Science 2.0

The first generation of World Wide Web capabilities rapidly transformed retailing and information search. More recent attributes such as blogging, tagging and social networking, dubbed Web 2.0, have just as quickly expanded people’s ability not just to consume online information but to publish it, edit it and collaborate about it—forcing such old-line institutions as journalism, marketing and even politicking to adopt whole new ways of thinking and operating.

Science could be next. A small but growing number of researchers (and not just the younger ones) have begun to carry out their work via the wide-open tools of Web 2.0. And although their efforts are still too scattered to be called a movement—yet—their experiences to date suggest that this kind of Web-based “Science 2.0” is not only more collegial than traditional science but considerably more productive.

“Science happens not just because of people doing experiments but because they’re discussing those experiments,” explains Christopher Surridge, managing editor of the Web-based journal Public Library of Science On-Line Edition (www.plosone.org). Critiquing, suggesting, sharing ideas and data—this communication is the heart of science, the most powerful tool ever invented for correcting errors, building on colleagues’ work and fashioning new knowledge. Although the classic peer-reviewed paper is important, says Surridge, who publishes a lot of them, “they’re effectively just snapshots of what the authors have done and thought at this moment in time. They are not collaborative beyond that, except for rudimentary mechanisms such as citations and letters to the editor.”

Web 2.0 technologies open up a much richer dialogue, says Bill Hooker, a postdoctoral cancer researcher at the Shriners Hospital for Children in Portland, Ore., and author of a three-part survey on open-science efforts that appeared at 3 Quarks Daily (www.3quarksdaily.com), where a group of bloggers write about science and culture. “To me, opening up my lab notebook means giving people a window into what I’m doing every day,” Hooker says. “That’s an immense leap forward in clarity. In a paper, I can see what you’ve done. But I don’t know how many things you tried that didn’t work. It’s those little details that become clear with an open [online] notebook but are obscured by every other communication mechanism we have. It makes science more efficient.” That jump in efficiency, in turn, could greatly benefit society, in everything from faster drug development to greater national competitiveness.

Of course, many scientists remain wary of such openness—especially in the hypercompetitive biomedical fields, where patents, promotion and tenure can hinge on being the first to publish a new discovery. For these practitioners, Science 2.0 seems dangerous: putting your serious work out on blogs and social networks feels like an open invitation to have your lab notebooks vandalized—or, worse, your best ideas stolen and published by a rival.

To advocates, however, an atmosphere of openness makes science more productive. “When you do your work online, out in the open,” Hooker says, “you quickly find that you’re not competing with other scientists anymore but cooperating with them.”

Rousing Success
In principle, Surridge says, scientists should find a transition to Web 2.0 perfectly natural. After all, since the time of Galileo and Newton, scientists have built up their knowledge about the world by “crowdsourcing” the contributions of many researchers and then refining that knowledge through open debate. “Web 2.0 fits so perfectly with the way science works. It’s not whether the transition will happen but how fast,” Surridge says.

One early success is the OpenWetWare project at the Massachusetts Institute of Technology (www.openwetware.org). Launched in 2005 by graduate students working in the laboratories of M.I.T. biological engineers Drew Endy and Thomas Knight, the project was originally seen as just a better way to keep the two lab Web sites up-to-date. OpenWetWare is a wiki—a collaborative Web site that can be edited by anyone who has access. It uses the same software that underlies the online encyclopedia Wikipedia. The students happily started posting pages introducing themselves and their work.

Soon, however, they discovered that the wiki was also a convenient place to post what they were learning about lab techniques: manipulating DNA, getting cell cultures to grow. “A lot of the how-to gets passed around as lore in biology labs and never makes it into the protocol manuals,” says Jason Kelly, a graduate student who now sits on the OpenWetWare steering committee. “But we didn’t have that.” Most of the students came from engineering backgrounds; theirs were young labs with almost no mentors. So whenever a student or postdoc managed to stumble through a new protocol, he or she would write down what was learned on a wiki page. Others would then add whatever tricks they had gleaned. The information was very useful to the labs’ members, notes M.I.T. grad student and steering-committee member Reshma Shetty, but “that information also became available around the world.”

