I'm a graduate student studying the molecular and biochemical evolution of HIV within patients and within populations. I also study epigenetic control of ERVs.
Endogenous retroviruses are weird, but how they got into our genomes and what they mean, evolutionarily, isnt too hard to understand (unless youre an IDiot). A retrovirus has to not only accidentally infect a germ-line cell (sperm/egg), that particular egg/sperm has to successfully mediate fertilization, and where the retrovirus randomly inserts has to not cause trouble for the resulting offspring (cell cycle arrest, cancer, etc), for an endogenous retrovirus to form.
But this scenareo, while highly improbable, has happened lots and lots of times (a large portion of your genome is retroviral), and it logically makes sense. The virus integrating into the host genome is part of a retroviruses life-cycle.
What we hadnt really thought was a possibility before, is a non-retrovirus becoming endogenous. Yes, there are some DNA viruses that associate closely with the host cell DNA without actually integrating, and integration can happen. HPV is normally a DNA virus that associates with our DNA in the form of an episome (snuggles up next to your DNA). HPV causes cancer when it snuggles up a bit too close, and is accidentally integrated. But HPV likes epithelial cells. Cant think of a way it would get into germ line cells (not to say it couldnt).
It just doesnt seem all that likely that a non-retrovirus could get integrated into our genomes and passed on vertically.
*shrug*
GUESS WHAT WE JUST FOOOOOOOOUND!!!!
Endogenous non-retroviral RNA virus elements in mammalian genomesQuick summary: Borna disease virus, an RNA virus that replicates in the host cell nucleus, stole the reverse transcriptase activity of LINE-1 elements to insert into our ancestors genome ~40 million years ago.
HAHAHAHAHA! *giddy clapping*
They found four of these guys in humans. One on Chromosome 10 (EBLN-1), one on Chromosome 3 (EBLN-2), one on Chromosome 9 (EBLN-3), and one on Chromosome 17 (EBLN-4).
Miracle of miracles, they found four BDV insertions in chimpanzees! One on Chromosome 10 (EBLN-1), one on Chromosome 3 (EBLN-2), one on Chromosome 9 (EBLN-3), and one on Chromosome 17 (EBLN-4).
Wonder of wonders, they found four BDV insertions in orangutans! One on Chromosome 10 (EBLN-1), one on Chromosome 3 (EBLN-2), one on Chromosome 9 (EBLN-3), and one on Chromosome 17 (EBLN-4).
Oh, no! Creationists are just going to have an aneurysm over this!!
There is no way. There is just no way, man, for Creationists to deal with this:
A negative sense ssRNA virus had to 'miraculously' perform this insanely improbable event dozens of independent times, all of which just so happened to perfectly insert themselves in the same location of the genomes of several different species, and the ones that inserted in the same locations just happen to have the exact same sequences, therefore the Garden of Eden and Jesus Christ died on The Cross for Our Sins.
Or, common descent.
For Petes sake, they found these insertions in everything from squirrels to lemurs to elephants. These insertions go back 40 million years.
Phylogenetic analyses demonstrate that the oldest primate EBLN observed must have appeared in an ancestor of primates after the separation between Strepsirrhini and Haplorrhini, implying that bornaviruses have coexisted with primates for an evolutionary history stretching at least 40 million years. Thus, bornaviruses are the first non-retroviral RNA virus whose existence in prehistoric times has been confirmed.AWESOME.
Linkage: YOOOOOOOOOONG!!! Beat me to it again!!
Life Science
Comments
Posted by: Sili | January 6, 2010 7:30 PM
I wish you would do a basic post on transposons, retrotransposons and retrovirus evolution.
In 1337 ;)
Posted by: mo | January 6, 2010 8:58 PM
That's very cool and very surprising. Question: Since non-retrovirus viruses are more common than retroviruses does this have any potential to help us with working out phylogenetic trees?
Posted by: Joshua Zelinsky | January 6, 2010 9:52 PM
I'm beginning to wonder whether on a genetic level, at least, eukaryotes (and maybe all living organisms) are going to turn out to be highly chimeric, with most (almost all?) of our genome consisting of viral (and other) DNA just sort of smooshed together -- co-opted, silenced, non-functional, dangerous, or whatever.
I wouldn't mind finding out that I'm actually a giant, frankenstein's-monster-like virus (Frankenvirus?) patched together out of near-random parts, with some cellular machinery to keep everything going -- I kind of like the idea, actually. I'm not sure what it would do to most people's sense of identity and uniqueness, though. And that kind of natural improvisation is just about the exact opposite of intellgent design.
Come to think of it, maybe the world was created for viruses, and we just exist to serve as their homes and breeding grounds. And God really is a giant virus.
I can see it now -- a vast congregation of viruses, bowing before the gigantic image of the divine bacteriophage...
Posted by: TotallyUncool | January 6, 2010 11:24 PM
TotallyUncool:
Bill Hicks beat you to the idea: "We're a virus with shoes".
Posted by: MarkW | January 7, 2010 7:42 AM
Cool news.
I learn stuff on this blog all the time.
Posted by: Mobius | January 7, 2010 9:34 AM
Fascinating and marvellous. But I fear you underestimate the ability of IDiots to rationalise the unreasonable, or just plain deny reality.
Posted by: SimonG | January 7, 2010 6:58 PM
Fascinating and marvellous. But I fear you underestimate the ability of IDiots to rationalise the unreasonable, or just plain deny reality.
