This was addressed recently by a fellow named PeterBorger on the CvE forum.
========
In the evolutionary community the shared retroviruses are commonly regarded as evidence of common descent. However, this may only be superficial.
First there is the claim that they do not serve any purpose. That should be scientifically proven. Maybe their function cannot be deduced from knocking them out, but that does not say anything about their function, since you can knock out genes with an open reading frame without any effect on the organism (genetic redundancies). Secondly, I would like to see the complete DNA sequences within the species and between the species before jumping to conclusions.
I checked one claim about the GLO pseudogene (the gene that catalyses the final step in vitamin c synthesis) that has been inactivated in the same spot in primates and is taken as proof for common ancestry. And, indeed a superficial look would immediately convince any evolutionist. However, if you have a careful look at the presented sequences you will discover that the replacement of nucleotides is not at random between the distinct species. Secondly, you will discover that it does not make a difference for the mutation rate of this gene whether it is functional or not, in contrast to what evolution theory would predict. Thirdly, it violates population genetics: why would the inactivated gene become fixed in the entire population, while the active gene conveys longivity. In addition, evolution never compensated for vitamin C uptake in the gut, and, finally, the gene is redundant anyway since the third step in vit c synthesis already yields vitamin C by spontaneous oxidation and is sufficient to avoid vit c deficiency. Also not unimportant, at least 2 primates are able to synthesize vitamin c in the liver, indicating the presence of an intact GLO gene (I once had a discussion about this gene with Dr D. Theobald (Talk Origin) so I know a bit about pseudogenes). However, at this level it is mostly speculation since we do not know a lot about it, yet.
In analogy to vestiges (appendix, tonsils) that shouldn't have a function according to evolution theory, it is far too early to say that this is proof for common descent. Show me the DNA sequences of these retroviruses in chimp and man, and I will respond in more detail.
Retrotransposons may have a function in epigenic regulation of gene expression (actually there is some proof for that. See: Dr. E. Max's website Talk Origin. Another one regulates the aghouti colour of fur in mice). It is thought that they may also play a role in eye colour (human), and some diseases like schizophrenia, and B.-W.-syndrome.
Evolutionists are free to claim these genes as evidence for common descent (as they did -- and still do -- for genetic redundancies, but which has actually contributed to the fall of natural selection as I will substantiate with scientific evidence in my forthcoming posting on genetic redundancy).
I foresee that ultimately there will be an unexpected (regulatory or stabilizing) function for these "vestiges".
Furthermore, read Spetner's book carefully on what he has to say on transposons. It makes sense. It will pay off to read opposite opinions. In summary, it is not an argument to take DNA sequences of which we do not know the function of as evidence for evolution. Our lack of knowledge described 98% of the DNA in the genome as "junk". This vision is increasingly proven to be wrong."
Note: link provided upon request.
===================
YES IT DOES. I haven't had this much fun since second grade recess.