After spending the previous chapters explaining Natural Selection, variation and their relations to evolution, Darwin shifts his focus to difficulties in the theory which he lays out in brief and will discuss in some depth over the next four chapters.
How, if all species descend from other species, do we have distinct well defined species instead of numerous variations of the same species, or transitional varieties? Just as natural selection preserves profitable modifications, it goes hand in hand with extinction as it diminishes those qualities that are less profitable. But to accumulate all of the many transformations necessary to distinguish the many distinct species inhabiting the earth today, Darwin questions why we do not find them in countless numbers buried in the crust of the earth. He attributes this to imperfections in the geological record. As members of a species move to differing environments the conditions favor different traits which in time cause the species to diverge. As they do these new characteristics, being better suited for their environments, will help them to prosper while the transitional varieties will, in time, become extinct.
Critics point to the impossibility of natural selection to account for the development of complex organs such as an eye and Darwin noted that if there were possible to find any such organ which could not be accounted for by numerous, slight, successive modifications his theory would break down. But he can find no such case.
In contrast he looks at organs which seem to have little apparent importance to natural selection. Darwin admits that here it is hard to know the cause of each slight variation or individual difference. Some of these may be vestiges of an earlier time when they were important for survival, some attributed to correlation, in some we may discover it's use in the future, and still in others it may be an organ that will die out in time.
Note- This chapter was added to later editions, thus it is missing in some versions of Origin of Species.
A serious objection, brought up by one of Darwin's critics is the appearance of defining characteristics like the length of ears and tails in some animals or folds in the enamel of teeth in others which are defining characteristics but seem to have no baring on their survival. Darwin says that some of these may be vestiges of what was once advantageous modifications, others may be attributed to correlation of another variation which we do not yet understand.
Next Darwin dedicates some time disputing the critiques of zoologist St. George Minvart who he seems to hold in little regard. Using the example of the giraffe, Darwin discuses many concepts that he has previously covered in countering Minvart's arguments. If the length of a giraffe's neck is so advantageous, and natural selection so potent, why haven't other animals developed the giraffe's ability to reach higher for food. There is food closer to the ground for those species and the competition for food high in the trees is amongst other giraffe's. Why advantageous mutations happen to some species in some places and not others is often a question that cannot be answered, but is not cause to doubt that natural selection exists. Some critics had questioned why, if the ability to fly were helpful to birds, the ostrich hadn't acquired the skill. Darwin cautions against the tendency for critics to be too sure of how one variation may have unexpected consequences and here he points out that flying would take up an enormous amount of food for the energy needed in such a large bird, something that is in short supply in the ostrich's desert home.
Darwin brings up and addresses a number of other very specific criticisms brought up by Minvart.
-Chapter 6 obviously added later as it relates chiefly to objections others have had to Origin of Species.