GDR writes:
...then we are all just a collection of atoms and everything is relative and thus philosophy is meaningless.
I always have trouble understanding why relative things are so deprecated in some people's minds. You see this usually with morality: if an objective morality tells us something is right or wrong, we should heed that. If a relative morality tells us the same thing, we should ignore it.
Ignoring the question of how we come to the determination that "everything is relative" if it is "just a collection of atoms"*, why on Earth ought that to stop us from philosophising about these relative things? For instance, we might argue about the morality of a non-vegan lifestyle regardless of whether cows are "just a collection of atoms" or not.
*ironically, I suppose we could do so via philosophy.