For my sins, I have spent many hours discussing evolution with creationists and ID proponentsists. The best evidence for evolution, in my opinion, is common genetic markers between different species. Commonly located endogenous retroviruses have no reasonable explanation other than endogenization (integration into the germline) in common ancestors. Creationists/ID proponentsists have done their best to try and discredit the evidence and proffer their own hypotheses, but they just don’t work. I critique their attempts in an FAQ I created, as well as answering common questions. Please have a look at the FAQ, a link to which appears in the following comment of mine. I have no qualifications in this subject, but I have made a special study of it. Graeme Finlay is a qualified expert in this subject, and a blogger for BioLogos. I would greatly appreciate any feedback/suggestions/corrections from him and from anyone else.
Here is the link to my endogenous retrovirus (ERV) FAQ.
And here is a link to Graeme Finlay’s book, Human Evolution.
Hi Barry! I have always enjoyed your contributions to this subject elsewhere on the interwebs, and I also find ERVs to be a fascinating topic since it hits a few topics that I really enjoy.
One aspect of the ERV argument that I think is often overlooked is the phylogenetic nature of the evidence. It isn’t just the similarities that matter, but the overall pattern of both similarities AND DIFFERENCES. When you can show that the differences also support common ancestry I think it really strengthens the argument and also counters the YEC claims about hot spots and relying on similarities.
One really good example is PtERV insertions in the chimp and gorilla genomes. There is an excellent paper on the topic found here. In that study, they found that both the chimp and gorilla genomes (as well as other primate genomes) were littered with PtERV insertions, but none were found in the human or orangutan genomes. If these PtERV insertions occurred in the ancestors leading up to the common ancestor of all apes or the common ancestor of the chimp/gorilla/human triad then those PtERV insertions should be found in the orangutan and human genomes, but they aren’t. Therefore, the concept of common ancestry would argue for these insertions occurring independently in the chimp and human lineages after the human/chimp split.
With this prediction in hand we can make other predictions. Most notably, since PtERV insertions occurred independently in the chimp and gorilla lineages they should NOT be found at the same spot (i.e. not orthologous) in each genome. That is what the authors of the paper looked at, and sure enough they were incapable of finding an unambiguous example of an orthologous PtERV insertion shared between the chimp and gorilla genomes. Out of 299 PtERV insertions they looked at across several primate genomes, they were able to find only a single PtERV insertion that mapped to an orthologous BAC clone between the chimp and gorilla genome. However, a BAC clone contains tens of thousands to hundreds of thousands of bases, so even this example can’t be said to be an orthologous PtERV insertion at single base resolution. The other insertions aren’t even close to one another, separated by at least thousands of bases.
If shared ERV insertions are the product of insertion into hot spots as YECs claim, then these observations blow that argument out of the water. The YEC explanation predicts that the bulk of PtERV insertions should be found at orthologous positions in the chimp and gorilla genome, but they aren’t. Evolution predicts that they should not be found at orthologous positions in the two genomes, and that prediction is supported by observation. This is one case where YEC and evolution make very different predictions, and it is evolution that wins out.
Thank you, T! 
I shall be looking at incorporating what you have to say in my FAQ.
This topic was automatically closed 6 days after the last reply. New replies are no longer allowed.