Thursday, January 17, 2008

Science 2.0: Great New Tool, or Great Risk?-SciAm debate

The following is an interesting article that is opened for comments by Scientific American:
The debate is about whether wikis, blogs and other collaborative web technologies could usher in a new era of science. Or not.


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). 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; as important as those papers are, 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."
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. "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. 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 open notebook, but are obscured by every other communication mechanism we have. It makes science more efficient." That jump in efficiency, in turn, could have huge payoffs for society, in everything from faster drug development to greater national competitiveness.
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.
The OpenWetWare 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. Students happily started posting pages introducing themselves and their research, without having to wait for a Webmaster to do it for them.
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. "But we didn't have that." Most of the students came from a background in engineering; theirs was a young lab with almost no mentors. So whenever a student or postdoc managed to stumble through a new protocol, he or she would write it all down on a wiki page before the lessons were forgotten. Others would then add whatever new tricks they had learned. This was not altruism, notes steering-committee member Reshma Shetty. "The information was actually useful to me." But by helping herself, she adds, "that information also became available around the world."
Indeed, Kelly points out, "Most of our new users came to us because they'd been searching Google for information on a protocol, found it posted on our site, and said 'Hey!' As more and more labs got on, it became pretty apparent that there were lots of other interesting things they could do."
Classes, for example. 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.
Laboratory management benefited too. "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, 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. 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"--not least to keep her lab pages from getting trashed by some random hacker. She did not relax until she began to understand the system's built-in safeguards.
First and foremost, says MIT's Kelly, "you can't hide behind anonymity." By default, OpenWetWare pages are visible to anyone (although researchers have the option to make pages private.) But 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 they did, the wiki automatically maintains a copy of every version of every page posted: "You could always just roll back the damage with a click of your mouse."
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, in December 2005. Even if incidents are rare in reality, 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.
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."
Under Bradley's radically transparent "open notebook" approach, as he calls it, 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," 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."
Still, Bradley says the more open scientists are, the better. When he started UsefulChem, for example, 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 anti-tumor agents. Rajarshi Guha at Indiana University offered to help us do calculations about docking--figuring out which molecules will be reactive. And there were others. So 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 April 2007 North Carolina Science Blogging Conference, 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. 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…’."
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 is another. "Chembark has morphed into the water cooler of chemistry," says 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," says PLoS ONE's Surridge. "Scientists don't blog because they get no credit."
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. (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 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, 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."


Enjoy!

Tuesday, January 15, 2008

Study challenges glacial melt-global warming theory!

Here we are. A roller-coaster ride that climate scientists subject us to.
The Inter-governmental Panel on Climate Change has injected fears of a doomsday approaching us.
No sooner has the Nobel gone to the protagonists of such a theory, a study at the University of California San Diego's Scripps Institution of Oceanography have come out with a shocker.
But that shocker may well pave the way for climate scientists to employ newer study strategies and approach the topic in a different way.
The researchers (Richard Norris, professor of paleobiology at Scripps Oceanography, and Andre Bornemann, a postdoctoral researcher at Scripps Oceanography and who continues the research at Universitat Leipzig in Germany) have found that though temperatures were much higher during the Cretaceous period (about 90 million years ago in the time of the dinosaurus) glaciers continued to be formed.
The temperatures then were found to be 35-37°C (95-98.6°F), about 10°C (18°F) warmer than today, thus creating a supergreenhouse climate.
Now this goes against the conventional thinking so far put forth and held by protagonists of the doomsday climatic changes.
What supports this research is that at least two other studies, one in Russia and other in New Jersey, found that sea level during that age actually fell by as much as about 25-40 m (82-131 feet).
The IPCC, in fact, has put out alerts saying that sea-levels would actually rise in the present age due to global warming. How then did sea levels 90 million years back fall despite the world simmering at 10°C more than present temperatures?
The new study, "Isotopic Evidence for Glaciation During the Cretaceous Supergreenhouse" is published in the January 11th issue of the journal Science.
It examined geochemical and sea level data retrieved from marine microfossils deposited on the ocean floor 91 million years ago during the Cretaceous Thermal Maximum.
They used two independent isotopic techniques and studied microfossils to gather geochemical data on the growth and eventual melting of large Cretaceous ice sheets. The researchers compared stable isotopes of oxygen molecules (d18O) in bottom-dwelling and near-surface marine microfossils, known as foraminifera, to show that changes in ocean chemistry were consistent with the growth of an ice sheet. The second method in which an ocean surface temperature record was subtracted from the stable isotope record of surface ocean microfossils yielded the same conclusion.
These independent methods provided them evidence to conclude that an ice sheet about 50-60 percent the size of the modern Antarctic ice cap existed for about 200,000 years.
Norris wonders how even the super-warm climates of the Cretaceous Thermal Maximum were not warm enough to prevent ice growth.
Then what about now?
The researchers suspect that past greenhouse climates may have aided ice growth by increasing the amount of moisture in the atmosphere and creating more winter snowfall at high elevations.
As humans continue to add large amounts of carbon dioxide and other greenhouse gases that accelerate the heating of the atmosphere and oceans, research on Earth's past climate conditions is critical to predict what will happen as Earth's climate continues to warm.
Will this new study warrant a change in an approach of scientists in taking what happened during the Cretaceous period as an input to current studies?
Maybe, we have missed something crucial!

