Recently in Irreducible Complexity Category

The core concept of Dr. Michael Behe’s recent book “The Edge of Evolution” (Behe, 2007) is that protein-protein binding sites are extremely unlikely to have developed by natural means, and therefore were designed by unknown intelligent agents. There is a lot of interest in this concept, as the tag cloud at PT indicates. A recent paper (Grueninger et al., 2008) on human design of binding sites undermines some of his key assumptions, but what is more interesting is an old paper cited in Grueninger that shows researchers have known for some time that evolution of protein-protein binding sites is not as difficult as Behe makes out. Indeed, his very premise was invalid from the beginning.

We learn at the Discovery Institute Blog about a recent lecture tour in Spain by ID creationists

Over an eight day period last January, Physicians and Surgeons for Scientific Integrity (aka DoctorsDoubtingDarwin.com, a rapidly growing, 277-member, physician group from 17 countries) sponsored a lecture tour in Barcelona, Malaga, Madrid, Leon and Vigo. It was titled “Lo Que Darwin No Sabia,” or “What Darwin Didn’t Know.” Tom Woodward, Ph.D. (author of Doubts About Darwin and Darwin Strikes Back) and myself (author of What Darwin Didn’t Know and Billions of Missing Links) lectured on eight occasions to exceptionally large audiences. Santiago Escuain was our translator extraordinaire. Rich Akin, the CEO of PSSI, put in enormous hours into making this trip a huge success.

El Pais reports on the ‘successful’ Spain Tour of ‘Lo que Darwin no sabía’. Of course, the DI does admit later on that the success was limited.

Dear Dr. Behe

Reflecting on your previous post, and the current one, I would like to note that both your mutation rates (10^-4) and effective population size (10⁹-10¹⁰) are too high. By a factor of around a hundred thousand.

The commonest estimates for HIV mutation rates are between 1x10^-5 and 4x10^-5, with 2.5x10^-5 the most common. Well, what’s a half log unit between friends? More serious is your population size estimate. Here I’d like to introduce you to the concept of effective population size.

Dear Dr. Behe

I’m sorry you couldn’t follow Ms Smith’s argument. I found it quite easy, an elegant detective story that built up its case clue by clue. However, even if you couldn’t follow it, the viroporin story was pretty hard to miss. That Vpu evolved over the space of a decade, when viral numbers were low, into a viroporin, a multisubunit structure with a function previously absent from HIV-1, was an obvious key challenge to your assertions.

Dear Dr. Behe

Abbie Smith has recently responded to your reply to her article on the HIV-1 protein Vpu. To refresh your memory, Ms Smith showed that the recently evolved viroporin activity of HIV-1 Vpu directly contradicts your statement that HIV has evolved no new binding sites since it entered humans (see “Edge of Evolution”, page 145 and 146). I see you intend to reply to my open letter at your Amazon blog, rather than engaging in open discussion here, or better yet, doing Ms Smith the courtesy of replying on her own blog. I hope that at least this time you will reply to the key argument Ms Smith made:

HIV-1 M Vpu is a viroporin.

SIV Vpu is not a viroporin, HIV-1 O Vpu is not a viroporin. This is a new activity that evolved in HIV after the split from SIV over a 10 year timeframe and is part of the reason that the HIV-1 M clade is the most common type of HIV in the world.

In the post about my review of Behe’s The Edge of Evolution, many complained that they couldn’t access the full text without a university subscription or paying a huge fee. I have checked Elsevier’s policies on this. Authors are not allowed to post the published PDF to their websites (you have to get that from Elsevier), but they can put up the unformatted, submitted preprint version of their articles, as long as they include the reference and DOI to the published version. So here is the reference: Nicholas J. Matzke (2007). “The edge of creationism.” Trends In Ecology and Evolution, In Press, Corrected Proof, Available online 24 October 2007. ScienceDirect, doi: 10.1016/j.tree.2007.09.004.

