I went to the Reasons to Believe website and searched their articles with the keywords "endogenous retroviruses". From what I can see, they all discuss the same misinformation already covered earlier in this thread.
1. Retroviral insertion is not random enough. That's false. Even in a best case scenario, insertional bias will only produce ~1% shared ERV's.
2. ERV's have function. Only a tiny fraction can be shown to have function, and even if they all had function they would still be smoking gun evidence for common ancestry.
3. PtERV1 is found in chimps and gorillas but not humans or orangutans. They forget to mention that they are not at orthologous positions in the chimp and gorilla genomes.
4. Departures from the expected phylogeny. There are known mechanisms that create these departures, such as ILS. It is expected that we will see a noisy phylogenetic signal if species evolved from a common ancestor. It is the ratio of noise to signal that matters, and they are reticent to even acknowledge the massive and overwhelming phylogenetic signal that sits out way above the noise.
5. Retroviruses can't produce ERVs in the first place. They acknowledge the case of ERVs being produced by an exogenous retrovirus in koalas, but they tell their audience to just ignore it for no apparent reason.
Nothing really original here. Just a rehash of what other creationist authors have written.
I ran across an article at ICR that made a claim about ERV's that I had not come across before:
First, genetic data indicate that these sequences are not millions of years old. Using the comparative tools of evolutionary genetics, secular scientists compared the gene sequences of viruses to their counterparts in animal genomes and found that, at most, the variation in these sequences indicates they can be no more than 50,000 years old.2 So, if these viral-like sequences are not millions of years old, then where did they come from?
[off topic note: the use of "secular scientist" still makes me giggle. What's next? Secular baseball players? Secular dentists?]
That's a bit convoluted, but their claim is pretty clear. They are claiming that ERVs are not older than 50,000 years. To support this claim, they cite:
Although the ultimate origins of RNA viruses are uncertain, it seems reasonable to assume that these infectious agents have a long evolutionary history, appearing with, or perhaps before, the first cellular life-forms (38). While the RNA viruses we see today may not date back quite this far, the evidence that some DNA viruses have evolved with their vertebrate hosts over many millions of years (24) makes an equally ancient history for RNA viruses a natural expectation. Yet a very different picture of RNA virus origins is painted if their gene sequences are compared; by using the best estimates for rates of evolutionary change (nucleotide substitution) and assuming an approximate molecular clock (21, 33), it can be inferred that the families of RNA viruses circulating today could only have appeared very recently, probably not more than about 50,000 years ago. Hence, if evolutionary rates are accurate and relatively constant, present-day RNA viruses may have originated more recently than our own species.
Well, that's a very different picture than the one painted by ICR. The scientific paper is saying that currently circulating RNA viruses originated no more than 50,000 years ago. It says nothing about ERVs originating within the last 50,000 years. On top of that, the article clearly states that there are examples of DNA viruses that have evidence for host/virus co-evolution over the last several million years. Strange that they didn't mention that (sarcasm implied). The paper also goes on to explain why comparison of circulating RNA viruses leads to these conclusions.
The rest of the ICR article hits the usual misinformation bullet points, such as some ERVs having function and no examples of extant exogenous retroviruses producing heritable endogenous retroviruses (see Koala Retrovirus [KoRV]).
Are you sure this is a valid method of calculating Orthologous ERV's?
Yes. ERV's are either orthologous or lineage specific. If they aren't lineage specific then they are orthologous. If only 82 human ERV's are lineage specific then the rest must be orthologous. The 203,000 human ERV's counted by the Human Genome Consortium was done by top scientists, so I see no reason to doubt it.
I tried to find an independent source and the best I could find was Orthologous endogenous retroviruses exhibit directional selection since the chimp-human split which says "Overall, we identified 336 chimp-human pairs of sequence from a variety of genomic locations".
They used several filters to narrow the field down which means they excluded a lot of ERV's from the study. They were looking for more recent insertions that are full length, so right away they are excluding about 90% of ERV's that are solo LTR's. Of the candidates, they further excluded older full length ERV's because they were focused on more recent insertions, as stated in the results section: