to a terrestrial habitat, where the cornea comes into play as an additional refractive element."
"The presence of multifocal lenses in representatives of all vertebrate classes studied thus far and their absence in cephalopods suggests a monophyletic origin for this lens design. Convergent evolution in so many vertebrate lineages is unlikely."

This should give Richard Dawkins (and others who think that eyes evolved easily) something to think about. Allowing an evolutionary perspective on the data, multifocal optics evolved once and then has been passed on to descendants with very little change. The same data permits a design perspective, as there is no hint here how such complexity evolved rapidly.

"The presence of at least four visual pigments [. . .] in the last common ancestor of jawed and jawless vertebrates suggests that the earliest vertebrates were able to sample a rich spectral light environment and enjoy the many advantages of colour vision. Our findings suggest that the eyes of these ancient animals were capable of forming well-focused colour images."

Early evolution of multifocal optics for well-focused colour vision in vertebrates
O. S. E. Gustafsson, S. P. Collin and R. H. H. Kroger
Journal of Experimental Biology 211, 1559-1564 (2008) | doi: 10.1242/jeb.016048

Jawless fishes (Agnatha; lampreys and hagfishes) most closely resemble the earliest stage in vertebrate evolution and lamprey-like animals already existed in the Lower Cambrian [about 540 million years ago (MYA)]. Agnathans are thought to have separated from the main vertebrate lineage at least 500 MYA. Hagfishes have primitive eyes, but the eyes of adult lampreys are well-developed. The southern hemisphere lamprey, Geotria australis, possesses five types of opsin genes, three of which are clearly orthologous to the opsin genes of jawed vertebrates. This suggests that the last common ancestor of all vertebrate lineages possessed a complex colour vision system. In the eyes of many bony fishes and tetrapods, well-focused colour images are created by multifocal crystalline lenses that compensate for longitudinal chromatic aberration. To trace the evolutionary origins of multifocal lenses, we studied the optical properties of the lenses in four species of lamprey (Geotria australis, Mordacia praecox, Lampetra fluviatilis and Petromyzon marinus), with representatives from all three of the extant lamprey families. Multifocal lenses are present in all lampreys studied. This suggests that the ability to create well-focused colour images with multifocal optical systems also evolved very early.

Robert Deyes

Switches, rheostats, electrical circuits and complex feedback loops that regulate household devices as well as national power grids are things that we have become so accustomed to in our own lives that we generally take them for granted. That is, until they break down. We saw this on a massive scale in the summer of 2003 when New York and other US and Canadian cities were brought to a stand still as power blackouts swept the east coast. A New Scientist report at the time claimed a total of 50 million people were affected (Ref 1). Needless to say, it took several days to bring things back to normal. The economic impact of the catastrophe cost the American and Canadian governments billions of dollars (Ref 1).

Switches turn genes on and off in the cell

Incredibly, regulated circuits and switches also exist inside the microscopic world turning genes on at the precise moments that their products are required and shutting them off when those same products become unnecessary, superfluous or even detrimental. In a fascinating study headed by a group at the Wistar Institute in Philadelphia it has now become clear that histones - proteins that are involved in packing DNA into individual chromosomes - play a fundamental role in regulating which genes are turned on and off in the cell (Ref 2). It appears that small molecular groups attached onto these histone proteins can serve as on/off switches that modulate which genes are on or off at any given moment. These molecular groups become attached to the histones as a result of multi-component machines that turn on genes. Karl Henry's group at the Wistar has revealed the functionality of one of these multi-component machines called the SAGA complex that attaches a molecular group called ubiquitin onto one of the Histones (Ref 2). What is surprising about the SAGA complex is that the removal of the ubiquitin molecular group from the Histones does not turn genes off. Rather it seems that both the addition and subsequent removal of ubiquitin, both by the SAGA complex, provide an essential sequence for turning genes on (Ref 2). This finding places an extra level of complexity to the previously held view that genes could be turned on or off through simple on/off switches. Now it appears that such switches operate through a specified order of molecular changes. In the case of SAGA, the correct order is absolutely critical if genes are going to be turned on correctly.

