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2 thoughts:
1. Other evolutionary mechanisms besides natural selection (and Kauffman's whatever he calls it) have strong theory behind them. Lynn Margulies (sp?) at Cornell first theorized endo-symbiosis as the origin of mitochondria. Symbiosis can also explain other evolutionary patterns found in nature. I will not be surprised when another evolutionary researcher theorizes yet another undiscovered, and rarer, mechanism. Evolution happens but it doesn't always happen by natural selection.
2. It has always seemed to me that the common usage of the word "God" (e.g. "God's Will") expresses exactly the epistemological uncertainty that Kauffman's ideas express. "God" is an ignorance-hiding way of saying "I don't know".