…and the full text is below the fold. Note that the unpublished version has a few minor differences from the published version. For example, it has more emphases which were kind of my way of jumping up and down on the smoking ruins of Behe’s core arguments in The Edge of Evolution.

I am pleased to announce that Trends in Ecology and Evolution (TREE) has just put up the article-in-press version of my book review of Michael Behe’s The Edge of Evolution. Here is the reference and link:

Nicholas J. Matzke (2007). “The edge of creationism.” Trends In Ecology and Evolution, In Press, Corrected Proof, Available online 24 October 2007. ScienceDirect, DOI.

The DOI link doesn’t seem to be working just yet, presumably that is temporary. And the other link is one of those nasty superlong ones, so if nothing works, go to the TREE website and click on “Articles in Press” to see it (you will have to have a subscription or university access to get the article; I will provide a partial quote below).

Writing this review was challenging. There are a great many things wrong with Behe’s book, and attempting to hit the most important points effectively, with just 750 words to work with, was quite a challenge. For example, there was no way to fit in anything about HIV, even though some really good points have emerged on that front in the last few months. Thanks to the PT crew for a great many helpful discussions, comments, etc. I also had Cavalier-Smith’s (1997) TREE review of Darwin’s Black Box, literally the article that got me into ID criticism in a serious way, to inspire me (despite some flaws in that review).

I tried to make every word count, so it is hard to pick a summary quote, but here is a bit from the middle:

Laurence Moran at Sandwalk comments on a video excerpt with Bill Dembski, recently touted by the Discovery Institute’s Robert Crowther. What is fascinating that despite more than a decade of Intelligent Design ‘research’ this is the best ID has to offer.

Ironically, Dembski starts of by stating that “what darwinists have done is hidden behind complexities of living systems”. How ironic can this be… While science, as I have shown in several examples, deals in explanations, pathways and hypotheses, Intelligent Design has contributed exactly zero to our scientific understanding of these systems. Worse, while Dembski mentions some complex systems, he also avoids some examples of complex systems science understands quite well how they may have evolved.

My thanks to Robert Crowther for presenting the “best’ response ID has to offer. You be the judge.

On ERV’s blog we find an article titled Irreducible Complexity Reflects Human Ignorance about Phillip Klebba, Professor of Chemistry and Biochemistry at the University of Oklahoma. It was Klebba’s relentless questions during the Q&A of Dembski’s talk at the Trinity Baptist Church Oklahoma University in Norman Oklahoma which forced Dembski to admit to the level of ignorance that is required for ID.

The Baptist Trinity Church had invited Dembski “to penetrate the university campus with the gospel” (source). After all, what better way to introduce the students to the gospel than through the ideas of William Dembski? Dembski presented a talk titled “Why Atheism is no Longer Intellectually Fulfilling: The Challenge of Intelligent Design to Unintelligent Evolution”. During the Q&A, Dembski found out that the students were not impressed by his arguments. While Dembski may have contributed to the successes of Atheism on the University, he also managed to show to the audience present why ID is scientifically vacuous.

Well, my own personal copy of Michael Behe’s new book The Edge of Evolution arrived via amazon.com today, so I suppose it is fair game. I have linked to a few early blog comments (see more from ERV), and Michael Ruse has a short newspaper comment out today. And several other reviews are coming out in the near future in Science, Discover, etc. None of them positive at all, but it’s amazing how much attention someone can get by sacrificing scientific rigour and inserting divine intervention instead.

I don’t have a full review of the book and I won’t for a bit since I am working on other things. But I want to get dibs on one peripheral but particularly shocking and egregious error that Behe makes in The Edge of Evolution. The error is simple but it points to what I have become convinced is the true core of the mishmash known as “intelligent design”: sloppiness and wishful thinking.

Review copies of Michael Behe’s new book The Edge of Evolution are now out – the book is officially coming out on June 5 – and now the reviews are starting. Mark C. Chu-Carroll at Good Math, Bad Math, has beat us all to the punch. I perceived many of these problems while giving The Edge of Evolution my own read-through, but it takes a mathematician to comment on Behe’s abuse of fitness landscapes and probability arguments with the appropriate sense of outrage.

