Literature

If proteins and enzymes could not recognise their targets, cellular chemistry would be in chaos. "It was realized early that recognizing molecules should be complementary in shape, akin of matching lock and key". The metaphor of lock and key has served many generations of biology students well - only when the protein key meets the substrate lock do the molecules bind and generate a response. However, "half a century of research has shown, however, that in numerous cases, the molecules need to deform in order to bind, as the key is not an exact fit for the molecular lock." What is to be made of these findings? "Why search for a key that does not match its lock exactly, and then require that the imperfect key warp its shape to fit the lock?" Is this an indication that evolution is a tinkerer and cannot get it right? Is it an example of biology making sense without an intelligent designer?
Actually no. The authors of new study of this phenomenon asked one simple question: "Does molecular recognition gain any advantage by such conformational changes?" They concluded that a definite advantage is present. "Optimal specificity is achieved when the ligand is slightly off target; that is, a conformational mismatch between the ligand and its main target improves the selectivity of the process." In more popular language: "The researchers' model shows that the key's deformation actually helps in discerning the right target. Although the energy required to deform the molecular key slightly lowers the probability of its binding to the right target, it also reduces the probability that it will bind to a wrong one by quite a bit."
"This simple mechanism is coined "conformational proofreading" and may explain the observed deformations in many biological recognition systems. Furthermore, conformational proofreading may turn out be a crucial factor affecting the evolution of biological systems, and it may also be useful in the design of artificial molecular recognition systems." The authors write: "Our analysis suggests that conformational changes upon binding may arise as the outcome of an evolutionary selection for enhancing recognition specificity in a noisy environment."
So, something that could have been interpreted as evidence for tinkering evolution is discovered to have advantages after all. Furthermore, it has potential for the design of human systems operating in noisy environments. By invoking "evolutionary selection", the authors suggest an evolutionary context for their work. However, there is no evidence that evolutionary selection was involved, and the link with evolutionary theory is gratuitous. This is another example where the questioning of imperfect design has led to the discovery of exquisite design. The simple question asked by the researchers emerges routinely from the perspective of Intelligent Design.

Conformational Proofreading: The Impact of Conformational Changes on the Specificity of Molecular Recognition
Yonatan Savir, Tsvi Tlusty
PLoS ONE 2(5) 2007: e468. doi:10.1371/journal.pone.0000468

Abstract: To perform recognition, molecules must locate and specifically bind their targets within a noisy biochemical environment with many look-alikes. Molecular recognition processes, especially the induced-fit mechanism, are known to involve conformational changes. This raises a basic question: Does molecular recognition gain any advantage by such conformational changes? By introducing a simple statistical-mechanics approach, we study the effect of conformation and flexibility on the quality of recognition processes. Our model relates specificity to the conformation of the participant molecules and thus suggests a possible answer: Optimal specificity is achieved when the ligand is slightly off target; that is, a conformational mismatch between the ligand and its main target improves the selectivity of the process. This indicates that deformations upon binding serve as a conformational proofreading mechanism, which may be selected for via evolution.

See also:

When Off-target Is Right On, Newswise,26 July 2007.

The fossil record shows a consistent pattern of rapid (sometimes explosive) variation followed by stasis. This is found in the Early Cambrian with the dramatic appearance of animal phyla and, subsequently, with rapid radiations affecting classes, orders and families. Gould's advice to treat stasis as data has not been taken seriously by neodarwinists, who continue to treat the phenomenon as a quirk of history rather than a pervasive characteristic of living things.
Thinking on this topic deserves to be rekindled by a major study of trilobites by Mark Webster. Trilobites have a fossil record stretching from the Early Cambrian to the Late Permian, and 9 orders, 180 families, about 5000 genera and over 15,000 species of trilobites have been described to date. Many of these species are poorly documented and unsuitable for inclusion in a systematic study of morphological variation.
Webster's work involved coding for different character states and finding ways to document the variability. "Overall, approximately 35 percent of the 982 trilobite species exhibited some variation in some aspect of their appearance that was evolving. But more than 70 percent of early and middle Cambrian species exhibited variation, while only 13 percent of later trilobite species did so." The research documented both rapid morphological variation and subsequent stasis. "There's hardly any variation in the post-Cambrian," Webster said. "Even the presence or absence or the kind of ornamentation on the head shield varies within these Cambrian trilobites and doesn't vary in the post-Cambrian trilobites."
In a commentary on these findings, Hunt writes: "This study, in establishing the reality of increased Cambrian variability for trilobites, implies that evolutionary processes in the distant past may have acted differently, or in a different balance than in more recent periods of time." It is important to put the new research into context, for what Webster has done is to use trilobites to quantify a trend that is far from unique.
Hunt goes on to consider two possible ways of making sense of the findings: "These explanations fall into two broad categories: genetic and ecological. The former suggest that Cambrian genomes were less constrained, or otherwise less apt to generate profoundly novel morphologies, whereas the latter invoke the relative sparseness of early animal ecosystems in allowing large evolutionary jumps to become successfully established." This debate gets really interesting if it is recognised that the trilobite record is representative of the norm. "We need to tease apart what's controlling this pattern of high within-species variation. There's a lot more work to do," says Webster. With more and more and more evidences emerging of initial complexity, methodologies based on ID have much to offer. One hypothesis is that radiations occur because organisms are designed to vary, but the process results in genetic impoverishment that leads to stasis.

A Cambrian Peak in Morphological Variation Within Trilobite Species
Mark Webster
Science, 317, 27 July 2007: 499-502.

Abstract: Morphological variation within species is a raw material subject to natural selection. However, temporal change in morphological diversity has usually been studied in terms of variation among rather than within species. The distribution of polymorphic traits in cladistic character-taxon matrices reveals that the frequency and extent of morphological variation in 982 trilobite species are greatest early in the evolution of the group: Stratigraphically old and/or phylogenetically basal taxa are significantly more variable than younger and/or more derived taxa. Through its influence on evolutionary tempo, high intraspecific variation may have played a major role in the pronounced Cambrian diversification of trilobites.

See also:

Hunt, G. Variation and Early Evolution, Science, 317, 27 July 2007: 459-460.

Fossils Older Than Dinosaurs Reveal Pattern Of Early Animal Evolution On Earth, Science Daily, July 26, 2007

Congratulations to Sean Nee for writing a most readable and informative review of Tim Friend's book on the untold story of the archaea. This features in large measure the research of Carl Woese, who has identified the archaea as the third domain of life (alongside bacteria and eukaryotes). "Woese pulled all the evidence together and made the intellectual leap that is now accepted: there is a third domain of life - the archaea. All of this is told, and much more."
For some of us, it is the "much more" that gives this story a special fascination. Not mentioned in the review, but essential to understanding Woese's contribution, is the claim that horizontal gene transfer was extensive in life's early history. Freeman Dyson draws attention to this in a recent essay: "Evolution was a communal affair, the whole community advancing in metabolic and reproductive efficiency as the genes of the most efficient cells were shared. Evolution could be rapid, as new chemical devices could be evolved simultaneously by cells of different kinds working in parallel and then reassembled in a single cell by horizontal gene transfer."
Consequently, Woese is known as someone who questions the role of Darwinism in the early earth. Here is Dyson again: "He presents evidence that Darwinian evolution does not go back to the beginning of life. When we compare genomes of ancient lineages of living creatures, we find evidence of numerous transfers of genetic information from one lineage to another. In early times, horizontal gene transfer, the sharing of genes between unrelated species, was prevalent. It becomes more prevalent the further back you go in time." Darwinism is perceived as a reductionistic approach which fails to do justice to appreciating and understanding complexity. Dyson writes: "Woese's main theme is the obsolescence of reductionist biology as it has been practiced for the last hundred years, with its assumption that biological processes can be understood by studying genes and molecules. What is needed instead is a new synthetic biology based on emergent patterns of organization."
Perhaps these issues were too controversial to go into a review in Nature. Nevertheless, Nee does slip in this comment: "It is probably no coincidence that Oxford's most famous popular writer on biology, Richard Dawkins, notoriously gave only a single page to the third domain of life in his take on biodiversity, The Ancestor's Tale, apparently more interested in things like cabbages." With his strong stance on the logical imperative of neodarwinism, it is understandable that Dawkins is not aligning himself with Woese's opposition to reductionism in biology, nor his rejection of Darwinism prior to the appearance of bacteria, archaea and eukaryotes.
With the proviso that "new ways of thinking" should include ID, we can let Dyson have the last word: "The reductionist physics and the reductionist molecular biology of the twentieth century will continue to be important in the twenty-first century, but they will not be dominant. The big problems, the evolution of the universe as a whole, the origin of life, the nature of human consciousness, and the evolution of the earth's climate, cannot be understood by reducing them to elementary particles and molecules. New ways of thinking and new ways of organizing large databases will be needed."

