Root and Branch
The DNA record does not give us a tidy tree because it encodes a lot of slightly different evolutionary histories in kindred animals, covering a very short span of recent time. With gorillas, chimps and humans we are talking no more than 8 million years. We may not end up with a tree even for the part that most interests us, the one on which humans hang. A thicket or bush, yes, but a clean-limbed tree, perhaps not. Thus the old question of the missing link has been transformed into a series of new questions that have immeasurably added to our understanding and leave us asking for more. That is the mark of a progressive research program.
There is a deep reason underlying the difficulty just mentioned. The ideas of species, genera and the rest of the taxa are invaluable in practical botany, ecology, the fisheries, etc., for sorting living organisms as they are now. Classes of living things really are distinct. But historically they are on a continuum. The species, as distinct and definite entities, fade away. I am no expert on Darwin, but it seems to me that he saw this very clearly.
When, thanks to Darwin, we turned from classification at a time to classification over time in the long haul, species began to drop out except as a convenient way to distinguish bits of the fossil record and match them with present life-forms. Because of the depth of the tree idea in the human mind (yes, back to Genesis and beyond), we have been fixated on the project of arranging definite species, like fruit, on a tree of descent. To exaggerate, there are no historical species to hang with exactitude. Not even our own, which we narcissistically call Homo sapiens (Latin for "wise man"). Anyone who reads Origin will notice that Darwin displayed only one curiously abstract tree diagram in that book. Starting in 1866, Ernst Haeckel, Darwin's great advocate in Germany, began to cover pages with exuberant trees of descent, including the first drawn tree of animal evolution. It is as if we have been trying to imitate Haeckel, but Darwin was the wiser man.
The human genome does have an incredible amount of historical information that we have only just begun to decode. Genetic anthropology is the liveliest of the human sciences today. It uses molecular biology to track the movements of peoples across the globe. It is a fabulous continuation of the program begun in another of Darwin's great books, The Descent of Man (1871). At the end of May this year, an enormous Creation Museum and Family Discovery Center opened near Cincinnati; innocent children are told that "The first man walked with dinosaurs and named them all!"
Perhaps we had better not speak of tree diagrams but of tree-ish diagrams or, to be Latinate, arborescent diagrams, as being the upshot of Darwin today. Even so--and here is my promised second open question--the representation of life on such diagrams may work well only for human-sized organisms: roughly speaking, from whales to mites, redwoods to lichen. Even that is misleading: Once we get down to fungi, classification is a mess. The action in evolutionary research today is, however, far below that, at the bacterial level. One fascinating idea is horizontal (or lateral) gene transfer. Bacteria, which don't have sex, probably pass genetic material from one to another, quite indifferent to who is descended from whom--from one species of bacterium to another. This idea was first circulated by C.R. Woese in 1977, and it has blossomed into a vigorous research program. By 2000 Scientific American had published a popular essay, "Uprooting the Tree of Life." It could be that the earliest life-forms had distinct origins; these then shared genetic material by passing it sideways, making life as a whole a bit more viable on a nasty planet. No unique primal ancestor after all.
Some biologists are pretty skeptical and doubt that horizontal transfer, if it exists, is a big deal. More radical souls are guessing that even mites and lichen benefit from horizontal transfer, via bacteria. (And maybe that's the problem with fungi.) You can sensibly take bets either way. I would bet that what we find out about bacteria in the next decade, including horizontal gene transfer, will wonderfully enrich our understanding of life and its origins. I might be ignorantly backing the wrong horse. Evolutionary theories are rich in open questions. That is what makes them so exciting.
Contrast that with pseudo-controversy and take, for example, Michael Behe, a professor at Lehigh University who must be the most ingenious and prolific anti-Darwinian biologist at work today. My use of "anti-Darwin" follows him. Unlike Ronald Numbers or Michael Lienesch, I do not speak of the antievolution movement or of creationism. This is because Behe says, in effect, "Sure, I believe in evolution by natural selection--it just doesn't do all it is supposed to." In his capacity as a biologist he does not officially argue for special acts of creation. So you cannot call him antievolution or creationist. But he is undeniably anti-Darwin. His first book was Darwin's Black Box (1996). His latest book is The Edge of Evolution: The Search for the Limits of Darwinism. The label "anti-Darwin" seems the right umbrella term for creationism, antievolutionism--and Behe.