Larry Gilman objects to my argument

Here. 

Lewis’s “Argument from Reason” gives me that fishy feeling I have whenever someone tries to get the jump on science by the power of pure reason.  As I learned from reading Lewis himself, logic only tells you that if you have one penny in a drawer and put another in, there must be two pennies in the drawer; it doesn’t and can’t tell you whether there is a penny in the drawer.  To know that, you must look.  Logic alone, no matter how pure, no matter how apparently compelling, can never tell us what is physically real, in a bureau, in a brain, or anywhere else.  We must look, and that looking we call “science.”  Lewis and Reppert, in effect, rule on what science can find before science has looked — whereupon I cry Foul.  Lewis even thought he could exclude a purely naturalistic, evolutionary origin for the human brain on the strength of the Argument from Reason (Ch. 3 of Miracles).  That’s an awful lot of biological history to settle without leaving one’s easy chair.  But despite my gripes, I think that the Argument from Reason draws attention to a fascinating and knotty class of problems.  If it were reclassified as the Problem of Reason, I would have no quarrel with it.

But my argument does not directly conclude that naturalism is false. What it concludes is that it cannot both be the case that the world is naturalistic AND that we make the rational inferences that constitute the scientific enterprise. There are two possible worlds, one with scientists in it which is not naturalistic, and a world without scientists which is naturalistic. Science is not a presupposition-free enterprise, it presuppose that there are scientists and that scientists do infer conclusions based on evidence. 

And, many people think that science is only allowed to appeal to materialistic explanations, otherwise it isn't science. That seems also to be deciding scientific questions without actually doing the science.