Literature

Lungfish are interesting animals, "dependent on their watery environment for food but dying if they can't breathe air with their lungs." It is not unusual for them to be mentioned in accounts of the evolution of fish to land-dwelling tetrapods because they demonstrate an ability to bridge the gap between water and air. (Outside this, they are not good candidates for being transitional).
Water-breathers have a distinctly different biology when compared to air breathers. "All air breathing land dwellers deal with acid - an excess of protons - by reacting protons with bicarbonate ions to create water and CO2, which is breathed out. To deal with too much base, breathing slows down, keeping CO2 and therefore protons in the body. Water breathing fish take a different approach, relying on metabolic processes at their gills and kidneys to restore a normal blood pH." So it is an interesting research question - how do lungfish deal with the problems?
"The lungfish have the best of both worlds" says Gilmour, one of the co-authors. Blackburn's summary is: "Like land dwellers, they rely more on air breathing to redress a more acidic blood pH, but their gills and kidneys deal with an excess of base to return blood pH back to normal, just like water breathing fish."
The research findings are interesting for students of origins. Lungfish do not demonstrate a transitional physiological system, but employ two developed systems side-by-side. They have an air-breathing system for controlling acidity (respiratory compensation) and they use their gills and kidneys to reduce excess base (metabolic compensation). In other words, the ability to operate in both watery and land environments requires two complex systems to be in place: one for living in water and the other for living in air. The case of lungfish shows that biological information precedes and permits biological function.

Mechanisms of acid-base regulation in the African lungfish Protopterus annectens
K. M. Gilmour, R. M. Euverman, A. J. Esbaugh, L. Kenney, S. F. Chew, Y. K. Ip and S. F. Perry
Journal of Experimental Biology 210, 1944-1959 (2007) | doi: 10.1242/jeb.02776

Abstract: African lungfish Protopterus annectens utilized both respiratory and metabolic compensation to restore arterial pH to control levels following the imposition of a metabolic acidosis or alkalosis. [. . .] These findings suggest that lungfish, like tetrapods, alter ventilation to compensate for metabolic acid-base disturbances, a mechanism that is not employed by water-breathing fish. Like fish and amphibians, however, extra-renal routes play a key role in metabolic compensation

See also:
Blackburn, L., Lungfishes' balancing act, Journal of Experimental Biology 210, 0ii (2007), doi: 10.1242/jeb.007419

Douglas Hofstadter is professor of cognitive science at Indiana University and his recent book, I Am a Strange Loop is yet another attempt to explain consciousness from within a "decidedly materialistic" paradigm. "He seeks an explanation of the phenomenon of consciousness using physical law only." According to this approach, "our feeling of a conscious "I" is but an illusion created by our neuronal circuitry".
So, what is it to be a person? Who am "I"? "If we posit that our consciousness is an illusion created by our thoughts "watching ourselves think" [as the philosopher of mind Daniel Dennett had previously suggested], we might ask "Who watches the watcher?"" Does me asking the question demonstrate that I am a person and that my consciousness is not an illusion? The offered response is 'no!' "The impression of having a mind is just another pattern of [neuronal] firings". This approach considers it entirely reasonable to expect that humans will, one day, construct machines with their own personalities.
Any alternative perspectives are traced back to Descartes and his dualist view of the world. This is unfortunate, because I doubt that most non-materialists see themselves as exponents of Cartesian philosophy. Some, for example, would want to identify information as a fundamental aspect of reality (an avenue of research that is excluded within the materialistic paradigm). Adoni (the reviewer) notes that a "surprising (to me) number of philosophers of the mind" are not materialists, but the review does not attempt to interact with any of their ideas. It is effectively declaring that non-materialists have nothing useful to say about consciousness.
Reading reviews like this is quite depressing. The materialist mind-set is a universal acid that eats away at everything, including itself. Consequently, the mind has to be a product of hierarchical levels of neuronal firings, and personality has to be an illusion. We are ultimately conscious machines. Why anyone with these views should think that our neuronal activity can have anything to do with truth and reality is a mystery to me!
But even more important, the materialist approach to consciousness is commonly dignified by the name "science". Other approaches, which are likely to be linked to Theism, are labelled "religion" and are excluded, on demarcation grounds, from science. This is an unacceptable situation, for as metaphysics, materialism has a philosophical standing that is entirely equivalent to Theism. It is simply that people choose to build their thoughts on different foundations. The paradox is that materialistic science wants to be realist and to have truth as a goal, but its approach to human consciousness can only support a post-modern philosophy which emphasises the socially constructed nature of reality and substitutes relativism for truth. And, for materialists, individuals have to seek for meaning and self-worth in existential experiences (an escape from reason) because the universal acid of rationalism has completely corroded realism and truth in human psychology.

Who Watches the Watcher?
Christoph C. Adami
Science 316, 25 May 2007: 1125-1126.

A review of I am a Strange Loop by Douglas Hofstadter
Basic Books, New York, 2007. | ISBN 9780465030781

According to Paul Rees "textbooks for GCE Advanced Level Biology have provided over-simplified and inaccurate accounts of Charles Darwin's contribution to the study of evolution over a period of many decades." The author has 20 years of teaching the subject and is now an academic in a British university. The paper reminded me of Jonathan Wells' book-length critique of the way US textbooks portray the classic 'evidences' advanced to support Darwinism. Rees' contribution is much more modest in what it attempts to do, but he is rightly concerned about the way the textbooks "have perpetuated myths about Darwin and his work". It would have been an interesting exercise for him to offer some analysis of the phenomenon, but maybe this would create a hostile reception, similar to that experienced by Wells.
An interesting addendum is his observation about "a worrying absence of references to Darwin in current A-level Biology specifications and some texts." This trend is also found in the US, where evolutionary biologists tend to point the finger at creationists and ID activists, inferring that the textbook authors are swayed by sales potential. This is quite unjust, as creationists and ID educators consistently call for more accurate information (rather than content that is cherry-picked to advance the case for Darwinism). But what can be said when the same trend of diminishing the significance of Darwin is observed in the UK? There is no parallel with the US case: this is not a trend linked to the market for textbooks. Maybe Darwinism is actually not as significant for biology as many would like to make it? Maybe the textbook authors have a problem showing its relevance to the curriculum? This may be a revolutionary thought to those who keep telling us that nothing in biology makes sense except in the light of evolution, but more and more people are coming to realise that Darwinism explains everything but predicts nothing. This is not something that fits well into the ethos of science.

