VIGEs

In the war in defence of scientific knowledge against creationists, there is hardly any more certain evidence of common ancestry than that from endogenous retroviruses, or ERVs for short. 

I will give a brief summary now, but much more detail is available via the links in the video description below.

Retroviruses - HIV is an example - replicate by integrating a copy of their genomes with the DNA of the cells of the host organisms they infect. The host cells then 'read' the integrated viral DNA and make more viruses.

ERVs are the remains of viruses that have entered the host genomes of species by integrating with their germline DNA (the DNA in sperm or egg cells) and have thereby become heritable. They can be passed down to offspring just like the traits for brown eyes or red hair.

When a retrovirus first enters the DNA of a sperm or egg cell, we call it endogenization, and we call the result an ERV. The non-fatal ones are usually broken. That's how they can be passed down to viable offspring. 

(From https://www.ncbi.nlm.nih.gov/pmc/articles/PMC509299/?tool=pubmed)

Now the essential fact to note (but creationists ignore it like the plague) is that when a retrovirus integrates with host DNA, it cannot target any particular spot or locus - in the DNA.

But the vast majority of ERVs present in the DNA, for example, in humans and chimps, are in precisely corresponding loci. The only viable explanation for them is that they were endogenized in common ancestors. Common inheritance accounts for their common locations. Separate endogenizations cannot account for it.  

(From https://strateias.org/vige.pdf)

One desperate notion that creationists will appeal to is the idea that at least some ERVs were not caused by retroviruses but designed into genomes to provide benefits. They call them VIGEs. Not the virus-induced gene editing of respectable science, but "variation inducing genetic elements". 

(take a short section from https://youtu.be/yYlx-vtvKpI around the 30 second mark)

The idea is that maybe some of these were designed into our genomes from the beginning, to be re-integrated in different parts of our genomes, rather like an unfolding puzzle

Yes, elements of ERVs do provide benefits, but never a complete, undamaged, functional retrovirus. They would be fatal.

And the bits and bobs that do do something useful do not have to be in the same locations in chimps and humans. 

(https://en.wikipedia.org/wiki/Isaac_Newton#/media/File:Portrait_of_Sir_Isaac_Newton,_1689.jpg)

The VIGE idea is a great example of a violation of parsimony. In the words of Sir Isaac Newton, "We are to admit no more causes of natural things than such as are both true and sufficient to explain their appearances. Therefore, to the same natural effects we must, as far as possible, assign the same causes."

But besides being unnecessary, VIGES don't even provide a viable explanation at all.

The real stakes in the heart of this idea are that -

1) The re-integration would be performed by the retroviral enzyme integrase, which, as has been proven, cannot target specific DNA loci. However many ERVs could have been VIGEs, and however many are supposed to be re-integrations, the VIGE idea cannot possibly explain the common locality of the re-integrations in the two species.

(From https://www.ncbi.nlm.nih.gov/pmc/articles/PMC509299/?tool=pubmed)

(From https://genomebiology.biomedcentral.com/articles/10.1186/gb-2006-7-11-241)

2) We have proof that ERVs are not designed-in parts of genomes. The Koala retrovirus KoRV makes that clear. It is a retrovirus currently endogenizing in koalas, with no VIGE in sight.