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How did the rivalry between the Church and science begin?

It started when the persecuted Christian minority had gained enough power to persecute others.

Priscillian, a Christian theologist, won his place in history for being the first Christian executed by the Christian authorities. In the year 385, shortly after Constantine had changed Rome’s religion to Christianity, Priscillian, with six of his companions, was sentenced to death for heresy: that is, not following the official line of the Church. For centuries to come, his execution set the stage for how the Church would deal with any of those subjects who questioned its teachings.

By the early Middle Ages, the Church, which had continued to consolidate its power, had established itself as the spiritual leader of the “civilized world”, and often as the political and economical superpower, successfully challenging rulers and states.

To strengthen its authority further, the Church positioned itself as the custodian of all truth, which it alone was authorized to expound under the inspiration of the Holy Spirit. It eliminated any challenge to its teachings by giving explicit sanction to officially correct views of nature and scripture; and in 1231 it established the Inquisition to maintain and defend the integrity of the faith, and to examine and proscribe errors and false doctrines. Heretics became the enemy of society.

In the beginning, interpretation of the Sacred Scriptures formed the foundation for the science of the Church. However, whenever a new philosophy was adopted, it became an inseparable part of the Holy Teachings, impossible to question or challenge.