Sunday, January 6, 2008

Indian Science 'Circus' 2008 is like a 'wide ball'

What a comic affair the 95th Indian Science Congress in Vishakhapatnam (Andhra Pradesh) has turned out to be! Nobel Laureates are treated like film stars without a word of what they said being understood, and sessions are featuring recycled presentations, in many cases straight downloads from the Net.
The 95th Indian Science Congress in Vishakhapatnam (Andhra Pradesh) potrayed what Indians are known for best -- over-excited lot of jokers, when it comes to science and technology. More of noise than anything else.
Take the sessions, for instance. Each of the sessions were nothing but idiotic normative analysis, when its should have been scientists telling people what new things are being done that are applicable as solutions to instant problems indians face in every corner of the country.
That is not to be. Sadly, the event's theme -- ''Knowledge-based society using environmentally sustainable science and technology'' -- is too broad-based for any long-lasting impact made by the five-day event on any specific area of science.
In keeping with such a chaotic event, scientists appear to be just rambling off presentations that have been made over and over again in the past. So much so, that even the much celebrated Indian Space Research Organisation (ISRO) scientists made a mediocre presentation on the second day when they told a motley group of delegates about the power of space technologies in solving the mess that Indian educations lies in.
No prizes for guessing what the space scientists had to say -- that satellite-based technologies are a sure-shot solution for reaching out to school drop-outs in remote villages, that the space technology could also help in increasing the number of PhDs and MTechs who are short by as much as 30,000 and 40,000 respectively, and of course in helping doctors in a remote village be connected with specialists in the respective field to operate upon hapless persons needing to go under the knife urgently.
It is a lop-sided effort.
What these technologies do not do is convince school drop-outs to return to school. How can a student determined to begin working by stopping school to earn his family some (lots!) money be convinced by space technology to attend classes that are relayed via satellite links?
Or, how are people expected to just walk into a room where space tech is bringing material to help people complete PhDs and MTechs, when in the first place those very people are voluntarily looking at more lucrative professions, not to end up as lecturers and professors with meagre incomes in comparison with what MNCs have to offer?
The Science Congress is like a ''wide ball'' bowled by an erratic bowler. A systematic tackling of the ''lack-of-interest-in-science'' issue should begin by making science teaching an interesting exercise in schools. That requires expert teachers who have the ability to hold rapt attention of the students through unique teaching methods.
Unfortunately, what is holding the rapt attention of students today is the process of making a quick buck. Nothing scientific about that.
ISRO's chairman Madhavan Nair once rightly said only those who have a passion for research would survive being in the scientific community despite the lure of attractive pay packages offered by MNCs.
But how do you find those kind of people?
I think the science congresses should first focus on this issue -- generate more people with passion for research. Only then such events would fill up with people who come with solutions, or who have already come up with solutions for the masses.
Only then would science congress mean a more interesting event attracting more youth to its folds. This in turn would be able to popularise science, which is the very objective of the Indian Science Congress Association.
Otherwise, just forget future science congresses that have the blessing of the Union Government through a Rs 1 crore grant that comes its way every year.