Kauffman's reasoning is, in the main, faultless. It falls down, however, in two places. The first is his proposal that consciousness is based on the quantum mechanical properties of cellular substructures. Some recent work does show that certain proteins, in the dense milieu of cells, can manipulate electrons Santa-fashion, keeping all quantum possibilities open for as long as possible.Gee's review makes clear that one cannot be a half-hearted materialist, as Kauffman and all his followers want to be. If you really believe in the materialist magic of self-organizing complexity, then you do not believe in God, or for that matter, in the mind or free will.
This idea is fascinating, but Kauffman appears to speak as if such properties were confined to neurons in the brain. Nowhere does he explain why they should not exist in other kinds of cell - a flaw that exposes him to accusations of arguing that brain cells are somehow exceptional. By the same token, he dismisses, out of hand, the idea that "mind" might be an emergent property of the trillion-fold interconnectedness of billions of neurons - a casual swipe that goes against everything else he says in the book about complex systems.
The second failure is the whole God business. The concluding chapters are more readable than the rest (in a book that is often an eye-watering challenge to read), but they degenerate into a repetitive mantra in which Kauffman says that the "ceaseless complexity" of the world, while not being evidence for a Creator God, should somehow be "symbolic" of God, or, at least, of something "sacred." He cannot prove this logically, he says; he can only try to persuade us.
This appeal to a kind of primitive pantheism is both sincere and charming, but in the end it is simply more special pleading. The fact is that in Kauffman's scheme, God is unnecessary, even if reductionism fails, so in the end one wonders about the point of preserving a sense of God.
Henry Gee's review makes that clear, though it fails to elucidate Kauffman's theory in any detail. (But in fairness, I could not do it either.)
Here's the book: Reinventing the Sacred (Basic Books, May 2008)
See also: Now, if all those the butterflies would just appear out of nowhere. ...