It is hard to know where to begin---there are so many different issues here that are all interconnected. But let me just focus on information.

It seems to me that "information" is one of the most ambiguous words in our contemporary scientific lexicon. Before we can discuss its relevance to the problem of immanent teleology (as I prefer to say, rather than "design"), we need to disambiguate it in at least two ways:

First, we must distinguish between an ontological notion of "structure" or "pattern" and an epistemological notion of "information" as structure that is meaningful for a cognitive agent. I am a realist; I believe that there are natural kinds and that the word has its own inherent structure, at least in some respects. There are not just arbitrary categories that we impose on the world; rather, we discover structure in the world. Now, if you are willing to grant me that much, then perhaps you will agree as well that if there were no living things, there would be no "information" at all, only structure, because information is inherently structure that is meaningful, and meaning presupposes the existence of a cognitive agent (i.e., a living thing).

That is one distinction. The other distinction is between objective and subjective senses of information. By objective information, I mean information that it used by a given organism for its own purposes, and that would exist even if no other organism existed in the world. It is objective in the sense that it is not observer-dependent. I believe that information in this sense is utilized in the fundamental life processes of all organisms. But the problem arises when we forget that other organisms are centers of their own being ("pour soi" in the terminology of the existentialists) and speak as though all information were generated by our own observation acts. When we speak of the "information content" of DNA, for example, we are speaking subjectively of the information content of the sequence as it appears to us in the context of the Shannon theory. But this observer-dependent sense of information may have little or nothing to do with the way information is utilized by the organism. In truth, we do not know enough to say. Certainly, the naive view that the genome can be interpreted straightforwardly as a bit string is fast becoming passe (see the New York Academy of Sciences collection edited by L.H. Caporale, or the important work of Richard von Sternberg). Therefore, I do not believe it is useful to reify information when talking about organisms in the way that the Shannon theory does when talking about communication channels. Certainly, information in some broad sense is ubiquitous in living things, but the Shannon formalism probably has little relevance to information in the objective, or non-observer-dependent, semantic sense.

Bill's idea of the "conservation of information" is of course quite correct within the context of Chaitin's algorithmic information theory, but I do not think it useful for understanding the real world of living things. The problem is that Chaitin's idea applies to formal systems ("the theorems deducible from an axiom system cannot contain more information than the axioms themselves do"), but organisms are not formal systems! If we merely assume that they are, then we are begging the main question at issue.

As Robert Rosen wrote (Life Itself, p. 191): "The assertion that formalizations suffice in the exression of Natural Law, and hence, that causal entailment is to be reflected entirely in algorithms, is a form of Church's Thesis . . . If it were true, the consequences that follow from its truth would clearly have the most staggering implications for all aspects of human thought. For good or ill, it is not true, not even in mathematics itself."

It seems to me that information theory is simply the wrong formalism for thinking fruitfully about the problem of immanent teleology (or design, if you prefer). What is the right one?

Well, the generation of structure in the most general sense is best explained within the framework of quantum field theory, and in particular the notion of symmetry breaking. As Pierre Curie said 100 years ago, "It is the dyssymmetry that creates the phenomenon." I am not quite sure what the "conservation of information" thesis would have to say about the formation of an ice crystal, for example, but clearly it plays no part in the conventional physical understanding.

Now, equally clearly life transcends the sort of symmetry breaking that we find in inorganic forms of condensed matter. So the real problem, as I see it, is how to account for the fact that living things are constantly shifting matter around in such a way as to perpetuate their own existence, thus resisting the second law. Clearly, something is going on that transcends the ordinary laws of physics and chemistry, which in the end boil down to energy minimization, because the whole point of life is to expend work pushing uphill against energy gradients. Unfortunately, we simply do not have a clue how this is possible. And yet it clearly happens, so there has to be an explanation. I have speculated that it may be connected to some sort of topological conservation principle (as opposed to the Noether principle) possibly connected with Hans Frauenfelder's "minimum frustration principle" in the protein state of matter, which arises from the enormous size and innumerable self-interactions in proteins.

But I am no physicist, and this is just hand-waving. What is exciting is that there are more and more physicists and biologists saying that the current Darwinian-mechanistic picture is fundamentally flawed. So, when a critical mass of people start working on the problem, maybe we will make progress toward solving it. In the meantime, the most important thing we can do is get the word out that the whole natural selection-based view of life is a castle built on sand.