Saturday, September 22, 2012


I am now working on a children's show about the science of smell and so I've been doing a good amount of research on historical theories of olfaction. One of the famous monographs on smell is John E. Amoore's Molecular Basis Of Odor in which he uses space filling molecular models (non-computer generated physical models, this was 1970) to try to find correlations between the gross molecular shape of odorant molecules and overarching classes of "primary odors". Amoore is best known for making generalizations like: camphoraceous smells are molecularly "bowl-like" and accepted by a "bowl-like" receptor, musky smells are molecularly "petrie-like" and accepted by a "petrie-like" receptor, floral smells are molecularly "key-like", and so on.

The book is worth skimming even if many of its hypotheses are disproven or based on dated concepts of the senses but one thing I found particularly interesting is the way that some of the odorant molecules are illustrated using a combination of space filling models in silhouette and skeletal notation. Amoore used this as part of what he called the "shadow-matching method." I had never seen this before and was surprised because it is actually a great way to combine the best features of both modes of representation. Spacial dimensions are indicated without looking like a confusing, botryoidal jumble of spheres and all of the readability of skeletal notation is left intact. Obviously this can present some problems, especially for non-planar molecules, which are sometimes forced into a planar conformation for skeletal diagrams but still it's interesting you don't see it more often in textbooks. I know programs like pymol can do similar, more complex versions of this where the 3D Van Der Waals surface envelopes a 3D ball and stick model but what about just a simple representation like the below, are there any programs that do (a clear better aligned version of) that?

Saturday, September 15, 2012


The weird science issue is now printed and available in select locations. The articles are being incrementally uploaded to accompanied by a few articles I had nothing to do with (e.g. something about "bath salts" that I did not see until the day before the issue went to press). Certain articles are online in an expanded version (e.g. there will be two additional pages of Alexander Shulgin's lab notebook at and in European editions of the magazine) other things are only featured in the print editions (e.g. two unpublished photos by Carsten Höller). Stanislaw Lem's short story A Puzzle and my guest-editor letter are now available online, enjoy!