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).

Most people may be familiar with the concept of Irreducible Complexity, popularized by Michael Behe. Few may know that this concept was discussed in the early 1900’s by Muller as an outcome of evolutionary processes. In other words, the very same concept which had been argued to have been an inevitable outcome of evolutionary processes was much later used as an argument against Darwinian evolution by Behe.

In a recent posting on Talk Origins Chris Ho-Stuart discusses the history:

Chris Ho Stuart wrote:

Muller’s definition of “interlocking complexity” is exactly the same as the definition of “irreducible complexity” – a system of mutually independent parts that requires all those parts to be present for the system to work. However, Muller’s claim is that this is an EXPECTED result of evolution. Behe took the same definition, and claimed it was IMPOSSIBLE as a result of evolution.

The reason for the difference is basically that Muller was using evolution; and Behe was using a weird strawman of his own devising. Behe describes evolution as working by the gradual addition of parts, one by one. Muller, however, describes evolution as working by gradual modifications of parts. Muller’s description is the more accurate. New proteins don’t get added to systems particularly often; the vast majority of evolution is small modifications to proteins, to alter their amino acid sequence and hence their chemistry. Behe neglects this entirely; and hence omits the vast majority of evolutionary change.

The paper is “Genetic Variablity, Twin Hybrids and Constant Hybrids, in a Case of Balanced Lethal Factors”, by Hermann J Muller, in Genetics, Vol 3, No 5, Sept 1918, pp 422-499. You can read a scan of the paper online at http://www.genetics.org/content/vol3/issue5/inde…>.

Chris was not the only one who had pointed out Muller’s contributions.

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 95979 and 96005 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.

Dembski has posted a contest on his blog, seeking the best case of gradual evolution by cooption (hmm, sounds like something evolutionary biologists have been talking about for decades) in the case of human-designed technology.

I’m talking about an actual history of invention in which an initial technology does A, and then a small change allows it to do B, after which a further small change allows it to do C, after which co-opting an existing system (without extensive modification) allows it to do D, etc. The evolution of a motorcycle from a motor and a bicycle is not a good example in this regard because the motor and bicycle require extensive design-work to adapt them to each other.

I hereby nominate the gradual evolution of “intelligent design” during the descent with modification of the manuscripts of Of Pandas and People, reviewed in this series of posts.

I expect my $100 by week’s end. Seriously, though, speaking of cooption: Dembski’s last-ditch, backup-backup argument against cooption as an explanation of irreducible complexity – that we had no well-documented examples of natural cooption – was destroyed by Scott Minnich during the Kitzmiller v. Dover trial.