I suppose the most famous case of what you are talking about is the
Church's reluctant acceptance of Copernicus's heliocentric model of the
solar system, thereby giving up the ancient Ptolemaic geocentric model.
A classic study of this process is Thomas Kuhn's "The Structure of
Scientific Revolutions".  One link I found is:
http://www.emory.edu/EDUCATION/mfp/Kuhn.html  but there are many
others.

Reed
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