I think that most who think about this in this way don't have enough insight into how molecular science works or how cellular biology works. It's a non-argument for me.

Of course we're a collection of atoms. We're just not only that.

I'm subscribing to Holism, the way you defined it. Life is like a novel or an essay - a collection of letters, yes, but letters organized into sentences, sentences into paragraphs, paragraphs into chapters and chapters into the book that is something entirely different from ''a collection of letters''.

I think these increasing levels of organization don't stop. You must know of super-organism. However I'm a little confused because a community's (say a country itself) organization is modelled on the human body as indicated by terms as head-of-state, arms of the government, etc. but it also appears that masses of people behave like a bacterial culture in a petri dish (multiplying, spreading, consuming resources). So, it seems humans can think rationally, at least it's claimed as such, and they use their own body plans as blueprints for social organization yet, organized communities also share similarities to mindless micro-organisms.

Atoms are just another model. In quantum physics there are even smaller building blocks. Or rather the blocks disappear and turn into wave forms.

As to whether "you" are a collection of atoms, I think the answer is no. You are not your body. You are a mind, or the awareness inside a mind. You are not a physical object, though you are represented by physical processes (brain activity) in the physical world.

Is your body still the same even though the atoms change? That is the "ship of Theseus" problem. The answer is that your question is incomplete. In order to answer the question "is X the same as Y", the context needs to be established. The same with respect to what?

Is it the same with respect to the physical identity of it's particles (cells, molecules, atoms)? No. Is it the same with respect to it's quality as a body? Yes.

Of course we're a collection of atoms. We're just not only that. — StreetlightX

Yes, and you don't need us to tell you what the key differences are.

If we are a collection of atoms, in what sense can we be the same person when our atoms switch out? Most people believe that we are the same person for at least longer than a year. Another thing to keep in mind is the principle of holism: the view that you can't understand a whole thing as the sum of its parts, rather the whole takes a life of its own (no pun intended). — Purple Pond

These are much better questions. Split them up into two separate discussions under "Identity Over Time" and "Holism vs. Mereological Nihilism". Scrap the rest.

A thing to keep in mind is that 98 percent of the atoms in your body change each year. If we are a collection of atoms, in what sense can we be the same person when our atoms switch out? Most people believe that we are the same person for at least longer than a year. Another thing to keep in mind is the principle of holism: the view that you can't understand a whole thing as the sum of its parts, rather the whole takes a life of its own (no pun intended). What else should we know? — Purple Pond

It's like a water fountain isn't it? The fountain, spectacular or drab, is there in the form of a permanent loop of water but the water is changing with each moment.

When we see a crowd we see a structure that maintains its defining characteristic of "mass of people" even when the people constituting the crowd have changed over time.

I guess it's a matter of definition. What are you focusing on? Are you talking about this body, with its unique shape and this mind with its set of beliefs and memories? If you are then there's no change and you are you but if you're considering the atoms then you are not you at all.

The ship of Theseus is a similar problem. What exactly do you consider the identity of the ship? Is it the usage or is it the planks that make the ship? Which is the ship of Theseus will depend on the answer to that question.

I did think the same way then, quantum macanics. It sees us as a result rather than a definite object.