Introducing the extremophiles
Sean Nee
Nature, 448, 413-414 (26 July 2007) | doi:10.1038/448413a

BOOK REVIEWED-The Third Domain: The Untold Story of Archaea and the Future of Biotechnology, by Tim Friend, Joseph Henry Press: 2007.

First para: Envy the achievement of Carl Woese, who announced his discovery of the third domain of life on Earth a mere 30 years ago. Marvel at the fact that most people are unaware of this three-domain understanding of biodiversity. Admire the journalist Tim Friend who resigned from the newspaper USA Today to write this superb book introducing the public to the third domain. Buy it and enjoy the personalities, the adventures, the drama and the science too, all presented in an admirable mix that is a terrific read.

See also:

Dyson, F., Our Biotech Future, The New York Review of Books, Volume 54, Number 12, July 19, 2007.

Watching geckos dart with equal ease over walls, floors and ceilings must have engaged the attention of countless travellers. How do these little animals do it? It is only in recent years that the answers have been forthcoming. The adhesion comes from van der Waals forces between nano-sized spatulae located on hairs on the gecko's foot and the substrate. The gecko provides a superb demonstration of how nanofibres can be organised to have a macroscopic impact. Research to reproduce the adhesion effects has taken place in many countries and two significant papers report recent progress.
Lee and colleagues have sought to enhance the wet performance of adhesion by incorporating a "synthetic polymer that mimics the wet adhesive proteins found in mussel holdfasts". They report greatly improved adhesion properties. "The hybrid material, which they call a geckel nanoadhesive, proved in initial testing to be adherent under dry and wet conditions. It also adhered much longer under both extremes than previous gecko-based synthetic adhesives, a major issue in this area of research."
The other paper, by Ge and colleagues, reports on a gecko-inspired adhesive tape. "We have demonstrated for the first time a macroscopic flexible patch that can be used repeatedly with peeling and adhesive properties better than the natural gecko foot. The carbon nanotube-based tape offers an excellent synthetic option as a dry conductive reversible adhesive in microelectronics, robotics, and space applications."
One thing we can learn from this particular exercise in biomimetics is that the gecko does not demonstrate just a single trait with enhanced performance. There are issues of adhesion and delamination, self-cleaning, and achieving a sustained adhesive performance. What we have in the gecko is exquisite design and, for that, biomimetics needs a methodology that can relate well to intelligent engineering design concepts. For more on this, go here.
One report of the adhesive tape research says: "Work is now underway to make the tape self-cleaning as well". Interestingly, in 2005, Hansen and Autumn speculated that the nano-sized setae might be self-cleaning, but this ongoing activity suggests that there are more gecko secrets yet to emerge in this area!

A reversible wet/dry adhesive inspired by mussels and geckos
Haeshin Lee, Bruce P. Lee & Phillip B. Messersmith
Nature, 448, 338-341 (19 July 2007) | doi:10.1038/nature05968

The adhesive strategy of the gecko relies on foot pads composed of specialized keratinous foot-hairs called setae, which are subdivided into terminal spatulae of approximately 200 nm (ref. 1). Contact between the gecko foot and an opposing surface generates adhesive forces that are sufficient to allow the gecko to cling onto vertical and even inverted surfaces. Although strong, the adhesion is temporary, permitting rapid detachment and reattachment of the gecko foot during locomotion. Researchers have attempted to capture these properties of gecko adhesive in synthetic mimics with nanoscale surface features reminiscent of setae2, 3, 4, 5, 6, 7; however, maintenance of adhesive performance over many cycles has been elusive2, 8, and gecko adhesion is greatly diminished upon full immersion in water9, 10. Here we report a hybrid biologically inspired adhesive consisting of an array of nanofabricated polymer pillars coated with a thin layer of a synthetic polymer that mimics the wet adhesive proteins found in mussel holdfasts. Wet adhesion of the nanostructured polymer pillar arrays increased nearly 15-fold when coated with mussel-mimetic polymer. The system maintains its adhesive performance for over a thousand contact cycles in both dry and wet environments. This hybrid adhesive, which combines the salient design elements of both gecko and mussel adhesives, should be useful for reversible attachment to a variety of surfaces in any environment.

Carbon nanotube-based synthetic gecko tapes
Liehui Ge, Sunny Sethi, Lijie Ci, Pulickel M. Ajayan, and Ali Dhinojwala
Proceedings of the National Academy of Sciences USA, June 26, 2007, vol. 104, no. 26, 10792-10795 | 10.1073/pnas.0703505104

We have developed a synthetic gecko tape by transferring micropatterned carbon nanotube arrays onto flexible polymer tape based on the hierarchical structure found on the foot of a gecko lizard. The gecko tape can support a shear stress (36 N/cm2) nearly four times higher than the gecko foot and sticks to a variety of surfaces, including Teflon. Both the micrometer-size setae (replicated by nanotube bundles) and nanometer-size spatulas (individual nanotubes) are necessary to achieve macroscopic shear adhesion and to translate the weak van der Waals interactions into high shear forces. We have demonstrated for the first time a macroscopic flexible patch that can be used repeatedly with peeling and adhesive properties better than the natural gecko foot. The carbon nanotube-based tape offers an excellent synthetic option as a dry conductive reversible adhesive in microelectronics, robotics, and space applications.

See also:

Gould, P. Nanotube tape mimics gecko's sticky feet, NanoToday, Volume 2, Issue 4, August 2007, Page 12.

Hansen, W.R. and Autumn, K., Evidence for self-cleaning in gecko setae, Proceedings of the National Academy of Sciences USA, January 11, 2005, vol. 102, no. 2, 385-389 | 10.1073/pnas.0408304102

Nature's secrets yield new adhesive material, EurekAlert, 18 July 2007.

