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A Truly Alive Virus

Posted by michael on from the cross-breed dept.

cyclop writes "Microbiologists are puzzled by the genome sequence of the giant Mimivirus. It seems this virus has even more genes than many bacteria, is able to synthesize its own proteins and therefore is, by definition, alive. 'We are seeing an organism here. There is DNA, RNA and plenty of proteins,' says Didier Raoult, who reports the work in this week's Science."

67 comments

  1. Mimi Bobeck by Anonymous Coward · · Score: 0

    The Mimivirus makes bespectacled Cleveland department store workers very sick, and it is known for its extremely garish appearance.

  2. The articles didn't mention the other... by dpilot · · Score: 1, Funny

    name for the Mimivirus - Slashdotter

    --
    The living have better things to do than to continue hating the dead.
  3. Aha! by Black+Parrot · · Score: 2, Funny


    Now we know what happened to the missing human genes.

    --
    Sheesh, evil *and* a jerk. -- Jade
  4. Um, no.... by slowtech · · Score: 3, Interesting

    Having DNA coding for a lot of proteins does not make a virus alive. This virus has a lot of DNA (the poxvirii do as well), but that does not mean it has a metabolism. Virii use their host's metabolism to produce proteins.

    Whether you think virii are alive or not, there is nothing about this virus that suggests (from the linked PubMed abstract) that this virus is qualitatively different from any other.

    --
    "Well it's not Victory - but then it's not Death either."
    1. Re:Um, no.... by shpoffo · · Score: 1

      Can anyone share an insight as to how a virus uses the host's matabolism to make proteins?

      thanks

      .
      -shpoffo

    2. Re:Um, no.... by Ayaress · · Score: 3, Insightful

      Well, most viruses just have DNA or RNA. They enter a host cell, and the host (or more particularly, the polymerase and ribozomes in it) then proceeds to treat the new DNA as its own, producing the proteins incoded in it, which is mostly things like the protein "package" for the viral DNA. Viral DNA lacks the control sites that prevents normal cells from overproducing any particular protein, so the cell will continue to produce the viral proteins until it dies.

      However, this virus is unique in that it can produce at least some of its proteins without a host cell. It's not much, but its still metabolism, so it is alive by definition. However, from what I read in the cnrs.fr link from the article, it sounds like it can't, among other things, produce its own ribosomal RNA (feel free to correct me if I'm wrong, I haven't had biology since high school and there are some big words in that article), so its still dependant on host cells for reproduction, which makes it a virus by definition.

    3. Re:Um, no.... by William+Tanksley · · Score: 1

      Your wording is a little ambiguous. This virus carries information to produce these protiens, so it doesn't depend on the host cell's protiens; however, it can't produce them itself.

      It's NOT metabolism by any definition; it's just more information than is common.

      -Billy

    4. Re:Um, no.... by Ayaress · · Score: 1

      Really late reply since I was out of town on the weekend, and you'll never read this, but read the article before you act stupid. It does produce the proteins itself. Over 100 of them. Read that carefully. It produces the proteins by itself, without any help from a host cell. Furthurmore, it produces protiens by itself from more genes than most viruses have at all.

  5. Size? by tod_miller · · Score: 2, Interesting

    I thought the amount of genes didn't matter (could be junk genetics?)

    Remember the Macro-virus on Voyager? [IANAT]

    I didn't realise that Viruses weren't 'alive'...

    Since the 1960s, scientists have argued about whether viruses are living organisms or just a bundle of very large molecules.

    aaaah so - definition of life...

    Then the truly dumb dumb dumb stuff:

    A virus has to hijack another organism's biological machinery to replicate, which it does by inserting its DNA into a host. Bacteria, on the other hand, carry all that they need to reproduce independently, and thus qualify as alive.

    Well oil my ovaries, auto-reproduction [there might be a better word for it] here I come! [I am alive right?]

    OK I realise they don't mean asexual reproduction is the only way of being able to reproduce on your own.

    I guess some /.'ers could only reproduce by infecting someone elses DNA!! :-)

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    1. Re:Size? by A+beautiful+mind · · Score: 1

      "A virus has to hijack another organism's biological machinery to replicate, which it does by inserting its DNA into a host. Bacteria, on the other hand, carry all that they need to reproduce independently, and thus qualify as alive."

