Wednesday, December 08, 2010

DNA, Phosphorus, and Arsenic

Most of you know that DNA strands have a sugar-phosphate background. The bases in each strand are covalently linked to each other by phosphodiester linkages between the 5′ and 3′ carbon atoms of the deoxyribose sugar.

Recently there has been a claim by NASA-funded scientists that a certain bacterium can replace those phosphates with arsenic. Close examination of the Science paper has revealed that, at most, a few percent of the phosphorus atoms are replaced and even that amount is challenged. It has become abundantly clear from reading the paper that the bacteria absolutely required phosphorus and sufficient quantities were present in the media as contaminants.

I've already linked to Rosie Redfield's critiques of the paper and the press conference. Now I want to add Carl Zimmer's take on the whole affair—the title tells all: "This Paper Should Not Have Been Published".

Carl raises an issue that has cropped up in many of the comments sections of various blogs. Is criticizing a scientific paper appropriate outside of the peer-reviewed scientific literature? Is it ethical to cast doubt on the integrity of scientists when questioning the quality of their science?

Felisa Wolfe-Simon1 is the lead author of the study and she was the main spokesperson in the video below. Carl Zimmer asked her if she wanted to respond to the criticism of her paper and here's what she said, according to the Slate article,
"Any discourse will have to be peer-reviewed in the same manner as our paper was, and go through a vetting process so that all discussion is properly moderated," wrote Felisa Wolfe-Simon of the NASA Astrobiology Institute. "The items you are presenting do not represent the proper way to engage in a scientific discourse and we will not respond in this manner."
Carl asked some other scientists about this and the best quote comes from Jonathan Eisen,
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."
My own impression of this fiasco is that the scientific authors of the paper can be accused of bad science and the lead author, Felisa Wolfe-Simon, is guilty of grossly misrepresenting her work at the press conference. There really can't be any excuse for that behavior if you want to call yourself a scientist. Those who think this is impolite and unethical are dead wrong. It's an absolute requirement of good science that we point out to the general public when scientists are behaving badly, otherwise we lose all credibility.

As you watch this video keep in mind that the bacteria absolutely require phosphate in the media in order to grow and that only a few phosphorus atoms, at most, are replaced by arsenic in DNA. If you think that's what Felisa Wolfe-Simon is telling you then you need to work hard on your listening comprehension skills.

1. The name of the bacterial strain is GFAJ-1. Rumor has it that this stands for "Get Felissa a Job." I wonder how that's working out? Do you think the job offers are pouring in?


  1. Is criticizing a scientific paper appropriate outside of the peer-reviewed scientific literature?
    When science is done by press release, the doors have already been opened for full public discussion (such as in the blogs).

  2. Isn't this just another manifestation of the whole 'science is what you do in the lab, and doesn't apply to everyday life' problem? At first we complained about scientists who didn't apply skeptical evidence-based reasoning to their daily lives, now it seems that the divide is being made official.

  3. It's not a rumour that GFAJ-1 is an acronym for "Give Felisa A Job". She says it here:

    "Felisa Wolfe-Simon: So I kind of joked, well, I really need a job. And we were tossing around 'Give Felisa a Job', that'll work, GFAJ, 'Give Felisa a Job', and so that's what we're stuck with right now."

  4. I could not agree more. The study was, at best, poorly executed and the claims are not supported by the results. As this study has been so widely reported on in the media, scientists have a moral obligation to comment publicly on it. Contrary to Dr Wolfe-Simon’s assertions, a public debate is not only a ‘proper way to engage in a scientific discourse’, but it is in fact a vital part of good and transparent science. The authors should welcome the opportunity to publicly address the valid criticisms raised by their peers, just as they welcomed the opportunity to publicly present their data to the waiting press.


  5. Ye gods that's a cheesy, over hyped presentation. are they are all like that are are these guys grandstanding and hamming it up?

    "I'm ready for my close-up, Mr. Mille..."

  6. It's been interesting to watch this debate develop. As I'm outside the field, but the blogs, I wouldn't have got such a close ring-side view!

  7. I'm sure there are a lot of administrators with the "any publicity is good publicity" attitude that will be leaning on their deans to hire her.

  8. The paper is a joke but the bigger problem is preposterous claim that no one has a right to say anything about this paper outside the official publication after peer review.

    First of all, would that peer review, by any chance, be as obviously ridiculously bad as the one that preceded the paper? And why can she go to the non-peer review channels and her critics cannot?

    Bleh. To simplify, the authors have been caught lying for monetary gain, can't admit it now and are trying to come up with excuses. BTW, note this: "Received for publication 1 September 2010. Accepted for publication 8 November 2010." This basically says "accepted without revisions". Glamor mag's zeal to publish sensation strikes again.

  9. I love when she is saying that they don't know the mechanism by which As end up "substituting" P. Because it implies not only that the bugs are promiscuous enough not to see any difference between P04 and AsO4, but ALSO that the bugs have a distinct chemistry for synthesizing DNA. Hmmm.

  10. OMG, it's almost unbearable to hear this Felisa talk about her work in that pompous way. Totally loving her 15 minutes in the limelight, but then refusing to follow up on non-peer reviewed criticism. Good luck getting that job!

  11. anonymous says,

    I'm sure there are a lot of administrators with the "any publicity is good publicity" attitude that will be leaning on their deans to hire her

    No administrators or Deans are involved in hiring at any decent research university.

  12. One issue that has not been raised is the role of the revewers of the Science paper, and why they failed so spectacularly to point out the seemingly basic flaws in the paper.

  13. The "non-peer reviewed criticism of science is inappropriate" claim is perhaps what gets me the most angry in the whole situation. Livid, actually. It promotes the "private club" aspect of science, as if the researchers and formal reviewers have been smiled upon by the gods of knowledge that the underprivileged lower life forms have been deprived of, and they must now bestow this unquestionable sacred knowledge upon their subjects. Who must bend over and accept in silence.

    Yeah, fuck off, science is as full of crooks and idiots as any other field of human activity, and the fact that someone holds credentials doesn't mean all that much at all. Maybe probabilistically, they'd be more likely to spout something that's not pure bullshit, but that does not mean all of us spout non-bullshit, all the time. And open discourse is necessary to keep science transparent and fair, and to negotiate the errors that slip past peer review, which is also full of flaws, by the way. The very idea that all criticisms must be peer reviewed as well is fundamentally scary – the factors that bias the system to accept or reject certain papers and not others will not go away in the criticism round. And glamourmags are full of bias and hidden interests. in other words, censorship.

    The whole debacle is quite embarrassing, and I hope it doesn't do too much damage to the image of science in public opinion, which is already shitty enough.

  14. "No administrators or Deans are involved in hiring at any decent research university."

    Hahahahaha! OK, I almost laughed my coffee through my nose.

    That's like the 'No true Scotsman' fallacy. The fact is, it does happen, even at the 'best' universities, unless we care to define 'best' by something other than research impact, program productivity, or number of faculty with high professional honors.

  15. @Argon,

    You make it sound like administrators and Deans are commonly involved in deciding who to hire at major research universities.

    I was thinking mostly of hiring at the Assistant Professor level—that the kind of job Felisa is looking for. In my experience that's always handled by departmental search committees. Is your experience different? Which universities?

  16. Not directly involved but Deans often interview the candidate along with the department faculty members.