beef: where is it?

Dembski, while slamming the Templeton Foundation's lack of support for Intelligent Design, makes an interesting claim:

I frankly doubt that there is one research paper published in the natural sciences (I’m not talking about medical journals that discuss the efficacy of prayer in healing) that acknowledges the Templeton Foundation as having provided essential research support (e.g., in the form of salaries for lab techs, lab equipment costs, etc.) for that project to be completed. Templeton supports research in that fuzzy new discipline that it has largely invented, known as science-religion, and not in science per se.

I know for a fact that Discovery Institute tried to interest the Templeton Foundation in funding fundamental research on ID that would be publishable in places like PNAS and Journal of Molecular Biology (research that got funded without Templeton support and now has been published in these journals), and the Templeton Foundation cut off discussion before a proposal was even on the table. [emphasis added]

Now, Mr. Dembski, will you provide the titles of those papers? Strangely, they are nowhere to be found on the Discovery Institute's (recently updated) list of peer-reviewed research.

Update: Spent an hour slogging through citations (thanks, Scopus--and Evergreen library card-toting wife!), and have come to one definitive conclusion: if Dembski is right (and there's no reason to assume he's prevaricating, other than his previous "street theater" hijinks), then the research was performed by someone who isn't a ranking member of the Discovery Institute. We eagerly await the revelation.

Update Update: Wait no further. It's Douglas Axe.

Behold the power of the internets:

"Estimating the prevalence of protein sequences adopting functional enzyme folds," Journal of Molecular Biology 341 (5), pp. 1295-1315

"Extreme functional sensitivity to conservative amino acid changes on enzyme exteriors," Journal of Molecular Biology 301 (3), pp. 585-595

"An irregular β-bulge common to a group of bacterial RNases is an important determinant of stability and function in barnase," Journal of Molecular Biology 286 (5), pp. 1471-1485

"Active barnase variants with completely random hydrophobic cores," Proceedings of the National Academy of Sciences of the United States of America 93 (11), pp. 5590-5594

Update³: Well, so much for the "bombshell." It's our old friend, who Dembski declared was already calculating specified complexity.

Internet mavens have been pestering me for actual calculations of complexity involved in such systems. I address this in my forthcoming book (_No Free Lunch_), but such calculations are out there in the literature (cf. the work of Hubert Yockey, Robert Sauer, Peter Rüst, Paul Erbrich, Siegfried Scherer, and most recently Douglas Axe -- I'm not enlisting these individuals as design advocates but merely pointing out that methods for determining specified complexity are already part of biology).

However, and most important, Matt Inlay already debunked the relevance of Axe's work to Dembski's conception of Intelligent Design in a devastating PandasThumb article.

Yes, reference 31 is Axe 2000. Rather than tone the comment down, Dembski apparently decided to bump his claim up a notch or two. Now “preliminary indications” has evolved into “strong evidence”, and “perturbations” into “small perturbations”. Again Dembski implies that 30 amino acid substitutions is “gradual”. So even though Dembski himself admitted over a year ago that this claim was unsupported by Axe 2000, he felt no obligation to leave it out of future writings. Why correct when you can just reassert?

And now Axe is "fundamental" to ID. And the beat goes on, badumdump, badumdump...

Update⁴: I notice that Dembski cites Axe in his (never-used) witness report for the Dover Trial [pdf or html]

Final Update: Now that we know the Discovery Institute funded Axe (at least once, if not more), the omission of his work from their list of ID papers is curious. They've never been shy about trumpeting work that's only tangentially (or, arguably, not at all) related to ID--so why leave Axe out? Is the non-applicability of his research obvious even to DI's propagandists?