The Origin of Species is based on breeders experience and research., his own opinion on the fauna of many parts of the world which he explored on his 5 year journey around the world and loads of experiments and research done by himself and others.
Before Darwin all knowledge of the sort were merely incoherent facts, on his voyages in Beagle he wrote down his research and conclusions which he later published. After five years of voyaging he went back to England and worked there as a honorary scientist. In Darwin's voyages he, among other places, traveled to the coasts of South-America, Tahiti, New-Zealand, South-Africa and the Galapagos Islands where Darwin is thought to have made his most remarkable discoveries.
At first Darwin sent home geological reports which greatly helped explaining the development of the geological state of the earth. He believed that the world was changing rapidly, little by little, but not in colossal disasters as many believed at the time. He didn't follow the Bible and that has no doubt helped him with his discoveries.
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