I would say the problems with composition in particular tend to be underappreciated. James Rooney has an excellent work, " Material Objects in Confucian and Aristotelian Metaphysics: The Inevitability of Hylomorphism," which looks at leading theories of restricted composition (all “hylomorphic”), and the way in which they still leave composition largely arbitrary because they are committed to the notion that substances can contain other substances as parts.
The physicalist will want to say something like: “the causal efficacy men qua agents and animals are sufficiently explained by what they are made of.” But then they cannot explain this composition at all.
Now of course, few deny that men are “made of” flesh and blood, and flesh and blood are made of proteins and lipids, and that these are made of chemicals, which are made of protons, electrons, etc., which in turn are said to be excitations of universal fields, etc. None of this really gets to composition though. The move from “men are flesh and blood,” to “therefore how men act can be explained in terms of flesh and blood without reference to man,” is not obvious either. Indeed, it seems that, at least epistemically, flesh and blood are only understood in reference to man, and chemistry only in reference to substances, etc., so that the order of knowing is exactly opposite of how the prioritization of microphysics has it (a massive problem if higher levels are epiphenomenal, since the higher level cannot be the cause of our moving our lips to utter things about them).
More problematically still, there is no way to start from protons or molecules, or even flesh, and to say: “this is one whole man,” or “this is a freshly dead corpse not a man.” Rather, we go in the opposite direction, starting with the whole and defining composition by participation in the whole.
Now the principles of physics are more general than those of biology, since not all things are living, and perhaps this is where the confusion lies. Generality is mistaken for ontic and causal primacy. This mistake is perhaps more obvious if we look at matter and form as principles of substances. To be sure, these are most general, but you don’t get anywhere without specifying this or that form, and not any other, or this or that matter, and not some other. The most general is in this way least powerful on its own. To say that something is tells us nothing about it, to say it is living tells us much more, to say it is rational still more, to say it is this specific man even more still. What is most general has the widest applicability precisely because it is closest to determining nothing at all. Qbits and the like are not most general because they are fundamental, but because they are closest to being nothing at all.
The process of understanding has to proceed from first principles (however unclear at the time), to the more specific, and then return to the more universal with a fuller understanding of what it contains. This is the process of reversion (epistrophe)—the intellect going out to the many and returning more fully to the unifying one that contains them. This is, however, precisely the opposite of begining with the many and trying to build back to the one. The latter is how you end up with extensional definitions that have to presuppose the principle they are being called in to define. Leaving microphysics as a self-contained base would seem to lock this reversal in place, or else create a layering of sui generis realms that exist on top of each other but do not interact.
Now, it might seem odd to say life is a more basic principle than the inverse square law or some such, but that is perhaps due to the tendency to think of causation in strictly temporal terms. Whereas, life clearly contains the potential to experience such physical principles, and intellect to understand them. Hence, they are prior precisely in containing these in a more eminent way.
For example, something like salt exists in a more eminent way in the intellect. Any individual lump of salt is “soluable in water,” but in reality it only ever dissolves in water when it is placed in water. It is only instantiating some of its properties at any given time, depending on its immediate context, and is not itself much of an intelligible whole at all. But in intellect all of salt’s properties can be present at once, and so it is more what it is when known then when it simply is (where it is almost nothing, lacking the noetic quiddity it has in intellect).
The order of materialism is an inversion of this order. It says that salt, etc. is basic, and all its intelligible whatness, only realized in intellect, is variously illusory, causally inert, or at best some sort of extra description floating on top of the ontic bedrock of the physical. Yet this sort of thinking has often tended to bottom out in a bare shadow world noumena being posited as the most basic and most real, despite its being wholly indeterminate, and so really nothing at all (granted plenty of philosophies stop a bit above this, at the level of brute mathematical structure for instance).
The other irony here is the claim of “sufficiency,” when the most common response to, “but why this physics,” is “it’s a brute fact.” But I’ll grant that is a confusing topic because the “laws of physics” are both very general (applying everywhere) and strangely specific (seemingly radically contingent). I would tend to take this as a strong demonstration of the fact that they are not intelligible in themselves however, and so represent the outreaches of being, not its fullness (this is perhaps clearer in attempts to reduce physics to 1 and 0, or the potential for 1 or 0, which seems about as minimal as one can get before we’re not speaking at all).