Science v Intelligent Design: ERV v Behe

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Things are not going well for Michael Behe. First his concept of Irreducible Complexity is shown to be full of holes, then he publishes a paper with Snoke (so much for the claim that ID proponents do not get to publish) to argue that there are limits to evolution, only to be shown to be wrong soon thereafter by another publication which points out some of the unreasonable assumptions made by Behe. And more recently, after a very “successful” defense of ID in the Kitzmiller trial, Behe has published a book in which he, mostly ad hoc, claims that there are limits to evolution. Needless to say, scientists were once again not very impressed.

In one example, ERV took on Behe’s claim about HIV. It took Behe several months to respond and his response both lacked in civility as well as in scientific content. Perhaps by mistake, perhaps by design, Behe left commenting enabled and soon comments filled his blog page. While several of these comments show once again the problems with Behe’s familiarity with science, it is the lack of scientific content of Intelligent Design which I would like to point out.

In an exchange between David Rintoul and Tarnaak we run across the following comments

David Rintoul Wrote:
Tarnaak Wrote:

“It’s more correct to say that you are ignorant of the testable predictions that ID has and can, make.”

So I’ll admit I’m ignorant. No problem for me; I already admitted my ignorance re CD4 downregulation. Tell me about those testable predictions of ID, please.

[sound of crickets chirping]

Tarnaak Wrote:

See thats what I mean by dogmatic thinking, you wrote “sounds of crickets chirping” because you are sure that thereare none. Don’t you think it’s possible that you are wrong?

David Rintoul Wrote:

But only after you tell me about those testable ID hypotheses. What predictions can be made from ID, given that it is predicated on an unknown designer acting at an unknown time using unknown tools or processes?

Tarnaak Wrote:

I’m not really interested in discussing those hypotheses with you, you can easily google it or head over to the ID research lab Biologic and ask them.

Chirp Chirp

As to Behe’s problematic response, let me point out a mistake which most undergrads would not make:

Behe Wrote:

She first points out that the amino acid identity between the homologous chimp SIV protein with HIV Vpu is 39%, much less than that of other homologous viral proteins, and she seems to regard that fact by itself as remarkable. Yet the alpha and beta chains of human hemoglobin are only about 44% identical, and have virtually superimposable structures and very similar functions.

Students, how well does sequence identity correlate with structure?

Functionally meaningful sequence similarity may sometimes be reflected only in local structural similarity, but not in global fold similarity. If detected and used naively, such similarities may lead to incorrect fold predictions.

S Sri Krishna, Ruslan I Sadreyev, and Nick V Grishin A tale of two ferredoxins: sequence similarity and structural differences, BMC Struct Biol. 2006; 6: 8.

In other words, structurally similar proteins can show limited sequence similarity and two similar sequences can show little structural similarity.

Similarly in Analysis of Protein Sequence/Structure Similarity Relationships. the authors write

Our survey also emphasizes that unexpected sequence/structure relationships in region D? (unexpected dissimilarities PvM)are not uncommon. We briefly illustrate and describe important protein pairs in this region that exhibit large structural deviations despite high sequence similarity. These complex multidomain proteins exhibit conformational plasticity inherent to biological activity, critical mutations (in linker/ loop regions, for example), structural changes induced by ligands, and diversity of conformational requirements for functional activities.

And one of the papers which ERV quoted from states the following

Taken together, these results show for the first time that Vpu proteins from SIVcpz isolates, although quite diverse in sequence and predicted secondary structure from the HIV-1 subtype B protein, are capable of down-regulating CD4, which is one of the major functions of the HIV-1 protein.

Behe may not be used to this unexpected level of peer review, and I wonder how long it will take before he will also disable comments for his blog entry. Peer review has never been kind to Intelligent Design. ID’s own ‘peer reviewed’ journal PCID has not published for almost 2 years now.

Caveat Emptor

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Dear Gentle Readers: At the bottom of this essay, I’m collecting links to reviews of Behe’s book The Edge of Evolution, replies to reviews and so forth. Well, now the burden is off me, and I can devote my book-reviewing time to good books,... Read More


A newbie on the Amazon thread posts the following

You are very wrong, Dr Axe has published papers that suport the design inference:


As a well read poster points out

If you bothered to read them, Axe’s papers are not even a critique of evolution, and they are certainly NOT positive evidence for ID. His data demonstrate that alterations of protein structure lead to alterations of protein function. Where is the POSITIVE EVIDENCE for design in those observations? How are his observations incompatible with evolutionary theory? In fact, Forrest and Gross (Creationism’s Trojan Horse: The wedge of intelligent design, 2004) quote Axe as saying that he does not make an argument FOR design in any of his publications.


