Ever since the 1859 publication of Charles Darwin’s Origin of the Species, it has served an esteemed as well as troubled history. Since its publication, Darwin’s theory has become the foundation of biology and has provided fruitful understandings in human as well as natural history. However, as Dennis Alexander once commented, “philosophy is parasitic to Darwin’s theory” .
Over its 150 year lifetime, Darwin’s theory has undergone a wide association with many ideologies and philosophies that predicate on the idea of “natural selection” and “the survival of the fittest.” From psychology, sociology, philosophy, business, cosmology and many other disciplines, Darwin’s theory of evolution can sometimes be interpreted as Darwin’s “theory of everything.” However, the most notable ideological association has been the supposed claim of evolution’s secular, or somewhat atheistic basis. To ask a relevant question: is atheism somehow inherent in Darwin’s theory?
Perhaps the best evidences to properly answer that question can be found within the Autobiography of Charles Darwin, which he wrote later in life. However, it should first be noted that Darwin was never an atheist. He actually started out early in life wanting to join the priesthood, but then progressively moved towards deism and thus finally in agnosticism shortly after his publication of the Origins. It wasn’t until Darwin published The Descent of Man in 1871 where he showed a significant shift in his explicit use of language towards “evolution” instead of “creation.”
Consider this passage in Darwin’s Autobiography where he discusses the struggle regarding his belief in God:
Another source of conviction in the existence of God, connected with the reason, and not with the feelings, impresses me as having much more weight. This follows from the extreme difficulty or rather impossibility of conceiving this immense and wonderful universe, including man with his capacity of looking far backwards and far into futurity, as the result of blind chance or necessity. When thus reflecting I feel compelled to look to a First Cause having an intelligent mind in some degree analogous to that of man; and I deserve to be called a Theist. This conclusion was strong in my mind about the time, as far as I can remember, when I wrote the Origin of Species; and it is since that time is has very gradually, with many fluctuations, become weaker. 
An interesting comment by Darwin (I think anyway) follows:
But then arises the doubt, can the mind of man, which has, as I fully believe, been developed from a mind as low as that possessed by the lowest animals, be trusted when it draws such grand conclusions? 
Therefore, as Darwin finishes, “The mystery of the beginning of all things is insoluble by us; and I for one must be content to remain agnostic” (emphasis added). Darwin surely would have been against the notion of his theory being furthered for the gain of some particular secular worldview, especially that it might be interpreted as some anti-religious perspective. According to Darwin, this was by all means on the contrary.
-  Dr. Dennis Alexander’s lecture Darwin, Ideology and God (March, 2011) can be found on iTunes.
-  Charles Darwin, quoted from The Portable Atheist, ed. Christoper Hitchens (Da Capo Press: 2007) p. 96
-  Ibid.