I've mentioned it before. That dreaded 29+ Evidences for Macroevolution by Dr. Douglas Theobald. I took the time to examine what has been pontificated as the "smoking-gun evidence for evolution" and the "irrefutable evidence." What many Darwinians believe is the most irrefutable argument for their views is the evidence from endogenous retrovirus insertion sites. I am petrified of this evidence. In fact, I am biting my nails. After gathering a few facts, I sent the following email to Dr. Douglas Theobald, concerning this astounding piece of evidence:
Dear Dr. Douglas Theobald,
In your 2004 article “29+ Evidences for Macroevolution” you write (Part 4: The Molecular Sequence Evidence, Prediction 4.5: Molecular evidence - Endogenous retroviruses):
“Endogenous retroviruses provide yet another example of molecular sequence evidence for universal common descent.”
You then go on to propose how this molecular sequence evidence for universal common descent could be potentially falsified:
“It would make no sense, macroevolutionarily, if certain other mammals (e.g. dogs, cows, platypi, etc.), had these same retrogenes in the exact same chromosomal locations. For instance, it would be incredibly unlikely for dogs to also carry the three HERV-K insertions that are unique to humans, as shown in the upper right of Figure 4.4.1, since none of the other primates have these retroviral sequences.”
Consider this molecular sequence evidence for universal common descent falsified. Essentially, in order to falsify this evidence, we must find an outgroup species that shares with a species of a certain clade the same retrogene or retrogenes insertions, but these insertion sites are not shared by the other species of that clade. This is what it boils down to.
Interestingly enough, Barbulescu et al. (2001) have identified “a human endogenous retrovirus K (HERV-K) provirus that is present at the orthologous position in the gorilla and chimpanzee genomes, but not in the human genome.”
What we have here is an outgroup species (gorilla) that shares a retrogene insertion site with a species (chimpanzee) of a certain clade (human-chimpanzee clade), but this insertion site is not shared by the other species of that clade. This alone, by your own criteria, falsifies the retrogene evidence for universal common descent you advance in your article.
Similarly, Bonner et al. (1982) report that the endogenous retrovirus colobus type C virus CPC-1 is shared by the chimpanzee and the gorilla but it is absent from the human genome.
Also note that certain classes of type C retroviruses are found in wooly monkeys and the gibbon ape, but it is not found in African great apes [Lieber et al. 1975].
Humans and Asian apes lack PTERV1 retroviruses, but they are present in African great apes and Old World monkeys [Yohn et al. 2005].
To quote Yohn et al. 2005:
“For example, only one interval is shared by gorilla and chimpanzee; however, two intervals are shared by gorilla and baboon; while three intervals are apparently shared by macaque and chimpanzee.…If these sites were truly orthologous and, thus, ancestral in the human/ape ancestor, it would require that at least six of these sites were deleted in the human lineage. Moreover, the same exact six sites would also have had to have been deleted in the orangutan lineage if the generally accepted phylogeny is correct. Such a series of independent deletion events at the same precise locations in the genome is unlikely.”
In summary, the very criteria that you stated would falsify this evidence for universal common descent has been met, and hence this evidence is effectively falsified. I am writing you so that you might add a correction to your article and realize that this evidence has been falsified.
Barbulescu M, Turner G, Su M, Kim R, Jensen-Seaman MI, Deinard AS, Kidd KK, Lenz J. A HERV-K provirus in chimpanzees, bonobos and gorillas, but not humans. Curr. Biol. 11(10):779-83 (2001).
Bonner TI, Birkenmeier EH, Gonda MA, Mark GE, Searfoss GH, et al. Molecular cloning of a family of retroviral sequences found in chimpanzee but not human DNA. J. Virol. 43: 914–924 (1982).
Lieber MM, Sherr CJ, Todaro GJ, Benveniste RE, Callahan R, et al. Isolation from the Asian mouse Mus caroli of an endogenous type C virus related to infectious primate type C viruses. Proc. Natl. Acad. Sci., 72: 2315–2319 (1975).
Yohn CT, et al. Lineage-specific expansions of retroviral insertions within the genomes of African great apes but not humans and orangutans. PLoS Biol, 3:110 (2005).
There. Now I've gotten this load off my chest. That's some absolutely amazing piece of evidence.