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Viral Fossil Brought Back To Life 320

Posted by samzenpus from the what-could-go-wrong dept.
hey hey hey writes "In a controversial study, researchers have resurrected a retrovirus that infected our ancestors millions of years ago and now sits frozen in the human genome. Published online by Genome Research this week, the study may shed new light on the history of these genomic intruders, as well as their role in tumors. Although this particular virus, dubbed Phoenix, is a wimpy one, some argue that resuscitating any ancient virus is inherently risky and that the study should have undergone stricter reviews."
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Viral Fossil Brought Back To Life More

Viral Fossil Brought Back To Life

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  • Andromeda strain (Score:3, Insightful)

    by zeroharmada ( 1004484 ) on Wednesday November 01, 2006 @09:17PM (#16683129)
    need I say more
    • Mmm nothing ghastly. I'd say that if they beat it back then we'd own it these days as our immune systems are rather advanced in comparison.
  • A virus that's been sitting in our genome is resurrected. I wonder what else is in there? I know we have a whole host of transposons that like to jump around and usually don't do any harm.

  • because thats what we really need... (Score:4, Funny)

    by spagetti_code ( 773137 ) on Wednesday November 01, 2006 @09:21PM (#16683159)
    ...a new (retro)virus.

    I mean - I was just saying the other day to a friend, I haven't
    seen a new virus in ages... just the same old ebola, HIV,
    flu, H5N1, herpes... I mean YAWN. Where's the excitement in
    those? /sarcasm

    • Just because a virus exists doesn't mean it's going to immediately INFEKT TEH WORLLD! Smallpox the virus still exists in two chambers in Atlanta and Moscow. Smallpox the disease hasn't been seen for years.
      • It still exists in CDC Atlanta, and we know some still exists at Vector, but what's to say that Vector wasn't plundered during the collapse of the Soviet Union? Or at anytime? I think it's more than likely that some has worked it's way out at some point, or during the stock destruction in the 90's. Some microbiologists did not want to see those stocks destroyed. Oh, and Vector is in Siberia, not Moscow ;) I'm assuming your referring to the Moscow institute for viral preparation.
    • You people are so pessimistic. Next you'll be saying that my perfectly harmless experiments to re-animate formerly living tissue could somehow have unforeseen, disastrous consequences!

  • Very interesting (Score:5, Informative)

    by MillionthMonkey ( 240664 ) * on Wednesday November 01, 2006 @09:24PM (#16683185)
    Only 3% of the genome is genes, the rest is junk DNA which has a lot of interesting stuff like alternate versions of genes, commented out ideas, and coded critters like this one that sit in your DNA like "sunken ships". There are like 200 copies of reverse transcriptase in the human genome, different versions, all in this junk DNA. Reverse transcriptase has absolutely no legitimate purpose in a eukaryote. It can take a segment of RNA (usually viral RNA), convert it into DNA, and stich it into your genome. Only viruses need to do that. The RNA itself has code for reverse transcriptase, and we see it in our chromosomes all over the place, this gene that is useful to viruses and no one else. It's the most common gene in your body.

    Viruses have a lytic cycle where they express nasty genes and build capsids inside you, and a lysogenic cycle, where they adopt a different strategy- they get into your DNA, become part of the junk DNA, and they replicate during normal cell division along with all the rest of your DNA.

    Junk DNA has all sorts of nasty critters in it. One trick your body uses is to carpet especially infectious regions with methyl groups via cytosine methylation [wikipedia.org]. Basically the idea is that the methyl groups jam up the machinery that comes along to express proteins, so if the proteins are viral, you can "comment them out" that way. When a cell divides, both strands of its DNA have methylated cytosines in the same regions. After the DNA replicates you have two methylated daughter strands, each coupled with a brand new complimentary strand. This complimentary strand has no methyl groups on it. So a clever enzyme comes along, DNA methyltransferase. [wikipedia.org] It has a regulatory domain and a catalytic domain. The regulatory domain runs across the DNA feeling it for methyl groups. If it finds them on one strand, the catalytic domain deposits methyl groups on the other strand. That way, the stretch of DNA can be marked as "bad news" in a way that is heritable, despite the fact that no actual DNA sequence is being "inherited". As far as where the initial methylation signal came from, that can probably be put down to natural selection.

