Darwin’s book The Origin of Species was the most controversial and most important scientific book in the history of science. It’s arguably the greatest idea ever published and shook the earth at its core with its ideas about descent with modification, and natural selection. Darwin used scientific reasoning to understand nature. He used the scientific principals of experimentation and observation and inductive reasoning to back his theories about natural selection and descent with modification.
The reason why the book turned out to be so controversial was that the logical extension of Darwin's theory was that us humans were simply another form of animal and not the divine creatures that we were told we were. His theories made it seem possible that humans might just have evolved from other animals just as the great apes did. These ideas were thought of as blasphemy in those times and Darwin was vehemently attacked, particularly by the Church.
It should be noted that Darwin did not specifically refer to man in the origin of species but used other animals to demonstrate his points. Nevertheless his ideas could be extended to humans and put into question the ideas of religion and creationism. Its fair to say that most atheist today consider Darwin’s theories to be the main argument against god and/or religion.
Darwin himself seemed to by confused by the problems that had arisen from theory and did not see it as a explicit denial of God/Religion. This is evident in a letter wrote in 1860 between Darwin Asa Gray “a devout Presbyterian” who looked at the connection between natural selection to natural theology and published many reviews on how they are compatible with each other.
“With respect to the theological view of the question; this is always painful to me.— I am bewildered.– I had no intention to write atheistically. But I own that I cannot see, as plainly as others do, & as I [should] wish to do, evidence of design & beneficence on all sides of us. There seems to me too much misery in the world. I cannot persuade myself that a beneficent & omnipotent God would have designedly created the Ichneumonidae with the express intention of their feeding within the living bodies of caterpillars, or that a cat should play with mice. Not believing this, I see no necessity in the belief that the eye was expressly designed. On the other hand I cannot anyhow be contented to view this wonderful universe & especially the nature of man, & to conclude that everything is the result of brute force. I am inclined to look at everything as resulting from designed laws, with the details, whether good or bad, left to the working out of what we may call chance. Not that this notion at all satisfies me. I feel most deeply that the whole subject is too profound for the human intellect. A dog might as well speculate on the mind of Newton.— Let each man hope & believe what he can.”