So it is that we learn that the 'conversion' of the genetic instruction into protein through the initial step of transcription involves more than polymerases - the reading molecules that chug along the DNA and generate RNA. It is a carefully planned, well-orchestrated series of events involving molecular switches. We see a complexity that intuitively does not seem to be accessible to unguided assembly. As mathematician David Berlinski quipped, "wherever the biologist looks, there is complexity beyond complexity, the entanglement of things ramifying downward from the organism to the cell" (Ref 3).

What caused the east coast electricity blackout? According to the New Scientist report there were two crucial pieces of software that failed on that frightful day (Ref 1). As alarm systems failed, more lines shut down and voltages fluctuated, the entire network spun out of control with the inevitable consequence of a massive power shut down. America suffered its worst power cut in recent memory because the correct order of processes and procedures so essential for the smooth running of an electricity grid had not been met. What happened on that horrific day during the heat of the summer sun was due to operator failure and could have been easily prevented. The New Scientist report mentions, for example, that one engineer left for lunch when a critical maneuver needed to be carried out (Ref 2). It is profoundly ironic that one of America's worst power failures should occur at precisely the moment that intelligent agency left the scene. As with man-made designs, evidence points to an intelligence behind the precision functioning of the cellular world.

References

1. Celeste Biever (2003) 'Preventable' failures caused US power blackout, New Scientist, 20th November, 2003

2. Karl W. Henry, Anastasia Wyce, Wan-Sheng Lo, Laura J. Duggan, N.C.Tolga Emre, Cheng-Fu Kao, Lorraine Pillus, Ali Shilatifard, Mary Ann Osley, Shelley L. Berger (2003) Transcriptional activation via sequential histone H2B ubiquitylation and deubiquitylation mediated by SAGA-associated Ubp8, Genes & Development Vol 17 pp2648-2663

3. David Berlinski (1996), The Deniable Darwin, http://www.discovery.org (see 'Articles by Center Fellows')

The "Age of Fishes" was in the Devonian Period of Earth history, when placoderm fishes became the dominant group of vertebrates. Largely on the basis of their place low down in the Tree of Life, placoderms have been regarded as "early primitive fish" which were slow and dull. We now need to question the validity of this perspective and whether it owes more to evolutionary presuppositions than to evidence.

Masterpricis attenboroughi is revealed as viviparous

The great majority of modern fish indulge in spawning: females lay large numbers of eggs and males fertilise those eggs after they have left the mothers' bodies. The process appears inefficient because few of the eggs grow to mature adults. However, in the absence of predators (such as after an environmental crisis), it is a great way for populations to expand rapidly.

Some fish, like sharks and rays, fertilise internally. Some are ovoviviparous, whereby the eggs remain in the body cavity of the female for protection, but the mother does not provide the embryos with nutrients. The rest are viviparous, giving both food and protection before they are born. Palaeontologists had "suspected that some placoderms fertilised internally". This is because "The males of a sub-group of placoderms , called ptyctodontids, have clasper-like appendages dangling from their pelvic fins - these are reminiscent of the claspers of modern sharks that are used to inseminate females." How far were these placoderms like the sharks and rays? The new fossil finds show that at least some placoderms were viviparous.

"With the discovery of the embryos we can now be sure that at least some placoderms gave birth to live young" says Per Ahlberg at Uppsala University in Sweden.
[. . .]
"Our ongoing investigations suggest that viviparity is more widespread than previously thought in early placoderms," says Long [at Museum Victoria in Melbourne, Australia].

From an evolutionary perspective, these placoderms "had a remarkably advanced reproductive biology". The reproductive system for internal fertilisation and viviparity is far more complex that the system for spawning. Yet the complex system appears in the placoderms, which represent the first flowering of vertebrate life in the fossil record.

