The ID Update

Alongside all the public interest in sporting prowess, recent research has added significantly to our knowledge of how the human body actually works. Many characteristics we take for granted now appear to be critical success factors. Take, for example, our toes. We do not need long toes, like monkeys and apes, because our toes are not used for grasping branches. But are they vestigial - withered remnants of once-grand appendages? The answer is: most definitely not! Whilst it is possible to walk comfortably with longer toes, running is different. Increase toe length by just 20% and there is a doubling of the peak digital flexor impulses and the mechanical work required.

An image like this shows just how different the human foot is from the apes (Source here)

It emerges that the human body has numerous traits that all support the ability to run. In an informative piece in the New York Times, author Parker-Pope refers to the research into short toes saying that it:

"showed that the short toes of the human foot allowed for more efficient running, compared with longer-toed animals. Increasing toe length as little as 20 percent doubles the mechanical work of the foot. Even the fact that the big toe is straight, rather than to the side, suggests that our feet evolved for running. "The big toe is lined up with the rest, not divergent, the way you see with apes and our closest non-running relatives," Dr. Bramble said. "It's the main push-off in running: the last thing to leave the ground is that big toe." Spring-like ligaments and tendons in the feet and legs are crucial for running. (Our close relatives the chimpanzee and the ape don't have them.) A narrow waist and a midsection that can turn allow us to swing our arms and prevent us from zigzagging on the trail. Humans also have a far more developed sense of balance, an advantage that keeps the head stable as we run. And most humans can store about 20 miles' worth of glycogen in their muscles."

A few years ago, one of the authors, Daniel Lieberman, was involved in a related study. This was concerned with the gluteus maximus, said to be the the largest muscle in the human body. Parker-Pope also reports on this work, which found that the gluteus maximus is primarily engaged during running.

"Your butt is a running muscle; you barely use it when you walk," Dr. Lieberman said. "There are so many features in our bodies from our heads to our toes that make us good at running."

There would appear to be potential for clarifying the use of this muscle. It is important for posture, and another has made the comment: "As all weightlifters know, the primary purpose of the gluteus maximus is to raise the body from a deep squat." There is more to be said on these matters.

A noticeable element of this research is that the data are consistently interpreted in terms of natural selection pressures acting on natural variation. This is nothing unusual, because most biologists working in this field have come to accept Darwinism as their interpretative paradigm. Richard Dawkins speaks for many when he wrote in The Blind Watchmaker (Chapter 3) that "We have seen that living things are too improbable and beautifully designed to have come into existence by chance." Natural selection is perceived as giving direction to hereditable variation and results in incremental adaptation. This is how Lieberman and his colleagues approach the 'evolution' of short toes:

"The data suggest that having longer pedal phalanges, in the hallux and to some extent in the lateral toes, increases digital flexor force and work and might contribute to an increased risk of overuse injury during running. Although these effects presumably have negligible fitness consequences for habitually shod recent-modern humans who do not run long distances daily, they might have been significant enough to impose the kind of selective pressures that led to the observed changes in phalangeal size and shape during human evolution. For example, partial foot remains recovered at Hadar, Ethiopia, suggest that, by 3.6 million years ago, the lateral phalanges of A. afarensis were shorter than in the African great apes, but approximately 40% longer and more curved than in modern humans. This intermediate phalangeal morphology is thought to reflect a mixed behavioral repertoire comprising substantial arboreality and facultative terrestrial bipedalism."

What makes this a matter for concern is that no one appears to be talking about testing alternative hypotheses. It is as though the Darwinian explanation wins by default, and this does not make for healthy science. In particular, one hypothesis that is held by a great many people but is not admitted to academic debate, is that the human body is a product of intelligent design. The strength of this approach rests (a) in the holistic character of the alleged design; (b) the exquisite nature of the various characteristics; and (c) the claim that some of these features are irreducibly complex. (as in chapter 2 of Stuart Burgess' book The Origin of Man.

There are ways to test the Darwinian hypothesis. The presumed ancestor had elongated foot bones, illustrated here. To transform this stage to a short-toed human foot by natural selection demands gradual change and this is how the hypothesis can be tested. Where is the evolutionary pathway? Incidentally, the australopithecine feet should not be compared with the African great apes (as Lieberman) but with other ancestral apes contemporary with Australopithecus afarensis. This same line of reasoning about hypothesis testing means that design-based predictions of abrupt appearance can also be evaluated. Are evolutionists willing to allow this testing process to occur? Is this a debate that can be permitted in academic literature and in educational contexts?

Almost invariably, in the past, the idea that ID leads to testable hypotheses is blocked by the philosophical principle that all causes in science must be natural (law or chance). Despite repeated efforts to point out this is a metaphysical block, not one required by science, few take the time to address the point. However, it is encouraging to find some shifts in opinion from time to time. An example, surprising to most of us, is the concession Richard Dawkins gave to John Lennox in a debate last year.

"The deist god would be one that I think it would be [pause] one could make a reasonably respectable case for that. Not a case that I would accept, but I think it is a serious discussion that we could have." (The audio of this exchange can be accessed via http://www.fixed-point.org)

This is a welcome acknowledgement. For those wanting more input on this, the day after the debate, Melanie Phillips had an article in Spectator Magazine drawing attention to the significance of Dawkins' admission. The offer of a serious discussion is welcome. ID scientists do not ask for anything more than the freedom to present a respectable case. What is needed is for academics to abandon their doctrinaire attachment to methodological materialism in science.

Another perspective on this issue is to consider what needs to be done to build a robot that walks and runs. This task certainly focuses the mind and clarifies the issues. For an insight into the state-of-the-art, go here. PETMAN is wearing normal athletic shoes and exhibits a normal heel-to-toe gait. This robot is the product of intelligent design: many man-hours of effort by highly skilled scientists and engineers. Those who think natural selection acting on natural variations would do well to consider the immensity of the task they are expecting Darwin's mechanisms to accomplish.

Walking, running and the evolution of short toes in humans
Campbell Rolian, Daniel E. Lieberman, Joseph Hamill, John W. Scott and William Werbel
Journal of Experimental Biology 212, 713-721 (2009) | doi: 10.1242/jeb.019885

Abstract: The phalangeal portion of the forefoot is extremely short relative to body mass in humans. This derived pedal proportion is thought to have evolved in the context of committed bipedalism, but the benefits of shorter toes for walking and/or running have not been tested previously. Here, we propose a biomechanical model of toe function in bipedal locomotion that suggests that shorter pedal phalanges improve locomotor performance by decreasing digital flexor force production and mechanical work, which might ultimately reduce the metabolic cost of flexor force production during bipedal locomotion. We tested this model using kinematic, force and plantar pressure data collected from a human sample representing normal variation in toe length (N=25). The effect of toe length on peak digital flexor forces, impulses and work outputs was evaluated during barefoot walking and running using partial correlations and multiple regression analysis, controlling for the effects of body mass, whole-foot and phalangeal contact times and toe-out angle. Our results suggest that there is no significant increase in digital flexor output associated with longer toes in walking. In running, however, multiple regression analyses based on the sample suggest that increasing average relative toe length by as little as 20% doubles peak digital flexor impulses and mechanical work, probably also increasing the metabolic cost of generating these forces. The increased mechanical cost associated with long toes in running suggests that modern human forefoot proportions might have been selected for in the context of the evolution of endurance running.

See also:

Lieberman, D.E., Raichlen, D.A., Pontzer, H., Bramble D.M. and Cutright-Smith, E., The human gluteus maximus and its role in running, Journal of Experimental Biology 209, 2143-2155 (2006) | doi: 10.1242/jeb.02255

Parker-Pope, T., The Human Body Is Built for Distance, New York Times (October 26, 2009)

by Denyse O'Leary
ARN correspondent

In "When Listening to Music, Your Brain Is ‘Moving’ Even If You Are Not," a news release from the Society for Neuroscience (10/15/06), we learn,

One of the best-studied features in orientation maps is known as a pinwheel, a small region in which all orientations are represented in segments that appear to come to a point. "A long-standing question is, 'How are neurons arranged in the pinwheel centers?'" says R.C. Reid, PhD, of Harvard Medical School.

Reid provided the answer by using two-photon calcium imaging, which determines the physiological response of hundreds of cells simultaneously as well as their precise location in the cortical circuit.

"By recording from hundreds to thousands of neurons at each pinwheel center, we demonstrated that pinwheel centers are remarkably well organized," he says.

"Neurons selective to different orientations are arranged in an orderly manner even in the very center," he adds. "There was virtually no mixing of cells with different orientation preferences even at the center. Thus, pinwheel centers truly represent singularities in the cortical map." This finding is suggesting extraordinary precision in the development of cortical circuits.

and much else.

Ignore all the yap about evolution in the article, which is - as typical - intended to distract attention from the obvious conclusion.

