Some Not-Well-Developed Thoughts:
Whether wholes are more fundamental than their parts, or parts more fundamental than their wholes, is an important question. The terminology of “fundamental particles” decides the question in favor of parts. It reinforces the idea that the proper way to think of reality is from the bottom up, rather than from the top down.
In contrast, I think the correct way to think about reality is usually from the middle out (both up and down), starting at the level of human beings and the objects we encounter in everyday life. On this view, everything “below” the “middle level” would be a part of some mid-level whole (or at least would be something whose essential telos it is to belong to such a whole as a part), and everything “above” the “middle level” would be essentially just a group or “sum” (being entirely reducible to mid-level wholes), rather than an actual whole.
Even at the “middle level,” however, there does seem to be a difference between organic and artificial wholes. The parts of an organic being grow out of the being; it begins as a whole, and then articulates itself, as it were. A chair, in contrast, usually starts with the parts, which the carpenter then joins together into a whole.
I clearly have a lot of reading in the literature of mereology and metaphysics to do.