https://barryhisblog.blogspot.com/p/debating-john-heintz.html
The debate proposal is, "Common ancestry is the only viable explanation for large numbers of commonly located endogenous retroviruses (ERVs) in any two species". I shall be arguing in support of the proposal.
Opening comments
This debate is likely to become rather technical, but I will try to be as concise as possible. Further explanation and supporting material is available at my Frequently Asked Questions (FAQ) questions pages at https://barryhisblog.blogspot.com/p/endogenous-retroviruses-frequently.html
So, briefly, what is an endogenous retrovirus?
A retrovirus (HIV is an example) is a particular type of virus with a characteristic replication cycle. In the open environment, its genome is in the form of RNA which is packaged by and with proteins (enzymes). On contact with a target host cell, it attaches to it and spills its contents into the cell, and induces the production of a DNA version of its genome. This is done with a retroviral enzyme, reverse transcriptase. Another enzyme, integrase, does a cut and paste job on the host's nuclear DNA, integrating the viral DNA with it. The host then begins to dutifully transcribe the retroviral DNA back into RNA, resulting, by further stages, in the production and release into the environment of copies of the original virus.
A little bit more jargon
A retrovirus that is freely at large in the environment is called an, 'exogenous retrovirus', because it is not in any host cell's genes.
The DNA form of a retrovirus that has been integrated with a host cell's DNA is called a 'provirus'. That's when the host cell is a somatic (non-reproductive) cell.
But when a retrovirus integrates with the DNA of a gamete (a sperm or egg cell), it is called an 'Endogenous' RetroVirus - an ERV. It is potentially heritable, and can spread through a population by normal sexual reproduction.
The evidence that establishes an endogenous retrovirus has been inherited is twofold.
1) It is present in every nuclear cell of the organism. Viruses from the environment do not normally infect every cell. (Never, to my knowledge.)
2) It is present in precisely the same DNA location, or locus, in every nuclear cell. This is important. Surveys of integration loci in somatic cells from viruses in the environment prove that integrase, although they may integrate in 'preferred' regions, just like accidents in accident danger spots, cannot target precise host DNA loci. There is typically no repetition of locus within several hundred samples.
The only explanation for the facts 1) and 2) above is that an ERV is there, in every cell in the same locus because every daughter cell contains an exact copy of the DNA of the first single cell that the host organism started out as, the DNA including the ERV.
When we examine the genome of our own species, we discover that we share the vast majority of our ERVs, in precisely the same loci, with all the other members of our species. This means that for each shared ERV, there is an individual ancestor in our family tree that is common to all of us, who first caught that particular virus that integrated with one of his or her reproductive cells. That individual is just like mitochondrial Eve, and, if we are of the male persuasion, an individual we call Y-chromosome Adam. The two individuals bequeathed us our mt-DNA, and in the case of men, our Y-chromosomes.
Now when we come to what evolutionary science has concluded are our most closely related species, Pan troglodytes and Pan paniscus, and we compare all our ERVs, we find that the vast majority of them are in precisely corresponding DNA loci. The only reasonable explanation for this is that all these ERVs have been acquired from common ancestors. We have all inherited them from the same sources. I have found no other viable explanation for these commonly located ERVs.
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