by yusunkwon
Best. Freshmen. Evar.:
[Via Unqualified Offerings]

By Thoreau

I decided to give my freshmen a taste of real physics. I offered extra credit to anybody who could give me a useful critique of my grant proposal. Amazingly enough, two of my students actually rose to the occasion. Although they couldn’t really dissect the science, they could tell that I wasn’t really explaining why this would be significant for the field, and they told me what I’d need to say to convince them of the significance. (I guess some people just can’t appreciate the inherent AWESOMENESS of simulating a new technique for optical nanolithography and identifying the necessary molecular parameters.) They earned themselves some extra credit points for the upcoming midterm. Prior to this these students flew under my radar, but if this grant gets funded, they’ll be the first ones that I consider for research assistantships.

I don’t know many researchers who would do this but Thoreau accomplished something very useful. Not only were several deficiencies in the grant identified but the students may have lined up some nice work for themselves. A nice win-win situation.

Obviously there are barriers to overcome (e.g. proprietary information) but I wonder?

Technorati Tags: Knowledge Creation, Science, Web 2.0

by twoblueday
These three posts run the gamut from exuberance to wonder to doubt to reconciliation:

A Breakthrough In Taxonomy?:
So Much For Taxonomies:
Taxonomies Again — What Behavior Do We Want?:
[Via A Journey In Social Media]

They describe the process of creating taxonomies for a group of communities, an attempt to create some order. The very rapid path this took, from the excitement of a brand new idea, its implementation and then the very rapid feedback all demonstrate the power of Web 2.0. Life moves faster.

The problem here is probably a very old one. Some people feel better with a described space, using tags that mean specific things. The tags define the space. Others like the space to define the tags. There will always be a conflict here, between those who want an orderly desktop and those who prefer an unorganized one, especially if both types are represented in the community.

Neither view has a monopoly on wisdom. As brought out here, it is operational the difference between a search and a browse. Tags make searches much easier and allows people to find the exact information they want. The path to the information is sharply defined.

Browsers like to take a less defined path to the information. They like little cul-de-sacs and interesting dead ends. The surprise of new spaces is innervating for them.

One group will always find what they are looking for. The other will be surprised at the novel things they happen upon.

The approach described here was not satisfactory to the users, they let people know and the leaders of the taxonomy project quickly tried to reel it back in and find figure out what to do. They pulled back and asked “What question are we trying to answer?”

They understood that the problem was really getting new users on board as quickly as possible. Here a taxonomy would help them get started. But there are other ways to help newbies that would not disrupt the established users. Now they can try to fix the real problem.

Web 2.0 approaches allowed them to reach this conclusion in just a few days, rather than months, something that happened in the Web 1.0 world.

We tried this at Immunex, with defined tags being used for research projects. The Bioinformatic people spent months putting together the applications to allow tags to be attached to research projects. They finally rolled them out and they were a failure.

The problem was that the users could not define the tags. They were created by some unknown person. So what happens when a new project did not have an appropriate tag? Do you try and use something close, even though it might corrupt the system? Do you leave it blank, subverting the entire purpose? How do new tags get added? Who decides that they should be?

The tags never really got fully utilized. Research moved too fast to rely totally on pre-defined tags. Different people would categorize the same project differently. Without flexibility, too many projects would just get tagged with ‘Other’ negating the whole purpose.

A useful system has to be respectful of the users. It has to be malleable enough to have both structure and flexibility. It would also encourage browsing as easily as it does searching. Not easy things to do. But EMC will get to it faster by using a Web 2.0 approach.

Technorati Tags: Open Access, Social media, Web 2.0

Well, Science 2.0 must be the next full release after Science 1.5.b13, right? Not quite. It takes its lead from applying Web 2.0 approaches to scientific research. So, what is Web 2.0?

In 2005, Tim O’Reilly described in detail what he meant by Web 2.0. Since then, there has been a lot of discussion on just what this means, if anything. So, I am going to add my own two bits to the mix. There really are not many technical differences between Web 1.0 and 2.0. The differences come from how they are used, and how usable they are.

Web 1.0 is static. Web 2.0 is dynamic.

As mentioned in the Wikipedia article on Web 2.0, Web 1.0 was about displaying information. Web 2.0 is about conversations, about participation in the flow of information.

