Arsenic Death

July 9th, 2012

Yesterday, Science magazine published what are effectively two death certificates for arsenic life (1 2). These twin papers delve back into the experiments first conducted on the GFAJ-1 bacterium that led Felisa Wolfe-Simon and coworkers to conclude that this organism can grow using arsenic instead of phosphorus.

In the newest reports, Redfield and coworkers were more fastidious than FWS in their experimentation and reported that the presence of arsenate did not affect the growth of the bacterium when phosphate was limiting. They also found no covalently incorporated As in the DNA of GFAJ-1. Erb, et al. found similar results. You can read the papers for yourselves, but suffice it to say that these are findings that jive with everything we know about biochemistry excluding the one paper published by Wolfe-Simon. The only reasonable analysis is that until bona fide experimental evidence to the contrary is presented, there are no organisms we know of that can function by substituting As for P in their DNA.

To follow up on one of my earlier posts, unfortunately, Felisa Wolfe-Simon *still* does not get it. The first rule of getting out of a hole is to stop digging. Giving a statement like the following to USA Today does not help FWS’s cause:

The “new research shows that GFAJ-1 does not break the long-held rules of life,” says the editorial statement by Science. The bacteria, “is likely adept at scavenging phosphate under harsh conditions, which would help to explain why it can grow even when arsenic is present within the cells,” it says.

Wolfe-Simon says in response, “There is nothing in the data of these new papers that contradicts our published data.” Her team hopes to submit more data on the microbe for publication within a few months, she suggests.

Her latest collaborator also decided to pick up a shovel in commenting to the Washington Post:

Wolfe-Simon, now on a NASA fellowship at the Lawrence Berkeley National Laboratory, is collaborating with senior scientist John A. Tainer on wide-ranging studies of the bacterium. In an interview Saturday, Wolfe-Simon and Tainer said that they had produced tentative results in the Berkeley lab almost identical to the original results at a U.S. Geological Survey laboratory, and that they were busy finishing the research and preparing another paper.

Tainer said the two new studies in Science may have come to different results than theirs because of the methodologies used, the precision used to detect arsenates and the provenance of the cells. He said the authors of the two new papers “may well regret some of their statements” in the future.

“There are many reasons not to find things — I don’t find my keys some mornings,” he said. “That doesn’t mean they don’t exist. The absence of a finding is not definitive.”

Wolfe-Simon and her numerous collaborators had made samples of GFAJ-1 broadly available after her initial results caused a storm of controversy, but she and Tainer said they may have been contaminated or modified in transit.

Even the Catholic Church admitted it was wrong when faced with the overwhelming evidence that the Sun does not revolve around the Earth. And we’ve just discussed scientific megablunders with regard to Ronald Breslow and the space dinosaurs paper: when you are spectacularly wrong, you need to admit it for people to let you move on. Denying or ignoring your mistakes prolongs the story.

The second rule of getting yourself out of a hole is to grab a life-line if someone offers you one. Wolfe-Simon could have easily jumped on the “good news” of the GFAJ-1 story by embracing the bacterium’s remarkable resistance to arsenic—which was verified. Instead, it appears as though FWS has doubled down behind the initial report. I’ll keep an open mind when she presents her newest results, but I don’t expect much.

As an aside, it is interesting to note that Science (with a capital “S”) got dragged through the mud again. As if publishing the flawed initial report wasn’t bad enough, the magazine was forced to publish the Redfield and Erb papers prematurely because Redfield broke the embargo on her own paper at a decided to present the results yesterday at a popular conference on evolution. What a mess for Science!

12 Responses to “Arsenic Death”

  1. Special Guest Lecturer Says:

    Regarding the embargo breaking – it’s not really a mess and Redfield was not behaving badly. Both new Science papers had been peer reviewed and accepted. Their scheduling publication times were a subject to the publication needs of the journal, not because they were somehow not yet ready for dissemination.

