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Biotech Science

Most of Woolly Mammoth Genome Reconstructed 245

Posted by samzenpus
from the I-want-a-cave-bear dept.
geekmansworld writes "From the Washington Post, 'An international team of scientists has reconstructed more than three-quarters of the genome of the woolly mammoth using DNA extracted from balls of hair, the first time this has been accomplished for an extinct species.' Who wants a pet mammoth?"
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Most of Woolly Mammoth Genome Reconstructed

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  • by Anonymous Coward
    I for one welcome the new hirsute elephantine overlords
  • by thermian (1267986) on Thursday November 20, 2008 @09:01AM (#25831005)

    Given that they have yet to work out how many chromosomes the woolly mammoth had, or which of the DNA features are genuine mutations, and which are artefacts caused by damage since the death of the creatures from whom DNA was extracted, there's a fair distance to go yet.

    Still, I don't doubt this is a seriously fun project to be working on. I'd love to get involved.

    • by sakdoctor (1087155) on Thursday November 20, 2008 @09:09AM (#25831071) Homepage

      Just download god's genome checker.

      [x] Automatically fix chromosome errors
      [x] Scan for and attempt to recover bad base pairs

      • by Alpha Whisky (1264174) on Thursday November 20, 2008 @09:56AM (#25831489)

        Your post advocates a

        (x) technical ( ) religious ( ) time travel

        approach to resurrecting extinct species. Your idea will not work. Here is why it won't work. (One or more of the following may apply to your particular idea, and it may have other flaws.)

        ( ) Possibility of creating mutant monsters
        ( ) We are defenceless against brute force attacks
        (x) People will not put up with giant stampy animals roaming about
        (x) The police will not put up with giant stampy animals roaming about
        ( ) Requires too much cooperation from organised religion
        (x) Requires immediate total cooperation from government regulators
        ( ) Time travel isn't possible
        ( ) Time travel into the past isn't possible without a wormhole which was (is) in the past already

        Specifically, your plan fails to account for

        (x) Laws expressly prohibiting it
        (x) Lack of centrally controlling authority for mad scientists
        (x) We haven't even sequenced the whole genome
        (x) Being sued by Michael Crichton's estate
        ( ) Asshats
        ( ) Jurisdictional problems
        ( ) Unpopularity of weird old animals
        ( ) Public reluctance to accept weird old animals
        ( ) Huge existing animals occupying the evolutionary niche of the old ones
        (x) Susceptibility of DNA to damage
        (x) We don't even know how many chromosomes it should have
        ( ) Unavailability of any living relatives to carry the foetus to term

        and the following philosophical objections may also apply:

        (x) Ideas similar to yours are easy to come up with, yet none have ever
        been shown practical
        (x) Religions will argue about playing god
        (x) Pointlessness of an animal adapted for an ice age during a period of global warming
        ( ) What's dead should stay dead
        (x) There are better things to spend the money on

        Furthermore, this is what I think about you:

        (x) Sorry dude, but I don't think it would work.
        ( ) This is a stupid idea, and you're a stupid person for suggesting it.
        ( ) Nice try, assh0le! I'm going to find out where you live and burn your
        house down!

        • Shouldn't something along the line of "we don't know whether they taste nice" be in there?
          • Re: (Score:3, Informative)

            by vigour (846429)

            Shouldn't something along the line of "we don't know whether they taste nice" be in there?

            There have been some reports of Russians eating frozen Mammoth, but I'm not sure how true that is (I read it somewhere, but I can't remember where).

            Here are some quick links I found on the topic:
            link 1 [straightdope.com]
            link 2 [stupidquestion.net]

            • Re: (Score:2, Interesting)

              by BluenoseJake (944685)
              In the 1800s, members of the royal society had some Mammoth steaks from a frozen beast found in the permafrost in Siberia. They said it tasted like chicken.
        • Re: (Score:3, Informative)

          by ari_j (90255)
          This form needs a section for mitigating factors. Here, at least one applies: (x) Mammoth burgers are delicious.
    • Not to mention... (Score:4, Informative)

      by Moraelin (679338) on Thursday November 20, 2008 @09:17AM (#25831149) Journal

      Not to mention, didn't we also have this story about how the proteins affect the transcription too, and the same piece of DNA can be transcribed in a dozen different ways or not at all, depending on how those proteins regulate it? It seems to me like in that case it's like saying they decoded half of it.

