Bursty science depends on openness:
[Via Science in the open]
Image via Wikipedia

There have been a number of interesting discussions going on in the blogosphere recently about radically different ways of practising science. Pawel Szczesny has blogged about his plans for freelancing science as a way of moving out of the rigid career structure that drives conventional academic science. Deepak Singh has blogged a number of times about ‘bursty science‘, the idea that projects can be rapidly executed by distributing them amongst a number of people, each with the capacity to undertake a small part of the project.
[More]

There will be many of these little experiments – using online conversations for scientific endeavors. Even inside an organization, having an online area to ask for help can be useful. Trying to use email for this purpose has little effect.

There are several ways to  use Web 2.0 approaches to ask/answer questions. An online forum works well if it is substantially populated and active. A forum with a 3 month old unanswered question will not be very useful.

One approach that works is to have one person, or a small group, act as troubleshooters. They probably already exist in many organizations. They are the ones every one goes to when they have a problem in the lab.

They usually have a wide range of knowledge and often work to help people find a solutions to a research problem.

Have these people move online. A troubleshooting page on a wiki would allow questions to be asked. The troubleshooters have the opportunity to find answers. FAQs could be written to respond to the endless questions many troubleshooters receive.

Then when someone asks for some help, there is already a team with responsibility to find answers. And, because all this is open and transparent, the troubleshooters can finally get the well deserved credit they should.

Helping in the lab is generally invisible to others, particularly when evaluation time comes around. It is hard to document just what the help accomplished.

A troubleshooting wiki, on the other hand, would provide ample documentation on just what help was provided and the effect that help had on the organization. The ability to actually document who helps the organization move forward will be very valuable.

Technorati Tags: Education, Science, Web 2.0

by jeffpearce
Progress toward Public Access to Science:
[Via PLoS Biology: New Articles]

PLoS Chairman of the Board Harold Varmus applauds the newly enacted NIH public access policy as a positive step toward ensuring greater access to and better use of the scientific literature.

This very nicely discusses some of the recent changes that are making Open Access to scientific information a going concern. Anyone receiving money from NIH has to deposit the accepted manuscripts into PubMed Central and allow freely available viewing within 12 months.

He also mentions the continuing problem of copyright. Many journals require the authors to turn over all rights to the journal in order to have the paper published. This is becoming a problem in the Web 2.0 world, since the concerns of the author do not often match those of the publisher.

As Varmus writes:

Finally, unless authors modify their copyright agreements with journals before publication—something they are urged to do—journals will continue to retain inappropriate control over the use of their articles, which is currently confined largely to reading online for most articles in PMC.

Harvard has recently addressed this. Faculty members must grant a non-exclusive license to the University for it to post on a website it maintains, one that is open and free. Faculty can opt out of this on a case by case basis if the journal will not permit this.
Varmus comments:

Moreover, the nuisance of writing to the Provost every time a desired journal refuses to conform to the Harvard policy may cause faculty members to rethink their choice of venue, thereby minimizing use of the “opt-out” option.

The journals make their reputation based on the reputations of its author scientists. If a journal has a restrictive copyright policy, these scientists may go elsewhere, putting pressure on the journal to adopt more open access.

This story is not over yet. But it has the potential to revolutionize scientific publishing. Stay tuned.

Technorati Tags: Education, Science, Web 2.0

by Vik Nanda

Rethinking Outreach: Teaching the Process of Science through Modeling:
[Via PLoS Biology: New Articles]

How can we get high school students interested in science? Here is a program that matches students with researchers, with the purpose of building a physical model of the protein being investigated in the lab.
What an outstanding idea! Not only did these students learn a great deal about how research is actually done but they also were instrumental in helping the researcher have some of the tools he needed.

These sorts of interactions will always be needed. Humans like to interact personally with others. But, Web 2.0 technologies can make it easier for these sorts of interactions to take place. Meetup is a great example of this.

There are already hints that scientific meetings may take a similar path. Again, not to replace the conferences already taking place but as an adjunct.

Update: Of course, Web 2.0 approaches can also expand the reach of teaching and communications. A great example was the recent EDUCAUSE Learning Initiative Online Focus Session.

Technorati Tags: Education, General, Open Access, Technology

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.
[More]

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 Clearly Ambiguous
Work-in-Progress Culture:
[Via Transparent Office]
Michael Idinopulos makes a great observation – Web 2.0 is collaboration in public. Fewer closed doors and more open hallways.

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.To me, 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.

[More]

It will be a difficult transition for many people, since it may be harder for them to totally ‘own’ a work but the pathway that was taken will be available for others to follow; the nooks and crannies. It will be harder to end up in a dead-end when others are there to help you out. And, because of the Long Tail, there will be someone available to help.

Technorati Tags: Knowledge Creation, Social media, 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

by Airton kieling

[Via One Big Lab]

First draft of PSB proposal
PSB proposal up on Google Docs
PSB Open Science session proposal submitted!
PSB proposal up on Nature Precedings
PSB proposal accepted for a workshop

A very interesting progression from first draft to final approval. Exactly what one would expect for an Open Science advocate. While not all Science 2.0 approaches may be suitable for exposure on the open web, this was certainly a wonderful exercise to follow. And I learned something about the process they went though, just in case I ever want to do something similar.

I may have to find myself in Hawaii early next year, at the Pacific Symposium on Biocomputing. It’s the Big Island.

Technorati Tags: Open Access, Science

by belgianchocolate

Publishing On OpenWetWare – Lessons Learned 4 – Presenting:Python
[Via Programmable Cells]

This is the fifth report of the ‘Publishing on OpenWetWare’ series. In brief, I am writing an article on OWW from start to finish: initial writing -> collecting comments -> publishing on arXiv.org -> presenting at a conference. For other articles, see one, two, three, four. In this report, I’ll share my experiences in presenting the work at Pycon 2008.

This is the most recent part in a continuing series by Julius Lucks about publishing on OpenWetWare, an example of Open Science. Initially, OpenWetWare was a great site to find protocols of all sorts. It has been expanding very rapidly to incorporate many facets of Science 2.0. This is one such. It led to a presentation dealing with his work and you can read the ‘paper’ dealing with his topic: Python All A Scientist Needs. Python is the programming language used here and it presents many advantages useful for scientists. It includes a special package, BioPython, just for biologists, which is supported by the Open Bioinformatics Foundation. So, we see an entire network of Open Source organizations that produce tools that not only make their work easier but also the work of others. By embracing these tools, one can engage the entire network and help use all the knowledge contained in it to help solve problems.

Technorati Tags: Bioinformatics, Science, Social media