"The Natural History of Retroviruses" - Yingguang Liu and Charles Soper @ AiG, debunked by fellow creationist, Todd Wood

In a blog called "Answers in Genesis", in a post entitled "The Natural History of Retroviruses", Yingguang Liu and Charles Soper speculate that, because parts of some ERVs (endogenous retroviruses) perform functions either useful or essential for their hosts, they might have been created (as opposed to having been exaptated) in order to perform those functions. There are several problems with this idea, but from their point of view, the biggest problem is that they are shooting themselves in their creationist feet! See below.

Liu and Soper state that retroviral elements have been degraded by mutations. That is certainly true. So much for the creationist assertions that all DNA is functional, but their biggest problem is pointed out by fellow creationist Todd Wood in a blog post of his own. The problem is,

How come, if they are unrelated, do chimp and human ERVs share the same disabling mutations?

• "Since the human and chimp genomes are very similar, the majority of ERVs are the same and have the same apparent "disabling mutations." Given the separate origins of humans and chimps (Genesis 2:7), we've either experienced thousands and thousands of mutations that are exactly the same as chimps or those "mutations" were created that way in the beginning. Since creation is the simpler hypothesis, that means the apparent degeneration of human and chimp ERVs is precisely that: apparent. Like ERVs themselves, the "disabling mutations" were also put there for a reason." - Todd Wood, "Microbes continue: retroviruses"

So

either chimps and humans are unrelated, their ERVs are degraded, and the common mutations are a colossal coincidence (Liu and Soper)

or

chimps and humans are unrelated, and their ERVs are not degraded. (Wood).

Yet there is massive evidence that ERVs are degraded - evidence that Liu and Soper themselves go into in detail. Indeed, the results of the "Phoenix virus" experiment, that resurrected a fully working exogenous (free) retrovirus from a set of "broken" ERVs shows that ERVs are indeed the inherited remains of mutated proviruses, and that the mutations that have degraded them are different in different ERVs (countering the suggestion that their mutations are common due to some deterministic process, BTW). It turns out that if you correct or reverse the mutations in ERVs, you end up with huge numbers of working proviruses in every nuclear cell of your body - in other words, you end up very, very dead, very, very quickly.

There is clear evidence that ERVs common to different species do indeed share common mutations,  as Wood claims. See Shared mutations among ERVs in identical loci and the corroboratory nested hierarchies they fall into.

Perhaps the error that both parties make is the presuppositional assumption that they both make.

What was it now?

Yes, that was it: "Chimps and humans are unrelated."

An object lesson in how, when you start from a biased position and then try to "prove" it, never mind how much work you put into it, you end up failing to see even the most obvious problems with your ideas.