Indeed, Kelly points out, “most of our users came to us because they’d been searching Google for information on a protocol, found it on our site, and said, ‘Hey!’” As more and more people got on, it became apparent that the collaboration could benefit other endeavors, such as classes. Instead of making do with a static Web page posted by a professor, students began to create dynamically evolving class sites where they could post lab results, ask questions, discuss the answers and even write collaborative essays. “And it all stayed on the site, where it made the class better for next year,” says Shetty, who has built an OpenWetWare template for creating such class sites.

Laboratory management benefited too. “I didn’t even know what a wiki was,” recalls Maureen Hoatlin of the Oregon Health & Science University, where she runs a lab studying the genetic disorder Fanconi anemia. But she did know that the frenetic pace of research in her field was making it hard to keep up with what her own team members were doing, much less Fanconi researchers elsewhere. “I was looking for a tool that would help me organize all that information,” Hoatlin says. “I wanted it to be Web-based, because I travel a lot and need to access it from wherever I am. And I wanted something my collaborators and group members could add to dynamically, so that whatever I saw on that Web page would be the most recently updated version.”

OpenWetWare fit the bill. “I came to love the interaction,” she says, “the fact that people in other labs could comment on what we do, and vice versa. When I see how fast that is, and its power to move science forward—there is nothing like it.”

A wide cross section of biological researchers now work through OpenWetWare’s growing number of sites, such as SyntheticBiology.org, which includes postings about jobs, meetings, ethics discussions, and much more. OpenWetWare currently encompasses laboratories on five continents, dozens of courses and interest groups, and hundreds of protocol discussions—more than 6,100 Web pages edited by 3,000 registered users. A May 2007 National Science Foundation grant launched the OpenWetWare team on a five-year effort to transform the platform into a self-sustaining community independent of its current base at M.I.T. The grant will also support creation of a generic version of OpenWetWare that other research communities can use.

Skepticism Persists
For all the participants’ enthusiasm, however, this wide-open approach to science does create fear for some. Even Hoatlin found the openness unnerving at first. “Now I’m converted to open wikis for everything possible,” she says, “but when I originally joined I wanted to keep everything private”—in part to keep her lab pages from being trashed by some random hacker. She did not relax until she began to understand the system’s built-in safeguards.

First and foremost, Kelly says, “you can’t hide behind anonymity.” By default, OpenWetWare pages are visible to anyone (although researchers have the option to make pages private). Unlike the oft-defaced Wikipedia, the system will let users make changes only after they have registered and established that they belong to a legitimate research organization. “We’ve never yet had a case of vandalism,” Kelly says. Even if damage were done, it could be rolled back with the click of a mouse: the wiki automatically maintains a copy of every version of every page posted. Unfortunately, this kind of technical safeguard does little to address a second concern: getting scooped and losing the credit. “That’s the first argument people bring to the table,” says Drexel University chemist Jean-Claude Bradley, who created his independent laboratory wiki, UsefulChem (www.usefulchem.wikispaces.com), in December 2005. Even if incidents are rare, Bradley says, everyone has heard a story, which is enough to keep most scientists from even discussing their unpublished work too freely, much less posting it on the Internet.

Ironically, though, the Web provides better protection than the traditional journal system, Bradley maintains. Every change on a wiki gets a time stamp, “so if someone actually did try to scoop you, it would be very easy to prove your priority—and to embarrass them. I think that’s really what is going to drive open science: the fear factor. If you wait for the journals, your work won’t appear for another six to nine months. But with open science, your claim to priority is out there right away.”

Under Bradley’s radically transparent “open notebook” approach, everything goes online: experimental protocols, successful outcomes, failed attempts, even discussions of papers being prepared for publication. “A simple wiki makes an almost perfect lab notebook,” Bradley declares. The time stamps on every entry not only establish priority but allow anyone to track the contributions of every person, even in a large collaboration.

Bradley concedes that researchers may sometimes have legitimate reasons to think twice about being so open. If work involves patients or other human subjects, for example, privacy is a concern. If a scientist is planning to publish in a journal that insists on copyrighting text and visuals, prepublishing online could pose a problem. And if work might lead to a patent, it is still not clear whether the patent office will accept a wiki posting as proof of priority. Until that is sorted out, he says, “the typical legal advice is: do not disclose your ideas before you file.”

Still, Bradley states, the more open scientists are, the better. When he started UsefulChem, his lab was investigating the synthesis of drugs to fight diseases such as malaria. But because search engines could index what his team was doing without needing a bunch of passwords, “we suddenly found people discovering us on Google and wanting to work together. The National Cancer Institute contacted me, wanting to test our compounds as antitumor agents. Rajarshi Guha at Indiana University offered to help us do calculations about docking—figuring out which molecules will be reactive. Now we’re not just one lab doing research but a network of labs collaborating.”

