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Science

Hints of Life's Start Found In a Giant Virus 158

Posted by samzenpus
from the that's-a-big-one dept.
An anonymous reader points out this update on the world's largest virus, discovered in March. Chantal Abergel and Jean-Michel Claverie were used to finding strange viruses. The married virologists at Aix-Marseille University had made a career of it. But pithovirus, which they discovered in 2013 in a sample of Siberian dirt that had been frozen for more than 30,000 years, was more bizarre than the pair had ever imagined a virus could be. In the world of microbes, viruses are small — notoriously small. Pithovirus is not. The largest virus ever discovered, pithovirus is more massive than even some bacteria. Most viruses copy themselves by hijacking their host's molecular machinery. But pithovirus is much more independent, possessing some replication machinery of its own. Pithovirus's relatively large number of genes also differentiated it from other viruses, which are often genetically simple — the smallest have a mere four genes. Pithovirus has around 500 genes, and some are used for complex tasks such as making proteins and repairing and replicating DNA. "It was so different from what we were taught about viruses," Abergel said. The stunning find, first revealed in March, isn't just expanding scientists' notions of what a virus can be. It is reframing the debate over the origins of life."
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Hints of Life's Start Found In a Giant Virus

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  • by cirby (2599) on Thursday July 10, 2014 @06:48PM (#47428229)

    "It was so big we had to sterilize our lab equipment with a hammer."

    • by meglon (1001833)
      Pfft. Ours was so big... well... does the phrase "take off and nuke it from orbit" mean anything to you?
  • by aeschinesthesocratic (1359449) on Thursday July 10, 2014 @06:57PM (#47428279)
    How do viruses reproduce without complex lifeforms in which to do so? If it reproduces on its own, I don't think pithovirus can be classified as a virus. Then, in that case, what separates pithovius from the prokaryotes?
    • by ColdWetDog (752185) on Thursday July 10, 2014 @07:05PM (#47428313) Homepage

      It can't reproduce entirely on it's own, so it's not 'free living'. It does need a host. It's just it doesn't need the host for some of the tasks that most viruses need the host for.

      It would seem that, instead of being a primitive form that was at the base of the the genetic tree, it's more likely to be an offshoot. It hijacked some additional molecular machinery from an extant organism rather that figuring it out on it's own.

      • Doesn't this then lead us to a bootstrapping issue?

        If life started with a giant virus, and viruses reproduce by infecting living creatures... wence life?
        • Life started due to a discarded sandwich by a distracted timetraveler.

        • by RockDoctor (15477)

          If life started with a giant virus, and viruses reproduce by infecting living creatures... wence life?

          "Whence." Your spelling checker needs switching on.

          That is one of the discussions elaborated in TFA : did viruses initially need life forms to replicate on? Or did they force the development of modern life forms. Or ... was there an earlier form of organism, distinctly different from modern cells (post-3.5Ga ago) and modern viruses (also post-3.5Ga ago) which held an intermediate position between modern ce

      • by ColdWetDog (752185) on Thursday July 10, 2014 @07:20PM (#47428385) Homepage

        Oh, now I went ahead and read TFA. It's all complicated and confusing.

        The current thinking is indeed that viruses are an offshoot of 'modern' life (modern being sometime after the archea). These critters, because they contain gene sequences that seem to predate the prokaryote - eukaryote split and because we know that bacteria just love to transfer genetic information 'horizontally' - that is by tossing bits of DNA and RNA around so some unrelated organism can incorporate it into their genetic apparatus as opposed to simply eating it - that it may be that these big viruses started sometime after the RNA hypothesis took hold and created the first self replicating organisms. Or at least helped those first 'organisms' diverge and multiply.

        At least it's a testable hypothesis. Once you have sequenced a number of the big virus genes and compare them you would presumably get an idea how old they are.

        It would seem that even if this mechanism held, the critters would have had a long time to morph into another ecological niche so it would be hard to pin down what their function was (if any) at the beginning of life. But perhaps the Central Dogma is barking up the wrong tree after all.

    • by radtea (464814) on Thursday July 10, 2014 @07:09PM (#47428331)

      Then, in that case, what separates pithovius from the prokaryotes?

      Structure, from the sound of it, although mostly this is people committing various fallacies of reification and making false claims of "natural kinds".

      Everything is a continuum. Humans divide the continuum up using acts of selective attention. The only infinitely sharp edge is the edge of our attention (because we scale the edge to match the scale we are attending to, so whatever scale we are attending to seems to have a sharp division between the things we are selecting out.)

      "Species" do not have particularly crisp boundaries in the general case: they fade into each other, and we draw edges around them in more-or-less arbitrary ways. When we find new varieties we can either create new categories (by drawing new edges) or lump them into old categories (by moving old edges). Which move is to be preferred depends on the purposes of the knowing subject.

      • by rgmoore (133276)

        Everything is a continuum.

        That is an exaggeration. Things grow as a continuum, but they can get separated when the parts in the middle die off. You wind up with a branched structure because things really can get far enough separated that when the middle dies off they can't reconnect. For example, mammals really are distinct from other tetrapods because the forms that connected them died off and they've been developing in different directions ever since.

      • by Dan East (318230)

        Everything is a continuum. Humans divide the continuum up using acts of selective attention

        Your generalization is quite wrong. Humans classify organisms based on the evidence in front of them. Can you show me this continuum between a platypus and some other animal? How does that fit into the "everything is a continuum" that you speak of?