Toronto-based Canadian journalist Denyse O'Leary (www.designorchance.com) is the author of the multiple award-winning By Design or by Chance? (Augsburg Fortress 2004), an overview of the intelligent design controversy. She was named CBA Canada's Recommended Author of the Year in 2005 and is co-author, with Montreal neuroscientist Mario Beauregard, of The Spiritual Brain: A neuroscientist's case for the existence of the soul (Harper 2007).

There is a Web site of the upcoming event "Intelligent Design: Is it Viable?" It will be a debate between Dr. Francisco J. Ayala and Dr. William Lane Craig. Moderated by Dr. Bradley Monton. The debate will occur on Thursday, November 5, 2009 at 7 p.m. EST at Indiana University Auditorium.

Here you will find all of the information you need to attend the event.

Go to Web site...

In ScienceDaily, it is reported that thhe mantis shrimps in the study are found on the Great Barrier Reef in Australia and have the most complex vision systems known to science. They can see in twelve colours (humans see in only three) and can distinguish between different forms of polarized light.

Special light-sensitive cells in mantis shrimp eyes act as quarter-wave plates -- which can rotate the plane of the oscillations (the polarization) of a light wave as it travels through it. This capability makes it possible for mantis shrimps to convert linearly polarized light to circularly polarized light and vice versa.

Dr Nicholas Roberts, lead author of the Nature Photonics paper said: "Our work reveals for the first time the unique design and mechanism of the quarter-wave plate in the mantis shrimp's eye. It really is exceptional - out-performing anything we humans have so far been able to create."

More...

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And how did this evolve through only natural processes? Given enough time anything can happen?

On October 21st Richard Dawkins appeared on the syndicated Hugh Hewitt talk show to promote his new book, "The Greatest Show on Earth".

It was a lively and interesting discussion...

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Cornelius Hunter blogged on Dawkins afterwards. Here is the link.

Seeking God in Science: An Atheist Defends Intelligent Design by Bradley Monton is a breakthrough book in the origins debate. Why? Because an atheist professor of philosophy at a secular university has written a book to defend intelligent design. As Monton would admit, it's a partial defense, as he does not find ID arguments overwhelmingly convincing, but he also does not find them trivial, and he believes they should be allowed on the table and in the classroom for discussion. He even went so far as to defend ID in a public debate in 2008, and his position as a true educator seeking truth has brought the wrath of Darwinists and fellow atheists down on his head. Welcome to the club Dr. Monton!

His work on a rigorous definition of intelligent design in chapter 1 is worth the price of the book alone. While most ID proponents use sound byte definitions to communicate the essence of ID to the public, Monton develops a rigorous definition that he feels will help in testing ID theory. We wouldn't expect any less of a philosophy of science professor and we think his definition will generate a more meaningful dialogue. But don't worry, you don't have to be a philosopher to understand this book. Monton has done a great job of making his arguments accessible to the general reader. This book is now available at ARN.

Stephen Meyer, Michael Behe, David Berlinski and John West are all featured speakers at The Legacy of Darwin Intelligent Design Conference to be held at the Douglas County Event Center in Castle Rock Colorado this weekend October 30-31. The Conference fee is $10. For more information visit www.shepherdproject.com/idconf/notabene.html or call 1-800-253-1869. Registrations will also be taken at the door. The conference begins 7 pm Friday night.

By Robert Deyes
ARN Correspondent

When it comes to academic triumphs and laudatory honors it can be said that mycologist Paul Stamets has his fair share. Stamets has authored six books on mushrooms, holds over twenty patents, is a winner of the Collective Heritage Institute's Bioneers Award and owns a wholesale business selling alternative medicines. Today he also runs a facility that boasts twenty four laminar flow benches across four laboratories processing between 10-20 thousand kilos of mycelia each week. He has close to a thousand mycelium cultures growing at any given time and is renowned across the world for his view of fungi as the 'grand molecular dissemblers of nature'.

Stamets describes himself in his youth as a hippy with a stuttering habit who could not look people in the eye. He also fondly recalls once telling his charismatic Christian mother that the forest is where he goes to church on Sundays. He spent many years as a microscopist at the Evergreen State College in Washington studying mushroom mycelia with the aid of an electron microscope. There he developed an intense passion for all things fungal even to the extent that he now occasionally appears in public sporting a hat made from Amadou- a fungus that, he boldly maintains, was essential for the portability of fire during man's much-heralded migration out of Africa.

When it comes to mushrooms, Stamets' most radical concept, and perhaps his most attractive one, draws on a human parallel. In fact he proposes that that organized networks of mycelia under our feet form the earth's own 'internet' of sorts carrying antibiotics and enzymes as well as huge numbers of signaling chemicals across trillions and trillions of end branchings. In short, he sees our own Internet superhighway as a mere replica of a highly-successful system that already exists in nature's own backyard. Perhaps surprisingly these networks are not confined to land habitats. Indeed aquatic underwater mushrooms have been discovered in the streams of southern Oregon and mycologists are now busily investigating how these hydrophiles survive and affect surrounding ecosystems.

Agarikon is yet another fungal species that gets mycologists such as Stamets visibly excited. Otherwise known as the 'elixir of long life', this impressively-sized fungus has been used for years as an effective treatment for respiratory diseases such as tuberculosis and is now known to exhibit a very potent effect against the smallpox and flu viruses. There is strong evidence that the active anti-virals in Agarikon might also serve well in the present-day combat against H1N1 and H5N1. In fact so critical to human health are the medicinal properties of this remarkable organism that Stamets has embarked on his own mini-crusade to create the largest Agarikon genomic DNA library in the world.

On a more serious note, many environmentalists claim that today we are fully engaged in the biggest mass extinction event that our planet has ever known. Stamets is not one to shy away from sounding alarm bells and boldly adheres to the claim that 50% of all known species on our planet could become extinct over the next 100 years if swift action is not taken. His use of oyster mushroom mycelia to remove oil pollution is an outstanding example of how we might avert such a bleak endpoint. These saprophytic fungi are gateway species that break down toxic waste through the action of specialized enzymes and thereby allow damaged ecosystems to flourish and rebound. Oyster mushrooms have also been shown to have a dramatic effect on bacterial titers destroying coliform bacteria and Staphylococcus in contaminated waters.

The environmental resiliency of fungi has long fascinated mycologists, and future mycotechnologies might build on this salient property. While Prototaxites- a 30-foot long, 3-foot high mushroom that lived 350-420 million years ago stands as the archetypal giant fungus, the twenty two-hundred acre, one cell thick mycelium mat of Armillaria ostoyae (honey mushroom) now holds the record for the largest organism in the world. Thermo-resilient symbionts such as Curvularia confer a viral-dependent heat tolerance on many grasses allowing them to grow at elevated temperatures, as high as 104 F in some cases.

Fungi can be described as being parasitic, saprophytic, micorrhizal or endophytic in their modes of deriving nourishment. This so-called 'mycological guild' of complementary fungi is what gives rise to a healthy ecosystem. The interactivity of these fungi and other organisms is clearly visible in ant cultivars of the Lepiota mushroom which are used by thatch ants to stop a particularly aggressive parasitic fungus called Escovopsis from invading their nests. In a converse strategy, Metarhizium is a parasitic fungus that kills carpenter ants and is therefore finding application in the protection of buildings from these would-be aggressors. By using the non-sporulating stage of Metarhizium, Stamets has surpassed the carpenter ants' own ability to keep the fungus at bay thereby providing him with an effective treatment against carpenter ant infestations.

Despite such mycotechnological advances, Stamets describes the current state of the field as being under-respected, underappreciated and underfunded. Most importantly he remains steadfastly focused on restoring ecosystems for the enjoyment of generations to come. For those of us actively involved in the evolution/ID debate, Stamets' findings are likewise poignantly relevant. In fact he makes a stunning claim regarding computer and fungal networks noting how "we were destined to create the computer Internet at a time when the earth is in crisis".

That our understanding of network theory and its importance in fungal bioremediation should coincide with our earth's need for ecological intervention introduces a teleological, purposeful perspective to life that contradicts the contingency of orthodox Darwinism. After all a cosmos that is fashioned towards such an endpoint is incompatible with the random, directionless tenet of natural selection. As for the Christian faithful there is one proclamation that makes sense in our current predicament: Thank God that the forests are where mycologists choose to go to church on Sundays!

For further details on Stamets' work see How Mushrooms Can Save The World at http://tiny.cc/iecmw, (Login: Promega; Password: mushroom)

Darwinius masillae is the magnificently preserved Ida, the "eighth wonder of the world" unveiled earlier this year: "our Mona Lisa" and an evolutionary "Rosetta Stone". Afradapis is a newly discovered adapoid from Egypt, known from fossilised jaws and teeth. The controversies surrounding Ida have been the subject of comment here and here. A newly published cladistic analysis of 360 morphological features found in 117 living and extinct primates comes down on the side of Ida being more closely related to lemurs and lorises rather than ancestral to anthropoids.

