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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."
So what you're saying is we will now have zombie viruses?
We will bankrupt ourselves in the vain search for absolute security. -- Dwight D. Eisenhower
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!
Demented But Determined.
You're right, we should never research diseases. We might infect ourselves with them.
karma: ouch!
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?
In any case, I'd prefer it if they'd experiment with mouse retroviruses instead...
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.
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 it. If we were once tolerant of it and now are not, that implies some cost to the tolerance-granting genes, since we lost them . . . in that case, they may not be around to find, and even if they are, where do you look? If we acquired some new trait that made us vulnerable to this now-dormant virus, that's going to be even less helpful, and again, how do you tell? All of this boils down to, we've got a touch more information about origin, but it doesn't point us anywhere.
The real benefits of this research lie elsewhere - in the ability to recover and play with old viruses, see what they do, and possibly track their evolution through the genetic record, which may help us combat the change and spread of nasty current retroviruses like HIV.
"There are four boxes to use in the defense of liberty: soap, ballot, jury, ammo. Use in that order." - Ed Howdershelt
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.
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?
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.
The correlation between ignorance of statistics and using "correlation is not causation" as an argument is close to 1.
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 with the basics. I study retrovirus proteins, and our collaborators routinely use "live" HIV viruses to infect cells. The procedures are quite standard. In those experiments, often the HIV strain that is used can only infect cells one time and cannot replicate. The researchers in the article do the same thing.
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 serious threats. Really, this is pretty safe compared to ongoing work on, say, Ebola.
The correlation between ignorance of statistics and using "correlation is not causation" as an argument is close to 1.
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.
Table-ized A.I.
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.
Umbrella Corporation unavailable for comment.
I am the unwilling control for my Origin.
If it was never alive in the first place?
Scientists still debate 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, written by the Director of Virus Research at UC Irvine.
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 more likely to get caught in traps. It would only be possible if we could eliminate all the mice in the world, and then introduce these 'dumb' mice into the wild. What's the point of repopulating the world with dumb mice if we didn't want mice in the first place?
Second of all, if you read the article, you would know how the researchers 'fixed' the 'broken' viruses:
The team took ten versions of that virus (we carry more than thirty) and compared the thousands of nucleotides in the genetic sequence of each version. They were almost identical, but where they differed the researchers selected the nucleotides that appeared most frequently. That permitted them to piece together a working replica of the extinct retrovirus. "If you have a person with a lethal defect in the heart,'' Bieniasz explained, "and another with a lethal defect in the kidney, you could make one healthy person by transplanting the respective organs. That is what we did.Lastly, and not that it will necessarily assuage your fears, but a species that carries an endogenous retrovirus in its genome is far less likely to be infected by that virus. Some developmental biologists employ a well-characterized and naturally occurring chicken retrovirus, engineering it to misexpress a normal chicken gene of their choice. This way, they can see what happens if they express that gene everywhere within a developing organ, as opposed to the normal expression of the gene only within a small population of cells within that organ. (As an example, they are studying gene X, which plays a role in bone development, and is only expressed in cells that will become bone cells. They make a chicken retrovirus that also expresses gene X, and infect the wing of a developing chicken. Now all the cells in the wing express gene X, and not just those that were going to become bone cells.) In order to do this, these researchers must use eggs from chickens that do not carry endogenous copies of this virus in their genome. Eggs from chickens that carry endogenous copies of this naturally-occurring retrovirus in their genome are far less susceptible to infection by the engineered virus, and therefore are not experimentally useful. Such endogenous retrovirus-free chickens were specially bred.
Sure, there are always potential risks from any type of science. But it is important to know how risky something is, and weigh that versus the potential benefits.
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.
Were that I say, pancakes?
From what I was just reading now, maybe the RNA world which some theorists have speculated (theorized) predated the DNA biological world we presently live in was the place where something like viruses could reproduce themselves.
But I'm probably misunderstanding everything I read today.
My personal opinion?
I remember playing with a 6802 prototyping board with a flaky power-on reset circuit. (I used cheap switches from Radio Shack.) It had a monitor ROM, of course, then later it had BASIC in ROM. If power came up too fast, the ROM would not be ready to put the reset vector on the bus, and the CPU would jump somewhere else. Sometimes, if the reset button worked, I could look at RAM, and I would find bits and pieces of the ROM sitting out there. Until the thing stabilized, sometimes it was not particular interesting, but sometimes it would dump almost intelligible strings, or even clots of error messages or the symbol tables into video RAM.
I had read, at the time, about how computers with disk drives had to have good power-on reset circuits, or had to be booted up with no media in the drives, and media loaded after the operator stabilized the CPU. Otherwise, the disk drives would tend to get told to write random data on the disks, which, of course, kind of ruins the whole purpose of having disks.
I had also read that (some of?) the first computer viruses were inspired by some of the junk that was left in memory by such episodes of uncontrolled execution.
So I have tended to wonder whether it might not be the case that viruses are not some independent remnants of proto-life, but are rather the results of genetic accidents.
I'm not sure we could tell the difference from looking at the archeological record.
But it's interesting that one of the biologists the friendly article quotes made a comment that almost equated viruses with God.
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 is fluid exchange involved in reproductive (and most other) sex, and they do get around that way, since they tend to be floating around your body soon after they've gotten into one cell.
These are NOT active viruses, they're leftover bits that got swept up and tossed in the stew pot back when you were a monkey, shrew, fish, bacteria, or whatever. Most of the junk in your DNA has been put to some use, even if just to mark another section as not used. They can be used to trace evolution, by looking to see who's got what bits.
Here's your sig.
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 understandable for general audiences. I recall his describing endogenous retroviruses in the human genome and reverse transcriptase as a mechanism. His main argument seems to be that a number of hereditary diseases like sickle cell anemia, diabetes, and hemachromatosis (a problem in regulating iron absorption) are hereditary because they conveyed some advantage to survival in the past, such as resistance to bubonic plague or malaria. He also touches on research in non-coding DNA and transposons ('jumping genes') and epigenetics (on variables affecting whether genes show up actively in the phenotype or remain dormant in the genotype.) I found the book in Orange County Public Library. A website: http://www.survivalofthesickestthebook.com/ has excerpts,reviews, and the author's blog. Johnathan Prince, a professional writer, is listed as co-author, presumably helping to make the book understandable to general readers. That includes me, and I found it fascinating and educational.
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 this bulk being redundant copies of the same of very similar viruses.)
I'll never make that mistake again, reading the experts' opinions. - Feynman