ERV’s [sic] Utterly Debunked

My comments in red. For information on ERVs (endogenous retroviruses), click on "ERV FAQ" above. ERVs provide some of the clearest, and most unassailable evidence for common ancestry, which is why science-deniers try to attack it so desperately.

An example: "u/Glittering-Tonight-9" posted at Reddit. https://www.reddit.com/r/DebateEvolution/comments/k1w4bg/ervs_utterly_debunked/ He posts,

(Note the post title is suppose[d] to be click-bait as I really want to see if these arguments stand up to scrutiny) I’m not a creationist but I will be playing devil[']s advocate and coming up with the best arguments from creationist sources on ERV’s and see if they stand up to scrutiny. I even am stumped by some arguments but here we go:

Dishonesty is something that, lamentably, we have come to expect from creationists. I don't believe for a moment that "Glittering" is not a creationist, judging by what follows in his/her post. And the title, "ERV'[sic]s Utterly Debunked" smacks of desperation. That desperation is warranted in the face of the real facts regarding ERVs.

The first argument is that ERV insertion is not random and can account for shared ERV’s across certain species:A study, by Sverdlov

(1998) https://www.sciencedirect.com/science/article/pii/S0014579398004785 “reports,But although this concept of retrovirus selectivity is currently prevailing, practically all genomic regions were reported to be used as primary integration targets, however, with different preferences. There were identified ‘hot spots’ containing integration sites used up to 280 times more frequently than predicted mathematically.” [emphasis added]

Other classes of retroelement also show fairly specific target-site preferences. For example, Levy et al. (2009) https://academic.oup.com/nar/article/38/5/1515/3112509 report that Alu retroelements routinely preferentially insert into certain classes of already-present transposable elements, and do so with a specific orientation and at specific locations within the mobile element sequence. Moreover, a study published in Science by Li et al.(2009) https://science.sciencemag.org/content/326/5957/1260 found that, in the waterflea genome, introns routinely insert into THE SAME LOCI, leading the internationally-acclaimed evolutionary biologist Michael Lynch to note, “Remarkably, we have found many cases of parallel intron gains at essentially the same sites in independent genotypes. This strongly argues against the common assumption that when two species share introns at the same site, it is always due to inheritance from a common ancestor.” ( Quote source: https://www.sciencedaily.com/releases/2009/12/091210111148.htm )

Finally, Daniels and Deininger (1985) https://academic.oup.com/nar/article-abstract/13/24/8939/2358649 suggest that,

“…a common mechanism exists for the insertion of many repetitive DNA families into new genomic sites. A modified mechanism for site-specific integration of primate repetitive DNA sequences is provided which requires insertion into dA-rich sequences in the genome. This model is consistent with the observed relationship between galago Type II subfamilies suggesting that they have arisen not by mere mutation but by independent integration events.”

The topic is ERVs, not ALUs or other "insertions".

It is not argued that ERVs insert (integrate is the word used) in "random" loci. Rather, investigations into actual integration loci show that integrase, the retroviral enzyme that does the cut-and-paste of the viral DNA into the host DNA may have statistical tendencies to integrate in certain types of regions, but this is insufficient to support the idea that integrations at specific loci, down to base-level resolution, can be explained by "integration site preference". Common inheritance is the only viable explanation. See https://barryhisblog.blogspot.com/p/relationship-between-integration-sites.html 

Out of tens of thousands of ERV elements in the human genome, roughly how many are known to occupy the same sites in humans and chimpanzees? According to this Talk-Origins article http://www.talkorigins.org/faqs/comdesc/section4.html#retroviruses, at least seven. Let’s call it less than a dozen. Given the sheer number of these retroviruses in our genome (literally tens (hundreds) of thousands), and accounting for the evidence of integration preferences and site biases which I have documented above, what are the odds of finding a handful of ERV elements which have independently inserted themselves into the same locus?

The T-O article, written before the publication and analysis of whole genome sequences of the human and chimpanzee genomes, is well out of date. But that does not stop creationists from treating it as gospel™. A fine example of cherry-picking and cognitive bias (and, of course, intellectual dishonesty). The genome sequencing discovered that out of approximately 200,000 (yes, 200,000) ERVs and ERV fragments  in Homo and Pan, the vast majority are at precisely orthologous loci (exactly corresponding DNA locations, whose only explanation can be common inheritance). See https://barryhisblog.blogspot.com/p/from-table-11-of-initial-sequencing-and.html and https://barryhisblog.blogspot.com/p/do-shared-ervs-support-common-ancestry.html

1 final thing but it’s not as ‘important’ or as strong of an argument but here’s something I’m curious for answers about:

Yohn et al. (2005) http://www.somosbacteriasyvirus.com/orangutans.pdf report that,

“Horizontal transmissions between species have been proposed, but little evidence exists for such events in the human/great ape lineage of evolution. Based on analysis of finished BAC chimpanzee genome sequence, we characterize a retroviral element (Pan troglodytes endogenous retrovirus 1 [PTERV1]) that has become integrated in the germline of African great ape and Old World monkey species but is absent from humans and Asian ape genomes.“

Why would it be a surprise that retroviruses can integrate and endogenise independently in different species? The "argument" is incoherent, and betrays, right at the end, either that "Glitter" does not understand this subject at all, or is deliberately and knowingly trying to mislead his/her readers. But the latter explanation would be inconsistent with one who presumably believes in a god who disapproves of lies. It's a puzzle.