Stories
Slash Boxes
Comments
Search

News for nerds, stuff that matters

Slashdot Log In

Log In

Create Account  |  Retrieve Password

The Role of Retroviruses in Human Evolution

Posted by Zonk on Sat Dec 08, 2007 04:38 PM
from the gotta-love-that-twisty-tree-of-life dept.
Biotech Science
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."
+ -
story

Related Stories

[+] One Species' Genome Discovered Inside Another's 224 comments
slyyy writes "The Universtiy of Rochester has discovered the complete genome of a bacterial parasite inside the genome of the host species. This opens the possibility of exchanging DNA between unrelated species and changing our understanding of the evolutionary process. From the article: 'Before this study, geneticists knew of examples where genes from a parasite had crossed into the host, but such an event was considered a rare anomaly except in very simple organisms. Bacterial DNA is very conspicuous in its structure, so if scientists sequencing a nematode genome, for example, come across bacterial DNA, they would likely discard it, reasonably assuming that it was merely contamination--perhaps a bit of bacteria in the gut of the animal, or on its skin. But those genes may not be contamination. They may very well be in the host's own genome. This is exactly what happened with the original sequencing of the genome of the anannassae fruitfly--the huge Wolbachia insert was discarded from the final assembly, despite the fact that it is part of the fly's genome.'"
[+] Study Suggests Genome Instability Hotspots 72 comments
Dr. Eggman writes "Ars Technica reports on a new study that suggests not only that certain areas of the mouse genome undergo more changes, but that changes to those areas are more tolerable by the organism than changes in other areas. Recently published in Nature Genetics, the study examined the certain copy number variations of the C57Bl/6 strain in mice that have been diverging for less than 1,000 generations. The results were a surprising number of variations. While the study does not address it, Ars Technica goes on to recount suggestions that genomes evolved to the point where they work well with evolution."
Submission: Role of endogenous retroviruses in human evolution by mhackarbie (593426)
This discussion has been archived. No new comments can be posted.
The Fine Print: The following comments are owned by whoever posted them. We are not responsible for them in any way.

The Role of Retroviruses in Human Evolution 50 Comments More /

 Full
 Abbreviated
 Hidden
More
Loading... please wait.

  • Bringing back the dead? (Score:3, Interesting)

    by smooth wombat (796938) on Saturday December 08 2007, @04:41PM (#21626971) Homepage Journal
    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?

  • The thing about retroviruses... (Score:5, Funny)

    by Anonymous Coward on Saturday December 08 2007, @05:04PM (#21627073)
    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.

  • Hmm (Score:5, Interesting)

    by pclminion (145572) on Saturday December 08 2007, @05:17PM (#21627167)

    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?

    • 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.

    • Re:Hmm (Score:5, Interesting)

      by Harmonious Botch (921977) * on Saturday December 08 2007, @05:29PM (#21627265) Homepage Journal
      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.

      • Re: (Score:3, Interesting)

        by maxume (22995)
        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 me' and little else, thus making things interesting. So not so much leaving home as taking it over destructively. Throw in billions of years and trillions of organisms and it starts to get a little ridiculous trying to make any guesses at all.

      • Re: (Score:3, Insightful)

        by LordLucless (582312)
        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 (Score:5, Interesting)

      by cpricejones (950353) on Saturday December 08 2007, @05:32PM (#21627293)
      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 (Score:5, Informative)

      by fm6 (162816) on Saturday December 08 2007, @05:50PM (#21627389) Homepage Journal
      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? (Score:5, Interesting)

    by Tablizer (95088) on Saturday December 08 2007, @05:40PM (#21627341) Homepage Journal
    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.

    • Re: (Score:2, Informative)

      by Colin Smith (2679)

      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.
       

      • Re: (Score:3, Interesting)

        by Tablizer (95088)
        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 precambrian fossils such that we know soft bodies existed in relative abundance at that time. They just lacked many features we take for granted, such as eyes, mouths, digestive tracks, and limbs; and don't seem to match up well with Cambrian-and-forward life
    • 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.
    • 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. . .
    • It'd be pretty funny if "God" turned out to be a retrovirus....

  • Two SciFi novels I recommend (Score:5, Informative)

    by ridgecritter (934252) on Saturday December 08 2007, @05:58PM (#21627437)
    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: (Score:4, Funny)

    by Lost Penguin (636359) on Saturday December 08 2007, @05:59PM (#21627445) Homepage
    Umbrella Corporation unavailable for comment.

  • Can you bring a virus back from the dead... (Score:4, Informative)

    by RichPowers (998637) on Saturday December 08 2007, @06:08PM (#21627485)
    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.

    • Re: (Score:3, Insightful)

      by Vellmont (569020)

      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 or not.

    • Re:Oh no! (Score:5, Interesting)

      by Dr. Eggman (932300) on Saturday December 08 2007, @04:55PM (#21627021)
      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!

      • Re: (Score:2, Insightful)

        by GwaihirBW (1155487)

        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 m

      • 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 (Score:4, Insightful)

          by Cassius Corodes (1084513) on Saturday December 08 2007, @06:27PM (#21627621)
          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 (Score:5, Informative)

          by GwaihirBW (1155487) on Saturday December 08 2007, @06:27PM (#21627629)
          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.

        • Re: (Score:3, Informative)

          by TriggerFin (1122807)
          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

          • Re: (Score:3, Informative)

            by shawb (16347)
            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.)

    • Re: (Score:3, Funny)

      by krel (588588)
      You're right, we should never research diseases. We might infect ourselves with them.
    • 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...
      • 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 treatment by for example interferone can certainly help against several viral infections (but, again, you would generally need to administer it before you see any symptoms), but it would frequently also cause worse effects than the original disease.
        • 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 and the body's own immune system have been far more effective against viruses than any drug. As you said, the nature of most viral infections make them much more difficult to treat, since they've probably been reproducing exponentially for days before sym
      • In any case, I'd prefer it if they'd experiment with mouse retroviruses instead...

        I cannot use a keyboard, YIC.

    • Re: (Score:2, Informative)

      by cpricejones (950353)
      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 repli

    • Re: (Score:3, Insightful)

      by Daniel Dvorkin (106857)
      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.
    • 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 viruses didn't manage to replicate themselves without excising themselves from our genome- take your pick. The fact is that viruses that exist *now* are the ones you should be worrying about.

    • Re: (Score:3, Interesting)

      by drunken_boxer777 (985820)
      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 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

    • Re: (Score:3, Insightful)

      by belg4mit (152620)
      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.

    • Re: (Score:3, Informative)

      by bob19794 (1122211) *
      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 hemachromatosi

All trademarks and copyrights on this page are owned by their respective owners. Comments are owned by the Poster. The Rest © 1997-2010 Geeknet, Inc.