Thursday, October 29, 2009

Chemistry in Second Life paper in Chemistry Central Journal

Andrew Lang and I just published a review article on the chemistry content in Second Life:
Andrew SID Lang and Jean-Claude Bradley Chemistry in Second Life, Chemistry Central Journal 2009, 3:14.
This review will focus on the current level on chemistry research, education, and visualization possible within the multi-user virtual environment of Second Life. We discuss how Second Life has been used as a platform for the interactive and collaborative visualization of data from molecules and proteins to spectra and experimental data. We then review how these visualizations can be scripted for immersive educational activities and real-life collaborative research. We also discuss the benefits of the social networking affordances of Second Life for both chemists and chemistry students.
This is gratifying on many levels:

1. Andy and I met in Second Life a few years ago and it is fitting that we should finally have a paper highlighting our collaboration and the work of others doing chemistry in Second Life. In fact, our meeting and the resulting projects both inside and outside of Second Life is listed under the networking section of this paper.

2. We found a very appropriate Open Access journal to publish this work. We wanted this review to offer concrete examples of what can be done with chemistry in Second Life and it is loaded with images to illustrate as clearly as possible what these options look like.

Even though it has many educational components we did not want to submit it to a "chemical education" journal. Generally these types of journals require framing the work within a pedagogical theory. We have been through prolonged debates with reviewers around this issue on other papers and did not want to repeat the experience. There is an expectation in some circles that progress in education can only come about when built within the context of testable theories. At least the scope of many educational journals is tied to this viewpoint - and that is absolutely appropriate.

But it is interesting that we have had to rewrite sections of papers - not because the content was incorrect in any way - but because it did not conform to a conceptual format. It makes me realize how much scientific discourse is directed by the expectation of editors and reviewers, when the authors themselves might have preferred to present their content differently.

3. There is lots of useful content that is never published in peer-reviewed publications because it does not fit the mold. The example above fits in the category of describing tools without evaluating them in some quantitative way. So the third point of gratification is that we managed to zip up a number of small developments that might be useful to someone but by themselves were not the right size and shape to publish in the peer-reviewed system. This included the ChemTiles game and the EduFrag project, initiatives that were converted to or from a Second Life format.

Of course, the mechanism of using a review to assemble such content can't be used very often.

In the experimental sciences there are two other types of useful content that are difficult to publish formally: "failed" experiments and lab techniques. I've repeatedly discussed the importance of sharing the results of experiments with disappointing results as a strong motivation behind Open Notebook Science.

But just as important are the details of laboratory techniques - completely separate from the results they provide. In our lab, the measurement of solubility has proven to be far from trivial and we have reported several pitfalls, as well as some techniques which I think could save others much wasted effort.

When I was a graduate student at the University of Ottawa I found a way of visualizing column chromatography that I thought could be helpful to others in speeding up separations. The only mechanism available back in 1992 for wide dissemination of chemical information was peer-reviewed publication so that is what I did (Tet. Lett. 33(50) 7733).

In order to publish using that channel I had to format my communication accordingly. Instead of just reporting on the method (use a quartz column and an insoluble fluorescent agent mixed with silica gel), I had to evaluate the method systematically testing different solvents, stationary phases and specifications. It was a hassle and completely unnecessary to simply share the technique.

If I were doing this today I would just blog about it and record the details in my open notebook as I was experimenting with the technique. There is a good chance that someone else would have given me useful tips as well.

As it turned out, the feedback I did receive was a letter from a chemist who had been using the technique for many years. His use escaped our literature search because it only appeared in the experimental sections and thus did not show up on keyword searches - keep in mind this was before the era of computerized searching - and none of the reviewers knew about it either.

We published a Corrigendum accordingly and that was the full extent of the public scientific discourse. By any standard the new communication tools we have today are far more versatile for quickly and easily communicating this type of information.

4. Once again (here and here), we had no trouble using blog posts and wiki pages as references. The key consideration is: what is the most relevant document to link to. If you are blogging your work it is likely that blog posts will be the only citable option in many cases. In this instance we also wrote the article on a public wiki page, which limited our selection of peer-reviewed journals to those that allowed pre-prints.

I don't know how many journals that don't allow pre-prints would take articles that are based substantially on work that has appeared in public blogs and wikis. Since the article would require re-integration and re-writing of the work there wouldn't be any copyright issues.


At 3:19 PM, Blogger Unknown said...

Congrats on your paper!

I share some of your concerns. Faculty should not be discouraged from innovating and broadcasting their results by an expectation that they will evaluate according to one particular paradigm that happens to be dominant in the current discourse. This is a much more complex issue than it seems to be on the surface.

Interesting that you characterize chemistry education journals as requiring a pedagogical theory that your work is based in. I see JChemEd as a journal that (for better or worse) has had no such requirement over the years and instead publishes just the sort of things you describe (other than failed results). Perhaps that has changed in the reviewer culture over the years with the increase in the number of chemical education research faculty in chemistry departments. The main drawback to publishing in JChemEd has been the extremely long time period from submission to publication.

This is definitely a topic that needs more exploration and discussion on a large scale. I look forward to the conversation. :-)

At 3:21 PM, Blogger Jean-Claude Bradley said...

We tried to publish in JChemEd but they have a policy against pre-prints.

At 11:39 PM, Blogger Unknown said...

I'm with you on that one. A new editor is just starting at JChemEd--Norb Pienta. I expect there will be quite a few changes. Now might be a good time to ree-examine the policy on pre-prints.

At 6:10 AM, Blogger Jean-Claude Bradley said...

Liz - we did contact the editor of JChemEd but they stuck to the official policy:

"B. ACS Editors Policy on Papers on Preprint Server

1. A preprint will be considered as an electronic publication and, according to positions taken by most editors of ACS journals, will not be considered for publication. If a submitted paper is later found to have been posted on a preprint server, it will be withdrawn from consideration by the journal."

As more authors experience the freedom that comes from using pre-print servers such as arXiv and Nature Precedings, I think a significant number will elect to publish in journals that embrace that system. Ultimately the invisible hand of the free market will determine the outcome. If Nature thought that pre-prints would kill their business model they would not have started Precedings.

At 11:49 AM, Blogger Unknown said...

Who did you correspond with? Let me see if I can get the issue on Norb's radar if he isn't aware of it. I don't know if it's out of their hands Re: ACS policy. I know he'll be working on the time-to-print problem.


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