Meanwhile, in another part of the forest

I imagine a mad mathematician, suffering from the effects of some atypical stroke or perhaps just an extremely severe case of OCD, who could derive the most amazing results except that he kept going back to make sure that his earlier proofs worked. “Did I really prove the bit about the square on the hypotenuse? Maybe I should go over it just one more time…” If your understanding of modern biology depends upon the popular press, you may think that we’re stuck in the same fix. No matter how much evidence piles up for the gold-standard validity of natural selection and evolution in general, somebody is always on hand to insist that we need to re-examine the evidence. Of course, the public debate, like so much else in America, is queered by ideology and religion—the Creationist calling for a fresh look at old fossils is exactly as honest as a Republican insisting that we ought to start over again with health care reform. However, in biology, at least, the PR efforts of the cultural conservatives have an ironic effect. By endlessly focusing attention on the issues related to traditional Darwinism, they ensure that most people won’t notice that much of the most important new work in evolution doesn’t have much to do with the preoccupations of what is often called the New Synthesis—natural selection and speciation among multi-cellular animals and plants. I’m not just referring to the work done under the heading of Evo-Devo: that the development of individual organisms would shed light on the historical relationships between species and vice versa was already bruited in the 19th Century, though the advance of biochemistry means that the current version of ontology and phylogeny is less talk and more HOX. I’m also not talking about attempts to rethink evolution in the light of Odling-smee’s concept of niche selection, the various ways that the activities of organisms determine the selection pressures on their offspring—I think that idea is very important, but I recognize that we’re talking about a reversal in perspective here, vases and faces, rather than a new assertion about how things work. What has changed most drastically, it seems to me, is our understanding of what there is to explain.

The famous names of evolutionary biology in the last century were mostly zoologists, botanists, and paleontologists who shared a preoccupation with large and showy organisms, even if large and showy sometimes meant nematodes and fruit flies. For the most part, the makers of the synthesis demonstrated a disdain for the microorganisms that represent so much of the biomass and biochemical diversity of life on earth. While these bird watchers and entomologists weren’t paying all that much attention, the microbiologists decided to get evolutionary and in the process discovered that life on earth is rather different than we imagined. When I first began to read biology books, there were two and only two kingdoms of living things, animals and plants. Subsequently, it was noticed that the more salient division was between organisms with and without nuclei, the eukaryotes and prokaryotes. Circa 1960, you got points for knowing about that. A little later, things were broken down more finely with Robert Whittaker’s five-kingdom system (bacteria, protists, fungi, plants, and animals), but that didn’t last very long either. The analysis of ribosomal RNA led Woese and his allies to the discovery that some of the erstwhile bacteria were as genetically different from bacteria as they were from animals, plants, and fungi, indeed, that these organisms, which eventually came to be classified under the new taxon Archaea, were, if anything, more similar to us than to E. coli. These newly discovered creatures obviously had a history, and their existence also put the possible origins of already familiar organism in a new light that evidently demanded rather different kinds of explanations than what had been dreamed of in Ernst Mayr’s hundred years, including, for example, the dramatic episodes of symbiosis that apparently gave rise to the eukaryotes by endowing them with vital organelles such as mitochondria and chloroplasts and, more generally, the possibility that a much greater degree of genetic interchange occurs between organisms, thus not simply making it much harder to discover the true tree of life but raising the possibility that it wasn’t always a tree at all.

Much as modern literature is sometimes successful in making the reader aware of the strangeness of experience, recent discoveries have revealed how little we understand of the living things around us, how down right weird the biosphere actually is. Cthulu isn’t lurking in an adjoining dimension: half a mile underground, in boiling hot springs, in chemical spills, at the bottom of the sea, and—it’s a good bet—in your large intestines, microbes are exploiting every energetic chemical bond on the planet in ways more exotic than any brain-eating alien. Genetic probes inform us that thousands and thousands of such beings exist, though we don’t know how to culture many of them yet or identify them under a microscope—one coccus looks much like another—but their modes of life, metabolisms, and chemistries mark them off as more radically diverse than the all the animals, plants, and fungi put together. And that’s what a complete theory of evolution would have to explain.

The people at Panda Thumb and other venues who fight the good but thankless fight against the Creationists and Intelligent Design devotees have to repeatedly point out to their theologically inspired opponents that the theory of evolution is not the same thing as a theory of the origin of life. Nobody is claiming that Darwin had an explanation for biogenesis—at most he had a few odd thoughts on the topic. It is also the case that no knowledgeable person would suggest that any consensus has formed since Darwin as to how life began on this planet. Granted that the primary evidence is probably 4 billion years old, that problem may not be insoluble but it is definitely a cold case. Distinguishing theories of the origin of life from theories of the origin of species thus makes excellent sense. Thing is, I wonder if it goes far enough. Granted what we’re learning about the deeper diversity of existing life, especially the wide range of ways that energy flows in living things, shouldn’t we expect that an adequate and truly general theory of evolution is likely to require us to intercalate several stages between biogenesis and the era when life began to evolve according to the familiar rules and patterns of the modern synthesis?

For the record, these thoughts were inspired by Jan Sapp’s recent book The New Foundations of Evolution, which provides a detailed history of the advent of the new understandings of phylogeny inspired by microbiological research. Reading his book was rather like listening to a golden oldies CDs since so many of the important discoveries have taken place during my lifetime and, as something of a scientific fellow traveler or male groupie, I remember what I was doing when caught wind of them even if I didn’t really understand their importance.