Oxygen != heat, or even fire.
I've never heard of phlogiston being heat.
Fluorine can set things on fire, for example.
True, but the vast majority of fire people normally deal with is oxygen-related. Only knowing about oxygen being an oxidizer would be almost as useful as knowing about all of them, at least when you're thinking about fire. Only knowing about phlogiston would be exactly as useful.
"Emergence" or "quantum effects" to explain how the brain works might fall into this category. I'm not sure that counts. We expect it to be explained away, but we still don't understand it, and it still hasn't been.
Whoops! I seem to have gotten my phlogiston theory mixed up with my caloric theory, which stated that fire was in fact made of particles of caloric, a near-weightless fluid that flowed between bodies in contact, explaining heat and cold. Sheesh, alchemists loved conjecturing fluids.
I am looking for examples of mysterious answers that were eventually explained *away* by science. I can think of two: One is the belief that the behaviour of living things was explained by the mysterious force of elan vital, and not by mere chemistry; which was destroyed by the synthetisation of urea. The other is the special (and mysterious) role of the conscious observer in quantum mechanics, which was explained away by demonstrating that rocks can get entangled with electrons just as much as brains can. Can anyone furnish me with other examples?
I observe in passing that phlogiston is *not* such a mysterious answer. Eliezer is down on it, but I think unjustly so; for people did in fact perform experiments on phlogiston, including the final experiment to find the weight of the phlogiston that had passed out of the burning material and into the byproducts. It turned out that the phlogiston had negative mass... in other words, that the direction of the transfer had been misidentified. But if you think of phlogiston as `negative oxygen', it makes the same predictions as modern chemical theory. This is no worse a mistake than mistaking the direction of the current, a mistake which is *still* enshrined in our sign conventions; it is not a mysterious answer of the form "X->Y" with no details of X given and any value allowed for Y.
However, I digress. Mysterious answers blown away by experiments, anyone?