stanford medicine


Three Scientists

The science pages

Scientists built the web. Do they love web 2.0?

With Oprah proclaiming actor Ashton Kutcher the “king” of Twitter and Sarah Palin taking the title of “fastest-rising” search result on Google in 2008, it is easy to forget that the World Wide Web actually began as a tool for scientists.

Born on the Franco-Swiss border at nuclear physics lab CERN, the first Web site went live in 1990 after computer scientist Tim Berners-Lee showed the power of joining the Internet with hypertext — the now-familiar method of navigating through information using mouse clicks. The goal was to create a network to help the physicists share data.

“Suddenly the Web gave you something to look at. You could finally visualize the communicative power of the Internet,” says M. Mitchell Waldrop, author of The Dream Machine, a history of computing and of the Internet. “The Web exploded because there were all these oil-soaked rags already laying around and somebody tossed in a match.”

But the more-grown-up Web has some personality traits scientists aren’t especially interested in embracing — at least not for their work. In the past five years, the Web has become rife with sites that make it easy for users to share information and to collaborate online. These Web sites (think Wikipedia, YouTube, Facebook and Flickr) are what’s known as “Web 2.0” and they’ve brought publishing within the reach of anyone with Internet access. It is nearly effortless to upload a home video to YouTube and, with a little luck, turn it into a phenomenon like David After Dentist, a video of a child experiencing an existential crisis while still feeling the effects of his anesthetic. (The video has logged more than 21 million viewings.)

The popularization of social bookmarking, blogging, social networking — all Web 2.0 phenomena — has moved the Web from static, printlike pages to an increasingly conversational, collaborative medium. Web 2.0 is, among other things, premised on the notion that users read from and write to the Web. “Once people started to realize the bits flow both ways — that the Web is not just something we look at — we started to see file sharing, social networks and a whole cluster of tools that are now called Web 2.0,” says Waldrop, who is also editor for editorials at Nature. “People realized they could contribute in addition to just consuming and they are still figuring out how to use that.”

The popularity of these services speaks for itself: According to the Pew Internet & American Life Project, 52 percent of all U.S. adults watch videos on YouTube, 35 percent use Facebook or MySpace, and 47 percent use Wikipedia.

And as these services have become household names, a constellation of applications for scientists started to gather under a “Science 2.0” banner: video journals and wikis for sharing protocols, and even social networks for researchers along the lines of Facebook. Their aim is to make scientific collaboration as easy as sharing videos of trips home from the dentist. Not many scientists are biting, though.

“Obviously the Web has transformed biomedicine and we should not forget that,” says Henry Lowe, MD, the medical school’s senior associate dean for information resources and technology. “There are many scientific resources available via the Web, PubMed being the obvious example. These resources have been transformative in opening up science to the world.”

But Web 2.0? Not so much.

“I believe we are at the very beginning of a transformation in the biomedical sciences,” Lowe says. “It is going to take a decade because these things move slowly.”

“Scientists have fallen behind the curve,” says Geoff Bowker, PhD, executive director of the Center for Science, Technology and Society at Santa Clara University. “I think you see more exciting Web 2.0 projects in business applications.”

Bowker is not alone in his opinion. “Anecdotally, there has been very low engagement in the scientific community with any of the Web 2.0 collaborative tools,” says Diana Rhoten, PhD, a School of Education alum and a program director at the Social Science Research Council. Rhoten was a program manager at the National Science Foundation’s Office of Cyberinfrastructure when many of the first Science 2.0 applications were being built. “We are right at that moment where the technology has been put out there, but there hasn’t been a social shift that will push them to success.”

The slow shift to Science 2.0 applications may arise from sociological issues rather than technological ones.

A simple generational difference is at work to a certain extent, says Bowker. “The base problem is use and habit: Suppose you come along with some great new tool for me, but that new tool means that I need to learn a new system,” he says. “Suddenly I go from being an expert to being a neophyte with a steep learning curve. The cost of the adoption of the new technology is too high and that can act as brakes on the adoption of any kind of new networking technology.”

“Typically one’s willingness to share depends on seniority.”

And beyond the adoption cost, Science 2.0 developers have built in an assumption that what works well for Wikipedia will also work well for science. That may eventually hold true, but today the social structures that support scientific research may not be conducive to Web 2.0-style collaboration. “Science has always been a community endeavor, but it has not historically been a collaborative endeavor,” says Rhoten. “There is a big cultural shift to be made. The incentive structure does not fully reward collaborative endeavors.”

That’s because while science is cooperative, it’s also competitive — very much so. And sharing information about one’s research in progress could give competitors an edge. “Typically one’s willingness to share depends on seniority: The more senior you are, the more willing you will be to share information,” says Bowker. That means younger researchers, who are likely more comfortable with the new Web tools, still won’t use them.

Scientists are promoted on the basis of publication in peer-reviewed journals, not for how they work together in the laboratory, points out Rhoten. There is no prevailing system yet for measuring collaborative contributions to science — for example, managing a database. As such, it is impossible to know how to reward researchers for those contributions, even though contributions like managing a database arguably add value to science. Compounding the problem, Web 2.0 applications are usually premised on heavy doses of almost anonymous collaboration. (As an illustrative exercise, try to name the last Wikipedia author you noticed.)