When I first heard of treadmill studies involving chimps and humans, I wondered if the researchers would be open to design paradigms as well as Darwinian adaptation. Would they get beyond the narrow conceptual window exhibited by another group studying assisted bipedalism in orangutans? The answer to that question would appear to be no.
"The researches collected metabolic, kinematic and kinetic data from five chimpanzees and four adult humans walking on a treadmill. The chimpanzees were trained to walk quadrupedally and bipedally on the treadmill. Humans walking on two legs only used one-quarter of the energy that chimpanzees who knuckle-walked on four legs did. On average, the chimpanzees used the same amount of energy using two legs as they did when they used four legs." This is certainly an interesting result. Those who have declared human upright movement to be associated with numerous bad design features will be given food for thought by this research. Those who already recognise design in the human body will regard the new data as strengthening this understanding.
The researchers, however, pursue an adaptationist agenda. The new study is said to provide support "for the hypothesis that walking on two legs, or bipedalism, evolved because it used less energy than quadrupedal knucklewalking." Also, "it has been hypothesized that the reduced energy cost of walking upright would have provided evolutionary advantages by decreasing the cost of foraging." OK, this is an adaptationist hypothesis, but it needs to be tested. Demonstrating an energy differential does not prove a hypothesis: in this case it just stimulates a hypothesis.
This is a situation where the Adaptive Landscape concept may be helpful. When considered holistically, bipedalism involves a whole raft of characters, all of which are needed to form a workable organism. Bipedalism involves arched feet, strong big toes, long legs, upright knee joints, angled femur bones, upright hip joints, straight back, upright skull, flat face and a very fine sense of balance. Taking all these characters into account means that the adaptive landscape looks like to very sharp peaks separated by a wide plain. We could call the peaks Mount Ape Improbable and Mount Human Improbable. The claim that there is an incremental route for an apelike animal to move from one peak to the other has so far eluded Darwinians. The authors comment: "why our unique two-legged gait evolved remains unknown." We have no evidence that apes have ever climbed a Mount Improbable, and there is a long way to go before an adaptive story based on the "evolutionary advantages [of decreased] cost of foraging" can begin to be convincing. Studying evidences of a "more extended hip and a longer hindlimb" do not get close to a holistic appreciation of the issues.
In 2002, a film was produced with the name Most Vertical Primate. In it, a chimpanzee becomes a competent skateboarder. A trailer can be found here. The task of training the chimpanzee to skateboard was impossible. One foot had to be tied to the board and the other positioned carefully so that the animal could get a grip with its toes. Even then, the chimp could not steer or balance. The film of skateboarding was pierced together from tiny clips of a few seconds each. Stuart Burgess, a design engineer, concluded: "Despite the title of the film, the film actually demonstrated that apes are not designed to be vertical!"

Chimpanzee locomotor energetics and the origin of human bipedalism
Michael D. Sockol, David A. Raichlen, and Herman Pontzer
Proceedings of the National Academy of Sciences US, published July 16, 2007, 10.1073/pnas.0703267104
http://www.pnas.org/cgi/content/abstract/0703267104v1?

Bipedal walking is evident in the earliest hominins [Zollikofer CPE, Ponce de Leon MS, Lieberman DE, Guy F, Pilbeam D, et al. (2005) Nature 434:755-759], but why our unique two-legged gait evolved remains unknown. Here, we analyze walking energetics and biomechanics for adult chimpanzees and humans to investigate the long-standing hypothesis that bipedalism reduced the energy cost of walking compared with our ape-like ancestors [Rodman PS, McHenry HM (1980) Am J Phys Anthropol 52:103-106]. Consistent with previous work on juvenile chimpanzees [Taylor CR, Rowntree VJ (1973) Science 179:186-187], we find that bipedal and quadrupedal walking costs are not significantly different in our sample of adult chimpanzees. However, a more detailed analysis reveals significant differences in bipedal and quadrupedal cost in most individuals, which are masked when subjects are examined as a group. Furthermore, human walking is ~75% less costly than both quadrupedal and bipedal walking in chimpanzees. Variation in cost between bipedal and quadrupedal walking, as well as between chimpanzees and humans, is well explained by biomechanical differences in anatomy and gait, with the decreased cost of human walking attributable to our more extended hip and a longer hindlimb. Analyses of these features in early fossil hominins, coupled with analyses of bipedal walking in chimpanzees, indicate that bipedalism in early, ape-like hominins could indeed have been less costly than quadrupedal knucklewalking.

See also:

Study Identifies Energy Efficiency As Reason For Evolution Of Upright Walking, Science Daily July 17, 2007

Burgess, S. The Origin of Man, Day One Publications, 2004.

The past year has been marked by numerous claims about science disproving God. The terms evidence and reason appear to have been comandeered by some scientists, falsely implying that Christianity has no place for clear thinking or for grappling with data. Studies have been published to show that eminent scientists tend to be atheists, and the conclusion is drawn that science leads people to abandon faith in God.
A new study by social scientists confirms that there is a secularising trend in the beliefs of the science community, but the authors question whether science has anything to do with it. "The first systematic analysis in decades to examine the religious beliefs and practices of elite academics in the sciences supports the notion that science professors at top universities are less religious than the general population, but attributes this to a number of variables that have little to do with their study of science."
The lead researcher is quoted as saying: "Our study data do not strongly support the idea that scientists simply drop their religious identities upon professional training, due to an inherent conflict between science and faith, or to institutional pressure to conform." Furthermore, the researchers found little to distinguish social scientists from scientists, which is another indication that the sciences are not exerting any distinctive influences above those of other academic disciplines.
The authors flag up childhood experience of religion as a major factor in their study. "Academic science has a disproportionately large number of people raised with no religion, potentially producing many more people who do not believe in God." The authors discuss this significant finding in their paper, offering tentative leads, and pointing to further research. I found this comment interesting: "Scientists lament a lack of scientific understanding among the U.S. population (Scientific American 2005; Lakoff 2005). While the general American public may indeed have a less than desirable understanding of science, our findings reveal that academic scientists may have much less experience with religion than many outside the academy." This is worth our attention, not only because there is an important debate here, but also because not a few have noted that the criticisms of Christianity emerging from some vocal scientists do not get beyond the teenager level of sophistication. These opinion-formers have only a rudimentary appreciation of the beliefs they are criticising! This new research could explain why.
For an ID exposition of why academics in general are affected by a cultural secularising tendency, see Phillip Johnson's Reason in the Balance: The Case Against Naturalism in Science, Law and Education (1998).

Religion among Academic Scientists: Distinctions, Disciplines, and Demographics
Elaine Howard Ecklund and Christopher P. Scheitle
Social Problems, May 2007, Vol. 54, No. 2: 289-307.

Abstract: The religiosity of scientists is a persistent topic of interest and debate among both popular and academic commentators. Researchers look to this population as a case study for understanding the intellectual tensions between religion and science and the possible secularizing effects of education. There is little systematic study, however, of religious belief and identity among academic scientists at elite institutions, leaving a lacuna of knowledge in this area. This absence of data exists at a time when the intersection between religion and science is reaching heightened public attention. Especially with increased tensions surrounding teaching evolution in the public schools, understanding what kind of resources scientists have (particularly in terms of their own religious beliefs and practices) to transmit science to a broader religiously-motivated public is crucial. Using data from a recent survey of academic scientists at twenty-one elite U.S. research universities, we compare the religious beliefs and practices of natural and social scientists within seven disciplines as well as academic scientists to the general population. We find that field-specific and interdisciplinary differences are not as significant in predicting religiosity as other research suggests. Instead, demographic factors such as age, marital status, and presence of children in the household are the strongest predictors of religious difference among scientists. In particular, religiosity in the home as a child is the most important predictor of present religiosity among this group of scientists. We discuss the relevance these findings have for understanding issues related to current theory and public debate about the intersection between religion and science.

See also:

Scientists May Not Be Very Religious, but Science May Not Be to Blame, University of Buffalo News, 23 July 2007.

