Darwin's theological reflex and a new species of scientist
Much of the scientific opposition — that is, opposition from scientists — that Darwin faced when he published Origin was about God. Pretty much every priest in England at this time was a natural scientist. Studying the natural world was a way of studying God's creation.
As Carlyle said, in a quotation that Darwin liked, "through every star, through every grass-blade, and most, through every Living Soul, the glory of a present God still beams." Natural science was a way of connected preachers to the creator. (It also filled the days of large numbers of intelligent and otherwise unproductive men.)
And hence most of the scientists critiquing Origin were priests, or at least theologically trained, and had to preserve their own status as scientists who had attributed to God what Darwin was now claiming for evolution.
Darwin did still believe in God, just about, when he wrote Origin. William Phipps' excellent book Darwin's Religious Odyssey (US link) details the way in which religious language occurs in Origin. (The book as a whole charts Darwin's changing theological beliefs throughout his life.)
Darwin wrote: "as natural selection works solely by and for the good of each being, all corporeal and mental endowments will progress towards perfection."
This is, of course, a basic error. Evolution is not a perfecting mechanism but an adaptive one. What is perfectly suited to one time and place is imperfectly suited to another. Darwin didn't just know that about evolution, he is the genius who realised it. Why the error?
Phipps explains that there is no conflict with God working through secondary causes and that this language is part of the background culture — the New Testament encourages Christians to "go towards perfection." There is also "a vestige of Paley's Natural Theology", and remember that Darwin studied Paley very carefully and closely at Cambridge. From Phipps:
Paley stated that perfection was the Creator's intention in making structures such as the eye. The epoch-making Origin ends with an affirmation that evolutionary law was impressed by God upon nature...
Darwin also talks in Origin about the Creator breathing life into "a few forms". The origin of life itself is beyond his scope, but Darwin is happy enough to implicate Eden as the origin of things. Creator and creation was a generic word, not necessarily implying anything theologically specific. And by implying a long-range purpose of evolution (somewhat dishonestly) Darwin was giving religious people enough room to accept his theory without destroying their wider belief.
However, when dealing with the priest-scientists who attacked his book, Darwin was less forgiving. Prominent men like Sedgwick, Herschel and Lyell, whose respect Darwin wanted and felt upset at not having, tried to refute Darwin's arguments using a variation of Paley's argument about the eye. They had to do this. Darwin's theory implied an incredibly old world, one which was not compatible with the Eden story. Sedgwick's scientific work took that story literally.
Darwin's argument against Paley was shattering. Paley had argued that the incredible complexity of an eye (cornea, iris, pupil, retina etc) proved God in the same way that the intricacy of a telescope proved a craftsman. As Phipps says:
Darwin suggested God's method is too sophisticated for comparison with the relatively simplistic way a human works... He criticised the assumption that God lacks the ability to construct the eye in a more complex manner than a telescope engineer might operate.
That defence, says Darwin, diminishes Him as a supreme being. So if you believe in the God Paley and his followers believed in, there is very little you can say to claim the work of evolution for God. Why, as Darwin asked, would the Almighty concern himself with the myriad variations in pigeon aesthetics just to bring a little pleasure to pigeon fancier?
Darwin was enough of a theist to let some implications of the unresolvable question of the universe's origins creep into his conclusion in Origin. He was also enough of a theist to see that the Paley argument was simply a jerk reaction. It was not a viable proposition, merely a reflexive argument to deny the inevitable changes evolution came with.
In The Expression of Emotions in Man and Animal (US link), Darwin talks about how paying attention to a reflex can inhibit it. He describes making a bet with some men that if they took snuff they would not sneeze. Because they all wanted to sneeze and were willing it to happen, they didn't.
The conscious wish to perform a reflex action sometimes stops or interrupts its performance, though the proper sensory nerves may be stimulated. For instance, many years ago I laid a small wager with a dozen young men that they would not sneeze if they took snuff, although they all declared that they invariably did so; accordingly they all took a pinch, but from wishing much to succeed, not one sneezed, though their eyes watered, and all, without exception, had to pay me the wager. Sir H. Holland remarks that attention paid to the act of swallowing interferes with the proper movements; from which it probably follows, at least in part, that some persons find it so difficult to swallow a pill.
Darwin's great skill was paying attention. He looked so closely at everything. He was brought up with the same theological reflexes as Paley, but he paid close and constant attention to them, so much so that they no longer worked for him and he was able to see the world differently, without becoming a materialist or an atheist (at that point).
It is nice to think of this as a variation in the species. He didn't quite make it as a country priest who practised natural theology. The Beagle voyage stopped that track cold. But he was in all other respects of class and culture one of them.
He retained some of the base assumptions they did, but deviated sufficiently to write and defend Origin. He stayed at home, supported the local church and studied science like they did. But he was more dedicated to truth and less concerned with dogma. They didn't leave a patch of lawn un-mown for twenty years as an experiment in speciation.
After Darwin, the close link between priests and biologists got weaker and weaker. Perhaps Origin was the point at which one species diverged from the other.