Frances Bacon had several ideas that went against the church, and he worked to spread these ideas to other people. Francis Bacon developed a scientific method that would essentially show people how to do real science themselves. This went against the church because now there would be more people doing science and publishing proof that said there was no divine power, and that everything was governed by scientific laws. He also modified the education of children, and taught then to look at things with an analytical and logical perspective, rather than believing that God controlled everything in the universe. The church was not happy with this: now the children would grow up believing in science and so the population who still believed in the divine power would diminish.
Rene Descartes is considered the founder of analytical geometry, which we still use today. He showed that everything could be reasoned through logic and physical proof. This went against the church because it is hard to prove something like divinity and the earth being the center of everything. Bacon also developed the theory of the conservation of momentum, which again shows that everything is governed by scientific laws, not God. This reflected poorly on the church, because they wanted everyone to believe that everything was governed by the divine power. Descartes and Rene showed that everything was governed by the same laws, even the planets in the solar system, and these ideas were very controversial.
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