      YESSSSSSS

      By this definition, the recording industry is DEAD! We just need to decide if virii is on the same level as them, or higher.

      --
      It takes a man to suffer ignorance and smile
      Be yourself no matter what they say
    2. Re:Size? by aminorex · · Score: 2, Funny

      If the gender balance of Slashdot is as similar to
      the gender balance in my upper division undergrad
      science courses as I think it is, the vast majority
      of /.'ers could only reproduce by infecting someone
      else's DNA.

      --
      -I like my women like I like my tea: green-
  6. 3 categories of life... by tod_miller · · Score: 2, Funny

    Although biologists sometimes divide life into three categories,

    Alive, dead, and that feeling you get at 3pm on a Sunday afternoon....

    Or:

    Us, them, and my little friends in the test tube...

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    #hostfile 0.0.0.0 primidi.com 0.0.0.0 www.primidi.com 0.0.0.0 radio.weblogs.com
  7. Spelling nazi by Anonymous Coward · · Score: 2, Funny

    Check dictionary.com. The proper plural for virus is viruses. It is not "virii". Those who use silly false plurals end up looking like ignoramii.

  8. Evolution proof ? by Jesrad · · Score: 4, Interesting

    This virus is not yet self-reproducting, but I think it might just evolve a bit more and complete that last step. It's a nice demonstration of evolution in action, I think.

    --
    Maybe we deserve this world ?
    1. Re:Evolution proof ? by Anonymous Coward · · Score: 4, Interesting


      This virus is not yet self-reproducting, but I think it might just evolve a bit more and complete that last step. It's a nice demonstration of evolution in action, I think.

      Perhaps it was once a bacterium which lost its selfreproductivity in a bid to maximize parasitivity.

    2. Re:Evolution proof ? by Ayaress · · Score: 3, Interesting

      Perhaps it was once a bacterium which lost its selfreproductivity in a bid to maximize parasitivity.

      Evolution or not, that would have been my first guess, too, from its size and the volume of its genome. However, if that were the case, you'd expect the genes it does have to be like their equivalents in bacteria, which isn't the case. The cnrs.fr link says that it shares key gene sturctures in common with viruses like smallpox.

      An interesting possibility would be that it's actually a sort of "hybrid." A mutation in the protien structure of the viral coat might cause the abnormally large size (a reduction in the bonding angles, perhaps), allowing for the fused genome of the host bacterium and the original virus, along with various key molocules from the bacterium to all be packaged into the virus, instead of just the viral DNA alone.

    3. Re:Evolution proof ? by DrKyle · · Score: 3, Informative

      A mutation in the protien structure of the viral coat might cause the abnormally large size (a reduction in the bonding angles, perhaps), allowing for the fused genome of the host bacterium and the original virus, along with various key molocules from the bacterium to all be packaged into the virus, instead of just the viral DNA alone.

      It's long been known that the viral coat proteins can only accept a certain amount of DNA to be packed inside them. A good example of this is the use of Lambda libraries 10 years or so ago which could only hold maybe 10 to 15kb which had to be removed from the viral genome first to make space. The idea that a mutation which allows this virus to hold more is a good one. If you have the room to store something, and events such as integration, excision and recombination allow for your genome to increase in size when infecting a cell, then the genome will increase in size. Just like anything in life: glove compartments, houses, hard drives - when you get more space you end up filling it rather quickly.

      But to say this virus is, or even could be either evolving towards bacterialhood or evolving away from it is quite ludicrous. Sure, you can have a bacteria with less than 300 genes, but those themselves are forced to live as obligate parasites. Even if this virus did manage to get just the right combination of genes which could allow it to "live" outside of a host, it would be like giving me blueprints to build a radio on a deserted island - useless, the virus doesn't have the machinery to use the information itself.

    4. Re:Evolution proof ? by Anonymous Coward · · Score: 0

      I don't think it is, at least no more so than any other virus with different traits.

      If this was the first organism around, it wouldn't be able to pass on its genes and would die out. Assumably viruses evolved as parasites from single celled organisms, and shed as much redundant stuff as they could.

      I don't think there's any way for this thing to evolve from something further from being self reproducing to where it is (in the absence of something to hijack).