The evolution of textbook misconceptions about Darwin
Paul A. Rees
Journal of Biological Education, 41(2), Spring 2007, 53-55.

Abstract: Textbooks for GCE Advanced Level Biology have provided over-simplified and inaccurate accounts of Charles Darwin's contribution to the study of evolution over a period of many decades. They have credited him with field skills and insight that he did not possess, and repeated several historical inaccuracies. Darwin's strength was as a synthesiser of information but, at least in his early life, he was not a particularly observant or careful field biologist. The specimens collected on his voyage on HMS Beagle were largely identified and analysed by others, but this is rarely acknowledged. This article criticises the historical accuracy of the treatment of Darwin and his ideas in a range of A-level textbooks, and notes a worrying absence of references to Darwin in current A-level Biology specifications and some texts.

"He's a young astronomer with dozens of articles in top journals; he has made an important discovery in the field of extrasolar planets; and he is a proponent of intelligent design, the idea that an intelligent force has shaped the Universe." His academic credentials are impressive; Guillermo Gonzalez has an international reputation. David Lambert, director of the MacDonald Observatory, has an assessment that should carry some weight: "I would have said he was a serious tenure candidate."
However, others think differently. "I would have voted to deny him tenure," says Robert Park, a physicist at the University of Maryland in College Park. "He has established that he does not understand the scientific process." Also, "in 2005, Gonzalez's rising profile led a group of 131 faculty members to sign a petition disavowing intelligent design."
Others, looking on, have real concerns about academic freedom. "There is a pattern happening to everybody who's pro intelligent design," says one pro-design biologist, who declined to be named because his own tenure process has just begun. "The same thing could happen to me," he says. "I don't want to get into trouble."
There are deep and significant differences here about the philosophy of science, and the hostile deniers are convinced that ID is incompatible with science. This is a battle that has to be fought, because this "academic hostility" is fundamentally wrong. These people conveniently forget that the pioneers of science were all advocates of ID. There are numerous philosophers of science who recognise the legitimacy of ID within science - the recent high profile case involving Professor Anthony Flew is witness to that. Those who claim that ID advocates do "not understand the scientific process" are nearly always advocates of the philosophy of naturalism: nature is all there is. They are using their version of the scientific process to ram atheistic philosophy into our minds. We must ensure that science does not become an ideological weapon, and this is why we need university leaders and other opinion formers to defend academic freedom and allow the issues to be explored openly and honestly.

Darwin sceptic says views cost tenure
Geoff Brumfiel
Nature 447, 364 (24 May 2007) | doi:10.1038/447364a

Abstract: Astronomer blames setback on his support of intelligent design.

See also:
Crowther, R. World's Premiere Scientific Journal Reports on Iowa State's Denial of Tenure to Guillermo Gonzalez, Evolution News & Views. May 23 2007.
Excerpt: "I am not appealing the tenure decision on the grounds of religious discrimination" (Guillermo Gonzalez).

The Darwin Exhibition constructed for the American Museum of Natural History has received many accolades. However, are people getting the Darwin of history, or are they being presented with a cardboard Darwin, constructed by people who have a particular agenda? It is worth asking this question, because it has happened many times before. For example, the "warfare thesis" between science and Christianity was the invention of Thomas Huxley and his allies. Theirs was not a fair view of history and they had the agenda of shifting the power base in society from 'the Church' to the scientific elite.
Unfortunately, Darwin has become an iconic figure for many people. This has emerged in recent discussions regarding the teaching of evolution in schools: any criticism of Darwin's theory has been interpreted as an assault on science. This is a deplorable state of affairs. Any serious educationalist ought to be encouraging students to think critically, and it is good scholarship to examine arguments for and against any theory. Hiram Caton has contributed a worthy critique of the new exhibition. Particularly welcome is his recognition that there was serious scientific criticism of Darwin's theory. "The Exhibition promotes an extreme version the triumphalist legend. Viewers are told that the Origin of Species caused a sensation, not only in Britain but around the world [. . .]. It is well established that while evolution was widely accepted by 1870, natural selection was not widely accepted among scientists; [. . .] Darwin's scientific apologists made serious criticisms."
We are fast approaching the bicentennial of Darwin's birth. The indications are that the hype will increase and peak in 2009. What we must not do is allow the myth-makers an easy ride.

Getting Our History Right: Six Errors about Darwin and His Influence
Hiram Caton
Evolutionary Psychology, 2007. 5(1): 52-69

Abstract: The Darwin Exhibition created by the American Museum of Natural History is the centerpiece of the bicentennial of Darwin's birth. It opened in November 2005 and will circulate to a number of museums before terminating at the London Natural History Museum in February 2009. The Exhibition is also a major contributor to online instruction about evolution for schools. The quality of the Exhibition's narrative is accordingly of some significance. This paper argues that the narrative is the legendary history that dominates public opinion. The legend has been thoroughly disassembled by historical research over recent decades. My criticism is organized as six theses. (1) Publication of the Origin was not a sudden ("revolutionary") interruption of Victorian society's confident belief in the traditional theological world-view. (2) The Origin did not "revolutionize" the biological sciences by removing the creationist premise or introducing new principles. (3) The Origin did not revolutionize Victorian public opinion. The public considered Darwin and Spencer to be teaching the same lesson, known today as "Social Darwinism", which, though fashionable, never achieved dominance. (4) Many biologists expressed significant disagreements with Darwin's principles. (5) Darwin made little or no contribution to the renovation of theology. His public statements on Providence were inconsistent and the liberal reform of theology was well advanced by 1850. (6) The so-called "Darwinian revolution" was, at the public opinion level, the fashion of laissez-faire economic beliefs backed by Darwin and Spencer's inclusion of the living world in the economic paradigm.

