The ID Report

by Denyse O'Leary
ARN correspondent

Here's an interesting article in New Scientist by Bob Holmes on a new approach to how animals become separate species ("Accidental origins: Where species come from", March 10, 2010):

Everywhere you look in nature, you can see evidence of natural selection at work in the adaptation of species to their environment. Surprisingly though, natural selection may have little role to play in one of the key steps of evolution - the origin of new species. Instead it would appear that speciation is merely an accident of fate.

So, at least, says Mark Pagel, an evolutionary biologist at the University of Reading, UK. If his controversial claim proves correct, then the broad canvas of life - the profusion of beetles and rodents, the dearth of primates, and so on - may have less to do with the guiding hand of natural selection and more to do with evolutionary accident-proneness.

[ ... ]

"When it works, it works remarkably well," he says. "But it only works in about 6 per cent of cases. It doesn't seem to be a general way that groups of species fill out their niches."

The otherwise most informative article is marred by the constant need to claim that Darwin was not wrong - but obviously, if Pagels is right, Darwin was indeed wrong, and so are all the people fronting his cause. Natural selection acting on random mutation was, precisely, Darwin's proposed mechanism.

No one supposes that natural selection doesn’t occur. But is it the main driver of new species, as Darwin thought, and Pagels doubts?

Pagels dances very nervously indeed around that point (presumably from fear of joining the Expelled, given that his genome research has failed to back Darwin up.

So, for a free copy of Expelled, which details what happened to a variety of people who questioned establishment Darwinism, based on its failures of evidence, and provide the best answer to this question: What do you think of Pagels’s evidence? Is it critical? Is he just blowing smoke? Will he be forced to recant?

Here's where you enter, which you do by posting a comment, 400 words or less. If you are new to Uncommon Descent, you will need to sign up.

Here are the contest rules, not many or difficult. The main thing is 400 words or less. Winners receive a certificate verifying their win as well as the prize. Winners must provide me with a valid postal address, though it need not be theirs. A winner's name is never added to a mailing list. There is no mailing list. Have fun!

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

by Denyse O'Leary
ARN correspondent

I see where Discovery Institute has put up a podcast with me, on "Is the Brain Just an Illusion"?

This must be one of the ones I did in Seattle in 2007, when they asked me to come and explain the book.

What I always ask is, "If the brain or the mind are an illusion, whose illusion are they?"

This question is modelled on the Jewish zen: "If the mind is an illusion, whose arthritis is this?"

On this episode of ID The Future, Anika Smith interviews science writer Denyse O'Leary about her book, The Spiritual Brain: A Neuroscientist's Case for the Existence of the Soul.

In the book O'Leary and her co-author Mario Beaurogard, neuroscientist and Associate Professor at Université de Montréal, explore the question of whether or not the mind is an illusion as materialists believe. The Spiritual Brain looks at whether religious experiences come from God or are merely the random firing of neurons in the brain. Drawing on his own research with Carmelite nuns, Beauregard shows that genuine, life-changing spiritual events can be documented. He and O'Leary offer compelling evidence that mind creates matter, rather than matter creating mind.

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

On the supposed evolutionary origin of religion:

Did you know that: Religion is good for you; also, Religion is bad for you; also, Religion makes no difference; also, Religion can be explained by a God gene, or a meme, or part of the brain . . . or whatever the editor of your local paper's "Relationships" section will buy for this weekend's edition?

You didn't know any of those things? Aw, no surprise. But never fear: One outreach of the new atheist movement, currently making its way around the lecture rooms of the nation, is the academic attempt to account for religious belief, and to do so on any basis whatsoever, except one.

We will get to that forbidden one in a moment. First, let's look at the permitted ones.

[ ... ]

Okay, so what is missing from this picture?

First, common sense: Suppose I told you that flossing your teeth (1) helped; (2) didn't help; (3) made no difference; (4) can be explained by . . . (choose an option). What would you reasonably conclude about the state of the evidence?

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).

Robert Deyes
ARN Correspondent

The Spanish Paseos Por La Naturaleza (A Walk Through Nature) series continues with an exploration of catalytic RNA within the larger context of the RNA world. Pulling together key lines of evidence from molecular biology, this installment builds a linchpin case against the fragile trusses of naturalistic causation.

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 third installment can be found at:
El ARN catalitico - un catalizador indigno de una discusion seria acerca del origen de la vida (See also OIACDI)

by Denyse O'Leary
ARN correspondent

When Britain's Guardian newspaper first introduced its "evolutionary agony aunt", this writer thought - a spoof for sure. But where evolutionary psychology is concerned, it can be genuinely hard to tell.

