A paper published in the Proceedings of the National Academy of Sciences makes the startling claim that all flagellar genes “originated through the successive duplication and modification of a few, or perhaps even a single, precursor gene” (see abstract below). While consistent with Darwinian evolution, such excessive hyperevolution was too much even for the hyperevolutionists at the Panda’s Thumb (go here), who are now distancing themselves from its conclusion. What’s going on here? How could people publish such a ridiculous result, and in PNAS of all places? Let me suggest the following hypothesis: Liu and Ochman, the authors of the piece, are really ID advocates who are pulling a Sokal-style hoax, pushing the envelope to see how extreme they can Read More ›

I posted a reference the other day to a peer-reviewed paper by two Finnish ID-supporters that I claimed supported ID. The paper highlighted that evolutionary methods work to the degree that they are directed. As is typical with our detractors, whenever a pro-ID paper by pro-ID scientists comes out in a peer-reviewed biology journal, they try their best to show that it doesn’t actually support ID. An example is the following post at PT by Steve Reuland: pandasthumb.org…the_proid_paper In reading Reuland’s critique, try to keep track of “rational design,” “directed evolution,” and “Darwinian methods.” Reuland conflates the last two. In so doing, Reuland completely misses the boat. So let me spell it out: DIRECTED EVOLUTION IS NON-DARWINIAN. DARWINIAN EVOLUTION IS Read More ›

About one year ago, Sahotra Sarkar and I debated ID and evolution in front of an overflow audience at the University of Texas-Austin. Sahotra and I had known each other since the mid-1980s, when we were graduate students sharing Bill Wimsatt as our primary advisor. As background for the UT debate, Sahotra sent me a couple of chapter drafts from his forthcoming book on “creationism” — a book now available from Blackwell. One criticism that came up both during the debate [here’s some post-debate commentary], and in discussions at Austin bars afterwards, was the perception that ID bad guys circumvent the normal processes of scientific review by arranging debates in front of lay audiences, instead of academic peers. Having just Read More ›

Rarely does the public catch a glimpse of how Darwinists actually behave toward colleagues who disagree with their view of biological origins. Thus, as a public service, I’m presenting here a correspondence, initiated by Darwinists and unsolicited by our side, that provides readers of this blog with such a glimpse. Briefly, a Johns Hopkins biologist named David Levin sent an unsolicited and wonderfully insulting letter to Michael Behe (the entire letter is given toward the bottom of this post). Levin also attached a pdf of a Nature article (see the very bottom of this post). As it is, Levin copied Ken Miller, Richard Dawkins, and the usual suspects. Ken Miller, thinking that Levin had a slam-dunk against ID, then suggested to Levin that he also send me what he had sent Behe (presumably to crush my spirits). Here, then, is the exchange. To trace the chronology, you’ll need to start from the bottom and work your way up. I post Mike Behe’s response to Levin with Mike’s permission. After Behe’s response and my second response to Levin, we never heard from him again.

—– Original Message —–
Date: Thu, 22 Feb 2007 23:36:44 -0600
To: “David E. Levin”
From: “William A. Dembski”
Subject: Re: Fw: Evolution of a biochemical pathway by gene duplication and specialization
Cc: richard.dawkins AT zoo.ox.ac.uk, robison AT nucleus.harvard, aorr AT mail.rochester, rdoolittle AT ucsd, Kenneth_Miller AT Brown, lziska AT asrr.arsusda, Lisa West , Behe

Dear Dr. Levin,

I receive many unsolicited emails asking me to comment on how the theory of intelligent design deals with this or that objection to it. You are asking me to respond to an informal letter that you wrote to Michael Behe sketching out some worries you have about his notion of irreducible complexity. Let me suggest you write up your thoughts in a formal article and submit them to a peer-reviewed publication. Once it’s accepted, I’ll be happy to look at it more closely and offer comment. As it is, Michael Behe was gracious enough to send you some comment on your letter (I’ve pasted his comments below for continuity), though he appears much less impressed with your work than you are.

In your note to me below you write: “you seem incapable or unwilling to discuss the data or the inescapable conclusion that emerges from them.” Actually I’m quite willing. If you would like me to speak at your campus on the topic of intelligent design and address your data, I can put you in touch with my speakers bureau.

