The Searchers

AUTHORS: William A. Dembski and Robert J. Marks II

SOURCE: Proceedings of the 2009 IEEE International Conference on Systems, Man, and Cybernetics. San Antonio, TX, USA – October 2009, pp. 2647-2652

COMMENTARY: Allen MacNeill

First, congratulations to Drs. Dembski & Marks! Publication is the life blood of all career academics and the living heart of the intellectual process. It takes courage and hard work (and a little bit of luck) to get your original work published, and more of the same to weather the criticism that inevitably ensues. But, just as one cannot have a fencing match without an opponent, real progress in any intellectual endeavor cannot come from consensus, but only from the clash of ideas and evidence.

And so, to specifics:

I have no quibble with most of the mathematical analysis presented. Indeed, given the assumptions upon which the authors' Conservation of Information (COI) theory is based (with which I do not necessarily agree, but which are clearly presented in their paper), the analysis presented is apparently not completely outside the domain of No Free Lunch (NFL) theorems in general.

However, the same cannot be said for the application of these ideas to biological evolution. To be specific, consider the following quote [Dembski & Marks (2009) pg. 2651, lines 2-5]:

"From the perspective of COI, these limited number of endpoints on which evolution converges constitute intrinsic targets, crafted in part by initial conditions and the environment." [emphasis added]

This is indeed the crux of the issue vis-a-vis biological evolution. While it is clearly the case that Simon Conway-Morris asserts that there is an apparently limited number of biological "endpoints", it is neither the case that Morris' viewpoint represents the core of evolutionary theory, nor that his point is relevant to the analysis of COI presented in Dr. Dembski and Marks' paper.

To be specific, the highlighted qualifier from the quote above – crafted in part by initial conditions and the environment – is precisely the issue under debate between evolutionary biologists and supports of intelligent design (ID).

Taken at face value, this qualifying simply phrase means that, given specific starting conditions and a specific time-varying environmental context, the various mechanisms of evolution (e.g. mutation, natural selection, genetic drift, inbreeding, etc.) tend to converge on a relatively limited set of genotypic and phenotypic "endstates" (i.e. what could be loosely referred to as "evolutionary adaptations").

This is simply another way of defining evolutionary convergence, and in no way constitutes evidence for intrinsic evolutionary teleology. On the contrary, it simply provides support for the hypothesis that, given similar conditions, similar outcomes result.

Furthermore, it assumes that virtually all characteristics of living organisms are adaptations (that is, genotypic/phenotypic characteristics that fulfill some necessary function in the lives of organisms). However, this is manifestly not the case, nor is it an absolutely necessary component of current evolutionary theory. On the contrary, many (perhaps the majority) of the characteristics of living organisms are not adaptive. This is certainly the case at the level of the genome, as evidenced by the neutral and nearly neutraltheories of molecular evolution.

Finally, Morris' (and, by extension, Dembski and Marks') position completely omits any role for historical contingency, which both the fossil and genomic record indicate are of extraordinary importance in macroevolution. As Dembski and Marks state, the "endpoints" (perhaps it would be more precise to refer to them as "way stations") of macroevolution depend fundamentally on initial conditions and the environment. But this is not fundamentally different from Darwin's position in the Origin of Species:

"The complex and little known laws governing variation are the same, as far as we can see, with the laws which have governed the production of so-called specific forms. In both cases physical conditions seem to have produced but little direct effect; yet when varieties enter any zone, they occasionally assume some of the characters of the species proper to that zone." [Darwin, C. (1859) Origin of Species, pg. 472, emphasis added]

Moreover, Dembski and Marks' analysis completely ignores the appearance (or non-appearance) of new genotypic and phenotypic variations, and on the accidental disappearance of such characteristics (via extinction), without regard to the adaptive value of such characteristics, or the lack thereof.

In other words, Dembski and Marks' analysis, while interesting from the standpoint of what could be called "abstract" search algorithms, completely fails to address the central issues of evolutionary biology: the source of evolutionary novelty (i.e. the "engines of variation"), the effects of changing environmental conditions on the actual forms and functions of living organisms, and the fundamental importance of historical contingency in the ongoing evolution of genotypes and phenotypes.

