The Role of Retroviruses in Human Evolution

mhackarbie writes "The current edition of the New Yorker magazine has up a story about endogenous retroviruses in the genomes of humans and other species. Although researchers have known about such non-functional retroviral 'fossils' in the human genome for some time, the large amount of recent genomic data underscores just how pervasive they are, in a compelling tale that involves humans, their primate cousins, and a variety of viral invaders. Some researchers are even bringing back non-functional viral remnants from the dead by fixing their broken genes."

Bringing back the dead?

Some researchers are even bringing back non-functional viral remnants from the dead by fixing their broken genes."

So what you're saying is we will now have zombie viruses?

Re:Bringing back the dead?

Zombie viruses, huh? Now might be a good time to take stock in really tiny shotguns.

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Is this a bad time to point out that you may just have missed a comma? :P

-:sigma.SB

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Didn't Jurassic Park teach us anything. Instead of T-Rex eating our lawyers we'll have our lawyers keeling over dead from fossil viri.

Re:Bringing back the dead?

Either way, lawyers die, which shows there is no downside meddling in genetic engineering.

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Well, all the lawyers can rest easy that either way, you too will die.

Re:Bringing back the dead?

Are viruses even alive in the first place?

Re:Bringing back the dead?

"Viruses and aberrant prion proteins are often considered replicators rather than forms of life, a distinction warranted because they cannot reproduce without very specialized substrates such as host cells or proteins, respectively.."

Life [wikipedia.org]

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Natural selection is a general principle that applies to anything that reproduces -- things that reproduce well will continue to exist and spread, and when variation occurs, those variants that are best equipped to survive and reproduce successfully in a g

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Why, its a plan that is almost entirely without a drawback, as far as I can see..

The thing about retroviruses...

See the thing about retroviruses is that once they work their way into the genome, they begin to do wack things. They predispose the person to wear bell bottom geans, listen to funk music, wear tube socks, and any number of out of fashion things. They begin to force the person to speak in archaic manners, eg "Thou hast been up intowards my grill!" So I think it's safe to say that we need to eliminate retroviruses as a mechanism of mutation. There comes a time to let certain things go.

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Hey! I resembleth thine remark, thou clod insensitiveth!

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Groovy!

Hmm

How do we know the the retrovirus genome didn't originate with the hosts themselves? Did these viruses evolve truly independently, or might they have started out as fragments of genetic code from some larger organism which somehow escaped and became self-sufficient?

In other words, when we look at the human genome and say, "This is riddled with retroviruses!" is it not possible that the retroviruses were actually there all along, and only later became able to leave the parent cell and operate independently?

Are retroviruses actually just chunks of "rebel DNA" from our own genome, or possibly from some other species?

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hat you're describing is probably possible, but for any given stretch of DNA encoding the right polymerases, it's a lot more likely that it's a retrovirus that lost the ability to leave the cell than that it's a transposon that gained that ability.

Aaargh, learn to use the preview button

What you're describing is probably possible, but for any given stretch of DNA encoding the right polymerases, it's a lot more likely that it's a retrovirus that lost the ability to leave the cell than that it's a transposon that gained that ability and then lost it again.

Is what I meant to say.

Re:Hmm

That is a damn good question.

A 'rebel DNA leaving home' must have happened at least once, in some species, otherwise how could viruses exist? They seem way too complex to have happened by chance, and they can't evolve until they are complex enough to infect.

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Do they really infect? Or do they do something else?

My impression is that bacteria are in the habit of absorbing random fragments of DNA from their environment. I can see where some accident would cause such a fragment to carry the instruction 'replicate m

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I'd imagine other forms of life to be more complicated than viruses, and the general consensus seems to be that they developed by random chance - they can't evolve until they're complicated enough to reproduce.

