Monthly Archives: April 2008

General, Open Access, Web 2.0

Science in the open

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University 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.

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General, Open Access

Teaching science

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structure 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.

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Open Access, Science, Web 2.0

Old versus New

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sheet music 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.

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Knowledge Creation, Open Access, Web 2.0

Public collaboration

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leafby 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.

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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.

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General, Knowledge Creation

Slides gone bad

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This is pretty hard to believe. 65 slides! And there are so many things wrong with each slide: horrible colors, too much clutter on slides, fonts too small. Just to name a few.

Each slide would have to take several minutes to get through, by which time everyone is zoned out and does not get the message. And, with no context, the slides can not be understood by anyone who was not present.

These are nice examples of what not to do.

Your moment of (slideument) Zen:
[Via Presentation Zen]

Coke_ppt_3

Coke3_3 Coke_ppt2_3

Three sample slides for your contemplation courtesy of a 65-slide PowerPoint deck from the world’s biggest brand.

Source: Coca-Cola Japan. Go to the site (investor relations page) and download the presentation slides (1.5MB pdf) and enjoy the journey yourself. The slide deck is ‘the real thing.’ H/T Samuli.

• What’s a Slideument?

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Science, Web 2.0

Discussing Science 2.0

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toolsby 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.

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Knowledge Creation, Web 2.0

Justifying Social Software

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galaxyby NASA /Hubble Heritage Team

Justifying Social Software:
[Via A Journey In Social Media]

It’s true that most organizations won’t move forward with significant investments without some sort of justification.

And it’s also true that the category of “productivity software” is perhaps the most difficult thing to justify.

So, I thought I’d spend this post on the flavors of business value we’re seeing from our internal environment.

How People Think Of Justification
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Chuck’s blog is getting to be one of my favorites. His metaphor about boulders vs. sand is absolutely right. It is a nice way to describe a power law curve with its Long Tail. The boulders are the big hits at the left of the curve, what everyone has been used to dealing with applying old style approaches to things like distribution costs. But, various web technologies, especially Web 2.0, have brought the Long Tail to innovation and social networks.

Now, instead of a few big boulders, companies can harness the huge amount of sand present in their organizations. This can be done in ways that not only help employees do their jobs but can also save the company money, enhance its IP portfolio and make the company a better place to work. As Chuck noted, employees really appreciate what the interactive web provides, viewing it as a major company benefit.

If done right, an intranet built on Web 2.0 technologies becomes a way to retain employees as well as attract new ones. Pretty good for something that can be built on OPen Source and could be launched in an afternoon.

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