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As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

The Longest Running Failed Prediction in Creationism

AUTHOR: G.R. Morton

SOURCE: Answers in Science

COMMENTARY: Allen MacNeill

First, today is the 150th anniversary of the original publication of Charles Darwin's Origin of Species. So many people have written about this event that it would be superfluous for me to write about it here. However, some of what has been written about the Origin lately, mostly by creationists and supporters of "intelligent design", is that Darwin's theory of evolution by natural selection is "crumbling" and will soon be "dead".

Admittedly, I have written recently that the "modern evolutionary synthesis" is dead (see here for more), but in doing so I have taken pains to point out that the theory of evolution itself is most assuredly not dead. On the contrary, it is very much alive. Indeed, it has never been more vigorous than it is today.

But that's not what the creationists are saying. What they're saying (or trying to say) is that the whole concept of evolution itself is dead: the Earth and everything on it was created a relatively short time ago, and even if life on Earth has changed (a little), all of that change has been guided by the deity of the Abrahamic religions (Judaism, Christianity, Islam, Mormonism, etc.) Indeed, just this morning a new podcast was launched at the website of the Discovery Institute, in which neo-Paleyist and ID creationist John West asserts once again that "Darwinism is dead".

Is this news? And is it new? How long have creationists been predicting the demise of Darwin's theory of evolution? Apparently, they've been doing so since a few decades before Darwin published it. G. R. Morton has compiled a short list of quote from creationists predicting the impending overthrow of the theory of evolution (you can read it here). He introduces his anthology of science denialism with this:

In recent reading of [Dr. William] Dembski and other ID proponents I saw them make a claim which has been made for over 40 years. This claim is one that the young-earthers have been making. The claim is that evolution (or major supporting concepts for it) is increasingly being abandoned by scientists, or is about to fall. This claim has many forms and has been made for over 162 years. This is a compilation of the claims over time. The purpose of this compilation is two-fold. First, it is to show that the claim has been made for a long, long time. Secondly, it is to show that entire careers have passed without seeing any of this movement away from evolution. Third, it is to show that the creationists are merely making these statements for the purpose of keeping hope alive that they are making progress towards their goal. In point of fact, no such progress is being made as anyone who has watched this area for the last 40 years can testify. The claim is false as history and present-day events show, yet that doesn't stop anyone wanting to sell books from making that claim.

Morton's quotations from creationists begins with a quote dating to 1825, 34 years before Darwin published the Origin of Species. Apparently, what many historians have asserted was true: that the idea of evolution was "in the air" in the mid-19th century, and that Darwin simply codified and provided evidence for an idea that was already becoming generally well-known and at least partially accepted. The fact that Alfred Russell Wallace came up with the same mechanism that Darwin did for descent with modification — natural selection — is further evidence for the idea that evolution was "in the air" at the time.

It still is, and even moreso. Not only has the theory of evolution not "crumbled", it is currently undergoing its most rapid expansion since 1859. Darwin's original theory was limited strictly to biological evolution, but now his theory is being extended into astrophysics, geology, economics, psychology, sociology, and even literature and art history. It is this tremendous success that upsets the opponents of Darwin's theory, and that impels them (in the face of overwhelming evidence to the contrary) that the most widely accepted, most generally applicable, and most analytically powerful theory in all of science is on its way out.

In other words (and true to their creationist roots), they stare reality in the face and deny it.

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As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

Intelligent Design is Boring

At a thread at another website discussing the idea that ID is "boring", an ID supporter wrote this:

"[ID] is boring to Will [Provine] I suspect (and to others for the same reason) because they rule out the possibility of an intelligent designer."

Actually, knowing Will Provine pretty well and hearing him say that ID is "boring" on several occasions, I can confidently state that the reason he finds it "boring" is that whenever something interesting in biology is discovered and somebody asks "Why is that thing the way it is?" Will hears most ID supporters answer "Goddidit". His opinion of ID is that it's a science-stopper because rather than suggesting new and interesting ways of trying to figure out how something came to be the way it is, he thinks that IDers simply throw up their hands and say "It's too complicated, so God / the Intelligent Designer must have done it".

