The ID Report

Robert Deyes
ARN Correspondent

The Spanish Paseos Por La Naturaleza (A Walk Through Nature) series continues with a review of Biologic Institute researcher Douglas Axe's thesis on the probabilistic barriers that make a neo-Darwinian explanation for the origin of protein folds untenable. Given his scientific background, Axe is well qualified to argue against the undirected origin of protein structure and convincingly counters those who extravagate over the much-heralded modular transfer of folds between proteins.

The Paseos Por La Naturaleza series aims to further strengthen the global influence that the Intelligent Design movement already enjoys and raise awareness of important academic resources that are today challenging orthodox Darwinism and revitalizing the call for a fresh perspective on scientific discourse.

The fifth installment can be found at:

Como los pliegues proteinicos derrumban el edificio neo-darwinista (see also darwinodi.com)

by Denyse O'Leary
ARN correspondent

As long as it’s NOT about their love for evolution. It is common to hear that the Nazis utterly lacked morality. Of course, that satisfies deep anger. But is it true? University of California professor Richard Weikart’s recent book, Hitler’s Ethic: The Nazi Pursuit of Evolutionary Progress (Palgrave Macmillan, 2009), offers an illuminating answer: No.

Hitler’s Ethic (a companion to his From Darwin to Hitler, Palgrave Macmillan, 2004) demonstrates that the Nazis indeed had an ethic. It flowed directly and painstakingly from evolutionary theory, as understood in Germany at the time.

I wish I had said this stuff. Come to think of it, I at least reported it here. Subscribe to Salvo, one of the few pubs worth reading these days, if you are not a gorilla somewhere.

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 Kevin Wirth, ARN Director of Product Development and Media Relations

Today marks the official publication of Dr. Caroline Crocker's book "Free to Think" (now available online at Amazon and Barnes & Noble). As we celebrate our national independence from the the tyrannical rule of King George over the American colonies so many years ago, it's fitting that we be reminded of our need to be free from other forms of injustice that are present with us today. Two of those injustices are, amazingly, freedom of speech and academic freedom. Both of these issues are addressed in Dr. Crocker's autobiographical account of her experience as a professor at George Mason University (GMU).

This long-awaited response to critics of Dr. Crocker puts to rest some of the often unscrupulous hype surrounding her departure from GMU in May 2005 (for example, see my earlier blog post on SKEPTIC Magazine's treatment of her back in October of 2008). Many of her critics have remarked that there was nothing at all unusual about Dr. Crocker's departure, since her contract simply ended and that was that - happens all the time. But Dr. Crocker reveals that the truth of the matter is anything but typical or usual.

Dr. Crocker, who appeared briefly in the 2008 movie Expelled, was an untenured adjunct professor at GMU and had signed a 3-year contract extension, which others also read. In her book, Crocker recounts how her good fortune was short lived, however, as she became the victim of a bait-and-switch scheme in which her original contract was changed to a one-year term shortly after being accused of teaching creationism in her classes - a charge she steadfastly denies. In fact recent evidence has come to light from one of her former students that a student who Dr. Crocker caught cheating retaliated against another student and made allegedly false accusations against Dr. Crocker, which eventually culminated in the loss of her job as a professer at GMU. The appeals process as told by Dr. Crocker was little more than a railroading and a denial of her academic freedom per GMU's own code - and readers are provided with her first-ever complete retelling of what happened in her own words as well as her response to the findings of her grievance committee (all documented in Appendix IV).

Many of Dr. Crocker's critics make the point that she SHOULD have been let go for teaching creationism. However, according to Dr. Crocker, all she did was challenge her students to think outside the box a bit and come to their own conclusions based on ALL of the available evidence, not just the usual consensus views of science. Crocker relates in her book exactly how and what she taught her students, including many in-class interactions. Readers will be left to decide whether they believe her approach was reasonable. I submit most readers will concur that she did nothing to warrant the treatment she received.

The broader question posed by Dr. Crocker (and hence the title of her book) is how far should we go in controlling the freedom we should give educators who desire to stimulate the thinking of their students? And likewise, how much leeway should be given to students who question consensus views of science? Dr. Crocker's story reveals a very disturbing lack of latitude among GMU officials. Unfortunately, the short-leash policy illustrated by GMU is all too common in many academic institutions across America.

But if that was not enough, even more alarming is what occurred afterward as she sought legal redress. According to both Crocker and her attorney Ed Sisson (who also wrote a compelling preface for this book), the law firm representing her interests in the GMU fiasco was being considered for hire by GMU on another unrelated matter with one stipulation - they must first agree to drop Crocker as a client before signing on the dotted line. And the travesty is, the law firm agreed to do so, and soon after dismissed Sisson from the firm after a 14-year career with them.

As Michael Behe, author of the book "Darwin's Black Box" writes in support of Dr. Crocker's account, this story is "guaranteed to make your blood boil."

Seattle area writer and Darwin skeptic Kevin Wirth is a founding member of ARN (formerly Students for Origins Research) and is also the founder of Leafcutter Press.

He is the Senior editor, contributor, and publisher of the book "Slaughter of the Dissidents: The Shocking Truth About Killing the Careers of Darwin Doubters" by Dr. Jerry Bergman (2008). This is the most comprehensive book published to date documenting the extent and types of discrimination against Darwin Dissidents.

