The ID Update

by Denyse O'Leary
ARN correspondent

A friend sent me this item on the purely random evolution of the wiener dog (dachsund):

Our findings suggest that retrogenes may play a larger role in evolution than has been previously thought, especially as a source of diversity within species," said the study's first author, Heidi G. Parker, Ph.D. of NHGRI. "We were surprised to find that just one retrogene inserted at one point during the evolution of a species could yield such a dramatic physical trait that has been conserved over time."

In the past, retrogenes have been recognized as an important source of changes that have fueled the divergence of species. However, the dog findings are the first example of a retrogene that has spurred significant and long-lasting variation within a single species.

And it just happened to be conserved, too, by survival of the fittest. Amazing.

News flash!

Toronto (July 27, 2009) North of Lake Superior, Canadian wildlife biologists are reporting a dismaying reduction in wolf packs, with a few haggard, starving survivors haunting fast food dumpsters near riverside hunting lodges, in hopes of a stale donut or two.

Highly efficient wild packs of dachshunds have been attacking established timber wolf packs and seizing their moose kills.

Geez Freeple, a Toronto University-based wildlife biologist, explained, "Evolution bred the dachshunds to have short legs and weak jaws, so they never actually get anywhere near the kill until after the wolves have brought it down and opened it up. After that, it is an easy matter for the dachsunds to drive off the wolves. They just yap incessantly. Same principle as driving guests away from the dachshund owner's house. Of course, the wolves meekly surrender in just the same way as the house guest does and slink off.

"It continually amazes me that anyone doubts the power of unguided Darwinian evolution."

(Note: To avoid misunderstanding, this is not a serious post.

There are NO packs of wild dachshunds running loose in the boreal forests of Canada.

No Geez Freeple works at the University of Toronto.

No boreal wolf would see the dachshund as anything but about 2 kg of pleasant guts to devour, all the sweeter if it just had a meal of dog food.

And the yaps would cease pretty quickly too.

Also just up at The Post-Darwinist

Speciation: If you don't sleep together, you soon won't cheep together?

Darwinism and popular culture: A columnist reminds me of its easy, empty phrases

Common descent, uncommon descent, and, hey, a ladderinto ...

Darwinism and popular culture: Well, aren't we all 30 per cent banana anyway?

Uncommon Descent: Contest Question 7: "Foul anonymous Darwinist blogger exposed. Why so foul?" Winners announced

Darwinism and academic culture: Why so many scientists no longer believe Darwin

Darwinism and popular culture: Real biology vs. Darwinism

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).

Synopsis Of The Third Chapter Of Signature In The Cell by Stephen Meyer
By Robert Deyes
ARN Corrspondent

ISBN: 978-0-06-147278-7 Imprint: HarperOne

"Watson, with his wild hair and perfect willingness to throw off work for a Hedy Lamarr film, and Crick, a dapper and no longer especially young fellow who couldn't seem to close the deal on his dissertation"(p.59). These are the uninspiring words that Stephen Meyer uses to describe the two men who would ultimately unravel the structure of DNA and thus ring in the molecular biology revolution.

With the chemical composition of DNA sufficiently well established, the world of science appeared poised for a major shake-up in its understanding of heredity. Still, the road of discovery up until that time had been anything but a 'walk in the park'. While important details concerning the components of DNA had been ironed out as early as 1909, several erroneous turns at the beginning of the twentieth century had thrown biologists 'off piste' into thinking that protein and not DNA lay at the heart of heredity.

In the 1940s the pioneering work of Erwin Chargaff brought heredity firmly back into its rightful place. Having shown unequivocally that DNA was made up of non-equal proportions of its constituent bases, Chargaff recognized that DNA might possess a language-style code that could act as the medium for inheritance. The intellectual journey that led James Watson to Cambridge University's Cavendish Laboratory in 1951 eventually finished of course with a stunning confirmation of Chargaff's suspicions.

Key to both Watson's and Crick's triumphant entry into the DNA race was their uninhibited drive to ask questions even if that meant revealing their ignorance. While others feared tarnished reputations should they expose any gaping holes in their understanding of the matter at hand, Watson and Crick had little to lose in their rise from obscurity. The Watson-Crick duo took valiant stabs at the DNA structure problem using data that others, notably Rosalind Franklin and Linus Pauling, had amassed. Indeed history tells of the tensions that existed between these rivals although many considered Watson and Crick to be nothing more than laughable 'know nothings' who had no business being where they were.

Using little more than plastic and metal models Watson and Crick brought substance to the idea that a double helix with phosphate backbones running on the outside accorded best with the data. The 'staircase structure' that they ultimately arrived at was in all senses revolutionary as was the nine hundred word-long 1953 Nature paper they published just weeks later. Famously, Crick entered the Eagle pub just around the corner from the Cavendish laboratory to inform the masses that the 'secret of life' had at long last been found.

Meyer does a marvelous job in conveying the personal tensions that so characterized the DNA story. His extensive coverage of 'turning point' historical moments reveals an in-depth knowledge of the subject matter. Like few other scientific discoveries, that of the structure of DNA brought fundamental changes to our understanding of the chemistry of life since life itself could no longer be considered to be a mere product of matter and energy. As Meyer elaborates, information in the form of a DNA code had emerged as the critical player in defining the hereditary makeup of nature.

Synopsis Of The Second Chapter Of Signature In The Cell by Stephen Meyer

ISBN: 978-0-06-147278-7 Imprint: HarperOne

When the 19th century chemist Friedrich Wohler synthesized urea in the lab using simple chemistry, he set in motion the ball that would ultimately knock down the then-pervasive 'Vitalistic' view of biology. Life's chemistry, rather than being bound by immaterial 'vital forces' could indeed by artificially made. While Charles Darwin offered little insight on how life originated, several key scientists would later jump on Wohler's 'Eureka'-style discovery through public proclamations of their own 'origin of life' theories. The ensuing materialist view was espoused by the likes of Ernst Haeckel and Rudolf Virchow who built their own theoretical suppositions on Wohler's triumph. Meyer summed up the logic of the day

"If organic matter could be formed in the laboratory by combining two inorganic chemical compounds then perhaps organic matter could have formed the same way in nature in the distant past" (p.40)

Darwin's theory generated the much-needed fodder to 'extend evolution backward' to the origin of life. It was believed that "chemicals could "morph" into cells, just as one species could "morph" into another" (p.43). Appealing to the apparent simplicity of the cell, late 19th century biologists assured the scientific establishment that they had a firm grasp of the 'facts'- cells were, in their eyes, nothing more than balls of protoplasmic soup. Haeckel and British scientist Thomas Huxley were the ones who set the protoplasmic theory in full swing. While the details expounded by each man differed somewhat, the underlying tone was the same- the essence of life was simple and thereby easily attainable through a basic set of chemical reactions.

Things changed in the 1890s. With the discovery of cellular enzymes the complexity of the cell's inner workings became all too apparent and a new theory that no longer relied on an overly simplistic protoplasm-style foundation, albeit one still bound by materialism, had to be devised. Several decades later, finding himself in the throws of a Marxist socio-political upheaval within his own country, Russian biologist Aleksandr Oparin became the man for the task.

Oparin developed a neat scheme of inter-related processes involving the extrusion of heavy metals from the earth's core and the accumulation of atmospheric reactive gases all of which, he claimed, could eventually lead to the making of life's building blocks- the amino acids. He extended his scenario further, appealing to Darwinian natural selection as a way through which functional proteins could progressively come into existence. But the 'tour de force' in Oparin's outline came in the shape of coacervates- small, fat-containing spheroids which, Oparin proposed, might model the formation of the first 'protocell'.

Oparin's neat scheme would in the 1940s and 1950s provide the impetus for a host of prebiotic synthesis experiments, most famous of which was that of Harold Urey and Stanley Miller who used a spark discharge apparatus to make the three amino acids- glycine, alpha-alanine and beta-alanine. With little more than a few gases (ammonia, methane and hydrogen), water, a closed container and an electrical spark Urey and Miller had seemingly provided the missing link for an evolutionary chain of events that now extended as far back as the dawn of life. And yet as Meyer concludes, the information revolution that followed the elucidation of the structure of DNA would eventually shake the underlying materialistic bedrock.

Meyer's historical overview of the key events that shaped origin-of-life biology is extremely readable and well illustrated. Both the style and the content of his discourse keep the reader focused on the ID thread of reasoning that he gradually develops throughout his book.

Synopsis Of The First Chapter Of Signature In The Cell by Stephen Meyer

ISBN: 9780061894206; ISBN10: 0061894206; Imprint: HarperOne

In August of 2004, philosopher Stephen Meyer published an article in the Proceedings Of The Biological Society Of Washington. The article raised media interest and outrage because it was the first to "advance the theory of intelligent design" in a peer-reviewed scientific journal. The editor Richard Sternberg lost his position as a result of the ensuing debacle.

Just a few months later, renowned British philosopher Antony Flew shocked the world by reversing his life-long atheistic commitment and announcing his support for an idea reminiscent of that proposed by the modern intelligent design movement. That same month the ACLU declared it would be filing charges against the Dover, Pennsylvania school board for approving the teaching of Intelligent Design in its science classes.

Much of the controversy in all the above cases stems from a misunderstanding over what the intelligent design movement does and does not purport to explain. As many in the movement have re-iterated throughout the years, intelligent design is not in any way synonymous with biblical creationism. In the words of Stephen Meyer "intelligent design is an inference from scientific evidence, not a deduction from religious authority" (p.8).

In his recent book Signature In The Cell, Meyer presents a fresh outlook on one of the most compeling facets of the Intelligent Design case- that of biological information in DNA. When Watson and Crick published their famous paper in 1958, they not only solved the mystery of the structure of DNA but also unearthed the computer program-like nature of the information that it carried. While experience tells us that such information has its origins in the activity of conscious beings, evolutionary biologists have dismissed such a connection in biology. As an alternative, they have as we all know placed their belief in the blind activity of natural selection.

It would seem ironic therefore that these same scientists would then employ design-evoking metaphors such as 'code' and 'language' to describe DNA. They of course qualify this by stating that the apparent design of DNA is merely illusionary. Still as Meyer hammers home, the mystery of the origins of DNA and life itself remains one that modern day biology is finding difficult to unravel.

Meyer provides a lucid and personal account of his own experiences as a scientist and philosopher revealing to the reader the watershed events that led to his move towards the intelligent design alternative. Foremost in his initial exposee are the meetings he conducted with Charles Thaxton who, in his co-authorship of the book The Mystery Of Life's Origin, rejuvenated the idea of intelligent causation in biology.

Uncommon Descent: Contest Question 7: "Foul anonymous Darwinist blogger exposed. Why so foul?" featured the opposite outcome from Contest Question 6. Only one person entered Question 6 (winner announced here , possibly because most of us are sick of hearing the term "crisis" used to mean any situation (in this case, genomics) that someone finds upsetting. That's good news, really. Maybe we'll go back to saving "crisis" for the next eruption of Krakatoa or Pinatubo. Basically, there are no "crises" in cosmology or genome mapping.

Anyway, 198 people responded to Contest Question 7. Now, to recap, the topic had come up unexpectedly. An avatar blogger, "Canadian Cynic," had been posting obscenities for years against Canadian women (wives, mothers, grandmothers, sisters, daughters) who espoused traditional values. I somehow got in his sights because of my interest in the intelligent design controversy.

The problem wasn't so much with the vile stuff he said but with the fact that no one knew who he was. But the enterprising Wendy Sullivan, the "Girl on the Right", found out, and allowed the world (his clients, colleagues, suppliers, acquaintances, neighbours, anyone who might be interested, really) to know that that is how he spends his time when he is not developing or writing about software.

That's all we wanted, really. Just to end the secrecy. The rest, we were pretty sure, would take care of itself. Okay, so that's history, but it raised an interesting question for Contest 7: Why do so many Darwinists spout so much filth, hostility, and aimless detraction?

In other words, why would stuff that earns applause at Panda's Thumb and After the Bar Closes get you kicked out of Uncommon Descent? And, incidentally, Darwin and his associates would doubtless be much more comfortable at Uncommon Descent than at Panda's Thumb or After the Bar Closes? What cultural change does this signify?

The part I find most interesting is that in polls, people like Canadian Cynic would doubtless proclaim themselves great defenders of the rights of women, more volubly maybe than men who would never behave that way in print.

Most of our 198 entries responded to one aspect or another of this charged issue., but a number were genuine entries. After reading them over and thinking about them, I found I could not choose between two entries, EndoplasmicMessenger at 105 and Cannuckian Yankee at 163, so I am declaring them joint winners. Both need to provide me with a postal address if they wish to receive their free copy of the Expelled DVD.

Here are their entries, reproduced:

Go here for more.

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).

Toucans are able to alter the flow of blood through their large bills, which make-up 30-50% of their body area. The effect is very significant: the toucan bill is now understood to make a major contribution to temperature regulation.