The only way ID can impress its followers is by keeping them ignorant about what ID is all about. Some might conclude that this is ‘by design’ :-)

[chirp chirp]

Still no predictions…

PvM Wrote:

The only way ID can impress its followers is by keeping them ignorant about what ID is all about. Some might conclude that this is ‘by design’ :-)

Clearly by design in the many cases were the refuted arguments of the ID/Creationists are reused in front of fresh audiences. This could also be part of a cynical ploy to keep up their jealous needling of the scientific community.

No doubt the ID/Creationist leaders see scientific peer review as thwarting their attempts to set themselves up as the adored authority figures of a subservient following. It is amazing how often they and their followers will make confident-sounding stupid statements in their attempts to impress.

Peer review is a healthy process that helps to keep one honest and circumspect about one’s claims, and it tends to blunt the ideological delusions of grandeur isolated minds tend to conjure up about themselves as they loose touch with reality.

Maybe Mats or BJ Bond could explain to us about those testable predictions of ID?


His data demonstrate that alterations of protein structure lead to alterations of protein function.

Wow. There’s a shocker. No one saw that coming. I guess that’s it for “Darwinism”, then.

Note, even though the Amazon site says comments are disabled, they aren’t. Here is my comment to Behe’s reply to Korthof…

Korthof’s opening sentence is…

“Readers interested in ‘Intelligent Design Theory’ will be disappointed.”

Korthof explains… “But, there is no design theory in this book. There are a bunch of observations and suggestive allusions to a theory. But not a coherent treatment of design theory. Even ‘nonrandom mutation’, which is an important part of Behe’s design claims, occurs only 3 times in contrast to ‘random mutation’ which occurs 171 times. Is it really unfair or unreasonable to expect in this book a coherent description of design theory after more than 10 years since his Darwin’s Black Box?”

Korthof sums up nicely why my expectations resulted in disappointment when I read through the Edge of Evolution.

Dr. Behe, many times you have suggested the key to understanding is at the microscopic level. Yet you refrain from exploring the obvious non-random mechanism available from quantum physics.


That blog on Amazon is a howler. Behe should learn from Dimski in that the best way to present IDC is in a venue where you control the discussion (delete and ban anyone who questions IDC).

Well, it has been fun discussing evolution and ID on an open forum with the likes of Bornagain77 (aka Philip Cunningham) and Joe G. When they are allowed to get into full howling batshit stupidity mode, they can do more damage to the ID cause than a roomful of Dembskis.

You gotta wonder why Behe left the comments open on that thread after closing them on all the previous entries. And you really gotta wonder why he hasn’t shut it down before it got to 140 comments and counting.

Albatrossity (aka David Rintoul)

Well, I spoke too soon. I just checked the Amazon site, and all of the comments have disappeared. There is still a box where you can post comments, but posting a comment there seems to have been futile.

I guess Behe woke up. Too bad. Did anyone save that thread? Unfortunately I did not…

Oops. Apparently there was only a momentary glitch in the amazon server, or my connection, or both. Everything still seems to be there.

Carry on.

Well, I read through Behes ‘quoted paper’

Re “to argue that there are limits to evolution,”

Well of course there are limits to what evolution can do. Evolution hasn’t (at least not directly) produced 747’s (junkyard or not), spring-powered mousetraps, pocket watches, mountains that look like dead presidents, or peer reviewed articles.


Henry J, but evolution created food, (bird)dance and sex. I rest my case.

Thought Provoker (aka Quantum Quack): Dr. Behe, many times you have suggested the key to understanding is at the microscopic level. Yet you refrain from exploring the obvious non-random mechanism available from quantum physics.

I’m not sure which quantum process is being referred to here, but most of ‘em are as random as it is possible to get. So much so that they are used to generate truly random numbers the world over.

And ‘quantum mechanism’ mooted as a source of biological variation will be, at the microscopic level, so indistinguishable from random as to make no odds.

Hi David,

Thank you for feeding the troll… err.. um… providing a thoughtful response.

Have you heard of quantum GHZ states? It displays a lack of randomness that some call “quantum weirdness”.

Here is a link on After the Bar Closes where we have been discussing it.

Where Behe is looking (at the microscopic level) quantum effects are very significant. Quantum effects are the only reasonable source for either randomness, or a lack thereof.

This has the makings of a possible scientific ID Hypothesis. So, as a challenge, I have been presenting my version of it.

If, by chance, Panda’s Thumb wanted to Guest Host the ID Hypothesis, I would attempt to defend it for entertainment’s sake. If someone will let me know, I will put together a cleaned up version for everyone to poke holes in.

My email is dfcord[AT]

About this Entry

This page contains a single entry by PvM published on October 17, 2007 10:33 PM.

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