Thanks for this useful summary, which is gratifying to me, at least, in telling me I wasn’t making nonsense up in my previous comments on the subject. And on one point I was vindicated, in that when I’ve suggested the chemical properties of compounds cannot be predicted from the constituent elements, there were those who denied it. That very fact ought to tell us that “something is going on.”
It seems to me that, in part at least, the answers to this are that dealing with substances holistically is intractable to the mathematical, abstracting methods of modern science. If a brain were, in fact, irreducible to the sum of individual “algorithmic” nerve impulses, then modelling it in simplified form would be minimally informative, and replicating it exactly impossible in practice. It’s a clear case of searching for the keys where the light is, rather than where you lost them. In fact, because the brain is so complex, one could search for reductionist explanations forever, without ever realizing that the whole approach is wrong.
The whole point of the AT approach, I think, is that a substantial form is such a unity, so a holistic methodology of some sort would need to be developed. The only specific example I can think of is that of Goethe (see here, which of course (like Thomism itself) was conceived at a much less developed state of science and has been largely ignored in the modern explosion of science.
In practice, it seems, science deals with the problems you raise largely by formulating a new, higher level, science: physics can’t predict chemistry, so you investigate chemistry empirically. If AT thinking is true, the conceptual error only comes from the assumption that, if someone gets round to serious work, the bridge from physics to chemistry will be found (an example you mention).
A more serious error would come from not taking the holistic form of chemical compounds seriously, eg by using the principle of reductionism to argue that water cannot have macro-structures, or that we can ignore the whole organism in, say, evolution and need explore only the molecules.
This subject has has many implications. For example, as I mention in one the blogs linked above, it brings insights into what are deemed “random causes” in nature.
Secondly, it suggests that much important knowledge can only be gained by the holistic functions of the mind (this was Goethe’s insight) - and that links in to the protracted discussions here about knowledge of God or morality requiring something more “intuitive” than deductive logic from evidence.