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here's a certain phrase that gets tossed around in reductionist philosophical circles from time to time, concerning "the map and the territory". For its users, this is trying to capture the disconnect between normal human understanding of the world, and the world as described by microscopic physics, that of fundamental particles. The idea is presented something like this: our concepts, such as "human", "dog", "chair", "cloud", etc., are maps, and therefore fundamentally unreal -- the territory, that is, the real actual universe, does not have these things, it only has fundamental particles. We can use our maps if they give us reasonably good results, but we shouldn't confuse the map and the territory. Only fundamental particles are truly real.
This can sound reasonable at first glance, but is in fact a load of trollop. To begin with: what, exactly, is being aided by the use of these maps? Human beings? According to the theory, there is no such thing as human beings, only fundamental particles, so it's entirely unclear where the subject of these distinctions even is. People can hand-wave and say that we're particles fooling ourselves into thinking that we're humans, but this is incoherent -- particles as such do not have thoughts, and cannot be fooled; if there's something there that is doing the misunderstanding of reality, we already have something other than fundamental particles.
But this isn't even the real contention with the map/territory framing. Let's turn to the metaphor itself. We have a map, and on it are drawn a bunch of mountains, which we are discussing. Someone comes up to us and says "It's all well and good to have a map, but you know, there aren't really anything such thing as mountains. In the territory itself, there are only rocks." This statement is obviously absurd. Yes, the mountains are made of rocks -- but the reason that there are mountains on the map is precisely because there are mountains in the territory. If there were no mountains in the territory, our map would be bad, and we should make another one. It is the same in the real world. Our concepts of human beings can be thought of like a map -- and they correspond to reality in the same way. The mountains on a map are smaller than, and not as detailed as real mountains, and are represented in symbols; likewise, our concepts of human beings have their own translation in our minds to make them comprehensible. However, these concepts correspond to actual, physical human beings (and dogs, and chairs, and clouds), and this is what makes the map a good one (or a bad one).
It is certainly true that things have parts, and material things have material parts. However, it is an unacceptable leap to say that the parts are the only thing that matter, and indeed, the only things that have reality. In fact, with most things, we understand the parts via their place within wholes, and it is the whole that gives the part its comprehensibility. For most purposes, the whole is substantially more real than the part (take, for example, the pseudo-fact that your body replaces itself materially every seven years -- the parts are clearly not the chief driver of what's going on here).
The icing on the cake here is that the concepts of "fundamental particles" are just as much maps as anything else. Anything we talk or think is a "map" -- we just have to do our best to make our maps good, accurate, and honest, responsive to the real world of real things.