I am sure we will have much more on Behe’s latest starting in June. My first take is that The Edge of Evolution is basically an incompetent attempt to provide a biological foundation for the silly assumptions that were made in Behe and Snoke’s (2004) mathematical modeling paper in Protein Science. (You will recall that it received its most thorough critique here at PT and also in a rebuttal written in Protein Science by Michael Lynch; and a biological rebuttal in this 2006 paper in Science – see also summary by Adami.)

The PNAS Early Edition webpage has just posted a series of papers from the December 2006 National Academy of Sciences Sackler Colloquium, “In the Light of Evolution: Adaptation and Complex Design,” organized by Francisco Ayala and John Avise. The series of papers, on topics ranging from color vision to beetle horns, is now available (I will post the list below the fold). Eugenie C. Scott (aka Genie) was invited to speak at this meeting about evolution education and the history of opposition to it, and the speakers wrote papers to be published in PNAS and a forthcoming NAS volume.

Genie brought me on as a coauthor on the paper she was asked to write. This became:

Although many have read the transcripts of the Kitzmiller v. Dover trial (HTML version | PDF version) and found them interesting, reading the transcripts does not give the full sense of what it was like to be in the Kitzmiller courtroom. In real life, in addition to the witness answering questions, the lawyers and witnesses were constantly referring to exhibits that were digitally projected onto a large screen on the right wall of the courtroom. Usually the exhibits were just documents, but when the science witnesses testified, their powerpoint presentations contain fossils, flagella, and everything else in between. I think it is safe to say that the testimony is much easier to understand when read with the demonstrative exhibits available (the exhibit lists and a few exhibits are available online).

However, it takes a lot of work to convert the slides to web format, add captions, embed them in HTML, etc. But as a first step, I and others at NCSE have done this for Kevin Padian’s testimony (testimony+slides | just slides).

There has been a spate of interest in the blogosphere recently in the matter of protein evolution, and in particular the proposition that new protein function can evolve. Nick Matzke summarized a review (reference 1) on the subject here. Briefly, the various mechanisms discussed in the review include exon shuffling, gene duplication, retroposition, recruitment of mobile element sequences, lateral gene transfer, gene fusion, and de novo origination. Of all of these, the mechanism that received the least attention was the last – the de novo appearance of new protein-coding genes basically “from scratch”. A few examples are mentioned (such as antifreeze proteins, or AFGPs), and long-time followers of ev/cre discussions will recognize the players. However, what I would argue is the most impressive of such examples is not mentioned by Long et al. (1). Below the fold, I will describe an example of de novo appearance of a new protein-coding gene that should open one’s eyes as to the reach of evolutionary processes. To get readers to actually read below the fold, I’ll summarize – what we will learn of is a protein that is not merely a “simple” binding protein, or one with some novel physicochemical properties (like the AFGPs), but rather a gated ion channel. Specifically, a multimeric complex that: 1. permits passage of ions through membranes; 2. and binds a “trigger” that causes the gate to open (from what is otherwise a “closed” state). Recalling that Behe, in Darwin’s Black Box, explicitly calls gated ion channels IC systems, what the following amounts to is an example of the de novo appearance of a multifunctional, IC system.

Over at the Discovery Institute’s Media Complaints Division, Michael Behe seems to be a wee bit concerned by the attention that a recent Nature paper is getting, moaning that, “It seems some scientists have discovered that one way to hype otherwise-lackluster work is to claim that it discredits ID.”

OK. To start with, watching Michael Behe whine about someone else using ID to hype “otherwise-lackluster work” creates a concentration of irony so dense that four mining firms have put in bids for that post. Sorry, but I had to get that one out of my system. Now that I’ve more or less managed to get that minor issue out of the way, let’s look at what, for lack of a better term, we will have to call the “substance” of Behe’s complaints.

