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Confused about Arsenic

Today’s Washington Post has an article by science reporter Marc Kaufman on the high-profile arsenic bacterium reported two weeks ago in Science that irritated the hell out of me. The article is entitled “Study on Arsenic-based Life Takes a Beating on the Web: Criticisms May Have Implications for Vetting of Future Research,” and its thesis is summed up in its lead, which states that “a torrent of criticism in the blogosphere has turned a widely reported scientific triumph into a scientific football—with much discussed implications for how research will be evaluated and presented in the future.”

There are a lot of things wrong with Kaufman’s article. First, the notion that it is only the “blogosphere” that has been critical of the findings reported by Felisa Wolfe-Simon and coworkers is just plain wrong. Yes, as soon as Wolfe-Simon announced on Thursday, December 2, at a NASA/Science sponsored press conference that she had discovered a bacterium living in the mud under Mono Lake that used arsenic in place of phosphorus in many of its biomolecules, serious scientists who maintain blogs began to criticize the work.

However, unlike Kaufman, who uncritically trumpeted Wolfe-Simon’s work in a front-page story in the December 3 Post, serious journalists also began to question the findings. The first article that I’m aware of that picked up on the scientific criticism appeared in Slate on Tuesday, December 7. Written by the highly respected science journalist Carl Zimmer, “This Paper Should not Have Been Published: Scientists See Fatal Flaws in the NASA Study of Arsenic-based Life” cites a number of scientists, some of whom had blogged their doubts, on why the Wolfe-Simon paper was rubbish and the poor vetting Science had done in accepting the paper for publication.

C&EN’s Carmen Drahl listened to the press conference and dashed off a lead “Science & Technology Concentrate” on the work just before press time on December 2. In it, she wrote, “When grown in arsenic-rich environments, the new bacterium, a member of the Halomonadaceae family plucked from sediments at California’s briny, arsenic-rich Mono Lake, contains arsenic in its proteins, metabolites, and DNA, according to mass spectrometry and X-ray spectroscopy measurements.” I was startled when I read that on page late Thursday afternoon, and after returning the concentrate pages to the production editor handling them, I poked my head into Carmen’s office.

“Do they have any idea where the arsenic is incorporated into the bug’s biomolecules?” I asked.

“It’s pretty fuzzy,” Drahl replied. There was some suggestion that the arsenic could replace phosphate in the nucleic acid backbone or in phosolipids, she said, but another scientist at the press conference, chemist Steven Benner, had suggested that that wasn’t really likely.

I arrive at the office early each morning, and the first thing I do is read the Post. I was startled when I read Kaufman’s article, which contained a graphic showing where the arsenic would replace phosphorus in double-helical DNA. Kaufman opened with a soft lead—“All life on Earth – from microbes to elephants and us – requires the element phosphorus as one of its six components.” He then wrote: “But now researchers have discovered a bacterium that appears to have replaced that life-enabling phosphorus with its toxic cousin arsenic, raising new and provocative questions about the origins and nature of life.” To his credit, Kaufman does cite Benner’s reservations, but he does it deep in the long story, well after Wolfe-Simon has waxed on about the “flexibility” of life.

I also get the New York Times and the Wall Street Journal at my office, and I looked and saw that both had front page stories on the Wolfe-Simon paper. The Journal’s story was as breathless as Kaufman’s; the Times a bit less so. I decided to download the Wolfe-Simon paper from Science and read it myself.

Not long after, Carmen poked her head into my office to tell me that Cambridge University nucleic acid chemist John D. Sutherland, with whom Carmen had worked previously on origin-of-life stories, had e-mailed to tell her that the Wolfe-Simon results were almost certainly physically impossible. Arsenate linkages in DNA would spontaneously hydrolyze on first exposure to water, Sutherland suggested, just as Benner had at NASA’s press conference, but more emphatically. Carmen called to ask whether Sutherland would be willing to submit a letter to C&EN with that statement, and he said he would.

I told Carmen that she should start working on a story about chemists’ reservations about the arsenic claims. Her story was posted as “Latest News” on C&EN Online on December 8. It was our lead “News of the Week” story in the December 13 print edition. In it, she quotes Sutherland as well as Penn State’s Nicholas Winograd, Stanford’s Keith Hodgson, and Ghent University’s Laszlo Vincze on the analytical techniques used by Wolfe-Simon; and Scripps Research Institute’s Gerald Joyce, who is one of the world’s leading chemists working on origin-of-life questions.

So, no, it’s not only blogs that are questioning the Wolfe-Simon paper.

Another problem with Kaufman’s story, though, is the suggestion that there’s something unique about the criticism appearing primarily on blogs. One of Wolfe-Simon’s coworkers is Ronald Oremland of the U.S. Geological Survey, who spoke yesterday about the ruckus at a press conference at the American Geophysical Union meeting in San Francisco. (This team sure seems to like press conferences.) Kaufman writes of Oremland: “He said that when people launch online attacks on the work done by him and biochemist Felisa Wolfe-Simon, he doesn’t really know who is behind them. ‘I don’t want to get involved in what can end up in a Jerry Springer situation, with people throwing chairs,’ he said.”

