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.
Yes, I think that is correct. Certainly we don't seem to be able to foresee them. Whether God does or not is really a theological problem. I'm not sure this can ever be a problem for science.