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I think the great divide between believers and agnostics/atheists is illustrated quite well by this interview, even though neither participant acknowledges it.
Sure, science (which is absolutely reductionist) has limits on what it can reveal. It cannot tell us anything at all about the super-natural, be it God or the miraculous soul, which would likely be a good analogy for Kauffman's creative agency, which he says obviously exists and yet is clearly non-scientific.
The divide arises when those limits of science are discussed. The liberal scientist says, "OK, beyond this lies the unknown," whereas the believer invents something to fill the darkness.
I think Kauffman is just one of those scientifically literate people who doesn't actually think scientifically... who, when he reaches the edge of what is scientifically knowable (and therefore what is knowable, imo) he can't admit that saying "I don't know" is the only justifiable answer to questions outside that boundary.