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Tuesday, August 29, 2006

Google Apps for Education

Google is now offering a service to educational institutions to permit branding and account management for Gmail, Google Calendar and Google Chat. Here are some of the applications Google suggests:

Gmail - Give students email with huge storage capacity, less spam, search tools to help them find information fast and built-in instant messaging.

Google Talk - Keep students in contact even when not on campus with instant messaging and voice calling over the Web.

Google Calendar - Help students stay on top of their schedules, share plans with others and keep up-to-date on campus events.
There is currently a beta period where institutions that sign up will get free access. This seems to imply that there will be a charge for latecomers.

Now if Google will just create an assessment module, Course Management Systems like WebCT will have trouble justifying their price tag.

Thanks to Stewart Mader for the link.

Tuesday, August 22, 2006

Chemistry Central and Fully Open Access

Hot off the presses from Sciencebase:
A new open access site for chemists - Chemistry Central - launches today as part of the newly announced Open Access Central group of sites from the makers of BioMedCentral.

CC collates peer-reviewed research from a range of open-access journals and makes available the original research articles as soon as they are published.

Deputy Publisher and former chemist Bryan Vickery explains the motivation, “We have seen increasing interest from chemists in the open access publishing model and, having launched two chemistry-specific titles in the last 18 months, the time seemed right for BioMed Central to create an open access publishing website to meet the needs of chemists,” he says.

On the CC roster are OA articles from Geochemical Transactions, the Beilstein Journal of Organic Chemistry, and chemistry-related articles from BMC Pharmacology, BMC Biochemistry, and BMC Chemical Biology.

It is hard to tell exactly what this will mean for Open Access chemistry research. Right now the vast majority of articles on Chemistry Central are better classified as bioinformatics related, although there are a few articles on analytical and organic chemistry.

There are certainly some intriguing opportunities laid out in the current system. For example, they are making their software and templates available for someone to start a new Open Access journal in a chemistry sub-field or interdisciplinary topic. That is actually really cool and I hope that this catalyzes the creation of novel useful information channels.

However, I am concerned that part of the model is based on author publishing fees on the order of $1000/article, similar to the PloS and PloS One models. Note that authors from institutions who are members can publish free of charge. Drexel is not a member as of yet.

Not all Open Access journals are funded by author fees. In the realm of organic chemistry the Beilstein Journal of Organic Chemistry and Arkivoc are funded using different mechanisms and provide what I would call Fully Open Access on the front as well as the back end. I think that this is where Open Access can really become a fully free and democratic process, with no barriers from the author and subscriber to share knowledge freely.

Notwithstanding all of these details and caution, this is a very important story for the chemical community to monitor.

Friday, August 18, 2006

Quality Control and Peer Review

Anyone following the current debate about Open Access scientific publication is well aware that peer review is a big factor in these discussions. For example, see Pedro Beltrao's recent discussion at Science Foo Camp.

I have found that this issue is of particular concern to librarians, who would like to be able to categorize all publications into two neat piles: reliable and unreliable. That makes it convenient to simply ignore anything that is not on the reliable list. Since librarians cannot be experts in every field, they have to rely on other criteria, such as a notice that a document has been peer reviewed.

Unfortunately, it is often assumed that peer reviewed information is reliable. This can be a dangerous assumption.

For example, in our research on the synthesis of anti-malarial compounds, we designed our experiments based on information found in peer-reviewed journal articles. Over time, we found some contradictory information in the literature about the solubility and spectroscopic properties of one of the compounds we were trying to make and this cost us some time.

I think that this was a great lesson for my students about how to use the chemical literature. The only way to confidence in science is to look for redundancy in independent reports. Peer review (from anonymous people who do not repeat experiments in a paper) cannot be used as a short cut to assessing reliability.

Of course if the papers that mislead us had links to the raw data of their experiments we would have been able to spot these errors much more quickly. This is a huge advantage of doing open source science.

With the proliferation of new forms of scholarship, it is no longer effective to teach our students that there is such a thing as reliable literature. There is uncertainty in every information source. We should teach them to find the same information from several different sources and then discuss the confidence we can derive from the aggregate results.

