David Weinberger is worried about the 'Universe as Computer ' idea, and confused by some metaphors, and wishes we'd stick to something comfortably obscure, like quantum mechanics.
David, I think what Kelly is getting at is quantum mechanics- Hydrogen bonds with Oxygen by finding the minimum energy state, thus solving a complex wavefunction equation with a single quantum resolution (join or not join). In effect all the probabilities are evaluated at once in the quantum superposition. Not sure what that has to do with Wolfram's thesis though.
Universe as Computer does explain determinism differently. Wolfram shows that complexity can emerge from very simple rules, in Cellular automata and many other interacting systems. However, although deterministic, they are not predictable. The only way to find out what comes next is to run the program.
He proposes a theory of computational equivalence, based on the Church-Turing thesis that any sufficiently advanced computer can simulate any other. He shows that he can make a Turing-complete computer from his simple cellular automaton with the emergent complexity, and thus it could perform any computation. Running a program will take the same amount of time (to within an order approximation - eg Order(n) Order (n2), or whatever).
Thus although the world is deterministic, following known physical laws, you can't find an analytic solution that gives the answer - there are no short cuts.
You just have to live it and see what happens next.