Two psychologists have argued that "resistance to science" in adults has its origins in the experiences of childhood. In particular, they claim, there are two adult traits that can be traced back to childlike characteristics. These are a reliance on "common-sense intuitions" about the world around us, and a sensitivity to the "trustworthiness of the source" when information is provided by trusted teachers/parents.
First, I am not taking issue with the idea that the experiences of childhood affect our adult lives. I am sure a paper could equally be written on 'attraction to science' being traced back to childhood (which happens to be my own experience).
Second, there is a tension between the authors' primary example of resistance to science (denying evolution) and the other examples (alternative medicine, spirits, astrology, ESP, divination). I do not think these can be lumped together in this way. By and large, in the US, evolution-doubting is widespread among the Christian community, but these same people do not indulge in the other cases of "resistance". Indeed, the Christian community tends to regard them as 'New Age' practices which are linked to an evolutionary world view that has no place for a Sovereign Creator God. In this spiritual vacuum, New Age practices flourish. Rationalism in the physical world spawns irrational existentialism in the religious world. Significantly, there is no interaction with thoughts like this by the authors of the paper.
Thirdly, and this is the most important point, the authors have a very narrow understanding of 'science' and 'scientific ideas'. This is best illustrated by the way they handle the mind/brain issue. "The strong intuitive pull of dualism makes it difficult for people to accept what Francis Crick called "the astonishing hypothesis". Dualism is mistaken - mental life emerges from physical processes." This statement is false because the authors are not presenting the conclusions of science, but the presuppositions of many neuroscience scholars. The authors are presenting an input as an output! The presupposition (that the human mind and consciousness "emerges from physical processes") has never been demonstrated empirically. Indeed, some of us predict that consciousness will never be understood by working within this naturalistic paradigm. These authors are confusing scientism with science. Any departure from the tenets of scientism are interpreted as "resistance to science" - which, in the case of evolutionary theory and understanding consciousness + the human mind is a travesty of the issue. Anyone one who reads Darwin on Trial by Phillip Johnson (for example) and thinks this is an example of "resistance to science" is sadly under a delusion.

Childhood Origins of Adult Resistance to Science
Paul Bloom and Deena Skolnick Weisberg
Science, 18 May 2007: 316, 996-997 | DOI: 10.1126/science.1133398

Abstract: Resistance to certain scientific ideas derives in large part from assumptions and biases that can be demonstrated experimentally in young children and that may persist into adulthood. In particular, both adults and children resist acquiring scientific information that clashes with common-sense intuitions about the physical and psychological domains. Additionally, when learning information from other people, both adults and children are sensitive to the trustworthiness of the source of that information. Resistance to science, then, is particularly exaggerated in societies where nonscientific ideologies have the advantages of being both grounded in common sense and transmitted by trustworthy sources.

See also:
Why do some people resist science? By Paul Bloom and Deena Skolnick Weisberg

In a recent blog, I described some introductory words in a paper by Eugenie Scott and Nicholas Matzke as Darwinian spin. They declared evolutionary theory to be "replete with explanations for complex biological structures" and that it "continues to make progress in explaining such fascinating structures". To prove my point, just look at the current issue of Nature, where Wallace Arthur reviews the book: From Embryology to Evo-Devo. He asks: "How do novelties arise? We can't yet agree on a definition for them, let alone answer this fundamental question. But we can see the nature of the challenge ahead." Arthur describes a research agenda in its infancy, at the stage of sorting out research objectives. He is right, and Scott + Matzke are wrong.
This is a serious point to make, because it affects what we teach students about the subject and what message goes out to the general public. Scott + Matzke claim to be acting in the interests of science education; but their message is not an accurate portrayal of what the research community have achieved. The reality is that the community have a prospect ahead of them. "As Wagner [the author of one of the chapters] says: "One of the main sources of intellectual excitement in devo-evo (sic) is the prospect of understanding major evolutionary transformations.""
Implicit in the comments of Arthur and of Wagner is the recognition that Darwinism does not have the answers, and that the ID insistence on addressing the issue of novelty is on target.

The search for novelty
Wallace Arthur reviews From Embryology to Evo-Devo: A History of Developmental Evolution
Nature 447, 261-262 (17 May 2007) | doi:10.1038/447261a

Excerpt: Third, and most important in my view, the origin of novelty is becoming one of the major themes of evo-devo. Attention is shifting from the retention of the old (as in recapitulation) to the creation of the new (be it an eye, a leg, a feather or even a whole body plan). Both the historical and the current importance of novelty emerge repeatedly in the book. How do novelties arise? We can't yet agree on a definition for them, let alone answer this fundamental question. But we can see the nature of the challenge ahead.

