The story is told in Adrian Desmond and James Moore's authoritative biography Darwin: The Life of a Tormented Evolutionist. Desmond and Moore point out that Darwin lost his faith many years before his publication of his magnum opus on evolution. When his young daughter Annie died at the age of 10, Darwin came to hate the God whom he blamed for this. This was in 1851, eight years before Darwin released his Origin of Species.

Around the time of Annie's death, Darwin also wrote that if Christianity were true then it would follow that his grandfather Erasmus Darwin and many of his closest family friends would be in hell. Darwin found this utterly unacceptable, given that these men were wise and kind and generous. Darwin's rejection of God was less an act of unbelief as it was a rebellion against the kind of God posited by Christianity. A God who would allow a young girl to die and good people to go to hell was not anyone that Darwin wanted to worship.

Now when Darwin published his work on evolution, the American biologist Asa Gray wrote Darwin to say that his book had shown God's ingenious way of ensuring the unity and diversity of life. From Gray’s point of view, Darwin had exposed divine teleology. Darwin praised Gray for seeing a point that no one else had noticed. In later editions of his books, Darwin went out of his way to cite the English writer Charles Kingsley, who described evolution as compatible with religious belief. To the end of his life, Darwin insisted that one could be "an ardent theist and an evolutionist."

Darwin’s most ardent champion, Thomas Henry Huxley, took a different view. Huxley was vehemently anti-Christian, and he was attracted to Darwin’s theory precisely because they saw it as helping to overthrow the Christian case for divine creation. Huxley noted that evolution’s “complete and irreconcilable antagonism” to Christianity constituted “one of its greatest merits in my eyes.”

So why didn’t Darwin correct his over-enthusiastic advocate? Here is where the story gets complicated. Over time, Darwin's hostility to Christianity did play a role in his scientific views. While Darwin was originally very modest about evolution--a theory to account for transitions from one life form to another--he became increasingly insistent that evolution was an entirely naturalistic system, having no room for miracles or divine intervention at any point. When Darwin's co-discoverer of evolution, Alfred Russel Wallace, wrote him to say that evolution could not account for man’s moral and spiritual nature, Darwin accused him of jeopardizing the whole theory. “I hope you have not murdered too completely your own and my child.” Darwin's ultimate position was that it was disastrous for evolution to, at any point, permit a divine foot in the door.

This history is important because we can embrace Darwin's account of evolution without embracing his metaphysical naturalism and unbelief. Dawkins, Provine and others are in a way confusing the two faces of Charles Darwin. They are under the illusion that to be an evolutionist is essentially to be an atheist. Darwin, to his credit, rejected the equation of these two stances as illogical, even if he didn't always maintain, within his own life, a clear distinction between his science and his animus toward God.