Archive for November, 2006

I was reading Pragmatism by William James and came across an interesting passage in which James quotes from a letter he received from Wilhelm Ostwald–winner of the 1909 Nobel Prize in Chemistry for “catalysis and associated fundamental studies on chemical equilibria and rates of reaction.”

“Chemists have long wrangled over the inner constitution of certain bodies called ‘tautomerous.’ Their properties seemed equally consistent with the notion that an instable hydrogen atom oscillates inside of them, or that they are instable mixtures of two bodies. Controversy raged; but never was decided. ‘It would never have begun,’ says Ostwald, ‘if the combatants had asked themselves what particular experimental fact could have been made different by one or the other view being correct. For it would then have appeared that no difference of fact could possibly ensue; and the quarrel was as unreal as if, theorizing in primitive times about the raising of dough by yeast, one party should have invoked a ‘brownie,’ while another insisted on an ‘elf’ as the true cause of the phenomenon.’”

I think today we would say that there is a practical difference between these two descriptions and that tautomeric solutions are best described as “instable mixtures of two bodies.” One-hundred years later, Ostwald’s point still seems relevant though. I wonder how many hours I’ve spent at a chalkboard arguing over two conceptions of the same fact, either of which make no practical difference whatsoever…

William James was a chemist before he was a famous psychologist and philosopher. He entered the Lawrence Scientific School at Harvard in 1861 to study chemistry, but lasted less than a year. He later graduated from Harvard Medical School.

Wilhelm Ostwald was on loan to Harvard University from 1904 to 1905—two years before James gave his lectures on Pragmatism—from his home University of Leipzig, Germany. He was close to retirement at the time and increasingly interested in the philosophy of science as is evident from his correspondence with James.

Bear with us for this post as we send out the bat signal to attract the chemical informatics crowd. I’m talking about the Peter Murray-Rusts of the world, who draw their superpowers from the glow of fluorescent lighting as they sit and hammer out code for hours on end.

On their blogs, Joerg Wegner and Murray-Rust took the rest of the chemistry blogosphere to task for not including more minable data, using standards such as Chemical Markup Language (CML). CML is used to include metadata on chemical structures and compounds that people post on the Internet. While it’s essentially invisible to human readers, search engines can use the extra data to sift through content on the Internet more efficiently for information that is specific to user-defined queries about chemical structures or substructures.

Aside from that gibberish in the last paragraph, we know nothing about the subject of informatics and making chemically-minable data. Since we’re basically starting this blog from scratch, we want to try to get all the informatics stuff right from the beginning.  I notice that using the latest version of ChemDraw (Ultra 9), you can save structures as CML files (in addition to the “usual” .cdx).  Where is the proper place to put this CML code?  In the image file?  Can it go anywhere in the blog post?

We also have the following questions:

1. Is CML the “standard” way of including structural information in electronic form? For instance, how does SciFinder or Beilstein store this information? If they don’t use CML, why don’t we just do it the way these programs do it, since they are the main tools already used by chemists?

2.  How do you recommend tagging images of chemical structures?  Is a name and CAS number good?  Is this unnecessary if the CML data is in there?

3.  Is there anything else we’re missing?

Thanks! 

This video of Sacha Baron Cohen (as Ali G) interviewing Boston College Professor T. Ross Kelly is excellent. After watching it a couple of times, I’m still not sure that Kelly knows exactly what happened.

The next time you expect to evolve a gas, please work in da hood and be sure to check your Hilfiger’s for contaminants.

Welcome to an experiment in fun: yet another blog about chemistry. While all aspects of chemistry interest us, I’d say were a little bit partial to the educational side of the field, which is often ignored at major research institutions. We’re not just talking about classroom stuff. Course material is certainly cool, but we’re also interested in the ethical, managerial, philosophical, political, practical, and operational aspects of chemistry and chemical research. We plan to incorporate some “non-blog” material over time, and there’s a chance this site could grow into a nice little resource for some of the ignored aspects of our field. Then again, we may never get there. We’re simply going to play it by ear, making sure we’re having fun doing whatever it is we do.

So, set your bookmarks, change your blogrolls, and pull up a chair. Enjoy your time at ChemBark.