I'm mostly thinking individual cells in a multicellular organism (i.e. lung cells in a person). It is indeed very hard to understand what they are optimizing for. Obviously, the organism as a whole is under selective pressure, but I'm not sure how much an individual cell in a given organism actually "feels" the pressure. Like, they undergo many cell cycles during one organism's life, but they're not really evolving or being selected during each cell cycle. Of course, this isn't always true as tumors definitely display selective pressure and evolution. But for normal tissue, I prefer to think of cells as dynamical systems operating under energetic and mass flux constraints. They're also constrained by the architecture of the interactions of the genes and proteins in the cell. All that adds up to something that looks a lot like evolutionarily optimized phenotypes, but I think that might be a bit deceptive, as the underlying process is different. It's not at all clear to me though. You're really getting at some deep questions! You might find this paper interesting in that regard:

https://www.nature.com/articles/nmeth.3254

Regarding reducibility and observability of time series, you might also find work from James (Jim) Sethna's lab at Cornell interesting. The math can be a bit hairy, but I think they do a pretty good job at distilling the concepts down so that they're intuitive. The overall idea is that some complex systems have "sloppiness", like some parts of the system can have any kind of weird, noisy behavior, but they don't change the overall behavior that much. Other parts of the system are "rigid", in that their behavior is tightly connected to the overall behavior.

https://arxiv.org/abs/2111.07176v1

You ought to get yourself connected with some folks at the Santa Fe Institute, if you haven't already. I know one affiliated professor, let me know if you want an introduction. At the very least, if you like podcasts, check theirs out. It's called "Complexity" and it's quite good.