Wednesday, 11 January 2017

Something Fishy About Retroviruses

Un-rooted phylogenies, estimated from a reverse transcriptase protein alignment.
Marine origin of retroviruses in the early Palaeozoic Era | Nature Communications.

Retroviruses are enough to induce extreme denialism in creationists because they can't be explained in terms of intelligent (sic) design, or design of any sort, but they can easily be explained by standard genetic evolutionary theory. In fact, they can only be explained by evolution.

Retroviruses are a class of related RNA viruses which, on gaining entry to a host cell, insert the DNA counterpart of their RNA into the genome, making themselves practically invisible to the normal antibody defences of the host. They can lay dormant for many years before being activated and, if they infect the germ-line cells, can be passed on to the next generation.

It gets slightly more complicated than that. Although these so-called endogenous retroviruses (ERVs) have their origins as pathological retroviruses, the retroviruses themselves may have their origins in the genome of the same or another species as mutated retrotransposons. Retroransposons are transposable genes that can be relocated within the genome. It is believed that mutations in these could produce pathological versions which can become exogenous. So, ERVs may actually be part of a host's original DNA, gone wrong.

Over the years, as an integral part of the host's genome, they are liable to random mutations and become part of the general junk DNA, also being susceptible to occasional gene duplication. A few may become exapted in part for other functions but generally they just exist, doing nothing other than embarrassing creationists and gradually accumulating mutations like the slow ticking of a clock.

As ERVs accumulate random mutations, the number of differences between versions in different species is a measure of their separation over time so they can be arranged into nested hierarchies, just like species can be by comparing their respective genomes.

Now Pakorn Aiewsakun and Aris Katzourakis of Oxford University's Zoology Department, by analysing a group of 'fish-like' ERVs (FLERVs) have shown that this group, and thus retroviruses as a whole, originated very early in the evolutionary history of vertebrates, in a marine environment at or around the time that jawed fish were evolving and long before there were any terrestrial vertebrates.

Abstract
Very little is known about the ancient origin of retroviruses, but owing to the discovery of their ancient endogenous viral counterparts, their early history is beginning to unfold. Here we report 36 lineages of basal amphibian and fish foamy-like endogenous retroviruses (FLERVs). Phylogenetic analyses reveal that ray-finned fish FLERVs exhibit an overall co-speciation pattern with their hosts, while amphibian FLERVs might not. We also observe several possible ancient viral cross-class transmissions, involving lobe-finned fish, shark and frog FLERVs. Sequence examination and analyses reveal two major lineages of ray-finned fish FLERVs, one of which had gained two novel accessory genes within their extraordinarily large genomes. Our phylogenetic analyses suggest that this major retroviral lineage, and therefore retroviruses as a whole, have an ancient marine origin and originated together with, if not before, their jawed vertebrate hosts >450 million years ago in the Ordovician period, early Palaeozoic Era.


These viruses are as old as vertebrates themselves, older than any other viruses we know about.

Aris Katzourakis,
Palaeovirologist at the University of Oxford, UK.
Co-author.
Quoted in Nature News
So these viruses, that in humans, cause AIDS, shingles, different forms of herpes, some cancers, hepatitis B, etc., etc., have their origins long before there were humans and long before there were even terrestrial vertebrates and they may well have originated as accidental mutations in retrotransposons as an inevitable consequence of imperfect genetic replication.

Can an intelligent (sic) design advocate help me out here, please?

Why should these ERVs not be regarded as evidence of undirected, mindless evolution over millions of years and why should their phylogeny not be regarded as evidence of their co-specific evolution over time? Maybe it would be easier to explain how they fit in an intelligent (sic) design model. Why would anything that can be remotely regarded as intelligent design retroviruses that become rendered harmless over time due to mutations and then simply hang around in a hosts genome, slowly changing over time but doing nothing other than adding marginally to the hosts energy requirement in that they have to be replicated along with the rest of the genome every time a cell splits into two? Some 5-8% of the human genome is believed to have originated as ERVs.

Oh, of course, ID proponents, no doubt whilst vigorously denying that ID has anything to do with religion, will invoke mystery and 'The Fall' to explain ERVs. In doing so however, they'll give away the fact that ID is not science but a religion or, more properly, a superstition and one based on Bible literalism and fundamentalism after all.

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