08 March 2011

Arsenic life, four months later: pay no attention to the internet

ResearchBlogging.orgTo recap: In early December, NASA holds a press conference relevant to astrobiology, wherein Felisa Wolfe-Simon announces a paper on a very interesting bacteria. The bacteria is indisputably arsenic tolerant, but Wolf-Simon and her eleven co-authors claim that the bacteria is not just tolerating arsenic, but using it in place of phosphorus. Before the weekend is out, strong criticisms of the paper appear on blogs. Wolfe-Simon initially refuses to respond to anything that isn’t in a peer-reviewed journal, but later relents and put up a FAQ on her website.

Now, criticisms are appearing in the peer-reviewed literature, like this one by Rosen and colleagues. The analysis is quite a helpful one in many ways, providing good background information on things like how cells can use arsenate (arsenolipids instead of phospholipids, for instance).

Their summary is that there is no “fatal flaw” in the paper that rules out the possibility of bacteria using arsenic (“no positive data” is how they put it) and that there needs to be more research.

Unfortunately, if you’re hoping to see how they accommodate criticisms from other researchers that some argued disproved the notion of arsenic being used in DNA, you’ll be disappointed. This paper not only tries its best to ignore the widespread commentary about the original paper on the blogosphere, it dismisses it. Here’s all they say:

This study has generated significant commentary, often as anonymous electronic communications.

This conflicts with my impression, which was that almost all of the commentary was signed. There was Rosie Redfield and Alex Bradley. Carl Zimmer got a dozen researchers to comment, all with their names in place. There was so much written in the blogosphere about arsenic life, that some of the commentary was pseudonymous (which, as many emphatically point out, is different than being anonymous). But the most prominent critics of the Wolfe-Simon and company paper were certainly not anonymous.

Writing an entire article evaluating the arsenic life paper without any references to what happened on blogs is both disingenuous and bad scholarship. To compress all that online commentary into a single one-liner borders on the unethical, because it so profoundly distorts the events following the release of the paper.

If there had not been such a public thrashing of ideas about this paper online, I doubt a journal have even considered publishing this review of the arsenic life paper (which still hasn’t been officially published yet). So the authors and editor take advantage of the controversy to publish a review, all the while tut-tutting and wagging their fingers at those nasty anonymous bloggers and refusing to do anything but give the most oblique acknowledgment of their role.

I imagine that Wolfe-Simon and some press people at NASA might be happy, though, since this article reinforces the rigid conventions that they promoted in the early days following the release of the paper. But it’s long past time those conventions change.

Additional: Only a few hours after I wrote this, I learned of another short paper commenting on arsenic life that appeared in January. Silver and Phung do not look upon the internet all favourably, referring to “the magic and nonsense that floods cyberspace.” But they do note the online criticisms and provide multiple links to them, mainly, but not exclusively, from new gathering organizations.

More additional: The authors have responded. This has generated my own follow-up post.


Rosen BP, Ajees AA, McDermott TR. 2011. Life and death with arsenic. BioEssays: in press. 10.1002/bies.201100012. (DOI link may not be working yet; try http://onlinelibrary.wiley.com/doi/10.1002/bies.201100012/abstract if it isn’t.)

Silver S, Phung L. 2011. Novel expansion of living chemistry or just a serious mistake? FEMS Microbiology Letters 315(2): 79-80. DOI: 10.1111/j.1574-6968.2010.02202.x

Wolfe-Simon F, Blum J, Kulp T, Gordon G, Hoeft S, Pett-Ridge J, Stolz J, Webb S, Weber P, Davies P, Anbar A, & Oremland R. 2010. A bacterium that can grow by using arsenic instead of phosphorus. Science. DOI: 10.1126/science.1197258

Hat tip to Jonathan Eisen for the Silver and Phung paper.


Rosie Redfield said...

The authors cite a 'personal communication' about arsenic-DNA interactions, but not any of the signed online communications that first raised most of the issues they discuss.

Such misappropriation of ideas hasn't formally been classed as scientific misconduct, but it should be.

Joe Chemler said...

There are a few more peer-reviewed articles published last month. I've provided a quick summary here:

Unknown said...

(Comment cross-posted from David Dobbs' place) It sounds to me like someone told Rosen et al. there was blog criticism and they just reported that second hand. Of course, if so, they should have added "(Smith, pers. comm.)". And a Google search for "arsenic criticism" would have taken them straight to the relevant links (which link to yet more relevant links), so there's hardly any excuse for not being able to find the "electronic communications" they dismiss. Nevertheless if Rosen et al. are anything like the majority of academics in the departments I've worked in, I suspect they have never read a science blog (or if they have, they didn't know that's what they were reading). Bloggers like Carl Zimmer and Phil Plait loom large in our world (ba dum tisk), but frankly most academics have no clue who they and other 'famous' science bloggers are, much less the rest of us. They haven't heard of Wired. They read Science and Nature in dead tree format. New Scientist and Scientific American are for punters. So while I'm not excusing them for their lazy scholarship on this point, it's worth stepping back and trying to understand their world view, and ours.

Addendum: having seen Rosie Redfield's comment just now, it seems they did cite a 'pers. comm.'

truth_coming said...

I was one of the earliest critics of the problematic claim of arsenic life. As a matter of fact, I posted a blog article (http://blog.sina.com.cn/s/blog_502041670100n4u8.html) on the same day the Science paper went online and then immediately concluded it is a sevcerely flawed research with a very likely invalid conclusion (http://blog.sina.com.cn/s/blog_502041670100n5rw.html). Then my scholarly formal written Technical Comment was sent to my microbiological peers for comments and then submitted to Science on December 15, 2010. However, this Technical Comment was rejected in March by Science but soon published in Logical Biology (http://im1.biz/albums/userpics/10001/LB2011V11N1A1_AsLife_P1.htm).
Since then I have been watching the progress in Science on the resolution of this great controversy and post weekly comment there (http://news.sciencemag.org/sciencenow/2010/12/arsenic-researcher-asks-for-time.html).
From what has happened so far, I think Science has done a great harm to science by first publishing a hype in high-profile and then by dragging an insubstantial discovery indefinitely?