The problem is that our knowledge is limited. Once we have a better understanding of certain biological processes, we may be able to find the right abstractions.
You might be missing the point. Biological systems are the result of Natural selection, and the processes of Natural selection are fundamentally irrational. Any biological system, including our own brain, is essentially the outcome of a random, irrational process. There may be cases where we can arrive at some abstractions, but such cases may be the exception, not the norm.
In that irrational assumes sentience, OK. The randomness being "we can't possibly predict all the elements that went into X happening" OK. But neither of those matters in making an abstraction: the biological components didn't evolve outside of chemistry and physics. We can argue about how much detail would be needed, but is there really anything we can't abstract?