      • Re: (Score:3, Interesting)

        transcription is the process of producing things from DNA, in sequencing like they did you're reading the (static) strains of DNA - not its products. Proteins regulate the expression of DNA, i.e. its products like RNA and proteins - you're confusing the two. To make a comparison: transcription is like running a program to see which data is produced. The data in itself regulates in most software the control-flow of the program and this is your feedback loop. The DNA however is stored on disk, it degrades but
        • Re:Not to mention... (Score:5, Informative)

          by thepotoo (829391) <[thepotoospam] [at] [yahoo.com]> on Thursday November 20, 2008 @11:13AM (#25832277)

          The big achievement here is the defragmentation of all that DNA

          The folks at 454 Life Sciences made reconstructing a genome from lots of little pieces pretty simple by using an algorithm that looks for common fragments (ex AAGGCTTCTA and CTTCTATCTGG probably go together to form AAGGCTTCTATCTGG).

          They also pretty much pioneered modern sequencing techniques.

          The news here (IMHO) is that we've been able to read the genome of an extinct animal. That is an impressive achievement, a few BP errors notwithstanding. If we have multiple copies of the genome (multiple cells), we should be able to figure out what the correct sequence is (mutations are random, and no two cells will have the same mutations). Hair is not exactly the prime target for sequencing due to its exposure to UV light (UV light wreaks havoc on DNA), but with a little work we should be able to the actual sequence.

          So at the end of the day, the Nobel prize goes to the guy who can figure out how many chromosomes a mammoth had. I'd like to say "just use the number that elephants have" but 7 million years (last common ancester) is easily enough time for chromosome duplication to occur.

          • Re:Not to mention... (Score:5, Informative)

            by kmcarr (1185785) on Thursday November 20, 2008 @01:11PM (#25834109)

            The folks at 454 Life Sciences made reconstructing a genome from lots of little pieces pretty simple by using an algorithm that looks for common fragments (ex AAGGCTTCTA and CTTCTATCTGG probably go together to form AAGGCTTCTATCTGG).

            Spoken like one who has never actually tried to assemble a genome sequence. Trust me, there is absolutely nothing simple about it. And while 454 Life Sciences (now a division of Roche Diagnostics) pioneered a new technology for generating raw DNA sequence data they did not pioneer the assembly process. Sequence assembly algorithms are a long and well studied problem.

            They also pretty much pioneered modern sequencing techniques.

            While 454 was first to the market with a next-generation sequencing platform they are currently in heavy competition with the Illumina/Solexa platform. And then there is Pacific Bioscience due to release a platform in 2010 which could eat both their lunches.

            • Re: (Score:3, Informative)

              by thepotoo (829391)

              Well, kmcarr, I bow before your expertise. I've never sequenced a genome, let alone the type of massively parallel sequencing you've done (you're the guy that worked on Arabidopsis sequencing, right?)

              In my defense, however, I only said that 454 had made life a lot easier for people doing sequencing, not that the algorithm itself was simple. I also note that you yourself used their pyrophosphate technique - to say that it's anything but a huge technological leap forward is to undercredit it. I repeat, 454

        • I _know_ the classic theory about DNA being everything, and the proteins just regulating what gets transcribed. What I'm referring to is the recent article linked to even on Slashdot: "The Gene Is Having an Identity Crisis" [slashdot.org], where they claimed that it just isn't so. They claimed exactly what I wrote there: that the same gene can be transcribed in a dozen different ways, based on what those proteins say, and that half your heredity is actually in those proteins.

    • by Hatta (162192)

      They need to be sequencing the Dwarf Mammoth [nytimes.com], that would be a much more viable pet.

