The conduct of science: Organic change

Most scientific research is about incremental improvements to existing theories. Every so often, though, an anomaly shakes things up, offering upstart ideas the chance to dislodge reigning ones. In December 2010 NASA, America’s space agency, announced a discovery which would, if confirmed, engender just such a shift. Their paper, published in Science, reported the isolation of a new species of bacterium. Where DNA of all known organisms is built on a backbone of phosphates, derived from phosphorus, GFAJ-1, as the microbe NASA’s boffins found in Mono Lake, California, is known, instead sported arsenates, chemical compounds based on arsenic. Since arsenic is toxic to other lifeforms, that would make the microbe different from anything else found on Earth.

Within a week of publication, however, scientists around the world began poking holes in the study. Its extraordinary and, they felt, unfounded claims called for extraordinary measures. So rather than pursue the usual, lengthy process of submitting papers to journals, which send them on to specialists in the field for formal evaluation, they tore the study apart in blogs and on Twitter.

In response, NASA scientists hid behind peer review, as the time-honoured practice is known, insisting they will only entertain such “formal” criticism. They can hide no more. Last week Science published two papers outlining failed attempts to replicate the results.

The first, by Tobias Erb, a microbiologist at ETH Zurich in Switzerland, and his colleageus, shows that even though GFAJ-1 can indeed grow in remarkably high concentrations of arsenic, it nonetheless needs small quantities of phosphates in order to survive. This contradicted the original paper’s claim that the phosphates found in GFAJ-1 were insufficient to sustain life. In the second paper a team led by Joshua Rabinowitz, from Princeton University, and Rosie Redfield, at the University of British Columbia, reported the bacterium’s DNA contains traces of arsenic but that its role is not as central as NASA’s boffins had claimed.

Dr Redfield, an early and vocal critic of the arsenic-life hypothesis, has blogged about her findings over the past year. The paper she and Dr Rabinowitz had submitted to Science has been available for months on arXiv, a free online repository. This is unusual; researchers wanting to reveal their full finding prior to publication in Science and other leading journals which charge hefty subscription fees for providing access to the world’s best research need special dispensation from the publisher to do so.

This policy is looking increasingly unsustainable (see article in this week’s print edition). Peer review takes months and requires journals to act as intermediaries. The internet means that research can be subjected to unofficial, but no less diligent, scrutiny in a matter of days. Physicists and astronomers, the primary users of arXiv, have long since embraced this new model. Nowadays, a paper’s publication in a prestigious physics journal serves merely as a stamp of approval, not a way to disseminate findings. The arsenic-life palaver demonstrates that other disciplines are beginning to follow suit.

Also published on economist.com.

References:

  1. Wolfe-simon et al.Science, 2011
  2. Reaves et al.Science, 2012
  3. Erb et al.Science, 2012
  4. Scientist in a strange landPopular Science 2011
  5. Redfield on NASA’s claimsRRResearch 2010
  6. Redfield’s paper on arXiv, 2012

 Image from here.

Publishing on preprint servers… do you do it?

In following up the arsenic in DNA story for The Economist, Rosie Redfield has brought some interesting issues to light. Dr Redfield, who blogs on this network, has recently published a paper in Science showing that NASA’s claims about finding an organism that has arsenic instead of phosphorus in its DNA weren’t true. Interestingly, her paper was available on arXiv, a preprint server, since February this year.

Before making it available on arXiv, she got in touch with Science to know if she can do this. Of course, physicists do it all the time. But Rosie figured that if Science publishes physics, then it must allow it too. To that end she asked and got this answer:

Posting of a paper on the Internet may be considered prior publication that could compromise the originality of the Science submission, although we do allow posting on not-for-profit preprint servers in many cases. Please contact the editors for advice about specific cases. We provide a free electronic reprint service to authors that allows visitors to the authors’ web site free access to the published version of the Science paper on Science Online immediately after publication.

Interestingly, Nature says the same thing but with more clarity than Science:

Nature journals do not wish to hinder communication between scientists. For that reason, different embargo guidelines apply to work that has been discussed at a conference or displayed on a preprint server and picked up by the media as a result. (Neither conference presentations nor posting on recognized preprint servers constitute prior publication.)

Our guidelines for authors and potential authors in such circumstances are clear-cut in principle: communicate with other researchers as much as you wish, whether on a recognised community preprint server, by discussion at scientific meetings (publication of abstracts in conference proceedings is allowed), in an academic thesis, or by online collaborative sites such as wikis; but do not encourage premature publication by discussion with the press (beyond a formal presentation, if at a conference).

How many people in the biological and chemical sciences really know about this? How many actually practice it? The only example I am aware of is Rosie’s. Do you know of others?