We left Darwin in a troubled frame of mind. The fossil record seemed to offer little support to his theory (then again, it offered little support to any other theory). By the time we reach the end of chapter 10, ‘On the geological succession of organic beings’, he’s feeling far more chipper:

“[A]ll the chief laws of palaeontology plainly proclaim, as it seems to me, that species have been produced by ordinary generation: old forms having been supplanted by new and improved forms of life, produced by the laws of variation still acting round us, and preserved by Natural Selection.”

What happened? I’m not entirely sure. Chapters 9 and 10 are sisters — they are summarized together — but they tell different stories. Chapter 9 was big on geology, and low on biological specifics. Reading chapter 10 in isolation, you’d never guess that the fossil record was such a tattered and faded document as its predecessor made out. We’ve seen, in chapters 6 and 7, for example, how good Darwin is at arguing with himself, at pre-empting our objections and addressing them, but these two geological chapters don’t talk to one another as much as you might expect.

There is one message, however, that we can carry over from the previous chapter — the world is very old. When you combine that with one of this chapter’s messages — that, if you look at the rocks, you see fossils appearing, sticking around for a bit, and disappearing, that starts to look like something not predicted, or explained, by natural theology. Once again, Darwin shows that the idea that species are specially and individually created is a poor fit to the data. Of course, species might appear fully formed and vanish like pieces removed from a game board. But Darwin has a better idea.

Descent with modification, says Darwin, can explain why once a group such as trilobites or ammonites goes extinct it never comes back. It can explain why Australia and South America’s fossil animals belong to the same groups as those continents’ living animals, and why history is a much better guide than environment to the species you find in a place (“how slight is the relation between the physical conditions of various countries, and the nature of their inhabitants”). And it can explain why, as you look back through the fossil record, the gap between modern groups narrows, and missing links appear. To illustrate this, he turns to the work of the man who would become his, and evolution’s, enemy, Richard Owen:

“[W]hole pages could be filled with striking illustrations from our great palaeontologist, Owen, showing how extinct animals fall in between existing groups. Cuvier ranked the Ruminants and Pachyderms, as the two most distinct orders of mammals; but Owen has discovered so many fossil links, that he has had to alter the whole classification of these two orders; and has placed certain pachyderms in the same sub-order with ruminants: for example, he dissolves by fine gradations the apparently wide difference between the pig and the camel.”

To explain the patterns of extinction and origination, Darwin turns, not surprisingly, to natural selection. Things disappear because something better comes along. As an analogy, he uses invasive species. Invaders must be fitter — many British species have naturalized successfully in New Zealand, so they “may said to be higher than those of New Zealand”, even though “the most skilful naturalist from an examination of the species of the two countries could not have foreseen this result”.

He also turns to domestic species. Pigeons et al. aren’t just something Darwin wheels out early on and then dispenses with. He uses them in just about every chapter.

“[W]hen a new and slightly improved variety has been raised, it at first supplants the less improved varieties in the same neighbourhood; when much improved it is transported far and near, like our short-horn cattle, and takes the place of other breeds in other countries. Thus the appearance of new forms and the disappearance of old forms, both natural and artificial, are bound together.”

Although that doesn’t mean that we should expect evolution to create regularity. His theory explains more than it predicts:

“I believe in no fixed law of development, causing all the inhabitants of a country to change abruptly, or simultaneously, or to an equal degree. The process of modification must be extremely slow. The variability of each species is quite independent of that of all others. Whether such variability be taken advantage of by natural selection, and whether the variations be accumulated to a greater or lesser amount, thus causing a greater or lesser amount of modification in the varying species, depends on many complex contingencies, on the variability being of a beneficial nature, on the power of intercrossing, on the rate of breeding, on the slowly changing physical conditions of the country, and more especially on the nature of the other inhabitants with which the varying species comes into competition. Hence it is by no means surprising that one species should retain the same identical form much longer than others; or, if changing, that it should change less.”

Once again, as when he discussed the blurry boundary between species and varieties, Darwin is using irregularity and uncertainty as evidence.

Is life, every day, in every way, getting better and better? Whether palaeontology gives Darwin quite as much support as he thought is an open question. The fact that many organisms remain recognizable across massive stretches of geological time suggests that stabilizing, or purifying selection is also an important force, selecting against the extremes. Stasis is data, to quote the punctuated equilibrium guys (seeing as ‘data’ is plural, shouldn’t that be ‘stases are data’?). And there’s no guarantee that a selection pressure will be in place long enough to create changes that show up in the fossil record.

On the other hand, adaptation is all around us — in the evolution of antibiotic resistance, say. And we are getting better (although still not perfect) at reading the imprint of different forms of selection, both positive and stabilizing, in genetic data.

Understanding the links, or differences, between microevolution and the patterns seen in the fossil record is a tricky business. Take two recent papers in PNAS.

In 2007, Gene Hunt published a study arguing that directional change in the fossil record was rare: of the 250 lineages he looked at, 95% showed either stasis or a random walk — only 5% showed any evidence for directional selection.

“The rarity with which directional evolution was observed in this study corroborates a key claim of punctuated equilibria and suggests that truly directional evolution is infrequent or, perhaps more importantly, of short enough duration so as to rarely register in paleontological sampling.”

But last year, Matthew Wills and his colleagues revealed that many Crustacean lineages show a trend to increasingly complex bodies, in terms of more differentiated limbs, through geological time.

“These results provide a rare demonstration of a large-scale and probably driven trend occurring across multiple independent lineages and influencing both the form and number of species through deep time and in the present day.”

Whether macroevolution is microevolution writ large is one of the big questions of evolutionary biology. It’s also one of the things that some evo-devo researchers, such as Sean Carroll, hope they can help to answer by revealing the genetic (i.e. microevolutionary) bases of change to form (i.e. what shows up in the fossils).

I seem to be ending all these posts by going, well, there’s this one bunch of guys says one thing, and then there’s this other bunch of guys says something else. But that’s the way it is, and like most of the questions that Darwin set loose, it’ll be a long time before this one is settled.

On Wednesday: Geographical Distribution.