Saturday, March 15, 2008

Science 2.0

Science 2.0: Great New Tool, or Great Risk?
Wikis, blogs and other collaborative web technologies could usher in a new era of science. Or not / M. Mitchell Waldrop


The explosively growing World Wide Web has rapidly transformed retailing, publishing, personal communication and much more. Innovations such as e-commerce, blogging, downloading and open-source software have forced old-line institutions to adopt whole new ways of thinking, working and doing business.

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 blogs, wikis and social networks 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 the traditional variety, but considerably more productive.

"Science happens not just because of people doing experiments, but because they're discussing those experiments," explains Christopher Surridge, editor of the Web-based journal, Public Library of Science On-Line Edition (PLoS ONE).

[http://scholarship20.blogspot.com/2007/12/plos-one-post-publication-peer-reviewed.html]

Critiquing, suggesting, sharing ideas and data--communication is the heart of science, the most powerful tool ever invented for correcting mistakes, building on colleagues' work and creating new knowledge. And not just communication in peer-reviewed papers ... [snip].

The technologies of Web 2.0 open up a much richer dialog, says Bill Hooker, a postdoctoral cancer researcher at the Shriners Hospital for Children in Portland, Ore., and the author of a three-part survey of open-science efforts in the group blog, 3 Quarks Daily [http://www.3quarksdaily.com/]. "To me, opening up my lab notebook means giving people a window into what I'm doing every day. That's an immense leap forward in clarity. [snip]

Of course, many scientists remain highly skeptical of such openness--especially in the hyper-competitive biomedical fields, where patents, promotion and tenure can hinge on being the first to publish a new discovery. From that perspective, Science 2.0 seems dangerous: using blogs and social networks for your serious work feels like an open invitation to have your online lab notebooks vandalized--or worse, have your best ideas stolen and published by a rival. To Science 2.0 advocates, however, that atmosphere of suspicion and mistrust is an ally. "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, says PLoS ONE's Surridge, scientists should find the 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 "crowd-sourcing" 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," he says.

[OpenWetWare]

The OpenWetWare [http://openwetware.org/] project at MIT is an early success. Launched in the spring of 2005 by graduate students working for MIT biological engineers Drew Endy and Thomas Knight, who collaborate on synthetic biology, the project was originally seen as just a better way to keep the two labs' Web sites up to date. OpenWetWare is a wiki--a collaborative Web site that can be edited by anyone who has access to it; it even uses the same software that underlies the online encyclopedia Wikipedia. [snip]. But then, users discovered that the wiki was also a convenient place to post what they were learning about lab techniques: manipulating and analyzing 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 of Endy's who now sits on the OpenWetWare steering committee.

[snip]

[snip] Instead of making do with a static Web page posted by a professor, users began to create dynamically evolving class sites where they could post lab results, ask questions, discuss the answers and even write collaborative essays. "And all stayed on the site, where it made the class better for next year," says Shetty, who has created an OpenWetWare template for creating such class sites.

[snip] "I didn't even know what a wiki was," recalls Maureen Hoatlin of the Oregon Health & Science University in Portland, 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 harder 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 needed to access it from wherever I was. 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, which Hoatlin saw in the spring of 2006, fit the bill perfectly. "The transparency turned out to be very powerful," she says. "I came to love the interaction, 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."

Numerous others now work through OpenWetWare to coordinate research. SyntheticBiology.org [http://syntheticbiology.org/], one of the site's most active interest groups, currently comprises six laboratories in three states, and includes postings about jobs, meetings, discussions of ethics, and much more.

In short, OpenWetWare has quickly grown into a social network catering to a wide cross-section of biologists and biological engineers. It currently encompasses laboratories on five continents, dozens of courses and interest groups, and hundreds of protocol discussions--more than 6100 Web pages edited by 3,000 registered users. A May 2007 grant from the National Science Foundation launched the OpenWetWare team on a five-year effort to transform OpenWetWare to a self-sustaining community independent of its current base at MIT. The grant will also support development of many new practical tools, such as ways to interface biological databases with the wiki, as well as creation of a generic version of OpenWetWare that can be used by other research communities such as neuroscience, as well as by individual investigators.

