This chapter of the Origin, the last before its conclusion, is something of a grab-bag of miscellaneous points. As is typically the case for such chapters, its author is clearly wrapping things up, drawing them together for the big conclusion to come. At the same time, it presents some of Darwin's stronger points, albeit more in favour of the principle of common descent (what we now refer to as "the fact of evolution") than of that of his mechanism behind evolution (natural selection). This is not to say that the latter goes unsupported (indeed Darwin makes some cogent arguments for it); rather it is that it is simply not the point of this chapter to make the case for natural selection. Here, as in the last chapter, Darwin contrasts his view of the living world against that of what was then "the ordinary view of special creation", and finds the latter wanting. And here, as in the last chapter, I am somewhat surprised that he has chosen to make these arguments so late in his work. This is essentially opposite to how I (and, I like to think, most other modern biologists) would present their case: first show the data, and then explain how the theory fits it. The "data" here is the genealogical organisation and common ancestry of all life, which itself is not necessarily obvious, and in Darwin's time required some hefty arguments in order to be taken seriously, arguments which he has provided in these latter parts of his book. But he has not provided them in such a way that they require an understanding of his theory in order to make sense. He refers to his theory here, but any other theory involving common descent (Lamarck's being the one most often presented to beginning students in biology) would be as apt. Once again, I am somewhat perplexed at the organisation of this book, although I will not deny that it works as presented.
The first topic brought up in this chapter is of classification. Darwin's view on this head is entirely modern: Classification should be genealogical. Einstein once said that "the most incomprehensible thing about the world is that it is comprehensible." Darwin notes a similar point in biology: the hierarchical classification that we all take for granted (even those of us who are not biologists are familiar with it on an intuitive level) should be remarkable, if we were honestly to assume that every living thing was made independently of every other. That this is not the case is a compelling argument in favour of common descent; at the very least it should be a noteworthy puzzle. The universe, as far as biological classification is concerned, is eminently comprehensible. And yet, Darwin's lengthy discussion of the topic gives no imminent indication that this was regarded as particularly revelatory. The idea of evolution had been in the air for over half a century by the time that Darwin wrote publicly about it; it could well be said that, like Galileo's popularisation of the heliocentric model of the Solar System, the world was ready to hear about it when Darwin wrote about it, even if it required to be convinced.
This is not to say that there were not contemporary alternatives to the principle of genealogically based classification (which requires common descent). Darwin lists a couple: similarity of form in closely-related organisms either "gives some unknown plan of creation" or is "simply a scheme for enunciating general propositions and of placing together the forms most like each other". Neither of these is satisfactory; for either to be true would require a tremendous amount of coincidence that looks very much like common descent. In contrast, common descent does not provide any substantial difficulties that are eased by assuming either of these alternatives.
Darwin quotes Linnaeus a few times in this chapter: "The characters do not make the genus, but the genus gives the characters." Most of this chapter regards character evolution, so this is an apt point. There is still debate as to how best to define taxa, whether it should be by some suite of characters unique to the group in question or by some limits to its genealogical makeup. The latter is harder to overturn, assuming that the phylogeny used to define the group is accurate, but the former is more satisfying. The risk there is that, after the group is defined according to its shared ancestral character states, some critical character will be found to have been misinterpreted, or some member with an abnormal character state will be discovered or found to be basal, calling into question the basis for the group's identity. Certainly, when starting work on a new group, it can be easier and more intuitive to start with the assemblage of organisms and to try to figure out what they have in common, and with modern molecular phylogeny this is exactly what happens. However, a genuinely objective system would require a completely consistent set of diagnostic features which would definitively place an organism within or without a group, rather than requiring its genealogy to be known (which in any event is often difficult to determine). Personally, I prefer the character-based definition, but this requires frequent updating as our understanding of the evolutionary history of the group is improved. Ultimately, what we take for significant characters in a group is dictated by our understanding of the group's evolutionary history, which in turn is based on a number of sources. So ultimately, Linnaeus is right, but not in quite the way that we (or I, at least) first read him: rather than the genus indicating which character states are significant (here meaning that they are constant within the genus in question), the genus indicates which characters -- variable within the containing group, and constant within the genus under discussion -- are important to use as diagnostic markers.