No spoof. The Guardian burbled proudly, "A mere 150 years after Darwin published On the Origin of Species, we are proud to introduce our very own Evolutionary Agony Aunt" in the person of Carole Jahme, author of Beauty and the Beasts: Woman, Ape and Evolution and star of comedy Carole Jahme is Sexually Selected, described as a combination of Charles Darwin and Charlie Chaplin. We were told that her column will shine the "cold light" of evolutionary psychology on readers' problems, in sharp contrast to the glossy magazines.

Carole counsels her troubled readers by citing the behaviour of chimpanzees, other apes, and monkeys. And with what result?

Go here for the rest.

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 Robert Deyes
ARN Correspondent

Santa Fe Institute economist Brian Arthur believed that much of what we see in global economic patterns can be explained by a process of "locking in" of historical events (1). Notably, the success of the QWERTY keyboard or the increased sales of the VHS video system over its arch rival Beta Max did not depend so much on any inherent better quality of the winning system but rather on small details in the history of innovation that, over time, lead to the establishment and the overwhelming success of particular technologies (1). Once such winning technologies became wide-spread, they became a locked and established part of our culture.

Arthur undoubtedly received much of his insight from long conversations that he had with biophysicist Stuart Kaufman as the two of them thrashed out the concepts of biology and economic policy in an attempt to reconcile both under the umbrella of their unifying theory of complexity (1). It was clear that a great number of parallels could be drawn between these two otherwise distinct areas of research.

From an origin of life standpoint, Kauffman has long been unconvinced by the usual crop of prebiotic synthesis experiments. There is after all no basis upon which to suppose that amino acids and nucleotides could randomly form long polymer chains with specific functions such as we see in the cell (2). Following such a realization Kauffman became enthralled by the idea that maybe there was a self-organizing process through which compounds could come together in an autocatalytic cycle- a closed cycle of catalysts that converted one molecule to another in a self sustaining fashion (3). What was interesting about Kauffman's idea was the manner through which he reached it- a multidisciplinary environment, such as the Santa Fe Institute with economists, political analysts and archaeologists coming together to look for a common thread uniting the emergence of complexity in lost civilizations, economically autonomous states and ultimately life's biochemistry.

One of Kauffman's favorite concepts- the 'adjacent possible'- describes a collection of molecules that are not actually in existence within the universe but are nevertheless one reaction step away from being synthesized (4). Thus the adjacent possible always exists since, once new molecules are synthesized, there is a new set of molecules that can always be made from these in a single reaction. Kauffman proposes that, ever since its origin, the earth's biosphere has been expanding into the adjacent possible as new molecules and compounds have become available (4). From a thermodynamic stance, the expansion of the biosphere into the adjacent possible would represent a displacement from equilibrium that, according to Kauffman, would provide the necessary chemical potential for driving the actual state of molecular diversity into the infinite adjacent possible. In other words many diverse molecules would emerge over time amongst which some would have the necessary properties to behave as biological catalysts. Given enough time, anything could happen.

While captivating in simplicity and imaginative content, Kauffman's cogitations on the emergence of life have done precious little to shake off the explanation-critical question of how specificity had arisen within his proposed autocatalytic cycles. The operative units of such cycles, namely proteins and nucleic acids, could not all exhibit low specificity if a self-reproducing metabolic cycle were to be in any way sustainable. Philosopher Stephen Meyer's exegesis on this matter is profoundly relevant. "It does not follow, nor is it the case biochemically" writes Meyer "that just because some enzymes might function with low specificity, that all the catalytic peptides (or enzymes) needed to establish a self-reproducing metabolic cycle could function with similarly low levels of specificity and complexity" (5). As Meyer later adds:

"For the direct autocatalysis of integrated metabolic complexity to occur, a system of catalytic peptide molecules must first achieve a very specific molecular configuration. This requirement is equivalent to saying that the system must start with a large amount of specified information or specified complexity...Self organizational models either failed to solve the problem of the origin of specified information or they "solved" the problem at the expense of introducing other unexplained sources of information. Kauffman's models provided only the best illustration of this latter "displacement problem."" (5)

Kauffman's concept of an infinitely expanding adjacent possible dies an early death when one starts dealing with actual numbers. Consider, for example, the number of possible amino-acid sequences that we can come up with for a protein that is 200 amino acids in length (numbers that are cited by Kauffman himself; 6). Proteins are made up of 20 different amino acids most of which are precisely arranged so as to attain specific functions. This means that for a protein that is 200 amino acids long, there are approximately 20exp200 possible ways that these amino acids can be lined up (ie 10exp260 proteins). Given that the total number of particles in the known universe is estimated to be around 10exp80 and considering Kauffman's own calculation for the total number of reactions since the big bang as being 10exp193, it is easy to see that the universe has not been around for long enough to cover even a small fraction of these 10exp260 proteins (6). In fact, Kauffman posits that it would take 10exp67 times the current age of the universe to cover all possible protein combinations for a protein of this size (6).

