It is extremely easy muddle together the scientific concepts of atoms and elementary particles, and the philosophical idea of atomism, and speak wrongly as a result. The worst example I've ever seen of this, which appears frequently in science textbooks (and which I have mentioned here before), runs something like:
"The ancient Greeks incorrectly thought that the atom was an indivisible entity. But modern science has shown that the atom can be further sub-divided."
This is such a crass error that it is almost unbelievable that it appears in so many textbooks. To understand what has gone wrong, consider the following analogy:
Joe moves to Brooklyn. He has heard reports of "the best bar in Brooklyn," one that has the best drinks at the best prices, served by the best bartenders. He spends a few weeks exploring, after which he dubs Bar X "the best bar in Brooklyn."
But couple of months later, he stumbles upon another bar, Bar Y, which has even better drinks at even better prices, served by even better bartenders. He therefore declares, "The best bar in Brooklyn does NOT have the best drinks at the best prices, served by the best bartenders."
Obviously, he is making a mistake: what happened is that he is awarded the title "the best bar in Brooklyn" too early. He should have awaited further pub crawling results before naming Bar X the best.
And this is just what happened in modern science: when chemists discovered elements such as hydrogen, oxygen, and carbon, they thought that they had found the indivisible particles that Greek philosophers had discussed.
The chemists were wrong. A century or so later it turned out the things they had named "atoms" were not really atomic at all. So what actually happened was the 18th and 19th century chemists had jumped the gun, and awarded the title "the indivisible particles" too soon. They certainly had not "proved" the ancient Greek atomists incorrect!
But there are more subtle ways to go wrong on this topic. For instance, physicist Alex Small mingles the philosophical and scientific issues involved, and thus makes a couple of mistakes that, while less egregious than the above textbook gaffe, are errors nonetheless.
First, he says of Averroes' defense of Aristotle's idea that the universe must be a plenum, "Ironically, his defense of incorrect science was used to carve out a space in which science could eventually thrive."
However, modern science has certainly not proved Aristotle's idea here "incorrect." Yes, modern science relies on the idea of "particles." But, when examined closely, these "particles" appear as probability densities smeared out across space, hardly the atoms the ancient Greek atomists were talking about! But even more apropos here, consider the quantum vacuum:
"According to present-day understanding of what is called the vacuum state or the quantum vacuum, it is 'by no means a simple empty space', and again: 'it is a mistake to think of any physical vacuum as some absolutely empty void.' According to quantum mechanics, the vacuum state is not truly empty but instead contains fleeting electromagnetic waves and particles that pop into and out of existence."
So, according to this interpretation of quantum physics, Aristotle apparently turns out to be correct: Space is full through and through, with no absolutely empty void. Now, is it really correct to say is that the quantum vacuum confirms Aristotle's idea that space is a plenum? And what's more, does it show that space must be a plenum, which Aristotle argued? Well, to answer those questions, we are going to have to do philosophy: physics can't possibly tell us how to interpret what Aristotle was saying!
Small then adds:
"However, given the paucity of evidence for atoms during the time in question (my recollection is that evidence for them didn't really come into play until the 18th century) it is hard for me to treat older ideas for or against atoms as no [sic] more than wildass speculation."
But, as we have seen the evidence for "atoms" that came into play in the 18th century was not actually evidence for "atoms" in the Greek sense at all: the things that were identified as atoms then turned out to be not atomic! And perhaps we can call all philosophy "wildass speculation," but genuinely philosophical issues can't be resolved by physics, any more than they can be resolved by plumbing or free throw shooting. The ancient Greeks were engaged in sophisticated philosophical speculation about the nature of space itself, and whether it could possibly be a continuum. How the findings of modern physics relate to that speculation, if they do at all, is a philosophical question, one which no field theory or bubble chamber experiment can answer.