It is quite chaotic messy. I’m not sure how perfectly organized you think things are, but they only look neatly organized when you look at the whole thing from very far away, and you lose most of the detail when you look at an image of what large scale collections of mass looks like. Also, all mass exerts gravitational force on all other mass. So things are kept in relatively proportional distances from one another because everything is constantly pulling towards its center. We have things like orbits on a small scale that we can rationalize is neat and organized, but even orbits aren’t perfect. There are obviously many things that aren’t in orbit like an unfathomable number of asteroids, stars and other cosmic material that randomly floats through space.
Also, there doesn’t appear to be a center of the universe. Expansion appears to be more or less uniform everywhere, which is another puzzling fact of the universe.
We don’t actually know! According to the Big Bang theory the universe should have been a pretty much uniform arrangement of atoms–something happened back in the very early universe that disrupted the uniform arrangement, and once that happened you got parts of the universe that were more dense than others and so began to clump together simply due to gravity. We don’t know what that “something” was, though.
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