The ID Report

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).

by Denyse O'Leary
ARN correspondent

Listen to these, and don't have a fight with someone on your cell phone while driving:

1.

Moving the Goalpost: How Darwin's Theory Survives

It's easy to win the game when you can move the goalpost.

On this episode of ID the Future, biologist and Discovery Institute Senior Fellow Jonathan Wells explains how Darwinism, unlike football, has only one rule: survival of the fittest. The fittest are those who survive, and Darwinists are determined to survive at all costs—even if it means moving the goalpost.

Go here to listen.

(Note: This one is quite interesting because Wells talks about how his observation that a specific type of speciation needed by Darwinism has not been observed was recently distorted in a science mag to say that speciation - as such - has never been observed. This tells me that the commitment of many scientists to Darwinism is not to the idea of speciation as such, but to a broader philosophical commitment to a method by which it must happen, a method that supports broader philosophical ideas. Remember that 78% of evolutionary biologists are pure naturalists - no God and no free will.)

2.

Is the Cell Like a Computer?

On this episode of ID the Future, Casey Luskin interviews Dr. Donald Johnson, author of Probability's Nature and Nature's Probability: A Call to Scientific Integrity. As both a chemist and a computer scientist, Dr. Johnson explains how the cell uses programming code, much like a computer, and he elucidates how the information is processed and converted from proteins into DNA. Listen in as Dr. Johnson shares the science of how the cell is like a computer.

Donald E. Johnson holds PhDs in Computer & Information Sciences from the University of Minnesota and in Chemistry from Michigan State University. He can be reached at his website,ScienceIntegrity.net.

Go here to listen.

(Note: In two important way, cells are not like computers. When my machine is bust, it is just bust, and my local nerd must visit. If I need a new one, it must be bought and unpacked, and inevitably, I will need him back again as something is sure to go wrong. Millions of cells die every day and are replaced, with no loss of function. Fancy that, computer!)

3.

Alfred Russel Wallace: Champion of Natural Selection or Intelligent Design?

On this episode of ID the Future, CSC's Robert Crowther takes a look at Alfred Russel Wallace, who, along with Darwin, co-presented the theory of natural selection in letters to the Linnean Society of London over 150 years ago. Contrary to Darwin, Wallace actually believed that it was possible to detect design in nature. What would modern Darwin defenders make of Wallace today? Listen in and find out.

Go here to listen.

(Note: Actually, they have been doing a number on Wallace for centuries, as Mike Flannery points out. Go here or here for an example. Wallace, with thought design played a role in evolution, was just not as useful for propaganda purposes and was of a much lower social class than Darwin. Here is somewhat from my review of Flannery's book.)

4.

Deepening Darwin's Dilemma With Jonathan Wells

This episode of ID the Future features biologist and Discovery Institute Senior Fellow Jonathan Wells, who explains why Darwin saw the Cambrian explosion as a serious argument against his theory. Darwin countered it by supposing that fossils of the ancestors of Cambrian animals once existed, but were destroyed.

Listen in and learn how the discovery of microscopic and soft-bodied Precambrian fossils makes Darwin’s excuse sound hollow.

(Note: It gets better. The Smithsonian sat on the Cambrian fossils for decades because they did not support Darwin's theory. Yes, yes, that Smithsonian, currently alleged to have pressured California Science Center into cancelling a Cambrian film that - I gather - raises the Cambrian problem. [Almost all modern phyla of life forms appeared rather suddenly about 550 million years ago. This is just not the story Darwin was telling and he knew it and so did his supporters, and now so do more and more people.])

Any chance all those dusty drawers in the Smithsonian's cellar will be seized as evidence? Maybe we could learn something, and not about the current functionaries' e-mails.

Free advice to the public in general, not to anyone in particular: Do NOT feed bones to the shredder. Nor paper clips. Never feed anything but paper to the shredder, and feed paper with staples only if the firm warrants that the shredder will accept staples.]

5.

"A Matter of Dismal Wet Plops": Stephen Meyer Interviews David Berlinski on Darwinism

This episode of ID the Future features a clip from the recent "Signature in the Cell" event in Tampa, FL, featuring Stephen Meyer, Michael Medved, David Berlinski and Tom Woodward. Listen in as Dr. Meyer interviews Dr. Berlinski about the questions that led him to criticize Darwinism.

(Note: Besides being brilliant, Berlinski, a mathematician, is as funny as heck - not always a common combination. We are all familiar, I suppose, with the genius who doesn't get a joke. Well, that's not him, as the title of this pod suggests. I had a lot of fun reading his Devil's Delusion, a shot at publicly funded nonsense in science, of which many people are getting royally tired. Science advisor to Marie Antoinette, check your e-mail.

Never forget: Most people fund science because they think it will help find cures for cancer or get one's country a Nobel Prize in physics [and ain't we proud!] or offer one's kid a stable, respectable job wearing a lab coat. So take that away - make science mean folly about Stone Age Man, exposed e-mail plots, court cases about broken contracts, reasonable doubts subjected to inquisition and persecution - and what happens?

One thing that might very well happen is that people who used to just sigh and pay the bill might start thinking differently. As in ... we've got the headache already, Now, where is the payload?)

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).