The Toco Toucan(Source and video here)

The newly published research needs to be considered in the context of history: for many people have wondered about the unusually large beak (the toucan has the largest bill relative to the body size of birds). The authors draw attention to previous speculation:

"In the hall of animal oddities, the toucan's enlarged bill is the avian example of exaggeration, being a source of debate since Buffon labeled it a "grossly monstrous" appendage. Even Darwin was intrigued, stating that "toucans may owe the enormous size of their beaks to sexual selection, for the sake of displaying the diversified and vivid stripes of colour with which these organs are ornamented". More recent explanations for the oversized bill include fruit peeling, nest predation, social selection in the context of territorial defense, and, finally, serving as a visual warning."

Since this is Darwin's year, it is worth highlighting his comments which were made as part of an argument for sexual selection. The justification of his interpretation is (a) that the idea is not incredible; and (b) that there is no greater improbability in thinking toucans have large beaks because of sexual selection than in thinking male pheasants should be "encumbered with plumes" for the same reason.

"This leads me to remark that it is not at all incredible that toucans may owe the enormous size of their beaks to sexual selection, for the sake of displaying the diversified and vivid stripes of colour, with which these organs are ornamented. The naked skin at the base of the beak and round the eyes is likewise often brilliantly coloured; and Mr. Gould, in speaking of one species, says that the colours of the beak "are doubtless in the finest "and most brilliant state during the time of pairing." There is no greater improbability in toucans being encumbered with immense beaks, though rendered as light as possible by their cancellated structure, for an object falsely appearing to us unimportant, namely, the display of fine colours, than that the male Argus pheasant and some other birds should be encumbered with plumes so long as to impede their flight."
(Darwin, C. R. 1871. The descent of man, and selection in relation to sex. London: John Murray. Volume 2. 1st edition. Chapter 16. The quoted words are on page 227).

The reason why many have not found this hypothesis convincing is that both male and female toucans excel in bill size, and both sexes have bills that are brightly coloured. The other hypotheses that have been explored have not fared any better. Take the fruit peeling idea: toucans eat fruit, but is there an advantage in having a large bill to do this? There are many other frugivorous birds, but none display notable large bills. Before moving on to consider the new research, it is worth pausing to reflect on the adaptationist paradigm. What Darwinists have done is persuade people to think that plausible speculations deserve to be considered as science. The tried-and-tested empirical approach is replaced by just-so stories, which become the basis of adaptationist 'science'. People have the view that Darwin's strength was his detailed knowledge of empirical observations, but this case may help to illustrate why this image is false. Darwin's theory did not emerge from the data but was brought in as an interpretative screen through which the data was viewed. There were numerous places where the fit was not good, but people did not perceive them because of Darwin's skill in telling persuasive stories.

The researchers have documented the function of thermoregulation after noting the network of blood vessels between the horny and bony parts of the toucan bill. They chose to work with the toco toucan because it has the largest bill of all the toucans.

"The bill has a network of superficial blood vessels supporting the horny ramphotheca. Therefore, the toucan's bill combines all the important features of a candidate thermal radiator: It is enlarged, uninsulated, and well vascularized. It is, however, crucial that blood flow be adjustable in order to control heat exchange from the bill. We examined whether the toucan's bill can operate as a thermal window for heat loss, capable of being "opened" within and above the thermal neutral zone and "closed" to conserve metabolic heat at lower temperatures. We used infrared thermography to examine the effects of changing ambient temperature on the heat exchange profile of different regions of the bird's body."

The findings were spectacular:

"The bill radiated a great deal of heat at high temperatures and when the toucan flew, indicating that, like elephants and rabbits do with their ears, the toucans flush their bills with blood to cool down. At lower temperatures, the difference between air temperature and bill temperature dropped, meaning that the toucans were restricting blood flow to their bills. Based on its size, a toucan's bill can theoretically account for anywhere from 5% to 100% of the bird's body heat loss [. . .]. When the toucan is in flight, its bill is the most efficient heat-shedder ever reported, losing four times more heat than the bird produces while at rest. That's about four times more efficient than either elephants' ears or ducks' bills."

The earlier explanations assumed adaptation, whether the trait is the consequence of sexual selection, fruit peeling, nest predation, social selection - territorial defense or visual warning. These analyses are now revealed as over-simplistic. They all assume that the only thing to be explained is the large bill. Once a driver for adaptive change is found, a new just-so story is invented. The new explanation is full of complexity: the bill has an internal structure involving vascularity, and the bird has the ability to control the flow of blood so as to achieve thermoregulation. This is an integrated system with feedback mechanisms - and this is not amenable to the 'one driver - one trait' mentality that has dominated the thinking of adaptationists. These systems, however, fit readily within the design paradigm because here we recognise complex specified information.

Heat Exchange from the Toucan Bill Reveals a Controllable Vascular Thermal Radiator
Glenn J. Tattersall, Denis V. Andrade, and Augusto S. Abe
Science, 325, 24 July 2009: 468-470.

Abstract: The toco toucan (Ramphastos toco), the largest member of the toucan family, possesses the largest beak relative to body size of all birds. This exaggerated feature has received various interpretations, from serving as a sexual ornament to being a refined adaptation for feeding. However, it is also a significant surface area for heat exchange. Here we show the remarkable capacity of the toco toucan to regulate heat distribution by modifying blood flow, using the bill as a transient thermal radiator. Our results indicate that the toucan's bill is, relative to its size, one of the largest thermal windows in the animal kingdom, rivaling elephants' ears in its ability to radiate body heat.

See also:

Price, M. A Bird With a Big Air-Conditioning Bill, ScienceNOW Daily News (23 July 2009)

by Denyse O'Leary
ARN correspondent

A friend writes,

This weekend I watched Alien From Earth- a documentary that outlines the consternation that the 'Man of Flores' has caused amongst evolutionary anthropologists. Here is what Nature science editor Henry Gee had to say on the matter ('Evolution of the Gaps' is once again all too evident):

Despite decades of patient work we still know rather little about the evolution of humanity ... the remains we have are very scarce and very meager and that means that there are probably lots of different species that existed, lived for hundreds of thousands of years and then became extinct and we know nothing about them ... All you need is just one to completely blow apart your well entrenched comfortable idea of the linear progress of evolution.

Basically, it's not clear that the one-metre tall humans who occupied Indonesian island Flores for millennia lived any differently from other ancient humans, so the obsession with classifying them as a different species sounds like just that - an obsession.

See also:

Flores find a clear misfit for human evolution sequence?

The little lady of Flores files

First "hobbits" [an early name for Flores humans], now Pygmies?

Also just up at The Post-Darwinist:

Top Ten mysteries in science 2007 (Golden oldie!)

Human evolution: We know little, and with good reason

Academics as conformists?: No, they just want to be non-conformists, like everybody else

David Tyler: Used to be horse feathers, but now it's dinosaur feathers?

David Tyler: Tetrapod family tree looks like a bush

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

In "Second Genesis: Life, but not as we know it," Bob Holmes (New Scientist, March 11, 2009) provides a summary of attempts to create artificial life (paywall).

We're still stuck with Life 1.0, the stuff that first quickened at least 3.5 billion years ago. There's been nothing new under the sun since then, as far as we know.

That looks likely to change. Around the world, several labs are drawing close to the threshold of a second genesis, an achievement that some would call one of the most profound scientific breakthroughs of all time.

However,

Venter's team at the J. Craig Venter Institute in Rockville, Maryland, plans to remove the genome from an existing bacterial cell and replace it with one of their own design. If successful, this will indeed result in a novel life form, but it is a far cry from the ultimate goal of a second genesis, as Venter would be the first to admit.

Other teams, however, are striving directly for that ultimate goal. The most ambitious of them do not even rely on the standard set of molecular parts, but seek to redesign a living system from first principles. If successful, they would provide an entirely new form ...

Meanwhile, others look for a shadow biosphere, an independent type of life sharing the planet with us.

My sense is that the people who use existing manufactured parts will have the best luck with their work.

Here's University of Colorado (Boulder) philosophy prof Carol Cleland'sargument in Astrobiology Magazine (12/01/06) for looking for a shadow biosphere:

The discovery of a shadow microbial biosphere would be philosophically and scientifically important. It is clear that familiar Earth life has a common origin, and hence represents a single example of life. Logically speaking, one cannot generalize on the basis of a single example. If we are to achieve a satisfactory understanding of the general nature of life, we need examples of unfamiliar forms of life.

Also, Holly Hight asks ("Does Earth harbour a shadow biosphere of alien life," Cosmos: The Science of Everything, 16 February, 2009 ):

Finding life that doesn't fit with the types we already know would be a strong indication that life developed more than one time here on Earth, increasing the chances of finding it elsewhere, said Paul Davies, an astrophysicist at Arizona State University in Tempe.

But nobody has ever seriously searched for microorganisms - or any form of life - different from the carbon-based, DNA-centred type of life about which we have long known.

If we do look, Davies said, "It's entirely feasible that we'll find a shadow biosphere," he told reporters at the annual meeting of the American Association for the Advancement of Science (AAAS) in Chicago.

"Our search for life [has been] based on our assumptions of life as we know it. Weird life and normal life could be intermingled, and filtering out the things we understand about life as we know it from the things we don't understand is tricky."

It must be hard to write science fiction these days.

Also just up at Colliding Universes:

Cosmology: Crisis of the month - gravitation

You never know what'll turn up useful

Multiverse: Getting comfortable with a zillion of everything that is unique

Podcasts in the intelligent design controversy: Origin of life (with Charles Garner)

Origin of life: This time it's salt water

Colliding Universes is my blog on competing theories about our universe.

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).

Some icy winds are blowing through the corridors of academia. What we are seeing is the linking of the intellectual 'consensus' with power, peer esteem and funding. The freedom to follow the evidence wherever it leads is being steered into a 'freedom' to strengthen the consensus (but not to question it). These issues are raised in a retirement interview with Thomas Bouchard, the Minnesota psychologist known for his study of twins raised apart. He pointed out the way this was affecting his own discipline (although I'm omitting references to specific issues):

"But we still have whole domains we can't talk about. One of the great dangers in the psychology of individual differences is self-censorship." [. . .]
"But people had enormous amounts of data [showing this] that they didn't publish because it did not fit the prevailing belief system." [. . .]
"There are a lot of people who simply won't talk about those things. Academics, like teenagers, sometimes don't have any sense regarding the degree to which they are conformists."

The human face of academia - and of science (source here)

These issues were picked up by Nicholas Wade in The New York Times. He recognised that Dr Bouchard was describing a situation that is widespread.

"Journalists, of course, are conformists too. So are most other professions. There's a powerful human urge to belong inside the group, to think like the majority, to lick the boss's shoes, and to win the group's approval by trashing dissenters.
"The strength of this urge to conform can silence even those who have good reason to think the majority is wrong. You're an expert because all your peers recognize you as such. But if you start to get too far out of line with what your peers believe, they will look at you askance and start to withdraw the informal title of "expert" they have implicitly bestowed on you. Then you'll bear the less comfortable label of "maverick", which is only a few stops short of "scapegoat" or "pariah"."

Wade wanted to make the point that scientists are not exempt from this human tendency. Indeed, it is vital for science that they guard against it.

"Conformity and group-think are attitudes of particular danger in science, an endeavor that is inherently revolutionary because progress often depends on overturning established wisdom." [. . .]
"The academic monocultures referred to by Dr. Bouchard are the kind of thing that sabotages scientific creativity."

A bit of history of science will help here. Why is it that science did not flower after the young plant started so well among the ancient Greeks? Why did Islamic science falter in the Middle Ages? Why did Chinese science not get beyond some promising technological innovations? The answer is that in each case, the thinking of the scholars was dominated by a consensus ideology. Instead of testing ideas by reference to the natural world, they showed their allegiance was to Aristotelian philosophy (or to the equivalent in the cases of the Arab and Chinese cultures). Why did science develop in 17th Century Europe? It is because the scientists were consciously throwing off Aristotelianism and resolving to test their theories of the natural world by reference to observations of nature. The experimental method was the hallmark of their enquiries. Many have seen the Christian culture of those days as the handmaiden to science: they had come to distrust the unaided power of the human mind. One such scholar is Peter Harrison, whose book The Fall of Man and the Foundations of Science brings a refreshing perspective on this period of history:

"The strength of Harrison's argument is his insistence that experimental science grew out of the acute awareness that attaining knowledge is not an easy, natural process. In a postlapsarian world, strategies must be devised to overcome the inherited infirmities of original sin, as well as circumscribe the difficulties of apprehending nature, which had become less intelligible since the Fall. A scientist would have to create controlled environments so that experiments could be performed and repeated, and naturalia observed and described."