Re:Hmm

To understand this, you can do sequence comparisons between retroviral genes and our own genes. For example, retroviruses have an enzyme called reverse transcriptase. This enzyme is a type of polymerase. We have many polymerases in our body, and if RT developed from one of them, then there would be very substantial sequence similarity. This is one way to figure out what proteins do if you do not know their function. You compare their amino acid sequence to other known proteins and see if they are similar. This is very common, and it is how researchers establish relationships between retroviruses to understand how they evolve. For example, HIV is a member of the subgroup of retroviruses called lentiviruses, and these viruses have many things in common. HIV has a cousin called SIV (simian immunodeficiency virus) that is very similar. A really good reference is Coffin, RETROVIRUSES, from Cold Spring Harbor Press.

Re:Hmm

You're not the first to have that thought. It was part of the premise of Greg Bear's SF novel, Darwin's Radio. He, in turn, got the idea from various scientists, cited in the back of the book. (Sorry, no copy at hand.)

Cambrian explosion?

Such viruses may be responsible for the Cambrian Explosion. A new kind of virus may have helped "share good ideas" like eyes, nervous systems, enzymes, etc. between different species of early animals. This may have propelled evolution by allowing life to mix and match instead of each branch having to reinvent stuff from scratch.

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Such viruses may be responsible for the Cambrian Explosion.

Or maybe... The big change at the Cambrian was a mutation which allowed the creation of shells and bones.
 

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Or maybe... The big change at the Cambrian was a mutation which allowed the creation of shells and bones.

I don't see those as a significant trigger mechanism. Early Cambrian fish hardly had any bones, I would note. And there's now plenty of soft-body pre

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This sounds like some wishful thinking do you have any references?

Since most retrovirus markers are useless remnants and are just artifacts of past events. They are not a means of propagating "good ideas" since they are largely non-functional.

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Some people take offense at implying their ancestry is of apes, imagine now that it's actually a hodgepodge from all sorts of animals like ducks and sea cucumbers. . .

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It'd be pretty funny if "God" turned out to be a retrovirus....

Two SciFi novels I recommend

that have emergence of HERVs at the core of their plotlines are Darwin's Radio and Darwin's Children, by Greg Bear. Good reads, both.

Next up:

Umbrella Corporation unavailable for comment.

Can you bring a virus back from the dead...

If it was never alive in the first place?

Scientists still debate [wikipedia.org] if viruses meet the definition of life as we know it. I'm certainly not qualified to render an opinion on the matter; I just think it's fascinating how viruses occupy this gray area between our definitions of living and non-living.

Here's a PDF of a SciAm article about this very debate [uvm.edu], written by the Director of Virus Research at UC Irvine.

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I just think it's fascinating how viruses occupy this gray area between our definitions of living and non-living.

Life or living is just a word, not reality. If a virus is alive or not alive is about as interesting a question as asking if submarines swim o

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I for one sort of welcome our semi-overlords.

Too late. Resistance WAS futile! :P

Re:Oh no!

Obviously if enough individuals survived with cells reproducing its DNA containing the retrovirus for it to become a species-wide "fossil" it was either not very harmful or possibly even beneficial to our ancestors. You might be able to make the case that perhaps we have since lost the ability to combat these retroviruses, but then we must consider the possibility that in some individuals these portions of dormant virus data have been reactivate naturally. If this has occurred and we are indeed now ill equipt to fight it, then it would have been observed as some disease and possibly classified as a genetic disorder. Who knows, by reactivating these, we have discover the cause, and subsequently the cure (as obviously we naturally beat it once) to some terrible genetic malady!

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Well, the cure might or might not be so easy . . . if we already knew it was a genetic malady, there's a good chance we knew the gene to some degree, and finding out that it's an ancestral retrovirus gives fairly minimal new information on how to address

Reactivated retroviruses

If I have beneficial bacteria in my gut that keeps dangerous ones from living there, perhaps we can revitalize some harmless retrovirus to compete for the niche that the AIDS retrovirus lives in.