Darwin elaborates: important characters are prone to vary. Things that are critical to an organism's way of life can easily converge, and so we have fish and dolphins superficially resembling one another when in fact they are very different animals. The phylogenetically important characters do not vary, and are not affected (at least, not within the more primitive members of the group in question) by natural selection. (Here, incidentally, is the one point in this chapter where an understanding of Darwin's theory is actually important to his arguments in favour of common descent. Even still, it could as well be brought up later in the book, had he chosen to present common descent first and natural selection later.) This is not to say that such characters never vary; indeed, characters that are highly conserved in one group (and so are reliable indicators of membership in that group) can be highly variable in another, related group; furthermore, these characters may have ample and even equal value to members of each group. On the face of it, things that unite a group may be of trifling importance, but consistent: Darwin gives the example of an inflection in the jaws of marsupials, which is indeed diagnostic, but probably not significant to the animals' physiology. Another example that Darwin gives, which betrays his lack of understanding of biochemistry, is the colour of algae: this is known (and has been for a long time) to be related to the biochemistry of the pigments used in collecting light, and of great physiological as well as phylogenetic significance. In any event, this is what Darwin means in his invocation of Linnaeus: we cannot guess what aspect of an organism's anatomy is significant to determining its classification without reference to other organisms, both similar and dissimilar. "Hence, as has often been remarked, a species may depart from its allies in several characters, both of high physiological importance and of almost universal prevalence, and yet leave us in no doubt where it should be ranked. Hence, also, it has been found, that a classification founded on any single character, however important that may be, has always failed; for no part of the organisation is universally constant."
Darwin returns to his prior point with remarkable pithiness: "all true classification is genealogical." He addresses this now from the other angle: the question of descent itself implies the existence of ancestors. We classify the descendents of a single genus in several, but those little changed from the common ancestor may be placed in the same genus as that ancestor. Does this make sense? To some extent, perhaps; and yet, all members of the lineage will have undergone some amount of adaptation. It would be true to say that they have all evolved for the same period of time, but this is not necessarily relevant. Did they all proceed through the same number of generations in that time? If not, the amount of evolutionary pressure that could be brought to bear on any one descendent lineage is not necessarily comparable to that of any other. Even if they have, the number of cell cycles undergone by one individual (each of which, on a smaller scale, presents its own opportunity for mutation and selection) may not be the same as another, and once again the lineages may not be comparable. So we may reasonably ask whether it is proper to put any living organisms in the same genera as their far-removed ancestors. But this is a question that is itself far removed from Darwin's discussion, and one which is still discussed today.
Returning to Darwin's observations, he notes that relatedness in character states follows certain patterns. Specifically, a member of one group resembling members of another will do so only in generalities; the first will not resemble any one member of the second group more than any other -- unless some members of that group are obviously less derived, in which case they will be the ones to which the member of the first group will bear a resemblance. This is a very important point, and one which requires us again to return to Linnaeus's dictum: what we regard as important in defining a group requires that we look around to related groups. Darwin concludes his discussion of classification with another nice quote: "We shall never, probably, disentangle the inextricable web of affinities between the members of any one class; but when we have a distinct object in view, and do not look to some unknown plan of creation, we may hope to make sure but slow progress."
The next section is ostensibly about Morphology, but is actually more about Homology. It should be mentioned here that Darwin uses the modern terminology in distinguishing actual homology (a term defined in its modern form some ten years earlier by Richard Owen) from analogy (a term not used in Owen's treatise) -- I do not know when the term first eneterd into use, but it is unlikely that Darwin introduced it here, as he does not define it. Much of Darwin's attention in this section focusses on serial homology, the phenomenon in which structures within the same organism can be seen to have developed from similar primordia. Thus our arms and legs have similar skeletal structures, and our vertebrae are all fundamentally similar, based on the same essential pattern. Owen went further, to suppose that the bones of the skull were themselves highly modified vertebrae, an idea that has since fallen from favour. (One of the hallmarks of any type of homology is that homologous structures arise through similar processes, but the plates of the skull have a very different embryonic origin from the components of the vertebrae, thus ruling out the possibility of homology.) Darwin also cites Owen's observation that more highly advanced forms (by which he means organisms more removed than their contemporaries from their common ancestor) have fewer similarities in their serially repeating body parts. Thus, to give a modern example, insects have only three pairs of functional legs, while their ancestors, the crustaceans, have several. Darwin cites Huxley as well, who says that serially homologous structures are not formed one from another, but all from some primitive precursor. Darwin corrects this view, though, pointing out that that precursor could well be, and usually is, present in even highly-derived modern forms.
