Following the Evidence Where It Leads: Observations on Dembski's Exchange with Shapiro
Replying to Bill Dembski's article ("Is James Shapiro a Design Theorist?") and seeking to account for what we see in living things, University of Chicago microbiologist James Shapiro rightly recognizes that some sort of genetic engineering has taken/is taking place. Change is too clearly directed toward function, and takes place too rapidly, to be the product of neo-Darwinian processes. He wants to limit the genetic engineering to purely natural processes, though. He lists natural genetic engineering, horizontal DNA transfer, interspecific hybridization, genome doubling and symbiogenesis as possible sources of change. The evidence for most of these kinds of processes is based on similarity: similarity of DNA sequence, primarily, but also similarity of structure or form.
What is missing, though, is a demonstration that these processes can in fact generate the kinds of change that are needed, and that they can occur without intelligent guidance. Just because two things look alike does not mean that there is an evolutionary path between them. Similarity does not constitute proof of common descent. Rather, the existence of an evolutionary path and the mechanism for traversing it must be demonstrated, not assumed.
This is the aim of our research -- to determine what kinds of transitions in form or function are possible for living systems. We have begun with proteins, because they are experimentally tractable. If natural genetic engineering can't be done here, it can't be done at all.
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.
I agree that there is plenty of work to do to determine what kinds of natural evolutionary processes occur in living organisms as we know them. That's what we are doing. But if the answer is that natural processes can accomplish very little, the question of where living systems came from in the first place becomes highly relevant.
Let's take it further. What if we detect pervasive signs of design, or information input, that require intelligent agency? At what point does the possibility of intelligent design become acceptable to the broader scientific community?
Shapiro has faith that one day it will be possible for science to address these questions. I think scientists are already addressing them.