Addenda for my reply to Kirk Durston

July 2, 2008

Over at Recursivity, I left a comment in response to some things Kirk Durston said about my analysis of a paper by Doug Axe.  Blogspot doesn’t like my formatting, so I have moved the last few paragraphs here, and posted the link to this message on Jeffrey Shallit’s blog.

The last two paragraphs:


4.  The occurrence of functional islands in sequence space is far less rare than you let on, Kirk.  The scope of the problem for you is illustrated (briefly, and among other places – I apologize for the shameless self-promotion) here, here, and here.

5. Said occurrence may be far more common than you let on, Kirk.  Studies such as those of Chiarabelli et al. (Chemistry and Biodiversity 3, 840-859, 2006) show  that folded sequences are rather common (20%!) in collections of random polypeptides.  This is a large part of the problem of function, and it’s not nearly the impossibly inaccessible one you imply.


Here is the rest of the comment, in case anyone is wondering about what the fuss is about:

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