Darwinius was proposed to be on the right branch - an ancestor of apes and humans - but the new study puts it as a dead end on the left branch (Source here)

One of the criticisms of the original report of Darwinius is that the authors did not provide a comprehensive cladistic analysis, but only referred to anthropoid-like characters. That analysis is still not forthcoming, but a new paper by Seiffert and colleagues considers dentition and jaw morphological features for a comprehensive set of primates, including Darwinius. The claim for anthropoid-like characters is put in a new light, because so many adapiform animals (ancestors of lemurs and lorises) have them.

"It has long been known that some adapiform lineages evolved derived morphological features that are also seen in living and extinct anthropoids (for example, fused mandibular symphyses, upper canines with mesial grooves, enlarged and spatulate upper and lower incisors, short and tall rostra). The phylogenetic significance of these features has been a source of ongoing debate for decades."

Their significant finding is that Afradapis (their newly reported fossil species - an undisputed adapiform) has numerous anthropoid-like characters. This leads the authors to conclude that evolutionary convergences are in plentiful supply.

"Of all known fossil prosimians (including Darwinius), Afradapis provides perhaps the most detailed examples of derived anthropoidlike adaptations in its dental and mandibular morphology. As is the case for many of the morphological features that some have argued link adapiforms to anthropoids, however, the anthropoid-like features of Afradapis (fused mandibular symphysis with transverse torus, deep mandibular corpus, deep masseteric fossa, large upper molar hypocones, absence of P2/2 and presence of an enlarged P3 with a honing facet for the upper canine) are not present in the most primitive undoubted fossil anthropoids, such as Biretia and Proteopithecus, indicating that the features are likely to have been acquired through convergent evolution."

The implication, then is that the Darwinius team have been misled by characters that have turned out not to be diagnostic of anthropoid affinities. This conclusion has been picked up and discussed by many commentators, such as Gibbons:

"When they scored Ida and Afradapis against those other primates, Seiffert and colleagues found that adapids do share some traits with anthropoids, such as the loss of a third upper and lower premolar. But these traits evolved more than once among primates, the team reports tomorrow in Nature. They are the result of convergent evolution, which is the acquisition of the same biological trait in unrelated lineages - and, thus, do not indicate inheritance of the trait from a shared ancestor."

Several significant consequences follow from this research. Not least is the reminder that tracking human ancestors by identifying missing links is an exercise fraught with methodological difficulties. As has been previously noted, human evolution data can be likened to a pointillist painting. Like a pointillist painting, evolution is only apparent from a distant vantage point. Close up, we see masses of data, but no coherent picture.

Another issue to address concerns convergent evolution and the problems this phenomenon creates for cladistic analyses. How do we know what characters are primitive and what are derived? Here is an opportunity for human interpretation to be concealed behind a scientific analysis. The extent to which convergences can be invoked raises suspicion in the minds of some:

"One of the researchers who studied Ida, however, responds that Ida and Afradapis look more like the group that gave rise to anthropoids than the group that gave rise to lemurs and lorises - and that there are too many traits to dismiss as convergent evolution. "The complete convergence postulated for Afradapis seems implausible to me," says paleontologist Philip Gingerich of the University of Michigan, Ann Arbor."

The best outcome of all this is for scientists to demonstrate more humility in handling data. So many seem to grasp at some data and brandish 'evidence' as though it provides a definitive answer to controversy. But this is not how data should be handled in research. Data needs to be interpreted and history shows that there is always more than one way of interpreting it. If we can all adopt a 'multiple working hypotheses' approach when using the scientific method, it will be progress indeed.

Convergent evolution of anthropoid-like adaptations in Eocene adapiform primates
Erik R. Seiffert, Jonathan M. G. Perry, Elwyn L. Simons & Doug M. Boyer
Nature 461, 1118-1121 (22 October 2009) | doi:10.1038/nature08429

Adapiform or 'adapoid' primates first appear in the fossil record in the earliest Eocene epoch (~55 million years (Myr) ago), and were common components of Palaeogene primate communities in Europe, Asia and North America1. Adapiforms are commonly referred to as the 'lemur-like' primates of the Eocene epoch, and recent phylogenetic analyses have placed adapiforms as stem members of Strepsirrhini, a primate suborder whose crown clade includes lemurs, lorises and galagos. An alternative view is that adapiforms are stem anthropoids. This debate has recently been rekindled by the description of a largely complete skeleton of the adapiform Darwinius, from the middle Eocene of Europe, which has been widely publicised as an important 'link' in the early evolution of Anthropoidea. Here we describe the complete dentition and jaw of a large-bodied adapiform (Afradapis gen. nov.) from the earliest late Eocene of Egypt (~37 Myr ago) that exhibits a striking series of derived dental and gnathic features that also occur in younger anthropoid primates [. . .] The specialized morphological features that these adapiforms share with anthropoids are therefore most parsimoniously interpreted as evolutionary convergences. [. . .]

See also:

Gibbons, A., New Primate Fossil Poses Further Challenge to Ida, ScienceNOW Daily News (21 October 2009)

Dalton, R., Fossil primate challenges Ida's place, (21 October 2009), 461, 1040 | doi:10.1038/4611040a

ARN launched its Darwin or Design Radio Broadcast today The Bridge FM family of stations in the New York and New Jersey area. The show airs each Saturday morning at 10 A.M Eastern time and ARN shares hosting duties with Dr. Tom Woodward with the C.S. Lewis Society. Those outside the broadcast area can listen in on the streaming web broadcast available at www.BridgeFM.org.

For the most recent broadcast with Dennis Wagner (October 24th), we've put together two extraordinary offers. Keep in mind that we can only promise to keep these offers posted through Thursday, October 29th!

OFFER #1:

(V070SK): This is the Phillip Johnson DVD Collection. Ten of the best of Phillip Johnson videos produced by ARN, including interviews, lectures, debates and a special tribute to Phil from his friends and foes. Normally these videos sell for $25 each, but you can save 50% when you purchase the entire collection of ten DVDs for only $125 U.S ($175 Foreign). To purchase this special offer, go to the following link: http://www.arn.org/arnproducts/videos/v070sk.htm. And remember - you can't get these videos anywhere else because they were produced by ARN.

The Phillip Johnson DVD collection includes:

V001 - Focus on Darwinism: An Interview with Phillip Johnson
V002 - Darwinism on Trial, Lecture at UC Irvine
V004 - Darwinism: Science or Naturalistic Philosophy: Debate with William Provine at Stanford University
V008 - Can Science Know the Mind of God? Lecture at Princeton University
V009 - Blind Watchmaker: Lecture at the University of Wales
V028 - How Darwinists Think: Lecture at Northern Michigan University
V029 - Raising Questions about Evolution in the Schools: Lecture at Northern Michigan University
V036 - The Right Questions: An Interview with Phillip Johnson
V040 - An Evening with Phillip Johnson: A Tribute to Phil from his Friends and Foes
V057 - One Nation Under Darwin: Lecture by Phillip Johnson

OFFER #2:

(B037) ARN is offering 45% discount off Phil Johnson's The Wedge of Truth hardback book. Dr. Phillip Johnson is one of the founding fathers of the intelligent design movement and there is no better place to start learning about ID than this book. Normal price is $18 US $28 Foreign. Sale price for this hardback edition is only $10 U.S which includes FREE shipping! ($20 Foreign). To view this offer, please visit the following link: http://www.arn.org/arnproducts/php/book_show_item.php?id=38

Shallow water light ranges from the ultraviolet to red (wavelengths 360 nm - 650 nm). Going deeper, the extremes disappear and the spectrum narrows to a blue (approx 480 nm). Of the fish species whose colour vision has been tested to date, all except one can see in the ultraviolet (UV). The exception is the scabbardfish, which is the subject of a new research paper. The authors find that the fish that are sensitive to UV have a pigment that absorbs UV light, but the scabbardfish lacks this pigment and has, instead, a pigment that is violet-sensitive.

The scabbardfish (Lepidopus fitchi) is now the only fish known to have switched from ultraviolet to violet vision, or the ability to see blue light. (Credit: Carol Clark, Emory University) (Source ScienceDaily)

The researchers have looked at the molecular structure of the relevant pigments and their absorption spectra.

"[T]hey used genetic engineering, quantum chemistry and theoretical computation to compare vision proteins and pigments from scabbardfish and another species, lampfish. The results indicated that scabbardfish shifted from UV to violet vision by deleting the molecule at site 86 in the chain of amino acids in the opsin protein.
"Normally, amino acid changes cause small structure changes, but in this case, a critical amino acid was deleted," Yokoyama says."

The hypothesis is that the shift from UV to violet vision was adaptive. Since the lampfish is also a benthopelagic marine fish, the adaptation explanation must also address why the lampfish has retained UV vision.