We need a fresh appraisal of developments in contemporary society. Scientists who step outside the 'consensus' are given a rough ride. Science leaders are being perceived by the public as arrogant. They are behaving like priests who understand their role to dispensers of knowledge. Bill Dembski refers to a "powerful new caste of scientists who have appointed themselves the guardians of humanity and the priests of a new social order." He continues:

"Scientists are as fallible as the rest of us, as are their scientific theories. Indeed, the history of science is filled with failed scientific theories that once were confidently asserted and now have been radically modified or even abandoned (see Thomas Kuhn's "The Structure of Scientific Revolutions"). The new scientific priesthood, however, has raised the stakes considerably for the mischief that science can do. In claiming to find and then resolve problems that threaten to overwhelm humanity, they have invaded the political scene, commanding vast research moneys and attempting to force on the wider population government-sanctioned programs for social control."

In the light of these trends, it is not surprising that ID scientists are regularly portrayed as enemies of reason and as subversive influences in the academic world. He/she who has eyes to see, let them see.

Behavioral Geneticist Celebrates Twins, Scorns PC Science
Constance Holden
Science 325, 3 July 2009, 27 | DOI: 10.1126/science.325_27 (restricted access)

Last month, the Behavior Genetics Association held its annual meeting in Minneapolis, home of the world-famous Minnesota Study of Twins Reared Apart. Attendees took the occasion to honor psychologist Thomas Bouchard, the man who started it all. Bouchard, 71, is retiring after 40 years at the University of Minnesota, Twin Cities, and has moved to Steamboat Springs, Colorado. Bouchard spoke with Science at the meeting; his comments have been edited for clarity and brevity.

See also:

Wade, N. Researcher Condemns Conformity Among His Peers, The New York Times, (Tierneylab, 23 July 2009).

by Denyse O'Leary
ARN correspondent

The significant thing about this Scientific American podcast on the recent disfavour into which evolutionary psychology has fallen is that no one appears to be throwing a fit about it.

This looks like another one for the Top Ten Darwin and Design stories of the year. But basically, it makes sense. You can only sound like the "Relationships" section of the weekend paper for so long, while pretending to do some kind of science, before people who actually do some kind of science start to get a bit nervous about what they are expected to endorse.

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

Michael Bloomberg, check your messages. In "Weak Link: Fossil Darwinius Has Its 15 Minutes: Skepticism about a fossil cast as a missing link in human ancestry" (Scientific American, July 21, 2009), Kate Wong observes,

And in an elaborate public-relations campaign, in which the release of a Web site, a book and a documentary on the History Channel were timed to coincide with the publication of the scientific paper describing her in PLoS ONE, Ida's significance was described in no uncertain terms as the missing link between us humans and our primate kin. In news reports, team members called her "the eighth wonder of the world," "the Holy Grail," and "a Rosetta Stone."

The orchestration paid off, as Ida graced the front page of countless newspapers and made appearances on the morning (and evening) news programs. Gossip outlets, such as People and Gawker, took note of her, too. And Google incorporated her image into its logo on the main search page for a day.

And then it all just melted away, with SciAm being only the latest source to say, "Hey, wait a minute. Shut off the canned wonder track for a minute, will you?"

I will certainly propose for this overall story as a down-list item for the ten top Darwin and Design stories of the year (here is 2008's list). It's rare indeed that popular media actually revolt against a proposition in "evolution," even one as patently foolish as this one - but evidently it happens. And who knows? - raindrops seldom fall solo. More Wong:

Critics concur that Ida is an adapiform, but they dispute the alleged ties to anthropoids. Robert Martin of the Field Museum in Chicago charges that some of the traits used to align Ida with the anthropoids do not in fact support such a relationship. Fusion of the lower jaw, for instance, is not present in the earliest unequivocal anthropoids, suggesting that it was not an ancestral feature of this group. Moreover, the trait has arisen independently in several lineages of mammals—including some lemurs—through convergent evolution. Martin further notes that Ida also lacks a defining feature of the anthropoids: a bony wall at the back of the eye socket. “I am utterly convinced that Darwinius has nothing whatsoever to do with the origin of higher primates,” he declares.

The real story here is the desperate need for a secular materialist establishment to find icons of evolution to venerate, Bloomberg-style - and it won't be their fault if they don't get a bunch more bogus relics.

My instinct about what went wrong is this: Popular media consider themselves gatekeepers when it comes to creating a craze, and they resent scientists, like the Ida team, who usurp their time-honoured right. Hence their swift revenge.

Also just up at The Post-Darwinist:

Darwinism and pop culture: Attempts to pretend that Darwin did not extend his theory to human society

Francis Collins: The Good News guy faces tough questions now

Darwinism and popular culture: Attacking Collins hurts science, Chris Mooney argues

Uncommon Descent Contest 6 winner announced: Why waste a crisis, especially in genomics?

Extinction: A 62-million-yearitch?

Enforcement of Textbook Orthodoxy Annals: Xist Gene X-ed

So when is Harlequin going to come out with their Neanderthal romance series?

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).

Popular science magazines, television programmes and many educational resources convey the message that birds are descendants of the dinosaurs. Every year brings new evidence from the Jehol Biota of northeastern China that is claimed to strengthen the scientific case. Feathered dinosaurs have started to adorn the pages of National Geographic and elsewhere. A lavishly illustrated book with the title Feathered Dinosaurs has been published recently by Oxford University Press. For many the issue is settled: any dissent is regarded as inexcusable. So it is noteworthy that a leading dissenter, Alan Feduccia (from the Department of Biology, University of North Carolina), has reviewed the book in Trends in Ecology & Evolution.

A picture is worth a thousand words - but is it true? (source here)

As many are aware, the Jehol Biota includes avian fossils, but these have not gained the headlines. Proto-feathers and dino-birds have been centre stage. Feduccia notes:

"New tantalizing material has resulted in unprecedented understanding of the early avian radiation, but has also provided a bonanza for paleontological speculation and controversy."

After a few complimentary words, Feduccia switches on critical analysis mode. He points out that the selective reading of evidence, together with ignoring of counter evidence, has led to an imaginary world masquerading as science.

"Although Long and Schouten promote the orthodoxy of 'feathered dinosaurs', compelling evidence for any proto-feathers in these fossils has always been lacking, and new evidence shows that the filamentous fibers on the small 'feathered dinosaur' Sinosauropteryx represented a complex mesh work of supportive skin collagen fibers; and the body outline on the specimens encloses the fibers. Furthermore, new evidence suggests that feathered microraptors and other groups of plumed maniraptorans are derivatives of the early avian radiation that produced an aviary at all stages of flight and flightlessness."
"The small theropod Compsognathus, 'compys' of Jurassic Park, is depicted with a covering of down-like proto-feathers, and modeled after the roadrunner; it is given an expanded throat sac 'critical for temperature regulation' and a pattern of small spots and bars for camouflage. Yet, there is no evidence for any type of feathers in the 'compys' (and, in fact, evidence to the contrary) or for endothermy; unfortunately, no references are provided in the text to papers marshalling evidence contrary to the dogma of feathered dinosaurs, part of an alarming trend in paleontology towards censorship by lack of citation."

Feduccia considers that history is repeating itself. In the 1860s, "Thomas Huxley envisioned a dinosaurian origin of birds via the flightless ratites" but was effectively rebuffed by Richard Owen who pointed out that the ratites were derived forms, with pedomorphic traits. This was confirmed in 1956, in the work of Gavin de Beer.

"[Owen's] statement should also provide a cautionary note for advocates of today's bird origin orthodoxy, which, among myriad problems, calls for all the sophisticated avian aerodynamic flight architecture to have evolved as exaptations, in earth-bound theropod dinosaurs: '. . . science will accept the view of the Dodo as a degenerate Dove rather than as an advanced Dinothere.'"

The closing paragraph returns to an appreciation of the book, and ends with a sentiment that will be shared by many:

"Feathered Dinosaurs is, despite my reservations on interpretation, a beautiful book, and the life poses of the Mesozoic menagerie are dazzling. The 'Fantasia' of feathered theropods aside, depictions of the Early Cretaceous birds are truly exceptional, the best to date. I particularly recommend the images of the flightless oviraptorosaurs. Hopefully, this book will help lead a new generation of students to go beyond the current unchallengeable orthodoxy of feathered dinosaurs to unravel the long-kept secrets of the Mesozoic."

A colorful mesozoic menagerie
Alan Feduccia
Trends in Ecology & Evolution, 24(8), August 2009, 415-416 | doi:10.1016/j.tree.2009.03.002

Review of:
Feathered Dinosaurs: The Origin of Birds by John Long, illustrated by Peter Schouten. Oxford University, Press. 2009. hbk (280 pages) ISBN 978 0 19 537266 3

See also:

Tyler, D.J. Dino skin shows no trace of protofeathers, ARN literature Blog (11 January 2008)

by Denyse O'Leary
ARN correspondent

Here's my Mercator.Net story on Francis Collins as new NIH head:

President Obama has chosen an evangelical Christian as the new head of the National Institutes of Health. He is coming under fire from both sides of the culture wars.

[ ... ]

Of course, his advocacy of faith as a public scientist has received mixed reviews, to the point of attracting histrionics about looming "theocracy."

But now that Collins faces confirmation hearings before the Senate, the focus will shift from his persona to his view on issues relevant to his new job. He seems much more relaxed about abortion and human embryonic stem cell research than the average evangelical leader, so it will be interesting to see if he attracts any flak on that account.

Go here for more.

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 was the question:

Here's On the Epistemological Crisis in Genomics by Edward R Dougherty, which moved in Current Genomics, April 2008.

Abstract

There is an epistemological crisis in genomics. At issue is what constitutes scientific knowledge in genomic science, or systems biology in general. Does this crisis require a new perspective on knowledge heretofore absent from science or is it merely a matter of interpreting new scientific developments in an existing epistemological framework? This paper discusses the manner in which the experimental method, as developed and understood over recent centuries, leads naturally to a scientific epistemology grounded in an experimental-mathematical duality. It places genomics into this epistemological framework and examines the current situation in genomics. Meaning and the constitution of scientific knowledge are key concerns for genomics, and the nature of the epistemological crisis in genomics depends on how these are understood.

He kvetched,

The rules of the scientific game are not being followed. Given the historical empirical emphasis of biology and the large number of ingenious experiments that have moved the field, one might suspect that the major epistemological problems would lie with mathematics, but this is not the case. While there certainly needs to be more care paid to mathematical modeling, the major problem lies on the experimental side of the mathematical-experimental scientific duality. High-throughput technologies such as gene-expression microarrays have lead to the accumulation of massive amounts of data, orders of magnitude in excess to what has heretofore been conceivable. But the accumulation of data does not constitute science, nor does the a postiori rational analysis of data.

What's happened since? Another black hole?

Contest question, for a free copy of Expelled?: What rules of science are relevant for genomics. Are they being followed?

This one didn't attract a lot of entries and they were all from the same person. Principally, I suppose, that is because many people interested in genomics react to the "crisis" the way I reacted to a recent claim about a "crisis" in cosmology around gravity. To most of us, a crisis is when you lock yourself out of the house and see through the window that the dog has tipped the candlabra and set fire to the carpet. If you don't do something useful right this minute, you soon won't have a house or a dog.

Okay, and the winner is, by acclamation, Lock, for 2:

From Edward R Dougherty: "But the accumulation of data does not constitute science, nor does the a postiori rational analysis of data."

I assume he uses an a priori framework with which to make that judgement?

Of course he does. And rightly so. And that lens is the one science should be using (and does ... but not consistently).

Here is the insanity ... science uses this lens religiously, except that when doing so the evidence points to religious conclusions.

Denyse, you asked: "What rules of science are relevant for genomics?"

Available empirical data examined consistently through the lens of the 'law of non-contradiction'.

"Are they being followed?"

Really now ... is that question necessary?

While Lock says he already owns Expelled, it may make a handy gift item, so he needs to be in touch with me at oleary@sympatico.ca, to arrange shipment of his prize.

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

In "Why microbes are smarter than you thought," Michael Marshall at New Scientist (June 30, 2009) intros and links many stories of the amazing ways microbes manage without brains and can even appear to think ( well, not really, but ... ). Here's my favourite, but go here for more:

Many single-celled organisms can work out how many other bacteria of their own species, are in their vicinity - an ability known as "quorum sensing".

Each individual bacterium releases a small amount of a chemical into the surrounding area - a chemical that it can detect through receptors on its outer wall. If there are lots of other bacteria around, all releasing the same chemical, levels can reach a critical point and trigger a change in behaviour.

Pathogenic (disease-causing) bacteria often use quorum sensing to decide when to launch an attack on their host. Once they have amassed in sufficient numbers to overwhelm the immune system, they collectively launch an assault on the body. Jamming their signals might provide us with a way to fight back.

How about a culturally (so to speak) adapted version of "Suicide is Painless"?

