On science blogs this week: Arsenic bugging

December 09, 2010

ARSENIC, THE BOLD CASE. I hope you're not bored with those arsenic-eating aliens, because there's more, much more.

Mono Lake
Last week belonged to scifi and its hopeful fancy, egged on by the National Aeronautics and Space Administration and abetted by the journal Science, that NASA researchers had discovered arsenic-based extraterrestrials on the Saturn moon Titan. Or somewhere. (They ended up settling for earthly bacteria in a lake in California.)

This week belongs to science with a small s but a big megaphone, shouting "Waitaminnit! Wait just a damn minnit!" One intriguing aspect of this debate is that not many of the traditional media have followed up last week's frivolity with this week's high seriousness. There's plenty of fodder to be had out there, but it's mostly on blogs — so much that I'm able to touch only on a small portion of what's being said.

First, there's controversy over the accuracy of the paper itself. Second is an issue that transcends this paper: what kind of analysis — and what sort of venue — is right for criticizing scientific research? Writing about the arsenic bug threatens to become my life's work, so I'll take the efficient (=lazy) way out and concatenate the commentary under subheds.

CRITIQUES OF THE SCIENCE. The consensus is that Rosie Redfield's extended blog post on December 4 has been the most important critique of the arsenic bug paper. It's telling, persuasive, and — not least — colorful. Redfield, a microbiologist at the University of British Columbia and therefore an expert in the field the paper is about, did not phrase her devastating blog analysis politely. The tone of the comments she's sending to Science, which she has also posted, are a bit different.

The blog post is very long, and much of it a technical slog I'm not equipped to comprehend, let alone evaluate. The bottom line, Redfield says, is that the paper

doesn't present ANY convincing evidence that arsenic has been incorporated into DNA (or any other biological molecule).

There are some disagreements among the 198 post comments (at last reading), but the general mood is one of "You go, girl!" and that's good enough for me. I'm convinced.

Another persuasive analysis is this December 5 guest post by microbiologist Alan Bradley at We, Beasties. Bradley states forthrightly, "The claim" [that the bug substitutes arsenate for phosphate in its DNA] "is almost certainly wrong." Read it all for the biochemical explanation, but the short version is that DNA with an arsenate background would have hydrolyzed quickly in water, and GFAJ-1's DNA didn't.

In his commentary on the commentaries by Redfield and Bradley, Neuron Culture's David Dobbs writes:

If the paper is as weak as these critiques hold, NASA appears to have been not just overzealous but reckless — and Science not only went along for the ride, cheering wildly, but put all the gas in the car.

Timid, isn't he? I urge you to read this post in particular for Dobbs's comments — too long to excerpt in full here — on what the arsenic bug tale tells us about the state of science journalism. But I can't deprive you of this remark, which certainly made me look into the mirror while trying not to blush:

So we get what we got: some measured check on the hype from the best journalists, but mainly, since the claimed findings are ambitious, an especially fascinated version of “This looks damned interesting, and is truly interesting if true, and [this next part usually doesn't get actually written] I sort of hope it is true, ‘cuz it’s cool.”

Carl Zimmer consulted several scientists for his piece on the controversy that ran in Slate on Tuesday, and most of them were critical of the paper. It was a good and useful piece, but the next day Zimmer showed why it is blogging, rather than conventional articles, that can be a communications marvel.

In the Slate piece he was able to quote only bits of what his sources told him, and we all know how frustrating that is. But in his Wednesday blog post at The Loom, Zimmer quoted what they all had to say. In full. Boyohboyohboy.

A seminal moment, folks. The blog becomes The Newspaper of Record.

Although he has been critical of the paper to reporters, at his blog Tree of Life, evolutionary biologist Jonathan Eisen, who is also academic editor-in-chief at the top-tier journal PLoS Biology, on Tuesday pleaded for an end to personal attacks:

I have seen so much out there about the failings of the paper reviewers, about the intelligence of the authors and the bloggers critiquing the authors, and a whole lot of uneducated guesswork about why some of the things associated with this story happened the way they did. I think it is perfectly fair to express opinions about the original paper, about the press releases and conferences and about the actions of any of the players here. But I do not think it is reasonable to go beyond that and to attack the people themselves. Let's try and make this an open discussion of science and science reporting and not a venue to spout derogatory comments about the people involved.

CRITIQUES OF THE PROPER VENUES FOR CRITIQUES OF SCIENCE. At Code for Life on Saturday, Grant Jacobs kicked things off with an extended analysis based on a CBC article about the Redfield critique. It had included the NASA response, which was (this is my reading of the subtext) that this distinguished government agency didn't get into gutter brawls with pestiferous blogging ruffians; dignified NASA scientists would discuss their work only in the refined milieu of "real" science journals.

Jacobs points out that research gets discussed outside of journal pages all the time, and cites an example from when he was a grad student spectator at a Usenet debate over the Mitochondrial Eve research when the the Internet was young.

Something similar was the theme of much of the blogging in response to NASA's snooty refusal to engage: the horselaugh, followed by examples from faculty lounges, journal clubs, and email exchanges. You've seen it too, when you've been at scientific meetings, sometimes in the form of fairly vicious verbal brawls. Arguing that the only proper place for scientific debate is journals is just a denial of reality.