        "Species" do not have particularly crisp boundaries in the general case:

        Uh, they most certainly have extremely crisp boundaries. Species are classified by the ability of two organisms to breed with one another. There isn't any "crisper" boundary than that. Once two lineages are different enough, it is no longer possible for them

        • by psnyder (1326089) on Thursday July 10, 2014 @10:25PM (#47429115)

          Uh, they most certainly have extremely crisp boundaries. Species are classified by the ability of two organisms to breed with one another.

          The "Species problem" [wikipedia.org] shows this not to be the case. The specific issue you mention is in the introduction:

          "Another common problem is how to define reproductive isolation, because some separately evolving groups may continue to interbreed to some extent, and it can be a difficult matter to discover whether this hybridization [wikipedia.org] affects the long-term genetic make-up of the groups."

          That being said, I was taught the same way as you and only learned differently when I started teaching it myself. Now when I explain classification, I try to intersperse phrases like "usually classified as..." or "One good way to classify it is...". I usually try to reinforce that there are many ways to classify, show them the most common way(s), and encourage them to make their own classifications if those ways fail. This is especially prevalent in biology where phylogenetics [wikipedia.org] (usually based on RNA, dividing groups into clades) is currently intermixing with more traditional taxonomy [wikipedia.org] (usually based on morphological traits, dividing groups into Linnaean classification)[1] [wikipedia.org].

        • platys and swordtails are different species and they interbreed without any hassle.

        • by PhilHibbs (4537)

          Consider the continuum as it extends over time and space. Everything is and/or was a continuum, but occasionally holes and tears in the continuum occur that cause the appearance of hard distinctions between species.

    • Great questions, I have come to believe that a virus is not a life form. Its only role is to transfer segments of DNA from one life form to another. It is how information is sent without individual contact.Is very important part of evolution because it saves time.
    • by Anonymous Coward on Thursday July 10, 2014 @07:16PM (#47428361)

      There are many differences between viruses and prokaryotes, but the main thing that seperates them from life is that they don't have ribosomes (https://en.wikipedia.org/wiki/Ribosome). Ribosomes are necessary for the production of proteins and no known virus encodes thier own ribosomes (they use the ones from their host cell). Some viruses, such as the one mentioned in the link, do encode genes to make some tRNA (needed for translating the genetic code into protein).

  • the others call him Morris Worm.

  • I for one welcome our new viral overlords.

  • Maybe at some point we'll regard this thing as being on a continuum from mis-folded proteins to intelligent life such as whales. In the meantime, people will argue about whether or not it's really a virus.

  • by Anonymous Coward

    Don't thaw it out! I've seen the the BLOB movie, I know how this turns out...

  • 30,000 years? (Score:5, Interesting)

    by Tablizer (95088) on Thursday July 10, 2014 @09:43PM (#47429015) Journal

    The sample being 30,000 years old doesn't seem significant because it's quite recent relative to the history of life, and even primates. The same kind of virus or a close relative is probably still around and the sample age probably has nothing to do with its size, but rather a happenstance of observation in that we tend to study old things harder than we do current things, and thus notice more.

  • "Chantal Abergel and Jean-Michel Claverie were used to finding strange viruses..."

    Is this the modern version of, "It was a dark and stormy night..." ?

    • LOL
      I can't mod anymore but if I could you would get a funny.
      Now I want to hear the rest of the novel. :D

  • OK, so I actually RTFA.

    They immediately recognized the organism’s viruslike shape — imagine a 20-sided die, with each face a hexagon

    I'm having a hard time fitting together 20 hexagonal faces. OTOH, the herpes virus is shaped like a regular icosahedron.

    • by PhilHibbs (4537)

      Truncated icosahedron, maybe?

      • by RockDoctor (15477)
        Truncate an icosahedron ... 5 faces at each vertex, so they'll truncate to form pentagons, and the triangular faces would go to hexagons.

        Congratulations. You've just invented the (soccer) football. While channelling Buckminster Fuller.

        • by PhilHibbs (4537)

          It's possible that an organism might resemble the hexagonal parts of a buckyball but not the pentagonal parts if the pentagonal parts are uneven or convex.

          Although this [kameleon.ba] looks just like a normal icosahedron. I can't find a transalation other than an automated one [google.co.uk].

          • by RockDoctor (15477)

            It's possible that an organism might resemble the hexagonal parts of a buckyball but not the pentagonal parts if the pentagonal parts are uneven or convex.

            I can't work out how you can have the hexagonal faces of a buckyball without having the pentagonal faces, since the edges that define the hexagonal faces also define the pentagonal faces. I'm not sure that what you're describing is possible or if you're trying to describe a 5-cornered square.

            Although this [kameleon.ba] looks just like a normal icosahedro

  • I think the summary rather overstates the case. This virus, if a virus it is, doesn't so much hint at the origins of life as it puts a new perspective on the origins of viruses. The origin of life probably lies much further back in time than the emergence of viruses, certainly if viruses are 'degenerated' life-forms, evolved from cellular life.

    Seen in this light, this new virus could be a primitive virus; but it rather begs the question whether 'virus' is actually a well-defined, mono-phyletic group. It see

    • by RockDoctor (15477)
      All of those questions are definitely on the table.

      After the Human Genome was published, I wondered why the fuck Craig Venter went off on his boat to do shotgun PCR on random buckets of seawater. Though this work isn't directly related to that, it's marking Venter's decision to forgo the complexities of culturing organisms as being a truly inspired insight. (And I'm not even a biologist! I deal with dead things and I can see the importance of this choice.)

  • Then merged to become life as we know it. This is a hypothesis proposed by some science scientists like Robert Hazen.
    Although we dont see pre-life metabolic fossils, some viruses could be pre-life reproductive fossils.

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