Paper from the colloquium: In the light of Evolution

John Gerhart and Marc Kirschner offer a radical theory of variation: one that majors on the regulatory elements rather than on the genes themselves. Coming from the Evo-Devo school, this theory offers numerous novel avenues of thought.
First, there are real problems with many traditional models of phenotypic variation. The models work in a limited way with single traits, but they do not handle complex variations at all well. In such cases, selection has to act on several traits concurrently and mutations (the source of variation) just may not be forthcoming. Consequently, "evolution may be impeded".
Second, it is not widely realised that there is a remarkable "metazoan toolkit of conserved functional components and processes". These were all in place by the end of the Precambrian. These are referred to as "conserved core processes". "They comprise an enormous toolkit, and the genes encoding them comprise the majority of the genetic repertoire of the animal. They have changed very little in the course of animal evolution since the Cambrian, even though animal anatomy and physiology have changed."
Third, if the toolkit and the genes encoding them have not changed since the Precambrian, what has? The answer offered is the regulatory system. The metazoan toolkit was so powerful and versatile "that post-Cambrian animals could largely omit further functional innovation at the gene product level (protein and functional RNA evolution) and instead exploit regulatory innovation to diversify anatomy, physiology, and development." As an example, the authors point out (from genome analysis) that 79% of mouse genes retain Precambrian sequences.
Whilst the authors go on to discuss many aspects of this theory and point out some empirical data that appears to provide validation (but see comments from Wells on this), it is pointed out here (and by Wells) that this theory does not address the origin of complex specified information. All the essential genetic information existed in the Precambrian and is accepted by the authors almost as a gift bequeathed to Phanerozoic animals and plants. The Cambrian organisms possessed the innate capacity to vary. "If the capacity to develop large phenotypic differences already exists in the organism as self-inhibited alternate states, and these can be elicited by simple signals (weak linkage), then large evolutionary steps can be made with a modicum of genetic change. In such cases, the distinction blurs between evolutionary gradualism and saltation (the generation of significant traits by single mutations)."
Curiously, this paper can be read as a vindication of concepts developed by ID scholars: if you want to develop models of variation involving complex specified information, you must start out with complex specified information. For more on this, go here and here.

The theory of facilitated variation
John Gerhart and Marc Kirschner
Proceedings of the National Academy of Sciences USA, published May 9, 2007, 10.1073/pnas.0701035104

This theory concerns the means by which animals generate phenotypic variation from genetic change. Most anatomical and physiological traits that have evolved since the Cambrian are, we propose, the result of regulatory changes in the usage of various members of a large set of conserved core components that function in development and physiology. Genetic change of the DNA sequences for regulatory elements of DNA, RNAs, and proteins leads to heritable regulatory change, which specifies new combinations of core components, operating in new amounts and states at new times and places in the animal. These new configurations of components comprise new traits. The number and kinds of regulatory changes needed for viable phenotypic variation are determined by the properties of the developmental and physiological processes in which core components serve, in particular by the processes' modularity, robustness, adaptability, capacity to engage in weak regulatory linkage, and exploratory behavior. These properties reduce the number of regulatory changes needed to generate viable selectable phenotypic variation, increase the variety of regulatory targets, reduce the lethality of genetic change, and increase the amount of genetic variation retained by a population. By such reductions and increases, the conserved core processes facilitate the generation of phenotypic variation, which selection thereafter converts to evolutionary and genetic change in the population. Thus, we call it a theory of facilitated phenotypic variation.

See also:

Wells, J. What's New? Books & Culture, September/October 2006, Vol. 12, No. 5, Page 45

Paper from the colloquium: In the light of Evolution

Eugenie Scott and Nicholas Matzke, from the National Center for Science Education, offer their analysis of how ID is making "a serious challenge not in the world of science, but in the world of public educational policy." It is a paper that reworks the NCSE position without contributing any new ideas to the debate.
These authors reveal an unqualified confidence that evolutionary theory has the answers. It is "replete with explanations for complex biological structures." It "continues to make progress in explaining such fascinating structures". They assert that there is "no serious scientific challenge to evolution." Underpinning theory are "fertile and unifying evolutionary principles". Anyone challenging such robust scholarly accomplishments must be deemed lacking in academic credibility, inevitably with a political or religious agenda! (If you don't recognise this as Darwinian spin, or if you want more input on this, go here).
Unfortunately the paper is very weak in its handling of complexity. Although the authors recognise the terms "irreducible complexity" and "specified complexity", they very quickly discard them in favour of mere "complexity". Thus, we read, "complexity is not a reliable marker of intelligent agency." Yes, exactly - that is why the terms irreducible complexity and complex specified information are needed! Failure to engage with ID arguments leads to a paper that completely misses the mark.
The authors do make a good point when they write: "complex biological 'machines' are always, upon investigation, found to be cobbled together from preexisting modules with other functions. Biological designs are not really 'purposeful arrangements of parts,' they are really adaptations of parts originally used for some other purpose." But this is a contrived assertion! What we find in the biological world, in most cases, is exquisite design and not the tinkering design of Darwinism. If we consistently found "cobbled together" design, the ID community would be much smaller than it is. Also, biomimetics, as a mushrooming interdisciplinary research activity, would not exist. Similarly, Systems Biology would have great difficulty developing a coherent methodology for research.
The authors go to great lengths to derive ID from creation science. No one will deny that connections can be made. However, Scott and Matzke overlook the fact that the ID community is capable of learning, of modifying its thinking, of maturing in its approach to science, philosophy and to education. What is needed is not an inferred 'guilt by association' exercise, but an engagement with the arguments. Unfortunately, there is very little of the latter for those who take the trouble to read the paper.

Biological design in science classrooms
Eugenie C. Scott and Nicholas J. Matzke
Published online before print May 9, 2007
Proceedings of the National Academy of Sciences USA, 10.1073/pnas.0701505104

Abstract: Although evolutionary biology is replete with explanations for complex biological structures, scientists concerned about evolution education have been forced to confront "intelligent design" (ID), which rejects a natural origin for biological complexity. The content of ID is a subset of the claims made by the older "creation science" movement. Both creationist views contend that highly complex biological adaptations and even organisms categorically cannot result from natural causes but require a supernatural creative agent. Historically, ID arose from efforts to produce a form of creationism that would be less vulnerable to legal challenges and that would not overtly rely upon biblical literalism. Scientists do not use ID to explain nature, but because it has support from outside the scientific community, ID is nonetheless contributing substantially to a long-standing assault on the integrity of science education.