"Scabbardfish spend much of their life at depths of 25 to 100 meters, where UV light is less intense than violet light, which could explain why they made the vision shift, Yokoyama theorizes. Lampfish also spend much of their time in deep water. But they may have retained UV vision because they feed near the surface at twilight on tiny, translucent crustaceans that are easier to see in UV light."

The researchers found several other amino acid sequence variants that could not be linked to any change in function. This stimulated some salutary comments from the authors:

"It is very common that evolutionary biologists infer the possibility of adaptive evolution of various genes by using computer programs, which compare the nonsynonymous and synonymous nucleotide substitutions per site. However, these analyses not only predict a significant number of false-positives but also fail to predict many positively selected sites; consequently, the positively selected amino acid changes inferred by the statistical methods must be tested by using experimental methods."

In the Press Release, Yokoyama is quoted as saying: "Evolutionary biology is filled with arguments that are misleading, at best". The research team is to be commended for connecting changes in amino acid sequences with changes in phenotypes and then relating all to the living environments. This is good science and a big contrast from the story-telling approach. Adaptation can be studied in a rigorous way, and analyses like this are a demonstration of what is possible.

The words "evolutionary" and "evolution" are used by the authors in their paper. It is strange that evolutionary biology has a fixation of the e-word when there are so many different meanings given to it. In this case, we have a study of adaptive change involving the change of a single amino acid in the opsin protein. This can be understood as a means of the organism becoming fine-tuned to its environment. Darwinian mechanisms appear to be adequate for understanding the data. It should not be necessary to point out that 'fine-tuning' is qualitatively different from 'constructing' the visual apparatus of the organism. Fine-tuning is only possible when the eye is functioning. This point can be better appreciated when the change involves the deletion of existing biological information - as it is in this case. Adaptation is not the route to create biological novelties: microevolution is not macroevolution.

There is a design-orientated way of approaching these data. What if organisms are designed to vary so that they can adapt to changes in their environment? In such cases, mechanisms for fine-tuning can be understood as designed mechanisms, thereby shifting the focus away from the biological world being the product of chance + necessity and towards a world resulting from purposeful intelligent agency.

Evolutionary replacement of UV vision by violet vision in fish
Takashi Tada, Ahmet Altun and Shozo Yokoyama
Proceedings of the National Academy of Sciences, October 13, 2009, 106(41), 17457-17462 | DOI: 10.1073/pnas.0903839106

Abstract: The vertebrate ancestor possessed ultraviolet (UV) vision and many species have retained it during evolution. Many other species switched to violet vision and, then again, some avian species switched back to UV vision. These UV and violet vision are mediated by short wavelength-sensitive (SWS1) pigments that absorb light maximally ([lamda]max) at approximately 360 and 390-440 nm, respectively. It is not well understood why and how these functional changes have occurred. Here, we cloned the pigment of scabbardfish (Lepidopus fitchi) with a [lamda]max of 423 nm, an example of violet-sensitive SWS1 pigment in fish. Mutagenesis experiments and quantum mechanical/molecular mechanical (QM/MM) computations show that the violet-sensitivity was achieved by the deletion of Phe-86 that converted the unprotonated Schiff base-linked 11-cis-retinal to a protonated form. The finding of a violet-sensitive SWS1 pigment in scabbardfish suggests that many other fish also have orthologous violet pigments. The isolation and comparison of such violet and UV pigments in fish living in different ecological habitats will open an unprecedented opportunity to elucidate not only the molecular basis of phenotypic adaptations, but also the genetics of UV and violet vision.

See also:

Seeing Blue: Fish Vision Discovery Makes Waves In Evolutionary Biology, ScienceDaily (17 October 2009)

Tyler, D. Adaptations affecting dim-light vision in vertebrates, ARN Literature blog (10 September 2008)

by Denyse O'Leary
ARN correspondent

Even though I am not a creationist by any reasonable definition, I sometimes get pegged as the local gap tooth creationist moron. (But then I don't have gaps in my teeth either. Check the unretouched photos.)

As the best gap tooth they could come up with, a local TV station interviewed me about "superstition" the other day.

The issue turned out to be superstition related to numbers. Were they hoping I'd fall in?

The skinny: Some local people want their house numbers changed because they feel the current number assignment is "unlucky."

Look, guys, numbers here are assigned on a strict directional rota. If the number bugs you so much, move.

Don't mess up the street directory for everyone else. Paramedics, fire chiefs, police chiefs, et cetera, might need a directory they can make sense of. You might be glad for that yourself one day.

Anyway, I didn't get a chance to say this on the program so I will now: No numbers are evil or unlucky. All numbers are - in my view - created by God to march in a strict series or else a discoverable* series, and that is what makes mathematics possible. And mathematics is evidence for design, not superstition.

The interview may never have aired. I tend to flub the gap-tooth creationist moron role, so interviews with me are often not aired.

* I am thinking here of numbers like pi, that just go on and on and never shut up, but you can work with them anyway. (You just decide where you want to cut the mike.)

Also just up at the Post-Darwinist:

Darwinism and academic culture: ID film banned

Darwinism and academic culture: Darwinists blither on in the face of the gathering storm

Biotechnology: The quest to bring back extinct animals

Fun with Mark Steyn, but when isn't Mark Steyn fun?

Toronto-based Canadian journalist Denyse O'Leary (www.designorchance.com) is the author of the multiple award-winning By Design or by Chance? (Augsburg Fortress 2004), an overview of the intelligent design controversy. She was named CBA Canada's Recommended Author of the Year in 2005 and is co-author, with Montreal neuroscientist Mario Beauregard, of The Spiritual Brain: A neuroscientist's case for the existence of the soul (Harper 2007).

When I took a course leading to the Certificate of Higher Education, we had some lecture inputs on psychology. The rationale was to show how educational strategies can be informed by the findings of psychologists. My abiding memory of these lectures concern the way the thinking of Sigmund Freud was presented: I was astounded that the lecturer was so uncritical of Freundianism. It was as though the great man was an oracle and we were expected to absorb his words rather than appraise them. At the time of taking the course, I was aware that Freud was no scientist. He did not test out his ideas using an experimental approach. Rather, he used his ideology-based theory as a filter through which to interpret the data. It was a useful experience for me - reinforcing the distinction between ideology and empirically based science.

In view of this, I welcomed reading the concerns expressed in an editorial in the current Nature. The opening paragraph reads:

"Anyone reading Sigmund Freud's original works might well be seduced by the beauty of his prose, the elegance of his arguments and the acuity of his intuition. But those with a grounding in science will also be shocked by the abandon with which he elaborated his theories on the basis of essentially no empirical evidence. This is one of the main reasons why Freudian-style psychoanalysis has long since fallen out of fashion: its huge expense - treatment can stretch over years - is not balanced by evidence of efficacy."

Disillusionment with Freud has not led to a better understanding of humanity (source here)

The stimulus for the editorial was a report issued by a report into the current status and future prospects of clinical psychology in the US. This found that a very high proportion of practitioners put more emphasis on their personal experience than on scientific evidence. This leads to a situation where craft practices prevail and interest in science is low. The US is not alone with these problems: go here and here.

"[M]any psychologists continue to use unproven therapies that have no clear outcome measures - including, in extreme cases, such highly suspect regimens as 'dolphin-assisted therapy'."

Questions are raised in the Editorial about the educational programmes leading to professional qualifications. The American Psychological Association is the accrediting body for the United States and Canada. However:

"The APA requires that such courses have a scientific component, but it does not require that science be as central as some members would like. In frustration, representatives of some two-dozen top research-focused graduate-training programmes grouped together in 1994 to form the Academy of Psychological Clinical Science (APCS), with a mission to promote scientific psychology."

The Editorial points out the scientific advances that could support clinical psychology: neuroimaging, molecular and behavioural genetics, and cognitive neuroscience. However, the link between the science and clinical practice is not explained, and it is worth asking whether the lukewarmness of practitioners towards science is because they have not been able to translate the science into therapeutic interventions. These practitioners are pragmatists: they are looking for therapies that they can use. They will not need to be brow-beaten into using scientific psychology if the findings are relevant to their profession.

Without wishing to denigrate in any way the empirical work being done in science laboratories, there is a problem with the theoretical framework adopted by most researchers. Here is one psychologist writing about free-will and his perception of science:

"[T]here can be no such thing as free will for the committed scientist, in his or her professional life. Thus, science itself presupposes that every phenomenon has a cause. We may speak of "spontaneous combustion" or a "spontaneous abortion" or even "spontaneous applause", but in each of these cases, some cause is more than likely . . . it is essential to a sober, naturalistic worldview." (Source here)

In this quote, the writer says that "science itself presupposes that every phenomenon has a cause", but he means that every phenomenon has a natural cause. He refers to a naturalistic worldview. Now this is a real problem. Instead of science being a search for truth, the writer is using science to pre-empt discussion about causation. But what if there are intelligent causes as well as natural ones? How would naturalistic science ever know? The author quotes Daniel Dennett approvingly:

"By trying to answer the questions, by sketching out the non-miraculous paths that can take us all the way from senseless atoms to freely chosen actions, we open up handholds for the imagination. The compatibility of free will and science . . . is not as inconceivable as it once seemed."