Read more (at The Questionable Authority):

On UcD, the following statement by Behe is being discussed. I will show that IC or falsification of IC has nothing to do with Intelligent Design since IC is merely a negative statement about natural selection, and flawed by definition. Nevertheless, this is a good opportunity to expose the fallacies behind ID think and educate people about its flaws and why it has remained scientifically vacuous.

Behe Wrote:

The National Academy of Sciences has objected that intelligent design is not falsifiable, and I think that’s just the opposite of the truth. Intelligent design is very open to falsification. I claim, for example, that the bacterial flagellum could not be produced by natural selection; it needed to be deliberately intelligently designed. Well, all a scientist has to do to prove me wrong is to take a bacterium without a flagellum, or knock out the genes for the flagellum in a bacterium, go into his lab and grow that bug for a long time and see if it produces anything resembling a flagellum. If that happened, intelligent design, as I understand it, would be knocked out of the water. I certainly don’t expect it to happen, but it’s easily falsified by a series of such experiments.

Note that Behe’s claim does not logically follow: Namely that if something cannot be explained by one of the processes of evolution, namely natural selection that we then have to assume that it was intelligently designed. Even though we have no competing explanations as to who, what, how or when. In other words, ‘intelligently designed’ becomes a place holder for our ignorance.

On Nobel Intent, John Timmer discusses amongst others the contrived dualism of many ID relevant claims

He also relied a lot on the “contrived dualism” argument: design was supported by the failure of evolutionary explanations, because no other alternative was possible. This was stated with extraordinary specificity when Behe answered questions, as he more or less claimed that ID was accessible to experimental studies because finding the limits of evolution would reveal design (more on that later).

Anyone who has been a “creationism watcher” for any length of time is familiar with the venerable creationist tactic of “quote mining.” Since creationists, essentially universally, can’t (or don’t want to) deal with actual scientific data pertaining to evolution, they attempt maintain a facade of respectibility by quoting statements from biological authorities. This can take many forms; for example, for the 1987 Supreme Court Edwards v. Aguillard case, the creationist lawyer Wendell Bird, apparently with the help of Paul Nelson, assembled a massive 500-page brief that consisted almost entirely of thousands of quotes from authorities on every topic bearing on “creation science”, from astrophysics to biology to philosophy to religion. This failed to convince the Supremes, but Bird turned his brief into a large two-volume book, The Origin of Species Revisited. Other elaborations on creationist quote-mining include various “Quote Books”, including The Quote Book (1984 booklet, inserted in Creation magazine I believe) and The Revised Quote Book (1990) from Answers in Genesis, the Handy Dandy Evolution Refuter (now online), and Henry Morris’ That Their Words may be used against Them (comes with CD!). Then we have endless collections of quotes on creationist websites, 50 of which were recently surveyed and ranked against the Talk.Origins Quote-Mine Project. Sometimes these quotes evolve and mutate over time (here is an example from Of Pandas and People), and sometimes they even spontaneously generate from thin air, as with this imaginary quote from Clarence Darrow.

You may be saying, “Surely this is a problem, but only famous authorities get quote mined. It would never happen to me!” Think again. On September 5, 2006, an article I coauthored in Nature Reviews Microbiology on flagellum evolution was published on the NRM website as an Advanced Online Publication. Before the ink was even dry – heck, before the ink was even wet, the October issue hasn’t come out yet – Casey Luskin at the Discovery Institute is quote mining it! The mining occured in Luskin’s insta-response to the revised edition Chris Mooney‘s book The Republican War on Science. Check this out:

Jonathan Wells (2006) The Politically Incorrect Guide to Darwinism and Intelligent Design. Regnery Publishing, Inc. Washington, DC.^Amazon

Read the entire series.

No book on “intelligent design” would be complete without a mention of the concept of irreducible complexity. Jonathan Wells’s The Politically Incorrect Guide to Darwinism and Intelligent Design does not disappoint in this regard; it is the actual discussion of irreducible complexity that is very disappointing and down right misleading.