For a long time, trilobite eyes served as an icon of complexity in the Cambrian. As time passes, this has been supplemented by many evidences of advanced morphologies (for examples, go here and here). Analysis of the genomes of so-called "primitive" organisms has revealed genes that are also found in more sophisticated animals. This new research reveals viviparity in some placoderm fish. How much more evidence do we need to show that Darwinian gradualism is in tension with the data?

Looking for patterns of oviparous, ovoviviparous and viviparous animals allows some generalisations. Mammals (with the exception of monotremes) are viviparous and there are a few cases of vivipary in reptiles, fish and insects. But when the focus changes to look at the details, and when the interpretive framework is the Tree of Life, then there are many difficulties. In a comment on the Nature news item, David Bump draws attention to the problems the authors have identified:

"...the complex behavioural, morphological, and physiological mechanisms required for successful copulation and internal fertilisation in chondrichthyans (Hamlett & Koob 1999) must have evolved independently and non-reversibly 12 times in teleosts..." It also claims that "Live bearing evolved from egg laying independently in all classes of vertebrates except birds, and also in many invertebrate clades." That's a lot of independent, sudden appearances of a complex reproductive strategy. It must take a lot of faith to believe in all that being the result of purely natural evolutionary processes, which haven't yet been shown to be capable of producing such changes.

This is a fair comment. We need a different paradigm - one that is not embarrassed by the riches of biological information found in supposedly primitive life-forms.

Live birth in the Devonian period
John A. Long, Kate Trinajstic, Gavin C. Young & Tim Senden
Nature 453, 650-652 (29 May 2008) | doi:10.1038/nature06966

The extinct placoderm fishes were the dominant group of vertebrates throughout the Middle Palaeozoic era1, yet controversy about their relationships within the gnathostomes (jawed vertebrates) is partly due to different interpretations of their reproductive biology. Here we document the oldest record of a live-bearing vertebrate in a new ptyctodontid placoderm, Materpiscis attenboroughi gen. et sp. nov., from the Late Devonian Gogo Formation of Australia (approximately 380 million years ago). The new specimen, remarkably preserved in three dimensions, contains a single, intra-uterine embryo connected by a permineralized umbilical cord. An amorphous crystalline mass near the umbilical cord possibly represents the recrystallized yolk sac. Another ptyctodont from the Gogo Formation, Austroptyctodus gardineri, also shows three small embryos inside it in the same position. Ptyctodontids have already provided the oldest definite evidence for vertebrate copulation, and the new specimens confirm that some placoderms had a remarkably advanced reproductive biology, comparable to that of some modern sharks and rays. The new discovery points to internal fertilization and viviparity in vertebrates as originating earliest within placoderms.

See also:

Dennis, C., The oldest pregnant mum, Nature 453, 575 (28 May 2008) | doi:10.1038/453575a

Morelle, R. Fossil reveals oldest live birth, BBC News, 28 May 2008

Mother fish, Museum Victoria News, 29 May, 2008 (with two video clips)

Robert Deyes

Real life compounds and real life experiments were the themes of a Nature Biotechnology article about a biologically-based machine that could play Tic Tac Toe (In the UK, the game of Naughts and Crosses) against human players. A Nature review of the paper told of a machine that could make 'decisions' that would not only allow it to win but win every time (Ref 1). Tic Tac Toe is of course a very simple game to play the idea being that the first to generate a row of either three crosses or 'zeros' on a nine-square grid wins the game. This new version of the game on the other hand was different and involved a rather contrived set of operational rules. Designed by Milan Stojanovic and Darko Stefanovic the machine was made up of nine individual square holes or wells, rather like a waffle, each containing a special concoction of biological enzymes. Play would begin when the human player added magnesium to each well of the waffle, triggering off a series of reactions in the process (Ref 1,2). The machine would then 'make' its first move, always from the center square of the nine-square waffle visible through special enzymatic reactions that caused the well to change colour. The player would be forced to then make their first move in the top left most square and, in the process, add a special piece of DNA to all of the wells (Ref 1,2). Thus every well was 'informed' of the player's first move. And so it went on, each time the human player being obligated to add special pieces of DNA to each of the remaining wells. The most that the human player could ever hope for was a draw (Ref 2). Nevertheless, it seemed from Stojanovic's and Stefanovic's design plan that complex biological 'machines' could be designed to make decisions based on inputs fed into it by human agents. Artificial Life had apparently made a move out of the computer-based simulation.