Gene, M. Science Does Not Lead to Atheism (Telic Thoughts, 19 July 2007)

The selectionist/neutralist controversy has continued for nearly 40 years, and a resolution is not in sight. NeoDarwinists like to think that Neutral Evolution is compatible with neoDarwinism, but this is a bit like their attitude to Punctuated Equilibrium: everything worth saying has to be compatible with neoDarwinism! Meanwhile, the controversy goes on. . .
In a recent PNAS review paper, Masatoshi Nei argues that our knowledge of genetics is such that, as far as genes controlling phenotypic characters are concerned, conservation is a more applicable description than evolution. "Phenotypic evolution occurs primarily by mutation of genes that interact with one another in the developmental process. The enormous amount of phenotypic diversity among different phyla or classes of organisms is a product of accumulation of novel mutations and their conservation that have facilitated adaptation to different environments. [. . .] It appears that the driving force of phenotypic evolution is mutation, and natural selection is of secondary importance."
This is, of course, not the message that you get from neoDarwinists, who continue to emphasise adaptive causation. In their view, natural selection is essential to explain the origin of complexity, and they are not impressed by the neutralists diminishing of the role of natural selection.
Whilst this paper can be discussed in various ways, I want to focus on the educational issues. We have here a controversy about the relative significance of mutations and natural selection. It is not a minor matter. NeoDarwinists feel very strongly about it. Take, for example, Richard Dawkins critiquing Michael Behe in The New York Times (July 1 2007):

The crucial passage in The Edge of Evolution is this: "By far the most critical aspect of Darwin's multifaceted theory is the role of random mutation. Almost all of what is novel and important in Darwinian thought is concentrated in this third concept."
What a bizarre thing to say! Leave aside the history: unacquainted with genetics, Darwin set no store by randomness. New variants might arise at random, or they might be acquired characteristics induced by food, for all Darwin knew. Far more important for Darwin was the nonrandom process whereby some survived but others perished. Natural selection is arguably the most momentous idea ever to occur to a human mind, because it - alone as far as we know - explains the elegant illusion of design that pervades the living kingdoms and explains, in passing, us. Whatever else it is, natural selection is not a "modest" idea, nor is descent with modification.

Then compare with Nei, who says this:

Although this type of statement is quite common in the evolutionary literature, it is obvious that any advantageous genotype is produced by mutation including all kinds of genetic changes. Natural selection occurs as a consequence of mutational production of different genotypes, and therefore it is not the fundamental cause of evolution.

This is an issue which is educationally very important, and it also happens to be relevant to ID arguments. It is not in the educational interests of students to prevent such issues being discussed by teachers, and nor should it be deemed a "religious intrusion" into science when neoDarwinism is subjected to critical scrutiny.

The new mutation theory of phenotypic evolution
Masatoshi Nei
Proc. Natl. Acad. Sci. USA, 10.1073/pnas.0703349104, Online 17 July 2007.

Recent studies of developmental biology have shown that the genes controlling phenotypic characters expressed in the early stage of development are highly conserved and that recent evolutionary changes have occurred primarily in the characters expressed in later stages of development. Even the genes controlling the latter characters are generally conserved, but there is a large component of neutral or nearly neutral genetic variation within and between closely related species. Phenotypic evolution occurs primarily by mutation of genes that interact with one another in the developmental process. The enormous amount of phenotypic diversity among different phyla or classes of organisms is a product of accumulation of novel mutations and their conservation that have facilitated adaptation to different environments. Novel mutations may be incorporated into the genome by natural selection (elimination of preexisting genotypes) or by random processes such as genetic and genomic drift. However, once the mutations are incorporated into the genome, they may generate developmental constraints that will affect the future direction of phenotypic evolution. It appears that the driving force of phenotypic evolution is mutation, and natural selection is of secondary importance.

See also:

Dawkins, R. Inferior Design, The New York Times, July 1, 2007 [for link, go here]

Scordova, Prominent NAS member trashes neo-Darwinism, Uncommon Descent, 18 July 2007

According to Winston Churchill, "History is written by the victors." The losers are variously portrayed as a scourge on society that the world is best rid of. The Warfare Thesis was invented towards the end of the 19th Century to replace the hegemony of the established church with the new hegemony of scientism, and ever since that time, the advocates of naturalism have been reinforcing the warfare myth and claiming victory for science against the forces of darkness (which generally means Christianity). The 1925 Scopes Trial in the US was slotted into this format and it now appears that the Dover trial is getting the same treatment.
In Nature, Kevin Padian has reviewed three books that tell the story of the Dover trial: where the decision of the Education Board in Dover, PA to incorporate Intelligent Design into the science lessons of students was declared to be an act of "breathtaking inanity" by the judge. The judge accepted the documents prepared for the prosecution by the National Center for Science Education. The president of the NCSE is none other than the reviewer, Kevin Padian. According to him, after the trial, "Intelligent-design proponents sputtered and fumed; the usual right-wing commentators fulminated; no one has since taken the Discovery Institute seriously."
Spin is ubiquitous in this review. The DI scholars are likened to "persecuted pilgrims who then turn around and ostracize anyone who doesn't agree with them"; after mentioning the textbook Of Pandas and People, the judge is said to have "proscribed bogus criticisms of evolution in science classes"; apparently, "Behe's notions of 'irreducible complexity' and the status of intelligent design as science were shredded by attorney Eric Rothschild", and Dembski gets "withering criticism from actual mathematicians". Needless to say, these comments (and others like them) are content-free. There is nothing offered that goes beyond opinion. This review is a sop to those who want to be associated with the victors (identified by Padian as those who side with the Enlightenment). For an antidote, read "Setting the Record Straight about Discovery Institute's Role in the Dover School District Case". It is unfortunate that Nature is prepared to treat such a partisan essay as though it were a work of scholarship.
Churchill is also responsible for this thought: "History will be kind to me for I intend to write it". I like to think that he was in a humorous mood at the time. However, Padian and the historical revisionists appear to be deadly serious and so it behoves us all to check things out and take people to task for indulging in spin.

The case of creation
Last year's Dover trial resulted in intelligent design being removed from the science curriculum
Kevin Padian
Nature, 448, 253-254 (19 July 2007) | doi:10.1038/448253a

First para: Three new books use as a centrepiece the court case of Kitzmiller et al. versus Dover Area School District, which played out for six weeks in late 2005 at the state capital of Pennsylvania. This trial was the latest in a series of American 'Scopes trials', named after the 1925 prosecution of Tennessee teacher John Scopes, who was fined $100 for flouting a state law that prohibited the teaching of evolution in state-run schools. Scopes volunteered to be the test case, knowingly breaking the law. Famed attorneys Clarence Darrow and William Jennings Bryan argued the case. Scopes lost, Tennessee was ridiculed, a few other states passed similar legislation, and the divide between fundamentalists and secularists in the United States was irrevocably cleft.

See also:

Dembski, W., Kevin Padian: The Archie Bunker Professor of Paleobiology at Cal Berkeley, Uncommon Descent, 20 July 2007.
[putting the record straight about Dembski receiving "withering criticism from actual mathematicians."]

Biomimetics has rapidly emerged as a route to innovative technology and academic publication. Various indicators show that the growth from 1990 to the present has been exponential. Hesselberg says that the favoured methodology to date has been mechanism-driven biomimetics. This starts with an engineering problem, finds potential solutions in the natural world and uses the best as inspiration to develop an engineered product. Well-known examples are the invention of Velcro and the development of Lotus-Effect (self-cleaning) materials.
Two other biomimetic approaches are explained by the author. Both are organism-driven, where organisms are studied for their potential. One approach is focused, where there is a particular phenomenon that is considered to have commercial potential. A good example is gecko feet. The other approach is integrative, where several aspects of an organism are considered concurrently. A widely cited example of this is cockroach locomotion. The case study Hesselberg presents in his paper concerns integrative organism-driven biomimetics relating to ragworms. Despite most people knowing them only as fish bait, these animals give multi-functional inspiration to novel endoscopes, displacement pumps and multifunctional robots.
The reason for drawing attention to this paper is that biomimetics nearly always involves teams of highly skilled people. "The multidisciplinary aspect of biomimetics is very strong, with many active groups including computer scientists, physicists, chemists, and philosophers working alongside biologists and engineers." The implication is that nature's secrets are not easily revealed, and certainly not easy to mimic.
Hesselberg also notes that "the field is still lacking an analytical framework". This has set me wondering whether this is related to the influence of Darwinism within the academic world. According to Darwinism, design is only apparent. It does not reveal an intelligent agent at work. Incremental natural variations combined with natural selection are deemed to be adequate causal agents. The Darwinists themselves predict that this leads to a "tinkering" style of design, but is this what we observe? The reason why biomimetics has taken off is not because people are uncovering designs of the tinkering variety, but designs that are exquisite and holistic. This is particularly apparent in the integrative organism-driven biomimetics reviewed by Hesselberg. Biomimetics as an interdisciplinary discipline may well find that Intelligent Design is superior to Darwinism for underpinning its analytical framework.