Web 2.0 uses many new approaches for dealing with information including wikis, weblogs, syndication, aggregators, RSS, podcasts, forums and mashups. These often require the active participation of users. They have been used to create hugely popular social media sites, such as Facebook and YouTube, where the very content seen by all is created totally by the users. User-generated content.
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by Wolfgang Staudt
The science exchange:
[Via Science in the open]

How do we actually create the service that will deliver on the promise of the internet to enable collaborations to form as and where needed, to increase the speed at which we do science by enabling us to make the right contacts at the right times, and critically; how do we create the critical mass needed to actually make it happen? In another example of blog based morphic resonance there has been a discussion a discussion over at Nature Networks on how to enable collaboration occurred almost at the same time as Pawel Szczeny was blogging on freelance science. I then hooked up with Pawel to solve a problem in my research; as far as we know the first example of a scientific collaboration that started on Friendfeed. And Shirley Wu has now wrapped all of this up in a blog post about how a service to enable collaborations to be identified might actually work which has provoked a further discussion.
[More]

Open Science is really in the very early stages. It may very well evolve into an important adjunct for research. Collaborations are the prime driver of much of today’s science.

Collaboration is difficult in some organizations. Without it, they will not be able to effectively solve the difficult questions in science today. The organizations that can harness effective collaborations will survive and flourish.

Currently, collaborations are usually set up using well known social networking skills honed through years of experience. Who you know is important. What Open Science holds the potential for, when it comes to collaborations, deals with who you don’t know.

OS can leverage an online community so that connections can be made that would have been difficult or impossible if face time was required. However, it will take a little work, like porcupines mating, to make this really effective.

Part of the reason for this is trust. Science has some free loaders, people who take short cuts. Not many but they can degrade interactions until trust is established. which takes a little time. Reputation is an important part of this trust.

There are many examples of peer reviewers abusing the process and scooping someone on a paper that they held up in review, giving the reviewer time to replicate the work in his lab and submit a paper.

Grant proposals have been abused in a similar fashion. Researchers have altered data in order to fit a preconceived hypothesis. Collaborating with such people is a possible danger without more information.

So trust and reputation will have to be a part of OS, particularly since the participants may not meet face to face. But reputation and trust are a common problem with many Web 2.0 approaches.

One way Web 2.0 surmounts this is the very openness and transparency that gives it power. Ebay, for example, would not work if people did not trust the seller to have the item and the buyer to have the cash. Being able to see how each rates the other help establish trust.

Research has shown that what is important in human social networks is not that the network prevents cheats or freeloaders from existing. It is that the network has a method for identifying them and expelling them from the network if they fail to change.

Now OS will not be like Ebay, which is a site of commerce. But the power of many eyeballs watching the interactions will help apply social norms to the most egregious behavior. A reputation lost in the open like this will be very difficult to untarnish.

Another important aspect of scientific collaborations is power, a very human trait. Scientists with power (i.e. large, well funded labs) sometimes have a very different view of a collaboration than those with a small lab and a single grant. People often tend to confuse large and well-funded with innovative.

Remember well funded does not always mean cutting edge investigations of important questions. Sometimes it means doing what everyone knows will work, just more of it with greater efficiency. Risk is many times found in the smaller labs, not the larger, something also seen in corporations. The unwillingness to take a risk, found in many large organizations, often make collaboration with smaller, risk-taking groups problematic.

But on the Internet, this sort of power is defused somewhat. There is a leveling effect, allowing many more researchers to have an equal voice. On the Internet, no one knows you are a dog. They also may not know whether you have a lab of 40 researchers and $10 million in grants. What will be important are your ideas and how you treat others in the network.

So, watch as this discussion happens out in the open, as it should. Become part of it if you can.

Technorati Tags: Open Access, Science, Social media, Technology, Web 2.0

TGIF: Davidson Seamount:

[Via Deep Sea News]

I’ve been fiddling around with the formatting for the YouTube videos. Looks like it is working.

This is an excellent example of what can be done to spread science around. Nice graphics and an interesting story.

Technorati Tags: General, Science

by cesstrelle74
Web 2.0: In defense of editors:
[Via Bench Marks]

Ran into a few very interesting (and very different) articles last week, which I wanted to comment on (more posts to follow).
First up is a blog posting on Sciencebase that quotes chemist (and blogger) Joerg Kurt Wegner, with a proposal that the solution for information overload is to do away with editorial oversight and instead rely on social software. Now, obviously, I’m heavily biased here, and I admit that up front. I’m an editor, it’s what I do for a living, and if I didn’t think I made valuable contributions, I would do something else. That said, there are several problems with Wegner’s proposal.
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Web 2.0 encourages people to publish quickly, then work to make it better. This may not be the best route for many scientific endeavors, particularly biological ones.

