An Old Fallacy In A New Packaging

I remember a few years ago my college chemistry professor was talking about atomic theory and how successfully it was applied at the beginning on the 20th century. Concerning whether atoms actually exist or whether they are simply a convenient fiction, he said, "Of course we know they exist, we can take pictures of the damn things!"

This is in fact begging the question. The existence of atoms is the very assumptions of the theory. If we "took pictures" of them and found out they were not atoms, it would show the theory to be self-contradictory; the fact that the pictures we can take (using electron microscopes) show them to be atoms shows only that the theory is consistent.

Dr. Bitterwolf I expect would argue that this is proof that the world is just a bunch of atoms colliding with each other. But he'd be arguing using a petitio principii. But that tends to happen when you absolutize science.