At least, I think I see. Kauffman wants to stop being a reductionist, but he doesn't want to stop being a materialist.
Reductionism is inadequate reductionism. Even major physicists now doubt its full legitimacy. Biology and its evolution cannot be reduced to physics alone but stand in their own right. Life, and with it agency, came naturally to exist in the universe. With agency came values, meaning, and doing, all of which are as real in the universe as particles in motion. "Real" here has a particular meaning: while life, agency, value, and doing presumably have physical explanations in any specific organism, the evolutionary emergence of these cannot be derived from or reduced to physics alone. Thus, life, agency, value, and doing are real in the universe. This stance is called emergence. Weinberg notwithstanding, there are explanatory arrows in the universe that do not point downward. A couple in love walking along the banks of the Seine are, in real fact, a couple in love walking along the banks of the Seine, not mere particles in motion. More, all this came to exist without our need to call upon a Creator God.Something is missing here, ... and what is missing is magic. That is, if we want mind to come from mud, we need either God or magic. Kauffman doesn't want God and he hopes that "emergence" is the magic that just sort of happens.
Well then, I always find myself asking, why isn't life, and all kinds of stuff, spontaneously emerging all around us? It should be, if Kauffman is right, but it never is.
That said, I read his earlier book and enjoyed it. I just didn't believe it.