Saturday, August 22, 2009

E-Biomed 2.0?

Last week the Open Access publisher Public Library of Science (PLoS) launched a new initiative called PLoS Currents (Beta).

Announcing the new development on the publisher's blog, PLoS chairman and co-founder Harold Varmus described PLoS Currents as "a new and experimental website for the rapid communication of research results and ideas".

Essentially, researchers are being invited to submit raw preprints — along with datasets and preliminary analyses — to PLoS Currents. These will then be made freely available online without first being subjected to "in-depth peer review".

In response to the recent worldwide H1N1 influenza outbreak, Varmus added, the first PLoS Currents research theme is influenza. This will encompass all aspects of influenza, influenza virology, genetics, immunity, structural biology, genomics, epidemiology, modelling, evolution, policy and control.

It is fitting (and surely no accident) that the launch of PLoS Currents should have been announced by Varmus: For it was as director of the US National Institutes of Health (NIH) that in 1999 Varmus proposed E-Biomed — "a community-based effort to establish an electronic publishing site" that would provide "more effective use of electronic methods for disseminating the results of biomedical research".

E-Biomed was to be a fully searchable, online open-access database that would contain full-text versions of both post-publication biomedical research and preprints.

In the event, as Rob Kling, Joanna Fortuna and Adam King pointed out a few years later, "in less than a year, the E-Biomed proposal was radically transformed, eliminating the preprint section, instituting delays between article publication and posting to the archive, and changing the name to 'PubMed Central'."

The radical defanging of E-Biomed, they added, was a consequence of "highly visible and highly influential statements made by publishers and scientific societies against the proposal."

Widely criticised

In short, E-Biomed was seen as a direct challenge to the vested interests of scholarly publishers, who were sufficiently powerful that they were able to successfully eviscerate E-biomed, and turn it into a pale shadow of Varmus' original intention.

What was particularly controversial about E-Biomed was the plan to make research available on the service without first subjecting it to a process of in-depth peer review. It was this above all, points out Jocelyn Kaiser on the Science blog, that led to the E-Biomed proposal being "shot down."

Critically, opponents argued that the director of the NIH was planning to dispense with scholarly journals, and with traditional peer review, and Varmus was widely criticised as a result.

"I must have known that I was not going to be at NIH for much longer," Varmus joked to New Scientist in 2003, "because this caused a tremendous political argument: what the hell was I trying to do to destroy the publication industry."

But it was not just publishers who criticised E-Biomed. One of the fiercest critics of the proposal was fellow open-access advocate Stevan Harnad, who characterised some of the ideas outlined by Varmus as "needless armchair fantasising".

And responding to Varmus' suggestion that readers of papers in E-biomed should be free to add comments to them, Harnad complained: "There is an echo here of a naive proposal we hear over and over again, that open commentary might somehow substitute for peer review."

For that reason Harnad advised Varmus: "don't associate the proposal any more closely with the quackish idea that spontaneous opinion polls could serve as a basis for calibrating one's reading."

PLoS Currents, we should note, will be making use of Google Knol — where research will be gathered together in collections and "community interaction, comment and discussion will enable commentary and conversations around these findings."

Varmus' status as a former NIH director has clearly helped too: PLoS Currents will also include a new independent database called Rapid Research Notes, which will be housed at the National Center for Biotechnology Information (NCBI) — a division of the National Library of Medicine at NIH.

So radical?

Looking back one is bound to ask: Was the E-Biomed proposal really so radical and, as some at the time argued, dangerous? As Varmus explained in his proposal, papers posted on E-Biomed would get there by one of two routes: "(i) Many reports would be submitted to editorial boards. These boards could be identical to those that represent current print journals or they might be composed of members of scientific societies or other groups approved by the E-biomed Governing Board. (ii) Other reports would be posted immediately in the E-biomed repository, prior to any conventional peer review, after passing a simple screen for appropriateness."

In other words, only a part of the database would have housed papers that had not gone through traditional publication channels.

As Varmus says in his recently published book The Art and Politics of Science, "Many of these articles would simply be online versions of existing journals, accepted for publication after traditional peer review by established editorial boards. Some would be articles submitted to and reviewed by the editorial boards of new online journals formed to publish within the E-Biomed system."

And those articles that had not been peer-reviewed, he adds, "would be clearly delineated from articles that were reviewed by traditional methods."

As to the proposal that people should be able to comment on papers in E-Biomed, this feature is now a standard component of open-access publishing.

Ten years on, it seems, the concept of E-Biomed is far less shocking than when Varmus first proposed it.

Nevertheless, given the reception E-Biomed received, says Kaiser, Varmus has been careful to stress that papers published in PLoS Currents should be regarded as preliminary, and to point out that it is expected that they will subsequently be published in peer-reviewed journals.

Ten years to see the light of day

Finally, it might help to point out that the E-Biomed concept was heavily influenced by the development of the physics preprint server arXiv, which had been founded by theoretical physicist Paul Ginsparg in 1991. And PLoS Currents has undoubtedly been influenced by arXiv as well.

Today arXiv hosts over half a million papers, and around 5,000 new papers are added each month. And the database is no longer confined to physics alone: it now accepts papers in mathematics, computer science, quantitative biology, quantitative finance and statistics as well.

Like PLoS Currents (and as was envisaged with one section of E-Biomed) none of the papers submitted to arXiv undergo in-depth peer review. Many are, however, subsequently published in a traditional manner. (As Kling et al. put it, "the vast majority" of papers posted in arXiv, "are eventually published in peer-reviewed journals or peer-reviewed conference proceedings").

Importantly, arXiv has not caused the sky to fall in. Indeed, it appears to have had very little impact on traditional scholarly journals.

Although it does not peer review papers submitted to it, however, arXiv does have a moderation process, and some articles are subsequently removed or reclassified (a process, incidentally, that has its own critics).

PLoS Currents will have something similar. As Varmus explains on the PLoS blog, "unsuitable submissions [to PLoS Currents] will be screened out by a board of expert moderators led by Eddie Holmes (Center for Infectious Disease Dynamics, Pennsylvania State University, USA) and Peter Palese (Department of Microbiology, Mount Sinai School of Medicine, USA)."

All in all, some may be tempted to conclude that it is a great shame it has taken ten years for Varmus' original idea for E-biomed to see the light of day; and a great shame that it has taken eighteen years for the biomedical research community to catch up with physicists when it comes to the rapid dissemination of their research results.

On the other hand, the ten-year delay has at least allowed PLoS to make use of cutting-edge technologies like Google Knol (which only became available last year).

Perhaps we should think of PLoS Currents as E-Biomed 2.0?