Biomimetics and the case of the remarkable ragworms
Thomas Hesselberg
Naturwissenschaften, Volume 94, Number 8 / August, 2007, 613-621.

Abstract: Biomimetics is a rapidly growing field both as an academic and as an applied discipline. This paper gives a short introduction to the current status of the discipline before it describes three approaches to biomimetics: the mechanism-driven, which is based on the study of a specific mechanism; the focused organism-driven, which is based on the study of one function in a model organism; and the integrative organism-driven approach, where multiple functions of a model organism provide inspiration. The first two are established approaches and include many modern studies and the famous biomimetic discoveries of Velcro and the Lotus-Effect, whereas the last approach is not yet well recognized. The advantages of the integrative organism-driven approach are discussed using the ragworms as a case study. A morphological and locomotory study of these marine polychaetes reveals their biomimetic potential, which includes using their ability to move in slippery substrates as inspiration for novel endoscopes, using their compound setae as models for passive friction structures and using their three gaits, slow crawling, fast crawling, and swimming as well as their rapid burrowing technique to provide inspiration for the design of displacement pumps and multifunctional robots.

Today, we are familiar with the metaphor of the cell as a factory, taking in raw materials and converting them, via elaborate processing equipment and complex chemistry, into usable products. But this metaphor is not the only one. The author of a recent review writes: "The history of cell theory offers a rich lesson in the use of metaphor and analogy in scientific thought. The first account of the cell likened it to an empty room, but it has also been conceptualized through the metaphors of a building stone (Baustein), an elementary organism (Elementarorganismus), a chemical laboratory or factory, a motor and a machine."
Of particular interest for this blog is the situation when Darwinism was in its infancy: "The dominant metaphor in the second half of the nineteenth century described the body as a 'society' or 'state' of cells (Zellenstaat). Cells were 'citizens' arranged into separate classes or professions according to their functions, together making up the 'economy of the organism'." "Using the physiologist Ernst Brucke's (1819-1892) proposal that cells be considered 'elementary organisms' (itself an analogy to the way the chemical elements came together to form complex molecules), evolutionary zoologist Ernst Haeckel (1834-1919) gave the cell-state metaphor a Darwinian spin: higher plants and animals, he argued, were evolved into colonies of these elemental organisms and humans were little more than a complex colony of protozoan-like cells with a highly evolved division of labor." So, the cell was conceived as a simple building block, and organisms were portrayed as assemblages with varying degrees of complexity.
The metaphor changed when the focus became process. "The metaphor of the cell factory or laboratory was employed chiefly when the topic of discussion was physiology, and in particular the problem of metabolism. [. . .] For those interested in metabolic activities, wanting to know how these little things worked rather than where they came from, the factory or laboratory metaphor was far more suggestive than the comparison to an elementary organism. This may explain why the metaphor of the cell factory emerged as a serious competitor to the elementary organism metaphor in the early twentieth century. It was then that biologists began to turn away from the construction of phylogenetic trees of the sort made popular by Haeckel towards more experimental investigations of cell activity guided by the mechanistic principles of chemistry and physics." The author concludes with comments on literal cell factories in the age of biotechnology.
The theme of the paper is worth further consideration by us. Thus, empirically-based biologists discovered that the cell was quite different from the simple ("empty room") concept favoured by Haeckel and many other Darwinists. Those who keep repeating the mantra that nothing in biology makes sense except in the light of evolution would do well to reflect on how Darwinism perpetuated a false metaphor of the cell and it needed a new generation of empiricists to move the subject on.
However, such was the hold of Darwinism that a way of maintaining the myth of simplicity was found. Ultimately, the cell had to be simple (they thought), so that incremental changes (mutations) could occur and be selected naturally. Then Michael Behe came along with his book 'Darwin's Black Box'. The ultimate can now be known: at the level of molecular biology. Researchers were finding complexity right down to the molecular level, and some of these mechanisms allow the recognition of irreducible complexity. 'Simplicity' is a word that should never be used when talking about cells!

The cell's journey: from metaphorical to literal factory
Andrew Reynolds
Endeavour, Volume 31, Issue 2, June 2007, Pages 65-70.

The concept of the cell has been based on metaphor since its inception, and the history of cell theory has continued to rely on metaphor and analogy. In the nineteenth century, cells were most popularly conceived either as building stones or elementary autonomous organisms from which larger organisms are composed. With advances in physiology and the rise of modern biochemistry in the early twentieth century, the chemical factory or laboratory became the dominant metaphor for this biological unit. Today in the twenty-first century, the metaphorical imagery has become a reality, with cells acting as chemical factories for the synthesis of commercially valuable bio-products. The history of the cell shows how metaphors act as conceptual tools, with particular strengths for facilitating different sorts of questions and experimental techniques.

It was in 1967 that W.D. Hamilton published his seminal thoughts on "extraordinary sex ratios", suggesting ways of understanding why "Fisher's principle" for 1:1 being the equilibrium ratio has many exceptions in nature. Records of the butterfly Hypolimnas bolina living on the Samoan islands reveal extreme ratios and also extreme fluctuations of those ratios. Media reports have majored on the thought that this is evolution in action: "Evolution occurs in the blink of an eye" (LiveScience) and "Butterfly shows evolution at work" (BBC). Since the media have rarely heeded Phil Johnson's sound advice to distinguish the different meanings of the word "evolution", it is useful for us to consider the research with this in mind.
Sex ratios are distorted by the presence of a maternally inherited bacterium which has the effect of selectively killing male embryos. The authors report ratios of >99% female to nearly 1:1. These were different on different islands and at different times. The genetics of this shift of sex ratios is summarised in one paragraph with some supporting online data. There is not enough information here for anyone to either confirm or challenge their conclusions. However, more substantial evidence for "suppression genes" had previously been published in 2006, and for the sake of this discussion, we will accept that "the shift in sex ratio was caused by the spread of host suppressor genes."
What we should be aware of is that the source of these genes is unknown. Various options exist. A novel mutation is a possibility (the 2006 study considered the suppression was controlled by a single locus). Another avenue to explore is that the gene had existed previously in the population (or sub-populations) of butterflies.
So the story concerns a genetic trait restoring the sex ratio of a species of butterfly living in the Samoan Islands. This seems to be a straightforward case of natural selection of a gene whose presence is directly related to the survival of male butterflies. The lead author comments: "To my knowledge, this is the fastest evolutionary change that has ever been observed". It is true it is rapid, but we might be forgiven the thought that if it were not rapid, the species would last little longer than its lifecycle!
In terms of its significance for evolutionary theory, this research is on a par with the peppered moth: there is no insight into speciation and there is no change in complexity of the organism. It is an observation that is perfectly compatible with Darwinism, ID and creation-based biology. The lead author is quoted as saying: "We're witnessing an evolutionary arms race between the parasite and the host. This strengthens the view that parasites can be major drivers in evolution". This is much more controversial. There is widespread view in ID circles that these genetic skirmishes actually lead to genetic impoverishment. Parasites may drive change, but it is likely to be towards extinction. To justify the "major driver" claim, the genetics of the process need to be analysed in much greater detail.

