It wasn't that much "a mystery" , more that there were those who lived in denial, like Mach. On the positive side, much before Mach, there was obvious scientifi

It wasn't that much "a mystery" , more that there were those who lived in denial, like Mach. On the positive side, much before Mach, there was obvious scientific progress. Not much later after Lavoisier: https://en.wikipedia.org/wiki/Atomic_theory#Avogadro https://en.wikipedia.org/wiki/Atomic_theory#Avogadro "Avogadro was able to offer more accurate estimates of the atomic mass of oxygen and various other elements, and made a clear distinction between molecules and atoms." (Since 1811). Mach and similar simply denied what was already discovered, often not even wanting to consider that, sticking to their beliefs. Mach was "physicist and philosopher," not a chemist. Not having a definitive proof for physical existence doesn't mean that chemistry haven't already used the concepts. Today too there are scientists who after they became prominent for some work start to spread the false beliefs, some realizing that at the moment they are too hard to disprove, even when most of the experts don't believe them. And some get more influence than it would be scientifically valid. The progress is not something automatically guaranteed, it's always the result of hard work and perseverance.