May 21, 2011


Free Science, One Paper at a Time (David Dobbs, May 11, 2011, Wired)

Jonathan Eisen’s quest has solidified his conviction that science needs to radically rework the way it collects and shares its data, methods, and findings. He has plenty of company. A growing number of prominent scientists want to replace the aging journal system with something faster, cheaper, and richer. The current system, they note, grew out of meeting notes and journals published by societies in Europe over three centuries ago. Back then, quarterly or monthly volumes could accommodate the flow of ideas and data from most disciplines, and the printed journal, though it required a top-heavy, expensive printing and publishing infrastructure, was the most efficient way to share those ideas.

“But now,” says Jonathan Eisen, “there’s this thing called the Internet. It changes not just how things can be done but how they should be done.”

As Stanford biochemist and PLoS co-founder Patrick Brown put it a few years ago, “What seemed an impossible ideal in 1836, when Antonio Panizzi, librarian of the British Museum, wrote, ‘I want a poor student to have the same means of indulging his learned curiosity, … of consulting the same authorities, … as the richest man in the kingdoms,’ is today within reach. With the Internet, we have the means to make humanity’s treasury of knowledge freely available to scientists, teachers, students and the public around the world.”

“The existing system worked well for quite a while,” says Jonathan Eisen. “But it was not designed by theory. It was designed by constraints.” In a world that provides communications conduits far larger and faster, those constraints have now made science’s traditional pipeline a bottleneck.


To get a sense of how the current system curbs science, consider a rare case in whichresearchers attacked a big medical problem with an open-science model. In 2004, in the United States, a network of government and private researchers, including large drug companies, used open-science principles to accelerate research into Alzheimer’s. The project, as Gina Kolata aptly described it in the New York Times last summer, “was an agreement … not just to raise money, not just to do research on a vast scale, but also to share all the data, making every single finding immediately available to anyone with a computer anywhere in the world. Before that, researchers worked separately, siloing off much of their work. Now methods and data formats were standardized. The data would immediately enter the public domain, where anyone could build on it.”

An extraordinary project ensued. The U.S. National Institute on Aging contributed over $40 million, and 20 companies and two nonprofit groups kicked in another $25 million to fund the first six years. The program produced an explosion of papers on early diagnosis and helped generate more than 100 studies to test drugs or other treatments. It greatly sped and opened the flow of findings and data. According to the New York Times, the project’s entire massive database had been downloaded more than 3,200 times by last summer, and the data sets containing images of brain scans was downloaded almost a million times. Everyone was so pleased with the results that they renewed the accord this year. And all because, as a researcher told Kolata, “we parked our egos and intellectual-property noses at the door.”

The language used here — everything entering the public domain, the dismantling of silos, the parking of egos and IP padlocks — might have been lifted from an open-science manifesto. And even Big Science appreciated the outcome. To open-science advocates, this raises a good and somewhat obvious questiknowleon: Why don’t we do science like this all the time?

Part of the answer, strangely, is the very thing at the center of science: the paper. Once science’s main conduit, the paper has become its choke point.

It’s not just that the paper is slow, though that is a huge problem. A researcher who submits a paper to a traditional journal right now, for instance, won’t see the published piece for about a year. She must wait while the paper gets passed around among editors, then goes through rounds of peer review by experts in her field, who might and often do object not just to her methods or data but to her findings and interpretations. Finally, she must wait while it moves through an editing, layout, and publishing pipeline that itself might run anywhere from 2 to 12 weeks.

Yet the paper is not simply slow; it’s heavy. Even as increasingly data-rich science has outgrown the paper’s ability to deliver and describe all that science has to offer — its deep databases, its often elaborate methods — we’ve loaded it up needlessly with reputational weight and vital functions other than carrying data.

The paper is meant to be a conduit for the real content and currency of the science: the ideas, methods, data, and findings of the people who do science. But the tremendous publishing and commercial infrastructure built around the academic paper over the last half-century has concentrated so many functions and so much value in the journal that the paper itself, rather than the information in it, has become science’s main currency. It is the paper you must buy; the paper you must publish; the paper you must cite; the paper on which not just citations but tenure, reputation, status, and even school rankings are built.