    • Re: (Score:2)

      by bky1701 ( 979071 )
      "Only 3% of the genome is genes, the rest is junk DNA which has a lot of interesting stuff like alternate versions of genes, commented out ideas, and coded critters like this one that sit in your DNA like "sunken ships"." So, you mean, it's like Microsoft source code?

    • Re:Very interesting (Score:4, Interesting)

      by Dr. Eggman ( 932300 ) on Wednesday November 01, 2006 @09:39PM (#16683375)
      I had read recently in Popular Science that said researchers discovered that alot of what we thought was junk DNA is actually regulatory code that operates in coordination and in response to the environment of protiens and enzymes to turn genes on and off and change the folding of the DNA structure itself. I think they called the idea, the epigenome, if anyone else knows more. (I forget which issue. It may have been Scientific American instead.)
    • Only viruses need to do that. The RNA itself has code for reverse transcriptase, and we see it in our chromosomes all over the place, this gene that is useful to viruses and no one else.

      Was the original genome 1.0 written by Microsoft, by any chance? I suggest we start looking in our DNA for Bill Gates' copyright notices.

    • Re: (Score:2, Insightful)

      by E++99 ( 880734 )

      Only 3% of the genome is genes, the rest is junk DNA...

      Based on what? We only JUST mapped out the 3% that encodes protiens (the genes). Science does not know what the rest of the DNA does or does not do. There is certainly no study that I can find that offers proof that it is unused. It's the furthering of the trend of treating ignorance as if it were knowledge. If they had intellectual honesty, instead of proclaiming DNA 97% junk, they'd proclaim themselves 97% ignorant. Labeling of it as "junk," esp

      • Re:Very interesting (Score:5, Informative)

        by MillionthMonkey ( 240664 ) * on Wednesday November 01, 2006 @10:36PM (#16683827)
        "Only 3% of the genome is genes, the rest is junk DNA..."
          Based on what? We only JUST mapped out the 3% that encodes protiens (the genes). Science does not know what the rest of the DNA does or does not do. There is certainly no study that I can find that offers proof that it is unused. It's the furthering of the trend of treating ignorance as if it were knowledge. If they had intellectual honesty, instead of proclaiming DNA 97% junk, they'd proclaim themselves 97% ignorant. Labeling of it as "junk," especially in our infancy, or rather fetushood, of understanding DNA, is the absolute pinnacle of scientific arrogance. Maybe next they'll look up at the sky, and seeing clear proof of life around one star, and none around the others, declare all the rest "junk stars."

        Dude, I'll just refer you to the Wikipedia page on Junk DNA [wikipedia.org] (the bold tags are mine):

        In molecular biology, "junk" DNA is a collective label for the portions of the DNA sequence of a chromosome or a genome for which no function has yet been identified. About 97% of the human genome has been designated as "junk", including most sequences within introns and most intergenic DNA. While much of this sequence is probably an evolutionary artifact that serves no present-day purpose, some may function in ways that are not currently understood. In fact, recent studies have suggested functions for certain portions of what has been called junk DNA. Moreover, the conservation of some junk DNA over many millions of years of evolution may imply an essential function. Some consider the "junk" label as something of a misnomer, but others consider it apposite as junk is stored away for possible new uses, rather than thrown out; others prefer the term "noncoding DNA" (although junk DNA often includes transposons that encode proteins with no clear value to their host genome).
        And I didn't even edit that on Wikipedia before replying either.

        You can call it something else if you're offended, but the DNA itself won't have its feelings hurt if you call it junk.

        • You can call it something else if you're offended, but the DNA itself won't have its feelings hurt if you call it junk.

          Arguably, if a human is offended by the use of the term "Junk DNA", then the DNA's feelings were hurt, since the ability to even have that emotional response was coded for by the respondee's DNA.

          But it's not whether the DNA's feelings are hurt, it's whether people are misled by the name. I agree with the grandparent, that using the term "junk" to refer to something that's mostly just not u

        • Re: (Score:3, Interesting)

          by espressojim ( 224775 )
          As a bioinformatician who recently published a paper in Nature Genetics on Conserved Non Coding regions (non gene regions that are more highly similar than expected - the base pairs are the same), I'd have to call "Bullshit!" on this wikipedia article.

