I tend to think of these layers as orders of physical complexity, and the development being "stochastic" I think is key to understanding it. Its almost random, but with feedback that gives certain permutations evolutionary weight over others. Might be near what D&G refer to when they talk about strata, with one stratum emerging from another.
And another crazy thing to try to understand is the time scale, the different time scales across these advancements from one order to another. Its like certain critical developments (again pseudo-random) actually function to hasten the very processes that led to them. Or like the emergence of prokaryotes as a result of a eukaryote subsuming some virion, one system swallowing another system and keeping it intact. In such a situation, the swallowed system becomes an organ in the larger one, and a whole slew of production opportunities are likely opened right up.
Maybe the cytoplasm is a more hospitable envrionment for such-and-such swallowed virion, and enables it to crank out protein complexes at a faster rate. Don't know, but that sort of thing is par for the course, seemingly.
