Science v Intelligent Design: ERV v Behe

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