See sentence in BOLD below. Large portions of Darwin's actual letter are included before and after the sentence in BOLD below, showing that this is clearly not out of context:

C. DARWIN TO C. LYELL.

Ilkley Wells, Yorkshire,
November 23 [1859].

My dear Lyell,

You seemed to have worked admirably on the species question; there could not have been a better plan than reading up on the opposite side. I rejoice profoundly that you intend admitting the doctrine of modification in your new edition;† nothing, I am convinced, could be more important for its success. I honour you most sincerely. To have maintained in the position of a master, one side of a question for thirty years, and then deliberately give it up, is a fact to which I much doubt whether the records of science offer a parallel. For myself, also, I rejoice profoundly; for, thinking of so many cases of men pursuing an illusion for years, often and often a cold shudder has run through me, and I have asked myself whether I may not have devoted my life to a phantasy. Now I look at it as morally impossible that investigators of truth, like you and Hooker, can be wholly wrong, and therefore I rest in peace. Thank you for criticisms, which, if there be a second edition, I will attend to. I have been thinking that if I am much execrated as an atheist, etc., whether the admission of the doctrine of natural selection could injure your works; but I hope and think not, for as far as I can remember, the virulence of bigotry is expended on the first offender, and those who adopt his views are only pitied as deluded, by the wise and cheerful bigots.

Charles Darwin,
Life and Letters, 1887, Vol. 2, p. 229

 

These difficulties and objections may be classed under the following heads:—First, why, if species have descended from other species by fine gradations, do we not everywhere see innumerable transitional forms? Why is not all nature in confusion, instead of the species being, as we see them, well defined?

Secondly, is it possible that an animal having, for instance, the structure and habits of a bat, could have been formed by the modification of some other animal with widely different habits and structure? Can we believe that natural selection could produce, on the one hand, an organ of trifling importance, such as the tail of a giraffe, which serves as a fly-flapper, and, on the other hand, an organ so wonderful as the eye?

Thirdly, can instincts be acquired and modified through natural selection? What shall we say to the instinct which leads the bee to make cells, and which has practically anticipated the discoveries of profound mathematicians?

Fourthly, how can we account for species, when crossed, being sterile and producing sterile offspring, whereas, when varieties are crossed, their fertility is unimpaired?

See sentences in BOLD below. Portions of Chapter 6 in Darwin's Origin of Species are included before and after the sentences in BOLD below, showing that these are clearly not out of context:

Organs of extreme Perfection and Complication.

To suppose that the eye with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, absurd in the highest degree. When it was first said that the sun stood still and the world turned round, the common sense of mankind declared the doctrine false; but the old saying of Vox populi, vox Dei, as every philosopher knows, cannot be trusted in science. Reason tells me, that if numerous gradations from a simple and imperfect eye to one complex and perfect can be shown to exist, each grade being useful to its possessor, as is certainly the case; if further, the eye ever varies and the variations be inherited, as is likewise certainly the case; and if such variations should be useful to any animal under changing conditions of life, then the difficulty of believing that a perfect and complex eye could be formed by natural selection, though insuperable by our imagination, should not be considered as subversive of the theory. How a nerve comes to be sensitive to light, hardly concerns us more than how life itself originated; but I may remark that, as some of the lowest organisms, in which nerves cannot be detected, are capable of perceiving light, it does not seem impossible that certain sensitive elements in their sarcode should become aggregated and developed into nerves, endowed with this special sensibility.

I much regret that want of space prevents my having the satisfaction of acknowledging the generous assistance which I have received from very many naturalists, some of them personally unknown to me. I cannot, however, let this opportunity pass without expressing my deep obligations to Dr. Hooker, who, for the last fifteen years, has aided me in every possible way by his large stores of knowledge and his excellent judgment

Down, November 29th [1859].

This shall be such an extraordinary note as you have never received from me, for it shall not contain one single question or request. I thank you for your impression on my views. Every criticism from a good man is of value to me. What you hint at generally is very, very true: that my work will be grievously hypothetical, and large parts by no means worthy of being called induction, my commonest error being probably induction from too few facts. I had not thought of your objection of my using the term "natural selection" as an agent. I use it much as a geologist does the word denudation-for an agent, expressing the result of several combined actions. I will take care to explain, not merely by inference, what I mean by the term; for I must use it, otherwise I should incessantly have to expand it into some such (here miserably expressed) formula as the following: "The tendency to the preservation (owing to the severe struggle for life to which all organic beings at some time or generation are exposed) of any, the slightest, variation in any part, which is of the slightest use or favourable to the life of the individual
[page 127]
which has thus varied; together with the tendency to its inheritance." Any variation, which was of no use whatever to the individual, would not be preserved by this process of "natural selection." But I will not weary you by going on, as I do not suppose I could make my meaning clearer without large expansion. I will only add one other sentence: several varieties of sheep have been turned out together on the Cumberland mountains, and one particular breed is found to succeed so much better than all the others that it fairly starves the others to death. I should here say that natural selection picks out this breed, and would tend to improve it, or aboriginally to have formed it...

Thank you heartily for what you say about my book; but you will be greatly disappointed; it will be grievously too hypothetical. It will very likely be of no other service than collocating some facts; though I myself think I see my way approximately on the origin of species. But, alas, how frequent, how almost universal it is in an author to persuade himself of the truth of his own dogmas. My only hope is that I certainly see very many difficulties of gigantic stature.

If you can remember any cases of one introduced species beating out or prevailing over another, I should be most thankful to hear it. I believe the common corn-poppy has been seen indigenous in Sicily. I should like to know whether you suppose that seedlings of this wild plant would stand a contest with our own poppy; I should almost expect that our poppies were in some degree acclimatised and accustomed to our cornfields

More letters of Charles Darwin. 2 vols., London, John Murray, 1903, Ch 6, p 450