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?
The constant free-fall acceleration used to be "explained" by the inertial mass being equal to the gravitational mass, which was, of course, a mystery in itself. It took General Relativity to show that only one type of mass is needed. Specifically, gravity is not really a force (but a spacetime curvature), and the Newton's second law Fgrav=ma for gravity is only an approximation, valid for not very heavy and not very fast objects.
"Because GR" is a less mysterious answer (thanks, Jack) than the previous model (Newton's universal gravitation), because it makes better predictions, but the mystery is still there: why does matter curve spacetime?