Extraordinary Flux in Sex Ratio
Sylvain Charlat, Emily A. Hornett, James H. Fullard, Neil Davies, George K. Roderick, Nina Wedell, Gregory D. D. Hurst.
Science, 13 July 2007: Vol. 317, p. 214, DOI: 10.1126/science.1143369

The ratio of males to females in a species is often considered to be relatively constant, at least over ecological time. Hamilton noted that the spread of "selfish" sex ratio-distorting elements could be rapid and produce a switch to highly biased population sex ratios. Selection against a highly skewed sex ratio should promote the spread of mutations that suppress the sex ratio distortion. We show that in the butterfly Hypolimnas bolina the suppression of sex biases occurs extremely fast, with a switch from a 100:1 population sex ratio to 1:1 occurring in fewer than 10 generations.

See also:

Bryner, J. Evolution Occurs in the Blink of an Eye, LiveScience, 12 July 2007

Butterfly shows evolution at work, BBC News, 12 July 2007

Hornett, E.A., Charlat, S., Duplouy, A.M.R., Davies, N., Roderick, G.K., Wedell, N. and Hurst, G.D., Evolution of Male-Killer Suppression in a Natural Population, PLoS Biology Vol. 4, No. 9, e283 doi:10.1371/journal.pbio.0040283

A simulation model of early biological evolution has been developed which claims to advance our knowledge of how the first gene families developed. Although we know very little about how the genotype relates to phenotype, it was necessary for the architects to build something about this into their model. They postulated that the death rate of an organism is determined by the stability of the least stable of their proteins. Initial conditions were as follows: "Our evolution dynamics runs start from an initial population of 100 organisms, each having the same one primordial gene in their genomes. Initial gene sequence is random."
The simulation was executed using a cycle of 4 steps: "(i) random mutation of a nucleotide in a randomly selected gene with constant rate m per unit time per DNA length; mutations leading to the stop codon are rejected to ensure the constant length of protein sequences; (ii) duplication of a randomly selected gene within an organism's genome with constant rate u; (iii) birth of an organism via duplication of an already existing organism with constant rate b (the genome is copied exactly); and (iv) death of an organism with the rate d per unit time."
After running the model, the number of genes increased, but never exceeded 10. "We found that out of 50 simulation runs starting with different starting sequences, 27 runs successfully resulted in a steady exponential growth of the population, whereas in 23 runs the population has quickly gone extinct." Numerous characteristics of the simulations are reported, with this comment: "Based on these observations, we conjecture that biological evolution, exponential population growth, and existence of stable genomes are possible only after the discovery of a narrow set of specific protein structures."
Their general conclusion: "Together, these results and their analysis suggest a plausible comprehensive scenario of emergence of the protein universe in early biological evolution."
One of the principles of simulation is that models are first verified (they perform as they were designed) and second validated (they provide a realistic model of the real world). Unfortunately, there is nothing in the paper about validation. This does raise concerns. The first relates to the descriptor: "advantageous": "We find that exponential population growth is possible only after the discovery of a very small number of specific advantageous protein structures." The problem is: what gives the protein structure an advantage? In the real world, proteins are advantageous because they do something useful by virtue of the way they fold. In the model, the proteins do not have functions and the only significant differences relate to their stability.
The model starts with organisms possessing 1 gene and, after the simulation of biological evolution, they never have more than 10. Compare this with the real world, where a minimal genome of less than 200 genes has to be regarded as a dream.
The authors correctly state: "Our model of natural selection is minimalistic and is limited in its scope". Also: "This work is in progress." The authors suggest their model relates more closely to viruses: "our model can be directly applicable to (and can be experimentally tested on) the evolution of RNA viruses, which often encode for a handful of proteins, all of which are essential for the virus." This is far more realistic. If the authors had focussed on this rather than making grandiose claims about modelling early biological evolution, their work would deserve more respect.

A First-Principles Model of Early Evolution: Emergence of Gene Families, Species, and Preferred Protein Folds
Konstantin B. Zeldovich, Peiqiu Chen, Boris E. Shakhnovich, Eugene I. Shakhnovich
PloS Computational Biology, 3(7): e139 doi:10.1371/journal.pcbi.0030139

Abstract: In this work we develop a microscopic physical model of early evolution where phenotype - organism life expectancy - is directly related to genotype - the stability of its proteins in their native conformations - which can be determined exactly in the model. Simulating the model on a computer, we consistently observe the "Big Bang" scenario whereby exponential population growth ensues as soon as favorable sequence-structure combinations (precursors of stable proteins) are discovered. Upon that, random diversity of the structural space abruptly collapses into a small set of preferred proteins. We observe that protein folds remain stable and abundant in the population at timescales much greater than mutation or organism lifetime, and the distribution of the lifetimes of dominant folds in a population approximately follows a power law. The separation of evolutionary timescales between discovery of new folds and generation of new sequences gives rise to emergence of protein families and superfamilies whose sizes are power-law distributed, closely matching the same distributions for real proteins. On the population level we observe emergence of species-subpopulations that carry similar genomes. Further, we present a simple theory that relates stability of evolving proteins to the sizes of emerging genomes. Together, these results provide a microscopic first-principles picture of how first-gene families developed in the course of early evolution.

Sea anemones, jellyfish and corals are all cnidarians, a phylum that goes back to the Late Precambrian. Geneticists studying this group of organisms have made much use of the starlet sea anemone Nematostella vectensis. Whilst previously reported research has been concerned with specific genetic elements, a new study reports on a comparative analysis of the whole genome. The sea anemone genome has been found to contain about 18,000 protein-coding genes with many of the same gene families that are found in other sequenced animals. This is where the surprises start.
The authors write: "The sea anemone genome is complex, with a gene repertoire, exon-intron structure, and large-scale gene linkage more similar to vertebrates than to flies or nematodes, implying that the genome of the eumetazoan ancestor was similarly complex." Elizabeth Pennisi observes: "This implies that even very ancient genomes were quite complex and contained most of the genes necessary to build today's most sophisticated multicellular creatures." Eugene Koonin of the National Center for Biotechnology Information was interviewed about the research. He said that it is surprising to find such a "high level of genomic complexity in a supposedly primitive animal such as the sea anemone". It implies that the ancestral animal "was already extremely highly complex, at least in terms of its genomic organization and regulatory and signal transduction circuits, if not necessarily morphologically."
The comparative study had some additional surprises. Writing in The Scientist, Melissa Lee Phillips points out: "The study also found that these similarities were absent from fruit fly and nematode genomes, contradicting the widely held belief that organisms become more complex through evolution. The findings suggest that the ancestral animal genome was quite complex, and fly and worm genomes lost some of that intricacy as they evolved."
Some have inferred that the vertebrate genome must therefore be primitive, but this fails to do justice to the observed sophistication. The implication of this research is that we are not tracking an evolution of complexity with time, but we have identified the sudden emergence of complexity in the Precambrian. It is the genetic equivalent of the 'Cambrian explosion'!
A hint of this was published in 2005 in a study of the Wnt gene family, which encodes secreted signalling molecules that control cell fate in animal development and human diseases. "Cnidarians and bilaterians have at least eleven of the twelve known Wnt gene subfamilies in common; [. . .] This unexpectedly complex inventory of Wnt family signalling factors evolved in early multi-cellular animals about 650 million years (Myr) ago, predating the Cambrian explosion by at least 100 Myr."
Researchers have looked for simplicity but have found complexity. They have selected organisms described as primitive and have proved them to be advanced. One evolutionary developmental biologist is quoted as saying: "The work is truly stunning for its deep evolutionary implications". He's right, but not in the sense he intended: when the data is profoundly at variance with evolutionary expectations, it is time to consider whether a new paradigm is needed.

Sea Anemone Genome Reveals Ancestral Eumetazoan Gene Repertoire and Genomic Organization
Nicholas H. Putnam, Mansi Srivastava, Uffe Hellsten, Bill Dirks, Jarrod Chapman, Asaf Salamov, Astrid Terry, Harris Shapiro, Erika Lindquist, Vladimir V. Kapitonov, Jerzy Jurka, Grigory Genikhovich, Igor V. Grigoriev, Susan M. Lucas, Robert E. Steele, John R. Finnerty, Ulrich Technau, Mark Q. Martindale, and Daniel S. Rokhsar
Science, 316, 6 July 2007: 86-94.

