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NASA Science

Genome of Controversial Arsenic Bacterium Sequenced 56

Posted by timothy
from the there's-gotta-be-some-arsenic-somewhere dept.
Med-trump writes "One year ago a media controversy was ignited when Felisa Wolfe-Simon and her colleagues held a press conference to announce the discovery of a bacterium that not only survived high levels of arsenic in its environment but also seemed to use that element in its DNA. Last week, the genome of the bacterium, known as GFAJ-1, which gets its name from the acronym for 'Give Felisa a Job.' (No joke!), was posted in Genbank, the public repository of DNA sequences for all who care to take a look. But it doesn't settle the debate over whether arsenic is used in DNA."
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Genome of Controversial Arsenic Bacterium Sequenced

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  • by ByOhTek (1181381) on Thursday December 08, 2011 @12:02PM (#38303678) Journal

    We geneticists come up with some of the most goofy names for genes.

    Smaug is a fun one.
    So is "MADD", which stands for "Mothers Against Dumpy Drosophela"

    • Re: (Score:3, Informative)

      by jinushaun (397145)

      Don't forgot Sonic Hedgehog (SHH), an important protein used in development.

      • by Guppy (12314) on Thursday December 08, 2011 @12:38PM (#38304142)

        Don't forgot Sonic Hedgehog (SHH), an important protein used in development.

        Which ends up being an unfunny problem for doctors, that have to explain to a mom that her baby's congenital malformation is caused by a "Sonic Hedgehog Mutation": http://www.nature.com/nature/journal/v439/n7074/full/439266d.html [nature.com]

        • by nedlohs (1335013) on Thursday December 08, 2011 @01:38PM (#38305040)

          Of they could not be stupid and say "caused by an SHH Mutation".

        • Don't forgot Sonic Hedgehog (SHH), an important protein used in development.

          Which ends up being an unfunny problem for doctors, that have to explain to a mom that her baby's congenital malformation is caused by a "Sonic Hedgehog Mutation": http://www.nature.com/nature/journal/v439/n7074/full/439266d.html [nature.com]

          I think Shakespeare may have had a particular point about the meaning of names... hmm.

        • by Anonymous Coward

          I also like the "I'm Not Dead Yet" (INDY) gene that they had found in fruit flies.

        • by izomiac (815208)
          OTOH, humorless names also become problems because they're not memorable. Most patients give an admirable effort in pronouncing or remembering the name of their prior illnesses, but there are limits. "Mysthenia Gravis" or "Lambert-Eaton syndrome" are simply beyond what many people can tell their future doctors, and they have even a rougher time trying to spell them for Google. Latin is a bit better than an eponym, but neither is useful when forgotten. OTOH, if a mother mentions a "hedgehog" then any doc
          • by RockDoctor (15477)

            "Mysthenia Gravis" or "Lambert-Eaton syndrome" are simply beyond what many people can tell their future doctors, and they have even a rougher time trying to spell them for Google.

            I almost hate to say this, and certainly hesitate before typing this, but "Darwin Award, anyone?"

            Remove (from your gene pool) the ones with spelling and/or writing problems (or thinking problems, to not realise this might be a problem in the future), and eventually the number of people with such problems will decrease. If we wer

      • by zarmanto (884704)
        Funny; I thought caffeine was the most important compound used in development...
      • by Niedi (1335165) on Thursday December 08, 2011 @12:51PM (#38304336)
        Anything that involves Drosophila in gerneral and especially Christiane Nüsslein Vollhard is just plain silly....
        examples (along with the translation if necessary)
        Spätzle (a swabian kind of noodle), wingless, toll (either great or crazy), Gurke (cucumber), tube, Pelle (husk/peel), Krüppel (cripple) etc....

        Basically they tried to destroy/deactivate/mutate random genes necessary for the development of the fly, without knowing what they'd hit. Then they looked for larvae or flies that looked weird or behaved funky and named them with whatever they associated with it. Finally they took the animal and tried to find the gene they deactivated. If successful, they'd give that original name to the gene, no matter how stupid the name was and no matter how important the gene is. Hilarity ensued.
    • by mwfischer (1919758) on Thursday December 08, 2011 @12:34PM (#38304094) Journal

      I googled Mothers Against Dumpy Drosphela and this site came up.

      http://jpetrie.myweb.uga.edu/genes.html [uga.edu]

      You people are strange. I like you.

      • When he says that the table does not align on Firefox, well, he's not kidding. Not even ordering seems to be preserved!

      • I knew it would involve UGA somehow. My anatomy teacher in high school worked on Drosophila there and had some of the funniest stories about her times in the lab.
  • by zarmanto (884704) on Thursday December 08, 2011 @12:33PM (#38304078) Journal
    While the rest of this is intriguing and all, I was actually more interested in whether or not she ever got the job... it seems that she did, from a note in the title article:

    Wolfe-Simon is now at working (sic) at Lawrence Berkeley National Laboratory (LBNL) with John Tainer.

    Good for her.

    • Re: (Score:2, Insightful)

      by Anonymous Coward

      Wolfe-Simon is now at working (sic) at Lawrence Berkeley National Laboratory (LBNL) with John Tainer.

      Good for her.