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

In "The Quantum Life" (Physcisworld.com, July 1, 2009), Paul Davies, astrobiologist and director of BEYOND: Center for Fundamental Concepts in Science at Arizona State University, examines the case for quantum mechanics kickstarting the origin of life (Q-life):

But why should quantum mechanics be relevant to life, beyond explaining the basic structure and interaction of molecules? One general argument is that quantum effects can serve to facilitate processes that are either slow or impossible according to classical physics. Physicists are familiar with the fact that discreteness, quantum tunnelling, superposition and entanglement produce novel and unexpected phenomena. Life has had three and a half billion years to solve problems and optimize efficiency. If quantum mechanics can enhance its performance, or open up new possibilities, it is likely that life will have discovered the fact and exploited the opportunities. Given that the basic processes of biology take place at a molecular level, harnessing quantum effects does not seem a priori implausible.

It's intriguing, the way he attributes to "life" and, elsewhere, "evolution" the attributes of a planning and thinking intelligent agent.

He almost persuades himself but

Although at least some of these examples add up to a prima facie case for quantum mechanics playing a role in biology, they all confront a serious and fundamental problem. Effects like coherence, entanglement and superposition can be maintained only if the quantum system avoids decoherence caused by interactions with its environment. In the presence of environmental noise, the delicate phase relationships that characterize quantum effects get scrambled, turning pure quantum states into mixtures and in effect marking a transition from quantum to classical behaviour. Only so long as decoherence can be kept at bay will explicitly quantum effects persist. The claims of quantum biology therefore stand or fall on the precise decoherence timescale. If a system decoheres too fast, then it will classicalize before anything of biochemical or biological interest happens.

. So we are now into the business of persuading ourselves that, based on a few studies, that would not be the normal fate of Q-life. And in the end,

How would Q-life evolve into familiar chemical life? A possible scenario is that organic molecules were commandeered by Q-life as more robust back-up information storage. A good analogy is a computer. The processor is incredibly small and fast, but delicate: switch off the computer and the data are lost. Hence computers use hard disks to back up and store the digital information. Hard disks are relatively enormous and extremely slow, but they are robust and reliable, and they retain their information under a wide range of environmental insults. Organic life could have started as the slow-but-reliable "hard-disk" of Q-life. Because of its greater versatility and toughness, it was eventually able to literally "take on a life of its own", disconnect from its Q-life progenitor and spread to less-specialized and restrictive environments - such as Earth. Our planet accretes a continual rain of interstellar grains and cometary dust, so delivery is no problem. As to the fate of Q-life, it would unfortunately be completely destroyed by entry into the Earth's atmosphere.

All this reminds me of a beautiful Edith Wharton short story, "Pomegranate Seed", on line here, and not wrecked by some clueless ethnicity/class/gender-driven analysis. The point of the story is that it looks as though a ghost drove a story character to suicide - but there is no actual evidence. (If you ever think of writing a ghost story, take Wharton as your guide. What make her stories work is: No one can prove anything happened, apart from catastrophic emotional impacts, and yet everyone is sure that something happened.)

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).

According to C.R.C. Paul, "the search for gradual change in the fossil record is a cautionary tale". The instigator of the search was, of course, Charles Darwin, whose theory predicted that a pattern of small incremental changes would be found in the fossil record as well as in contemporary life forms. It is well known that Darwin did not find what he was looking for. On the Origin of Species included a whole chapter (X) to explain how the theory could be reconciled with the fossil record, using the argument of its "extreme imperfection". This argument held sway for over 100 years. Palaeontologists adopted Darwin's explanation, presenting the few cases of gradual change that they did manage to identify as a great achievement.

[Paul refers to the] "belief that the fossil record should contain abundant evidence of gradual evolutionary (i.e. morphological) change, which we all accepted (myself included) until Eldredge and Gould (1972) proposed the alternative punctuated equilibrium model."

The fossil record provides an important test for Darwinian gradualism - but what weight can we give to the evidence we find? (Source here)

During this 100 year period, some examples of "genuine evolutionary trends" were reported but, Paul points out, "there are far too few of them". Even the classic trend examples "do not bear close scrutiny". The cases of Micraster, Zaphrentis and Gryphaea are not as robust as once was thought.

"[F]or over 100 years palaeontologists sought examples of evolutionary trends in the fossil record and yet they remain stubbornly rare. In contrast, no one reported examples of stasis during this interval. We did not even have a name for lack of morphological change - it was regarded as lack of information."

So strong was the focus on gradual change that few found morphological stasis interesting. It was not even deemed worthy of reporting. Published literature became biased in favour of gradual transformation. A major characteristic of the fossil record - stasis - was neglected until Eldredge and Gould launched Punctuated Equilibrium in 1972.

"In over a century the very rare examples that were found were accepted as evidence of a general pattern in the fossil record, whereas the more abundant patterns, unbiased random walks and stasis, were ignored. The analyses of Paul (1999) and Hunt (2006, 2007) are very different, yet both agree that trends are rare in the fossil record. With the benefit of hindsight it seems amazing that it took so long for us to recognize that the vast majority of fossil species do not change significantly throughout their stratigraphical ranges."

Paul draws attention to the analytical approach of Hunt, whose methods are described as "robust".

"Hunt (2007) analysed the frequency of the three patterns in a large sample (251 characters in 51 taxa), covering benthonic and planktonic microfossils and macrofossils (mammals, fish and molluscs), as well as size, shape and other characters. He found that in only 13 characters (5.2%) was directional change (trends) best supported, whereas unbiased random walks and stasis were best supported in 123 (49%) and 115 (45.8%) cases. Hunt commented that since there was an historical bias in favour of trends, 5% was probably an overestimate."

The remainder of Paul's paper is concerned with the probability of fossilisation. He concludes that most animals with skeletons are likely to have become fossilised. Impoverishment of the record is linked to active erosion of fossiliferous strata.

Darwin regarded the fossil evidence as potentially providing a valid test of his theory. He predicted gradual transformation. Since he did not observe it, he invoked "extreme imperfection" to preserve the theory. This explanation is no longer credible. The fossil record must now stand as evidence that refutes Darwinian gradualism. Those examples of gradual morphological change represent, at best, 5% of observed trends, but it is possible they are simply extreme cases of random walk trajectories. In a eureka moment of clear thinking, Stephen Jay Gould declared that Neodarwinism "as a general proposition, is effectively dead, despite its persistence as textbook orthodoxy". Those who represent analyses like this as religiously motivated and out of bounds for consideration in school science lessons are doing a great disservice to education and to the students they claim to be defending.

The Fidelity of The Fossil Record: The Improbability of Preservation
C. R. C. Paul
Palaeontology, May 2009, 52(3), 485-489 | doi 10.1111/j.1475-4983.2009.00872.x

Abstract: The fidelity of the fossil record reflects how accurately it preserves the history of life. Since Darwin's time any mismatch between our theories and the fossil record has been attributed to the imperfections of the record. For over a century scarcity of gradual evolutionary trends was explained in this way until the punctuated equilibrium model was proposed. A null hypothesis that all morphological patterns in the fossil record are unbiased random walks can be rejected because it predicts far more apparent trends than exist. Current best estimates suggest that trends occur in at most 5% of characters. When an organism dies either it becomes fossilized or it doesn't. To be confident a species has not been preserved the probability against preservation must be significantly larger than the total number of individuals of that species that ever existed. For skeletized species preservation was the norm not the exception. Nevertheless, fossils must then avoid subsequent destruction and be discovered to be useful.

See also:

Gould, S.J. The Structure of Evolutionary Theory, Harvard University Press, 2002, page 1004 (for reflective comments on the effective death of Neodarwinism quote).

Hunt, G., 2007. The relative importance of directional change, random walks, and stasis in the evolution of fossil lineages. Proceedings of the National Academy of Sciences of the United States of America, 104(47), (November 20), 18404-18408 | doi: 10.1073/pnas.0704088104

Synopsis Of The Second Chapter Of Nature's IQ By Balazs Hornyanszky and Istvan Tasi
ISBN 978-0-9817273-0-1
By Robert Deyes
ARN Correspondent

Defense, Disguise, Perception is the descriptive title that Hornyanszky and Tasi have chosen for the second chapter of their book Nature's IQ. And the delivery of the facts is as convincing and thought-provoking as ever. Coupled with its vivid illustrations, the chapter lays out a set of arguments that are easily accessible to the expert and non-expert reader alike. The underlying principle of their text is simple- intelligent design lies at the heart of many of nature's phenomena.

As Hornyanszky and Tasi show from the onset, the natural world is replete with innovative defense mechanisms that afford potential prey with the protection they need. For many of those doing the eating, an aversion towards highly toxic prey such as the poisonous sea snake is one that is deeply ingrained into their instinctive fabric. It has to be. After all, one bite-sized morsel taken out of a creature such as a sea snake would be lethal to most prospective predators. The fire-bellied toad cautions all who might dare nibble at its poisonous flanks by flipping onto its back and displaying the red and black markings on its belly.

Warning-style markings are of course common-place throughout nature as are rapidly deployed disguises or masquerades that ward off would-be attackers. Many a high school student will learn about eye spots on moth and butterfly wings, designed as they are to give the impression that a much larger, potentially dangerous beast lies waiting. Bearers of such disguises often times exhibit associated behaviors only showing their disguises when threatened. The copper-band butterfly fish has the astonishing ability to move backwards so as to make the eye spot on its large tail look as if it really is at the front.

In the case of the American four-eyed frog, white and black nodes on its back stand out as realistic three-dimensional imitations of much larger mammalian and cephalopod eyes. These frogs exhibit the extraordinary ability to turn their backs to wherever danger is lurking, lifting their hind legs into a position that makes their fake eyes look all the more face-like and therefore less enticing for the hungry onlooker. For evolution pundits this theatrical act defies their version of the story of life since, in the words of Hornyanszky and Tasi "the simultaneous appearance, via chance mutations, of the pseudo-eyes and the knowledge of just what to do at precisely the right moment is, to put it mildly, highly improbable" (p.30).

As artful masters of disguise go, the treehopper Umbonia spinosa takes some beating. Making the most out of its thorn-like dorsal protrusion, this particular insect instinctively flattens its underlying body against the stems of rose bushes to avoid detection. The Atlantic Halibut about which Darwin himself wrote in The Origin Of Species, maintains its anonymity by also lying flat, camouflaged against the sand covered sea bottom. How would either of these creatures know that to lie still in their respective environments is the best way to eschew the grasp of a predator?

For these and all their earlier examples, Hornyanszky's and Tasi's intelligent design inference shines through as they reason in favor of irreducibly complex, genetically inherited systems that require both phenotypic and behavioral traits in order to achieve their respective functions. Knowledge of the most appropriate behaviors is not something that is learned but rather is genetically hard-wired into these creatures from birth. In order for such behaviors to be effective, they must have appeared in tandem with the phenotypic traits with which they are so evidently associated. Therein lies the designed IQ that we observe in many fauna.

Horyanszki's and Tasi's superb treatise is a 'must read' for all who are interested in the ongoing debates over the origin of animal behaviors. It is bound to shake the unquestioned acceptance of the Darwinian story of life that today pervades many a field of science.

For more information and to order Nature's IQ go to http://www.arn.org/arnproducts/php/book_show_item.php?id=129

Sean P. Harris, for the Austin Independent Examiner, reported that Governor Rick Perry announced his appointment of board member Gail Lowe to replace Don McLeroy as chairperson of the Texas State Board of Education. Gail Lowe is a Lampasas newspaper editor and has been a member of the State Board of Education since 2002. She is also a proponent of Intelligent Design.

More...

In the battle over how to teach evolution in public schools, Thomas Jefferson's demand for a "separation between church and state" has been cited countless times. Many argue that the controversial alternative to Darwinian evolution, intelligent design, is an exclusively religious idea and therefore cannot be discussed under the Constitution. By invoking Jefferson's principle of separation, many critics of intelligent design assume that this visionary Founding Father would agree with them. But would he?

More...

In the LA Times, Charlotte Allen gives her take on the New Atheists.

"My problem with atheists is their tiresome - and way old - insistence that they are being oppressed and their fixation with the fine points of Christianity. What - did their Sunday school teachers flog their behinds with a Bible when they were kids?"

"Read Dawkins, or Hitchens, or the works of fellow atheists Sam Harris ("The End of Faith") and Daniel Dennett ("Breaking the Spell"), or visit an atheist website or blog (there are zillions of them, bearing such titles as "God Is for Suckers," "God Is Imaginary" and "God Is Pretend"), and your eyes will glaze over as you peruse - again and again - the obsessively tiny range of topics around which atheists circle like water in a drain."

More...

