The natural inference from this is that descent and natural selection are one and the same thing.

Again:-

“If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down.  But I can find out no such case.  No doubt many organs exist of which we do not know the transitional grades, more especially if we look to much-isolated species, round which, according to my theory, there has been much extinction” (p. 189).

This makes “my theory” to be “the theory that complex organs have arisen by numerous, successive, slight modifications;” that is to say, to be the theory of descent with modification.  The first of the two “my theory’s” in the passage last quoted has been allowed to stand.  The second became “the theory” in 1872.  It is obvious, therefore, that “the theory” means “my theory;” it is not so obvious why the change should have been made at all, nor why the one “my theory” should have been taken and the other left, but I will return to this question.

Again, Mr. Darwin writes:-

“Although we must be extremely cautious in concluding that any organ could not possibly have been produced by small successive transitional gradations, yet, undoubtedly grave cases of difficulty occur, some of which will be discussed in my future work” (p. 192).

This, as usual, implies descent with modification to be the theory that Mr. Darwin is trying to make good.

Again:-

“I have been astonished how rarely an organ can be named towards which no transitional variety is known to lead . . .  Why, on the theory of creation, should this be so?  Why should not nature have taken a leap from structure to structure?  On the theory of natural selection we can clearly understand why she should not; for natural selection can act only by taking advantage of slight successive variations; she can never take a leap, but must advance by the slowest and shortest steps” (p. 194).

Here “the theory of natural selection” is opposed to “the theory of creation;” we took it, therefore, to be another way of saying “the theory of descent with modification.”

Again:-

“We have in this chapter discussed some of the difficulties and objections which may be urged against my theory.  Many of them are very grave, but I think that in the discussion light has been thrown on several facts which, on the theory of independent acts of creation, are utterly obscure” (p. 203).

Here we have, on the one hand, “my theory,” on the other, “independent acts of creation.”  The natural antithesis to independent acts of creation is descent, and we assumed with reason that Mr. Darwin was claiming this when he spoke of “my theory.”  “My theory” became “the theory” in 1869.