Paper from the colloquium: In the light of Evolution

According to Michael Lynch, "the myth that all of evolution can be explained by adaptation continues to be perpetuated by our continued homage to Darwin's treatise in the popular literature. For example, Dawkins' agenda to spread the word on the awesome power of natural selection has been quite successful, but it has come at the expense of reference to any other mechanisms, a view that is in some ways profoundly misleading." Despite all the textbooks and most popular literature giving the impression that adaptive forces are the key to understanding evolutionary transformation, there are very real questions as to "whether natural selection is a necessary or sufficient force to explain the emergence of the genomic and cellular features central to the building of complex organisms."
Lynch describes evolution as "a population-genetic process governed by four fundamental forces." These are: natural selection (which is adaptive), mutation, recombination and genetic drift (which are non-adaptive). "Given the century of work devoted to the study of evolution, it is reasonable to conclude that these four broad classes encompass all of the fundamental forces of evolution."
The body of Lynch's paper is really a manifesto for non-adaptive forces being central to our understanding of organismal complexity, so that the features of interest "may be nothing more than indirect by-products of processes operating at lower levels of organization."
This is probably the most significant paper in the colloquium. It demonstrates the vulnerability of the adaptationist paradigm to critical scrutiny. "If complexity, modularity, evolvability, and/or robustness are entirely products of adaptive processes, then where is the evidence?" Significantly, it is questioning like this that has been ruled inadmissible in the education of biology students in several US states!
But what happens when the non-adaptive 'forces' (with the addition of migration) are critiqued and found to be inadequate for creating complex specified information? What if we come to the conclusion that biological information demands intelligent causation? What is needed is a rational exploration of these issues, not a "religious adherence to the adaptationist paradigm" nor a demarkationist blocking of ID concepts from the domain of science.

The frailty of adaptive hypotheses for the origins of organismal complexity
Michael Lynch
Published online before print May 9, 2007
Proceedings of the National Academy of Sciences USA, May 15, 2007, vol. 104, suppl. 1, 8597-8604 | doi 10.1073/pnas.0702207104

Abstract: The vast majority of biologists engaged in evolutionary studies interpret virtually every aspect of biodiversity in adaptive terms. This narrow view of evolution has become untenable in light of recent observations from genomic sequencing and population-genetic theory. Numerous aspects of genomic architecture, gene structure, and developmental pathways are difficult to explain without invoking the nonadaptive forces of genetic drift and mutation. In addition, emergent biological features such as complexity, modularity, and evolvability, all of which are current targets of considerable speculation, may be nothing more than indirect by-products of processes operating at lower levels of organization. These issues are examined in the context of the view that the origins of many aspects of biological diversity, from gene-structural embellishments to novelties at the phenotypic level, have roots in nonadaptive processes, with the population-genetic environment imposing strong directionality on the paths that are open to evolutionary exploitation.

Paper from the colloquium: In the light of Evolution

One presumes that Francisco Ayala intended this paper to set the scene for the colloquium. He argues that Darwin's main contribution was to find natural mechanisms that accounted for the apparent design of living things. This, he claims, links Darwin with Copernicus as the two architects of the Scientific Revolution: with Darwin addressing the biological world and Copernicus the workings of the universe. This is highly contentious history, but even more troubling is the philosophy of science emanating from Ayala. His view of science is that all explanations of natural phenomena must necessarily be in terms of "chance and necessity" (a phrase included in the keywords). Thus, "The theory of evolution conveys chance and necessity jointly enmeshed in the stuff of life; randomness and determinism interlocked in a natural process that has spurted the most complex, diverse, and beautiful entities that we know of in the universe. [. . .] And this is the conceptual revolution that Darwin completed: the idea that the design of living organisms can be accounted for as the result of natural processes governed by natural laws."
It is this vision of science that excludes intelligent causation as a matter of principle and pre-empts all discussion of design and information linked to intelligent agency by declaring it 'out of bounds'. This is a demarcationist agenda, which ends up concluding that which was assumed at the outset. With Ayala's philosophy of science, if the cosmos and living things were intelligently designed, no one could ever know!
The paper is full of unqualified compliments to Darwin's genius. It is a market promotion exercise rather than an academic paper. Again, historians of science would want to take issue with many of the points made. However, my concern here is with the presentation of natural selection (and Darwin's references to "my theory"). "Natural selection accounts for the "design" of organisms because adaptive variations tend to increase the probability of survival and reproduction of their carriers at the expense of maladaptive, or less adaptive, variations." Also, "Mutation and selection have jointly driven the marvelous process that, starting from microscopic organisms, has yielded orchids, birds, and humans." When ID scholars focus their attention on the inability of mutations and natural selection to deliver specified complexity and novel structures, they are informed that they are being simplistic and Darwinism has several other mechanisms in its portfolio. Nevertheless, not a hint of this is manifest in Ayala's paper. "The number of mutations that can be tested, and those eventually selected, in millions of individual animals over millions of generations is difficult for a human mind to fathom, but we can readily understand that the accumulation of millions of small, functionally advantageous changes could yield remarkably complex and adaptive organs, such as the eye."
This is traditional Darwinism, alive and well, robustly critiqued by both ID scholars and by Ayala's peers - yet presented in this colloquium as the essence of evolutionary theory!

