It kinda seems like everyone just takes it for granted that everything in the universe is made of atoms, but is there actually any evidence? it seems like they can't really be observed, so there probably isn't any empirical evidence. Is it still just completely theoretical? A theory doesn't really sound like a solid foundation on which to base other theories... If there's no evidence of atoms, then how can people posit the existense of protons, or electrons, or quarks, etc? it seems like a kind of weak framework on which to build an understanding of the universe, asuming that we can really even understand the universe in any objective way...
of course, i could be completely wrong about all of that. I haven't really studied any of this in great detail. I'm just interested to hear (or at least read) your thoughts on the matter.
I think about that sometimes as well. Atomism was originally posited by Leucippus in Ancient Greece. At that time it was mere theory. However, the name atom was perhaps mistakedly given to what we now know as the atom whereas in Leucippus's views, subparticles would be the real atoms, or if we find yet another smaller particle, then those would be the atoms in Leucippus' theory. In 5th century BC it was indeed just a theory.
Mathematical calculation has created a stronger inference and scientific objective interaction with what we know of as the atom and sub-particles infers that they exist. However, as we find with the wave/particle duality, our idea of matter is perhaps more subjective than we could have comprehended before. Einstein touched on the idea that our 'reality' is completely mandated by our limited comprehension, what we are able to perceive, our consciousness.
Direct observation through one of the senses, albeit with mechanical assistance, has been the last step in 'observing' the atom. Of course, what mandates that something is 'real' simply through your observation through senses? What makes anything real? If we have limited comprehension then how can we mandate what is real and what isn't real?
We can observe interactions outside our own ability to interact that alters what we observe through our senses, but what says that what we perceive through our senses or infer through the senses of other entities on earth (Sonar, etc) are the only things that exist?
The whole idea seems rather subjective to me.
Atoms are an inference that show objective intractability. The idea is to expand the scope, definitions are always subject to change.
The whole idea with science is to work with what we
can comprehend and interact with and make inferences to the unknown based on those interactions. In the scientific realm, if those interactions are repeatable and predictable, then we infer it is real.
Do not base your other "theories" on there being gravity. 
I didn't think about it like that. Maybe electricity is "magic"... I don't think there's a very good definition of what magic is, electricity could be called magic. 