  • by owlnation (858981) on Thursday November 20, 2008 @09:04AM (#25831035)
    the numbers of woolly mammoths has tripled in the past six months...
    • Re: (Score:3, Funny)

      by genner (694963)

      the numbers of woolly mammoths has tripled in the past six months...

      They're breeding.....nature finds a way.

      Ummm....where's that helicoptor.

    • Actually, the number of physical mammoths is still zero.

      However, we are reconstructing the source code, and when we succeed, we can compile as many mammoths as we need.
  • by squoozer (730327) on Thursday November 20, 2008 @09:05AM (#25831041)

    As a kid I always thought that Wooly Mammoths died out aroud the same time as the dinosaurs but I heard a while back that they might have been around until a couple of thousand years ago. I now know that man hunted them to the dinosaur date is wrong but when did the last one shed it's mortal coil?

    • Re: (Score:3, Informative)

      My understanding is that the woolly mammoth is one of the first casualty of the infestation Earth by the human species : they went extinct partly because of the warming climate, partly because of overhunting.

      • by SQLGuru (980662)

        Good thing they are thinking about bringing back Neaderthal man, too....
        http://www.statesman.com/news/content/news/stories/nation/11/20/1120mammoth.html [statesman.com]

        Basically the same article but with additional content about Neaderthal DNA, too.

        Layne

        • Re: (Score:2, Interesting)

          by Hal_Porter (817932)

          Neanderthals would make a good servant race, like in Planet of the Apes. What could possibly go wrong.

        • But of course... otherwise we'd be overrun with Mammoths...

          Skinner: Well, I was wrong. The lizards are a godsend.
          Lisa: But isn't that a bit short-sighted? What happens when we're overrun by lizards?
          Skinner: No problem. We simply unleash wave after wave of Chinese needle snakes. They'll wipe out the lizards.

          Lisa: But aren't the snakes even worse?
          Skinner: Yes, but we're prepared for that. We've lined up a fabulous type of gorilla that thrives on snake meat.
          Lisa: But then we're stuck with gorillas!
          Skinner: No,

      • by aliquis (678370)

        They surely must have had genetics to survive warm-ages? If not they must have been a short-lived species.

        • Re: (Score:3, Funny)

          by Hognoxious (631665)

          They surely must have had genetics to survive warm-ages?

          Genetics, no. Gillettes, yes.

          Sadly, things were a bit primitive back then. Instead of the 97 steel blades we have now there was only one - and made of flint at that. By the time the poor creatures had even one leg shaved, they'd died of heat exhaustion.

          And that, children, is why mammoths are extinct.

      • by Whiteox (919863) <htcstech AT gmail DOT com> on Thursday November 20, 2008 @09:51AM (#25831441) Journal

        They were quite recent: They survived on Wrangle Island (Artic) and St Paul Island (Bearing Sea) as dwarfs until 1700 BCE.
        They were also found on the Channel Islands off California and disappeared around 40,000 BCE. They are still digging them up, preserved, in the permafrost of Siberia.
        Humans did hunt mammoths, sabre-tooths etc.

    • There are no stupid questions. But there are stupid places to ask them. Try [google.ie] elsewhere [google.ie], for better sources of information.

      • by owlnation (858981) on Thursday November 20, 2008 @09:47AM (#25831383)

        There are no stupid questions. But there are stupid places to ask them. Try elsewhere, for better sources of information.

        Really? Considering the amount of SEO spam that's corrupted Google search results, considering the cabals, corruption and low quality of most wikipedia results, and considering that many of the world's experts on most science and technology fields ARE regularly reading slashdot, then I seriously doubt there IS ANY better place to ask a science related question than on this site.

        Of course, the downside is that there are some grumpy, elitist pedants here.

        • >Considering the amount of SEO spam that's corrupted Google search results,

          I'll admit that Google isn't as good as it used to be, but it is still very good. Very few of my searches turn up many irrelevant SEOd pages on the first page or two of results. And when you do get a lot of irrelevant results, it is usually pretty easy to filter them out.