Personally, I don't find ID boring for quite the same reason, as I don't always see ID supporters resorting to the "Goddidit" pseudoexplanation. No, the reason I tend to find most ID boring is it's relentlessly negative. That is, people like Michael Behe and William Dembski observe something marvelously complicated and say "That's Irreducibly Complex!" or "That's Complex Specified Information, so it couldn't have evolved via naturalistic means"...and then they leave it at that. No alternative means of creating the marvelously complicated thing is proposed (unless you credit Behe's "puff of smoke" pseudoargument).

Furthermore, I generally don't see ID supporters doing any original empirical research. In particular, I don't see any of them going out into the field (my favorite place to discover things) or into the lab and "getting down and dirty" with some biological phenomenon that they find absolutely fascinating.


My friend, Harry Greene (the world's authority on rattlesnakes) is my idea of a real scientist. He absolutely loves snakes, talks about them at the drop of a hat, has spent his entire professional life studying them in the field and in the lab, and has revolutionized our understanding of the ecology, ethology, and evolutionary biology of reptiles. To me, he's the epitome of an evolutionary biologist, because he has what we call "a feel for the organism" which goes far beyond simply studying it as an experimental subject.


And my friend, Lynn Margulis (the world's authority on endosymbiosis) is also my idea of a real scientist. She absolutely loves getting knee-deep in the mud of some tropical lagoon and scraping scum off of rocks to look at under the microscope. She's spent her entire professional life studying microorganisms in the field and in the lab, and has revolutionized our understanding of the evolutionary biology of microorganisms. Like Harry, she's the epitome of an evolutionary biologist, because she also "a feel for the organism" which leads her to discover things nobody ever thought to look for before, such as symbiotic bacteria embedded in the cell membranes of symbiotic protozoa from the guts of termites.

I have yet to meet or hear about or read about any ID supporter who does anything like what Harry and Lynn do. Yes, Michael Behe is a biochemist, but the things he does in his laboratory at Lehigh have little or nothing to do with ID. And William Dembski wouldn't know an actual living organism if it lunged out and bit him on the ankle.

Biology, and especially evolutionary biology, is that branch of the natural sciences founded and maintained by people who loved and were obsessed with nature and natural things. Darwin and Wallace and Fisher and Haldane and Wright and Dobzhansky and Mayr and Simpson and Stebbins and Hamilton and Trivers and Margulis and the two Wilsons (Edward O. and David Sloan): these are my heroes, and they are the "naturalists" (see how the word has another, much more positive meaning?) who have been the inspiration for my research, insignificant as it is compared with theirs.

And all that IDers can generally do is say "No, you're wrong, it can't happen that way, in fact it can't happen at all without a deus ex machina?" Ugh: boring, pointless, and most of all, no "feel for the organism".

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As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

Just Another One of the Boyz in the Banned...

Just a quick note to say that I have apparently once again been "moderated" off of the threads at Uncommon Descent. Apparently my comments were cutting a little too close to the bone. One could almost say I'd been Expelled (No intelligence Allowed)...

And to Timaeus and others from UD: I will be indirectly responding to some of the posts at Uncommon Descent here (time and weather permitting, of course).

The IDEA Dodo Tries to Fly...

AUTHOR: Allen MacNeill

SOURCE: Original essay

COMMENTARY: That's up to you...

URGENT: Really big news from the national IDEA Center: They aren't dead...yet!

Well, that's nice. But if you follow the link, you will find that according to their own report, the IDEA network currently includes

"...about [sic-1] a dozen IDEA Club chapters that are active or in-formation.[sic-2]"

Interesting; back in December 2005, Dr. William Dembski wrote that

"...there are thirty such centers [sic-3] at American colleges and universities..."

From 30 "centers" (i.e. "clubs") in December 2005 to "about a dozen that are active or in-formation" in January 2009. To me (and admittedly I'm not a mathematician...more's the pity), that indicates a decline of at least 60% since 2005. And that assumes that all of the clubs included in the "dozen that are active or in-formation" now actually exist. That is, they meet now and then, and a few people show up for their meetings.

Of course, we have no way of empirically verifying whether any of the "about a dozen" clubs actually exist or not. However, what anyone with a web connection can empirically verify is that the links to "active" IDEA clubs posted at the national IDEA Center have not changed. They are all either dead (i.e. they return a 404: File Not Found message) or they lead back to old press releases from the national IDEA Center.