The issue is not one of introducing the miraculous to science (which is an impossible scenario) but insisting that there is continuity from senseless atoms to conscious humanity. By excluding intelligent causation, naturalistic science is making a statement about the nature of reality. The assertion does not emerge by the use of the scientific method, but is a dogmatic imposition. Unfortunately, this materialistic mindset is widespread among behavioural geneticists and neuroscientists. If their philosophical stance is wrong, and there are no checks and balances in their science, then they will never understand the human condition. This does not give confidence that their work will lead to therapeutic interventions that will help patients.

This is not to defend "unproven therapies" but to flag up a problem not mentioned in the Editorial. Freud imposed theory onto data, but so also does naturalistic science. We need to be encouraging a science that is free to explore the evidence wherever it leads and which builds into its methodologies the means to challenge its most cherished presuppositions.

Current Status and Future Prospects of Clinical Psychology
Timothy B. Baker, Richard M. McFall, and Varda Shoham.
Psychological Science in the Public Interest, 9(2), November 2008, 67-103.

Excerpt from Summary: Clinical psychologists' failure to achieve a more significant impact on clinical and public health may be traced to their deep ambivalence about the role of science and their lack of adequate science training, which leads them to value personal clinical experience over research evidence, use assessment practices that have dubious psychometric support, and not use the interventions for which there is the strongest evidence of efficacy. Clinical psychology resembles medicine at a point in its history when practitioners were operating in a largely prescientific manner.

Psychology: a reality check
Editorial
Nature 461, 847 (15 October 2009) | doi:10.1038/461847a

Abstract: If clinical psychology in the United States wants to remain viable and relevant in today's health systems, it needs to publicly embrace science.

For more blogs on the nature of humanity, go here, here and here.

Those who live in the Los Angeles area are invited to attend a gala premiere screening of Illustra Media's new documentary, Darwin's Dilemma: The Mystery of the Cambrian Fossil Record next Sunday, October 25th at 7:00 pm at the University of Southern California. The event is sponsored by the American Freedom Alliance.

This premiere was originally scheduled for the California Science Center, but the Center canceled the event just a few days ago, leaving the organizers virtually no time to find a new location. If you live in the Los Angeles area, you can show your support for free speech to debate the evidence for intelligent design by attending this important event!

More...

by Denyse O'Leary
ARN correspondent

For Uncommon Descent Provide the Code: for Dawkins' WEASEL Program, we have declared a winner - 377 responses later - and it is Oxfordensis:

It seems that Dawkins used two programs, one in his book THE BLIND WATCHMAKER, and one for a video that he did for the BBC (here's the video-run of the program; fast forward to 6:15). After much beating the bushes, we finally heard from someone named "Oxfordensis," who provided the two PASCAL programs below, which we refer to as WEASEL1 (corresponding to Dawkins's book) and WEASEL2 (corresponding to Dawkins's BBC video). These are by far the best candidates we have received to date.

Go here for more.

Note: Apparently, Bill Dembski is taking care of the award.

Toronto-based Canadian journalist Denyse O'Leary (www.designorchance.com) is the author of the multiple award-winning By Design or by Chance? (Augsburg Fortress 2004), an overview of the intelligent design controversy. She was named CBA Canada's Recommended Author of the Year in 2005 and is co-author, with Montreal neuroscientist Mario Beauregard, of The Spiritual Brain: A neuroscientist's case for the existence of the soul (Harper 2007).

Review Of The Eighth Chapter Of Signature In The Cell by Stephen Meyer
ISBN: 9780061894206; Imprint: Harper One

By Robert Deyes
ARN Correspondent

In the middle ages, Moses Maimonides debated heavily with Islamic philosophers over the Aristotlean interpretation of the universe. By looking at the stars and seeing their irregular pattern in the heavens, he concluded that only design could have generated the star arrangements he observed (1). In the process he ruled out necessity and the Epicurean ideology of chance. Centuries later Isaac Newton similarly opted for design as the best explanation for the origins of our solar system. Writing in his General Scholium for example Newton left us with no doubt over where his focus lay:

"This most beautiful system of sun, planets, and comets could only proceed from the counsel and dominion of an intelligent and powerful Being" (2).

Still, with the revolutions in thought brought forth by the likes of Pierre Simon Laplace and of course later Charles Darwin, the stage was set for chance and necessity to become the only players permissible in scientific discourse (1). Today science operates under the conviction that the material world "is all there is, and that chance and impersonal natural law alone explain, indeed must explain, its existence" (3).

So, what of chance? When statisticians refer to chance events what they really mean is that the exact combination of physical factors that cause these events are so complex that their occurrence cannot be reasonably predicted. Implicit in an appeal to chance is the negation of any sort of law-like necessity or Maimonidean-style recourse to design. On the flip side, Stephen Meyer reminds us in Signature In The Cell that that chance hypotheses can be eliminated when "a series of events occurs that deviates too greatly from an expected statistical distribution" (p.180).

A casino player winning 100 bets consecutively while spinning a roulette wheel is an obvious example of such a deviation. But low probability in itself is not enough for detecting design. Indeed fundamental to this particular non-chance alternative is the recognition of some sort of discernible pattern- 100 wins on a roulette wheel for example- that compels us to suspect that an intelligence somewhere is directing the outcome.

For Meyer such insights were seeded through conversations he held with philosopher William Dembski in the hallways of academia as he grappled with questions relating to life's origins. Much to the chagrin of the Darwin-faithful, today Dembski not only contends that design, "is a legitimate and fundamental mode of scientific explanation on a par with chance and necessity" but also argues that there exists a set of criteria for reliably detecting design in biology (1).

Pattern discernment, Dembski asseverates, can be retrospectively applied; that is, to events that have already occurred. Indeed as any spy buff will attest, cryptoanalysts routinely decode signals only after these signals have been generated and transmitted. Intelligent involvement in such cases can either be ruled in or out through a thorough examination of the available probabilistic resources (4).

In Signature In The Cell Meyer builds on Dembski's cornerstone case and uses a seemingly non-ending supply of illustrations to firm up his own supportive arguments. But the reader is nevertheless left pondering over what relevance such illustrations have to the matter at hand, namely demonstrating that the origin of life requires more than just chance. Meyer meticulously alleviates such concerns with a component-by-component breakdown of the probabilistic resources of our cosmic landscape. He writes:

"There are a limited number of opportunities for any given event to occur in the entire history of the universe. Dembski was able to calculate this number by simply multiplying the three relevant factors together: the number or elementary particles (10⁸⁰) times the number of seconds since the big bang (10¹⁶) times the number of possible interactions per second (10⁴³). His calculation fixed the total number of events that could have taken place in the observable universe since the origin of the universe at 10¹³⁰" (pp.216-217).

Applying his calculations on limits to biology Meyer notes:

"the probability of producing a single 150 amino acid protein by chance stands at about 1 in 10¹⁶⁴. Thus for each functional sequence of 150 amino acids there are at least 10¹⁶⁴ other possible non-functional sequences of the same length...Unfortunately that number vastly exceeds the most optimistic estimate of the probabilistic resources of the entire universe- that is the number of events that have occurred since the beginning of its existence" (p.217).

While such a rationale has already been advanced in the peer-reviewed literature (5), it is as profoundly relevant today as it was in its original context. Those design heisters who acrimoniously steal intelligent design away from the realm of biology do so at a tremendous cost to us all. Intelligent design is after all not 'pie in the sky' story telling. It is rigorous science.

Literature Cited
1.William Dembski (2002), No Free Lunch: Why Specified Complexity Cannot Be Purchased Without Intelligence, Rowman & Littlefield Publishers, Inc, Lanham, Maryland, pp.1-3

2. Nancy R. Pearcey and Charles B. Thaxton (1994), The Soul of Science: Christian Faith and Natural Philosophy; Crossway Books; Wheaton, Illinois, p.91

3. Guillermo Gonzalez and Jay Richards (2004), The Privileged Planet, How Our Place In The Cosmos Is Designed For Discovery, Regnery Publishing Inc, Washington D.C, New York, p.224

4. For a review of probability as relates to the biological context see Robert Deyes and John Calvert (2009), We Have No Excuse: A Scientific Case for Relating Life to Mind, Intelligent Design Network, See http://www.intelligentdesignnetwork.org/We_have_no_excuse.pdf

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

by Denyse O'Leary
ARN correspondent

In the Huffington Post, Rick Smith (October 9, 2009) notes

In a 2005 article for the United Kingdom's Philosophical Transactions of the Royal Society of London, physicist Henry Stapp and psychiatrist Jeffrey Schwartz showed that sustained concentrated attention on any particular mental experience-a thought, an insight, an image, even a fear-not only kept the brain circuitry involved open and alive but also eventually produced physical changes in the brain's structure. In effect, by increasing attention, you are creating brain architecture specifically suited to the challenges before you. Little wonder, then, that performance should grow dramatically.