Darwin's greatest discovery: Design without designer
Francisco J. Ayala
Proceedings of the National Academy of Sciences USA, published May 9, 2007, 10.1073/pnas.0701072104

Darwin's greatest contribution to science is that he completed the Copernican Revolution by drawing out for biology the notion of nature as a system of matter in motion governed by natural laws. With Darwin's discovery of natural selection, the origin and adaptations of organisms were brought into the realm of science. The adaptive features of organisms could now be explained, like the phenomena of the inanimate world, as the result of natural processes, without recourse to an Intelligent Designer. The Copernican and the Darwinian Revolutions may be seen as the two stages of the one Scientific Revolution. They jointly ushered in the beginning of science in the modern sense of the word: explanation through natural laws. Darwin's theory of natural selection accounts for the "design" of organisms, and for their wondrous diversity, as the result of natural processes, the gradual accumulation of spontaneously arisen variations (mutations) sorted out by natural selection. Which characteristics will be selected depends on which variations happen to be present at a given time in a given place. This in turn depends on the random process of mutation as well as on the previous history of the organisms. Mutation and selection have jointly driven the marvelous process that, starting from microscopic organisms, has yielded orchids, birds, and humans. The theory of evolution conveys chance and necessity, randomness and determinism, jointly enmeshed in the stuff of life. This was Darwin's fundamental discovery, that there is a process that is creative, although not conscious.

Last December, a colloquium was held in Irvine, CA, with the general title "In the light of evolution". This choice of words is an allusion to Dobzhansky's oft-quoted statement that "nothing in biology makes sense except in the light of evolution". A series of colloquia are planned, all seeking to "interpret phenomena in various areas of biology through the lens of evolution". The December event was the first and it took as its theme "Adaptation and Complexity".
The organisers were very aware that this is "a time of resurgent societal interest in supernatural explanations for biological complexity. Especially in the United States, proponents of intelligent design (ID)-the latest reincarnation of religious creationism - argue that biotic complexity can only be the product of a supreme intelligence (i.e., God)." Of course, this is not how the ID community sees the issue. ID arguments major on the rationale for making design inferences. The options for causal explanations are extended from 'Law + Chance' to 'Law + Chance + Design'. This approach is perceived as important for truth and for the integrity of science, because otherwise science gets moulded by the philosophy of naturalism (nature is all there is). This threat to science is neither perceived nor addressed by the organisers.
There is an easy way to show that design inferences are inappropriate - and that is to show the superiority of the explanations based on Law and Chance. However, the failure of the evolutionary community to deliver on this is one of the most important factors behind the sustained interest in ID. The authors of the introductory essay recognise that they do not bring strong, mature arguments to support their claims: "150 years after Darwin the challenge of understanding nature's complexity remains in many regards in its infancy." They go on to refer to new tools to help understand this complexity, but do not acknowledge that the data uncovered by these tools have influenced many in the direction of ID.
The papers are currently in the Early Edition of the PNAS website, all open access. Selected papers will be the subject of further comment on this blog.

In the light of evolution I: Adaptation and complex design
John C. Avise and Francisco J. Ayala
Published online before print May 9, 2007
Proc. Natl. Acad. Sci. USA, 10.1073/pnas.0702066104

Abstract: This paper serves as an introduction to this PNAS supplement, which resulted from the Arthur M. Sackler Colloquium of the National Academy of Sciences, "In the Light of Evolution I: Adaptation and Complex Design," held December 1-2, 2006, at the Arnold and Mabel Beckman Center of the National Academies of Sciences and Engineering in Irvine, CA. It is the first in a planned series of colloquia under the umbrella title "In the Light of Evolution" (see Box 1). The complete program is available on the NAS web site at www.nasonline.org/adaptation_and_complex_design.

Now that the opossum genome has been sequenced, both winners and losers have emerged. The main loser is the 'Genes-R-Us' school, who have argued that genes are the only really interesting components of the genome. This group is a loser because the "vast majority of the opossum's genes are identical to other placental mammals". Genes do not distinguish marsupials from placentals, but the non-coding elements (previously referred to as 'Junk DNA' are distinctly different. Thus, "most of the genetic difference between marsupials and placental mammals comes from non-coding sequences, not proteins."
The Evo-Devo community appears to consider itself a winner. The new research "is bound to make the [evolutionary developmental biology] community very happy, because they've been saying all along that it's the regulation of genes that is what's driving the changes that we see in the evolution of animals." Some of this confidence is, however, misplaced: it is one thing to say that gene regulation is the key to understanding the difference between placentals and marsupials, but linking this to origins is theory-laden. The data does not speak for itself but is interpreted, often through an evolutionary filter.
The ID community is also a winner. ID scholars have long been sceptical of the genetic reductionism displayed by most evolutionary biologists, and have also been quick to recognise the functionality of much of the so-called Junk DNA. These scholars have much in common with evo-devo, but see the regulation system as an extraordinarily complex system that invites design inferences when considering origins.
ID scholars will also welcome the recognition that marsupials are not primitive mammals: "The study helps to erode a common misconception that marsupials are somehow an archaic or second-rate category of mammal. One scientist comments on the discovery of a gene that encodes for a unique form of T-cell receptor not found in placental mammals: this "knocks that assumption on its head [. . .] It shows that they have a very sophisticated immune system, but one that's very different."

Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences
Tarjei S. Mikkelsen, et al.
Nature 447, 167-177 (10 May 2007) | doi:10.1038/nature05805

We report a high-quality draft of the genome sequence of the grey, short-tailed opossum (Monodelphis domestica). As the first metatherian ('marsupial') species to be sequenced, the opossum provides a unique perspective on the organization and evolution of mammalian genomes. Distinctive features of the opossum chromosomes provide support for recent theories about genome evolution and function, including a strong influence of biased gene conversion on nucleotide sequence composition, and a relationship between chromosomal characteristics and X chromosome inactivation. Comparison of opossum and eutherian genomes also reveals a sharp difference in evolutionary innovation between protein-coding and non-coding functional elements. True innovation in protein-coding genes seems to be relatively rare, with lineage-specific differences being largely due to diversification and rapid turnover in gene families involved in environmental interactions. In contrast, about 20% of eutherian conserved non-coding elements (CNEs) are recent inventions that postdate the divergence of Eutheria and Metatheria. A substantial proportion of these eutherian-specific CNEs arose from sequence inserted by transposable elements, pointing to transposons as a major creative force in the evolution of mammalian gene regulation.