We can forget the idea of ever being able to cover the full panoply of amino-acid combinations for a 200 amino-acid long protein. Nevertheless can we find solace in the context of the cell where catalytic events may speed up the rates of reaction and thus cram the adjacent possible into the incredibly short? The answer here is an even flatter no. To understand why, we must visit another of Kauffman's key ideas, that of 'self-organized criticality' (7). When we say that cells are subcritical, what we are really saying is that they have an extremely constrained rate of expansion of molecular diversity- much more constrained than Kauffman's adjacent possible biosphere. If it were much faster, cells would invariably die. We now know that viruses and bacteria are well below this so-called error catastrophe (7).

What does this mean for the exploration of the vast molecular space? Simple- the organization of molecules into a cellular 'living' context does nothing to shorten the time required to find those 200 amino-acid long proteins that are going to perform useful functions. In fact, because of their subcritical state, the search for functional proteins in a cell only becomes more drawn out. Molecular biologists Jean Jacques Toulme and Richard Giege point out how nature just has not had the time to visit the vast extent of combinatorial space that defines the protein world (8). In true neo-Darwinian style, they nevertheless assure us that the current repertoire of proteins could easily have evolved from a selected few precursors (8). If that is not blind faith, I do not know what is.

Further Reading
1. M. Mitchell Waldrop (1992), Complexity, The Emerging Science At The Edge Of Order And Chaos, Simon & Schuster, New York, pp.49
2. ibid p.122
3. ibid p.123
4. Stuart Kauffman (2000), Investigations, Published by Oxford University Press, New York, p.142-144
5. Stephen Meyer (2009) Signature In The Cell: DNA And The Evidence For Intelligent Design, Harper Collins Publishers, New York, p.262
6. ibid, p.142
7. ibid pp.152, 207-209, 216, 244
8. Jean-Jacques Toulme and Richard Giege (1997), Une introduction a la science des aptameres; Atelier de formation INSERM, 'Strategies combinatoires pour la selection d'oligonucleotides a fonction predefinie: applications en biologie'

by Denyse O'Leary
ARN correspondent

Here's the reason I asked why human evolution should be taught in school:

I just came across this fact: Human evolution: Little is known other than basic outline

Contrary to widely heard huffing, there are huge gaps in our understanding of early humans. In Nature's 2020 Visions (7 January 2010) Scroll down to Leslie C. Aiello, and we learn

Most of the recent effort in hominin palaeontology has been focused on Africa and Europe. But the announcement in 2004 of the small hominin Homo floresiensis in Indonesia was a warning that we are naive to assume we know more than the basic outline of human evolutionary history. ... Go here for more.

Sorry to be so long judging this one, but there were 143 posts and I had several local issues to deal with at the same time. Now, to business: The winner is Collin at 8. His succinct entry appears below. I would also have awarded a prize to EvilSnack at 48, for this entry, but I only received one copy of David Berlinski's The Deniable Darwin. I will see if I can procure another copy, but if not EvilSnack may contact me anyway. I have other prizes on my shelf.

Winners need to be in touch with me at oleary@sympatico.ca, with a valid postal address. Their names will not be added to a mailing list. There is no mailing list.

Here's Collin:

Human evolution ought to be taught in schools because it is one of the best cases for common descent. This is probably a result of the extra interest among scientists concerning human evolution.

Even creationists and students sympathetic to ID ought to be taught the best argument for Darwinism so that if they want to argue against it they do so against the best scenario the opposition has to offer. Otherwise, those supportive of traditional Darwinism will sense a straw man argument and end up being inoculated against further, more refined and honest arguments.

Some careless creationists in the '80s made this mistake causing further, more compelling arguments to be dismissed before being further evaluated.

Human evolution, being taught, does inform students of a lot of ideas that are not necessarily against ID or even creationism. Presumably even creationists (most of them) will concede that homo erectus did exist as some kind of now-extinct species. Students can be presented with the fact of the bones (or lack thereof) and they can make their own conclusions. My hope is that teachers will present evolution's best arguments but not endeavor to indoctrinate students. Maybe that is a fine line, but it can be done, and is the honest way to go about it.

What swayed me was Collin's emphasis on hearing both sides honestly represented by their own advocates. If schools do not teach students to evaluate on that basis, they are not worth the money we spend on them.

Consider a simple example: Most days, I ride the Toronto Transit System, which features a vast array of busboard ads and subway posters advocating every cell phone offer imaginable. You can be sure that the sales person will not emphasize strongly to the customer, "Our offer is the cheapest - but, of course, we do sign you up for three years, and it costs you $300 to cancel."