          "mammoths die out" (no quotes) gets very good results.

          The wiki also has a decent, if somewhat short article on mammoths. Generally, the wiki articles you have to

      • I think you're looking for this [letmegoogl...foryou.com]
    • by Comboman (895500) on Thursday November 20, 2008 @09:39AM (#25831319)
      Dinosaurs died out 65 million years ago. Mammoths became extinct about 10,000 years ago, though some scientists believe that there were still pockets of mammoth populations on isolated islands as late as 3500 years ago.
    • Mammoths were one of the many large mammal and bird species that went extinct coinciding with the global expansion of man. Even our ancestral cousins, the Neandertals, disappeared abruptly when Cro-Magnon man arrived on the scene. A wave of extinctions descended down through America at about the same time people arrived. The most likely conclusion is that one our Cro-Magnon predecessors learned how to hunt in groups, they tended to kill everything large almost everywhere they went.
  • by Farmer Tim (530755) <<roundfile> <at> <mindless.com>> on Thursday November 20, 2008 @09:05AM (#25831043) Journal

    And I thought cats were disgusting...

  • by oodaloop (1229816) on Thursday November 20, 2008 @09:05AM (#25831045)
    with those from the Tasmanian Devil ala Jurassic Park. What could possibly go wrong?
    • by aliquis (678370)

      Or the myostatin "bug" found in belgian blue? =P

    • Re: (Score:3, Informative)

      by theaveng (1243528)

      Um.... I thought they used frog DNA to fill-in the missing sequences. Which is how supposedly "sterile" dinosaurs were able to give birth.

      • They weren't sterile (obviously). Each and every one was suppose to be female but due to the frog's DNA (and ability to switch genders), well, they got it on, bow chicka and etc.

    • by Chris Burke (6130)

      So you want us to have gigantic mammoths, spinning around at high speed, eating everything they see (especially rabbits)? Are you insane, or just trying to one-up Jurassic Park for doomed-ness?

  • by wytten (163159) <(wytten) (at) (cs.umn.edu)> on Thursday November 20, 2008 @09:10AM (#25831075) Homepage

    It could be the solution of how how to maintain legacy systems in generations to come. They just need to start mapping the genes of a COBOL programmer.

    • Re: (Score:3, Funny)

      by Thanshin (1188877)

      > They just need to start mapping the genes of a COBOL programmer.

      Why would you do that? They are evil!

      Little green scaly evil punks. Always with their traps and their "I'm dragon subtype I can reach godhood before level 6". Bah!

      Mark my words. You'll regret not having cloned griffins first.

      • by Whiteox (919863)

        Almost as bad as those FORTRAN lifeforms. They tend to turn up when least expected and have no idea about micro-computers

    • by DarthVain (724186)

      Pffft. After the fall of man, the only thing left will be cockroaches, and Cobol programmers...

  • There are woolly mammoths in the latest World of Warcraft expansion. They're huge, fierce, and scary looking.

  • http://www.nytimes.com/2008/11/20/science/20mammoth.html?partner=permalink&exprod=permalink [nytimes.com]

    right NOW, we can do this

    apparently it would be tedious, but a number of technical hurdles have been overcome lately to the point where this is really conceivable to do, and the talk about doing it isnot theoretical, but practical

    1. most recent modern genome decoders don't care that the dna is shredded into pieces
    2. encapsulated in keratin (hair), the dna is not so tainted by bacterial dna like it is in bone
    3. a new technique allows modifying modern elephant dna 50,000 genomic sites at a time, rather than one by one, so the proper egg can be arrived at after a few generations of reconstruction, implanted in a female elephant, and voila

    this can be done, right NOW!

    amazing

    even more freaky: we can do the same, right now, with neanderthal!

    using chimpanzee as a starting point for ethical considerations, we can also, right NOW, bring a neanderthal back to life

    that's pretty freaky. these guys wouldn't be dumb. someone would have to explain to the guy that he is not the last of his species, he's an artifically reconstructed clone of a guy who died 50,000 years ago. no one of his kind exists anymore

    but we revived a wooly old friend of yours too. here's a spear, happy hunting

    just don't eat the dodo
    or the quagga
    or the irish elk
    or the auroch
    or the sabretooth though

    really really freaky and amazing

    • Comparing the averages, Neanderthals had about 100 cc more brain matter than we regular humans do.