Sea anemones are seemingly primitive animals that, along with corals, jellyfish, and hydras, constitute the oldest eumetazoan phylum, the Cnidaria. Here, we report a comparative analysis of the draft genome of an emerging cnidarian model, the starlet sea anemone Nematostella vectensis. The sea anemone genome is complex, with a gene repertoire, exon-intron structure, and large-scale gene linkage more similar to vertebrates than to flies or nematodes, implying that the genome of the eumetazoan ancestor was similarly complex. Nearly one-fifth of the inferred genes of the ancestor are eumetazoan novelties, which are enriched for animal functions like cell signaling, adhesion, and synaptic transmission. Analysis of diverse pathways suggests that these gene "inventions" along the lineage leading to animals were likely already well integrated with preexisting eukaryotic genes in the eumetazoan progenitor.

See also:

Pennisi, E., Sea Anemone Provides a New View of Animal Evolution, Science, 316, 6 July 2007: 27.
Melissa Lee Phillips, M.L. Surprises in sea anemone genome, The Scientist, 5th July 2007
Kusserow, A., et al., Unexpected complexity of the Wnt gene family in a sea anemone, Nature 433, 156-160, (13 January 2005)

We are indebted to Gould and Lewontin for pointing out so eloquently to adaptationists that biological structures should be explained in context and not as independently constructed adaptations. They wanted to revive the great historic themes of developmental morphology and the bauplan in which some features are, like spandrels, consequences of a larger-scale architecture. David Hartl has chosen to remind readers of this emphasis in his review of a book on the origins of genome architecture.
At the outset, some garbage must be cleared away. Adaptationists have tended to develop lazy ways of thinking and rarely seek out ways to test their offered scenarios. "Glib generalizations [according to the author] come from the assumption shared by many biologists that natural selection is the only mechanism of evolutionary change, and hence every observed feature of organisms must have come about because of natural selection." This mechanism is highly prized because they think it can do anything. They claim it is the great creator of complexity. But the concept is qualitative, not quantitative, and there are inadequate checks to avoid the pathways to fantasy. "This conveniently licenses anyone to concoct any adaptive story about anything biological and put it forward as a serious contribution to the science of evolution."
Michael Lynch, the book's author, has come to the view that many complex structures cannot be explained using adaptation. "The recurring theme is that many of the major molecular features of genes and genomes in multicellular organisms can be explained without invoking natural selection. The list will raise some eyebrows: it includes the transition from the RNA world to DNA, streamlining of microbial genomes, variation in nucleotide composition within and among genomes, centromere expansion, proliferation of transposable elements, growth of untranslated regions in messenger RNAs, origin of spliceosomes and the proliferation of introns, origin of modular gene regulation, variation in the architecture of organelle genomes, mRNA editing in plant organelles and the evolution of sex chromosomes."
"The problem with natural selection is that if it explains everything, it explains nothing, and instead it becomes an exercise in story telling. [. . .] The challenge for those who would invoke natural selection as causing any biological feature is therefore to propose a specific adaptive mechanism, to deduce attributes that would differ according to which hypothesis were correct and then to make the necessary observations or comparisons."
What a welcome airing of these issues! And wouldn't it be good if biology students could be alerted to such thinking before they get brainwashed by neo-Darwinism?

The spandrels of the genome
Daniel Hartl
Nature Genetics, 39, 811 (July 2007) | doi:10.1038/ng0707-811

BOOK REVIEWED - The Origins of Genome Architecture by Michael Lynch, Sinauer Associates: 2007

See also:
Gould, S.J. & Lewontin, R.C. The spandrels of San Marco and the Panglossian paradigm, Proceedings of the Royal Society of London, B. 1979, 205, 581-598.

In his July editorial in The Scientist, Richard Gallagher marks the 35th anniversary of the term "Junk DNA" by asking the question "Is it time to retire provocative descriptors such as "junk DNA"?" His answer is negative, and he proceeds to justify the term on the grounds that: "junk DNA works as a catchy moniker that helps frame the debate for the general public while evoking passionate debate among scientists". This blog has drawn attention previously to the way evolutionary biologists like to frame the debate for the general public: instead of equipping the public with the concepts and resources to make informed judgments, the objective appears to be to safeguard Darwinism to ensure the public do not revolt!
There is no doubt that "Junk DNA" has been a controversial term within the scientific community. However, for many years, the sceptics were in a minority. The general public were presented with overwhelming evidence that our genomes are "filled with the remains of extinct genes" that are of marginal interest until advantageous mutations bring them back again into centre stage. The Framers made sure the public got the message: "...the designer made serious errors, wasting millions of bases of DNA on a blueprint full of junk and scribbles. Evolution, in contrast, can easily explain them as nothing more than failed experiments in a random process . . ." (Kenneth Miller, 1994) and "DNA differs from written language in that islands of sense are separated by a sea of nonsense, never transcribed" (Richard Dawkins, 2004).
The policy of retaining the term to help frame the debate for the general public is actually very misleading. Recent research is uncovering a mass of functionality that suggests the term actually promotes falsehoods in the name of science.
Even more significantly, Gallagher writes: "The latest iniquity to befall junk DNA is the attempted hijack by proponents of Intelligent Design. Some of them would have us believe that their movement has provided the tools to find function in junk DNA. A withering critique by Pim van Meurs can be found on the Web site, The Panda's Thumb, along with an entertaining and educational thread of 150 or so comments."
This comment is also seriously misleading. The key contribution ID scientists have made is to predict functionality for some, if not most, of the supposed junk DNA. This prediction has emerged partly from an appreciation of the exquisite complexity of living things (including its DNA) and partly from a scepticism about the capabilities of Darwinian mechanisms to achieve large-scale transformations. It was also provoked by declarations like this from Phillip Kitcher (philosopher of science at Columbia University) in 2005: "A lot of the DNA in there is not needed -- it's junk. If it's intelligently designed, then God needs to go back to school." A more judicious assessment would be: ID scientists have risen to the "Junk DNA" challenges thrown at them, and have shown that ID thinking does make successful predictions. It may be concluded that any continuing refrain about ID not making predictions is just more "framing" of the debate for the masses.

Junk Worth Keeping (Editorial)
By Richard Gallagher
The Scientist, July 2007

First Para: June 30, 1972, was a high point for the lexicon of biology. That day, Susumu Ohno coined (or at least publicly introduced) the term "junk DNA." In a talk titled "So Much 'Junk DNA' in our Genome," Ohno argued that the frequency of deleterious mutations restricts the number of serviceable genes to around 105 and that the great bulk of our DNA is merely the debris of failed duplication. "The earth is full of extinct species," he said. "Is it a wonder that our genome, too, is filled with the remains of extinct genes?"

See also:

Junk DNA, ResearchID.org (June 2007)

Pearson, A., Why 'junk DNA' may be useful after all, New Scientist, 11 July 2007.

