John Herschel, Cambridge professor, noted mathematician and astronomer, and leading light of Victorian philosophy of science, was well known for his combination of Christian faith and rigorous scientific methodology. In a letter to Charles Lyell in 1836, he expressed his preference for "natural" causes over the "miraculous", even to account for the appearance of new species: 

"He that on such quest would go must know nor fear nor failing

To coward soul or faithless heart the search were unavailing -- 

Of course I allude to that mystery of mysteries the replacement of extinct species by others. Many will doubtless think your speculations too bold -- but it is as well to face the difficulty at once. For my own part -- I cannot but think it an inadequate conception of the Creator, to assume it as granted that his combinations are exhausted upon any one of the theatres of their former exercise -- though in this, as in all his other works we are led by all analogy to suppose that he operates through a series of intermediate causes & that in consequence, the origination of fresh species, could it ever come under our cognizance would be found to be a natural in contradistinction to a miraculous process -- although we perceive no indication of any process actually in progress which is likely to issue in such a result."

Darwin and much of the reading public would have encountered this text in its public version, in Charles Babbage's Ninth Bridgewater Treatise (London, 1837). By following such views, Darwin simply fulfilled this standard of science, albeit by discovering the "process actually in progress" that Herschel doubted he'd ever see. He would draw on this accepted tradition of reasoning to defend his theory, referring to the "mystery of mysteries" in the Introduction to his On the Origin of Species (1859).