Summarized, the argument is this: if only nature exists, then when I think and reason and prove things, the only thing that’s happening is that atoms are moving in my brain because other atoms pushed them. Human reason is caused only by nature, by the sum total of all the material events, from the Big Bang through evolution to photons of light stimulating my optic nerve to send electrical charges to my brain now. Why should I trust my reasoning, then, if it is caused by nothing but blind, unintelligent material forces? If there is no supernatural Mind, if my material brain is not moved by or in touch with or aware of any superior Spirit or Mind (however many material means and intermediaries he may use), then I have destroyed the credentials of my thinking, including that very act of skeptical thinking. Then I can’t help how my tongue happens to wag. Then I think a certain thing is true only because atoms and wind and weather and digestion and electricity have necessitated it, not because a wise and good Father God is teaching his children through many material intermediaries, as a teacher teaches students through blackboards and books. If there is no supernatural, then science is like listening to a broadcast of the news when there’s no broadcaster, no one on the other end. The television set and the wires are like the universe and our bodies and senses: the means of communication. God is like the broadcaster. Would you pay attention if you thought the broadcast just happened and there was nobody there? Would you pay attention to your own thinking if you believed it was nothing but the inevitable echoes of the evolutionary belch of the primordial slime?
--from Angels and Demons, by Peter Kreeft