In a bold and incisive paper, philosopher Owen Anderson writes: "In what follows I explain the principle of uniformity as developed by Lyell, consider its philosophical grounding in Humean empiricism and epistemological naturalism, and argue that, although Lyell himself may have believed in the theistic view of God, this principle raises questions about the role of God and natural evil in the world. By identifying the role that uniformitarianism has played in subsequent science and understanding its role as a nonempirical interpretive principle, I show how fideism can be avoided at the level of first principles." Among the many issues raised, I draw attention to just one. This concerns the fundamental importance of interpretive principles (or paradigms) in science.
There is a tendency for scholars in the Lyell tradition to think that empirical evidence can be gathered objectively and that analysis leads to robust knowledge. However, Lyell filtered the data available to him by an unarticulated interpretive principle. Anderson seeks to revise our perceptions of Lyell's contribution by focusing attention on his philosophical roots. "Just as the Aristotelians gathered huge amounts of data and yet because of false interpretive principles drew false conclusions about the world, so any other "science" is only as good as its interpretive principles."
Lyell appeared to have been deeply influenced by the philosopher David Hume. "Lyell's principle requires a radical form of empiricism as developed by David Hume. Hume's invective against anything that appears to be metaphysical or theological has had immeasurable influence on the modern mind. He believed that there were only two sources of knowledge and ruled out the idea of special revelation." The picture that emerges involves two competing philosophical stances: naturalism and theism. Although Lyell professed to be a theist, his thinking was that of a naturalist. "For the naturalist to maintain that he or she is simply working with the evidence while the theist is importing theology is for the naturalist to ignore his or her own interpretive assumptions. The theist will maintain that the material world and its past cannot be entirely explained through secondary causes and that, although God has created these causes and endowed the human mind with the ability to know them, they do not exhaust what humans should know about the formation of the world (there is also the redemptive work of God in history). Neither of these interpretive principles can claim to be neutral or "just following the evidence where it leads"."
The great strength of this paper is the way the author frames the science-faith debate. The differences are not about scientific methodology, nor about the role of reason. The fundamental differences are philosophical, particularly relating to naturalism and theism. Those who think that the term "theistic scientist" is an oxymoron would do well to read what Anderson has to say.

Charles Lyell, uniformitarianism, and interpretive principles
Anderson, Owen
Zygon, 42(2), June 2007, 449-462.

Abstract: I examine the development of Charles Lyell's principle of uniformity and its influence on the development of modern geology and biology and argue that distinguishing between philosophical starting points and empirical findings is essential for clarity in the discussion between science and religion. First, I explore Lyell's arguments against catastrophism and how these were both empirically and religiously motivated. I then consider how David Hume's empiricism, theory of causation, and rejection of miracles influenced Lyell. Using these insights, Lyell formulated his principle of uniformity, which he believed was based on current empirical findings, and rejected explanatory hypotheses that used the biblical Flood or other catastrophist accounts as violations of uniform causation and introductions of theological concepts into empirical science. I next examine the influence of Lyell's principle on Charles Darwin. Although Lyell opposed Darwinism for most of his life, Darwin relied heavily on Lyell, as is evidenced by references throughout The Origin of Species. I contend that the most important aspect of Lyell's principle for Darwin is that it makes natural evil (the struggle for survival) a process that has always been occurring rather than something introduced after the Fall as recorded in Genesis. Finally, I discuss the role that uniformity plays for Lyell, Darwin, and modern science as an interpretive principle rather than as an inference from empirical data, and I conclude by noting that keeping the distinction in mind between interpretive principles and empirical findings will help clarify debates between science and religion.

Earlier this year, Liu and Ochman made some dramatic claims about how the bacterial flagellum evolved: by the simple processes of successive duplications and diversifications. They discounted lateral gene transfer (LGT) as having had any significant influence. This received much applause, one critical blog and it was briefly reviewed here.
In a recent contribution to Current Biology, we read: "there are some caveats we evolutionists should consider before hailing Liu and Ochman as our next champions in the war against unreason." The caveats are to be welcomed. It was surprising to read the uncritical acclaim accompanying the publication of the original paper and a more measured assessment of its bold claims is to be welcomed. However, the reference to "war against unreason" is misguided. The authors are referring to ID, yet ID scientists are strong defenders of reason. Their reason leads them to make design inferences, and design inferences are totally unacceptable to scientists who have adopted the philosophy of naturalism.
After mentioning with approval the blog by Matzke, the authors write: "Equally problematic, we think, is their conclusion that "proteins forming the flagellum, the rod, hook and filament proteins, originated in an order that mirrors the 'inside-out' flagellar assembly process". Common sense might suggest such a scenario, but only rooted trees, which Liu and Ochman do not provide, can prove it."
Regarding the LGT claim, the authors (one of whom is a champion of LGT) write: "Critics of LGT often assume that trees with little resolution, because they do not show statistically significant conflict, must be in agreement and support vertical descent. But most often there is simply insufficient signal. Making vertical descent the null hypothesis is to assume that which was to be proved - and in this case to give false credibility to the claim for a common evolutionary history." This argument is very interesting, because it is closely related to arguments that have often been made by ID scientists. The problem of "little resolution" is widespread and the result is that researchers end up confirming their own assumptions.
It is obviously important that scientific debate be encouraged. There are serious problems linked to researchers apparently proving their presuppositions. We ask: when will this critical thinking be applied to science itself? Many scientists assume naturalism and then go on to 'prove' that naturalism can explain everything. This approach to science is one of the things ID scientists are seeking to change.

Evolution: Reducible Complexity - The Case for Bacterial Flagella
W. Ford Doolittle and Olga Zhaxybayeva
Current Biology, 17(13), 3 July 2007, R510-R512 | doi:10.1016/j.cub.2007.05.003

Abstract: A recent paper, which will surely figure centrally in the debate between evolutionists and Intelligent Design creationists, proposes a (perhaps too simple) scheme for the evolution of bacterial flagella.

See also:
Sequence similarities in the bacterial flagellum: what do they mean? ARN Literature Blog, 04/19/07

For over 30 years, the public have been led to believe that human and chimpanzee genetics differ by mere 1%. This 'fact' of science has been used on innumerable occasions to silence anyone who offered the thought that humans are special among the animal kingdom. "Today we take as a given that the two species are genetically 99% the same." However, this "given" is about to be discarded.
Apparently, it is now OK to openly acknowledge that those who are involved in this research have never been comfortable that the 1% figure was an accurate summary of the scientific information. But more recent studies have made it impossible to sustain the old orthodoxy. They have raised "the question of whether the 1% truism should be retired." One zoologist is quoted as saying: "Now it's totally clear that it's more a hindrance for understanding than a help."
"Researchers are finding that on top of the 1% distinction, chunks of missing DNA, extra genes, altered connections in gene networks, and the very structure of chromosomes confound any quantification of "humanness" versus "chimpness." [. . .] In the December 2006 issue of PLoS ONE, Hahn and co-workers reported that human and chimpanzee gene copy numbers differ by a whopping 6.4%, concluding that "gene duplication and loss may have played a greater role than nucleotide substitution in the evolution of uniquely human phenotypes and certainly a greater role than has been widely appreciated."" The diversity of relevant factors that are mentioned suggest that the problem has been one of oversimplification leading researchers to draw unwarranted conclusions from limited data.
The zoologist quoted above is also quoted as saying: "For many, many years, the 1% difference served us well because it was underappreciated how similar we were." Another researcher is quoted thus: "In the end, it's a political and social and cultural thing about how we see our differences." It is comments like these that can give sociologists of science a field day, for they reveal how social context influences what results are emphasised and what are overlooked. In this particular case, evolutionary biologists need to take full responsibility.
It is good to see a start being made in setting the record straight. Steve Jones, professor of genetics at University College London, writes: "DNA is beside the point. To concede so much to biology risks taking such privileges away from ourselves. [. . .] Chimps may resemble Homo sapiens in a tedious and literal sense, but in everything that makes us what we are H sapiens is unique indeed. Biology, in its proof of our physical similarity to other primates, underlines its own irrelevance."
It should be a "given" that humans are different from animals. If anyone struggles with this intellectually, then it may be appropriate to learn something from history. Let's be mindful that our knowledge of the relevant issues is limited.

Relative Differences: The Myth of 1%
Jon Cohen
Science 316, 29 June 2007: 1836.

Abstract: Genomewise, humans and chimpanzees are quite similar, but studies are showing that they are not as similar as many tend to believe

See also:

Jones, S., View from the lab, Daily Telegraph, 26/06/2007