Finding the melting or boiling point of a compound is a great way to make that point. Use a company catalogue, Wikipedia, a textbook and Google and see if there is consensus. For example, the boiling point of ethanol is listed as 78.4 C in Wikipedia, 78.3 C on this website, 78.30 C on this website and 78.5 C here. Based on this we can be reasonably certain that the boiling point is between 78 C- 79 C and that may be all that we need for our application. Finding the accurate value for that first decimal place is going to require a lot more research.

Unfortunately most of these information sources do not reveal the details of the original experiments where the boiling point was determined, which would be extremely helpful in this case. However, before you start bashing Wikipedia and web pages as being inherently unreliable, take a look at the official information compilations that are out there. For example, MSDS (Material Safety Data Sheet) is considered by chemists to be the standard information source for chemical safety. In the course of our research, I was disturbed to find that benzene was listed as an incompatibility for sulfuric acid. This is the very first reaction I cover in the chemistry of aromatics!

I found this to be even more disturbing:
The quality and accuracy of MSDSs varies widely. One recent study showed that of 150 randomly selected MSDSs, information was accurately identified in Health Effects in 37%, in First Aid Procedures in 76%, in Personal Protective Clothing in 47%, and in Occupational Exposure Limits in 47%.
Unfortunately, there does not appear to be a simple way to get to the original experiments where the MSDS information was obtained. At least on Wikipedia you can ask the author directly for the source if it is not listed.

For a nice discussion on the issue of reproducibility in peer reviewed publications see Chris Surridge's post on the PLoS blog.

UsefulChem space of the month

From the August 2006 Wikispaces newsletter, here is a concise summary of the UsefulChem project:

August's Space of the Month is great blend of the principles of open
content and open source applied to science and education.

Our Space: UsefulChem is an Open Source Science project aiming to share real time results from the Bradley chemistry lab at Drexel University. The main objective right now is to make compounds to fight malaria.

Our Community: The main contributors currently are Khalid Mirza (grad student), James Giammarco (undergrad), Lin Chen (undergrad), David Strumfels (grad student), Alicia Holsey (grad student) and Jean-Claude Bradley (Principal Investigator).

Our Experience with Wikispaces: After evaluating several wiki solutions we settled on Wikispaces because it offered a clean simple interface, RSS feeds, rapid indexing on Google and a free hosted option. Our objective is not only to communicate our research work directly to the world but also to offer solutions that can be easily replicated by other scientists at minimal or no cost. The coupling of the organizing power of Wikispaces with the chronological recording of Blogger creates an optimal vehicle for the dissemination of Open Source Science.

Monday, August 07, 2006

Back from BCCE

Here are some notes on the BCCE 06, the Biennial Conferences on Chemistry Education at Purdue last week:
  1. I gave two talks: one with Mark Ott on screencasting and podcasting chemistry courses and one on games specifically for organic chemistry.
  2. I attended the sessions that I could find related to podcasting in chemistry. Alan Kiste talked about using enhanced podcasts to supplement his organic chemistry class.
  3. Bob Hanson opened my eyes to the power of AJAX for chemistry. He had a demo where highlighting a word pulled up more info without having to reload the page. His first example was Google Suggest, where suggestions come up as the user types.
  4. Richard Zare gave a very entertaining Keynote talk about general ways to solve problems. He demonstrated all kinds of brain teasers, both chemical and general. His basic point was that people don't solve problems in an organized way and that is ok. Let the students feel comfortable with the messiness of thinking. I agree.
  5. I finally got to see a little demo of the First Person Shooter Critical Mass chemistry game (Gabriela Weaver). They used the gun to shoot some crates and to heat up a reactor. It will be interesting to play when they are done.
  6. Zangyuan Own showed some pretty impressive data about delivering chemistry courses customized for different kinds of Multiple Intelligences. Unfortunately, the material was only available in Mandarin. He was also handing out handsome decks of playing cards with a different element showcased on each card.

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