No totally indirectly by means of elements and compounds and rules of proportions. Later brownian motion seemed further indirectly give evidence for atoms. Only today do we have STM's and AFM's to directly detect atoms, but even they do it indirectly by getting data and using advanced mathematics that would convert it into geometry. Only indirectly did Einstien figure out that gravity is curviture of some barelly defined spacetime term, and that was by means of a system of reference frames which barelly has anything to do with curviture of some still undiscovered quantum field. Alway's we have to puzzle things out, and what we end up with is a finite theory that incompletelly describes nature.
Every theory incompletelly describes nature.
Taken at face value the stars are just fixed points on a crystal sphere that rotates around us. The earth must be the center of the universe. One supergenius greek took the wierd phenomenon of retrograde motion as evidence something else must be going on. His theory was later resaid by Copernicus. Kepler assumed as everyone would that the orbits must be circular, yet the data just wouldn't fit.