A paper that just came out in Advance Online Publication section of Nature, Murphy et al. 2006, reports the first in situ structure of a flagellar motor in a spirochete, Treponema primitia. Such things have been done before, for the bacterial lab rat Salmonella, but spirochetes are a whole different bacterial phylum, and they have weird flagella. First, instead of the flagella sticking outside of the cell and doing what any self-respecting flagellum would do, the flagella of spirochetes rotate entirely within the periplasm (the space between the inner and outer membrane, which includes the cell wall). You might think that there would be no room for the flagellum to rotate in such a restricted space, or that it would tear apart the membranes – but intuitions are very unreliable at the sub-microscopic scale. The intracellular rotation of the flagella evidently cause the whole cell to gyrate, moving it through liquid in a corkscrew-like fashion.

This post contains my commentary on the Annotated Bibliography on the Evolution of the Immune System, now online in the NCSE Kitzmiller archive. The Annotated Bibliography describes the significance of each publication listed in the Supplementary Material for the recent Nature Immunology article on the “immune system cross” during Behe’s testimony in Kitzmiller v. Dover. For article, click here. For the full Annotated Bibliography, click here. The Annotated Bibliography has reached an approximately final state, but I would still be interested in any additional comments people might have. My overall point with all this, of course, is that unless and until ID proponents (1) acknowledge the existence of this scientific literature, (2) admit that their previous statements about the nonexistence of this literature were wrong, and (3) substantively rebut this literature, providing a better and more detailed explanation for the immune system, then they aren’t even beginning to be scientifically serious.

As you read through this, keep in mind the Discovery Institute’s hiliarious commentary in their recent book attempting to rebut to the Kitzmiller decision, Traipsing Into Evolution:

Consider [Judge Jones’s] skewed summary of the evidence relating to the irreducible complexity of the immune system. He cited Kenneth Miller’s speculative assertions as if they were facts, while refusing even to mention biochemist Michael Behe’s detailed rebuttal during the trial. (Traipsing, p. 45, italics added)

Speculative? I guess in ID-Land, dozens of publications in top journals confirming key expectations is “speculation”, whereas the vague statement that divine intervention occurred sometime, somewhere, for unspecified reasons is considered rock-solid. Even better, Traipsing then quotes from Behe’s “detailed response” to the immune system section of Jones’s opinion. However, the book neglects to point out that Behe tried exactly the same silly arguments in his direct testimony at trial, and they were specifically debunked on cross-examination. For more on Behe’s “detailed rebuttal”, see here.

Here in the pounding-nails-into-the-ID-coffin department of the Panda’s Thumb, we are still hard at work. Longtime PT posters Andrea Bottaro, Matt Inlay, and I have just published a “Commentary” essay in May 2006 issue of Nature Immunology. (Update: Subscription no longer required. Thanks to NI.) See the NCSE announcement and more background at the NCSE Evolution Education and the Law website.

The article is:

Bottaro, Andrea, Inlay, Matt A., and Matzke, Nicholas J. (2006). “Immunology in the spotlight at the Dover ‘Intelligent Design’ trial.” Nature Immunology. 7(5), 433-435. May 2005. (Subscription no longer required: DOI | Journal | Google Scholar | PubMed | Supplementary Material)

Therein, we review the now-notorious episode in the Kitzmiller case where, during Eric Rothschild’s dissection of Michael Behe, Rothschild challenged Behe’s claims about the scientific literature on the evolutionary origin of the immune system by piling up on Behe’s podium a stack of books and articles on the evolution of the immune system. Behe responded that he had not read most of it, but dismissed it out of hand, and this cavalier attitude seems to have been one (of many) factors that impressed Judge Jones and persuaded him to issue the thorough, detailed ruling that he did.

Update: I’ve added some substantial comments 81029 and 81054 that might be lost in the comment roll, but add some important perspective to Behe’s arguments.