Best wishes,
Bill Dembski

—– Original Message —–
At 09:26 AM 2/22/2007, David E. Levin wrote:

Dr. Dembski,

You seem to have missed the point of my letter to Behe. It was not to bring to his attention the Kellis et al. paper. That was merely the starting point, the prerequisite understanding from which my work followed. It did not escape my notice that you had nothing whatever to say about my demonstration of how a real biochemical pathway has evolved to a more complex state. Perhaps all the biochemistry and genetics is beyond you.

Still, your criticism of the Kellis et al. paper was telling. Lets see, you asserted that it is now three years old, as though its age as some bearing on the validity of its conclusions. You clued into the phrases computational algorithm and statistical analysis as though such things invalidate any conclusions the authors might derive. These guys sequenced and assembled the genome of a species and aligned its eight chromosomes with the 16 chromosomes of another species. Yes, they used computers and statistics to assist them in their analysis. Its a 10 megabase eukaryotic genome! You sort of need computers and statistics to crunch all that information.

Whats important here is to look at the remarkable picture that emerges from this work. A species ancestral to the bakers’ yeast underwent a whole-genome duplication, followed by loss of most of the duplicated genes. This is how bakers’ yeast arrived at current genomic organization. As I said before, there is no other way to interpret these data. But you seem incapable or unwilling to discuss the data or the inescapable conclusion that emerges from them. I am taken aback by the extreme level of intellectual dishonesty that pervades the intelligent design circle. Your tactic is always to deflect and misdirect. Never mind the data, its old, or it uses statistics, or it presupposes common descent. Why are you so afraid of the data? Its as though you creationists have closed your eyes, covered your ears with your hands and are muttering to yourselves My mind is made up, dont confuse me with facts.

As for your assertion that nonteleological evolutionary mechanisms are not sufficient to drive the evolutionary process, I have provided an excellent example of precisely how this happens. Deal with it!

David E. Levin, Ph. D.
Professor
Dept. of Biochem. & Molec. Biol.
Johns Hopkins Bloomberg School of Public Health
615 N. Wolfe St.
Baltimore, MD 21205

Ph. (410) 955-snip
fax (410) 955-snip

—– Original Message —–
At 01:26 PM 2/22/2007, Michael Behe wrote:

Hello, Professor Levin, nice to meet you. Well, I see that even though you work in Baltimore, you’ve managed to avoid acquiring any Southern charm. Most folks consider it rude to send insulting, unsolicited mail to people you’ve never met, even if you don’t like their views. I hope at least you are polite toward people who agree with you.

Thanks for sending me the brief report on your work. Clearly you are excited about it, so I hope you don’t mind that I find it unimpressive even if your interpretation of events is correct. Here’s how I see your scenario: Roughly a hundred million years ago the ancestor of S. cerevisiae had a well-regulated, multicomponent pathway, including a prodigy protein, Mpk1, that had several activities. That complex pathway is taken by you for granted, as an unexplained starting point. Then the genome duplicated. In one of the duplicated copies of the prodigy protein a point mutation caused it to lose one of its pre-existing abilities. In the other copy of the prodigy protein, although it hasn’t happened yet in nature, you have in your own lab demonstrated that, by golly, a simple mutation can cause the other pre-existing ability to be lost too. I’m afraid I find all of that unsurprising. It has been known for quite a long time that mutations can inactivate protein functions.

The single gain of function in your whole story is the new binding site for Rlm1. That, however, is a comparably modest change; since the consensus binding sequence for MADS-box proteins is about ten nucleotides, with considerable redundancy, such a sequence would be expected to occur by chance perhaps every ten kilobases or so, and either to have been present in some segment of the population at the time of the genome duplication, or to be produced by point mutation very shortly thereafter. Such sites are thought to be gained and lost continually. At the very best then, assuming that modern Mpk1 eventually does lose the ability to activate SBF, according to your own scenario we are left with yeast that does pretty much the same thing with two very similar pathways that its ancestor did with one. And that meager (potential) result required enormous evolutionary resources: a hundred million years, whole genome duplication, and huge numbers of yeast likely many orders of magnitude more than the numbers of a vertebrate species that would be available in a similar span of time.