      Please don't hold it against LBL - most of the people I've spoken to here think the paper was bullshit. I'm not sure what Tainer was thinking; his lab normally does crystallography and small-angle X-ray scattering (SAXS), which rarely stray into controversial territory. We do have the necessary equipment to verify her claims, however, if that's possible. I'm just not looking forward to the in

      • by geekoid (135745) <dadinportland@ya ... m minus math_god> on Thursday December 08, 2011 @01:23PM (#38304772) Homepage Journal

        The paper was fine. Her handling of some of the samples may not have been what one would want.
        The sensationalism is the problem. Her conclusion, while unexpected and quite possible wrong, are fine based on the experiment.
        This will be worked out like science is worked out. People will try to recreate it, and the DNA will be put under a Mass Spec.

        All of which is in the article.

        Shit. I just realized you posted AC. So, you are crap. Normally I don't bother with AC, but since I wrote it, I'll post it.

      • by Anonymous Coward

        Wolfe-Simon is now at working (sic) at Lawrence Berkeley National Laboratory (LBNL) with John Tainer.

        Good for her.

        Please don't hold it against LBL - most of the people I've spoken to here think the paper was bullshit. I'm not sure what Tainer was thinking; his lab normally does crystallography and small-angle X-ray scattering (SAXS), which rarely stray into controversial territory. We do have the necessary equipment to verify her claims, however, if that's possible. I'm just not looking forward to the inevitable public reaction if she holds another hand-waving press conference; the DOE doesn't need that kind of publicity.

        - a Berkeley Lab scientist

        I would be tempted to hold YOUR comment against LBNL, except you might not actually be a scientist there and just a troll (I hope so), and even if you are, your attitude might actually not be representative.

        She published a paper, and put her data out there. She drew a conclusion from the data that others don't agree with, but she explained her reasoning with supporting data. Working in "controversial territory" is nothing to be ashamed of. She may be right, she may be wrong, let actual data settle the qu

        • My concern is that it appears that she seems to have been ostracized and punished by members of the scientific community for publishing her paper. Science and peer review aren't supposed to inject personal feelings into research. It's not supposed to be a case of liking or disliking her data but, whether or not it's accurate.

          • by Anonymous Coward on Thursday December 08, 2011 @01:55PM (#38305272)

            The criticism of Dr. Wolfe-Simon has largely focused on the publicity surrounding the paper. The paper itself has problems but in and of themselves these would not reflect too badly on Dr. Wolfe-Simon, because the conclusions as stated in the paper are not too extreme and are supported by the evidence in the paper, such as it is.

            However, she and her lab orchestrated a rather extreme degree of publicity for the paper, even though it was likely unwarranted based on the quality of the results, with much of it focusing on what a great scientist she was and how groundbreaking these findings were. Considering that the findings are widely disputed and possibly false, which is sort of the opposite of good and groundbreaking science, this rubbed a lot of people the wrong way.

            • Re: (Score:3, Insightful)

              by Anonymous Coward

              Same AC here.

              I should elaborate: Sometimes a result that is disputed and possibly false ends up becoming good and groundbreaking science. However, this will only be the case after it has been confirmed independently and the disputed issues addressed. Publicizing it immediately, before that process occurs, as though this uncertain and doubtful piece of science is the gospel truth, is irresponsible.

              • The BIG problem was getting the PR people involved. They started hyping it as if it were the discovery of the century. A paper with 'weird' results is fine - even if it turns out wrong. A paper with a dozen PR flacks hyping an entirely new paradigm in molecular biology not so much.

            • I'm not a geneticist, nor a professional scientist; just a layman & space enthusiast following the story. It seems to me she's trying to cast herself as a poor female being attacked by the male 'establishment', even though some of her most vocal critics are women. The scientific method ought to be the only criteria of judgment here. Has anyone duplicated her results?
  • If you actually sequence the genome, then you know if their is Arsenic in it. You look at what you sequences and see if it says anything but "ATCG", because all of those letters code for nucleotides containing phosphates.

    You see those letters code for very specific chemicals Adenine, Cytosine, Guanine and Thymine, none of which have Arsenic.

    When you change the nucleotides, you get something BESIDES ATCG. A prime example of this is RNA, a similar chemical that has no Thymine. Instead it uses Uracil wh

    • by Anonymous Coward

      This is simply not true (otherwise known as bull cookie)

      The authors claim that some of the posphor in the ACTG bases may have been substituted by arsenic. All currently available genome sequencers "read" bases by either PCR based (Sanger, Illumina, Roche, Pac-bio or Ion-torrent) or ligation based (Solid) techniques. These techniques do not discriminate on the phosphor group.

      In addition even if the arsenic in the DNA would interfere with the sequence, genome sequencing is not single molecule sequencing; So i

      • by gurps_npc (621217)
        Your comment indicates a lack of reading comprehension skills. And a lack of intelligence.

        Let me ask you a simple question:

        Someone gives you a written Portuguese book.

        You have a Spanish translation program.

        Would you then run it through the Spanish translation program and claim you have 'translated it"?

        NO OF COURSE NOT, ONLY A MORON WOULD DO THIS.

        I totally agree that if you use PCR (which I have experience in - minimal, but recent), or a ligation based system (of which I have read), on an arsenic bas

    • Well, I might have no clue how you sequence a gene or genome today, but I would guess the procedure would involve using traditional rna in a non-arsenic environment to multiply the dna before analysing it.

      This process would of course not preserve the arsenic.
      To get better tools, you would have to look at how the adapted lifeform reads and processes its dna, and how the cells factories actually translate the messenger rna, as this might be different.
      See
      http://en.wikipedia.org/wiki/Genetic_Code#Variations_to_ [wikipedia.org]

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