Michael Behe is known as the author of the concept of Irreducible Complexity (IC, but see [note 1]). However, he has given several different, not entirely consistent, definitions of IC. Everyone is familiar with the “multiple parts” definition, fewer will be familiar with the “neutral mutational steps” definition (1) and fewer still with the idea that amino acids interactions themselves are IC (2, see my critique of this). Indeed, Behe’s recent paper with David Snoke (3) relied on a combination of the last two definitions (see our critique), and Behe also used the latter definition in the Dover trial (3).

A paper just out in the journal Science has effectively refuted the claims of the Behe and Snoke paper (4)

Pat Hayes at Red State Rabble (which ought to be on everyone’s daily reading list) calls attention to something I didn’t know: Bill Dembski endorsed the Bible Code nonsense (also reproduced here), identifying it with his intelligent design detection methodology:

At the same time that research in the Bible Code has taken off, research in a seemingly unrelated field has taken off as well, namely, biological design. These two fields are in fact closely related. Indeed, the same highly improbable, independently given patterns that appear as the equidistant letter sequences in the Bible Code appear in biology as functionally integrated (“irreducibly complex”) biological systems, of the sort Michael Behe discussed in Darwin’s Black Box.

The relevant statistical methodology is identical for both fields. As a result, the two fields stand to profit from each other. For instance, my forthcoming book, The Design Inference, gives a thorough account of universal probability bounds, i.e., how small a p-value one needs to eliminate chance decisively. (Although the literature on universal probability bounds dates back to the French probabilist Emile Borel, it seems not to have been engaged by the Bible Code researchers.)

This convergence of the Bible Code and biological design should not seem surprising. There is a tradition within both Judaism and Christianity of speaking of two “books” where God reveals himself—the Book of Scripture, which is the Bible, and the Book of Nature, which is the world. I commend Jeffrey Satinover for his efforts to read both books.

The Bible Code nonsense has been thoroughly debunked: See here for a compendium of dissections, and see also Chaper 14 in Mark Perakh’s Unintelligent Design. Does Dembski still assert the identity, and has he profited from the lesson of the Bible Code? Not visibly. His design detection methodology has been debunked as thoroughly as the Bible Codes, yet IDists still claim that they have a methodology for detecting design. They are in the same boat: a convergence of cranks.

RBH

Two threads combine in this posting. First my comments on the Beckwith thread where I show how Dembski and Behe use the term specification or purpose to refer to “function”, and secondly a thread on strings in which the concept of purpose arose again.

First let’s revisit Dembski’s and Behe’s position on function which shows that their use of the term specification or purpose clearly refers to function.

van Till Wrote:

However, when it comes time for Dembski to support his conviction that the bacterial flagellum is specified, the procedure becomes considerably more casual, almost facile. Speaking on the specification of biological systems in general, Dembski simply asserts that, “Biological specification always refers to function. An organism is a functional system comprising many functional subsystems. In virtue of their function, these systems embody patterns that are objectively given and can be identified independently of the systems that embody them. Hence these systems are specified in the sense required by the complexity-specification criterion.”NFL, p. 148.In these four brief sentences the foundation of Dembski’s entire strategy for certifying the specification of biotic systems is laid.

Or in Behe’s terms “a purposeful arrangement of parts” where purpose and function are interchangeable.

Behe Wrote:

Q The whole positive argument for intelligent design as you ve described it, Professor Behe, is look at this system, look at these parts, they appear designed correct?

A Well, I think I filled that out a little bit more. I said that intelligent design is perceived as the purposeful arrangement of parts, yes. So when we not only see different parts, but we also see that they are ordered to perform some function, yes, that is how we perceived design.

Page 44 of Behe’s cross examination on Day 11 of the Kitzmiller trial. See also Analysis of Behe’s Testimony, Part 1: Purpose and Function at “Dispatches from the Culture Wars”

It seems that Dembski has decided to ‘decisively’ move the goalposts of ID further out and although in earlier writings he did mention the possibility of ‘front loading’, he also considered such possibilities to be unlikely and ‘deistic’ in nature.

