A recent 2008 paper, "Retroviral promoters in the human genome," in the journal Bioinformatics (Vol. 24(14):1563–1567 (2008)) discusses the fact that "Endogenous retrovirus (ERV) elements have been shown to contribute promoter sequences that can initiate transcription of adjacent human genes. However, the extent to which retroviral sequences initiate transcription within the human genome is currently unknown." The article thus "analyzed genome sequence and high-throughput expression data to systematically evaluate the presence of retroviral promoters in the human genome."
The results were striking:
We report the existence of 51,197 ERV-derived promoter sequences that initiate transcription within the human genome, including 1743 cases where transcription is initiated from ERV sequences that are located in gene proximal promoter or 5' untranslated regions (UTRs).
[…]
Our analysis revealed that retroviral sequences in the human genome encode tens-of-thousands of active promoters; transcribed ERV sequences correspond to 1.16% of the human genome sequence and PET tags that capture transcripts initiated from ERVs cover 22.4% of the genome. These data suggest that ERVs may regulate human transcription on a large scale.
(Andrew B. Conley, Jittima Piriyapongsa and I. King Jordan, "Retroviral promoters in the human genome," Bioinformatics, Vol. 24(14):1563–1567 2008)
From this it is obvious that the theory that ERVs represent 'junk DNA' and are residues left by unknown viral infections, is pure nonsense.
If the ERVs have such extensive functions, then it is clear that they must have been there from the beginning - otherwise transcription and translation would have been seriously impaired, and in all likelihood could not take place. Species extinction would have followed in short order, and the human species demolished. This leaves the common descent from some proto-human-chimpanzee theory high and very dry.