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Saturday, June 24, 2006


This is the last week of the online CONFCHEM and my presentation is up there.

The conference is run by mailing list. If you have any interest in lurking or participating this week just sign up with the instructions at the bottom of this page.

Here is my abstract:


Expanding the role of the organic chemistry teacher through podcasting, screencasting, blogs, wikis and games

Jean-Claude Bradley (Drexel University)

Technology is enabling new ways to channel the relationship between teacher and student. The ability to provide an archive of recorded lectures in rich and convenient formats like screencasts, podcasts and vodcasts enable an instructor to explore additional means to integrate class material through activities such as games, blogs and conversation. This presentation will describe the implementation of such technologies in a university level organic chemistry class. See http://chem241.wikispaces.com.

Tuesday, June 20, 2006


There has been a lot of talk lately about PLoS ONE, an open access online journal based on the existing Public Library of Science (PLoS) format. PLoS ONE aims to be more inclusive, aiming to publish reports that are scientifically sound, without assessing importance.

This seems like a step in the right direction towards the dissemination of laboratory results. However, it is uncertain exactly what this will cost the authors:

From an interview of Chris Surridge, the managing editor of PLoS ONE, Richard Poynder reports:

RP: Will the article processing charges for PLoS ONE be the same as those applying to the journals, which I understand have just risen from $1,500, to between $2,000 and $2,500 per paper?

CS: Hopefully the rate can be lower. One of the driving forces of PLoS ONE is that we want to be able to publish lots of papers. To that end we are setting up the system in a completely scaleable way so that we can cope with as many papers as people want to publish with us. One of the advantages of doing so is that we can start getting economies of scale, and this will keep author fees as low as possible.

I wonder if this model can really support the open sharing of scientific information, when the barrier to contribution excludes anyone who is not well funded. I know that I would much rather spend $2000 on chemicals, lab equipment and students. But I would be very interested in a breakdown of how that money is spent to better appreciate the model.

So, for now, I still maintain that self-archiving is the way to go for the lowest barriers on both the sender and receiver sides.

Thanks to Glyn Moody for the link.

Monday, June 19, 2006

Back from Frye

I just returned from an intense two weeks at the Frye Leadership Institute at Emory. There were about 50 participants, mainly from the IT and academic library domains. As a faculty member, it was really interesting to get a perspective of the university through other eyes.

There were a lot of talks but also some group work. Here is some work that my group did on our hypothetical university, Maverick U.

The main intersection with my interests revolved around social software and other non-traditional modes of communicating scholarship (especially scientific), including implications for tenure and promotion. The librarians were also very much interested in discussing their role in the archiving and retrieval of new forms of documents. Of course, nothing was resolved, but the dialogue is open and we'll continue to share our thoughts and experiments as we move forward.

The best part of all this was meeting and engaging with a group of terrific people, especially when we played Weboggle.

Saturday, June 03, 2006

Varmus on Open Science

Here is a candid little article from Wired on Harold Varmus and how Open Access in Biomedical research came about.

Free Radical
Harold Varmus won a Nobel Prize for changing how we think about cancer. Then he overhauled the NIH. Now he's battling to make all scientific research free and universally available.
Here is a quote about the original vision:
The conversation clicked with Varmus. Soon, he, Brown, Eisen, and David Lipman, an NIH colleague, drafted a proposal for “E-Biomed,” a public, one-stop repository of biomedical papers. Researchers could submit papers through a peer-review process similar to that used in the current journal system, or they could post work fresh out of the test tube.

I think that the part that we have yet to embrace is the posting of work fresh out of the test tube. As long as scientific research is published in an article format and its value is determined by a popularity contest of citations and peer-reviewed blessing, there will be little motivation to post work fresh out of the test tube. Especially when issues like competition and tenure are at stake.

The reality is that the impact of raw experimental data is usually unknowable at the time when it is generated. It may never be used by anyone (which is a guarantee if kept in a private lab notebook) or it may at some point answer a key question for an agent (human or otherwise) looking for a solution to an important problem.

My opinion at this point is that publishers or any kind of central repositories are not going to be as effective in communicating this kind of raw scientific data, unless it is readily available on the uberdatabases like Google or MSN. That's why Blogger makes an optimal vehicle to communicate raw experimental data: no cost, no gatekeeper and anyone looking on an uberdatabase will find your stuff.

Thursday, June 01, 2006

RSS in chemistry article

Edward Vawter has recently published an article: RSS explosion in chemistry and science. It is disappointing to see that chemistry publishers are basically still just using RSS as a means of distributing their tables of content. Although it is better than nothing, as a researcher, what I really want is to be able to track specific information using arbitrary keywords and chemical ID numbers. The only way that I am aware of being able to do this is through MSN.

Thanks to Christina Pikas for the link.

Chmoogle name change

Chmoogle, the chemical search engine I noted a while back, is now reporting that they have changed their name as a result of pressure from Google. They have a detailed statement about why they thought they would not have a problem. I have to admit that when I first heard about the site I assumed it was a Google project.

Their service is now available under eMolecules.

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