Assuming a non-religious stance, we are made of the atoms that make up everything else in the universe. Why are we categorized as humans, and not the stars that existed billions of years ago and exploded, making up what we see now? Why are we categorized as humans, and not the fish we evolved from?
There is an argument that the distinct edges behind objects are an artificial construct. To use your example where we assume everything is made of atoms, there's a blurry edge between a pattern of atoms which is human, and a pattern which is not. Indeed, we find many debates on abortion end up in these muddy and tricky waters.
I would argue there's no obligation to have such divisions (even though I admit to generally accepting that they exist, especially in speech). Daoism famously argues that everything is the Dao. Not that we are made up of the Dao, but that the Dao is all that is, and all that is is the Dao. The distinction between human and not in such a system is... complicated. I would fail to do the religion justice if I tried to sum it up in a sentence.
This would suggest these divisions are more social than anything, as Mauro ALLEGRANZA references in the comments. If you look at US history, you can watch the meaning of "human" change with respect to people with dark skin. Some words even change just based on context. If you say "this table is solid and rigid" it means something very different than is meant when a an experimental particle physics scientists say it. By their standards, our solid tables are rather flimsy and soupy. Surely they can't be relied upon to be stable on the scale of the precious nanometers or even picometers that the scientist is concerned with.
In the philosophy I have read which assumes distinct classifications of "stuff," I find a few major classes that one can look to:
- An epistemological approach where once one defines what an object is, and what is not, then one can classify by properties. This may be at the root of your question, based on the wording I see. Note that there's one cheat in the phrasing. First one must define what is an object, and what is not.
- An ontological approach, which typically classifies things as something far more fundamental than "chairs" and "humans." Many dualist approaches argue there is a "matter" and some not-matter material (such as "mind" or "soul"). This is outside of your particular argument (as you explicitly stated you are using an atomic physicalist perspective... thank you for specifying), but its definitely a pattern you will see which doesn't fit nicely into the atomic world you specified.
- A two step approach, where one first argues that the divisions you are used to using are arbitrary, and uses that to make an argument such as "we are all fish." This is then solidified back onto an argument with clear classification to prove their point.
- A method of inquiry, where one assumes that a division exists, and then seeks to define its meaning. In such approaches, one is always at risk of developing a classification which is inconsistent. In my experience with systems that use Dao, the things which use the word Dao start to feel inconsistent quickly, with the intent of driving you to stop using the words and feel the underlying reality. In this case, the purpose of the classification is not to be truthful, but to be a driving force that propels you forward.
Personally, I find I resonate well with a phrasing Alan Watts loved to use:
There are basically two kinds of philosophy. One’s called prickles, the other’s called goo. And prickly people are precise, rigorous, logical. They like everything chopped up and clear. Goo people like it vague. For example, in physics, prickly people believe that the ultimate constituents of matter are particles. Goo people believe it’s waves. And in philosophy, prickly people are logical positivists, and goo people are idealists. And they’re always arguing with each other, but what they don’t realize is neither one can take his position without the other person. Because you wouldn’t know you advocated prickles unless there was someone advocating goo. You wouldn’t know what a prickle was unless you knew what a goo was. Because life isn’t either prickles or goo, it’s either gooey prickles or prickly goo.
And, in summary, you say " I've seen people claim there's no such thing as human, or "specie", that we are fish." I've heard one step further. I've heard that we aren't humans, so much as highly advanced star-dust. The argument is the same, it's merely a question of how far you wish to go. If one does not make some point using this classification, it is very tricky to argue that the classification stands on its own.
There's no one single answer to this, because different philosophical --and scientific --systems categorize things very differently. It's perhaps easiest to say that the borders are set where they are because that's what makes sense in the specific philosophical, conceptual, religious or scientific framework making those particular categories. To question the categories is to question that conceptual system.
Monism describes all the universe as being of a single type of substance. If you think that substance is mental, you're an ideal monist. If you think that substance is physical, you're a physical monist. If you think the universe is two substances, you're a dualist. If you think those two substances are body and mind, you're a Cartesian dualist. If you think those two substances are good and evil, you're a moral dualist. If you think those two substances are yin and yang, you're a Taoist.
If you think that human beings are something intrinsically different from animals, you are part of a humanist tradition dating back to one part of the ancient world, and upheld in the modern world largely in the religious communities. If you think human beings are just one type of animal among many, then you're in different ancient tradition, or perhaps you're a Singerian Utilitarian, or a modern biologist.
To a chemist, gold, silver, hydrogen and helium are all different elements. They are the same, in being elements, but they are essentially different from each other. But to an atomic physicist, those are just different arrangements of protons, electrons and neutrons.
I could go on, and on with examples, but you get the point. Where you draw boundaries --if you draw boundaries --depends on what you believe, and what your goals are.
Because if you don't categorize the nature around you, you cannot interact with it.
You can't touch the planet, bend atoms or grab the weak force in your hand. You cannot even drink water if it is not "categorized". In order to drink water, you need to put all the water in the universe in two categories: the part that you need (e.g. a glass of water) and the rest of water.
In order to touch something, there should exist the category "thing", and "not thing" (so, touching applies only to the first category). If you need to bend something, in addition to the thing category, you need a new one thing that can be bent, and the rest of things. So, you cannot bend an atom, but you can bend a flexible bar. etc.
Strictly, you address nature as a bunch of systems, in order to interact with them, always upon the pattern subject interacting with objects. If those categories would not exist, I would not even be able to address you as "you": there would not be limits between you and me, there would not even be a "me", not even words, not even something as a unit or a whole (because in order for a whole to exist, a "nothing" is necessary, making both two categories) .
As for now, there's no accepted theory of interaction, an idea that Bertalanffy proposed.
While you are right to say that everything around us is made of the same building blocks, different combinations of those building blocks have different collective properties. For example, some combinations are liquid while others are solid. Some conduct electricity. Some conduct heat. Some are transparent. Some are inert. Some are mobile. Some reproduce. Some mobile combinations consume other mobile combinations, and so on.
A combination of the basic building blocks might, for example, have the properties of being mobile, of reproducing, of forming a shape that includes a pouch-like opening, a pair of short projections, a pair of longer ones and one single long projection, and of consuming other living combinations, other liquid combinations and other gaseous combinations. Humans use the term 'kangaroo' to refer to a combination of basic ingredients that possesses those qualities.
The categories you refer to are sets of combinations of basic building blocks where the combinations in the set share common properties.