I read Mike Syvannen's article, and found it both enjoyable and thought-provoking. I certainly found it to be quite understandable. That is to be expected, of course. I am a grad student in zoology. I read scientific papers on a daily basis and I am familiar with the terms and concepts that appear in scientific papers. I suspect that reading Mike's article would be a very different experience for someone who did not have a strong foundation in biology. Such a person would have been confronted with unfamiliar terms and concepts - lots of them, tightly packed, and with very little familiar ground in between.
That is not meant in any way as a criticism of the paper. The concept of horizontal gene transfer is complex. Understanding how horizontal gene transfer might affect evolution is even more complex. Learning how to read an unrooted phylogenetic tree is complex. Understanding what a phylogenetic tree is is complex. Understanding the mathematics involved in finding the best phylogenetic tree for a set of data is extremely complex. Evolution is a complex science, and complex things can be very difficult to explain in simple terms.
Intelligent design has been accused of being a number of things. Complex isn't one of them. Anyone can follow the basic ID argument: Evolution can't explain it, so God must be the explanation. Some of the IDers might try to wrap that up in some more complex-looking outfit, but the basic argument remains unchanged. In fact, they can't really change it much, since the sheer simplicity is a large part of their argument's appeal.
That's a difficult enough situation, but unfortunately it's just the beginning. Many of the IDers are not above taking advantage of the complexities of real science. It is very easy to misrepresent a complex concept, and it can be very difficult to correct the misrepresentation. This is exactly what is happening with Nelson's misrepresentation of Mike Syvannen's article.
Turns out Mike Syvanen is explaining why Darwin's tree of life -- Mooney and Nisbet's orthodox "common ancestry of all organisms on earth" -- may not be the case, because life may have arisen from multiple independent starting points.
That's a single, long sentence containing 37 words. I'm now going to try to explain, in as simple terms as I possibly can, why this misrepresents what Syvanen was actually arguing.
The conventional way that people have thought about evolutionary descent is as a tree, with all living things branching off from a single starting point - like the family trees that show all of the descendents of one couple. The reason that people have thought about evolution as having happened this way is because parent-to-child was the only way that anyone knew of for genes to be passed on. Over the last thirty to forty years, we have discovered that there are actually some other ways for genes to be passed on to someone else. It's been found that bacteria can transmit small pieces of DNA to other bacteria, that they can do this even between bacteria that are not part of the same species, and that the DNA can contain usable genes. People have seen this happen, and it looks like this kind of gene transmission has helped some kinds of bacteria to get resistance to antibiotics. It also looks like there are some species of virus that can move chunks of DNA from one species to another.
These kinds of non-traditional genetics seem to be more important in things like bacteria than they are in big, multicellular organisms. But way, way back in time everything that was alive was something like bacteria. If that kind of "sideways" movement of genes was important then, we might need to change the way we think about the evolution that was happening then. When we thought that traditional, parent to child genetics was all that went on, we could draw the lines of descent as all running straight from parents to children. But we can't draw those kind of lines if the "child" is also getting some genes from a somewhere else. Instead, we have to draw at least two lines leading to that child - one from the "parent", and one from any other bacteria that contributed genes. If we do that, we don't have a drawing that looks like a tree. We have a drawing that looks like a net.
What Mike Syvanen suggested is that life could have started several times in that "net" of parents, instead of just once. If he is right, then what it would mean is that not everything alive today is descended from a single species. Instead, it would mean that everything that is alive today is descended from a pool of species that were able to (and did) swap some genes back and forth. It doesn't mean that things alive today don't have common ancestry. It just means that the ancestry worked a little different, and a little bit messier, than we used to think about it.
That took 444 words, arranged in seventeen sentences over three paragraphs. It took about half an hour to write. It wasn't as clear as I hoped it would be, and there's a good chance that it would bore the hell out of anyone who isn't really interested in evolution (and maybe some who are). Paul Nelson's comment, on the other hand, was a complete misrepresentation of what was actually written, but it was short, clear, and to the point.
This is a problem. Evolution, like most of the natural world, is very complex. It is simply not possible to explain why Nelson was lying about what Syvannen said in anywhere near the number of words that it took him to do it. I suspect that Nelson and other ID proponents know this, and that is why they do it. I wish I could say that I know how we can counter that strategy, but I do not. A short and simple lie can sound a lot more compelling than a messy and complicated truth. That's just a fact, and it's something that we're going to have to continue to work around.