Schwartz is the lead author of The Mind and the Brain, which sets forth this thesis in more detail. Basically, our minds become what we focus attention on, and this can be good or bad for us, depending on what that is.

Meanwhile, this Dark Age blog post (October 11 2009) mentions both Mario Beauregard, the third author of the 2005 paper and yours truly as well.

Also just up at The Mindful Hack

Neurolaw: Mind readers bustle into the court room

Mind and society: Why you can trust the people, when they have a chance

Neuroscience: Stuff I didn't need to hear about what people care about, but pass along anyway

Atheism and pop culture: Religious commitment as mild dementia?

Toronto-based Canadian journalist Denyse O'Leary (www.designorchance.com) is the author of the multiple award-winning By Design or by Chance? (Augsburg Fortress 2004), an overview of the intelligent design controversy. She was named CBA Canada's Recommended Author of the Year in 2005 and is co-author, with Montreal neuroscientist Mario Beauregard, of The Spiritual Brain: A neuroscientist's case for the existence of the soul (Harper 2007).

Evolutionary theory does not boast of many laws, and those that do are not universal by any means. One of these is Dollo's law, which is said to date back to about 1890. It is really a hypothesis about the non-reversibility of evolutionary pathways. The authors of new research considered the relevance of the law to the molecular evolution of a protein structure and reported a significant constraint preventing reversibility.

"The extent to which our observations concerning the evolutionary reversibility of glucocorticoid receptors can be generalized to other proteins requires further research. We predict that future investigations, like ours, will support a molecular version of Dollo's law: as evolution proceeds, shifts in protein structure-function relations become increasingly difficult to reverse whenever those shifts have complex architectures [. . .]"

A few restrictive mutations meant the key would not turn (Source here)

A description of the work is provided by Carl Zimmer in The New York Times:

"Dr. Thornton and his colleagues [. . .] studied a protein called a glucocorticoid receptor that helps humans and most other vertebrates cope with stress by grabbing a hormone called cortisol and then switching on stress-defense genes. By comparing the receptor to related proteins, the scientists reconstructed its history. Some 450 million years ago, it started out with a different shape that allowed it to grab tightly to other hormones, but only weakly to cortisol. Over the next 40 million years, the receptor changed shape, so that it became very sensitive to cortisol but could no longer grab other hormones. During those 40 million years, Dr. Thornton found, the receptor changed in 37 spots, only 2 of which made the receptor sensitive to cortisol. Another 5 prevented it from grabbing other hormones. When he made these 7 changes to the ancestral receptor, it behaved just like a new glucocorticoid receptor.
Dr. Thornton reasoned that if he carried out the reverse operation, he could turn a new glucocorticoid receptor into an ancestral one. So he and his colleagues reversed these key mutations to their old form. To Dr. Thornton's surprise, the experiment failed. "All we got was a completely dead receptor," he said."

To find out why the receptor was inactive, the researchers looked for other mutations - and found 5. These were described as "restrictive" because when attempts were made to return the receptor to its supposed ancestral form, the additional mutations acted as blocks.

"Dr. Thornton argues that once the restrictive mutations evolved, they made it practically impossible for the receptor to evolve back to its original form. The five key mutations could not be reversed first, because the receptor would be rendered useless. Nor could the seven restrictive mutations be reversed first. Those mutations had little effect on how the receptor grabbed hormones. So there was no way that natural selection could favor individuals with reversed mutations."

Some significant comments on this research have been made by Michael Behe here and here. These comments are highly relevant to discussions of mechanisms of evolutionary transformation. At the outset, Behe said that the work was interesting and the conclusion was reasonable -

"but the result was exceedingly modest and well within the boundaries that an intelligent design proponent like myself would ascribe to Darwinian processes. After all, the starting point was a protein which binds several steroid hormones, and the ending point was a slightly different protein that binds the same steroid hormones with slightly different strengths. How hard could that be?"

Behe's central point is that the evolutionary pathway was relatively easily disrupted by a few other mutations, so it is not satisfactory to think that Darwinian processes can find a way over every hurdle. The conclusions of his first post are as follows:

* The central point of The Edge of Evolution was that if several amino acids of a protein must be changed before a certain selective effect is available, then that is effectively beyond the reach of Darwinian processes. Bridgham et al (2009) confirm that conclusion. [. . .]
* There is no reason to think the protein studied by Bridgham et al (2009) is unusual in its difficulty of developing a binding site for even a relatively closely-related substance. In fact, in the absence of strong opposing data, that should be the default, reasonable assumption.
* That same reasonable assumption counts strongly against any two unrelated proteins easily developing a binding site for each other.
* That reasonable assumption therefore negates all woolly Darwinian evolutionary scenarios where critical protein binding sites are assumed without justification to pop up when needed (such as, say, in the building of multiprotein structures like the cilium or flagellum).
* Thus the work strongly supports the conclusion of Edge that Darwinian processes are highly unlikely to have built the complex molecular machinery of the cell.

The conclusion of the second post is this:

"The bottom line is that, for a given evolutionary task, at best only a handful of proteins will likely be helpful to evolve, at worst none may help. To calculate the probability of, say, a helpful protein-protein interaction developing in response to any particular selective pressure, it's mistaken to gratuitously multiply odds by the total number of proteins in a cell. Combined with the point made by Bridgham et al (2009), that even tiny structural/functional changes may not be achievable by random mutation/selection, these considerations pretty much squelch the likelihood of Darwinian processes doing much of significance during evolution."

An epistatic ratchet constrains the direction of glucocorticoid receptor evolution
Jamie T. Bridgham, Eric A. Ortlund & Joseph W. Thornton
Nature 461, 515-519 (24 September 2009) | doi:10.1038/nature08249

The extent to which evolution is reversible has long fascinated biologists. Most previous work on the reversibility of morphological and life-history evolution has been indecisive, because of uncertainty and bias in the methods used to infer ancestral states for such characters. Further, despite theoretical work on the factors that could contribute to irreversibility, there is little empirical evidence on its causes, because sufficient understanding of the mechanistic basis for the evolution of new or ancestral phenotypes is seldom available. By studying the reversibility of evolutionary changes in protein structure and function, these limitations can be overcome. Here we show, using the evolution of hormone specificity in the vertebrate glucocorticoid receptor as a case-study, that the evolutionary path by which this protein acquired its new function soon became inaccessible to reverse exploration. Using ancestral gene reconstruction, protein engineering and X-ray crystallography, we demonstrate that five subsequent 'restrictive' mutations, which optimized the new specificity of the glucocorticoid receptor, also destabilized elements of the protein structure that were required to support the ancestral conformation. Unless these ratchet-like epistatic substitutions are restored to their ancestral states, reversing the key function-switching mutations yields a non-functional protein. Reversing the restrictive substitutions first, however, does nothing to enhance the ancestral function. Our findings indicate that even if selection for the ancestral function were imposed, direct reversal would be extremely unlikely, suggesting an important role for historical contingency in protein evolution.

See also:

Behe, M. Nature Publishes Paper on the Edge of Evolution, Evolution News & Views, 30 September 2009

Behe, M. Nature Paper Reaches "Edge of Evolution" and Finds Darwinian Processes Lacking, Evolution News & Views, 7 October 2009

Dolgin, E. Protein burns its evolutionary bridges, Nature News, 23 September 2009 | doi:10.1038/news.2009.940

As reported by Troy Anderson, for the Los Angeles Daily News, a brouhaha has erupted in Los Angeles County over a planned series of events exploring the conflict between his theories and "intelligent design" advocates.
A group that favors "intelligent design" had planned to premier a new documentary film at the California Science Center in Los Angeles later this month, but the center later canceled the event.

The group claims the cancellation was an act of censorship, made after the center was pressured by the Smithsonian Institution, but the center chalked it up to a contract issue, without elaborating.

Coined "The Darwin Debates: A Forum for Dialogue," the nonprofit American Freedom Alliance had planned to premier a new Illustra Media documentary, "Darwin's Dilemma: The Mystery of the Cambrian Explosion," at the California Science Center on Oct. 25.

More...

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Troy Anderson's definition of ID at the very end of the article, is really quite lame, and shows his lack of understanding of the scientific endeavours of pursuit of ID.

As reported in ENV by Anika Smith, Richard Dawkins, the world's leading public spokesman for Darwinian evolution and an advocate of the "new atheism," has refused to debate Dr. Stephen C. Meyer, a prominent advocate of intelligent design and the author of the acclaimed Signature in the Cell: DNA and the Evidence for Intelligent Design.