Skepticism Persists

For all the participants' enthusiasm, however, this wide-open approach to science still faces intense skepticism. [snip]

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 [http://usefulchem.wikispaces.com/] in December 2005. [snip]

However, the Web provides better protection that the traditional journal system, Bradley maintains. Every change on a wiki gets a time-stamp, he notes, “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."

[snip] "A simple wiki makes an almost perfect lab notebook," he 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 there are sometimes legitimate reasons for researchers to think twice about being so open. If work involves patients or other human subjects, for example, privacy is obviously a concern. And if you think your work might lead to a patent, it is still not clear that the patent office will accept a wiki posting as proof of your priority. Until that is sorted out, he says, "the typical legal advice is: do not disclose your ideas before you file."

[snip]

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 April 2007 North Carolina Science Blogging Conference [http://scienceblogging.com/], one of the first national gatherings devoted to this topic. The whole point of blogging is spontaneity--getting your ideas out there quickly, even at the risk of being wrong or incomplete. "But to a scientist, that's a tough jump to make," says Willard, head of Duke's Institute for Genome Sciences & Policy. "When we publish things, by and large, we've gone through a very long process of drafting a paper and getting it peer reviewed. [snip]

Still, 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 possible. Blogging is slowly beginning to catch on; because most blogs allow outsiders to comment on the individual posts, they have proved to be a good medium for brainstorming and discussions of all kinds. Bradley's UsefulChem blog is an example. Paul Bracher's Chembark [http://blog.chembark.com/] is another. "Chembark has morphed into the water cooler of chemistry," says Bracher, [snip] ... .

[snip]

The credit-assignment problem is one of the biggest barriers to the widespread adoption of blogging or any other aspect of Science 2.0, agrees Timo Hannay, head of Web publishing at the Nature Publishing Group in London. [snip] 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 on line, that will get easier to measure too."

Collaboration the Payoff

The acceptance of any such measure would require a big change in the culture of academic science. But for Science 2.0 advocates, the real significance of Web technologies is their potential to move researchers away from an obsessive focus on priority and publication, toward the kind of openness and community that were supposed to be the hallmark 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 afterwards as well: PLoS ONE not only allows users to annotate and comment on the papers it publishes online, but to rate the papers' quality on a scale of 1 to 5.

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. "We've recognized that the Web can completely change the way that communication happens." Among the efforts are Nature Network, a social network designed for scientists; Connotea, a social bookmarking site patterned on the popular site del.icio.us, but optimized for the management of research references; and even an experiment in open peer review, with pre-publication manuscripts made available for public comment.

Indeed, says Bora Zivkovic, a circadian rhythm expert who writes at Blog Around the Clock [http://scienceblogs.com/clock/], and 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 to go," Hooker adds. "But I'd be happy to bet that we're going to like it when we get there."

[http://www.sciam.com/article.cfm?id=science-2-point-0-great-new-tool-or-great-risk]

Edit This - 2008

Welcome to a Scientific American experiment in "networked journalism," in which readers—you—get to collaborate with the author to give a story its final form.

[This] article ... is a particularly apt candidate for such an experiment [as it is a] ... feature story on "Science 2.0," which describes how researchers are beginning to harness wikis, blogs and other Web 2.0 technologies as a potentially transformative way of doing science. The draft article appears here, several months in advance of its print publication, and we are inviting you to comment on it. Your inputs will influence the article’s content, reporting, perhaps even its point of view.

[snip]

[http://www.sciam.com/section.cfm?id=edit-this]

2 comments:

ChemSpiderMan said...

Gerry...I recently wrote an article for Drug Discovery News about collaborative science through Wikis and Blogs. Should be published soon. I encourage you to take a look at the work of Jean Claude Bradley at Drexel University. He runs UsefulChem: http://usefulchem.wikispaces.com/

Axel P. Mustad said...

Gerry - interesting article.

We work on developing a high quality ontological framework for nano- and converging technologies.

We have implemented an analytic classification engine and system for tracing the evolution and dependencies of ideas, 'the creative process', within a certain subject domain.

Together with universities, research institutes and industry we define an international cooperation in the field of knowledge sharing and cooperative industrial technology development for innovation financing in nano- and converging technologies, for accelerated development of publicly funded research and technological development projects.

Should anyone developing "science 2.0" systems be interested in collaboration; http://www.nqcg.com