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Let Science Be the Arbiter: A Reply to James Shapiro

In his response to Bill Dembski's article, "Is James Shapiro a Design Theorist?," Shapiro writes:

However, if he [Dembski] does not want to abandon the supernatural (as Michael Behe has repeatedly told me he does not) and if he wishes always to have recourse to a literal Deus ex Machina, then we cannot have a serious scientific discussion. Doing that requires respecting the naturalistic limits of science. I think it would be a very positive development for ID proponents to give up on all theological crutches and engage in a strictly naturalistic inquiry, independent of whatever their beliefs in final causes may be. Is Bill Dembski willing to do that?
It would be helpful for James Shapiro to clarify his commitment to naturalistic science. If he holds that the answers to the great questions of biology all reside in the material components of life and their arrangement, then he must realize this to be just another philosophical position. Right? It follows that if he has a valid criticism, it must be not merely that ID proponents approach their science with assumptions, but rather that their assumptions are inferior to his own assumptions.

So who is right? I think we all agree that science should be the arbiter here. Naturalism and ID both make testable claims about how things happen in the real world, so it ought to be possible to evaluate these positions by evaluating their respective claims.

If crutches are devices for propping up lame positions, then I completely agree that they should go, but let's be careful to call a crutch a crutch. 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.

There is no crutch here. The aspects of protein structure that appear to preclude a naturalistic origin have been described in detail. If Shapiro or anyone else were to show in detail how these are overcome by a naturalistic mechanism, then my argument would fall and I would let it fall. But the reverse needs to be true as well. Scientists who personally side with naturalism have to be willing to let naturalism fall, as otherwise they would be guilty of using a crutch to prop it up.