A spokesperson for the national IDEA Center (could it be Casey himself?) claims that they are diligently updating these links and will soon post a new map and list with new hot links to new active IDEA clubs. Well, could be; they will be able to do this if such clubs actually exist and are meeting now and then.

So, I propose a new empirical investigation (that's what science is all about, right?). Let's all return periodically to the page at the national IDEA Club that lists the links to "active" IDEA clubs and see if they have been updated. If they have, and they include information on recent activities at those clubs, then we can conclude that the IDEA club movement really isn't dead, it's just restin' on account of bein' tired and shagged out after a long squawk (like the Norwegian blue; beau'iful plumage...).

But, if the links don't get updated, or they are but there are no new activities listed, then we can conclude that their self-reports of their non-demise will have been greatly exaggerated.

As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

Oh, and here's the explanation of the sics:

[sic-1] "...about a dozen..." Odd, most people don't have trouble counting up to twelve. Is it "a dozen" or eleven, or six, or one, or what? If anybody should know, it should be the people in charge, right?

[sic-2] "in-formation" Would that have anything to do with Dr. Dembski's soi dissant "Law of Conservation of Information"? Or does it mean that a couple of people have been thinking about getting together to talk about ID sometime? Just curious...

[sic-3] Dr. Dembski's "ID centers", would those be the little group of two or three ID supporters huddled in a corner of the student union cafeteria, talking about the "evilutionists" and ending their "center's" activities with a prayer? Sounds like a major "ID research center" to me...

The "Intelligent Design" Movement on College and University Campuses is Dead

AUTHOR: Allen MacNeill

SOURCE: Original essay

COMMENTARY: That's up to you...

On 22 December 2005, I posted a critical analysis of a press release on the Kitzmiller v. Dover decision, written by Dr. William Dembski, one of the founders of the "intelligent design" movement (Dr. Dembski's press release is apparently no longer available online). My analysis of Dembski's press release was hosted by Ed Brayton at his blog, Dispatches from the Culture Wars (you can find it here). In my analysis, I noted that Dr. Dembski had made a series of statements that were so divergent from the actual facts that they could be interpreted as symptoms of delusional thinking on the part of Dr. Dembski, if not deliberate falsehoods.

Here's the claim by Dr. Dembski that I would like to re-examine in this post:

Three years ago, there was one Intelligent Design and Evolution Awareness (IDEA) Center at the University of California-San Diego. Now there are thirty such centers at American colleges and universities, including UC Berkeley and Cornell. These centers are fiercely pro-ID. [emphasis added]

Dr. Dembski strongly implied in his press release that these IDEA Centers were essentially research centers, such as those commonly found at college and university campuses.

Well, they aren't...or, rather, weren't. They weren't "research centers" or anything like it. They were clubs, similar to the kinds of student-centered special interest clubs that abound on most college and university campuses. Such clubs have several characteristics in common:

1) they are founded, supported, and run by students (sometimes with support from affiliated national organizations),

2) they often have to have permission from the administration to use classrooms or other facilities for meetings, and

3) they sometimes receive funding from students, derived from student activities fees.

To do these things, campus organizations typically have to show that they have no political or religious requirements or ties, as this could jeopardize the academic institution's not-for-profit educational status. This was a problem for IDEA Clubs, for several reasons:

1) they were usually founded, supported, and run by students who received encouragement and training to do so from the national IDEA Center, a spinoff of the Discovery Institute in Seattle, Washington, the political "nerve center" of the "intelligent design movement";

2) the IDEA Clubs often met in campus classrooms or other facilities; and

3) some IDEA clubs did in fact receive funding derived from student activities fees.

This was problematic for two simple reasons:

1) the Discovery Institute receives much of its funding from religious organizations, especially those supported by Christian "reconstructionist" Howard Ahmanson (that this is the case can be easily verified by reading the so-called "wedge document", formulated by the Discovery Institute as a fund-raising tool);

2) the IDEA Center required that the founders and officers of the IDEA Clubs they helped organize and support be Christians.

This was the case for the IDEA Club chapter founded at Cornell University, with whom I had several debates and public meetings. The requirement that the Cornell IDEA Club's officers be Christians was withheld from its membership by its founders until it was made public by their opponents. This caused dissension within the club and eventually led to the modification of this policy by the national IDEA Center administration.