Frankly, I’m puzzled why that is supposed to be an example of the power of Darwinian processes. Id be happy to cite it myself as an illustration of genome drift within tight limits set by severe constraints. The trivial changes the scenario involves would be expected to have been available in the yeast population a very short time after the initial genome duplication event. Yet here we are twiddling our thumbs, tens of millions of years later, still waiting for the scenario to complete itself. This suggests to me that your scenario is overlooking many complicating factors, such straightforward issues as whether genome duplications or gain/loss of regulatory binding sites or loss of protein function even in a duplicated copy are deleterious, and whether there are useful functions close by existing functions. Such questions plague any simplistic Darwinian scenario, including the ones you cite that were proposed for the blood clotting cascade, but it seems few people are willing to take the difficulties seriously.

I wish you well with your work, Professor Levin. But please don’t write to me again unless you can restrain your childish sneers.

Sincerely,

Mike Behe

P.S. – I apologize for bothering all the people who were copied by Professor Levin on his original email.

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Remember those disclaimers such as “this paper in no way endorses intelligent design” or “this article in no way challenges evolutionary theory” (see here for instance). Well here’s a disclaimer that appears right at the start of a forthcoming book on evolutionary computation — one that is being published through a recognized academic outlet: Disclaimer: The Editors are not endorsing evolution as a scientific fact, in that species evolve from one kind to another. The term “evolutionary” in the evolutionary computation (EC) simply means that the characteristics of an individual changes within the population of the same species, as observed in the nature. Way to go!!

Is there only one Designer of life or are their multiple designers? Here is James Shapiro’s take: Bacteria are small but not stupid:
Cognition, natural genetic engineering, and sociobacteriology

Bacteria as natural genetic engineers….

This remarkable series of observations requires us to revise basic ideas about biological information processing and recognize that even the smallest cells are sentient beings.

In the case of engineered products we often might think of designers (plural) versus a designer (singular). It may be that some Ultimate Intelligence created the universe and (by way of extension) engineers. But even for those of us who accept that there is an Ultimate Intelligence, it is not customary to say that God made automobiles and airplanes and genetically engineered food.

Can we find proximal sources of intelligent design of life without appealing directly to the Ultimate Intelligence? Even though I personally believe God was the Ultimate Creator of the universe and hence even the creator of the Wright Brothers, I generally still identify airplanes as the proximal intelligent design of the Wright Brothers. A similar issue may arise in identifying the Designer or designers of life on Earth.
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I was at the Dembski-Shermer Debate at Bridgewater College in Bridgewater Virginia last night. I had the privilege of finally meeting both William Dembski and Michael Shermer for the first time in person. They spoke to a crowd of about 350 people from Bridgewater College, James Madison University, and the surrounding community. The crowd was diverse from high-school educated carpenters to PhD trained scientists and philosophers. Symbolic of the diverse mix of people was an American pastor of a rural church and his wife, a Russian laser physicist!

Dembski won the debate, but I must salute Shermer’s honorable and courageous performance in the face of overwhelming odds. Read More ›

One of our readers, who goes by the call sign “late_model” asked for a thread on Wheeler’s thesis that information is more fundamental than matter and energy. Wheeler, was highlighted in Wired Magazine’s 2007 edition: Wired: What we don’t know.
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In 1981 Dennett and Hofstadter edited a compilation of essays entitled The Mind’s I: Fantasies and Reflections on Self & Soul . The book is a compilation of essays by Dawkins, Morowitz, Searle, Alan Turing, and several other big names on the nature of mind and intelligence. Since ID implies a mind of some sort, it is appropriate to ponder what a mind really is, and this is a surprisingly good book on the topic.

Dennett’s co-author, Hofstadter, makes an interesting remark about the ultimate mind:

one way to think of the universal wave function [of quantum physics] is as the mind– or brain, if you prefer–of the great novelist in the sky, God.

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What are the speed limits of naturalistic evolution? We know from experience it takes time to evolve a species. Would naturalistic evolution be fast enough in geological time to turn a cow into a whale, an ape-like creature into a human? What are the speed limits of evolution?
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Through a little detective work, I found out where some of the Discovery Institute’s research funding has gone. It was an obscure comment in a paper that clued me in. The funding was for an exploration into the fundamental Speed Limits of Naturalistic Evolution. What was the plight of this exploration?
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I’d like to encourage people on the ground in the UK to comment on this and what it is likely to mean. Senior academics support Truth in Science Monday, 01 January 2007 As reported yesterday in the Sunday Times, twelve senior academics have written to the Prime Minister and Education Secretary in support of Truth in Science. The group was lead by Norman Nevin OBE, Professor Emeritus of Medical Genetics, Queen’s University of Belfast and included Antony Flew, former Professor of Philosophy at Reading University and a distinguished supporter of humanism. “We write to applaud the Truth in Science initiative,” the letter said. Empirical science has “severe limitations concerning origins” and Darwinism is not necessarily “the best scientific model to Read More ›

[update: I just added the original text of Casey Luskin’s letter in addition to mine ]

In my post, UVa faculty alarmed by ID’s presence on their campus, I wrote about my concerns that another witch hunt was in the making.