          Please don't believe everything you read on wikipedia. It might have been right if I'd read that 5 years ago, but my work, and other people's work says otherwise.
          • Hey man, since you're an expert in the field, perhaps you'd consider bringing the Wikipedia article up to date.

    • Re: (Score:2)

      by iabervon ( 1971 )
      The part of the genome that doesn't code for proteins is hardly "junk". It's full of binding sites for regulatory molecules, sections that don't code for anything but help the molecule fold and unfold without breaking.

      It's also plausible that the viral sections you mention are kept so that the immune system can produce antibodies for them, by treating those sections of the genome as deactivated virus. This would give the organism as advantage to having those sections deactivated over not having them at all

    • Re: (Score:2)

      by Dunbal ( 464142 )
      Only 3% of the genome is genes, the rest is junk DNA which has a lot of interesting stuff like alternate versions of genes, commented out ideas, and coded critters

            I'm actually scouring the net to see if anyone has found a way to unlock our "Hot Coffee" mod...
    • And once we really understand how all this works, some new nazi ideologist will come along and create a "bird flu" that will selectively wipe out the "enemy" based on their junk DNA that differentiates them, while the soldiers on the "good" side can freely walk among the epidemic because they are of course genetically immune, by design of the viral weapon. Then an even greater enlightened visionary will come along who will investigate whether it's possible to fuck up just any dna whatsoever with "clever cod
    • ...the rest is junk DNA which has a lot of interesting stuff like alternate versions of genes, commented out ideas...

      So what are you saying....? Time to refactor? ;-)


  • Revival or restoration... I think that a fully restored 1967 Hemi Barracuda is a very nice car!

    Anyways, I was more expecting that the focus of controversy here would be evidence or other implications indicative of Nature's myriad ways to encourage evolution.

    • Re: (Score:2)

      by necro81 ( 917438 )
      Revival or restoration... I think that a fully restored 1967 Hemi Barracuda is a very nice car!
      The corollary is, of course, that a revival of the barracuda would be a bad idea. Look at the aweful spate of reintroduced (or "revived") american muscle cars: the mustang, the t-bird, the camero. Even if they are more advanced (and, sometimes, more powerful) vehicles, they pale in comparison to the original.

  • Link to the Original Article in Genome Research (Score:3, Informative)

    by jestill ( 656510 ) on Wednesday November 01, 2006 @09:29PM (#16683255) Journal
    The abstract [genome.org] with a link to the full pdf [genome.org] is available online. The pdf is available on campus from many universities. It is interesting that this is already in the news. This is not technically in print form yet, and was just posted to the journal's advance articles web site.
    • I think it made the news because it's a bit worrying.

      Biowarfare labs already know how to take a mild virus and amp up its virulence. Now scientists are digging up agents that are known to be infectious... You see where I'm going?

      Put it in that context, it's easy to see why TFA says that this type of lab work should be authorized at the (inter)national level & done under the highest level of containment.
      • I think it made the news because it's a bit worrying.

        I think it made the news because of the concern that the work should have been subject to greater review. The research was normal enough stuff, but nobody likes a mad scientist. Nobody. NOBODY you hear! HAHAHAHAHAhahahah........

        I'm not a mad scientist, honest. I'm being a penguin today.

  • Not very Intelligent design (Score:3, Insightful)

    by 140Mandak262Jamuna ( 970587 ) on Wednesday November 01, 2006 @09:31PM (#16683283) Journal
    If human beings were designed, it seems to be a poor design to include copies of viruses in it. But we mere mortal humble human beings dont have the intellect to fathom the Divine Intentions. All we can say for sure is that, unless you pay the priest 10% of your income and get dunked in a pool you will rot in Hell.
    • Haha. I love it. Please mod it up.

  • HERVs: 8% of Human Genome (Score:5, Interesting)

    by Rob Carr ( 780861 ) on Wednesday November 01, 2006 @09:34PM (#16683319) Homepage Journal
    Resuscitating this virus presented no danger. Human Endogenous Retroviruses (HERVs for short) make up 8% of the human genome.

    In this particular case, there were 30 copies of the virus in the genome. They worked backward to create the original virus. The resultant virus was disabled so that, after replicating once in a cell, the daughter viruses could not replicate. So there was no risk.

