The dubious arsenic bacterium

I didn’t post on the bacterium that supposedly evolved to incorporate arsenic into its DNA because I was ill, late to the party, and, frankly, not really equipped to judge that paper, which was published in Science.  In yesterday’s Slate, however, Carl Zimmer wades into the fray, talking to a number of scientists who attacked the study, including Rosemary Redfield of the University of British Columbia, who published a withering takedown of the original paper. Zimmer’s piece is straightforwardly called “This paper should not have been published.”

Zimmer’s interviewees are pretty unanimous in claiming that the evidence that arsenic was really incorporated into the DNA—the paper’s major finding—is unconvincing.  It might well have been a contaminant. Critics blame the paper’s appearance on shoddy science, credulous authors, and poor reviewers.

Zimmer asked two of the paper’s authors to respond to these criticisms, and they refused, claiming that they weren’t going to debate their results in the media.  As Zimmer reports, others see this as evasion:

While Redfield considers Wolfe-Simon’s research “flim-flam,” she think it’s fine for the NASA scientists to hold off responding to their critics. She is working on a formal letter to Science detailing her objections. But Jonathan Eisen of UC-Davis doesn’t let the scientists off so easily. “If they say they will not address the responses except in journals, that is absurd,” he said. “They carried out science by press release and press conference. Whether they were right or not in their claims, they are now hypocritical if they say that the only response should be in the scientific literature.”

Eisen’s right.  It’s incumbent on the authors, who flogged their paper via press conference, to at least give some sort of public response, if only to say that they’re looking into it and repeating their experiments.  This is a new era of science, in which reaction to a paper by fellow scientists can be virtually instantaneous, and not always pretty.  I, for one, welcome it.  I’d rather know now rather than later if there are problems with this “new life form.”  Further, these critiques and counter-critiques aren’t always easy to find when they’re in the scientific literature: many journals bury them somewhere in the online version.

23 Comments

  1. daveau
    Posted December 8, 2010 at 9:44 am | Permalink

    I agree. This was all over the news, and the authors at least need to acknowledge, but not necessarily defend, these issues via the same media. Live by the sword, die by the sword.

  2. Matthew Cobb
    Posted December 8, 2010 at 9:45 am | Permalink

    *Ouch*. To a non-specialist, Redfield’s critique looks pretty damning. If the arsenic isn’t in the bug’s DNA, it’s so much less interesting – merely a microbe surviving in a tough environment. For those who don’t know – last week the web was crawling with rumours about NASA making an annoucnement about ET. The Guardian website had a blog about it. All that came from the authors and NASA sexing it up… If they can’t back up their extraordinary claims, it’ll look bad. Interesting to reflect, however, that a junior scientist in Redfield’s position might have thought more than once, twice or twenty times about publishing such a damning critique – their reputation might be made, but it might also be forever blown…

  3. Sigmund
    Posted December 8, 2010 at 9:48 am | Permalink

    I read about this first on Bad Astronomy and was highly skeptical of how it was reported there. I think it behoves science bloggers to get things correct since science journalists often use science blogs as sources. Phil’s article was very unclear for the layperson whether we were talking about a new form of non DNA genetics (an amazing discovery) or simply a new biochemical adaptation that allows some bacteria to live in a toxic environment (not so amazing at all). The immediate comments to Phils article were calling the result “Utterly incredible” and “The greatest news of the 21st century. Nobel prize for them guys.”
    I work in genetics and could see that that the paper didn’t come anywhere close to this but I’m sure a lot of people don’t have the ability to simply download the paper and understand the actual results. Apparently a lot of science journalists contacted Phil afterwards to be updated on the story – and not to knock Phil Plaits scientific ability but I think it should be pointed out that just because NASA is funding a project it doesn’t mean that an astronomer is the best person to look at the results – particularly when the paper is entirely about microbiology and biochemistry. Science is so fragmented these days that nobody is an authority on anything but a small area of knowledge and, believe it or not, astronomy is very different to microbiology.

