"...[T]he decline of Darwin's faith began when he first started to doubt the truth of the first chapters of Genesis. This unwillingness to accept the Bible as meaning what it said probably started with and certainly was greatly influenced by his shipboard reading matter—the newly published first volume of Charles Lyell's Principles of Geology (the second volume, published after the Beagle left England, was sent on to Darwin in Montevideo)...

Inevitably, the more Darwin convinced himself that species had originated by chance and developed by a long course of gradual modification, the less he could accept not only the Genesis account of creation, but also the rest of the Old Testament as the divinely inspired Word of God. In his Autobiography, Darwin wrote, 'I had gradually come by this time, [i.e. 1836 to 1839] to see that the Old Testament was no more to be trusted than the sacred books of the Hindoos or the beliefs of any barbarian.'

When Darwin came to write up the notes from his scientific investigations he faced a choice. He could interpret what he had seen either as evidence for the Genesis account of supernatural creation, or else as evidence for naturalism, consistent with Lyell's theory of long ages. In the event, he chose the latter—that everything in nature has come about through accidental, unguided purposelessness rather than as the result of divinely guided, meaningful intention, and, after several years, in 1859 his Origin of Species was the result.

On the way, in 1844, he wrote to his friend, Joseph Hooker, “I am almost convinced... that species are not (it is like confessing a murder) immutable.” Concerning this, Ian Taylor writes, "Many commentators have pointed out that the 'murder' he spoke of was in effect the murder of God."

Having abandoned the Old Testament, Darwin then renounced the Gospels. This loss of belief was based on several factors, including his rejection of miracles: "the more we know of the fixed laws of nature, the more incredible do miracles become"; his rejection of the credibility of the Gospel writers: "the men of that time were ignorant and credulous to a degree almost incomprehensible to us"; his rejection of the Gospel chronology: "the Gospels cannot be proved to have been written simultaneously with the events"; and his rejection of the Gospel events: "they differ in many important details, far too important, as it seemed to me, to be admitted as the usual inaccuracies of eye-witnesses."

Summing up the above, he wrote, “by such reflections as these... I gradually came to disbelieve in Christianity as a divine revelation.”

On another occasion he wrote, “I never gave up Christianity until I was forty years of age.” He turned 40 in 1849. Commenting on this, Darwin's biographer, James Moore, says, "... just as his clerical career had died a slow 'natural death,' so his faith had withered gradually."

One immediate effect of Darwin's rejection of the Bible was his loss of all comfort from it. The hopeless grief of his later letters to the bereaved, contrasts sharply with the earlier letter of condolence quoted above. In 1851, his dearly loved daughter Annie, aged 10, died from what the attending physician called a "Bilious Fever with typhoid character." Charles was devastated, and wrote, "Our only consolation is that she passed a short, though joyous life." Two years later, to a friend who had lost a child, Darwin's only appeal was to “time,” which "softens and deadens... one's feelings and regrets"

One major factor that contributed to Charles's apostasy is worth noting--the role model of his father, Robert, and of his grandfather, Erasmus. Both were ' freethinkers', so disbelief was an acceptable trait within the Darwin family--perceived not as 'a moral crisis or rebellion,' but perhaps even as 'a filial duty'. Indeed, in 1838, when Charles had become engaged to Emma Wedgwood, a very devout Unitarian, Robert had felt the need to advise his son to conceal his religious doubts from his wife--other households did not discuss such things.

Surrounded as he was by unbelievers, and having soaked his mind in literature that rejected the concept of divine judgment in earth's history, Charles mused, I can hardly see how anyone ought to wish Christianity to be true; for if so, the plain language of the text seems to show that the men who do not believe, and this would include my Father, Brother, and almost all my best friends, will be everlastingly punished. And this is a damnable doctrine.' The descent into darkness did not stop there. In 1876, in his Autobiography, Darwin wrote, “Formerly I was led... to the firm conviction of the existence of God and the immortality of the soul. In my Journal I wrote that whilst standing in the midst of the grandeur of a Brazilian forest, 'it is not possible to give an adequate idea of the higher feelings of wonder, admiration, and devotion, which fill and elevate the mind.' I well remember my conviction that there is more in man than the mere breath of his body. But now the grandest scenes would not cause any such convictions and feelings to rise in my mind.”

In 1880, in reply to a correspondent, Charles wrote, “I am sorry to have to inform you that I do not believe in the Bible as a divine revelation, & therefore not in Jesus Christ as the Son of God.”

In the last year of his life, when the Duke of Argyll suggested to him that certain purposes seen in nature "were the effect and the expression of mind," Charles looked at him very hard and said, "Well, that often comes over me with overwhelming force; but at other times," and he shook his head vaguely, adding, "it seems to go away." And about the same time he wrote to his old friend, Joseph Hooker, “I must look forward to Down graveyard as the sweetest place on earth..." full text: Was Darwin a Christian? Did he believe in God? Did he recant evolutionism when he died?