      (I'm assuming you mean life emerging from nothing and evolving from there. If not ignore this.)

    5. Re:Evolution proof ? by e7 · · Score: 1

      You obviously never watched Gilligan's Island.

      --
      Corollary to Moore's Law: The IQ of new computer owners is declining.
  9. It's called VIRUSES not virii by hankwang · · Score: 4, Informative
    This virus has a lot of DNA (the poxvirii do as well)

    That geeks write "virii" in l33tspeak when they talk about computer viruses is one thing, but it's worse when this spelling pops up in scientific discussions. The plural is VIRUSES!

    If you follow latin rules for constructing the plural form, it would still be viri with a single i at the end.

    --
    Avantslash: low-bandwidth mobile slashdot.
    1. Re:It's called VIRUSES not virii by slowtech · · Score: 1

      Good point. I wasn't sure, but I was under the impression that both virii and viruses were acceptable. I was just trying to make it consistent - I didn't check.

      s/virii/viruses/g

      --
      "Well it's not Victory - but then it's not Death either."
    2. Re:It's called VIRUSES not virii by FFFish · · Score: 2

      Spelling it "virii" is A LOT MORE FUN than sticking to "viruses."

      Sheesh. Loosen up some!

      --

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      Don't like it? Respond with words, not karma.
    3. Re:It's called VIRUSES not virii by Alsee · · Score: 1

      My boxen have virusen!

      Ok it's lame joke, but not any lamer than whining about the plural of virus.

      -

      --
      - - You can't take something off the Internet! That's like trying to take pee out of a swimming pool.
    4. Re:It's called VIRUSES not virii by KanshuShintai · · Score: 1

      If you follow the latin rules it would be "virus", with a long mark over the 'u'. "Virus" is a fourth declension noun; the the second declension nouns are the ones that end in a long 'i' for their plural form.

      Either way, in English it's "viruses", though "virii" may as well be used as the plural for computer viruses, since it's come into such common useage.

    5. Re:It's called VIRUSES not virii by almightyjustin · · Score: 1

      Virii is completely bogus, but viri isn't valid either. That link is probably showing the genitive (standard practice for Latin dictionaries), not the plural. Virus was an uncountable noun in Latin (just like "slime" is in English), so the only possible plural in English is viruses. Check this out for an in-depth discussion.

      --

      Omnes arx vestrum sunt adiuncta nobis.

    6. Re:It's called VIRUSES not virii by Anonymous Coward · · Score: 0

      geeks write "virii" in l33tspeak...
      If you follow latin rules...

      Why not follow the geek rules? Are latin speakers somehow superior to geeks?

    7. Re:It's called VIRUSES not virii by Nutria · · Score: 1

      Sheesh. Loosen up some!

      Thank you, FFFish, for telling this to those humorless bastards.

      --
      "I don't know, therefore Aliens" Wafflebox1
    8. Re:It's called VIRUSES not virii by Anonymous Coward · · Score: 0

      There is no plural form of virus in latin, so giving it a latin plural is silly in any case.

      I assume that's why we don't use a latin plural for virus but we can for octopi (but octopuses is also correct). Who knows, maybe I'm wrong.

      P.S. - after looking it up in my dictionary I found the entry "virus -i", which makes it a second declension noun, not fourth.

    9. Re:It's called VIRUSES not virii by NonSequor · · Score: 1

      I've never seen any solid evidence to support the idea that it's a fourth declension noun. It's possible but not certain. From what I've seen it's an irregular neuter second declension noun declined as

      Nom: virus
      Voc: virus
      Acc: virus
      Gen: viri
      Dat: viro
      Abl: viro

      Regardless, it is neuter and one of the most consistent rules in Latin (and most of Latin's rules are very consistent) is that the plural nominative, vocative, and accusative forms of neuter nouns all end in -a. If it were a fourth declension neuter noun it would be pluralized as virua. I believe that all fourth declension neuter nouns have a singular nominative ending in -u anyway (e.g. cornu). Of course, it could be an irregular fourth declension noun, but the only irregular fourth declension noun I know of is domus. This is in contrast with the second declension which has a number of nouns with gender confusion.

      --
      My only political goal is to see to it that no political party achieves its goals.
    10. Re:It's called VIRUSES not virii by YOU+LIKEWISE+FAIL+IT · · Score: 1

      Nerds!