    • Dominic
      Posted December 8, 2010 at 10:01 am | Permalink

      You are right of course. I think this is one occasion when it is not fair to attack science journalists who have reported the story, but again there is so much pressure to put a spin on results to get funding for research – I do not see a way past this. We just have to rely on other experts to be sceptical. The researchers themselves should be – SHOULD be – open to criticism as long as it is not personal.

      • MoonShark
        Posted December 8, 2010 at 10:39 am | Permalink

        That’s how I felt about the BA coverage too, Sigmund.

      • JB
        Posted December 8, 2010 at 12:00 pm | Permalink

        Science journalists should at least know enough to ask physicists about physics and biologists about biology.

        In the NYT article on this story, major attention was paid to the breathless comments of some clueless astrophysicist, while the more level-headed “wait and see” comments of true experts like Gerald Joyce were buried below the fold.

        • Kevin
          Posted December 8, 2010 at 12:04 pm | Permalink

          I think because the paper was being presented as a “astrobiology” study, science journalists naturally gravitated to the “astro” part before understanding that they needed to be looking at the “biology”.

          A natural error.

          However, and forcefully, I will state that any astronomer who was called by a journalist for a pithy quote about this study should have done the sensible thing: turfed it.

          It’s not a sin to acknowledge that something is beyond your area of expertise.

          In this case, faking it has harmful consequences all around.

    • MadScientist
      Posted December 8, 2010 at 11:03 am | Permalink

      I think it’s just another example of how limited we all are in what we know. It’s a common mistake to assume that someone else knew what they were doing and the BA was just repeating the claims made in the press meeting.

  4. Posted December 8, 2010 at 9:55 am | Permalink

    I agree with you, if I learned anything in 10th grade math it was this; show your work. Whether the subject’s math, biology, or sasquatch, show your work.

    • Sajanas
      Posted December 8, 2010 at 12:56 pm | Permalink

      When I was in college, my professors liked to illustrate really important information by giving us the original research papers to read. Often these were papers that resulted in people getting Nobel Prizes, and one thing I always noticed is that they gave huge amounts of controls. If you leave any doubts in the minds of your readers, you have done a poor job of constructing your argument, and the more bizarre the claim, the better those controls had better be.
      A particular favorite was the discovery of RNA being able to catalyze an enzymatic reaction (in particular, an enzyme that cuts a pre-tRNA). Since no RNA had ever been known to do this, the researchers through the whole kitchen sink at it to make sure it worked. What resulted was very convincing once its results had been replicated.

  5. Posted December 8, 2010 at 10:00 am | Permalink

    While it is proper to analyze flaws in the methods of this paper, I think it is important to bear in mind that, even if all their experimental claims are true, the result was wildly overhyped. When Carl Zimmer writes “If the authors of the paper were right, we would have to expand our notions of what forms life can take”, I think he’s wrong. If the authors of the paper were right, we would have an interesting example of what extremophile bacteria are capable of, but we wouldn’t even begin to approach a redefiniton of what life is. This was evident from the initial press reports last Friday, even before Rosie Redfield posted her devastating takedown that showed they probably weren’t even right.

    • MadScientist
      Posted December 8, 2010 at 10:56 am | Permalink

      I think Carl was working on the notion that if arsenates can substitute for phosphates in the DNA backbone we may have to think about the development and metabolism of such creatures – how would they compare to the familiar beasts with phosphate in the DNA structure? Such conjectures deserve some consideration – after all the As and P ions have different sizes and properties. It would be interesting to see how an As based DNA worked and how it compared with normal DNA. However, the authors haven’t even convinced people in general that As had indeed replaced P to any significant degree.

    • MoonShark
      Posted December 8, 2010 at 11:03 am | Permalink

      What *is* the current biochemical definition of “what life is”, by the way? I don’t think I’ve seen one that limits it to particular elements. Is DNA (or RNA) even an absolute requirement?

      Also, as a chemistry student, regardless of the outcome of this dispute, I think it’s clearly interesting and worthwhile for researchers to be exploring the tolerances of cells to unusual compounds and environments. And it’s good to fire up the presses once in a while (as long as it’s not too overblow), to inspire new work.