See also:

Fairless, D., The awesome opossum gets sequenced, News@nature.com, 9 May 2007; | doi:10.1038/news070508-8

Lee Phillips, M., First marsupial genome released, The Scientist, 9th May 2007.

Glial cells have been known to neuroscientists for over a century and they perform numerous essential functions. Now we can add another. In the vertebrate eye, there are "radial glial cells spanning the entire retinal thickness" known as Muller cells. Shaped like an extended funnel, they are "oriented along the direction of light propagation". These cells "provide a low-scattering passage for light from the retinal surface to the photoreceptor cells", thus acting as optical fibres. Their function is to "mediate the image transfer through the vertebrate retina with minimal distortion and low loss".
For years, we have been told by "blind watchmaker" Darwinians that the eye is an example of bad design because light has to pass through the retina to reach the photoreceptor cells. These folk insist that a good Designer wouldn't have wired our retinas the "wrong" way. The response from those who advocate design has been to show that the eye is an example of optimum design: there are good reasons that can be advanced for having an inverted retina. This approach has satisfied many but certainly not all. The "bad design" claim is still widespread.
This new paper has finally nailed the argument: by revealing yet another level of exquisite design. The authors modestly say: "This finding elucidates a fundamental feature of the inverted retina as an optical system". They describe the Muller cells as "ingeniously designed light collectors". ScienceNow says: "For an organ that delivers such crystal-clear images, the eye is curiously designed. Its light-sensing rods and cones lie hidden behind a blanket of nerve cells that carry visual information to the brain. So what prevents those neurons from obscuring our vision? The answer may be surprisingly high-tech." So, in addition to optimal design arguments, we can now appreciate how these distinctive cells address completely the main perception of compromised design. One of the authors is quoted as saying: "Nature is so clever". Surely, it has to be myopic not to discern here the hallmarks of an intelligent designer. This is argument from evidence par excellence!

Muller cells are living optical fibers in the vertebrate retina
Kristian Franze, Jens Grosche, Serguei N. Skatchkov, Stefan Schinkinger, Christian Foja, Detlev Schild, Ortrud Uckermann, Kort Travis, Andreas Reichenbach, and Jochen Guck.
Proceedings of the National Academy of Sciences USA, May 15, 2007, vol. 104, no. 20, 8287-8292. | 10.1073/pnas.0611180104

Abstract: Although biological cells are mostly transparent, they are phase objects that differ in shape and refractive index. Any image that is projected through layers of randomly oriented cells will normally be distorted by refraction, reflection, and scattering. Counterintuitively, the retina of the vertebrate eye is inverted with respect to its optical function and light must pass through several tissue layers before reaching the light-detecting photoreceptor cells. Here we report on the specific optical properties of glial cells present in the retina, which might contribute to optimize this apparently unfavorable situation. We investigated intact retinal tissue and individual Muller cells, which are radial glial cells spanning the entire retinal thickness. Muller cells have an extended funnel shape, a higher refractive index than their surrounding tissue, and are oriented along the direction of light propagation. Transmission and reflection confocal microscopy of retinal tissue in vitro and in vivo showed that these cells provide a low-scattering passage for light from the retinal surface to the photoreceptor cells. Using a modified dual-beam laser trap we could also demonstrate that individual Muller cells act as optical fibers. Furthermore, their parallel array in the retina is reminiscent of fiberoptic plates used for low-distortion image transfer. Thus, Muller cells seem to mediate the image transfer through the vertebrate retina with minimal distortion and low loss. This finding elucidates a fundamental feature of the inverted retina as an optical system and ascribes a new function to glial cells.

See also:

Optical solution. ScienceShots

Sherriff, L. Living optical fibres found in the eye, The Register, Tuesday 1st May 2007

Ayoub, G. On the Design of the Vertebrate Retina, Origins & Design 17:1

Denton, M., The Inverted Retina: Maladaption or Pre Adaption? Origins & Design 19:2, Winter, 1999

The origins of language has long been discussed with little sign of any resolution. Now, "a team of researchers has rekindled an old hypothesis: that human language evolved from gesturing, rather than from vocal calls." Captive bonobos and chimpanzees were studied, to document manual gestures, facial signals and vocalisations. "The study distinguished 31 manual gestures and 18 facial/vocal signals. It was found that homologous facial/vocal displays were used very similarly by both ape species, yet the same did not apply to gestures. Both within and between species gesture usage varied enormously." One neuroscientist has commented: The greater variety of hand gestures "supports the idea that language evolved from manual gestures rather than animal calls".
This research has not been met with universal appreciation. Take this comment, for example: "Although all primates use vocal and facial expressions to communicate, only the great apes - chimpanzees, bonobos, orangutan and gorillas - use gestures as well, an ability they share with humans." Many people think that other animals do use gestures! Whilst manual gestures are only possible with animals having hands, gestures are possible with paws, tails, ears, fur and body posture. Maybe the reason why other animals are claimed not to use gestures is that their body language has not been formally studied. If gesturing is widespread as a means of communication, can there be any special significance of apes making gestures with limbs and hands? Human language remains a distinctive human trait.

Ape gestures and language evolution
Amy S. Pollick and Frans B. M. de Waal
Proceedings of the National Academy of Sciences USA, published April 30, 2007, 10.1073/pnas.0702624104

The natural communication of apes may hold clues about language origins, especially because apes frequently gesture with limbs and hands, a mode of communication thought to have been the starting point of human language evolution. The present study aimed to contrast brachiomanual gestures with orofacial movements and vocalizations in the natural communication of our closest primate relatives, bonobos (Pan paniscus) and chimpanzees (Pan troglodytes). We tested whether gesture is the more flexible form of communication by measuring the strength of association between signals and specific behavioral contexts, comparing groups of both the same and different ape species. Subjects were two captive bonobo groups, a total of 13 individuals, and two captive chimpanzee groups, a total of 34 individuals. The study distinguished 31 manual gestures and 18 facial/vocal signals. It was found that homologous facial/vocal displays were used very similarly by both ape species, yet the same did not apply to gestures. Both within and between species gesture usage varied enormously. Moreover, bonobos showed greater flexibility in this regard than chimpanzees and were also the only species in which multimodal communication (i.e., combinations of gestures and facial/vocal signals) added to behavioral impact on the recipient.