    In the human genome, the researchers point out, are the pieces from other viruses. 8% of the human genome codes for HERV proteins or their regulatory subunits [nature.com]. If these pieces are activated, they can reassemble to create a new, working virus. This happens naturally.

    All of these HERVs are viruses that, throughout human evolution, we and our ancestors have more or less come to terms with. At some point, many of them were probably devastating. But those that caught the virus, survived, and reproduced were able to mitigate the effects of the virus. These are viruses we've reached a "détente" with. They no longer rampage through the population. In fact, some of the proteins they produce are vital to our survival. One of these retroviral proteins permits implantation of the placenta. Without it, we'd all have placentas that don't attach to the uterine lining -- like mice, which as a result, aren't very complex when they have to be born.

    Yes, HERVs are related to cancer. This occurs naturally. They act in a transposon-like manner, and they can pop into areas where they either damage mechanisms that prevent cancer or control cell replication. If we don't study these viral remains, we won't learn about them, won't learn what we can safely disable further -- and what we don't dare eliminate from our genome because we are dependent upon it.

    These researchers were not Dr. Frankensteins, messing with things man was not meant to know. They were careful, they were deliberate, and theya re beginning the investigation into what could be an incredibly crucial topic in molecular biology.

    Remember -- these are viruses that we learned to live with, more or less. By studying them, we can learn to mitigate the damage they still present.

    • Re:HERVs: 8% of Human Genome (Score:4, Interesting)

      by the_humeister ( 922869 ) on Wednesday November 01, 2006 @09:41PM (#16683393)
      Kind of raises the quesion: if we were able to strip out all of this excesses DNA, would the resulting DNA still be useful?

      • Hell yes! I removed all that crap and compiled my DNA with -O4 -funfold-proteins -march=ubermensch and now I can flip a VW bus with one hand and paint fences with my mind! w00t!

        • Ah, so they finally ported Gentoo to humans?
        • and now I can flip a VW bus with one hand and paint fences with my mind! - isn't that the result of your DNA changing you into a one handed balloon-headed person?
      • From the parent:

        "One of these retroviral proteins permits implantation of the placenta. Without it, we'd all have placentas that don't attach to the uterine lining -- like mice, which as a result, aren't very complex when they have to be born."

        I'd be willing to guess that you'd have quite a different creature on your hands.
        • In which case, that part is not junk DNA - it is a gene, coding for a useful protein, which we wouldn't strip out (at least, not on purpose.)

          I'd like to know whether it's possible to strip out the transposons and transposon-like sequences - if they can insert into cell-management areas, causing cancer, then if we genetically modified ourselves to not have them, or not to express them, incidence of cancer should plummet.

    • Re: (Score:2)

      by Renraku ( 518261 )
      I read something the other day saying that a lot of people are infected with the same virus that causes genital herpes, but its in an inactive stage and will probably never activate, because their body keeps it in check.

      Something like 40% of the population has it, whereas only like 10% of people that have it get the traditional symptoms and pass it on.

      I bet a lot of virii are like this.
    • We can see the common marks the retroviruses left in human and chimpanzee DNA.

      See this paper [pnas.org] for a detailed treatment of how the family tree of the primates can be reconstructed by the retrovirus sequences in our genes.

      Pretty much the only available response from the ID crowd is that God created false evidence to test our faith.

    • Re: (Score:3, Insightful)

      by thefirelane ( 586885 )
      The resultant virus was disabled so that, after replicating once in a cell, the daughter viruses could not replicate. So there was no risk.

      Life will find a way.... have you learnt nothing?
    • "No Risk"
      By no means do I suggest that these researchers necessarily acted dangerously or that their research and research like it should be stopped, but I have to say that complex efforts with potentially "devastating" [your term] results should not be reassured against with phrases like "there was no risk". Your explanation of "The resultant virus was disabled so that, after replicating once in a cell, the daughter viruses could not replicate" only inspires a dubious curiosity for how this was done.