    • by genner (694963)
      Ok you are hearby banned from using the word "freaky" ever again.
    • by Moraelin (679338)

      Do we really want to do this to a sentient and intelligent species?

      For a start, the Neanderthal will be a circus freak for all his life. Whatever his other achievements or shortcomings would be, he'll still be that reconstructed Neanderthal. I doubt that he could have a normal job or relationship or interact normally with new people, without getting back to that aspect that he's the only Neanderthal in the world. Even assuming that all people he'll meet are nice and tactful, it's still that curiosity aspect

      • like picasso, the neanderthal [asa3.org]

        neanderthals didn't go extinct, they interbred. there's a little neanderthal in all of us

        its not so bleak as you presume. as a unique person, he'll enjoy rockstar status. there's also asshats that pick on people in wheelchairs, but do you see stephen hawking genuinely limited by that in life? you are giving too much credence to the reaction of the lowest common denominator, which he wouldn't come in that much contact with, and wouldn't rule his life

        • by Moraelin (679338)

          Actually, apparently there is exactly 0% Neanderthal in us, if you look at the DNA. You can see the differences between Neanderthals and the common ancestor (since that's what made them Neanderthals), and you can see the differences between humans and the common ancestor (since that's what makes us humans.) The two sets just don't overlap. All the genes that made Neanderthals be Neanderthals are not present in us.

          The easiest to look at is the mitochondrial DNA, since it's pretty small, and it's been mapped

  • My g/f was looking over my shoulder and proclaimed she already had a pet wooly mammoth and looked at me :(
  • by eclectro (227083) on Thursday November 20, 2008 @09:34AM (#25831279)

    Do they taste good??

    • by Whiteox (919863) <htcstech AT gmail DOT com> on Thursday November 20, 2008 @10:09AM (#25831595) Journal

      No. Mammoth meat probably smells and tastes like limburger cheese.

      University of Michigan paleontologist Daniel Fisher had a theory that early Americans of 10,000 years ago used frozen lakes as refrigerators to store mastodon and mammoth meat. He tested his theory when a friend's horse died of old age. Fisher dropped chunks of horse meat of up to 170 pounds below the ice in a nearby pond. He anchored some pieces to the bottom. Every week or so he cooked and chewed a piece of meat, and eventually swallowed each bite. The meat remained safe to eat well into the summer. The theory is that as the water warmed in the spring, lactobacilli (the bacteria found in yogurt & cheese) colonized the meat, rendering it inhospitable to other pathogens. So despite the smell and taste (similar to Limburger cheese), the meat remained safe to eat.
      http://www.foodreference.com/html/f-mammoth-meat.html [foodreference.com]

      • by TheLink (130905)
        But that's probably even less accurate than saying milk smells and tastes like limburger cheese.
      • Re: (Score:3, Insightful)

        Seriously, you think mammoth meat probably smelled and tasted like Limburger cheese because a guy stuck horsemeat in a pond for months, and then it smelled and tasted like Limburger? A couple of clues as to where you might have gone wrong - fresh horsemeat does not taste or smell like Limburger, and mammoth meat probably did not require long term pond storage before it could be eaten.

  • The correct tag for this would be eyreaffair, not jurassicpark. In The Eyre Affair there were resurrected mammoths wandering around the British countryside (and since they were an endangered species you weren't allowed to interfere with their migration patterns).
  • Mastodons?
    They seem to have lived later than the mammoths like 10,000 years ago [wikipedia.org]

  • How about making little potbellied woolly mammoths?

  • Yeah, but who wants 3/4 of a Wooly Mammoth? Aren't we at least 98% similar in DNA to earthworms? Let me know when the whole genome is reconstructed. :)

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