John Dalton brought atomism into the scientific mainstream when he used the concept to explain the law of multiple proportions. But it wasn't until the early 20th century that scientists fully accepted that matter really was made up of atoms. What exactly were the arguments that scientists put against it? I want books and articles that I can read and reference; specific scientists whose counter-arguments I can cite. This is for a Wikipedia article.
As I understand, most scientists accepted that atomism was a useful heuristic tool that chemists could find useful in their work, but physicists doubted that atoms were real because nobody had physical model. Is this true? I was told that when Bohr published his model of hydrogen, all doubts finally evaporated because Bohr's physical model could explain the spectral lines of hydrogen and how atoms bonded (electron shells).
I was also told that another reason scientists were uncertain about atoms is that chemists struggled to accurately measure the atomic weights of various elements and the exact makeup of various molecules. There were lots of conflicting measurements. Is this true?
As mentioned, I want contemporary books and articles that I can read and cite.
The tricky thing here is that what an "atom" might be was not a universally-agreed upon concept during this time, and so accepting or rejecting it depended on ones context for it. Dalton's idea of an "atom" — the "chemical atom" — was a mostly hypothetical concept devoid of real physical properties, and was not necessarily identical same as the Newton-Laplacian corpuscular approach to atomism as physical matter. This wishy-washy nature of the definition is what made some reject it along various lines. Two in particular stand out: that the idea of the "atom" was a purely metaphysical concept with no physical evidence (one sees this represented as late as Ernst Mach, though by his day he was an outlier for this position — he argued that anything that could not be directly observed should not be admitted into physical science), while the others rejected atomism because they felt there should be a "unity of matter" and a world with dozens of unique atoms didn't accord with that (one can think of this as a sort of neo-Aristotlean position). And there was a separate approach that indicated that the indivisible "atom" itself was possibly divisible — notably that of William Prout, who postulated that all atoms were actually composites of sub-atomic particles (this line of reasoning was highly motivating to J.J. Thomson's thinking about electrons, later, but most chemists of Prout's day considered it false). Prout's approach can be seen as an attempt to reconcile atoms with the "unity of matter" (he was imagining a single sub-atomic particle, not a multitude of them).
Even those who used atomism regularly, like 19th century chemists, questioned how literally the idea should be embraced. They found it a useful heuristic but felt that speculation on the actual nature of chemical elements unproductive, and basically worked around that. Some took this approach to an extreme to reject any dependence on any particular theory of atomism, and just saw chemistry as its own alternative sphere of work, but this was apparently an unusual position.
Anyway — as you can see this is tremendously murky, characterized by its lack of distinct theories battling with each other (it wasn't "I hate atomism, I prefer plenism," like you have in the 17th century, but more "atomism is an obviously useful assumption, but how real is it?"). What you have are two ideas of atomism (the Newtonian-Laplacian and the Daltonian) that were useful in different contexts but were ultimately not physically grounded in any kind of particulate understanding, and that gave enough uncertainty that you could doubt they were particularly true at a deep level. But their heuristic value was very clear; I don't think there were 19th century chemists of note whose work did not ultimately depend on Daltonian assumptions, for example, even if they didn't specifically subscribe to a particular nature of atoms. In this context you can see why the work of Thomson, Rutherford, and Bohr would suddenly make a big difference, as they began to actually give some physical anchoring to the question of what atoms really were, and would lead to a clear unification of both the physical atom and the chemical atom in a single concept.
This summary is taken from Helge Krage, "Particle science," in R.C. Olby, et al., Companion to the History of Modern Science (Routledge, 1990), 661-676.