Now he may have clarified his position:

Dembski Wrote:

Let’s cut to the chase: Is the designer responsible for biological complexity God? Even as a very traditional Christian and an ardent proponent of ID, I would say NOT NECESSARILY. To ask who or what is the designer of a particular object is to ask for the immediate intelligent agent responsible for its design. The point is that God is able to work through derived or surrogate intelligences, which can be anything from angels to organizing principles embedded in nature.

For instance, just because I hold to both Christian theism and ID doesn’t mean that God directly designed and implemented the bacterial flagellum by specifically toggling its components. It could well have happened by a process of natural genetic engineering of the sort envisioned by James Shapiro. The design would be no less real, but God’s role in the design would be distant, not proximal.

Philosophers have long distinguished between primary and secondary causes. The problem is that under the pall of methodological naturalism, secondary causes have been identified with purely materialistic processes. But it’s perfectly legitimate for secondary causes to include teleological processes. I develop all this at length in THE DESIGN REVOLUTION.

Anything from angels to organizing principles, I clearly see the scientific value of ID here. And the logical conclusion from Dembski’s admissions about front-loading is that natural explanations would be able to explain the origin of such features as the bacterial flagellum. Thus, lacking any further evidence, science would be unable to reach a conclusion of ‘intelligent design’ as the evidence would be hidden beyond our observations. In other words, Intelligent Design has moved itself further into the realm of scientific vacuity.

Not bad for a days work though. Boy do I wish Dembski had testified at the Dover trial.

I find it fascinating that Dembski on the one hand seems to be arguing that complex specified information requires a supernatural origin while on the other hand arguing that CSI can in fact be explained by natural law alone. Whether or not a supernatural designer was responsible for the front loading is a question science cannot answer. Which is exactly why Intelligent Design makes for poor science and good apologetics. As such, I start to understand more and more why Dembski has returned to apologetics.

Given the recent scientific progress, it may not come as a surprise to see ID proponents retreat to front-loading.

William Dembski has just blogged about a short comment I made this morning on The Thumb answering someone’s question about whether or not a detailed evolutionary model for the bacterial flagellum would deserve a Nobel Prize. In that comment, I pointed to this long web article I wrote on the evolution of the bacterial flagellum (which is already badly in need of an update), but I said that, no, such a model would clearly not deserve a Nobel, because it would be entirely routine and conventional – simply the application of the current paradigm (modern evolutionary theory) to fill in one more little gap in our knowledge of evolutionary history. Although creationists don’t realize it, discoveries showing how complex system evolved come out all the time in the scientific literature. (A number of examples are linked from my comment here.)

Dembski’s post in reply is entitled “To Explain the Flagellum � Just Look Up All the Homologies.” There are numerous dubious assertions in Dembski’s short post that would take all day to write up, but I just want to focus on one limited point for the moment. Will the ID advocates admit that they made a mistake in asserting that, except for the 10 proteins of the Type III secretion system, they other 30-40 parts of the flagellum were “unique”?

In “Darwin”s Black Box” (DBB), ID”s arch-biochemist Behe glibly labeled evolutionary hypotheses for the origin of “irreducibly complex” systems as “hops into the box of Calvin and Hobbes” (for those who don”t know what the heck this refers to, go here to learn about Calvin and Hobbes, and here for info on their box, or even better go spend some time here, and come back tomorrow). This overconfidence has come back to haunt him as more and more evidence accumulated in support of the evolutionary origin of his various IC systems, from the flagellum to the complement and clotting cascades.

The topic where the idea of unevolvability of IC systems has probably taken the most beating is the vertebrate adaptive immune system, where not only evidence for evolution has accumulated at a steady pace, but even more embarrassingly for Behe, it has developed exactly along the lines predicted by those “Calvin and Hobbes jumps” he originally dismissed. A recent paper in the journal PLoS Biology [1] is the latest turn in the death spiral of irreducible complexity of the immune system, and I think provides a good opportunity to take a look at how science works, as opposed to ID navel-gazing.