"Richard Dawkins claims that the appearance of design in biology is an illusion and claims to have refuted the case for intelligent design," says Dr. Meyer who received his Ph.D. in the philosophy of science from the University of Cambridge in England.

"But Dawkins assiduously avoids addressing the key evidence for intelligent design and won't debate its leading proponents, adds Dr. Meyer. "Dawkins says that there is no evidence for intelligent design in life, and yet he also acknowledges that neither he nor anyone else has an evolutionary explanation for the origin of the first living cell. We know now even the simplest forms of life are chock-full of digital code, complex information processing systems and other exquisite forms of nanotechnology.

More...

Michael Behe posts on ENV that Nature has published an interesting paper recently which places severe limits on Darwinian evolution.

Behe comments that "Before reading their paper, even I would have happily conceded for the sake of argument that random mutation plus selection could convert an MR-like protein to a GR-like protein and back again, as many times as necessary. Now, thanks to the work of Bridgham et al (2009), even such apparently minor switches in structure and function are shown to be quite problematic. It seems Darwinian processes can't manage to do even as much as I had thought."

More for details...

Review Of The Seventh Chapter Of Signature In The Cell by Stephen Meyer
ISBN: 9780061894206; ISBN10: 0061894206; Imprint: HarperOne

By Robert Deyes
ARN Correspondent

The distinction between historical and experimental science is one that extends back over the centuries and at its core seems easy to grasp. Whereas historical science has as its focus events that have defined the history both of our planet and larger cosmos, experimental science has its eye on the current operation of nature.

The 19th century philosopher William Whewell coined the term 'palaetiological sciences' to describe those fields of science, such as geology and paleontology, that have a historical perspective (1). Whewell's broad application of the term shone through in his two great works, his History of the Inductive Sciences and his Philosophy of the Inductive Sciences (1). Immanuel Kant used a similar distinction contrasting those sciences that describe "relationships and changes over time" with those that deal with the "empirical study and classification of objects...at present" (2).

As part of their analytical process, scientists routinely assess the validity of competing hypotheses to determine which best explain the data they have at their disposal. The late Cambridge philosopher Peter Lipton formally defined such a process of validation in his book Inference To The Best Explanation (3). Put simply, Lipton considered the best explanation for the occurrence of a natural event as one that obviously best identifies a likely cause. Lipton's formalization rode on the back of 19th century geologist Thomas Chamberlin's 'method of multiple working hypotheses' (4) and provided an improvement over Charles Peirce's abductive reasoning- the process through which an established rule is used to explain a tangible observation (5).

Abductive reasoning would have us say that given a rule such as "If it rains the grass is wet", the occurrence of wet grass must invariably lead to the conclusion that rain had fallen at some moment in the past (5). Nevertheless Peirce was quick to identify an inherent fallacy in such a thread of logic- a fallacy known amongst philosophers as the 'affirmed consequent'. According to one review:

"Affirming the consequent, sometimes called converse error, is a formal fallacy committed by reasoning in the form: If P, then Q. Q. Therefore, P. Arguments of this form are invalid in that [they] do not always give good reason to establish their conclusions, even if their premises are true." (5)

In the above illustration, the fallacy is all too evident since rain is quite obviously not the only causal agent that waters our lawns (summertime sprinklers and hose pipes stand out as self-evident alternatives!). The question that naturally follows is, given numerous causally adequate explanations, how might one go about deciding which supplies the greatest explanatory power?

One way is to resort to vera causa ("causes now in operation") as Darwin did when he used animal migration behaviors to explain common descent. According to Darwin "the simplicity of the view that each species was first produced within a single region captivates the mind. He who rejects it, rejects the vera causa of ordinary generation with subsequent migration, and calls in the agency of a miracle" (6). Darwin of course assumed that the 'now operational' variations observed in animal breeding could likewise explain macro-evolutionary changes throughout the history of life.

An alternative approach to the causal adequacy question is to seek out additional lines of evidence that either prop up or debunk competing explanations. Stephen Meyer expounds on this salient point in the seventh chapter of his most recent book Signature In The Cell,

"the process of determining the best explanation often involves generating a list of possible hypotheses, comparing their known (or theoretically plausible) causal powers against the relevant evidence, looking for additional facts if necessary, and then, like a detective, progressively eliminating potential but inadequate explanations until, finally, one causally adequate explanation for the ensemble of relevant evidence remains" (p.166)

Historical scientists are of course not the only group to employ such a procedural chain. Meyer's impressive list of distinguished professions- including clinical diagnosticians and forensic detectives- that are 'cause-focused' in their modes of operation, gives us much to ponder over. And his follow-on question is brilliantly relevant- might not intelligent design supply the most causally adequate explanation for the origin of biological information? The answer may surprise some. It turns out that by the same 'vera causa' line of reasoning used by Darwin 150 years ago, intelligent causation in biology remains a distinct possibility. After all, a cornerstone claim in the ID offensive is that we routinely observe intelligent agents as 'causes now in operation' that generate the same type of specified information as we find in DNA.

Meyer goes on to boldly entertain the idea that intelligent design presents us with the only causally adequate explanation for the origin of biological information and spends much of the remainder of his book tying together substantial evidence in support of his position. As for Darwin, one can only imagine how he might have felt coming back to find intelligent design legitimized through his very own criterion. My hunch is that he would have applauded the current state of debate.

Citations Listed
1. For a summary of Whewell's work, see biologist Robert J O'Hara's discussion at http://rjohara.net/darwin/palaetiology

2. Phillip R. Sloan (2006), Kant On The History Of Nature: The ambiguous heritage of the critical philosophy for natural history, Stud. Hist. Phil. Biol. & Biomed. Sci. 37 (2006), pp.627–648

3. Peter Lipton: Philosopher of science renowned for his account of inference and explanation, Obituary appeared in The Guardian, Thursday 13th December, 2007, See http://www.guardian.co.uk/news/2007/dec/13/guardianobituaries.obituaries1

4. For a detailed account of Thomas Chamberlin's work, see http://geology.about.com/od/history_of_geology/a/aa_geothinking.htm

5. See Absolute Astronomy, http://www.absoluteastronomy.com/topics/Abductive_reasoning

6. Charles Darwin (1859), The Origin of Species By Means of Natural Selection Or The Preservation of Favored Races In the Struggle For Survival, Modern Library Paperbacks Edition (1998), New York, p.488

by Denyse O'Leary
ARN correspondent

We are told (in a Nova program, Ghost in your Genes, October 16, 2007) ,

Scientists have long puzzled over the different fates of identical twins: both have the same genes, yet only one may develop a serious disease like cancer or autism. What's going on? Does something else besides genes determine who we are? In this program, NOVA reveals the clues that have led scientists to a new picture of genetic control and expression. One such clue is the surprisingly modest number of genes that turned up when technology made it possible to map the human genome. The Human Genome Project was originally expected to find at least 100,000 genes defining the human species. Instead the effort yielded only about 20,000 - about the same number as in fish or mice - too few, some believe, to account for human complexity. Learn more about the connection between epigenetics, aging, and cancer on the program's companion website.

"What's going on? Does something else besides genes determine who we are?"

Um, yes. Here are three obvious observations right away:

- All we need to know about any life form is not necessarily in its DNA, as the program makes clear. Frustratingly, the true causes and cures of cancer and autism are controversial and clouded.

But our DNA is not a book of magic in which all the answers are written, and it is too bad if anyone thought it was.

- Identical twins may have almost-identical DNA, but usually one is the dominant twin and the other the sub-dominant one. Also, they tend to separate as adults and have different experiences. Over a lifetime, these differences can add up.

- Also, humans are intelligent and make choices. Different choices lead to different outcomes. The fact that anyone should doubt that this occurs and would be important is a symptom of the damage materialism (= you are either a robot or a monkey) has done to science.

See also Identical twins does not mean identical minds

Intelligence: How much is heredity and how much is environment

How much brain do you need?

Hat tip: Stephanie West Allen at Brains on Purpose

Also just up at The Mindful Hack:

Neuroscience: More "brain in a vat" talk

Religion: Does religious literacy matter?

Religion: Putting God on trial once again

Learning and self-esteem

Mental health: Use of psychiatry as torture

Neurolaw: Simulated study stirs debate

Toronto-based Canadian journalist Denyse O'Leary (www.designorchance.com) is the author of the multiple award-winning By Design or by Chance? (Augsburg Fortress 2004), an overview of the intelligent design controversy. She was named CBA Canada's Recommended Author of the Year in 2005 and is co-author, with Montreal neuroscientist Mario Beauregard, of The Spiritual Brain: A neuroscientist's case for the existence of the soul (Harper 2007).

by Denyse O'Leary
ARN correspondent

This one's a bit of fun, but there is a serious purpose behind it. Go here to enter.