Posted by: SimonG | January 7, 2010 7:09 PM
You can interpret the design hypothesis in an unfalsifiable way. Deism is unfalsifiable, and anything that uses magic as an explanation is unfalsifiable.
I don't think many people realize that that's a bad thing. I can remember in one of my first philosophy classes, I learned that an argument I wanted to make was unfalsifiable, and my first attitude was something like "that's good; I win no matter what."
I think you have to teach enough epistemology for them to understand why unfalsifiable explanations are bad before they will even care about the evidence. Before that the attitude is "I don't really care what your evidence is, because I know it will fit into my unfalsifiable worldview".
Posted by: qbsmd | January 8, 2010 12:18 PM
It's okay, Abbie - YOU were the one to include the maximum likelihood tree, and those make me the happiest :)
Posted by: Ritchie Annand | January 8, 2010 1:16 PM
You are Pure Win.
Posted by: zer0 | January 9, 2010 11:25 AM
When Abbie first posted this article, I started a thread on the Topix Evolution Debate forum about it. (I post as Darwins Stepchild there.)
http://www.topix.com/forum/news/evolution/T4F78G4TNNVIDP4UL
(It gets off topic for a bit as I was relating some news about my dog. I am sure Abbie will understand.)
Anyway, this morning, someone from Japan going by chottom posted some interesting information.
http://chottomatte.net/2010/01/08/japanese-research-team-discoveres-the-first-virus-of-non-retroviral-origin-in-our-genome/
http://chottomatte.net/wp-content/uploads/2010/01/RNA_virus.jpg
http://genome.ucsc.edu/cgi-bin/hgTracks?insideX=115&revCmplDisp=0&hgsid=149148534&hgt.out2=+3x+&position=chr3%3A73110810-73112488&hgtgroup_map_close=0&hgtgroup_phenDis_close=1&hgtgroup_genes_close=0&hgtgroup_rna_close=0&hgtgroup_expression_close=1&hgtgroup_regulation_close=0&hgtgroup_compGeno_close=0&hgtgroup_varRep_close=0
Some of this is over my head, but I still thought I would pass it along.
Posted by: Mobius | January 9, 2010 12:55 PM
In passing: chottomatte is Japanese for "wait a moment".
Really cool virus news.
Posted by: Stephen Wells | January 18, 2010 10:15 AM
Yes indeed Stephen :)
BTW it is amazing how many interesting things you can find within the genomic databases if you learn how to use properly at least one genome browser (for example UCSC - my favorite).
Cheers
chottom
I intend to create and popular science blog but not enough spare time lately.
Posted by: chottom | January 20, 2010 1:02 AM
just some rhetorical questions:
If Theism is an unfalsifiable claim, why do atheists claim that it's false?
Where did the information in dna come from?
Common decent or common designer, wouldn't we expect similarities either way?
--"The man of science is a poor philosopher."-- Albert Einstein
A poor philosopher is a poor scientist.
Posted by: t. james archibald | January 21, 2010 2:00 PM
@t. james archibald
Theism isn't unfalsifiable; theistic beliefs make specific claims that can be demonstrated to be false. For example, studies show that prayer is ineffective at helping people recover from diseases. Deism (a belief in a creator who started the universe and was hands-off afterwords) is and therefore no atheist should ever claim to be certain that a deity does not exist, only that one is extremely unlikely, or that belief in one is unjustified.
Also, you need to read more philosophy to learn why unfalsifiable ideas are not respected by skeptical or scientifically minded people.
Other people understand information theory far better than I do. I recommend reading http://recursed.blogspot.com/2009/10/stephen-meyers-bogus-information-theory.html which explains that creating information according to any rigorously defined information theory is trivial, and creationists have their own special fuzzily defined version of information that can't be quantified or analyzed if you look at it closely.
You would expect similarities either way, but not the same similarities. As a quick example, cars are designed. Cars made by a given company this year may use certain technologies that weren't available last year, so you will see some change over time. You will expect to see the same problems solved in the same way for different models. You will expect differences to reflect differences in function, for example, SUVs and sports cars have more powerful engines than other vehicles, so you expect those engines to have similar features.
With evolution on the other hand, you expect to see a branching tree pattern everywhere. Pick any given gene and look at how similar that gene is to the same gene in other organisms and you can draw a tree where more similar genes are on closer branches. Also, these trees are predicted to be more or less the same for any gene you pick. For example, a Tasmanian Wolf is very similar in appearance to canines, but is in fact a marsupial. If it were designed, you would expect many of its genes to be very similar to wolf genes. If it evolved, you would expect its genes to be more similar to a kangaroo's than a wolf's despite the physical appearance.
You likely just though something like "but a designer wouldn't have to do it that way". That is what unfalsifiability means. Imagine if you and I were to walk through the woods with William Paley, and after he finds a watch on a rock and declares it to be designed I insist that the rock is also designed because, of course, someone could have taken a larger rock and carved it into precisely the shape it had for some aesthetic reason, and of course, to hold up the watch. How would you argue with me? Even if you find no tool marks on the rock, I can insist that this is because of the carver's skill in making it look as natural as possible. Is there any evidence you think you can provide that could change my mind?
Posted by: qbsmd | January 22, 2010 9:26 PM
@t. james archibald
Lisa: Dad, do you know what rhetorical means?
Homer: Do I know what rhetorical means?
Posted by: qbsmd | January 22, 2010 9:30 PM