      --
      One god, one market, one truth, one consumer.
    11. Re:It's called VIRUSES not virii by NonSequor · · Score: 1

      I'll take that as a compliment.

      --
      My only political goal is to see to it that no political party achieves its goals.
    12. Re:It's called VIRUSES not virii by Anonymous Coward · · Score: 0

      Sometimes being a nerd is a bad thing. Such as when you're arguing over the latin plural form of an ENGLISH word. Virus might be based off the latin word, but it's not the same word. It's english and the plural is viruses, look it up in any REAL dictionary.

    13. Re:It's called VIRUSES not virii by NonSequor · · Score: 1

      I agree and that's how I pluralize it. But I can't help but join in on these discussions where people are speculating on what the Latin plural would be if it had one.

      --
      My only political goal is to see to it that no political party achieves its goals.
  10. A Large Virus Named Mimi by DLWormwood · · Score: 2, Funny

    What would Drew Carry think?

    --
    Those who complain about affect & effect on /. should be disemvoweled
  11. Um, yes... by contagious_d · · Score: 5, Informative

    "This virus has a lot of DNA (the poxvirii do as well), but that does not mean it has a metabolism. Virii use their host's metabolism to produce proteins....."
    I have this funny feeling you didn't RTFA before you decided that this was a worthless story.
    From Nature: "It can make about 150 of its own proteins, along with chemical chaperones to help the proteins to fold in the right way. It can even repair its own DNA if it gets damaged, unlike normal viruses."

    --
    - /home is where the food is.
    1. Re:Um, yes... by Idarubicin · · Score: 3, Informative
      I have this funny feeling you didn't RTFA before you decided that this was a worthless story.

      I have a feeling the parent didn't read the story closely enough to decide that the grandparent was wrong.

      Nature's phrasing is a bit misleading. Mimivirus, like all other known viruses, requires the protein synthesis machinery of a host cell to reproduce and to carry out the synthesis of the proteins described. (For mimivirus, the hosts are amoebae.) I mean, it's impressively large--it carries a lot of genetic material inside its protein coat, and it's comparable in size to some of the smallest bacteria (mycoplasma)--but it's not alive.

      While the Nature blurb says that "it can make about 150 of its own proteins, along with chemical chaperones to help the proteins to fold in the right way. It can even repair its own DNA if it gets damaged, unlike normal viruses", what they mean is that it carries genes that when expressed by the host cell can carry out those functions. The virus, by itself, can't do protein synthesis, so it can't make the proteins that carry out DNA repair or other described functions.

      It's very interesting and unusual for a virus to carry genes for these functions--all other known viruses rely on their hosts to provide them, or do without--but it definitely doesn't make the virus alive. The grandparent poster is quite right, and it's made quite clear in the linked PubMed abstract to the original Science article. The Nature piece is in their News section, written by a staff writer. It's not a peer-reviewed article, and the terminology is regrettably confusing.

      --
      ~Idarubicin
    2. Re:Um, yes... by contagious_d · · Score: 1

      Ahh, you are right. I still think the great grandparent is wrong though, as his whole point was that this virus was not significantly different from other viruses.

      --
      - /home is where the food is.
  12. Look who just got on the clue train. by Anonymous Coward · · Score: 0

    See the very first post. Been there, done that.

    1. Re:Look who just got on the clue train. by DLWormwood · · Score: 1

      Funny, even though I browse with a "+1" for Anonymous posts, I didn't see that one... Maybe it was briefly modded down?

      --
      Those who complain about affect & effect on /. should be disemvoweled
    2. Re:Look who just got on the clue train. by Anonymous Coward · · Score: 0

      Try browsing at zero or -1, not +1. Thanks.

    3. Re:Look who just got on the clue train. by DLWormwood · · Score: 1
      I browse so that Anonymous posts get a "+1" (just like registered users), which should do the same thing.

      Or is there a bug in Slashcode that breaks this?

      --
      Those who complain about affect & effect on /. should be disemvoweled
  13. What is the plural of virii? by Anonymous Coward · · Score: 0

    It's viriii, right?

    1. Re:What is the plural of virii? by Anonymous Coward · · Score: 0

      No, read the grandparent carefully. He clearly says its \/1|2ll.