In "A Life of Its Own: Where will synthetic biology lead us?" (September 28, 2009 New Yorker mag), Michael Specter reports, "If the science truly succeeds, it will make it possible to supplant the world created by Darwinian evolution with one created by us."

Jurassic Park, anyone? Consider this:

... researchers have now resurrected the DNA of the Tasmanian tiger, the world’s largest carnivorous marsupial, which has been extinct for more than seventy years. In 2008, scientists from the University of Melbourne and the University of Texas M. D. Anderson Cancer Center, in Houston, extracted DNA from tissue that had been preserved in the Museum Victoria, in Melbourne. They took a fragment of DNA that controlled the production of a collagen gene from the tiger and inserted it into a mouse embryo. The DNA switched on just the right gene, and the embryo began to churn out collagen. That marked the first time that any material from an extinct creature other than a virus has functioned inside a living organism.

It will not be the last. A team from Pennsylvania State University, working with hair samples from two woolly mammoths—one of them sixty thousand years old and the other eighteen thousand—has tentatively figured out how to modify that DNA and place it inside an elephant’s egg. The mammoth could then be brought to term in an elephant mother. "There is little doubt that it would be fun to see a living, breathing woolly mammoth—a shaggy, elephantine creature with long curved tusks who reminds us more of a very large, cuddly stuffed animal than of a T. Rex.," the Times editorialized soon after the discovery was announced. "We're just not sure that it would be all that much fun for the mammoth."

The article discusses both the promise and the peril or reengineering nature.

Personally, I am a bit skeptical that an extinct creature can be resurrected from DNA alone, but ... wait! What I thought was passing traffic turned out to be a herd of tyrannosaurs heading off to eat the McDonalds.

So now to Uncommon Descent Contest Question 11: For a free copy of Stephen Meyer's Signature in the Cell (Harper One, 2009), how likely do you think biotechnologists will be in bringing back the Tasmanian wolf or the woolly mammoth? You can try the tyrannosaur too if you are feeling ambitious.

Here are the contest rules, not an extensive read.

Toronto-based Canadian journalist Denyse O'Leary (www.designorchance.com) is the author of the multiple award-winning By Design or by Chance? (Augsburg Fortress 2004), an overview of the intelligent design controversy. She was named CBA Canada's Recommended Author of the Year in 2005 and is co-author, with Montreal neuroscientist Mario Beauregard, of The Spiritual Brain: A neuroscientist's case for the existence of the soul (Harper 2007).

by Denyse O'Leary
ARN correspondent

Here's the latest UD Contest Question, so use this link to enter.

Addressing the Inbox, I discovered this most interesting tale about lotteries in Bulgaria, a tale that reminds me of a similar suspicious lotto in my own Canadian province of Ontario.

In Money Matters, at Australia's news.com, we learn that "Lottery numbers the same in consecutive draws in Bulgaria" (correspondents in Sofia, Agence France-Presse, September 16, 2009)

Here are the bullet points, and you can read the rest yourself.

- The numbers 4, 15, 23, 24, 35, and 42 were drawn two weeks in a row / File
- Same numbers picked in consecutive draws
- Review of the national lottery is ordered
- Probability is 4.2 million to one

Hmmmm. If these charges are true, I'm glad I am not in charge of that investigation. I would hardly want to hear all the lies people would probably try to tell me. Our Ontario premier, faced with a similar situation, fired the chair and the whole board of the lottery corporation and decided to start fixing the problem from scratch. I would recommend looking for statisticians and tough cops, not just anyone with the "power from behind" to sit through an endless board meeting.*

But here's the question that this and other questionable lottery stories leaves me with: The intelligent design theorists emphasize probability issues. Their chief knock against Darwinism is that it appears improbable. In the same way, an accidental origin of the fine-tuned values of our universe appears improbable. If I understand the matter correctly, the universe is assumed to be over 13 billion years old, or so, and Earth over 4 billion years old. (I assume these values for convenience as I believe them to be generally accepted.) So we can assume a basis for computing probability.

So, for a free copy of the Privileged Planet DVD, which addresses the fine tuning of the universe:

Uncommon Descent Contest Question 12: Can Darwinism beat the odds. If not, why not? If so, how?

You might want to look at Bill Dembski's No Free Lunch.

(Note: Thanks to Ilion Troas for alerting me to this story.)

*One alternative: Don't have a lottery at all. Lotteries attract vast moral hazard and corruption because they look like free money. I never supported the idea and don't buy tickets, and think that worthy causes should be funded in the usual ways, through taxes, donations, memberships, sponsorships, premiums, etc. But this mini-editorial is unrelated to the point of the contest question.

Toronto-based Canadian journalist Denyse O'Leary (www.designorchance.com) is the author of the multiple award-winning By Design or by Chance? (Augsburg Fortress 2004), an overview of the intelligent design controversy. She was named CBA Canada's Recommended Author of the Year in 2005 and is co-author, with Montreal neuroscientist Mario Beauregard, of The Spiritual Brain: A neuroscientist's case for the existence of the soul (Harper 2007).

The Indiana Memorial Union Board and the Secular Alliance of Indiana University will present a lecture by evolutionary biologist, author and atheist Richard Dawkins, titled "The Greatest Show On Earth: The Evidence for Evolution," Monday, Oct. 12, at 7 p.m. at IU Auditorium.

The event is free and open to the public. No ticket is required, and doors will open at 6 p.m.

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Michael Behe posts that Nature has published an interesting paper recently which places severe limits on Darwinian evolution.

The manuscript, from the laboratory of Joseph Thornton at the University of Oregon, is entitled "An epistatic ratchet constrains the direction of glucocorticoid receptor evolution". The work is interpreted by its authors within a standard Darwinian framework. Nonetheless, like the important work over the years of Michigan State's Richard Lenski on laboratory evolution of E. coli, which has shown trillions of bacteria evolving under selection for tens of thousands of generations yielding just broken genes and minor changes, the new work demonstrates the looming brick wall which confronts unguided evolution in at least one system. And it points strongly to the conclusion that such walls are common throughout all of biology.

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A debate between Dr. Francisco J. Ayala and Dr. William Lane Craig. Moderated by Dr. Bradley Monton. The debate will occur on Thursday, November 5, 2009 at 7 p.m. EST at Indiana University Auditorium.

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Intelligent design is the most likely explanation of the origin of life, an author and speaker at the University of Oklahoma said Monday night.

The way Stephen C. Meyer came to that conclusion, was using Charles Darwin's own scientific method of determining which cause to accept for scientific questions in the remote past.

"The irony of that is that a conclusion that points to intelligent design" is reached by Darwin's own methods, Meyer said.

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The news out of Oklahoma about Stephen Meyer's intelligent design presentation at the University on Sept. 28th is quite encouraging. Over three hundred people reportedly turned out for the lecture and discussion following. For all the potty mouthed bluster that local Darwin activists offered up ahead of time, almost everyone in attendance, whether for or against ID, was civil and respectful during the presentation and discussion.

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Recently, I noted here and here the growth of "neurolaw," the - in my view often misguided - attempt to apply neuroscience to crime and punishment. I've since had a chance to read the excellent article by Michael S. Pardo and Dennis Patterson, "Philosophical Foundations of Law and Neuroscience", to be published in the University of Illinois Law Review in 2010. It provides an overview and critique of this growing field (and explains why it should shrink instead).

On a personal note, all this reminds me so much of Freudianism. Once upon a time, many years ago during an argument, an amateur Freudian psychologist informed me that my problems - as he perceived them - were due to the fact that I hated my mother.

I had never imagined that. How could I hate my mother and not even know it? Well, he explained, the hatred was in my Unconscious ....

So I solved the problem immediately by just disbelieving in the Freudian Unconscious. I continued to disbelieve and to not hate my mother, so far as I know and my behaviour would suggest, for another 45 years. Of course, it is possible I have a Freudian Unconscious somewhere in which I hate my mother, but it has had no impact on my life.

Today, the same person would announce instead that he had found a "hate Mom circuit" in my hippocampal gyrus, or something.

So no, I don't think neurolaw is any more scientific than Freud's Unconscious. Finding someone's fingerprints - and only his fingerprints, not anyone else's - on the steak knife used to stab another patron in a bar plus a security videocam catching him stabbing that guy, now that's what I mean by "scientific." I don't mind paying taxes for a criminal justice system that deals in that sort of evidence, but I am very skeptical of this "neurolaw" craze.

I've always thought neuroscience should stay as close to medicine as possible. In medicine, as Sir William Osler put it, you cure sometimes, alleviate often, and comfort always. So neuroscience would never be a weapon against anyone; it might help or might not help, in cases of strokes or mental disorders, for example, but the first principle of medicine, as Hippocrates used to say, is "First, do no harm."

Psychic phenomena: Persistent paradox

Reptile brain: Even reptiles don't have one, or not exactly, anyway

Baby bigots? Or adults who pay too much for fishwrap?