New Scientist has an article by Mark Buchanan discussing horizontal transfer as a mechanism for the evolution of early life: “Horizontal and vertical: The evolution of evolution”
There’s a lot of “evolution doesn’t work the way we thought” stuff in the article, which focuses on Carl Woese:
How could modern biology have gone so badly off track? According to Woese, it is a simple tale of scientific complacency. Evolutionary biology took its modern form in the early 20th century with the establishment of the genetic basis of inheritance: Mendel's genetics combined with Darwin's theory of evolution by natural selection. Biologists refer to this as the "modern synthesis", and it has been the basis for all subsequent developments in molecular biology and genetics. Woese believes that along the way biologists were seduced by their own success into thinking they had found the final truth about all evolution. "Biology built up a facade of mathematics around the juxtaposition of Mendelian genetics with Darwinism," he says. "And as a result it neglected to study the most important problem in science - the nature of the evolutionary process."
In particular, he argues, nothing in the modern synthesis explains the most fundamental steps in early life: how evolution could have produced the genetic code and the basic genetic machinery used by all organisms, especially the enzymes and structures involved in translating genetic information into proteins. Most biologists, following Francis Crick, simply supposed that these were uninformative "accidents of history". That was a big mistake, says Woese, who has made his academic reputation proving the point.
I don’t see any inconsistency between the modern synthesis and the idea of horizontal gene transfer. This is a failure of history – of people reading only Ernst Mayr as a representative of the synthetic view. Other voices – especially Stebbins – emphasized gene transfer. The dynamics of genes themselves, as opposed to genes as mere parts of organisms, surely underlie the next generations of evolutionary theoriests, including Dawkins’ gene-centric perspective, and Williams’ idea of “levels of selection”.
Woese is working to discover modes of evolution of gene (and even sub-gene) replicators, before the “hardening” of genomes into organisms. Before the organismal level of selection existed, there can only have been the gene level (taking “gene” to mean replicating element). That’s not anti-synthesis, it’s what we would expect of replicators at the sub-organismal level.
It’s also no surprise as applied to horizontal transfer in more recent lineages. Humans have gotten DNA from viruses during the past few million years, some of which has been fixed in the genomes of the present population. That’s no challenge to the way we understand evolution, it’s saying that one kind of mutational process is acquisition of viral DNA. Likewise, the introgression of genes between species is no challenge to evolution. It is good evidence that speciation is a evolutionary process – otherwise boundaries between sister species would be impermeable.