See also:

Morell, V. The Handy Way of Speaking, ScienceNOW Daily News, 30 April 2007

Ape gestures 'show human links', BBC News, 1 May 2007.

Two criticisms of ID are commonly heard: (1) it is unfalsifiable; and (2) it is falsified by observations of imperfect adaptations. Taking the second objection first, philosopher Elliott Sober acknowledges that there is a valid response: 'How can anyone know what an intelligent designer wanted to achieve unless the designer tells us?' Those who continue to use this style of criticism would do well to digest Sober's comments.
However, the first criticism is, in Sober's judgment, more substantial. Nevertheless, Popper's criterion of falsifiability should not be invoked if the grounds are that design inferences are probabilistic. If Popper's criterion is used in this way, not only would ID be deemed unfalsifiable, but also much evolutionary theory! Consequently, Sober invokes the necessity of considering "auxiliary propositions" in evaluating ID's scientific claims. These propositions, in other contexts, allow theories to make specific predictions. In the context of ID, "we have no independent evidence concerning which auxiliary propositions about the putative designer's goals and abilities are true". Thus, the robust response to the second criticism (noted above) is actually a demonstration that the first criticism is valid.
Sober's paper certainly needs to be discussed within ID circles. Suffice to say here that his reformulated criticism interacts only with a small subset of possible ID enquiries that purport to explain why an observed design was selected from the range of options. This is not a substantial criticism because ID scholars are concerned with making design inferences, not identifying design goals.
Sober's criticism needs to focus more on the mainstream ID arguments relating to objective evidences of design and the recognition of irreducible complexity. The probabilistic recognition of design is an integral part of archaeological science and forensic science, and any philosophy of science that does not find a place for design inferences must be defective. Furthermore, it is not a convincing argument against irreducible complexity to talk about genetic drift or crossing valleys in the fitness landscape. What we need, on the part of critics of ID, is a more penetrating analysis of actual ID arguments.

WHAT IS WRONG WITH INTELLIGENT DESIGN?
Elliott Sober
The Quarterly Review of Biology, March 2007, vol. 82, pp. 3-8.

ABSTRACT: This article reviews two standard criticisms of creationism/intelligent design (ID): it is unfalsifiable, and it is refuted by the many imperfect adaptations found in nature. Problems with both criticisms are discussed. A conception of testability is described that avoids the defects in Karl Popper's falsifiability criterion. Although ID comes in multiple forms, which call for different criticisms, it emerges that ID fails to constitute a serious alternative to evolutionary theory.

See also:

What is Wrong with Sober's Attack on ID? Evolution News, Posted by Casey Luskin
(Part I): Defining ID and its Historical Origins (March 21, 2007)
(Part II): Comparing ID and Darwinism while Ignoring Darwinism's Epicycles (March 28, 2007)
(Part III): Ignoring the Widely Discussed Positive Predictions of Intelligent Design (March 30, 2007)
(Part IV): Sober's Regressive Arguments (March 31, 2007)

Junk DNA must be the most misleading phrase in the vocabulary of evolutionary biologists. Now that researchers have realised that "non-coding" does not mean "useless", discoveries of functionality are commonplace. The latest contribution concerns mobile genetic elements - transposons. "Large swaths of garbled human DNA once dismissed as junk appear to contain some valuable sections, according to a new study". It has been recognised that many of these elements have an association with genes that are significant for early development. According to one of the researchers, "We used to think they were mostly messing things up. Here is a case where they are actually useful".
Next time you hear someone saying that humans share useless genetic information with chimpanzees, it is worth remembering the comment (in the abstract) that conserved sequences are, by extension, functional sequences. We are likely to share elements because we have similar functional needs, not because the sequences are vestigial. Whilst design inferences do not exclude the concept of degradation, they do help to avoid the pitfall of thinking that non-coding sequences are junk and not worth researching. That has been shown to be an argument from ignorance.

Thousands of human mobile element fragments undergo strong purifying selection near developmental genes
Craig B. Lowe, Gill Bejerano, and David Haussler
Proceedings of the National Academy of Sciences USA, published April 26, 2007, 10.1073/pnas.0611223104

Abstract: At least 5% of the human genome predating the mammalian radiation is thought to have evolved under purifying selection, yet protein-coding and related untranslated exons occupy at most 2% of the genome. Thus, the majority of conserved and, by extension, functional sequence in the human genome seems to be nonexonic. Recent work has highlighted a handful of cases where mobile element insertions have resulted in the introduction of novel conserved nonexonic elements. Here, we present a genome-wide survey of 10,402 constrained nonexonic elements in the human genome that have all been deposited by characterized mobile elements. These repeat instances have been under strong purifying selection since at least the boreoeutherian ancestor (100 Mya). They are most often located in gene deserts and show a strong preference for residing closest to genes involved in development and transcription regulation. In particular, constrained nonexonic elements with clear repetitive origins are located near genes involved in cell adhesion, including all characterized cellular members of the reelin-signaling pathway. Overall, we find that mobile elements have contributed at least 5.5% of all constrained nonexonic elements unique to mammals, suggesting that mobile elements may have played a larger role than previously recognized in shaping and specializing the landscape of gene regulation during mammalian evolution.

See also:

'Junk' DNA Now Looks Like Powerful Regulator, Scientists Find
Science Daily, April 24, 2007