And so, to the purpose for this post: it appears from all indications that the IDEA Club "movement" (and, by extension, the "intelligent design movement" as a whole) is dead. You can verify this by going to the website of the national IDEA Center and clicking through the various links located there. I did that this morning, and found it very enlightening. To save you time, here is what I found (the links are listed first, followed by what they lead to):

Upcoming Events: empty (no events listed)

Press Releases:: except for a press release on "Expelled: No Intelligence Allowed" (the movie) and the online publication of the Spring, 2008 Light Bulb Newsletter (see below), the most recent press release is dated 11/11/06

Classes & Seminars: last updated spring 2004

IDEA Conferences: none

ORIGINS News Updates: last updated 2005

The Light Bulb Newsletter: started publication online (.pdf format) in 2002; listed as quarterly, but only eight out of twenty-six issues have been posted; most recent issue (Summer 2008) consisted almost entirely of a review of the movie "Expelled" (see link, above)

Listserves & Discussion Boards: none

Events Archive: last updated 05/24/07, previously updated on 07/26/03

Student Training Conferences: (for students interested in forming an IDEA Club) last conference held on 09/27-28/02

Ah, but this only indicates that the national IDEA Center is now moribund. Surely something is happening in the 35 international chapters, located at high schools, community colleges, colleges, and universities around the world? Well, here's the list, followed by what you find when you click on the link:

Armstrong Atlantic State University (GA): last updated 01/09/06; virtually no content

Baraboo IDEA Club (academic affiliation not listed) (WI): 404:File Not Found

Braeside High School, Nairobi, Kenya: IDEA Center press release, dated 09/15/03; when link to actual site clicked, received 404:File Not Found

California State University, Sacramento (CA): no events, no content, last updated 11/14/02

Cornell University (NY): when link to actual site clicked, received 404:File Not Found; blog last updated on 03/11/07

Fork Union Military Academy (VA): IDEA Center press release, dated 08/14/04; no actual website or content linked or listed at associated institution

Franciscan University of Steubenville (OH): IDEA Center press release, dated 03/12/04; no actual website or content linked or listed at associated institution

George Mason University (VA): IDEA Center press release, dated 04/06/05; no actual website or content linked or listed at associated institution

Hillsdale College (MI): IDEA Center press release, dated 09/20/03; no actual website or content linked or listed at associated institution

James Madison University (VA): IDEA Center press release, dated 04/06/05; no actual website or content linked or listed at associated institution

Midwestern State University (TX): IDEA Center press release, dated 04/13/04; no actual website or content linked or listed at associated institution

Myers Park High School (NC): when link to actual site clicked, received 404:File Not Found

Poway High School (CA): no content or events listed (no date listed for last update)

Pulaski Academy (AR): IDEA Center press release, dated 09/15/03; no actual website or content linked or listed at associated institution

Scripps Ranch High School (CA): IDEA Center main website homepage; no actual website or content linked or listed at associated institution

Seattle Central Community College (WA): when link to actual site clicked, received 404:File Not Found

South Mecklenburg High School (NC): IDEA Center press release, dated 08/14/04; no actual website or content linked or listed at associated institution

Stanford University (CA): IDEA Center main website homepage; no actual website or content linked or listed at associated institution

Tri-Cities IDEA Club (WA): no events listed; last updated on 05/08/08

University of California, Berkeley (CA): 403:Access Forbidden

University of California, San Diego (CA): when link to actual site clicked, received 404:File Not Found

University of Illinois, Urbana-Champaign (IL): IDEA Center press release, dated 04/06/05; no actual website or content linked or listed at associated institution

University of Mississippi ("Ole' Miss") (MS): IDEA Center main website homepage; no actual website or content linked or listed at associated institution

University of Missouri (MO): IDEA Center main website homepage; no actual website or content linked or listed at associated institution

University of Nebraska, Lincoln (NE): when link to actual site clicked, received 404:File Not Found

University of Oklahoma (OK): when link to actual site clicked, received 404:File Not Found

University of the Phillipines: IDEA Center press release, dated 07/11/04; no actual website or content linked or listed at associated institution