In another sense, Stojanovic's and Stefanovic's game was altogether very disappointing for those keen to demonstrate a simple route for generating complex feedback networks. After all, this biological machine had no powers to gain from experience and improve its strategy. Moreover, unlike the human players, Stojanovic's and Stefanovic's game did not display any ability to self-organize thought processes into winning strategies or chemicals into closed sets of catalytic reactions. It simply did what it had been instructed to do and all this within a very constraining set of conditions. The inventory list of components that Stojanovic and Stefanovic had used, for example, had been carefully selected for what was conceptually a very simple game. Each hole of the nine-welled waffle contained carefully designed DNA enzymes with YES, AND and NOT gates rather like the electrical circuit boards used in high school physics classes. The conditions within each hole of the nine-well waffle were carefully tweaked and fine-tuned to ensure that the reactions would work. The authors themselves reported how their initial attempts at playing the game resulted in, "further empirical improvements" to ensure that the machine worked (Ref 2). Indeed this biological machine never lost because it implemented the perfect strategy. In all fairness, Stojanovic and Stefanovic never designed their machine to learn from experience. Nevertheless they were successful at demonstrating just how difficult it is to design a biological machine that could carry out even the simplest of tasks - hardly what one would hope for those arguing for the natural emergence of complex biological systems.

The same sort of bleak findings have been reported in other studies designed to harness the practical benefits of bacteria. Drew Endy, a biologist at MIT, is a pioneer in making novel bacterial strains that might one day become bioproducers of disease targeting drugs (Ref 3). Yet for Endy and other biologists, the results of genetic engineering have been disappointing and frustrating to say the least primarily because of the time needed to engineer bacteria to do even the simplest of tasks (Ref 3). Endy has taken on the challenge of designing a library of genetic parts, or 'biobricks', that can be inserted into bacteria to achieve certain basic functions. Endy's work might one day soon provide an accessory shop of sorts where researchers can customize their bacteria rather like automobile aficionados might customize their car. Yet the problem with customizing bacteria in this way is that, over relatively short periods of time, the genetically engineered parts mutate and become non-functional. As Ron Weissman of Princeton reported,

"Replication is far from perfect. We've built circuits and seen them mutate in half the cells within five hours. The larger the circuit is, the faster it tends to mutate" (Ref 3).

As science writer Wayt Gibbs reminds us, scientists are coming to terms with the relative difficulty of engineering even the shortest stretches of DNA to achieve even the most basic of functions (Ref 3). Many of the products of these short pieces of DNA have proved to be toxic to the cells requiring careful tweaking and trimming before being successfully introduced into bacteria. In other words, biological entities such as bacteria do not lend themselves easily to even the smallest of changes in their molecular composition. They require precision-directed design if such viable changes in their molecular constitution are to be made.

References

1. The Nature Review of the paper written by Stojanovic and Stefanovic was published by Helen Pearson in Nature on the 21st of August, 2003 and can be found at http://www.nature.com/nsu/030818/030818-9.html

2. Milan N Stojanovic and Darko Stefanovic (2003), A deoxyribozyme-based molecular automaton, Nature Biotechnology, Volume 21 Number 9 pp 1069 - 1074.

3. W. Wayt Gibbs (2004) Synthetic Life, Scientific American, Volume 290 (5) pp 74-81.