Kauffman says that these phenomena cannot be explained by physics, but that they do have causal powers and so are real entities. He suggests that a process of emergence leads to these phenomena, and that we may regard the "creative process of emergence" as (a naturalized version of) God.
I have two problems with this.
(1) An inability of current physics to explain some phenomena should perhaps not lead us so quickly into a view of these phenomena as emergent entities. Physics seems to always be increasing the number of things it is able to explain. Just as relativity is able to make predictions that classical physics cannot regarding big stuff, and quantum mechanics is able to make predictions that classical physics cannot regarding small stuff, maybe a new field of physics will be developed that can make predictions involving this "emergent" stuff. Of course, maybe that's what Kauffman is working on here. I should really read the book, and learn something about physics, and read the article more carefully, before blogging about it, I suppose.
(2) Whatever the processes that lead to these phenomena are, I guess we can choose to call them (collectively) "God". But I don't know what this accomplishes. The processes may indeed be "stunning", "overwhelming", and "worthy of awe". Still, why call it "God"? The word has lots of heavy connotations. Certainly these processes are not what most people think of when they think of God. God is supposed to be a benevolent, intelligent, rational, etc. being. One could say that this conception is simply an anthropomorphic interpretation of these processes, I suppose. But, it seems that a naturalized God is just not God, but more science.
Clearly, Kauffman does not mean to suggest that these processes are actually what is talked about in the Bible. But, my question is, why bring God into it at all? Couldn't he just say "Hey, here's some weird stuff that we can't explain right now. It's pretty amazing." and leave it at that? I don't see how this is "sacred science" or how it is "using faith to explain anomalies".