    Redfield’s data was essentially available on her blog, and the Science manuscript was available to anyone for free on the ArXiv preprint server. The purpose of the embargo is so Science can maximize the press impact of the articles, but such a policy would have hindered the work being discussed at an important international biochemistry forum. What is Redfield supposed to do, give a high-profile lecture and pretend the work doesn’t exist when everyone in the room essentially already knows the story?

    Regarding FWS – it would definitely be more politically astute to stop defending what seems to be a failed hypothesis, but it doesn’t matter that much in the end. Either she and her collaborators (or others) will produce more careful results consistent with the initial hypothesis or they won’t. Science works!

  2. Rosie Redfield Says:

    Thanks, Special Guest Lecturer.

    Science explicitly permits researchers to present in-press results at conferences. But they requested that I not mention that our results were in press at Science, and that I not speak to the press. In my blog post about this I wrote:

    “My plan is describe the refutation results and the Science paper as a minor part of my talk, and to meet with whatever press the organizers arrange, either before or after my talk. I’ll make sure the journalists are aware of Science’s embargo, but I’ll happily talk with them about any aspect of the #arseniclife debacle. I’ll probably also mention the issues surrounding the embargo in my talk.”

    I don’t think this constitutes breaking the embargo, especially given the availability of the manuscript and the prior public discussion of its results.

  3. Paul Says:

    Yeah, my apologies for the lack of precision. Rosie Redfield did not break the embargo; her plans to speak of the work before the Science/media embargo was set to be lifted effectively forced Science to move up the day the embargo was to be lifted. Redfield’s plans to discuss the results are completely consistent with how she has approached this study as a model for “open science”.

    My main point is that Science does not look good here. They set an embargo for a story and then were pushed around and had to change it. Usually, journals are pretty effective at clamping down the flow of information with threats about scuttling a publication. Here, I think they were forced into a less common defensive posture.

    Anyway, I’m on my phone. More thoughts tonight.

  4. Paul Says:

    I’ve edited the last paragraph to reflect the comment above.

    I’m still thinking this whole embargo situation through. My original thought was that if you have an agreement with a journal that they will publish a paper and in return, you will respect any embargo on the paper, that it is somewhat unfair to expect to be able to talk about the work ahead of time. That was part of the agreement—one can easily argue that if you don’t like it, publish somewhere else (in a journal less concerned about these issues).

    With that said, any embargo enforcement so strict that it would hinder the presentation of data at a professional meeting/conference really represents a disservice to the scientific community. Also, the open nature of Redfield’s investigation has been manifest since the beginning, and I can only assume the editors of the journal knew about it.

    Fortunately, these points are moot. I am glad Science dropped the embargo such that this friction never became an issue.

  5. Paul Says:

    Ash at The Curious Wavefunction has a post up about the latest round of papers. His previous post, written following news of the acceptance of Redfield’s paper, was also excellent.

  6. Notanastrobiologist Says:

    The authors of the new studies may regret some of their statements….which do not contradict the original studies.

    #arseniclife has become an endurance test of inanity.

  7. Rhenium Says:

    I didn’t see the “may well regret some of their statements” part yesterday…
    Maybe it could be followed up with “Fools! I’ll destroy you all!”

  8. Exploring why NASA needed to believe in the arsenic-eating bacteria | Uncommon Descent Says:

    [...] Here’s Rosie Redfield on NASA’s ”cowardly responses.“ Also, “Arsenic bacteria”: Coffin, meet nails, and also Arsenic Death. [...]

  9. Paul Says:

    Carmen Drahl has a new article in C&EN featuring a wide array of quotes. Good stuff.

  10. wolfie Says:

    DNA is much more than a three bit byte computer. It is quite certainly a semiconductor (so what ?). Ninety percent are junk, and are probably responsible for the real secrets of heredity between generations. Think of methylation patterns. Allegedly, they are inherited among rats from mother to son and change quite rapidly.

  11. The Scienceblogging Weekly (July 13th, 2012) | Home Pests Says:

    [...] Arsenic Death by ChemBark [...]

  12. Martyn Says:

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