Foraminifera are protozoans with a hard calcareous shell. There are two major groups: benthic and planktic. Benthic organisms live on the sea floor whereas planktic are buoyant and live in the upper water layer as part of the plankton. Their shells, although mostly microscopic, are much studied because they are found in profusion in oceanic sediments. The geological history of the benthic forams goes back to the Early Cambrian, but planktic species first appear in Mid-Jurassic sediments.

"Traditionally, all planktic foraminifera have been seen as monophyletic [Suborder Globigerinina], descended from a single Early-Middle Jurassic ancestor, similar to the monophyletic origins of other planktic groups."

Streptochilus globigerus (credit: Kate Darling, source here)

Six years ago, Hart and colleagues reviewed evidence bearing on the ancestor of the planktic forams and suggested that its evolution was triggered by an oceanic anoxic event in the Early Jurassic. They introduce their paper with an acknowledgement of the problems:

"In a recent review of the earliest planktic Foraminifera (Globigerinina) Simmons et al. (1997) report that the origins of the group are '. . . still shrouded in uncertainty'."

The new research by Darling and colleagues has found that a planktic species, Streptochilus globigerus, is genetically the same as a benthic species, Bolivina variabilis. This is the first time such a lifestyle has been recognised in foraminifera. The technical term is tychopelagic.

"The word "tychopelagic" is used to describe organisms that usually live as benthos but can survive and grow in fairly large numbers as plankton and may be advected well offshore into open ocean assemblages. Such a lifestyle is known from diatoms, but until now has never been documented for foraminifera."

The implications are many. First, the sharp line drawn between benthic and planktic forams needs to be erased. The issue of buoyancy suddenly becomes secondary. The previous stance - that planktic forams were a radical evolutionary innovation - needs to be discarded. "Interestingly, buoyancy is generally assumed to be one of the major constraining evolutionary traits on the passage from benthos to plankton."

Secondly, the monophyletic radiation of planktic forams, with examples of both punctuated and gradual changes, needs to be re-examined. If tychopelagic forams are common, everything goes into the melting pot.

"The Cenozoic planktic foraminiferal phylogeny of microperforates, the group containing biserial and triserial forms, has generally presented taxonomists with problems. Many of these genera and species show discontinuous stratigraphic records, making ancestor-descendant patterns difficult to reconstruct. This could be the result of a lack of observation of the small forms, in a size fraction that commonly is not included in study. In our view, however, such ancestor-descendant relations simply do not exist."
[. . .]
"Appearances of biserial and triserial planktic forms in the geological record should therefore not be considered as necessarily discrete punctuated evolutionary events but as a series of excursions of expatriated tychopelagic microperforates into the planktic domain."

Thirdly, the concept of recolonisation has been underplayed by evolutionary biologists. They get as far as colonisation, but perceive this as a process of gradual adaptation under the influence of natural selection. They have given little thought to inbuilt capabilities of rapid adaptation to new environments - perhaps because this could be understood as a designed capability. Nevertheless, the authors of the new research recognise the ecological advantages possessed by tychopelagic organisms.

"The ability to survive in both planktic and benthic habitats should be seen as an extraordinary ecological adaptation for long-term survival. After mass extinctions in the plankton, e.g., as caused by bolide impacts and oceanic anoxic events, tychopelagic species are able to repopulate the pelagic realm and evolve into purely planktic forms."
[. . .]
"We thus argue that radiation and repopulation of the empty niche in the plankton after the end Cretaceous mass extinction may at least in part have occurred from benthic tychopelagic species rather than from nerito-planktic ones."

This research provides another angle on the hypothesis outlined in a previous blog that the fossil record has more to do with ecology and the colonisation/recolonisation of habitats than it has to do with evolutionary transformation.

Surviving mass extinction by bridging the benthic/planktic divide
Kate F. Darling, Ellen Thomas, Simone A. Kasemann, Heidi A. Seears, Christopher W. Smart and Christopher M. Wade
Proceedings of the National Academy of Sciences USA, online before print July 2, 2009, doi: 10.1073/pnas.0902827106 (abstract)

Abstract: Evolution of planktic organisms from benthic ancestors is commonly thought to represent unidirectional expansion into new ecological domains, possibly only once per clade. For foraminifera, this evolutionary expansion occurred in the Early-Middle Jurassic, and all living and extinct planktic foraminifera have been placed within 1 clade, the Suborder Globigerinina. The subsequent radiation of planktic foraminifera in the Jurassic and Cretaceous resulted in highly diverse assemblages, which suffered mass extinction at the end of the Cretaceous, leaving an impoverished assemblage dominated by microperforate triserial and biserial forms. The few survivor species radiated to form diverse assemblages once again in the Cenozoic. There have, however, long been doubts regarding the monophyletic origin of planktic foraminifera. We present surprising but conclusive genetic evidence that the Recent biserial planktic Streptochilus globigerus belongs to the same biological species as the benthic Bolivina variabilis, and geochemical evidence that this ecologically flexible species actively grows within the open-ocean surface waters, thus occupying both planktic and benthic domains. Such a lifestyle (tychopelagic) had not been recognized as adapted by foraminifera. Tychopelagic are endowed with great ecological advantage, enabling rapid recolonization of the extinction-susceptible pelagic domain from the benthos. We argue that the existence of such forms must be considered in resolving foraminiferal phylogeny.

See also:

Tiny marine organism lives double life to survive extinction, Planet Earth Online, 1 July 2009.

Hart, M.B., Hylton, M.D., Oxford, M.J., Price, G.D., Hudson W. and Smart, C.W., The search for the origin of the planktic Foraminifera, Journal of the Geological Society, 160, 2003, 341-343.

by Denyse O'Leary
ARN correspondent

Everybody seems to be taking a whack at evolutionary psychology these days, and David Brooks gets in his shot in "Human Nature Today" (New York Times, June 26, 2009).

Evolutionary psychology has had a good run. But now there is growing pushback. Sharon Begley has a rollicking, if slightly overdrawn, takedown in the current Newsweek. And "Spent" is a sign that the theory is being used to try to explain more than it can bear.

The first problem is that far from being preprogrammed with a series of hardwired mental modules, as the E.P. types assert, our brains are fluid and plastic. We're learning that evolution can be a more rapid process than we thought. It doesn't take hundreds of thousands of years to produce genetic alterations.

Moreover, we've evolved to adapt to diverse environments. Different circumstances can selectively activate different genetic potentials. Individual behavior can vary wildly from one context to another. An arrogant bully on the playground may be meek in math class. People have kaleidoscopic thinking styles and use different cognitive strategies to solve the same sorts of problems.

Evolutionary psychology leaves the impression that human nature was carved a hundred thousand years ago, and then history sort of stopped. But human nature adapts to the continual flow of information—adjusting to the ancient information contained in genes and the current information contained in today’s news in a continuous, idiosyncratic blend.

Sharon Begley's account, in my view, was not overdrawn, it was overdue. Re "Spent" - this sounds-like forgettable book takes evolutionary psychology to the shopping mall to show what we are genetically "hardwired" to buy and why, according to six (count 'em) big traits.

The book might have made a bigger splash before the recession hit. To listen to local retailers wail, many people just now have hardwired their wallets to their pockets. But surely Pleistocene cave men did the same thing, so there must be a module for that too somewhere in there ...

Essentially, two things killed evolutionary psychology: Neuroplasticity, as Brooks notes, and Occam's Razor. It's never been clear that EPs' selfish genes and brain modules ever existed, or ever needed to. Evolutionary psychologists keep looking for things that their current interpretation of human evolution can explain - which is to say, anything and everything, provided speculation is freely allowed.

Also just up at The Mindful Hack:

Neuroscience: The default brain network -humming along while we're idle

Evolutionary psychology: David Brooks on the growing pushback

Human evolution: Oldest hand-crafted flute so far is 35,000 years old

Meditation: Research scientist learns benefits personally

Neuroscience: Reducing minds to brains a deep dark rabbit hole?

Book review and online vids:The Mind and the Brain

Animal minds: Humans project guilt feelings onto their dogs?

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).

More and more people are realising that the living world is like a treasure trove packed full with engineering marvels. The agenda of biomimetics is to actively research the potential of applications inspired by animals and plants. The human body supplies some of these design ideas, and the one considered in this blog concerns the inner ear, or cochlea. Undoubtedly, researching organs like this leads to a new appreciation of the sophistication of biological systems.

Sound is collected in the outer ear, travels through the ossicles (or bones) of the middle ear and delivers pressure waves through the oval window of the cochlea (the inner ear) (Source here)

The people involved in the newly published work describe the cochlea as "an amazing sensory instrument that transforms sound frequencies into spatially and temporally-varying excitation patterns of the auditory nerve". It is particularly interesting to electrical engineers because: "It performs this task over a wide range of input frequencies and amplitudes using very little power. In humans, the approximate values of these performance metrics are three decades, 120 dB, and 14 W, respectively". The mechanism is described thus:

"The cochlea is a hydro-mechanical system; incoming sounds set up travelling waves on the basilar membrane (BM) and in the fluids that surround it. The properties of the BM scale approximately exponentially with position: The membrane gradually becomes wider and less stiff, and resonates at lower frequencies. Thus, high frequency sounds excite responses towards the beginning, or basal part, of the cochlea, while low frequency sounds excite responses towards the end, or apical part. In other words, the cochlea uses a frequency-to-space transformation to perform audio spectral analysis."

There is broader medical interest in any research with potential relevance to problems of deafness. Cochlear implants have been available for some years. They give some benefit to people whose hearing is impaired, but do not restore normal hearing. Electrodes are implanted to stimulate the the cochlear nerves using electrical impulses generated from sound reaching the subject. For an brief overview of the history of cochlea implants, go here. For more technical information, a paper by Kissiah (2007) is helpful.

However, medical applications are beyond the scope of the reported research. The researchers have their sights on constructing an electronic cochlea - not implanting electrodes but making a complete system. They are interested in radio-frequency devices, not audio-frequency applications. Their goal is to achieve a high speed of operation, an ability to handle a wide range of input frequencies and a reduced power requirement in use.

"The human ear is a very good spectrum analyzer," said Rahul Sarpeshkar, a professor at MIT who co-authored the paper [. . .]. "We copied some of the tricks the ear does, and mapped those onto electronics."
[. . .] To detect electromagnetic waves instead of pressure waves the MIT scientists used circuits, in place of cilia. Starting on the outside edge of the 1.5-mm by 3-mm-chip are tiny squares, each one corresponding to a different size radio wave.
As they spiral into the center, the squares become larger and larger. The outer spiral detects the highest energy, shortest frequency waves, while the center circuits detect less energetic, longer frequency waves.

The team have produced an "electromagnetic ear". This detects a very wide range of frequencies with no more energy than is used by a typical cell phone. What they have done is to combine an analogue spectrum analyser with digital signal processing. This reduces the power requirement to about 1% of a purely digital system.

"A simple cell phone takes 300 millivolts to detect one carrier wave," Sarpeshkar said. "We can do all 50 carrier frequencies with 300 millivolts." Other devices do exist that can examine a range of radio frequencies. They just require much more power to do so. The low power usage of the electromagnetic ear means it would be ideal for portable electronic devices.

One assessment of this work is as follows: "People have tried to construct electronic cochlea before, but this is the first demonstration that imitates the amplification we think happens in the ear to produce a device that works." The team is now working on RF transmission as well as signal analysis, because this has the best potential for commercial exploitation.

Since the discovery of DNA, it has been increasingly popular to refer to life as "digital". Darwinists, particularly, have latched onto this concept, because their mechanism (incremental changes filtered by natural selection) can be understood in terms of digital mutations. Artificial life software like Avida is 100% digital, and enthusiasts consider that their digital world gives them the power to experiment in an unprecedented way. One researcher, Richard Lenski, is quoted thus:

"It's also the power to manipulate almost any variable one can imagine, to measure variables with absolute precision, to store information that then allows one to trace back a complex chain of events, and to take evolved organisms and subject them to new sorts of analyses that one might not even have anticipated when first collecting the data."

But what if life is both digital and analogue? What if analogue information is independent of digital information? These are questions that Darwinians do not ask because they stretch beyond the horizon of the gradualist paradigm. What if analogue systems point to complex specified information that cannot be modified gradually without ruining functionality? The case of the RF silicon cochlea is significant. This device was only developed by the focused effort of intelligent design engineers. When we consider the human cochlea, we need to ask the question whether it could have been developed by digital tinkering or whether the sophisticated design principles embedded in the physical structure of the organ point to an explanation involving intelligent agency.