University of Texas, Dallas (TX): no events listed; last updated on 06/14/05

University of Victoria (BC): no events listed; last updated May, 1999

University of Virginia (VA): IDEA Center press release, dated 08/14/04; no actual website or content linked or listed at associated institution

Vanderbilt University (TN): IDEA Center main website homepage; no actual website or content linked or listed at associated institution

Wake Forest University (NC): IDEA Center press release, dated 04/06/05; no actual website or content linked or listed at associated institution

Western Baptist College (OR): IDEA Center press release, dated 04/06/05; no actual website or content linked or listed at associated institution

Westminster College (MO): IDEA Center press release, dated 04/06/05; no actual website or content linked or listed at associated institution

And there you have it: not one of the IDEA Clubs affiliated with an academic institution is still functioning. Indeed, only one of the clubs listed has even updated its website during the past year (the Tri-Cities IDEA Club).

UPDATE (01/04/09): The Tri-Cities IDEA Club website has now descended into "Under Construction/Placeholder" Hell, and so all of the current links to IDEA Clubs at the national IDEA Club website are currently non-functional.

Furthermore, a quick statistical analysis is also illuminating:

1) there are 39 IDEA Clubs listed, not 35 (as stated at the IDEA Club main website);

2) of the 39 listed IDEA Clubs, eight (21%) are located at high schools or community colleges;

3) four (17%) are located at religious institutions;

4) nine (23%) simply do not exist (i.e. have 404: File Not Found at their link); and

5) 18 (46%) have links that simply redirect to either a national IDEA Center press release or main website homepage.

These are the "intelligent design research centers" about which Dr. Dembski spoke so glowingly in his analysis of the effects of the Kitzmiller v. Dover Area School Board decision.

What can one conclude from this analysis? I conclude five things:

1) that the national IDEA Club website is essentially what is known online as a "shell site" (that is, a place-holder with no real content);

2) that the "movement" represented by the IDEA Club organization peaked in late 2005 or early 2006 (around the time of the Kitzmiller v. Dover trial);

3) since then (i.e. since Judge Jones issued his now-famous decision) it has died almost everywhere;

4) the majority of the output of the "intelligent design movement" consisted of press releases (and produced no empirical science of any kind); and

5) my conclusion in my critical review of Dr. Dembski's analysis of the Kitzmiller v. Dover Area School Board decision was essentially correct: he was (and probably still is) either delusional or a bald-faced liar.

So, why did I illustrate this post with a picture of a dodo? Because, like the "intelligent design" movement, the dodo was notorious for its stupidity and that fact that it is extinct.

UPDATE (09/01/09): All of the current links to IDEA Clubs at the national IDEA Club website are currently non-functional; if this keeps up, they may fossilize.

As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

Genetics and the Explanatory Filter

AUTHOR: Salvador Cordova

SOURCE: An Instance of Design Detection?

COMMENTARY: Allen MacNeill

There is a thread at Uncommon Descent in which the development of a commercial service for identifying Genetically Modified Objects (GMOs) is given as an example of industry use of William Dembski's "explanatory filter." Dembski claims that the "explanatory filter" can unambiguously identify "intelligently designed" entities, especially entitities in which information is encoded in a sequences of digital bits (as in the genetic code in DNA).

As one of the comments on the thread suggested that I would have a difficult time refuting this argument, my interest was piqued, and so here is my reply:

As has already been pointed out numerous times (not the least by William Dembski himself), Dr. Dembski has asserted that all biological entities are designed, as indicated by the fact that their nucleotide sequences are highly improbable, yet tied to a necessary biological function. However, if this is truly the case, then it should be literally impossible to separate GMO sequences from naturally evolved sequences using Dembski's "explanatory filter", since both types of sequences conform to his definition of "complex specified information."

However, since companies are able to distinguish between "natural" and GMO sequences at a level of reliability that real-world companies will pay them handsomely for their services, it is therefore clear that there is something fundamentally different between GMO sequences (i.e. sequences that really are designed by intelligent entities) and "natural" sequences (i.e. sequences that have evolved by natural selection and/or genetic drift). Therefore, I must conclude that, rather than providing evidence for the efficacy of the "explanatory filter," the ability to distinguish between genuinely "intelligently designed" and "natural" nucleotide sequences provides powerful evidence for the assertion that the difference between the two is the result of fundamentally different processes: "design" in the case of the former, and "natural selection/genetic drift" in the case of the latter.

