Lady Antu
Out of the things you listed gravity is the only theory. We have physical proof of cells, germs, photons, atoms, and tectonic plates, so you can't state that they are a theory, they are fact.
We have "physical proof" that objects are solid, and yet we also know that most objects consist of a sparse cloud of tiny nuclei and tinier electrons with most "solid" things actually being empty space.
All things that science says are falsifiable, meaning that at best we can say that something hasn't been disproven yet. This is what separates science from religion. Read Karl Popper's work on the subject.
Tectonic plates are a theory; no one has actually seen a tectonic plate, and while there is plenty of evidence for tectonic plates existing, this does not mean that they definitively exist in the form that we think they do. It could be that what we think are tectonic plates are actually something else, say, giant turtles, that only look like tectonic plates in the situation that we tend to observe them in, at the scale that we observe them from. A giant turtle, once removed from the earth, would look very different from a tectonic plate, but when it's buried underneath us and moving only very slowly, it might look like a tectonic plate..
Similarly for cells; they might also be tiny, translucent turtles that are too small for us to distinguish from actual cells. Germs might also be turtles, and maybe atoms are also turtles, and photons might be turtles as well; it's turtles all the way down.
The point of all this is, no matter how much evidence we have, there is always the chance that we're wrong, that what we're looking at is something that looks identical in the situations that we observe but that acts differently in situations that we haven't examined yet.
Cells are a theory. Germs are a theory. Atoms are theory. Photons are a theory. They all have plenty of evidence (and we have plenty of evidence for gravity), but "proof" is a lie spread by those who don't understand science..
