I really don't know how to answer your question, js1138 -- in principle. You be the judge:
Just in case you haven't seen Wolfram's book, A New Kind of Science, which was finally issued this year, here's a little sketch. Essentially, cellular automata are pictures of the output of computer programs. You load whatever instructions you want to test and let 'er rip. The output is graphical. So then you just watch what happens. In other words, you don't have a clue, going in, about what you're going to get as a result.
I don't know how this relates to chemistry (I know almost nothing about that discipline), except to say that it appears Wolfram's "new kind of science" stands the traditional approach of science on its head. The classical model of science makes an hypothesis, and then tests it. You know what you're looking for; the experiment is done to test whether it's "there" -- i.e., to validate or falsify the hypothesis.
What Wolfram is doing is simply saying, let's start, not with an hypothesis, but with a specification of initial conditions, and a set of instructions -- which could be anything from the simplest of computer programs, the digit sequence of pi, the distribution of primes, Fibonacci numbers, Turing machines, and so forth -- and just let the instruction set run through zillions of iterations. (Well, tens of millions....)
As mentioned, the output is graphical; so in effect, at the end of the day you have a "model" of an evolving system in pictorial form. Wolfram has modelled all kinds of things in this way, just about anything that came to his attention whose behavior could be described in digital processing terms. This information forms the instruction set of the program.
The really interesting thing is that, after something like 20 years of staying up all night fiddling with his programs and modelling whatever came to hand, he ended up with only 258 possible patterns -- his cellular automata -- of only four types or classes. The Class 4 type is of particular interest (apparently there are only 2 or 3 CAs of this type).
As a result of doing this kind of experiment, Wolfram surmises that systems that are not obviously simple (e.g., Class 1 or 2 CAs) are "computationally equivalent." Finally he has an hypothesis to test, which he did: He was able to successfully emulate a very high-level Turing machine with Rule 110. And he suspects that little crittur may be some kind of a "universal emulator."
As Wolfram puts it, "it is a general feature of class 4 cellular automata that with appropriate initial conditions they can mimic the behavior of all sorts of other systems."
He hopes that science can figure out ways to apply this insight in their respective disciplines.
But as they are assembled they aquire more complex attributes. They can become part of a system -- an object that we name, and perhaps even love or hate.
Going the opposite direction, the rules for assembly can be derived from the rules of quantum mechanics -- a simpler (!) set of objects and rules. We really don't know how elementary we can make the set of object and rules. Perhaps as simple as the rules for celular automata.
Here is an interesting question: can the creator of the rules forsee all the properties that emerge as the game is played. I think Wolfram argues that emerging patterns cannot be foreseen. So you might call this the God Game, and ask if god ever tries to make a stone He can't lift.