    2. Re:What is the plural of virii? by Anonymous Coward · · Score: 2, Funny

      The whole sequence of plurality is something like: viri, virii, viriii viriv, virv, virvi, virvii, virviii, virix, virx, virxi, et c.

    3. Re:What is the plural of virii? by Anonymous Coward · · Score: 0

      I know for sure that emacsii is alive and assimilating.

  14. Living Virus by delta_avi_delta · · Score: 1

    ... I'm not convinced it's alive. Certainly it's perkier than a prion, but...

  15. Living computer virus by Knights+who+say+'INT · · Score: 2, Funny

    How many people thought this was an interesting AI-based computer virus, perhaps employing genetic algorithms?

  16. Plurals, Latin, Greek, Us v Them by Anonymous Coward · · Score: 0

    If you follow latin rules for constructing the plural form, it would still be viri with a single i at the end.

    Latin Rules? It's GREEK you should look at.

    If it ends in -is, then the plural is -i
    If it ends in -us, then the plural is -ii

    IIRC,
    IANAG (I am not a Greek)

    1. Re:Plurals, Latin, Greek, Us v Them by hankwang · · Score: 1
      Latin Rules? It's GREEK you should look at. If it ends in -is, then the plural is -i. If it ends in -us, then the plural is -ii

      You are trolling: Inflection of substantives. Besides, there is no letter V in Greek.

      --
      Avantslash: low-bandwidth mobile slashdot.
    2. Re:Plurals, Latin, Greek, Us v Them by Anonymous Coward · · Score: 0

      There isn't in Latin either. There is a consonant sound u (as well as a vowel sound u). It's commonly written as a v, and it makes a w sound.

    3. Re:Plurals, Latin, Greek, Us v Them by Anonymous Coward · · Score: 0

      IT doesn't come from Greek..it comes from the Latin word meaning 'poison'

    4. Re:Plurals, Latin, Greek, Us v Them by Anonymous Coward · · Score: 0

      You are trolling: Inflection of substantives. Besides, there is no letter V in Greek.

      HAHAHAHAHAHA you sure made that guy look stupid!

  17. The Mimi virus by tcc · · Score: 0, Redundant

    Let's wait till Drew gets a hold of this :)

    --
    --- Metamoderating abusive downgraders since my 300th post.
  18. Re:Um, yes.... by VendingMenace · · Score: 4, Informative

    It is quite simple, really. The virus enters the host cell. From there it uses the hosts machinery (enzymes, ribozyme, protiens, ect) to carry out the replication of the viruses DNA (or RNA whatever the case may be).

    However, the virus is not just bare DNA or RNA (gennerally). It also contains a protien coat on the outside that serves to hold and protect the virus genome. So this too must be made in great quantities to hold all the vast numbers of genomes that have just been copied.

    So, in order for a virus to replicate in a cell, it must use the cells system to make BOTH the nucleic acid synthesis AND the protiens for the coat around the virus.

    Since this process of protien sythensis uses energy, the virus IS using the cells matabolism to make protiens.

    I hope that answers your question. :)

  19. Oh Great! by Sean+Johnson · · Score: 1

    Now we have to attribute and possibly congradulate the lowest scum of the earth (virus writers) for making possible real artificial intelligence. I can just see these virii as the stepping stones towards self-awareness in computer networks. Who'da thunk it!

    --
    >>>>>> Chewie, take the professor in the back and plug him into the hyperdrive.
  20. Doesn't produce own proteins outside of a cell by Bowling+Moses · · Score: 3, Informative

    From the Science article: "Surprisingly, Mimivirus genome sequence now reveal genes relevant to all key steps of mRNA translation: tRNA and tRNA charging, initiation, elongation and termination, with the exception of ribosome components themselves." I'm sure many people knew that when the Nature News link said "Mimi carries about 50 genes that do things never seen before in a virus. It can make about 150 of its own proteins, along with chemical chaperones to help the proteins to fold in the right way." they meant within a host cell, but I'm sad to say I didn't get that right away. I really should have--there's a guy in the lab next door who does EM and crystallography on virus particles so I know that the inside of a virus capsid is ~crystaline DNA or RNA so no protein production would be expected to take place within the capsid itself.

