Phlogiston Or Oxygen

Phlogiston was a theory of burning matter that said that a substance, phlogiston, came out of burning material, and was what actually burned. Stands to reason - you burn a piece of paper and what is left is smaller than what you started with. The phlogiston has come out of the paper.

The new theory said that something, oxygen, came out of the air and was added to a material while it was burning.

The phlogiston theory didn't describe all the data perfectly, but then the oxygen theory didn't, either. The phlogiston theory did a pretty good job at describing what would burn, and the fact that it emitted light and heat. The phlogiston theory did a poor job of explaining things like the fact that metals increased in mass when you burned them.

Adherents of the two paradigms simply couldn't talk to each other. One saw something being added, the other something being taken away. They had absolutely no basis for communication. The only resolution was when the oxygen theory began making more accurate predictions and younger scientists took to it. Eventually, the phlogiston scientists died off.

It is interesting that Priestly, who is labeled the discoverer of oxygen in all the high-school chemistry books, went to his death-bed arguing furiously that he did no such thing. He was a believer in phlogiston, and he believed that he had done what he set out to do, which was to extract all the phlogiston from air. He believed that dephlogisticated air would have such an attraction for phlogiston (for nature abhors a vacuum) that material would burn much faster in it. He produced it, and found that paper would nearly explode when burned in it. He was very pleased with the results. His opponents said that he had actually discovered how to make pure oxygen, and that is how he is remembered. (Story taken from TheStructureOfScientificRevolutions by Kuhn.)

Paradigm shifts are not a HegelianDialectic. One paradigm makes more compelling predictions than the other. People new to the field adopt that paradigm. Eventually the old one goes away. (Kuhn disputes the claim that the new paradigm necessarily makes better predictions than the old.)
I am reminded, for all the rabid blathering about the Church suppressing Galileo, that his fellow scientists were also skeptical. His theory still required epicycles to explain apparent planetary motion, and implied a stellar parallax that the instruments of the time could not measure.

The scientists weren't also skeptical because the Church wasn't skeptical. It was certain and hostile. Do you think its actions would deserve any more or less criticism had it turned out Galileo was incorrect?

The Galileo affair has been used to paint a simplistic view of the Renaissance Church.

Agreed. At the particular moment the church was trying to be simplistic, since they were in the middle of an effort to standardize their teachings. That's what Galileo was stepping on, although they were relatively lenient and he showed exceptionally poor tact. Things were different both before and after. But at the same time, this doesn't change that they were suppressing him, and neither does the skepticism of his peers.

But that's not the point. The point is that the old science-vs-religion saw is not a complete and accurate description of what happened. Some churchmen defended Galileo, many scientists did not.
The truth is much more complex than the "science vs religion" morality play version of events that is taught in history class.

I'm at a loss to understand what 'phlogiston vs. oxygen' has to do with 'religion vs. science'. I don't believe there was any religious doctrine at stake in the debate.

Nothing much, but both show that scientific progress often proceeds with bitter political rows and not by some sort of infallible higher proof. This is often a surprise to those not involved in science.
See also DarkSuckers.

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