The salesperson's competitor does that. The competitor shouts from busboards, subway posters, and billboards, "No contract, no cancellation fee!" That sets the customer thinking about what to ask next time, doesn't it?

Cell phones are a minor matter, of course. But later in life, the student will deal with job offers, marriage proposals, mortgage offers, investment advice, medical plans .... The advocate's offer can only be evaluated by hearing alternatives, clearly spelled out.

One of my major objections to "Darwinism-only" biology education is that - apart from the fact that I don't think it is true - it is not a good way to teach.

Other comments follow:

Read more!

By Robert Deyes
ARN Correspondent

2010 sees the beginning of a new series in Spanish exploring key findings from contemporary science that support the intelligent design inference. The series Paseos Por La Naturaleza (A Walk Through Nature) 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.
Second installment can be found at:

Paseos Por La Naturaleza

OIACDI

(transl: New Intelligent Design Book A Landmark Assault On Scientific Naturalism)

Synopsis Of Chapter Eleven, Signature In The Cell by Stephen Meyer
ISBN: 9780061894206; ISBN10: 0061894206; Imprint: HarperOne

By Robert Deyes
ARN Correspondent

Biological determinists will argue on the assumption that universal laws undergird the origin of life. Such an appeal to natural law is of course not a novel one. Indeed even thousands of years ago Aristotle philosophized over the existence of some universal organizing principle that could shape life into the easily identifiable forms we see today. From a protein sequence perspective Pennsylvania State University biochemists Gary Steinman and Marian Cole gave seemingly empirical substance to the idea that there were certain combinations of amino acids that were more likely to form as a direct result of amino-acid bonding energies.

Along the same grain, biophysicist Dean Kenyon became a die-hard advocate of the view that proteins first assembled into functional entities through the selective affinities that specific amino acids had for one another. To be sure, Kenyon believed that specific protein sequences were somehow predestined to form as a direct result of such constraints. The title of his much-respected tome Biochemical Predestination, which he co-authored with Steinman, became a spark that served to boost his credibility. But as his joint book garnered strength as a staple text for biochemistry graduate studies in the 1970s, Kenyon himself began to have personal doubts over the validity of his own proposition. Interviewed as part of the Discovery Institute's documentary Unlocking the Mystery Of Life, Kenyon's own testimonial brought clarity to the depth of his ongoing struggles:

"There was this enormous problem of how you could get together into one tiny sub-microscopic volume of the primitive ocean all of the hundreds of different molecular components you would need in order for a cell replicative cycle to be established. And so my doubts into whether amino acids could order themselves into meaningful biological sequences on their own without pre-existing genetic material being present just reached an intellectual breaking point. The more I conducted my own studies including a period of time at the NASA Ames Research Center the more it became apparent that there were multiple difficulties with the chemical evolution account".

I first learned of Kenyon's misgivings in the Foreword he wrote for another ground-shifting manifesto The Mystery Of Life's Origins where he noted how it was the information-bearing attributes of both polynucleotide and polypeptide sequences that he had found most vexing and unexplainable. For Stephen Meyer, his own philosophical pilgrimage brought him to the writings of Michael Polanyi who at the end of the 1960s argued that the language-style content of DNA could not be reduced to the mere operation of natural and physical laws. Just as the ink on a paper could not explain the message communicated on a printed page, so the information conveyed in a DNA molecule transcended the chemical and physical properties of its smaller component subunits.

The structures of DNA and RNA presented no escape chute for the chemical evolutionist. As with proteins, there were no constraining forces or 'differential affinities', this time along the phosphate backbones of DNA and RNA, that would make any given base sequence more likely than any other. Meyer transpicuously relays this point to the reader by comparing the base letters of DNA and RNA to magnetic letters on the metallic surface of a refrigerator (For further discussion see We Have No Excuse: A Scientific Case for Relating Life to Mind by Robert Deyes and John Calvert). In the same way that the placing of such letters into meaningful strings cannot be reduced to the magnetic forces between them and the refrigerator, so the information-carrying aspects we observe in DNA and RNA bases cannot be attributed to physical and/or chemical constraints.

Constructing his case on the shoulders of prominent philosophers and scientists, Meyer shows how the absence of biological determinacy is a fundamental feature of both codon/amino-acid assignments and the correspondence between amino acids and their respective tRNA molecules. The need for sequence "freedom" in DNA is imperative if it is to be a molecule of "virtually unlimited novelty" that can store information. To draw yet again from one of Meyer's outstanding depictions, there is no more inevitability in the assembly of functional genes from the ground up than there is in the construction of the palace of Versailles from bricks and mortar.

by Denyse O'Leary
ARN correspondent

A while back, I wrote about a self-absorbed female Darwinist* who was misshelving Mike Behe's Edge of Evolution in the "religion" section of the bookstore, to make some odd personal point:

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).