Endogenous NON-retroviruses!

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 genomes

Quick 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!!

Comments

#1 Sili
January 6, 2010

There is just no way, man, for Creationists to deal with this:

Since when do Creos “deal” with anything? Besides sticking their fingers in their ears and chanting LA-LA-LA-LA I CAN’T HEAR YOUUUU!! ?
#2 mo
January 6, 2010

I wish you would do a basic post on transposons, retrotransposons and retrovirus evolution.
In 1337
#3 Joshua Zelinsky
January 6, 2010

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?
#4 TotallyUncool
January 6, 2010

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…
#5 MarkW
January 7, 2010

TotallyUncool:

Bill Hicks beat you to the idea: “We’re a virus with shoes”.
#6 Mobius
January 7, 2010

Cool news.

I learn stuff on this blog all the time.
#7 SimonG
January 7, 2010

Fascinating and marvellous. But I fear you underestimate the ability of IDiots to rationalise the unreasonable, or just plain deny reality.
#8 SimonG
January 7, 2010

Fascinating and marvellous. But I fear you underestimate the ability of IDiots to rationalise the unreasonable, or just plain deny reality.
#9 qbsmd
January 8, 2010

But I fear you underestimate the ability of IDiots to rationalise the unreasonable, or just plain deny reality.

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”.
#10 Ritchie Annand
January 8, 2010

It’s okay, Abbie – YOU were the one to include the maximum likelihood tree, and those make me the happiest
#11 zer0
January 9, 2010

…therefore the Garden of Eden and Jesus Christ died on The Cross for Our Sins.

Or, common descent.

You are Pure Win.
#12 Mobius
January 9, 2010

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.
#13 Stephen Wells
January 18, 2010

In passing: chottomatte is Japanese for “wait a moment”.

Really cool virus news.
#14 chottom
January 20, 2010

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.
#15 t. james archibald
January 21, 2010

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.
#16 qbsmd
January 22, 2010

@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?
#17 qbsmd
January 22, 2010

@t. james archibald
Lisa: Dad, do you know what rhetorical means?
Homer: Do I know what rhetorical means?
#18 peter borger
November 23, 2010

Yeah, great news indeed…

First of all there is the RNA virus paradox. It says all RNA viruses, and their socalled remnants ERVs, have a common ancestor around 50 thousand years BP.

Still, ERVs are present in all known animals, which are allegedly millions and million years apart…a paradox.

Close-up scrutiny of ERVs reveals unexpected surprises. For instance, some found in coelecant and humans have the same unique features. Evolution? Common descent? Apparently not…

Could it be that main stream scientists are wrong about their interpretation that ERV are the ancient remnants of RNA viruses? Regarding the above facts, most probably YES.

What can an ERV be then? If anything?

Could it be that ERVs (containing gag and pol only) were designed as variation-inducing genetic elements (VIGEs)? Could it be they were controlled and regulated in the past, but due to their redundant character easily degenerate into junk DNA?

The origin of RNA viruses (gag & pol plus additional genes) is currenlty completely obscure. There is not a single scientist in the entire world who can tell you an plausible origin story, where RNA viruses have their origin…

Could it be that RNA viruses (such as HIV, Flue, RSV, etc) have their origin in VIGEs?

Could that be the case? Do Darwinians mix up cause and result?

Yes, that is moste likely the case.

RSV is a “simple” RNA virus that is able to cause carcomas (cancer). If we study the genetic components of RSV we observe again gag and pol. In addition, we vind part of a gene we know as src. This gene is a cell cycle control gene we find in all higher organisms, and itposseses a molecular on-switch and an off-switch.

Now look how RSV originated: The VIGE integrated near the SRC genen, and when it excised it accidentally picked up only the on-switch of the SRC gene. The births of an ocogene!

This is how all RNA viruses arose: from VIGEs.

Why is it plausible? Because this view solves the RNA virus paradox. And it explains RNA-virus-caused diseases as secondary.

Have a nice day,

Peter Borger, PhD
Biologist

PS: Humans and chims differ by hundreds of unique genes, including protein coding- and miRNA genes. As long as Darwinians don’t have a clue about such novelties, the independent integration of ERVs and the like, in specific sites in the genomes of primates, explains why they give an illusion of common descent. Mutations are not a random phenomenon, guys. For more information read my articles in the JOC.

~~~~
#19 radar
March 5, 2011

As usual, making up a long complicated story unsupported by evidence and then trumpeting the conclusions reached by an imaginative mind. Never has a Darwinist ever explained where information comes from and this ERV nonsense is just another black box event for them. Hey, we can make things sound complicated and make up a process out of thin air and assign millions of years to it and impress college students who want to get finals over with and go out on a date. Good thing real scientists like Borger are there to pop the balloon.
#20 W. Kevin Vicklund
March 6, 2011

As usual, making up a long complicated story unsupported by evidence and then trumpeting the conclusions reached by an imaginative mind.

Yeah, that’s pretty much all Peter Borger does. Oh, and misrepresent data. For example:

First of all there is the RNA virus paradox. It says all RNA viruses, and their socalled remnants ERVs, have a common ancestor around 50 thousand years BP.

Still, ERVs are present in all known animals, which are allegedly millions and million years apart…a paradox.

But that’s not what it says at all. It actually says that within each RNA virus family, almost all the extant “species” diverged from a common ancestor within the last 50,000 years. However, the families diverged much longer ago than that, but the dating method used is only reliable back to 50,000 BP. Any divergence older than that results in a saturated molecular clock.

A molecular clock is a way of measuring time from divergence based on counting the number of mutations and multiplying by the mutation rate. Say we have two species that recently diverged, and there’s a difference of 6 nucleotides per 100,000 bp. That means each species had three mutations per 100,000 bp since divergence (assuming constant and equal mutation rate). Now, if the mutation rate is 1 mutation per 100,00 bp per million years, we can say that the species diverged around 3 million BP. However, as more mutations accumulate, the more likely a new mutation will occur in the same spot as a previous mutation. The molecular clock won’t pick up this extra mutation, and will be increasingly in error as these accumulate. At a certain point, the likelihood of such a mutation occuring is so high that the molecular clock is unreliable to the point of being useless. We call the clock saturated at this point. It is similar to the limitations of carbon-dating, or more closely analogous, racemic dating.

For most types of life, the mutation rate is slow enough that the saturation point is billions of years. However, viruses have much faster mutation rates, mainly due to the lack of repair mechanisms.