      • JB
        Posted December 8, 2010 at 1:15 pm | Permalink

        There is no such definition, but this is as good as any: http://en.wikipedia.org/wiki/Life#Biology
        Note no DNA/RNA requirement.

        Unless the authors are complete frauds or incompetents, I believe they have at least demonstrated that this beast grows better with almost-no-phosphate/high-arsenate than with almost-no-phosphate/almost-no-arsenate. And that’s interesting (but not Publish In Science interesting).

        • JB
          Posted December 8, 2010 at 2:24 pm | Permalink

          Correction: they didn’t even demonstrate that. According to Table S1, their “control” low-P/low-As medium contained NO GLUCOSE and NO VITAMINS. WTF?? Maybe they are incompetents (maybe their reviewers are too).

    • Posted December 9, 2010 at 2:56 am | Permalink

      All known living creatures use phosphorus as a crucial component of their nucleic acids. If this bacterium turns out to be capable of building nucleic acids with arsenic instead of phosphorus, then I think it would be very reasonable to describe it as an expansion of our notions of the forms life can take. I don’t think Carl Zimmer said anything wrong here.

  6. MadScientist
    Posted December 8, 2010 at 10:46 am | Permalink

    This is why I prefer an open forum where anyone can check items submitted for review and comment on them. The only down side I see is that some other group may see an article and rush their own publication in a closed journal.

  7. Anonym
    Posted December 8, 2010 at 11:37 am | Permalink

    Is “shoody” anything like ‘shoddy’?

    • whyevolutionistrue
      Posted December 8, 2010 at 11:38 am | Permalink

      whoops! Fixed, thx.

  8. will tomlinson
    Posted December 8, 2010 at 4:50 pm | Permalink

    Here’s an interesting article from today’s UK Guardian, “Arsenic About Face” — http://www.guardian.co.uk/science/the-lay-scientist/2010/dec/08/2

  9. Adam M.
    Posted December 8, 2010 at 6:08 pm | Permalink

    It’s worse than Ida. I’m beginning to get suspicious of scientific press releases in general.

    How nice it would be if science journalists at least waited until findings got accepted before inevitably telling us about how each new overturns everything we knew.

  10. Matthew Cobb
    Posted December 9, 2010 at 1:16 am | Permalink

    There’s a really useful update from Carl Zimmer with reasoned quotes from loads of folks here:
    http://bit.ly/eOMsmI

  11. Steven
    Posted December 17, 2010 at 8:45 am | Permalink

    The lead author has responded:
    http://www.spacedaily.com/reports/NASAs_arsenic_life-form_scientist_answers_critics_999.html

    Personally, I think the high speed publish by PR is a bad idea. To presume it’s great because we get the information is to forget that science does not live in a bubble. It lives in the media universe and the media universe gets it wrong. Every time. I’ve yet to see ANY PR publication that didn’t distort the paper in an attempt to beef up the story.


6 Trackbacks/Pingbacks

  1. [...] The dubious arsenic bacterium and Life on Arsenic? and NASA arsenic story – let’s lay off the personal attacks on all sides and Scientific dissention: shouldn’t we all be nice? [...]

  2. [...] the whole article for details; read Redfield’s post; read Jerry Coyne’s post including comments, most of which are from people who know something relevant. Related postsOn [...]

  3. [...] Note the caveat. That is what is interesting in the internet age; people get their work out very quickly and it often gets circulated before the scientific community as a whole gets a chance to completely vet it (beyond the usual peer review process). This “arsenic based life-form fiasco” claim was an example of that. [...]

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  5. [...] you remember, this paper attracted huge attention because of its claim that a bacterium growing in Mono Lake, California, was able to incorporate [...]

  6. [...] of life.  Admittedly, soon after the paper came out it was pretty roundly attacked for its “shoddy science, credulous authors, and poor reviewers.”  Well, it’s been about a year and a half … enough time for some new research [...]

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