A Bio-Inspired Active Radio-Frequency Silicon Cochlea
Mandal, S.; Zhak, S. M.; Sarpeshkar, R.
IEEE Journal of Solid-State Circuits, June 2009, 44(6), 1814-1828 | doi: 10.1109/JSSC.2009.2020465

Abstract: Fast wideband spectrum analysis is expensive in power and hardware resources. We show that the spectrum-analysis architecture used by the biological cochlea is extremely efficient: analysis time, power and hardware usage all scale linearly with N, the number of output frequency bins, versus Nlog(N) for the Fast Fourier Transform. We also demonstrate two on-chip radio frequency (RF) spectrum analyzers inspired by the cochlea. [. . .] Our work, which delivers insight into the efficiency of analog computation in the ear, may be useful in the front ends of ultra-wideband radio systems for fast, power-efficient spectral decomposition and analysis. Our novel rational cochlear transfer functions with zeros also enable improved audio silicon cochlea designs with sharper rolloff slopes and lower group delay than prior all-pole versions

See also:

Bland, E. Human ear inspires universal radio antenna, Discovery Channel (June 8, 2009)

Is Life Analog or Digital? A Question for Edge discussion group from Freeman Dyson (2001)

by Denyse O'Leary
ARN correspondent

In "How to map the multiverse" (04 May 2009), Anil Ananthaswamy explains:

Greene's transformation is emblematic of a profound change among the majority of physicists. Until recently, many were reluctant to accept this idea of the "multiverse", or were even belligerent towards it. However, recent progress in both cosmology and string theory is bringing about a major shift in thinking. Gone is the grudging acceptance or outright loathing of the multiverse. Instead, physicists are starting to look at ways of working with it, and maybe even trying to prove its existence.

If such ventures succeed, our universe will go the way of Earth - from seeming to be the centre of everything to being exposed as just a backwater in a far vaster cosmos. And just as we are unable to deduce certain aspects of Earth from first principles - such as its radius or distance from the sun - we will have to accept that some things about our universe are a random accident, inexplicable except in the context of the multiverse.

Also

However, if our universe is part of a multiverse then we can ascribe the value of the cosmological constant to an accident. The same goes for other aspects of our universe, such as the mass of the electron. The idea is simply that each universe's laws of physics and fundamental constants are randomly determined, and we just happen to live in one where these are suited for life. "If not for the multiverse, you would have these unsolved problems at every corner," says Linde.

Let's see. We don't need to prove fine tuning. It's just there. But there's no evidence for the multiverse; it is an attractive idea because it makes our current cosmological values and fine tuning appear random. I love this line: " ... starting to look at ways of working with it, and maybe even trying to prove its existence".

Question: How fit are people in this state of mind to evaluate what they are seeing?

Also just up at Colliding Universes, my blog about competing materialist and non-materialist theories about our universe:

Cosmology: Crisis of the month - gravitation

Podcasts in the intelligent design controversy: Origin of life (with Charles Garner)

Origin of life: This time it's salt water

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

In "Science, Spirituality, and Some Mismatched Socks" (Wall Street Journal, May 5, 2009)", Gautam Naik explains how "researchers turn up evidence of 'spooky' quantum behavior and put it to work in encryption and philosophy.":

Last year, Dr. Gisin and colleagues at Geneva University described how they had entangled a pair of photons in their lab. They then fired them, along fiber-optic cables of exactly equal length, to two Swiss villages some 11 miles apart. During the journey, when one photon switched to a slightly higher energy level, its twin instantly switched to a slightly lower one. But the sum of the energies stayed constant, proving that the photons remained entangled. More important, the team couldn't detect any time difference in the changes. "If there was any communication, it would have to have been at least 10,000 times the speed of light," says Dr. Gisin. "Because this is such an unlikely speed, the conclusion is there couldn't have been communication and so there is non-locality."

Right, so there is no common-sense explanation of quantum mechanics. About the encryption?

Some researchers are using the uncertain state of photons to solve real-world problems. When encrypting sensitive data such as a bank transfer, both the sending party and the receiving party must have the same key. The sender needs the key to hide the message and the receiver to reveal it. Since it isn't always practical to exchange keys in person, the key must be sent electronically, too. This means the key (and the messages) may be intercepted and read by an eavesdropper. An electronic key is usually written in the computer binary code of "ones" and "zeros." Quantum physics permits a more sophisticated approach. The same "ones" and "zeros" can now be encoded by using the properties of photons, like spin. If someone intercepts a photon-based message, the spins change. The receiver then knows the key has been compromised. MagiQ Technologies Inc. of Cambridge, Mass., refreshes its quantum keys as often as 100 times a second during a transmission, making it extremely hard to break. It sells its technology to banks and companies. Dr. Gisin is a founder of ID Quantique SA in Switzerland. The company's similar encryption tool is used by online lottery and poker firms to safely communicate winning numbers and winning hands. Votes cast in a recent Swiss federal election were sent in a similar way.

We live in a mysterious world, where uncertainty is better for security than certainty - but at the quantum level only. The person who left his keys stuck in the front door all night is one dumb bunny and can be grateful that most thieves wouldn't expect to get so lucky, which is why he was the first person to discover the problem in the morning.

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

The guy had successfully hidden his identity for about five years, while posting all kinds of sexually charged abuse to the Internet about many people, including me. But now we know.

Wendy Sullivan, the Girl on the Right, has officially found out who the mysterious Canadian Cynic is. Here is stuff he has said about me. He is Robert PJ Day. Small business owner. Computer genius. Well-read book nerd. Anti-creationist debater

A Linux genius, apparently. [Foul language warning re his posts and any reports on them. ]

Here isthe contest question: Why do so many of Darwinists spout so much filth, hostility, and aimless detraction?

The winner will receive a free copy of Expelled.

Go here for more information, links to the above, and to enter.

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).

Paul Knauth and Martin Kennedy have been studying isotopic signatures in carbonate sediments. Indeed, they have "examined the chemical composition of all known limestones dating from the Neoproterozoic era, which stretched from 1 billion years ago up to the start of the Cambrian." The ratio of carbon-13 to carbon-12 is a frequently measured parameter, because plants preferentially absorb carbon-12. Similarly, freshwater is depleted in oxygen-18, oxygen isotope ratios are also interesting. "So sediments deposited in these conditions have a recognisable carbon-12 to oxygen-18 ratio." Significantly, the authors report that the 'modern' signature for land-derived sediments goes back - not to the Ordovician (where the record of land plants begins) - but to 850 Ma (which is Late Precambrian).

"Knauth says the balance of carbon-12 to oxygen-18 in the limestones is "screaming" that they were laid down in shallow seas that received extensive rainwater run-off from a land surface thick with vegetation."

"Screaming" is a strong word, but data itself does not scream. An interpretation placed on that data, however, can provide a compelling argument. The question to be addressed is whether that argument is strong, or whether the researchers are just shouting.

Was a moss and liverwort filled world responsible for oxygenating the atmosphere? (Source here)

There are several strands for analysis in this research. The first is whether the isotope ratios are best interpreted in the terms suggested. As well as the positive evidence from isotope fractionation, the researchers report finding a sparsely populated area of their data plots - which they named the "forbidden zone."

"If previous interpretations of carbon isotope data were correct, there would be no forbidden zone on these cross plots," Knauth said. "The forbidden zone would be full of Neoproterozoic data."
"These zones show that the isotopic fingerprints in limestone we see today started in the late Precambrian and must have involved the simultaneous influx of rain water that fell on vegetated areas, infiltrated into coastal ground waters and mixed with marine pore fluids. During sea level drops, these coastal mixing zones are dragged over vast geographic regions of the flooded continents of the Neoproterozoic," Knauth said. "Vast areas of limestone can form in these mixed pore fluids."

It will be interesting to find out what others make of this interpretation, but my initial reaction is that the argument is strong. The main objection thus far appears to be the lack of fossil evidence for vegetated land surfaces. This blog proceeds on the basis that the researchers have documented isotopic evidence strongly suggesting vegetated areas in the Neoproterozoic.

The second strand of analysis is concerned with the relationship between the evidence for vegetated land and the Cambrian explosion. The abstract includes the comment: "This facilitated a rise in O2 necessary for the expansion of multicellular life". The paper expands slightly with the words: "The terrestrial expansion of an extensive, simple land biota indicated by the isotope data may thus have been a critical step in the transition from the Precambrian to the Phanerozoic world". The press release accompanying advance publication says that the researchers "believe they have found the trigger for the Cambrian explosion". This, and the Science Daily reports suggest that the problem of the Cambrian Explosion may have been solved. "It was a massive greening of the planet [that] virtually set the table for the later explosion of life through the development of early soil that sequestered carbon, led to the build up of oxygen and allowed higher life forms to evolve". The New Scientist story says that the plants "turned the hitherto barren Earth green, created the first soils and pumped oxygen into the atmosphere, laying the foundations for animals to evolve in the Cambrian explosion that started 542 million years ago".

It has to be said that the Cambrian Explosion needs to be addressed on two fronts: biological and environmental. The new work adds nothing to the conundrums faced by biological science: the emergence of new body plans, complex organs and organelles. What it does do is contribute to the environmental story. If marine animals are to thrive, they need oxygenated waters. Accompanying this is the need for conducive water chemistry, suitable temperatures, appropriate food supplies, etc. Nevertheless, with these elements all present, life will not simply emerge to fill the space! To think this is to make the same mistake as the abiogenesis researchers who seem to think that if the building blocks are assembled, life just happens! The same problem is faced by astrobiologists: they get excited about finding a planet in the habitable zone with water - but this is just the environmental dimension. It provides a necessary but not sufficient condition. Real solutions are only obtained by the generation of complex specified information - which is the hallmark of intelligent design.

If it is the case that biological diversification is triggered by environmental factors, it can be argued that this is an indication of design in the workings of the natural world. Create a suitable environment, and it is filled with living things! Maybe the story of life on Earth is governed by ecology: where conditions are appropriate, the animals and plants that can live in those environments move in to colonise them. Ecology, rather than evolution from primitive ancestors, may be the key to understanding the development of living things.

The late Precambrian greening of the Earth
L. Paul Knauth & Martin J. Kennedy
Nature, 460, 728-732 (6 August 2009) | doi:10.1038/nature08213 (pdf here)

Many aspects of the carbon cycle can be assessed from temporal changes in the 13C/12C ratio of oceanic bicarbonate. [. . .] Here we compile all published oxygen and carbon isotope data for Neoproterozoic marine carbonates, and consider them in terms of processes known to alter the isotopic composition during transformation of the initial precipitate into limestone/dolostone. We show that the combined oxygen and carbon isotope systematics are identical to those of well-understood Phanerozoic examples that lithified in coastal pore fluids, receiving a large groundwater influx of photosynthetic carbon from terrestrial phytomass. Rather than being perturbations to the carbon cycle, widely reported decreases in 13C/12C in Neoproterozoic carbonates are more easily interpreted in the same way as is done for Phanerozoic examples. This influx of terrestrial carbon is not apparent in carbonates older than ~850 Myr, so we infer an explosion of photosynthesizing communities on late Precambrian land surfaces. As a result, biotically enhanced weathering generated carbon-bearing soils on a large scale and their detrital sedimentation sequestered carbon. This facilitated a rise in O2 necessary for the expansion of multicellular life.

When Earth greened over
Explosion of animal life could have been triggered by blanket of vegetation.
Eric Hand
Nature 460, 161 (8 July 2009) | doi:10.1038/460161a

Abstract: A thick, green carpet of photosynthetic life, on the scale of that seen today, exploded across Earth 850 million years ago - much earlier than thought - a new study suggests.

Francis Collins, well known as the genome mapper who sat with President Clinton and others on the White House lawn in 2000, is the new head of National Institutes of Health.

As others have noted, he may be as well known for his recent book, The Language of God, part personal testimony and part explanation of how there need be no conflict between faith and science.

Some are skeptical. David Klinghoffer writes,

Do you ever notice how religious believers are always cited by the media as "devout" precisely when they are equivocating on basic Judeo-Christian moral and theological tenets? Dr. Francis Collins has some startling ideas on abortion. Startling, that is, from an Evangelical Christian who is Obama's choice to head up the National Institutes of Health. He's a favorite church speaker with Evangelical audiences, especially on how Darwinism poses no threat to their faith.

Klinghoffer offers some examples of his concerns: Go here for more.

Cornelius Hunter blogs on "Evolution Wins Out in Hong Kong Curriculum".

More...

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Darwinists believe that all they need to do to dispatch with ID is to assert it is not science. They may think, "There...now that was easy." I suppose the historic sciences (forensic, SETI, etc.) are not science either. You can't have it both ways, yet they get away with it all the time.

Listen to Dr. Stephen C. Meyer's interview on the nationally syndicated Michael Medved Show. Meyer and Medved discuss the information revolution and the challenge it presents for Darwinism, as well as the argument for intelligent design from information.

Go to the ENV Web page to LISTEN...

In ENV...a science test given last month to thousands of teenagers in England, Wales, and Northern Ireland. One question asked students to compare Darwinian evolutionary theories with Lamarckian evolutionary theory, the theory of intelligent design and Biblical creationism.