From this discussion of the origins of serially homologous body parts, it is only natural that Darwin should turn to the subject of embryology in general. This is a topic that has recently exploded in evolutionary utility, the subject of evolutionary developmental biology, or "evo-devo". Here, Darwin's understanding of the topic is strikingly modern. Over and again he emphasises that "[t]he question is not, at what period of life any variation has been caused, but at what period it is fully displayed." Again: "at whatever age any variation first appears in the parent, it tends to reappear at a corresponding age in the offspring." In other words, not just an organism's form, but the regulation of development that produces that form, is heritable. We often think of there being "a gene for" a given trait, but in reality this is rarely the case: many, perhaps most, of our genes are for fairly standard things, like digestive enzymes or structural proteins. What varies amongst multicellular organisms like ourselves is more the patterns in which those genes are expressed than the genes themselves. For example, all of my genes for actin (a structural protein used, among other things, to make muscles contract) could be replaced by those from a chimpanzee, and nobody would be able to tell the difference unless they actually sequenced my genes. However, if the regulatory regions of my genome were to have been replaced with those of a chimpanzee's while I was growing up, I would have some distinctly chimpanzee-like characteristics, assuming that such replacements did not sabotage some essential bodily functions. To put it another way, the components are the same in most organisms; what changes is the way in which they are assembled.
Another point in which Darwin sounds strikingly modern is his view of the relationship of embryonic morphology to evolution. Haeckel famously said that "ontogeny recapitulates phylogeny" (a saying I find remarkable in its concentration of both syllables and jargon), meaning that an embryonic mammal was in fact a fish. Darwin, while not making a point of the matter, disagrees: rather, the embryo of a mammal resembles the embryo of a fish. Fishes may not develop much beyond that embryonic state in many ways (for instance, they retain the gill pouches that mammals lose) but in others they do depart from the common form (as in, for example, the development of fin rays). I am not well-read in Darwin's views of the matter, but in the first edition of the Origin he gives a very modern account of this relationship, even if he does not contrast it against Haeckel's view.
This is not to say that Darwin gets everything right here. He regards holometaboly in insects (the process in which individuals undergo a radical metamorphosis from larva through pupa to adult) as ancestral, and incomplete metamorphosis (a blanket term covering various alternatives now understood to be primitive amongst insects) to be derived. He gives no explanation for this, and supposes that incomplete metamorphosis arose from the juvenile insects being under the same ecological pressures as their adult counterparts. Certainly something like this has occurred in cephalopods, which lack the larval stages common to other mollusks, but in the case of insects we know this to be the wrong way around. Interestingly, this bears on a fundamental question in animal evolution, one of which Darwin either was unaware or chose to ignore: that of the point at which planktonic larvae arose. Darwin points out that he was amongst the first to have recognised barnacles as crustaceans, based on their obviously crustacean larval stage; obviously he regards crustacean larvae to have been ancestral, and the adult crustaceans to have adapted from that. But whether the larvae of other animals represent their ancestral state, from which the current adult form is a later development, or the adults were the original forms, and the larvae arose later to fill different ecological or life-history roles, is not a topic that Darwin broaches.
The remaining original section of this chapter is on vestigial organs. Darwin has already discussed this topic, and brings little new to it here. He is again impressively modern in his understanding of the matter, and I have little to add to his discussion. Likewise, his summary of the chapter is short and (almost) sweet, beginning with another impressively colossal Victorian sentence, enumerating his main points, and bringing little new by way of synthesis to the matter. This is not terribly surprising in a chapter devoted to the miscellaneous ideas that have not received discussion earlier, of course. All that remains now is his final summary, the capstone on the entire project.