      Indee
      • but what the hell do I know? Well, more than someone saying 'virii', by a long shot

              About grammar, probably. But I'm willing to bet you don't know shit about virii :)

              We say virii because our professors said virii. That's just the way it is.
      • I didn't use "virii." Someone else did. I'm not the world's greatest proofreader, but "virii" just sounds obnoxious. It's what most of my biochemistry professors used, and the same can be said for a lot of physicians I've worked with over the years. I just don't happen to like the sound of it, and so I go with the preferred version. If you're going to call someone ignorant, what about the person who accuses the wrong individual? Pulling up grammar in a biology/biochemistry argument is pedantic and ignorant.
        • We're arguing about grammar, and this ignores the most fundamental point:

          This is Slashdot.

        • "I'm frightened by the hordes that wish to stop all research because of mythical scenarios that don't even make sense."

          I think it's the "what if you're wrong" question that worries people.

          Sure, if your calculations are correct then yes, there is no risk, but if not.....
          • But it shouldn't.

            No one worries about people writing kernel code, accusing them of being "Dr. Frankensteins" because they might accidentally create a virus that will escape their machine, infect the Pentagon, and launch all our nuclear missiles.

            Biological viruses aren't any more magic than their machine counterparts.
            • We created the kernel, it's something that can be entirely understood by humans.
              We did not create life, it's something that cannot be entirely understood by humans.

              For every question abut kernel issues, someone knows the answer. The same is not true of biological scenarios. In this way, biological viruses are more mysterious, and that mystery opens the margin of error wider than some believe acceptable.
    • The resultant virus was disabled so that, after replicating once in a cell, the daughter viruses could not replicate. So there was no risk.


      Better: So the only risk was that someone messed up and the disabling mechanism didn't work.

      (Sorry, I've been a software engineer for too long, pessimism comes with the trade I guess)
      • Actually, being in a P3 lab, there were other safeguards.

        In working with fissionables, the usual goal is 3 fault tolerance. In other words, you make three mistakes and they don't combine to create "bad." A P3 lab is, in and of itself, 3 fault tolerant, the damage done to the virus was simply an added, extra layer.

        If anything, it was overkill on the safety measures. I can't blame them for that.

    • In this particular case, there were 30 copies of the virus in the genome. They worked backward to create the original virus. The resultant virus was disabled so that, after replicating once in a cell, the daughter viruses could not replicate. So there was no risk.

      Unfortunately, they used African sex-changing frog DNA to fill in the gaps and the daughter viruses chemically adjusted themselves to reproduce! Fortunately, the resultant virus is only dangerous to users of AOL and Xanga.
    • These researchers were not Dr. Frankensteins, messing with things man was not meant to know.

      No? Well, TFA says

      "Richard Ebright, a molecular biologist at Rutgers University in New Jersey, says any study that creates new viruses or activates old ones should be subject to a special review at the national or international level. What's more, he says, because the researchers couldn't be absolutely sure about Phoenix's infectivity, the study should have been carried out under Biosafety level 4 conditions--t
      • Ebright might say it, but does that make it right?

        The researchers weren't sure about the infectivity of the virus...they weren't sure it would be infective at all. This is a virus that was beaten by evolution and became a pet:

        In addition, the researchers showed that Phoenix could form particles capable of infecting mammalian cells in culture. Infectivity was very low, presumably because host cells have evolved mechanisms to resist uncontrolled virus propagation, as has been repeatedly observed for retrov

  • Relax... (Score:2, Funny)

    by Anonymous Coward
    What could possibly go wrong?!
  • With all the comments on junk DNA and non-functioning parts of the genome, its pretty clear than M$ has learned from mother nature and uses a similar development strategy for their code. No wonder Windows is so robust.
  • http://www.sysinternals.com/Utilities/RootkitRevea ler.html [sysinternals.com] has a tool that can help flesh out all those registry and file system API discrepancies for further study.

    Of course it's always safe to run AdAware[ http://www.lavasoft.com/ [lavasoft.com] ] and if you have the budget, purchase WebRoot[ http://www.webroot.com/ [webroot.com] ] for a fast, centralized cleaning in the enterprize environment.
  • So when does the virus mutate and start to gestate in humans? I hear that date for colonization is coming soon (December 21, 2012), and the secret government needs more clones. Oh whats that, it's just the hanta virus? WTF...?
  • I'm mostly frozen retrovirus genome?

    (OK, I don't know how to continue from here....)
  • Viruses don't live.
    They don't eat, excrete, convert energy, grow, reproduce or respond to stimuli.
    So they can't be brought back to life.

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