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A Response to Ann Gauger’s and Douglas Axe’s Comments

Continuing a conversation initiated by Bill Dembski (“Is James Shapiro a Design Theorist?“), Ann Gauger wrote:

So far, our research indicates that genuine innovation, a change to a function not already pre-existent in a protein, is beyond the reach of natural processes, even when the starting proteins are very similar in structure. No supernatural presuppositions here, just standard genetic engineering, with a result similar to what protein engineers have found any time they try to engineer a new function onto an existing protein template.

Douglas Axe wrote:

As an ID proponent, I’ve put forward the scientific case for thinking that the thousands of distinct structures that enable protein molecules to perform their specific tasks inside cells cannot have arisen in a Darwinian way. Moreover, the facts of this problem seem to preclude any naturalistic solution, Darwinian or not.

Ann and Doug, the problem of protein evolution is covered in detail in my book, and a relevant periodically updated bibliography is posted online. The 2001 draft human genome paper in Nature contains two figures that summarize the revolution that has occurred in our understanding of protein evolution (Lander, Linton et al. 2001).
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.
Doolittle, R. F. and P. Bork (1993). “Evolutionarily mobile modules in proteins.” Sci Am 269(4): 50-56. http://www.ncbi.nlm.nih.gov/pubmed/8235550.
Lander, E. S., L. M. Linton, et al. (2001). “Initial sequencing and analysis of the human genome.” Nature 409(6822): 860-921. http://www.ncbi.nlm.nih.gov/pubmed/11237011.