Chi. Chikyuu no Undou ni Tsuite

The setting is 15th-century Europe. It was a time when heretical ideas lead those to who possessed such a mindset to being burned at the stake for their beliefs.
The protagonist, Rafał, a child prodigy, is expected to major in theology, the most important subject at the time, at the university where he plans to skip a grade. One day, however, he comes across a mysterious man, and is now studying a possible "truth" in the midst of heretical thought!
(Source: Shogakukan, translated)