This suggests that the object of Darwin's Doubt was Darwin's own belief in evolution. But the letter itself suggests something different, something that I find even more interesting. Below is the entire letter, taken from volume 1 (pp. 315-17) of The Life and Letters of Charles Darwin, Including an Autobiographical Chapter, edited by his son Francis Darwin.
Down, July 3rd, 1881.
I hope that you will not think it intrusive on my part to thank you heartily for the pleasure which I have derived from reading your admirably written 'Creed of science,' though I have not yet quite finished it, as now that I am old I read very slowly. It is a very long time since any other book has interested me so much. The work must have cost you several years and much hard labour with full leisure for work. You would not probably expect any one fully to agree with you on so many abstruse subjects; and there are some points in your book which I cannot digest. The chief one is that the existence of so-called natural laws implies purpose. I cannot see this. Not to mention that many expect that the several great laws will some day be found to follow inevitably from some one single law, yet taking the laws as we now know them, and look at the moon, where the law of gravitation -- and no doubt of the conservation of energy -- of the atomic theory, &c. &c., hold good, and I cannot see that there is then necessarily any purpose. Would there be purpose if the lowest organisms alone, destitute of consciousness existed in the moon? But I have had no practice in abstract reasoning, and I may be all astray. Nevertheless you have expressed my inward conviction, though far more vividly and clearly than I could have done that the Universe is not the result of chance. But then with me the horrid doubt always arises whether the convictions of man's mind, which has been developed from the mind of the lower animals, are of any value or at all trustworthy. Would any one trust in the convictions of a monkey's mind, if there are any convictions in such a mind? Secondly, I think that I could make somewhat of a case against the enormous importance which you attribute to our greatest men; I have been accustomed to think, second, third, and fourth rate men of very high importance, at least in the case of Science. Lastly, I could show fight on natural selection having done and doing more for the progress of civilization than you seem inclined to admit. Remember what risk the nations of Europe ran, not so many centuries ago of being overwhelmed by the Turks, and how ridiculous such an idea now is! The more civilized so-called Caucasian races have beaten the Turkish hollow in the struggle for existence. Looking to the world at no very distant date, what an endless number of the lower races will have been eliminated by the higher civilized races throughout the world. But I will write no more, and not even mention the many points in your work which have much interested me. I have indeed cause to apologise for troubling you with my impressions, and my sole excuse is the excitement in my mind which your book has aroused.
I beg leave to remain,
Yours faithfully and obliged
Pay no attention to that racist behind the curtain. Francis Darwin footnotes the phrase "that the Universe is not the result of chance" with the following:
The Duke of Argyll ('Good Words,' Ap. 1885, p. 244) has recorded a few words on this subject, spoken by my father in the last year of his life. "... in the course of that conversation I said to Mr. Darwin, with reference to some of his own remarkable works on the 'Fertilisation of Orchids,' and upon 'The Earthworms,' and various other observations he made of the wonderful contrivances for certain purposes in nature -- I said it was impossible to look at these without seeing that they were the effect and the expression of mind. I shall never forget Mr. Darwin's answer. He looked at me 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.'"
So what Darwin was doubting was not evolution but his own belief or impression that the universe shows itself to be the product of intelligence, of mind. That is what he questions in light of evolution.
This isn't a gotcha! moment for Plantinga however. On the one hand, the letter could easily be understood as saying that doubting the belief in an intelligent creator opens the door to doubting all of our cognitive faculties. This is how Plantinga presents the issue, by taking it the further step of applying it to our belief in naturalism and even evolution itself, but Darwin could have been implying it in the letter already. Regardless, even if Darwin didn't apply it this way, it doesn't mean that we can't.
On the other hand, Darwin may just be applying his doubt to the beliefs that were inconvenient for him in some way. That's also a possible interpretation of the letter, but I think it's far too uncharitable. It accuses Darwin of being inconsistent and using ad hoc reasoning; worse than that, of doing so consciously. I'm very uncomfortable with charging Darwin with dishonesty.
On the third hand, perhaps Darwin was only applying this doubt to the thoughts we have before we turn a critical eye on them, our instinctive reactions prior to having the light of reason shone upon them. He doesn't say that in the letter either, but I think the letter could also be reasonably understood this way. In that case, he wouldn't be applying his doubt to evolution, because his belief in evolution is precisely the product of critical thinking. He doesn't doubt the process of reason or rationality, just the building blocks that the process works with.
Again, it's certainly possible that that's all Darwin meant. The problem is that there doesn't seem to be any reason for applying it to one and not the other. In fact, most arguments like Plantinga's explicitly question whether the process of reasoning could be trusted if our minds are what they are merely in order to increase the likelihood of our survival and propagation. It certainly seems that reason is veracious, but why should we trust this "seeming"? Perhaps it was useful to our survival to have an overwhelming impression of the veracity of reason -- just as Darwin had the occasional overwhelming impression that nature is a product of a divine mind -- regardless of whether reason actually is veracious. So Darwin's Doubt applies. Indeed, Darwin's Doubt is a universal acid, eating through every traditional concept and leaving in its wake ... well, nothing. It's an acid.
But now, to return to the elephant in the room, Darwin had the overwhelming impression that the order present in nature bespeaks of a divine mind. That strikes me as a pretty big deal. Moreover, this belief was still coming over Darwin with "overwhelming force", albeit intermittently, within a year of his death. And he gets himself out of that belief by suggesting that evolution by itself makes it difficult to see why our beliefs should be trustworthy, a point that kicks the door wide open to Plantinga's argument and the charge that naturalism is ultimately self-defeating. Again, Darwin may not have intended to apply his doubt to his own belief in evolution, but there's no reason it would apply to one and not the other. The point of course is not to challenge whether evolution is true but to challenge whether it's the whole story: if it were then the belief that it's the whole story would not be trustworthy.
(cross-posted at Quodlibeta)