"Unlike creationism, intelligent design is an inference from scientific evidence, not a deduction from religious authority," countered Meyer. "Intelligent design proposes that certain features of the universe and life are best explained by an intelligent cause rather than an undirected process such as natural selection."

More...

by Denyse O'Leary
ARN correspondent

In "Brain detects happiness more quickly than sadness" (Eurekalert), we learn:

The results, published in the latest issue of the journal Laterality, show that the right hemisphere performs better in processing emotions. "However, this advantage appears to be more evident when it comes to processing happy and surprised faces than sad or frightened ones", the researcher points out.

"Positive expressions, or expressions of approach, are perceived more quickly and more precisely than negative, or withdrawal, ones. So happiness and surprise are processed faster than sadness and fear", explains Aznar-Casanova.

The finding doesn't particularly support the famous "left brain, right brain" thesis, that is so embedded in popular culture that even your cousin, who never reads a book, knows about it.

Two theories are currently "competing" to explain the pattern of cerebral asymmetry in processing emotions. The older one postulates the dominance of the right hemisphere in the processing of emotions, while the second is based on the approach-withdrawal hypothesis, which holds that the pattern of cerebral asymmetry depends upon the emotion in question, in other words that each hemisphere is better at processing particular emotions (the right, withdrawal, and the left, approach).

When we are miserable, we should seek out people we believe to be right-brained (chances are they will intuit our needs), and when we are happy, we should go to the races with people who are left-brained. (And get them to help us decide where to place our bets).

Also, just up at The Mindful Hack:

Evolutionary psychology: Why it is on the way out, with last year's magazines

Daydreaming: Neuroscientist calls it key to creativity, unimaginative boss still calls it loafing

Empathy: Hath not a Jew eyes?

Free will: Understanding what it means

Neuroscience and science fiction: Can we cure everything by advanced technology?

The Mindful Hack is my blog on neuroscience and spirituality issues, which supports The Spiritual Brain.

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).

Professor Michael Reiss is Director of the Institute of Education, University of London. He gained notoriety last year for being sacked by the Royal Society for failing to say the 'right' things about creationism and ID in the context of school science education. Previous blogs have covered this story: here and here.

A new paper in the journal Evolution provides an opportunity to restate or retract. Reiss is unrepentant - he restates his case! His critics are almost all advocates of the "conflict" view of the relationship between science and religion. Ian Barbour is quoted approvingly: "In scientific materialism, science swallows religion. In biblical literalism, religion swallows science." There are strengths and weaknesses in Reiss' paper and this blog seeks to provide some constructive discussion of relevant issues.

In his discussion of the nature of science, Reiss draws attention to the work of Robert Merton and Karl Popper. Whilst there is much of value here, he writes, "most historians and philosophers of science would argue that there is more to the nature of science". He considers the "seminal contributions" of Thomas Kuhn and the concept of scientific paradigms, plus the related analysis of research programs by Lakatos. More recently, science has become "more influenced by politics; it is more industrialized; and it is more bureaucratic." Then comes the conclusion:

"The effect of these changes is to make the boundaries around the city of science a bit fuzzier. [. . .] Of course, if one accepts the contributions of the social study of science one finds these boundaries fuzzier still."

Whilst all this is helpful, it is not clear to me how this affects the subsequent argument of the paper. The paradigms affecting evolutionary biology are not analysed; nor the research programs of scientists involved with origins research. The fuzzy boundaries are not mentioned again. Reiss could have taken the opportunity to show the defenders of "scientific materialism" where they fit into the analysis - thereby constricting their comfort zone - but he does not. Later, he says that creationism "is not really a science in that its ultimate authority is scriptural and theological rather than the evidence obtained from the natural world". Creationists, of course, do not see any incompatibility between their ultimate authority and working with evidences from the natural world - but that is another discussion. If ultimate authority is an issue, what can be said of the many advocates of "scientific materialism"? What shall we make of Richard Lewontin's oft-quoted maxim: "Moreover, that materialism is absolute, for we cannot allow a Divine Foot in the door."? Does this statement imply that Lewontinism 'is not really a science in that its ultimate authority is philosophical materialism rather than the evidence obtained from the natural world'?

Let us move on to the worldview issue. Reiss draws on the work of others to provide a working definition: "A worldview constitutes an overall perspective on life that sums up what we know about the world, how we evaluate it emotionally, and how we respond to it volitionally." He applies this to student convictions about creationism or intelligent design, recognising that these students are not just confused about the details.

"A value of the worldview perspective is that it indicates the extent to which a belief in creationism or intelligent design for many students is not just a simple misconception to be remedied by some straightforward science teaching, as a belief that most of the mass of a plant comes from material extracted from soil might be, but rather a whole way of understanding the world - a "world view"."

The implications for science teaching are far reaching. It means that conflict strategies are counter-productive because students find them threatening and this is not a good learning environment. Teachers need to realise that they are there to teach, not to indulge in personal crusades against what they perceive as nonsense and ignorance.

"I do believe in taking seriously and respectfully the concerns of students who do not accept the theory of evolution while still introducing them to it. Although it is unlikely that this will help students who have a conflict between science and their religious beliefs to resolve the conflict, good science teaching can help students to manage it - and to learn more science."

There is wisdom in this approach. The problem comes if teachers (or the scientific community) think that they do not need to think about their own worldviews and their effect on scientific work. So often, teachers and science leaders retreat into a positivist stronghold and embark on a discourse to emphasis their objectivity. They completely forget Reiss' earlier discussion of the nature of science. Unfortunately, Reiss also appears to overlook the wider relevance of these issues. This point is picked in a blog on the Truth in Science web site:

"What is disappointing is that Reiss, in common with most evolutionists (whether secular or theistic) regards science as something separate from religion. He constantly contrasts 'religious worldviews' with 'the scientific worldview' as if science is a faith-free zone. However, the last half-century or so of work in the history and philosophy of science has abundantly shown that in each and every discipline of science, the facts are seen in terms of a theory, against the frame of reference of a paradigm (research programme), within a philosophical view of reality, and from a religious stance."

To conclude, it is worth looking at the application of Reiss' approach to school science teaching. The issue has become alive this week because the Assessment and Qualifications Alliance in the UK has set a GCSE biology exam paper with a question exploring the students' understanding of different theories of origins. The essence of the question was reported by The Daily Telegraph:

Pupils were presented with four "theories of how new species of plants and animals have developed". These included creationism, which is commonly known as the belief that the Earth and its species were created suddenly by God within the last 10,000 years, and intelligent design, its more recent off-shoot. Pupils were also presented with Darwinism and Lamarckism, the theory of organic evolution advanced by the French naturalist Lamarck.
They were then asked to match each theory with a sentence.
Pupils were supposed to place creationism with the observation that "fossils of all the different kinds of animals appear suddenly in the rocks, with no evidence of ancestors".
They should also have identified intelligent design as theory based on the "complicated way in which cells work".

Reaction has been rapid, and the AQA says it has withdrawn the question. The scientific materialists insist that only Darwinism and Lamarckism are entitled to be called scientific and that there is no case for putting creationism and ID at the level of "theory". ID scientist, Dr Steve Meyer, is quoted as saying: "The exam board should be commended, not attacked, for exposing students to competing ideas about the origin and development of life."

My interest is in whether the exam question was informed by the stance taken by Michael Reiss or whether it is a further example of muddled thinking. If worldview thinking is to be taken seriously, then the same evidence is likely to be handled differently by the science that emerges from each worldview. For example, whereas an evolutionist considers classification to be a matter of tracing ancestor-descendant relationships, a design theorist is open to the idea that some of the pattern may be better explained by design. We have the same data - but different interpretations. However, in the examination question, matching a theory with a sentence suggests that data brings its own interpretation. Data then is perceived as "magic bullets" to prove or disprove a particular theory. But this is not good science and it is not informed by worldview thinking. What might be more appropriate is to match different interpretations of the same data to theories springing from different worldviews.

Clearly, there is a lot of work to be done in developing a better understanding of the philosophy of science, and how philosophical materialism, theistic materialism, creationism and ID can relate meaningfully to science. Reiss is to be commended for proposing an approach that keeps the opportunity to dialogue open.

The Relationship Between Evolutionary Biology And Religion
Michael J. Reiss
Evolution, 63(7), July 2009, 1934-1941 | doi: 10.1111/j.1558-5646.2009.00714.x

ABSTRACT: Belief in creationism and intelligent design is widespread and gaining significance in a number of countries. This article examines the characteristics of science and of religions and the possible relationship between science and religion. I argue that creationism is sometimes best seen not as a misconception but as a worldview. In such instances, the most to which a science educator (whether in school, college or university) can normally aspire is to ensure that students with creationist beliefs understand the scientific position. In the short term, the scientific worldview is unlikely to supplant a creationist one for students who are firm creationists. We can help students to find their evolutionary biology courses interesting and intellectually challenging without their being threatening. Effective teaching in this area can help students not only learn about the theory of evolution but better appreciate the way science is done, the procedures by which scientific knowledge accumulates, the limitations of science, and the ways in which scientific knowledge differs from other forms of knowledge.

Synopsis Of The First Chapter Of Nature's IQ By Balazs Hornyanszky and Istvan Tasi
ISBN 978-0-9817273-0-1
By Robert Deyes
ARN Correspondent

Ethology, the field of biology that attempts to explain the origins of animal behavioral patterns, has traditionally focused on two possible sources for such patterns- those that are inherited and those that are environmentally induced. For the former of these two, the Darwinian mechanism is that which is most commonly advanced. The underlying axiom barely needs repeating- inherited behaviors have been acquired through gradual changes as a result of environmental selective pressures. In his 1973 Nobel lecture entitled Analogy As A Source Of Knowledge, Konrad Lorenz made his case in favor of the link between Darwinian gradualism and animal behavior. And yet in Nature's IQ, authors Balazs Hornyanszky and Istvan Tasi blast such a gradualistic inference and re-interpret the evidence in favor of the intelligent design alternative.

For many key anatomical features found in nature, a necessary behavioral pattern must be present if a desired function is to be fulfilled. The prominent bioluminescent bulb of the anglerfish for example must exhibit a slow waving motion if it is to lure its prey. As Hornyanszky and Tasi so vividly illustrate, any intermediate behavior on the way to becoming the fully-fledged comportment we see today, would have been inappropriate and insufficient for catching unsuspecting fry. In effect, anglerfish are endowed with an IQ that must have appeared at once and in parallel with its predatory anatomy if it were to provide any selective advantage.

We see the same principle playing out in the trap-like lures of other creatures such as the decoy scorpion fish, the Argentine Horned frog and the copper-head snake. Most prominent of all is the alligator snapping turtle which holds its mouth open for extended periods of time while waiting for a victim to catch sight of its worm-like wriggling tongue. The New Guinean dung spider is able not only to assume the appearance of bird droppings but also produce a characteristic 'dropping' smell as a way of enticing and trapping insects that normally feed on such a delectable meal. Hungry Egyptian vultures repeatedly throw stones at ostrich eggs as they try to access their next meal- a behavior that has been conclusively shown to be integral part of the vulture's genetic constitution.

Hornyanszky and Tasi maintain that for all such cases, both the anatomical features and the accompanying behaviors must have arisen all at once if the observed functions were to have been achieved. In short they build on biochemist Michael Behe's showcase volume Darwin's Black Box by inferring that many such anatomical-behavioral functional units are irreducibly complex and thereby inaccessible to a progressive accumulation of random mutations.

Hornyanszky's and Tasi's case in favor of intelligent design is made all the more compelling through the wealth of examples that they draw on as well as the rich illustrations that accompany many of these examples. In all, the first chapter of Nature's IQ provides a firm foundation in support of the Intelligent Design case and sets the tone for the chapters that follow.

For more information and to order Nature's IQ go to http://www.arn.org/arnproducts/php/book_show_item.php?id=129

Apparently, journalism faces something of an identity crisis, not least science journalism. The 6th World Conference of Science Journalists was held in London last week. Before it started, it was said that many attendees will be "wondering if this is journalism's swan song". An Editorial in Nature asked whether the role of science journalists is that of cheerleader ("to explain new scientific findings to the masses" and "for making the case for a thriving research enterprise to public and politicians alike") or a watchdog ("to cast a fair but sceptical eye over everything in the public sphere - science included").

The one question not being asked is: are science journalists letting us down? (Link to source here)

The root problem is that readers are deserting in significant numbers and with that comes declining advertising revenue. "Readers - and small ads, once a reliable earner - are migrating to the Internet." Science journalists and other specialists are being replaced by press releases:

"This contraction is perhaps particularly bad news for journalists with specialist beats such as science - the kind of journalists who need an informed understanding of what they are writing about, and know which experts can provide context, and where appropriate criticism, of new results. But publishers tend to see that kind of expertise as a luxury when money is tight, especially when the same space can be easily filled with material from press releases and wire services."

