Another choice quote from Zen and the Art of Motorcycle Maintenance:

Substance doesn't change. Method contains no permanence. Substance relates to the form of the atom. Method relates to what the atom does. In technical composition a similar distinction exists between physical description and functional description. A complex assembly is best described first in terms of its substances: its subassemblies and parts. Then, next, it is described in terms of its methods: its functions as they occur in sequence. If you confuse physical and functional description, substance and method, you get all tangled up and so does the reader. (p. 305)

I've been having trouble with some documentation I'm reviewing at work and I think this insight may help address the bad feeling I have about it. I'm sure his idea translates directly to complex software systems as well. They too have "assemblies" that interact with each other. It's important to understand that the assemblies exist and then learn how they interact with each other.