Blogophobia
Although wikis are gaining, scientists have been strikingly slow to embrace one of the most popular Web 2.0 applications: Web logging, or blogging.

“It’s so antithetical to the way scientists are trained,” Duke University geneticist Huntington F. Willard said at the January 2007 North Carolina Science Blogging Conference, one of the first big gatherings devoted to this topic. The whole point of blogging is getting ideas out there quickly, even at the risk of being wrong or incomplete. “But to a scientist, that’s a tough jump to make,” Willard says. “When we publish things, by and large, we’ve gone through a very long process of drafting a paper and getting it peer-reviewed. Every word is carefully chosen, because it’s going to stay there for all time. No one wants to read, ‘Contrary to the result of Willard and his colleagues....’”

Nevertheless, Willard favors blogging. As a frequent author of newspaper op-ed pieces, he feels that scientists should make their voices heard in every responsible way. Because most blogs allow outsiders to comment on the individual posts, they have proved to be a good medium for brainstorming and discussions. Bradley’s UsefulChem blog is one example. Chembark (www.blog.chembark.com) is another. “Chembark has morphed into the water cooler of chemistry,” says Paul Bracher, who is pursuing his Ph.D. in that field at Harvard University. “The conversations are: What should the research agencies be funding? What is the proper way to manage a lab? What types of behavior do you admire in a boss? But instead of having five people around a single water cooler, you have hundreds of people around the world.”

Of course, for many members of Bracher’s primary audience—young scientists still struggling to get tenure—those discussions can look like a minefield. A fair number of the participants use pseudonyms out of fear that a comment might offend some professor’s sensibilities, hurting a student’s chances of getting a job later. Other potential participants never get involved because they feel that time spent with the online community is time not spent on cranking out that next publication. “The peer-reviewed paper is the cornerstone of jobs and promotion,” PLoS ONE’s Surridge says. “Scientists don’t blog because they get no credit” for that.

The credit problem is one of the biggest barriers to many aspects of Science 2.0, agrees Timo Hannay, head of Web publishing at the Nature Publishing Group in London. (That group’s parent company, Macmillan, also owns Scientific American.) Once again, however, the technology itself may help. “Nobody believes that a scientist’s only contribution is from the papers he or she publishes,” Hannay says. “People understand that a good scientist also gives talks at conferences, shares ideas, takes a leadership role in the community. It’s just that publications were always the one thing you could measure. Now, however, as more of this informal communication goes online, that will get easier to measure, too.”

The Payoff of Collaboration
Acceptance of such measures would require a big change in academic culture. But for Science 2.0 advocates, the real significance is the technologies’ potential to move researchers away from an obsessive focus on priority and publication toward the kind of openness and community that were the supposed hallmarks of science in the first place. “I don’t see the disappearance of the formal research paper anytime soon,” Surridge says. “But I do see the growth of lots more collaborative activity building up to publication.” And afterward as well: PLoS ONE allows users not only to annotate and comment on the papers it publishes online but to rate the papers’ quality on a scale of 1 to 5.

Some universities may be coming around, too. In a landmark vote in February, the faculty at Harvard’s College of Arts and Sciences approved a system in which the college would post finished papers in an online repository, available free to all. Authors would still hold copyright and could still publish the papers in traditional journals.

Meanwhile Hannay has been taking the Nature group into the Web 2.0 world aggressively. “Our real mission isn’t to publish journals but to facilitate scientific communication,” he says. Among the efforts are Nature Network, a social network for scientists; Connotea, a social bookmarking site for research references patterned on the popular site del.icio.us; and Nature Precedings, a Web site where researchers can comment on unpublished manuscripts, presentations and other documents.

Indeed, says Bora Zivkovic, a circadian rhythm expert who is the online community manager for PLoS ONE, the various experiments in Science 2.0 are now proliferating so rapidly that it is almost impossible to keep track of them. “It’s a Darwinian process,” he says. “About 99 percent of these ideas are going to die. But some will emerge and spread.”

“I wouldn’t like to predict where all this is going,” Hooker adds. “But I’d be happy to bet that we’re going to like it when we get there.”