[abelaer]

(OP here) That's a good point---these mereologies tend to grow very fast with system size. Exponential is not even so bad. There is the 'redundancy' mereology for example, which scales with the Dedekind numbers. This appears quite often in information theory and neuroscience, but quickly becomes intractable.

As I see it, emergence comes in two flavours: a higher-order interaction among microscopic parts is already emergent in the sense that it is a non-atomic thing that determines the behaviour of atoms (I use atoms to refer to the 'singletons' or smallest elements of the theory, not necessarily physical atoms). But you're completely right in saying that there is another sense of emergence which only really happens for a 'thermodynamic' number of atoms. The difference seems somehow captured by the contrast between:

-- the whole is more than the sum of the parts -- the whole is less than the sum of the parts.

Both are commonly called emergence! If it turns out that you don't need to keep track of all birds in a flock to describe its behaviour, then we call that emergent because the whole is somehow less than the sum of the parts.

Your example of genetics is interesting, because it is actually what got me interested in this problem in the first place. I spent most of my PhD struggling with calculating up to 7-point interactions among genes, and you indeed need some clever tricks to make this tractable. I used causal discovery methods to rule out most potential interactions based on conditional dependencies. This is now a piece of open-source software: https://www.embopress.org/doi/full/10.1038/s44320-024-00074-...