Really? Sure, some of the comments posted in response to the news reports on the paper have been anonymous, but the blog postings cited by Zimmer certainly weren’t. Rosie Redfield, Forest Rohwer, Shelley Copley, and Alex Bradley are all clearly identified and links to their websites provided in the Zimmer article. They are all respected scientists who use their blogs or websites to communicate their ideas.

Other blogs provide even further insight into Wolfe-Simon’s arsenic saga. Paul Bracher at Chembark, for example, has a revealing and quite funny post entitled “Albert Eschenmoser and I Had Arsenic for Lunch” in which it becomes clear that, 1) Wolfe-Simon has had arsenic and DNA on her mind for a long time, and 2) she thinks a lack of knowledge of chemistry would be beneficial in her quest for arsenic-based life forms. Note to Kaufman: Blogs are an accepted form of serious communication among scientists.

Finally, as the subhead on the story suggests, Kaufman writes that bloggers have criticized the peer reviewers who vetted the Wolfe-Simon paper and that some bloggers “claimed that blogosphere review was the peer review of the future.”

I don’t plan on getting into the debate over what role social networking technology will play in vetting scientific research in the future. The point here is not that the peer review system somehow failed in allowing the Wolfe-Simon paper to be published. It’s that Science did a lousy job of administering peer review. If a single chemist familiar with nucleic acids had reviewed the paper, it would not have been published in its current form. Likewise, if a journalist who had listened to the Wolfe-Simon press conference had contacted the ACS Press Office and asked for the name of an expert to comment on the work—which none did—maybe the stories that appeared on the front pages of three of our leading newspapers would have been a little more circumspect.

7 Comments

  • Dec 18th 201012:12
    by Mygraine

    A very good post. However, I take exception with the statement “The point here is not that the peer review system somehow failed in allowing the Wolfe-Simon paper to be published.” Unfortunately, this is a key point. The paper is so bad (for example, the figures are not properly explained) that it could only be published through sheer negligence of the reviewers. Further, the very hyping of these very shaky results revealed shocking incompetence of the NASA officials and folks at SLAC National Accelerator Laboratory (http://www.ironlisa.com/SLAC_PressRelease.pdf) and the Lawrence Livermore National Laboratory (http://www.ironlisa.com/LLNL_PressRelease.pdf). So the real story is not about a formerly pink-headed girl who managed to trick the whole science establishment. It is about incompetence of the science establishment revealed by this story.

  • Pingback

    Dec 19th 201023:12
    by Quick Links | A Blog Around The Clock

    [...] New real blog post tomorrow. Some links till then…. A Funny Arsenic Smell Upstream — What questions is it fair to ask about squishy science? and Comments on Dr. Wolfe-Simon’s Response and Yet another reason why the Wolfe-Simon conclusion is so improbable and Arsenic and Old Wounds and Scientists and the News Media: Arsenic-Based Life Forms a Case Study? and Arsenic Bacteria 4: The Quest for Peace and Confused about Arsenic [...]

  • [...] Scientists and the News Media: Arsenic-Based Life Forms a Case Study? and Arsenic Bacteria 4: The Quest for Peace and Confused about Arsenic [...]

  • Dec 20th 201010:12
    by David Bradley

    I must say I wasn’t taken in by this As story. It’s two years ago that they were talking about As being metabolised by microbes in that lake, but the chemistry still doesn’t stack up.

    On a point of ethos though, you’re saying here that “Blogs are an accepted form of serious communication among scientists.” I believe that to be true, but how does that idea mesh with Prof Murray’s recent blanket criticism of the blogosphere?

    http://pubs.acs.org/doi/full/10.1021/ac102628p

  • Dec 20th 201017:12
    by Rudy Baum

    @David Bradley: There were a lot of people like yourself who weren’t taken in by the arsenic paper. But quite a few were, so I think C&EN’s coverage was appropriate.

    On Royce Murray’s editorial in which he criticizes science blogging, Royce speaks for himself, not me or C&EN or ACS. I actually was writing a post about Royce’s editorial, but David Kroll beat me to it on Terra Sigillata here, http://cenblog.org/terra-sigillata/2010/10/15/the-current-phenomenon-of-bloggers-should-be-of-serious-concern-to-scientists/#more-226.

  • Mar 14th 201119:03
    by Elizabeth Petro

    I wouldn’t describe Bracher’s post as “quite funny”; I would describe it as mean. I might go even further and describe it as not being without a whiff of misogyny, between the comments on Dr. Wolfe-Simon’s physical appearance and his describing a woman not only over the age of 18 but also with a PhD as a “girl”. It’s hardly the evidence I would have chosen to support the statement “Blogs are an accepted form of serious communication among scientists.”

  • Apr 20th 201101:04
    by Paul

    Petro left a similar comment on my blog, which I responded to here:

    http://blog.chembark.com/2010/12/08/albert-eschenmoser-and-i-had-arsenic-for-lunch/#comment-6575

    These types of ideas/conversations are exactly why blogs are necessary. No one has the guts to give brutally honest (negative) opinions to the “big names” in scientific print media. We need these sorts of discussions when the circumstances call for them.

    Also, “girl” is not necessarily demeaning (and in this case, was certainly not intended to be). The word is the opposite of “guy”.

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