“There is a need for a metric or method for isolating contributions to collaborative projects,” says Rhoten. “That’s not what Web 2.0 is about, so it creates a culture clash.”

Of course, the explanation could be much simpler than sociology, as Lowe points out. He says that the current crop of Science 2.0 applications may not offer enough utility to justify their use: “You really have to take the scientist’s perspective and ask, ‘What is the added value here? This is going to take some work on my part to maintain. What am I getting out of it in return?’ Frankly, most of the existing systems don’t really offer biomedical scientists much in return.”

But can big change be far off when even print journals are starting to play in the Web 2.0 pool? RNA Biology, for example, is requiring any author who submits an article about families of RNA molecules to also submit at least one summary of the article to be posted on Wikipedia. The journal then peer reviews the page before publishing it in Wikipedia. “This requirement ensures an easily accessible, high-profile and high-quality Wikipedia article is generated for each RNA family we publish,” writes Paul Gardner, associate editor of RNA Biology and a researcher at the Sanger Institute.

Eventually Web-only publishing could replace print journals. Bowker points to the physics community, with its arXiv repository at Cornell University ( “It’s interesting if you look at the physics community as the homeland of all of this,” he says. “Basically, people read physics papers not in journals; they read them at arXiv.”

A new movement called open-access publishing coalesced over the last decade, with the aim of making scientific information in peer-reviewed journals available to the public without cost. Open access to scientific papers has been a (contentious) point of discussion for approximately five years, but its supporters have been increasing in number and now include the Howard Hughes Medical Institute, Wellcome Trust, the National Institutes of Health and the Massachusetts Institute of Technology.

Open access could show how other aspects of scientific research on the Web could change very soon. Lowe sums up the inflection point nicely: “This is like a wave. It will travel and it is going to take time,” he says. “Some of the things we are going to see five years from now are going to be hard to imagine.”















New Web ToolsA Glossary

Hypertext: Text containing “links” to additional text that a user can retrieve by means of a mouse click or keystroke. Hypertext can also contain images and other rich media. The concept has been discussed in academic circles since the 1940s, but its first public demonstration came in 1968, when Douglas Engelbart, PhD, and his colleagues at Stanford Research Institute unveiled NLS or “oN-Line System.” In what has become known as the “mother of all demos,” Engelbart showed the public both the graphical user interface and hypertext in a single presentation.

Science 2.0: A term used to describe Web 2.0 (see below) tools targeted at the scientific community.

Social bookmarking: A system that allows users to share, store, tag and organize bookmarks, typically via a Web service such as Delicious.

Social network service: Most commonly a Web-based community of people that is self-organized according to social relationships, interests and/or activities. Facebook and LinkedIn are two prominent examples.

Web 2.0: A term used to describe a second generation of Web design and development that facilitates collaboration and the iterative manipulation of information. Web 2.0 has led to the development of blogs, social networks, content-sharing sites and wikis.

Wiki: A collection of Web pages that can typically be edited by any user. The massive online encyclopedia, Wikipedia, is the most noteworthy example of a wiki.

Science 2.0 sample pack Web 2.0 applications tailored for the scientific community

OpenWetWare is a wiki that has made it literally as simple to share laboratory information and protocols as editing a Wikipedia page. Originally called Endipedia, OpenWetWare was launched in 2005 by graduate students at MIT working in the laboratories of Andrew Endy, PhD, and Thomas Knight. Endy is now an associate professor of bioengineering at Stanford. In 2007, the National Science Foundation awarded the OpenWetWare team a grant to continue building the online community. Four years on, OpenWetWare is home to 5,847 users from around the world, including researchers from Harvard University, Baylor College of Medicine, MIT, Yale University, Stanford University, University of Cambridge and many others. On its pages, researchers can locate a protocol for the extraction of DNA from the tissue or embryos of mice, techniques for determining the size of objects in microns, or a protocol for freezing and thawing mammal cells.

The Journal of Visualized Experiments is a peer-reviewed Web journal that publishes videos demonstrating protocols (a paper also accompanies the video). The journal, also called JoVE, is designed to make experiments easier by showing researchers how a protocol works in real time. Its how-to videos run the gamut from pressure-polishing pipettes to harvesting hamster oocytes and mouse embryos.

Epernicus is a social network designed to help investigators identify people and techniques that can help them solve their research problems. Epernicus is similar to Facebook in that its users complete profiles and form networks of contacts, but its profiles are tailored to a scientific audience.

Nature Network is another social network for scientists, this one run by Nature Publishing Group. Nature has also created its own social bookmarking service, Connotea, which works like Delicious, a popular social bookmarking service.

Proteome Commons is a collaborative site for sharing information about proteomics (a proteome is the range of proteins expressed by a genome, cell, tissue or organ), as well as managing projects and data. As of this writing, the site has 306 members sharing some 12.5 million files or approximately 9.2 terabytes of data.






©2009 Stanford University  |  Terms of Use  |  About Us