(2) The idea that an "explanatory filter" can clearly and unambiguously distinguish between "intelligently designed" and "naturallly evolved" nucleotide sequences is directly contradicted by our experience with the structure and function of most adaptive genetic sequences. As just one example, consider the following nucleotide sequence: TTGACA-17 base pairs-TATAAT. Those of you with some knowledge of molecular genetics should immediately recognize this sequence as the "core" of a typical promoter; that is, a nucleotide sequence that is "recognized" (i.e. provides a binding site for) RNA polymerase during gene transcription. According to Dr. Dembski's model of "CSI", this sequence can only have come about via "intelligent design", because it has such a low probability of existing that for it to have arisen by chance is negligable.

However, as some of you may know, this sequence is actually the "consensus sequence" for the promoter. There are others, including (but not necessarily limited to) TAGACA-17 base pairs-TATAAT, TACACA-17 base pairs-TATAAT, ACCACA-17 base pairs-TATAAT, and TTCACA-17 base pairs-TATAAT. The probability of RNA polymerase binding to one of these alternative sequences is purely a function of how much the sequence deviates from the consensus sequence (i.e. it will bind least often to ACCACA-17 base pairs-TATAAT, as this sequence differs from the consensus sequence by three base pairs, whereas the other sequences differ by only one or two base pairs). The biological significance of this variability in base sequence in gene promoters is this: the regulation of gene expression is at least partly a function of the frequency at which such promoter sequences are bound to by RNA polymerase.

This means that deviations from the consensus sequence, rather than being "mistakes" which the "explanatory filter" should be able to identify as such, deviations from the consensus sequence are actually tied to the rate of gene transcription, which are in turn tied to rates of gene product function in the cell. For example, a gene product (i.e. protein) that is used very often in the cell would be coded for by a gene for which the promoter is very close to the consensus sequence, thereby causing the gene product to be synthesized more often. By contrast, a gene product used less often by the cell would be coded for by a gene with a promoter sequence that deviated more from the consensus sequence, and therefore would be transcribed and translated less often.

This means that deviations from the consensus sequence, rather than having less biological significance (and therefore more likelihood of existing by chance, and therefore less likelihood of being identified by Dembski's "explanatory filter"), would actually be just as biologically significant as the consensus sequence. In other words, if the "explanatory filter" is to be of any use at all, it must explain why random deviations from the consensus sequence (i.e. the "designed" sequence) are in reality just as important to cellular function as the consensus sequence itself, until suddenly (when none of the base pairs match the consensus sequence) the promoter stops functioning as a promoter at all. You can't have it both ways: either the functions of "deviant" promoter sequences are just as "designed" as the consensus sequences, or they aren't. But this means that essentially all nucleotide sequences are "intelligently designed", making the "explanatory filter totally useless for any meaningful investigation of genetic processes. Philosophically intriguing to a few theologically inclined non-scientists perhaps, but totally irrelevant to biology.

From the standpoint of natural selection, however, functions arising from deviations from the consensus sequence are exactly what one would expect, as natural selection is just as capable of exploiting random deviations as it is of exploiting "designed" (i.e. adaptive) sequences. Indeed, from the standpoint of natural selection, there are no such things as "designed" sequences; nucleotide sequences are only more or less adaptive, as reflected in their frequencies in populations. Some sequences are apparently not adaptive at all (i.e. they are not conserved as the result of natural selection) - we sometimes refer to such sequences as "junk DNA", although that term carries implications that do not reflect what we currently understand about non-adaptive DNA sequences. Other sequences (the ones that the "explanatory filter" is supposed to be able to distinguish) are adaptive at some level. However, the only way to tell if a sequence is actually adaptive is to be able to show, from the level of nucleotide sequence all the way up to phenotypic differences, that there is a statistically significant difference between the reproductive success (i.e. "fitness") associated with one sequence as compared with another. Until this is possible (and we are a long way from it), any attempt to rule out selection as the efficient cause of nucleotide sequences is pointless (as is the "explanatory filter").

--Allen