To get an idea of the paper’s excess weight, go to Cambridge, England, and find Mark Patterson. Patterson is a scientific-publishing old hand gone rogue. He formerly worked at two of the biggest scientific publishing companies, Elsevier and Nature Publishing Group (NPG), each of which puts out scores of journals. A few years ago he moved to the staff at PLoS.* Patterson is now director of publishing there, and since he joined, PLoS has leveraged open-science principles to become one of the world’s biggest publishers of peer-reviewed science and the biggest single publisher of biomedical literature. Readers like it because they get free access to good science. Researchers like it because their work reaches more readers and colleagues. PLoS’s success is heartening open-science advocates greatly — and unsettling the traditional publishers.

To describe PLoS’s innovations, Patterson likes to talk about how PLoS’s most innovative journal, PLoS One, deals with four essential functions of science that are currently wrapped up in the scientific paper: registration, certification, dissemination, and preservation. The current publishing regime, he argues, locks up these functions too closely in the current, conventional version of the scientific paper — even though some of these functions can be met more efficiently by other means.

So what are these functions?

Registration is essentially a scientific claim of discovery — a marker crediting a particular researcher with an idea or finding. The current system registers these contributions via a paper’s submission date. Certification is essentially quality control: ensuring a paper is solid science. It is traditionally done via peer review. Dissemination means getting the stuff out there — publication and distribution, in printed journals or online. And preservation, or archiving, involves the maintenance of the papers and citations to create a breadcrumb trail other researchers can later follow back to an idea or finding.

“The current journal system does all four of those things,” says Patterson. “But it doesn’t necessarily do them all well. The trick is finding a system that gets each of these done most efficiently, sometimes by other means, instead of having them all held by the publisher.” He and others contend that science would gain both speed and rigor by “unbundling” some of these functions from the paper and doing them in new ways.

PLoS loosens things up mainly in distribution and quality control. All of its journals are open-access — that is, free to read. Instead of making every would-be reader either buy a journal subscription or pay a per-article price of $15 to $50, PLoS collects a fee from the researcher to publish — usually about $1400 or so — and then publishes the paper online and makes it free. The author fee is substantial, but it’s actually a small addition to the other costs of doing science, and performs the essential function of getting it out there. It’s Panizzi’s dream realized: every poor schoolchild — or at least every schoolchild with web access — can read PLoS. Researchers like this, and it works. A recent study showed that on average, papers and data published open-access receive more citations than did those behind paywalls.

PLoS’s rapid growth has shaken things up. Some journal groups, such as Elsevier, have responded by allowing authors to pay to have a paper open-access on publication. Yet commercial publishers that do this tend to retain certain rights that PLoS does not, and they’re less likely to release underlying data, metadata about the publications, or other data and rights. And the practice creates a weird and uncertain market: You can go to, say, Neuron, and find, in the same issue, one paper you can download for free and another that costs $30. The difference? The authors of the latter paper didn’t pay the open-access fee.

Meanwhile, PLoS’s biggest, most cross-disciplinary journal, PLoS One, streamlines quality control in a way that’s more complex and raises more ire. The traditional route, peer review, generally involves having two or three experts evaluate the entire paper — data, methods, findings, conclusions, significance. The publisher relays these peer critiques to the author, usually with requests for either changes or clarifications. If the author answers those to the publisher’s satisfaction, the paper gets approved.

PLoS One uses a similar process but — crucially — asks its reviewers to judge only on technical merits, and not on any assessment of the paper’s novelty, significance, or impact. “The idea,” says Patterson, “is to let the importance be determined later by how much the paper’s ideas and findings and conclusions are taken up by the community. We’re letting the scientific community at large determine a paper’s value and importance, rather than just a couple of reviewers.”

You can certainly understand their fear that the marketplace will determine most papers have no value.

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Posted by at May 21, 2011 6:11 AM

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