I would like to thank the University of Virginia Magazine for publishing an abbreviated version of the letters to the editor which Casey and I wrote. The ID debate has dominated the last two issues in that section of the magazine.

The published version of the letters (including several by highly articulate pro-ID UVa alumni) can be found at: Origins of Life Revisited.
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Back in 1985 Denton wrote of the Molecular Clock Hypothesis which was concocted by Schlemiel Zuckerkandl:

…the idea of uniform rates of evolution [molecular clocks] is presented in the literature as if it were an empirical discovery. The hold of every evolutionary paradigm is so powerful that an idea [molecular clocks] which is more like a principle of medieval astrology than a serious twentieth-century scientific theory has become a reality for evolutionary biologists…the biological community seems content to offer explanations which are no more than apologetic tautologies.

Michael Denton, Evolution: A Theory in Crisis (1985)

Well this principle of “medieval astrology” used by evolutionary biologists continues to come apart.
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Judge Jones tours the American countryside seeking the adulation of our intellectual elite and extolling the genius of his Kitzmiller v. Dover decision. The press release below indicates that Jones let the ACLU essentially dictate his decision. Instead of original and impeccable reasoning, Jones uncritically took extensive material from the ACLU’s proposed “findings of fact and conclusions of law” and either copied it directly or modified it ever so slightly. Outside the legal system this is called plagiarism. But since judges are allowed to draw on briefs of the parties, this is called legal scholarship. Even so, courts frown on decisions in which judges extensively copy and paste from other briefs — which is exactly what Jones did! Wired Magazine voted Jones one of the sexiest geeks of 2005. Time characterized him as a legal genius. Truth be told, Jones is a narcissistic putz.

In case you have trouble downloading the Discovery article cited below, i.e., “A Comparison of Judge Jones’ Opinion …”, I’ve uploaded it on the UD server here: www.uncommondescent.com/documentation/Comparing_Jones_and_ACLU.pdf.

“Masterful” Federal Ruling on Intelligent Design Was Copied from ACLU

Seattle — The key section of the widely-noted court decision on intelligent design issued a year ago on December 20 was copied nearly verbatim from a document written by ACLU lawyers, according to a study released today by scholars affiliated with the Discovery Institute. [Go here.]

“Judge John Jones copied verbatim or virtually verbatim 90.9% of his 6,004-word section on whether intelligent design is science from the ACLU’s proposed ‘Findings of Fact and Conclusions of Law’ submitted to him nearly a month before his ruling,” said Dr. John West, Vice President for Public Policy and Legal Affairs at Discovery Institute’s Center for Science and Culture.

“Ironically, Judge Jones has been hailed as ‘an outstanding thinker’ for his ‘masterful’ ruling, and even honored by Time magazine as one of the world’s ‘most influential people’ in the category of ‘scientists and thinkers,'” said West. “But Jones’ analysis of the scientific status of intelligent design contains virtually nothing written by Jones himself. This finding seriously undercuts the credibility of a central part of the ruling.”

The study notes that, while judges routinely make use of proposed findings of fact, “the extent to which Judge Jones simply copied the language submitted to him by the ACLU is stunning. For all practical purposes, Jones allowed ACLU attorneys to write nearly the entire section of his opinion analyzing whether intelligent design is science. As a result, this central part of Judge Jones’ ruling reflected essentially no original deliberative activity or independent examination of the record on Jones’ part.”

Jones’ copying was so uncritical that he even reprinted a number of factual errors originally made by ACLU attorneys.

For example, Jones claimed that biochemist Michael Behe, when asked about articles purporting to explain the evolution of the immune system, responded that the articles were “not ‘good enough.'” Behe actually said the exact opposite: “it’s not that they aren’t good enough. It’s simply that they are addressed to a different subject.” Jones’ misrepresentation of Behe came directly from the ACLU’s “Findings of Fact.” Read More ›