Saturday, June 14, 2008

The retroviruses that are Endogenous

A blogger, SA Smith, phrased it in a way that, frankly, is hard for me to improve upon, so I'll just quote her:

If Darwin and Wallace had decided to open a resort in Cuba instead of going into science -- if every fossil were still hidden, then the second we found ERVs, common descent would have smacked us in the head like a sack full of doorknobs.

So, what are endogenous retroviruses (ERVs), and why is Ms. Smith so convinced that they are such powerful evidence in favor of common ancestry?

Let's start with the basics, shall we?

A retrovirus is pretty much what it sounds like. It's a virus that works backwards. Most viruses contain a double strand of DNA, locked within a protein coat, which is dumped into the cell. This double strand of DNA hijacks the cell's machinery and uses it to churn out more copies of itself. The DNA from the virus produces mRNA, the mRNA migrates to the cell's ribosomes and produces more proteins, and the DNA churns out more copies of itself. This is a massive oversimplification, and it doesn't apply to all DNA-based viruses, but for the purposes of this discussion, it's sufficient.

A retrovirus does this backwards. A retrovirus is a protein coat which contains single strands of RNA. Using an enzyme called Reverse transcriptase (also, pretty much, exactly what it sounds like), the RNA in the virus is reverse-transcribed into DNA which is then inserted in the genome of the cell they're attacking. That DNA then pumps out tons of copies of the virus, which then move on to infect other cells.

Now, these retroviruses have a very distinct genome of their own. As distinctive as a fingerprint, maybe even more so. In addition, they have a giant molecular flashing neon sign which says HERE IS WHERE A RETROVIRUS WAS INSERTED. Not literally. It's called the Long Terminal Repeat, or LTR, it's a specific type of sequence which has only ever been found in the genes encoded by retroviruses. Sandwiched between these two LTRs are the genes for the proteins that make up the virus. In other words, once a retrovirus has inserted itself into its host genome, it's easy to find, and the gene sequence in between those LTR signposts is easy to identify, and is so specific that a single virus can be identified within the genome.

Okay, so what?

Well, sometimes, not often, but sometimes, a retrovirus inserts itself into a germ cell, reverse-transcribes itself onto the genome of that germ cell, and becomes inactive. At this point, we call the retrovirus endogenous. This doesn't happen often, but it happens often enough that it's estimated that approximately 8% of the human genome is made up of remnants of ERVs, and because we have this giant molecular neon sign hanging on either side of them, they're pretty easy to nail down. So this ERV, newly dumped into a germ cell, gets passed from parent to child, and from that child to his or her children and so on. They get dumped into the genome at random points, but once they're there, they can stay in the genome, in pretty much the same place, for millions of years.

Every vertebrate species we've every looked at has ERVs, conserved so neatly that we can trace them back through the animal's ancestry, literally playing connect-the-dots by finding common ERVs between humans. Buried within the very molecules that make us, we have tiny molecular fossils which can be followed back millions of years.

So, let's look at the creationist viewpoint, and what this viewpoint would predict for ERVs. If all animals on earth were specially created, pretty much in their current form, then you'd expect all animals, including humans, to have completely different ERVs in completely different points of their respective genomes. In other words, we'd expect no commonality in the ERVs, either in location, or in species of ERV. If you looked at the human genome and found an ERV, then looked at the same locus in the Chimp genome, you would expect never to find the same ERV. The same applies for humans and Gorillas, and Humans and Orangutans. There should be absolutely no commonality between ERVs of different species.

However, if common descent is correct. If all animals share a common ancestor, then we should find commonalities between ERVs in a very specific, predictable pattern. Namely, animals which are more closely related should have more common ERVs than animals which are more distantly related. Humans should have a lot of ERVs in common with Chimpanzees, a few in common with other primates, and almost none at all with elephants. If we had none in common with Chimpanzees, or a lot in common with elephants, evolution (certainly the common ancestry of humans) would be disproved on the spot.

In other words, we can place these two predictions side by side and see how they match up with the available data. Is there no pattern whatsoever to ERVs in different animal species, or do we see this pattern predicted by common descent?

Well, guess what, the experiment has been done for humans and the other great apes eight years ago (Gene 2000 Apr 18;247(1-2):265-77). Sure enough, we share ERVs in common with all of the other great apes, and exactly as the theory of evolution predicts, we have more in common with chimpanzees, our closest living relative, than any of the others.

And it doesn't just work for humans. Other vertebrates have had their phylogenies worked out, and their relationship with other vertebrates and their ancestries worked. Time and time again, we can use ERVs to trace the lineage through a single species (for humans, for example, there are even a couple of ERVs which appear in some humans, but not all of them, indicating an extremely recent addition to the human genome), or between species. And that phylogeny can be laid neatly over the nested hierarchy that we've already constructed. This is easy to explain by a common ancestry. Actually, it's kinda hard to explain it any other way, but I'm willing to let the creationists try.

So by all means, what's the creationist explanation for Endogenous Retroviruses, and what evidence can you bring to bear to support that explanation?

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