Editors and peer reviewers perform a vital task - they make sure that the science is done right. It requires special training and a firm understanding of the topic to do this well. Even then there are some important mistakes, as recently happened in Proteomics, where a misleading and plagiarized article was published in February.

The editors/reviewers made a mistake in allowing publication. But the errors and plagiarism were discovered by well-educated people (mostly other scientists and interested individuals) on the web. And this information spread rapidly, forcing the journal to publish a retraction and pull the paper.

Science will need editors and peer reviewers from some time, since good science does require careful scrutiny by experts. But, of necessity, this will be a small group of people, who may not see the forest for the trees.

Perhaps some middle ground will be found between the old approaches and the Wikipedia’s of the world. I am sure that the editors of Proteomics, whose reputation was hurt by this, would have liked to have some way for a larger group to review before publication.

Preprints have been the standard way of sending a draft around to colleagues in order to get comments. Web 2.0 approaches using Open Science may hold similar appeal. Many hard science papers (physics, math, etc.) are online at very early points in the process.

The journal Nature is doing something similar with Precedings. These will be important adjuncts to the old way.

They will enhance but never replace. At least for scientists.

Technorati Tags: Open Access, Science, Technology, Web 2.0

by geishaboy500
Web 2.0 for Biologists-Are any of the current tools worth using?:
[Via Bench Marks]

David Crotty has been leading a discussion regarding the acceptance of Science 2.0 by scientists. Or rather the non-acceptance.

It is ironic to use Web 2.0 approaches to examine why scientists do not use Web 2.0 approaches. But entirely appropriate. Because these technologies will help researchers.

But not because we tell them so. No Internet technology ever became used simply because people were told so. They used it because it made it easier to do what they wanted to do.

What scientists can be told is how Web 2.0 will make their life easier. Once they can see how these approaches deal with the glut of data being generated and will help create knowledge, they will be ready for some of the more emergent aspects of Science 2.0.

This is a presentation I gave last weekend at the Southwest Regional Society for Developmental Biology Meeting. It’s an updated version of an earlier talk posted here. It’s kind of a 180 degrees turn from the previous talk, in that the first one was delivered to publishers, and this one was delivered to scientists. Here I’ve tried to include the thoughtful comments and helpful suggestions that readers made on the first talk, and have also tried to point out currently useful tools and interesting future directions. I don’t come at this subject from the point of view of a programmer, that’s not my background. I’m approaching it as 1) a publisher, who wants to build these tools into our journals and online products to make them more useful, and 2) as a former research scientist, with a thought toward what tools would have made my life easier when I was at the bench. The same caveat applies as last time-I work for a biology publisher, and am a former biologist. My comments and analysis of the culture here refer to that culture specifically (and I’ll try to avoid using the generic word “scientist” where it’s inappropriate). Different cultures have different needs. Certain fields of science collect types of data that more obviously fit in with Web 2.0 approaches. These approaches may not apply directly to the world of wet-bench biology, but they do serve as valuable pointers and directions worth watching. I want to be clear that I’m not writing Web 2.0 off as useless. What I’m interested in doing is separating the wheat from the chaff. Much of what is currently being done under this umbrella is useless and doomed. But there are some gems already available and despite many likely failures, aspects of those failures are worth recognizing and incorporating into future efforts.

If you read the first talk, sorry for the redundancies, and sorry for re-using some of the same jokes. I’ll work on new ones for the next presentation.

[More]

Technorati Tags: Science, Web 2.0

by m o d e

This site will be coming alive over the next week or so. We have a lot to cover and want it to be done without overwhelming anyone. SpreadingScience will make it easier for researchers to deal with the tremendous amount of information that threatens to overwhelm their efforts.

We do this through a teaching approach dealing with both Science 1.0 techniques to transmit information (papers, oral presentations and posters) as well as Science 2.0 ones.

What most scientists know about Science 1.0 comes from on the job training. We have developed some areas of good practice which permit much more effective use of their time for transferring information.

Science 2.0 approaches using online collaborative tools (wikis, blogs, podcasts) hold the promise of lowering many of the barriers to effective information transfer.

However, these tools must operate in a social network, even if it is online. Without an understanding of how the social networks of researchers are similar to those of other groups, and how they are different, the tools of Science 2.0 will not flourish.

This is where SpreadingScience has its greatest impact. Contact us to find out more about what we can do for your research organization.