One of the more civil examples came from David Kroll at CENtral Science:

As painful as her analysis might have been to read for the authors, NASA, and editors of Science, Redfield’s critique represents the future of post-publication peer-review. Already the present at journals such as those from PLoS where readers can comment on papers at the journal website, open public discussion of science immediately upon release of a paper will help science progress more quickly. No longer confined to the archaic correspondence to the journal that takes months to view, the internet and the science blogosphere is facilitating open discussion of peer-reviewed publications within hours and days of release.

Isis the Scientist, at On Becoming a Domestic and Laboratory Goddess, disagrees in part. While she approves of bloggers since she is one, she argues:

... the only thing that is going to answer that doubt is data. Data cannot be generated by blog discussion. Either those data exist and the paper should be retracted, or those data do not exist and more experiments need to be done ... Wolfe-Simon's response may not have been popular, but she is right. The real discussions about this work belong in the scientific literature.

At Byte Size Biology, computational biologist Iddo Friedberg muses about peer-review, both pre- and post-pub. He thinks what has happened to the arsenic bug paper may be an example of the peer-review system undergoing reform — and shows why scientists should be bloggers.

Yesterday, ScienceInsider reported that first author Felisa Wolfe-Simon had posted a statement on her Web site saying that she and her co-authors planned to respond in Science to critiques sent to the journal. The statement also said: "Meanwhile, we are preparing a list of 'frequently asked questions' to help promote general understanding of our work."

What do you suppose that means? Sounds as if maybe they're planning to respond outside the journal as well?

The statement also said that the journal is making the paper freely available, but apparently only for the next two weeks. Abstract here. You can get to the full-text PDF from the abstract, but it appears you'll have to register.

CRITIQUES OF PEER REVIEW. Bjorn Brembs Blog argues that journals like Science should be criticized — and subscriptions to them canceled — when they publish shoddy research. He does this while making a peculiar claim that Science (and its peer-review process) have not been criticized for permitting the arsenic bug paper through their filtering machinery. I guess he hasn't been reading the same blogs I do.

For example, he probably hasn't read this post by Anthony Watts, whose blog Watts Up With That is well known for climate-change deni — uh, skepticism. For Watts, the arsenic bug paper is an opportunity to bash the peer-review system and NASA's "flawed zeal to get some press coverage." He quotes from scientists' complaints in Zimmer's Slate piece and notes:

Of course if that was any of us saying the same thing about climate science, somebody would immediately label us “anti-science deniers”. Lets see if somebody comes up with a label for these people asking skeptical questions. Maybe “anti NASA space bug deniers”?

It's an odd feeling, finding myself in semi-agreement with Anthony Watts. And I have to acknowledge that he's managed one of the better bits of wordplay on the Cary Grant movie title "Arsenic and Old Lace." His hed: Arsenic and post-haste. There have been a lot of attempts, but most don't work.

The best movie pun, so far, is this hed: Arsenic about face. It sits atop Martin Robbins's post at TheLayScientist at the Guardian, a comprehensive summary of the Story So Far, Robbins concludes:

The journal system prevented the public from accessing the paper. Peer review failed. The research was over-hyped in NASA's original 'sphinx-like' press release. An embargo was enforced on information that had already leaked into the public domain, and even as speculation mounted news outlets were barred from reporting the facts. The paper itself wasn't even available until hours after the embargo lifted, and when the research was finally published, and scientists began to criticize it, NASA's press people issued a spectacularly ill-mannered and arrogant response.

At In the Pipeline, Derek Lowe sees the arsenic bug paper as simply part of a trend, even in major journals, to publish papers that shouldn't have made it through the system. He speculates that journals might be overcome by their desire to land high-profile papers. Or, he wonders:

Is it a problem with how they're assigning papers for review — who they go to, or how seriously the reviews are taken when they come back? I really don't know. I just know that we seem to be seeing a lot of embarrassing stuff in the literature these days. It's not supposed to work that way.

Are we seeing more embarrassing stuff? I don't suppose there's any way to quantify it, but I do wonder whether there really is proportionally more dreck out there than in olden days. If you take into account the metastasis of journals and the increased number of scientists, is the proportion of unworthy papers notably higher than in the past? Or is it just that, what with bloggery and social media and mobile phones that work anywhere on the planet, these things more often stand publicly revealed in all their shameful tatters?

ARSENIC MISCELLANY. At Embargo Watch, Ivan Oransky compares the behavior of public information officers at Science and NASA, and NASA flunks. He also flunks NASA for failing to observe its own code of conduct for release of information to the public.

If there's a new bacterium, won't there be new viruses that live on it? Not, perhaps, a surprising speculation, given that it comes from virologist Vincent Racaniello at his Virology Blog.

GFAJ-1 may have disappointed those who've been scanning the skies for ET, but at least a new extremophile with super-weird biochemistry makes it more likely there really is Life Out There. Doesn't it?

Nope, says Jennifer Frazer at The Artful Amoeba. And here's why.

HAD ENOUGH YET? I have. But if you haven't, the indefatigable Bora Zivkovic is collecting pretty near all the arsenic bug posts, and apparently intends to continue this public service for as long as it takes. Consult his ever-lengthening link list here.

He may be at it for a long time. This curious bacterium has legs, and I wouldn't be surprised if we're still talking about it in the new year.