Sure; I'm using atoms to refer to physical reality rather than abstractions people are applying to the top; atoms more in the indivisible sense, than what you think of in the physics lexicon.

I think your dichotomy is false. Human simplifications of the world are "real" in so far as they correspond with what they model (or else we'll get into a debate about what "real" means). The higher up in the abstraction stack you go, the bigger things (generally) you can model, but the details vary more. This may be more "real", or less "real", depending on what you're trying to model and how well the conceptual framework fits; e.g. you won't get far with modelling fluid as Newtonian marbles. The point being that it's not a binary proposition, the models are all approximations, and any "cause" you find is only with respect to a story people have made up about the way the world works.