(Background: Bill Dembski started it all by asking Shapiro, based on his observations, why aren’t you a design theorist? Then everyone had a say. Great stuff!)
Now, Shapiro tells Axe and Gauger:
Proteins evolve largely by shuffling and accreting functional subregions called “domains,” not through the Darwinian modifications of individual amino acids (Doolittle and Bork 1993). Domain accretion and shuffling are inherently natural genetic engineering processes (i.e. non-Darwnian) because they involve the rearrangement of extended DNA segments that encode the different domains. As my book details, we have many examples of this process mediated by mobile genetic elements in nature as well as its replication in living cells in the laboratory. Moreover, we know a great deal about the roles of mobile genetic elements as sources for completely novel domain coding sequences through the process currently known as “exoneration.”
I suggest you review this literature to see that well-documented natural processes are more than adequate to explain how protein evolution for new functionalities can occur in a purely natural and combinatorial fashion. One of the motives behind my book was to acquaint readers with these and other poorly known examples of revolutionary discoveries in molecular genetics and genomics that allow us to view evolutionary processes in a new light.
Well, they are definitely “poorly known.” Most non-ID folk are still insisting that “Darwin done it.” Over to Axe and Gauger …
By the way, James Shapiro is not to be confused with Robert “Dr. No” Shapiro (1935-2011), a skeptical origin of life chemist.
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