I recently came across this paper in the journal "Mobile DNA": Mobile DNA and the TE-Thrust Hypothesis: Supporting Evidence from the Primates.
In it, Oliver and Greene describe the evidence from primates to support the "TE-Thrust" hypothesis. In summary, this hypothesis states that transposable elements - mobile genetic elements - have been influential in evolution, particularly in large genetic rearrangements and the like. No arguments there. It then goes on to suggest that these are responsible for "macroevolution" (bleurgh) and the changes consistent with observed "punctuated equilibrium" in the fossil record.
I hate the term "macroevolution". It is made up, arbitrary and essentially meaningless. There is evolution. Full stop. Yes, it happens at different rates and evolutionary changes are of different scales but it is a broad continuum. Differentiating micro- and macro- helps no one but Creationists and IDers who want to stir up controversy where there is none. Besides, I don't know of any work where someone has shown that the scale of the genetic change is related to the scale of phenotypic change - you can have some pretty monstrous point mutations and some largely silent chromosomal translocations. Hype.
Macroevolution aside, the suggestion that TE-thrust has played an important role in the evolution of many lineages seems fair enough. They don't seem to want to leave it there, though. It seems that they think it is not just important but almost essential, and organisms with few TEs get stuck in "stasis" or even go extinct due to their lack of evolvability. I don't see why this necessarily follows - TEs are not the only way to have genetic change. We have a long history of analysing point mutations and other non-TE-related insertions/deletions etc. and know that they play at least some role. Furthermore, TEs are not the only repetitive sequences in the genome. Again, I just say: Hype. Why are people so obsessed with "paradigm shifts"? At best you end up looking over-eager, which makes people distrust your work and actually retards the shifting of paradigms. At worst, you end up looking stupid.
Don't get me wrong - I am not against the idea that TEs have contributed positively to the evolution of their hosts, and even that this contribution might have played an important role in their maintenance. Far from it, in fact: in my own PhD I developed a model in which occasional beneficial insertions could maintain an otherwise selfish mobile element in even a clonal population. I just think that caution is needed when assigning cause and effect to observed trends. Beneficial TE-mediated events can sweep TE-containing individuals through the population via hitch-hiking and can help their spread and maintenance. This does not mean that TE-lacking individuals are doomed.
The last thing to point out - and, to be fair the authors (kind of) say this themselves - is that regardless of the extent to which the TE-thrust hypothesis is right, most transposable elements are still "junk DNA". They may be junk that very occasionally do something useful but unless they regularly contribute to the fitness of an organism, they are junk. Worse than junk, even under TE-thrust most affects of transposable elements are still going to be negative because most large-scale mutations are deleterious. They also put an energetic load on the cell by increasing the amount of DNA that needs to be replicated. I am sure that ID/Creationists and other "it's not junk" fans will ignore this fact and jump on this paper as further evidence for their fantasies but it simply isn't true.
If you can get past the hype and hyperbole, though, this is an interesting paper and has some beautiful examples of how some important traits have evolved through traceable TE-mediated rearrangements. Evolution. It works, bitches.