Archer Opterix
The idea of atoms and the idea of a round earth are both ideas that belong to ancient Greek philosophy. The people who came up with these ideas didn't imagine they were doing science. Science had yet to be invented. They were doing philosophy. But answers they are, and they have stuck.
Well I think this is where the difference between science and philosophy occurs. Though the greeks speculated on the existence of atoms, science has gone the extra step to show that the atomic hypothesis is correct to the best level of probability.
That said ,just what the atom is is only known in the sense that we can understand the models that pertain to it.
The Bohr atom that is used in elementary school is replaced by the quantum orbital variety that is used in high school ,however even with the mathematical model, the human mind simply cannot
realize how an atom is actually structured.As jar is fond of saying, the map is not the territory.
I feel that the philosophers position is to stretch the envelope however, unlike the past centuries, it must now be subsumed by the rulings of science concerning what properties the world is allowed to possess.
"A man's ethical behavior should be based effectually on sympathy, education, and social ties; no religious basis is necessary. Man would indeed be in a poor way if he had to be restrained by fear of punishment and hope of reward after death."
Albert Einstein