Thank you so much, Hector, for your thoughtful and patient replies. I haven't been able to access McAllister's 2003 article, but I did read the Twardy et. al. reply, which I think fairly refutes McAllister's claims when interpreted in narrow terms. However, I did read a more recent piece by McAllister (2009) "What do patterns in empirical data tell us about the structure of the world", from which I can see that he hasn't given up! His two main points there, liberally interpreted, seem to be (1) 'noise' is relative and may be mined for further pattern (signal), and (2) there is a sense in which 'pattern' is in the eye of the beholder. I would agree fully with (1), while acknowledging the usefulness of provisionally disregarding noise in pattern extraction. While I think he may go too far in his case for (2), there is something in the spirit of it that would certainly be useful should we ever have to confront alien scientists! In any case, it seems a wise proviso for human researchers to bear in mind.
In your reply you say:
"I only point out that if the universe is deterministic as one may believe (as I do), then there is this fundamental incompatibility [between randomness and determinism]."
My point is that the universe can only be deterministic if it happens to coincide perfectly with some formalism, for only such deductive systems are truly deterministic (i.e. the only meaning that can actually be assigned to causality is logical implication within some deductive system). In other words (to put it somewhat outlandishly), the universe can only be deterministic if it is not natural but artificial; conversely, if it is natural, it cannot be fully and finally mapped in any formalism. On the other hand, we are not in a position to say that it is fundamentally indeterministic either, since (mathematical) randomness cannot proven. This is why I wonder at the basic human impulse to assert a "truth of the matter" one way or the other, since it seems hopeless to establish that. I hope I am not trying your patience too much, but I would very much value your feedback to these ideas.
You reply also:
"But a blueprint is a description which tells someone (if not you then nature) how to build something. The claim that only information makes a cup a cup rather than a human being is because both human beings and cups are made exactly of the same elementary particles and it is nothing but the way they are arranged that make one or the other. But let me know how that could be wrong from a purely materialist point of view."
While perhaps useful, I think it is a mistake to project human communication models upon nature. We should not assume that nature engages in some form of information processing or computation, along the lines utilized by human beings. We cannot assume that we possess the (complete) information involved in the structure of a natural thing, which is not made by us but found in an incompletely known state. In the sense hinted at by McAllister, the information is made by us, and we can never be sure how exhaustively (or correctly) it describes the real thing. We only know for certain the blueprints we literally make, not the blueprints we impute to nature.
Thanks again for the clarity of your thinking and your willingness to respond.
Dan