In addition, he is also the publisher of Caroline Crocker's book "Free to Think," which addresses her critics and relates her experience as an Expelled University professor from George Mason University.

To read more essays by Kevin Wirth, click here.

Copyright (c) 2010 by Kevin H. Wirth, all rights reserved. Quotes and links to this blog post are welcomed with attribution.

A Review Of The Case Against A Darwinian Origin Of Protein Folds By Douglas Axe, Bio-Complexity, Issue 1, pp. 1-12

By Robert Deyes
ARN Correspondent

Proteins adopt a higher order structure (eg: alpha helices and beta sheets) that define their functional domains. Years ago Michael Denton and Craig Marshall reviewed this higher structural order in proteins and proposed that protein folding patterns could be classified into a finite number of discrete families whose construction might be constrained by a set of underlying natural laws (1). In his latest critique Biologic Institute molecular biologist Douglas Axe has raised the ever-pertinent question of whether Darwinian evolution can adequately explain the origins of protein structure folds given the vast search space of possible protein sequence combinations that exist for moderately large proteins, say 300 amino acids in length. To begin Axe introduces his readers to the sampling problem. That is, given the postulated maximum number of distinct physical events that could have occurred since the universe began (10exp150) we cannot surmise that evolution has had enough time to find the 10exp390 possible amino-acid combinations of a 300 amino acid long protein.

The battle cry often heard in response to this apparently insurmountable barricade is that even though probabilistic resources would not allow a blind search to stumble upon any given protein sequence, the chances of finding a particular protein function might be considerably better. Countering such a facile dismissal of reality, we find that proteins must meet very stringent sequence requirements if a given function is to be attained. And size is important. We find that enzymes, for example, are large in comparison to their substrates. Protein structuralists have demonstrably asserted that size is crucial for assuring the stability of protein architecture.

Axe has raised the bar of the discussion by pointing out that very often enzyme catalytic functions depend on more that just their core active sites. In fact enzymes almost invariably contain regions that prep, channel and orient their substrates, as well as a multiplicity of co-factors, in readiness for catalysis. Carbamoyl Phosphate Synthetase (CPS) and the Proton Translocating Synthase (PTS) stand out as favorites amongst molecular biologists for showing how enzyme complexes are capable of simultaneously coordinating such processes. Overall each of these complexes contains 1400-2000 amino acid residues distributed amongst several proteins all of which are required for activity.

Axe employs a relatively straightforward mathematical rationale for assessing the plausibility of finding novel protein functions through a Darwinian search. Using bacteria as his model system (chosen because of their relatively large population sizes) he shows how a culture of 10exp10 bacteria passing through 10exp4 generations per year over five billion years would produce a maximum of 5×10exp23 novel genotypes. This number represents the 'upper bound' on the number of new protein sequences since many of the differences in genotype would not generate "distinctly new proteins". Extending this further, novel protein functions requiring a 300 amino acid sequence (20exp300 possible sequences) could theoretically be achieved in 10exp366 different ways (20exp300/5×10exp23).

Ultimately we find that proteins do not tolerate this extraordinary level of "sequence indifference". High profile mutagenesis experiments of beta lactamases and bacterial ribonucleases have shown that functionality is decisively eradicated when a mere 10% of amino-acids are substituted in conservative regions of these proteins. A more in-depth breakdown of data from a beta lactamase domain and the enzyme chorismate mutase has further reinforced the pronouncement that very few protein sequences can actually perform a desired function; so few in fact that they are "far too rare to be found by random sampling".

But Axe's landslide evaluation does not end here. He further considers the possibility that disparate protein functions might share similar amino-acid identities and that therefore the jump between functions in sequence space might be realistically achievable through random searches. Sequence alignment studies between different protein domains do not support such an exit to the sampling problem. While the identification of a single amino acid conformational switch has been heralded in the peer-review literature as a convincing example of how changes in folding can occur with minimal adjustments to sequence, what we find is that the resulting conformational variants are unstable at physiological temperatures. Moreover such a change has only been achieved in vitro and most probably does not meet the rigorous demands for functionality that play out in a true biological context. What we also find is that there are 21 other amino-acid substitutions that must be in place before the conformational switch is observed.

Axe closes his compendious dismantling of protein evolution by exposing the shortcomings of modular assembly models that purport to explain the origin of new protein folds. The highly cooperative nature of structural folds in any given protein means that stable structures tend to form all at once at the domain (tertiary structure) level rather that at the fold (secondary structure) level of the protein. Context is everything. Indeed experiments have held up the assertion that binding interfaces between different forms of secondary structure are sequence dependent (ie: non-generic). Consequently a much anticipated "modular transportability of folds" between proteins is highly unlikely.

Metaphors are everything in scientific argumentation. And Axe's story of a random search for gem stones dispersed across a vast multi-level desert serves him well for illustrating the improbabilities of a Darwinian search for novel folds. Axe's own experience has shown that reticence towards accepting his probabilistic argument stems not from some non-scientific point of departure in what he has to say but from deeply held prejudices against the end point that naturally follows. Rather than a house of cards crumbling on slippery foundations, the case against the neo-Darwinian explanation is an edifice built on a firm substratum of scientific authenticity. So much so that critics of those who, like Axe, have stood firm in promulgating their case, better take note.

Read Axe's paper at: http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2010.1

Further Reading

Michael Denton, Craig Marshall (2001), Laws of form revisited, Nature Volume 410, p.417