Technorati Tags: Social media, Web 2.0

by jurvetson
Working Transparently:
[Via Gurteen Knowledge-Log]
By David Gurteen

I am including almost all of the post bt David Gurteen for a reason. It brings together in one post the ideas espoused by several other people. So, I quote David, who quotes John who quotes Michael. Every step in the transfer of information is stated and linked, providing the very openness and transparency discussed in the post. David then brings in his personal experience and ands another wrapper with the article on Science 2.0.

All of this to weave his view on openness into the other views. I hope my small addition provides some more insight into the need for openness and transparency for Science 2.0 aproaches to be useful.

I wrote a Gurteen Perspectives article for Inside Knowledge Magazine recently titled Open and transparent? where I talked about the concept and need for openness and transparency in the way we work today. So I have been delighted to see others say similar things:

In this post KM 2.0 is about showing your workings out by John Tropea, John quotes from Michael Idinopulos:

“The real paradigm shift in Web 2.0, I believe, is the blurring the line between publication and collaboration. In the old days, people collaborated in private. They talked to their friends and colleagues, wrote letters. Later they sent emails. All the real thinking happened in those private conversations. Eventually, once the key insights had been extracted, refined, and clarified, they published: books, articles, speeches, blast memos, etc.”

“…the really exciting thing that’s happening in Web 2.0 and Enterprise 2.0 is that more and more of those private “pre-publication” interactions are happening in public (or at least semi-public). I think of this as the dawn of the “Work in Progress” culture. We no longer think that something has to be finished before we let strangers into the conversation.”

And then Gerry McKiernan in this post on Science 2.0.

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.

Take a look. How might you work more transparently?

Transparency and openness are the lubrications that allow human social networks to create knowledge rapidly. If any one person prevents the flow by holding onto critical information, the power of the network can be degraded.

This can be a problem in hierarchies, where information flows through a few chokepoints. A well connected, diverse social network can deal with this problem.

In fact, small groups of humans have always been able to identify who these people are and often use social norms to either make them comply or to shun them, particularly if other sources of the information can be found. If these chokepoints no longer are getting any information, the power they hold is greatly reduced.

Now, this may not always happen because of someone’s unique position in a small group. But the huge scaling properties of the Internet, the Long Tail and its enormous potential, means that it becomes much less likely that a single point of failure will damage the network.

The Internet was designed to route around ‘damage’ and so can diverse, connected human social networks. The Web makes it much less likely that one person will hold unique information. Thus it weakens their advantages.

Power comes from weaving information into unique knowledge - knowledge to make decisions.

The positive effects of openness and transparency can very rapidly overcome any small advantage of an individual holding information close. They lose any advantage they might have because very little information is that unique.

If these information hoarders gain little advantage by being closed, and if the social network uses peer pressure to identify free riders and to deal with them, then it would appear that behavior would rapidly converge towards openness and transparency.

In fact, the groups that can more rapidly create knowledge using human social networks will be the first to solve many of the complex problems we face today. Groups with choke points will be much slower and, in the type of natural selection we see all around, will become extinct. At least where the need is to understand complex processes.

Technorati Tags: Knowledge Creation, Open Access, Science

by dcJohn
Using Wikipedia to Reenvision the Term Paper
[Via EDUCAUSE Learning Initiative]

At the just held online EDUCAUSE Online Spring focus conference, Andreas Brockhaus and Martha Groom, both at UW-Bothell, just around the corner so to speak, discussed unusual aspects to classes taught by Groom. She required the students to either create a new page on Wikipedia or to substantially add to a previous page. No term paper. It was going up on Wikipedia.

Befitting a discussion about using new technologies in the classroom, you can see the Powerpoint presentation and hear the talk online. Almost like being there.

While there were some barriers to break through, the effect on the students and their writing was almost electric. Normally, only the teacher and a few other students might see what was written.

In this example, the entire Web could see what they wrote. To ameliorate this somewhat, she had the students work in groups.

Martha Groom has been using this approach for the last few years. There are still a few things to work on. Writing for an encyclopedia is different than working on an essay.

She has added a recursive approach to the project, with proposals and peer review before it hits the Web. The community nature of Wikipedia required the students to really give up proprietary feelings about the essays. Sometimes the give and take of online discussions could be a little harsh.

But Martha has continued to tweak the approach. Generally, the students were very happy with the results. The quality of writing was very high also. With such transparency, the possibility of plagiarism is infinitesimal. It really highlights the need for proper sourcing of the work. All very good things.

And, if a really good job is done, the student can point out the page to others as evidence of their scholarship. All in all, much better than a one-off term paper.

Technorati Tags: Education, Science, Web 2.0