The Endogenous Retroviruses that we share with chimps is one of the strongest pieces of evidence there is for evolution. And of course who else but Answers in Genesis would challenge this? The first thing that should be addressed is the claim that endogenous retroviruses are beneficient to the host. Blogger Abbie Smith has given the answer to this:
"As a defense against the argument that 'junk DNA', including nonfunctional ERVs, is evidence against their choice* of 'Designer', Creationists insist that ERVs are functional.
There is a very big difference between a functional ERV, and a functional component of an ERV. Creationists do not understand this (specific example here)
Yes, we have found a retroviral env that has been co-opted by mammals. Yes, somewhere around 100 human proteins might have evolved from co-opted gag proteins. Yes, we can find retroviral transcripts floating about cells, sometimes. But these are not examples of ERV functionality. They examples of evolution in action-- the host organism salvaging ERV parts for its own use.
Complete ERVs are recombined, mutated, and methylated into junk. When they regain some semblance of functionality, they cause disease! Which is no surprise, as exogenous retroviruses like HIV and HTLV cause AIDS, leukaemia, lymphomas, and various other autoimmune diseases.
ERVs specific to humans, called HERVs, have been tied to multiple cancers, including germ-cell tumors, breast cancer, seminomas, melanoma, ovarian cancer... And autoimmune diseases like multiple sclerosis, rheumatoid arthritis, psoriasis, and lupus (please see this source for more information).
These are just the human-specific ERVs. We have lots more."
Read here original post here.
So ERV's are still powerful evidence for evolution since they are inserted randomly into the genome and yet we find them in the same places in related organisms.