Re:Reactivated retroviruses

While that might seem a valid comparison it unfortunately wrong on to points

1. The role of your bacteria in your gut is not to prevent bad bacteria from living there but to help with digestion. However since bacteria on your skin do have this competition role I'll accept it as a valid point.

2. Viruses come, ursurp the mechanisms of the cell to make it produce copies, and then kill the cell to move on (in most cases). Hence using "good" viruses isn't going to make the bad viruses go away. What has happened with the "good" viruses is that they were once bad, but as part of their attack on a cell they merged their rna into our dna which become deactivated and over time changed into a new and positive role.

Re:Reactivated retroviruses

Unfortunately viruses don't compete directly in that potentially harmless way . . . HIV's niche is in your T cells (and others), reproducing itself until the cell explodes. Viruses [wikipedia.org] don't really prey on each other (they are simple RNA injection machines that parasitically use the replication mechanisms of cells they infect for reproduction. The only way for another virus to block it is to just kill all the potential target cells first (not so helpful) or to infect them with counter-RNA that neutralizes that of HIV. The problem with the second is that unless it's also doing dangerous things to you, that helper virus isn't going to be able to spread in order to combat the HIV. It's just not the same as gut bacteria - they take up residence on the limited available real estate, do some digesting of the food you helpfully provide, and defend their turf from unwanted invaders while managing their own reproduction and such, whereas viruses are hijackers by nature.

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Active viruses aren't typically transmitted as part of a person's DNA, as that would involve an usurped sperm or egg cell. As you imply, those cells don't reproduce themselves, so they don't make good homes for a virus, which would break them anyway. There

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Most of the junk in your DNA has been put to some use

Actually, that is pretty much false. About 2% of our DNA does anything to encode for protein. As a reference, the article states that about 8% of our DNA is relegated to fossil viruses (much of thi

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You're right, we should never research diseases. We might infect ourselves with them.

What are you talking about?

HIV is the only virus in which drug resistance is a problem - because most aren't affected by any drugs in the first place. Maybe you're thinking of bacteria [microbeworld.org]?

In any case, I'd prefer it if they'd experiment with mouse retroviruses instead...

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There are several other viruses that are affected to some degree by drugs, e.g. Tamiflu and many others. The main problem is that one generally wants to hit early in the lifecycle, as the point is to stop the exponential growth. The other problem is that t

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True, but there hasn't been any equivalent to penicillin, and something that broad-spectrum is probably impossible with viruses. Few could be considered life-saving, or even useful. Valacyclovir and similar drugs for herpes viruses, I suppose. But vaccines

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In any case, I'd prefer it if they'd experiment with mouse retroviruses instead...

I cannot use a keyboard, YIC.

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Viruses are relatively speaking, very simple. They have very few genes, and they have few functions. By comparison, simple bacteria often have several hundred times as many genes. If we want to understand how organisms work period, it's necessary to start

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Researchers work every day with viruses that are known to be incredibly dangerous, not just those that might be such as these putative retroviral fossils. So if you're worrying about something escaping the lab and causing a global pandemic, there are more

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too late. we've already revived ancient viruses from our genome and they are found to be extremely bad at infecting eucaryotes like us. it could be for any number of reasons, the RNA-i based defenses, millions of years of evolution, the fact these viruse

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I'm giving up mod privileges on this to comment.

If we "fix that part where they're drug resistant", it would make no difference, unless we could eliminate those viruses in the first place. It's like trying to populate the world with only mice that were m

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What do you mean "will?" It's nothing new, so they must have developed a "logical" retort by now.
We study HIV by infecting chimps and Rhesus monekys. Furthermore, it's long been thought/accepted
that HIV evolved from SIV.

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There is a book out this year that seems related to this discussion, called Survival of the Sickest by Sharon Moalem, a medical student with PhD.'s in neurogenetics and evolutionary biology. He writes this book in a conversational style fairly understandab