    Mimivirus does contain a lot of weird, weird stuff for a virus, including a number of DNA repair proteins, and truly bizarre, protein folding chaperones and a proline cis-trans isomerase. Doesn't make a damn bit of sense to me, but it'll be interesting to find out why it has them.

    Oh yeah. You know it's news when Science gives you 13 freakin' pages for your stuff as opposed to the usual miserly 3.

    1. Re:Doesn't produce own proteins outside of a cell by Muhammar · · Score: 1

      Mimivirus does contain a lot of weird, weird stuff for a virus, including a number of DNA repair proteins, and truly bizarre, protein folding chaperones and a proline cis-trans isomerase. Doesn't make a damn bit of sense to me, but it'll be interesting to find out why it has them

      Mimi is packed for a long trip. He knows, where he has his towel.

      --
      I doubt that we will ever figure out - and I suspect that even if we did figure out we couldn't do much about it
  21. Initial Report of the Mimivirus by xplenumx · · Score: 1
    For those interested in a bit more background on the Mimivirus (and have access to Science's archives), you can check out the group's previous report on the virus at:

    La Scola B, Audic S, Robert C, Jungang L, de Lamballerie X, Drancourt M, Birtles R, Claverie JM, Raoult D (2003) A Giant Virus in Amoebae. Science 299(5615):2033

  22. Its a bitch by Anonymous Coward · · Score: 0

    science/Evolution is a bitch isn't creationists!

  23. parthenogenesis by Anonymous Coward · · Score: 0
    Well oil my ovaries, auto-reproduction [there might be a better word for it] here I come! [I am alive right?]

    it's called parthenogenesis.

    interresting stuff, but it's a touchy subject in most major scientific circles (which tend to be somewhat male dominated -- coincidence?)

  24. Hmmm DNA computer template? by merlin_jim · · Score: 2, Interesting

    Wow this virus is self contained, has 800 kilobase pairs, can replicate its own proteins, uses a circular genome (think of a turing machine tape), and is capable of DNA self-repair, unlike every other organism in the world. And the scientists believe that over 90% of its DNA is actively used throughout its lifecycle.

    Sounds like an ideal building block for a genetic computer. I'm half-seriously wondering based on that 90% figure if it is in fact the left over of some pre-historic genetic computer?

    There are more mysteries here; the virus has genes common to all cellular life, but it itself is clearly not cellular. Unless this virus is a close relative of some precursor virus that initially combined with a bacteria to from the first nucelied cell, then this is an EXTREMELY improbable occurance.

    I mean form follows function, but in this case the form is present but not necessarily the function... parallel evolution doesn't really explain that...

    All the same, if I was a genetic computing microbiologist I'd be very interested in this guy...

    --
    I am disrespectful to dirt! Can you see that I am serious?!
    1. Re:Hmmm DNA computer template? by William+Tanksley · · Score: 1

      and is capable of DNA self-repair, unlike every other organism in the world.

      Pardon, but every organism in the world does DNA self-repair. If they didn't there would be almost NO succesful reproduction. von Neumann considered self-repair to be one of the three crucial elements of a self-preproducing machine (the other two are reproduction and self-diagnosis).

      And I'm not sure what you meant, but this virus doesn't replicate its own proteins -- it simply has the instructions for its own proteins encoded in it. Most viruses just depend on the cell having some that are close enough.

      -Billy

    2. Re:Hmmm DNA computer template? by merlin_jim · · Score: 1

      Pardon, but every organism in the world does DNA self-repair. If they didn't there would be almost NO succesful reproduction. von Neumann considered self-repair to be one of the three crucial elements of a self-preproducing machine (the other two are reproduction and self-diagnosis).

      I was unaware of that. However, this is still unique in that its a virus that does DNA self-repair...

      --
      I am disrespectful to dirt! Can you see that I am serious?!
  25. Is this the start of a new mememememe... by eno2001 · · Score: 1

    mememememememememe. Hehehe. I couldn't resist. ;P

    --
    -"...bad old ideas look confusingly fresh when they are packaged as technology" - Jaron Lanier (Digital Maoism on Edge.o
  26. Re:3 categories of life... oblig quote.. by talaphid · · Score: 1

    Alive, all dead, and mostly dead... "There's only one thing you can do if they're mostly dead [...] check their pockets for loose change."