At present, students of nature who are anxious to avoid metaphysics turn a favorable ear to Atomism. But it is not possible to escape metaphysics and cease to trace nature back to terms of thought, by throwing ourselves into the arms of Atomism. The atom, in fact, is itself a thought; and hence the theory which holds matter to consist of atoms is a metaphysical theory.
Newton gave physics an express warning to beware of metaphysics, it is true, but to his honor be it said, he did not by any means obey his own warning. The only mere physicists are the animals: they alone do not think: while man is a thinking being and a born metaphysician. The real question is not whether we shall apply metaphysics, but whether our metaphysics are of the right kind: in other words, whether we are not, instead of the concrete logical Idea, adopting one-sided forms of thought, rigidly fixed by understanding, and making these the basis of our theoretical as well as our practical work. It is on this ground that one objects to the Atomic philosophy.
Encyclopedia of Philosophical Sciences – VII. Being § 98, Attraction and Repulsion