What is singularly lacking from the Editorial comment is any discussion of ideology and worldviews. It is the concern of many of us that significant issues are waiting to be explored but the traditional media are just not interested. Denyse O'Leary puts her finger on the problem here, when she writes:

"Believing that materialism is the truth, many journalists assumed that their role was to promote materialism at the expense of traditional, spiritually oriented ideas about human nature. Journalism consciously modelled itself on science, with "objectivity" as a new standard. Journalism would provide trenchant criticism of the religious outlook that it replaced."

This situation has become unstable over the past decade because of the increasing problems of maintaining a materialist worldview. Opinion polls show that a majority of people are not persuaded by the design-free media output. They are increasingly aware of evidence for design! In a second post on this topic, O'Leary writes:

"But most science journalists are not really aware of this stuff because their template for understanding issues is simply to reinterpret all problems as support for materialism, with Darwinism as its creation story. For example,
* Fine-tuning of the universe = That proves that many flopped universes exist!
* Cells as super-computers = That just shows what Darwinism can do!
* Origin of life? = Harvard will spend $50 million on "the answer"!
* Hard problem of consciousness = Science (materialism) will solve it [no end date for evaluation of project suggested]
Almost all coverage of the intelligent design controversy in major media is provided by people who cannot acknowledge any problem with materialism. They think you must be a fraud or just plain stupid if you raise problems that cannot even exist, in their opinion. And remember, as far as they are concerned, their opinion is science."

For most part, science journalism reflects the materialistic philosophy that is promulgated by science leaders and science organisations. Busy journalists often produce reports that are popularised versions of the press releases issued by the researchers, with little attempt to evaluate the significance of the research. This year, Ida has provided a clear example of the problem. Darwin dissenters have a tough time getting their message across. Repeatedly, I have learned of scientists being interviewed and they have pointed out that their objections are based on scientific evidence - only to find that the media report paints their views as an expression of their religious convictions. The thought that the mainstream view is an expression of a materialistic worldview seems never to have occurred to these journalists.

The editorial closes with some fine words that are worth repeating:

"Science and journalism are not alien cultures, for all that they can sometimes seem that way. They are built on the same foundation - the belief that conclusions require evidence; that the evidence should be open to everyone; and that everything is subject to question. Both groups are comprised of professional sceptics. And whether it's directed towards an experiment or a breaking news story, each can appreciate the other's critical eye."

The word "everything" is important. We know that many science leaders and science organisations do not accept that materialism is "subject to question". They are not prepared to either re-assess their own presuppositions or to allow anyone with different presuppositions to represent science. Until this situation changes, these people should not be surprised that readers vote with their feet and find other media that does not ram an alien ideology down their throats.

Cheerleader or watchdog?
Editorial
Nature 459, 1033 (25 June 2009) | doi:10.1038/4591033a

Abstract: Science journalism is under threat. What can scientists do to help?

See also:

For more on materialism in science, go here, here and here.

Brainard, C. NSF "Underwriting" Coverage. . ., The Observatory (July 01, 2009)

Quacks, hacks and pressing problems with press releases, The Guardian (30 May 2009)

by Denyse O'Leary
ARN correspondent

Issue 9 of Salvo (Summer 2009) has come out, with many fine articles. The feature article is on the explosion of kids watching Internet porn.*

A number of interesting features on topics related to the intelligent design controversy:

Gimme that Spacetime Religion: Seeking Salvation in Science by Regis Nicoll, about the effort to transform Darwinism into a religion with all the trappings - except actual guilt for sin.

Wesley J. Smith, describing himself as a "Human Exceptionalist" talks about the effect that the growing practice of equating humans with animals and plants has on bioethics, pointing out, "If they really wanted to be reductionist, they could also say that because carrots are made out of carbon molecules, there is no distinction between carrots and humans either. You can't get far enough ahead of these guys in terms of satire."

Twin Features: The Big Problem That Design Convergence Posses to Darwinian Evolution by Hugh Ross: Remember the Tree of Life we were taught in high school, that proved Darwin was right? "The problem for the Darwinian perspective is this: Life forms that are only distantly rrelated, if at all, nevertheless show amazing similarities in their morphological features (some are identical). This is not what Darwinists expect." He recounts a good deal of examples, including Lenski's famous simulation, showing that repeated design is a better explanation. We are now down to the club moss of life, I guess. Turns up everywhere.

The Flop: Betting Against Darwin's Tree of Life by Casey Luskin: A great companion to the above. Luskin explains how a famous Darwinist, self-cited as one of the "world's leading experts on the tree of life" tried to bluff the Texas State Board of Education that Darwin's Tree of Life was in great shape - when current science lit shows it is collapsing. Or, as Eric Bapteste, an evolutionary biologist at the Pierre and Marie Curie University in Paris, said, "... today the project lies in tatters, torn to pieces by an onslaught of negative evidence." One of the world's leading experts should spend less time bluff and more time reading the evidence. Even the Texas Board can find this stuff out now. (If they don't, it won't be Luskin's fault.)

Old Bones: The Story of a Girl with a Birth Defect by Michael Cook: About a severely retarded child who lived over 500 000 years ago. "Now here's the remarkable thing. The hunter-gatherer Middle Pleistocene family of Cranium 14 must have cared for the child, or she would not have survived for at least five years, and perhaps as many as twelve. In the dry-as-dust words of the article, 'It is obvious that the [Sima de Huesos]' hominin species did not act against the abnormal/ill individuals during infancy, as has happened along our own history in many cultures.'"

My regular Deprogram column is about Phineas Gage - the Lecture Room Psychopath. It seems he wasn't a psychopath in his lifetime, but became one after his death, when he was needed to demonstrate to Psychology 101 students that brain injury radically changes personality. "Sadly, Intro to Psych 101 professors didn't need a workingman who had independently adapted to his disability - without government funding - and found work on his own. They needed an aimless, sociopathic drifter."

Only the first of these ID-relevant articles seems to be online. If you thought this was a hint that you should subscribe or buy just this one issue, or support Salvo - well yes, it is!

Americans, Happy July 4!

(*As a mother and grandmother, I would say key controllable factors are more chores, more sports, more homework, and more supervision. A busy, supervised kid is not watching porn whether it is available or not, for the same reason that a busy, supervised kid isn't smoking (or not often) even if he can buy cigs from a complicit shopkeeper.)

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).

As reported by Beb Leach in the London Telegraph, Prof. Richard Dawkins, the prominent atheist, has helped set up an atheist summer camp where children will be taught rational scepticism and sing John Lennon's Imagine...

The author of "The God Delusion", who stepped down from his post at Oxford University last year, has subsidised the five-day camp in Somerset.

Camp-goers will be given lessons in rational scepticism, as well as sessions in moral philosophy and evolutionary biology.

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Now, let me get this straight...according to the atheist, when Christians "propagandize" children regarding God, it's a form of child "abuse", but when Richard Dawkins propagandizes children regarding atheism, it is just wonderful "truth-telling".

The world of human phylogeny has been hit by a bombshell. Although scholars and textbooks are presenting chimpanzees as man's closest relatives, Grehan and Schwartz have revived the case for orangutans. They consider hominoids to be comprised of two sister clades: the human-orangutan clade (dental hominoids) and the chimpanzee-gorilla clade (African apes). They claim that humans and orangutans "share a common ancestor that excludes the extant African apes". Since it is received wisdom that chimps are the nearest relative to humans because we share over 98% of their genes and since humans are referred to as the "third chimpanzee", the ramifications of the new paper are immense!

Mr. Jiggs, a six-year-old orangutan at London Zoo, is capable of mopping his own quarters (credit B. A. Stewart and D. S. Boyer, source here)

Conceptual upheavals of this magnitude are unlikely to happen without major methodological modifications. This is the main concern of this blog. The authors do not start with DNA similarities but with morphological data. They note that, originally, the DNA comparisons were interpreted in the light of morphological analyses, but:

"Neither of two oft-cited morphological studies claiming to corroborate the interpretation of molecular data as supporting a close relationship between chimpanzees and humans took into consideration or provided justification for excluding most of the morphological features that have been documented as being shared uniquely by humans and orangutans."

The authors proceed to critique previous studies for the way they selected characters for cladistic analysis. They point out that these approaches incorporated characters considered to be derived within the ingroup "in spite of the fact that the feature is also common in the outgroup".

"Although a range of morphological studies have claimed to support a closer relationship between humans and chimpanzees or African apes, these studies have relied on many of the characters that we found to be problematic, and thus demonstrate how entrenched error becomes as it is unquestioningly passed on from and incorporated into one study after another."

Those familiar with the Kuhnian analysis of the practice of science will discern features here of 'working within the paradigm', with presuppositions unintentionally closing off avenues of enquiry. Conscious of the limitations of other work, Grehan and Schwartz explain and justify their selection of characters. One of their additional objectives was to include numerous fossil apes within their study.

"Our analysis of relationships between living and fossil taxa is based on a character matrix limited to hard-tissue characters that have been sufficiently well described in the literature to permit verification, and whose claimed character states as well as unique occurrence within a large-bodied hominoid clade we could corroborate via a broad outgroup comparison."

It is worth noting that their conclusion has deep roots. Schwartz was making points like this in 1984. His book The Red Ape appeared in 1987 and in a revised form in 2005. The paper has not come from authors who have suddenly hit on a quirky idea but it represents the mature judgment of two respected scholars.

What then shall be said of the DNA similarity data? The analysis of the authors is scathing. The key points are, in their own words:

"But the widely accepted notion that the 'greatest overall molecular similarity' is synonymous with 'most closely related' derives not from any empirical evidence but merely from the acceptance without question of the 'molecular assumption': namely, most recently divergent taxa will be most similar in their proteins and DNA because they will have shared a longer lineage of molecular change prior to their divergence and that the pace of molecular change was clocklike in nature. Nevertheless, despite claims to the contrary, the demonstration of molecular similarity does not a priori equate with a demonstration of homology, which must precede any hypothesis of phylogenetic relationship because a demonstration of similarity alone is only phenetic and must be subject to rigorous phylogenetic enquiry."

They cite previous work by Schwartz & Maresca that was the subject of a blog here. They argue that the published studies lack objectivity and have embedded tautologies. The New Scientist report summarises the argument against chimp/human genetic similarities by quoting one of the authors:

"Grehan, however, argues that this is not scientifically justified. He points out that traditional taxonomy makes a distinction between two types of similarity - "derived novelties" and "primitive retentions". Derived novelties are traits shared by two closely related species and are taken to have evolved in a recent common ancestor. Primitive retentions are older traits with a deeper evolutionary past shared by a larger group of species.
The problem with molecular systematics, says Grehan, is it fails to distinguish between the two. "It does not matter that more DNA similarities may be found between humans and chimpanzees if these similarities are really primitive retentions," he says."

A third element of the new paper is to set the argument for the human/orangutan relationship in a biogeographical context. Whereas the consensus view understands an emergence of humanity "out of Africa", there is a need for these issues to be addressed for the dental hominoid clade. The authors do this utilising data relating to the fossil species included in their analysis.

The significance of the paper is that the arguments relate to cladism (which is very widely used for assigning probabilities to evolutionary relationships) and phylogenomics (which is a standard tool for establishing evolutionary relationships). The authors have challenged the scientific consensus with some cogent and penetrating arguments. It is not just a dispute about the meaning of data, but how that data is selected and what presuppositions the researchers bring to their work. As such, the new paper provides us with a very important case study and sets the agenda for potentially very interesting discussions about methodology. If this is properly done, it will be to the health of the science community. Scientists with an openness to ID will welcome this debate, because many of critiques made by Grehan and Schwartz link directly to issues that concern us.

Evolution of the second orangutan: phylogeny and biogeography of hominid origins
Grehan, J.R. and Schwartz, J. H.
Journal of Biogeography, advance online 22 June 2009 | doi 10.1111/j.1365-2699.2009.02141.x (abstract)

Main conclusions: Humans and orangutans share a common ancestor that excludes the extant African apes. Molecular analyses are compromised by phenetic procedures such as alignment and are probably based on primitive retentions. We infer that the human-orangutan common ancestor had established a widespread distribution by at least 13 Ma. Vicariant differentiation resulted in the ancestors of hominids in East Africa and various primarily Miocene apes distributed between Spain and Southeast Asia (and possibly also parts of East Africa). The geographical disjunction between early hominids and Asian Pongo is attributed to local extinctions between Europe and Central Asia. [. . .]

See also:

Lawton, G. Could the orang-utan be our closest relative? New Scientist, 17 June 2009

Humans and Orangutan, Buffalo Museum of Science web resource.

As reported by ENV...the American public overwhelmingly rejects Darwinian theory in favor of intelligent design. When asked if life developed "through an unguided process of random mutations and natural selection," a standard definition of Darwinism, only 33 percent of respondents said they agreed with the statement. But 52 percent agreed that "the development of life was guided by intelligent design."

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