Tuesday, April 26, 2011

Importance of being obsessive-compulsive

Never underestimate the importance of naming. For instance, I would probably never read the excellent paper by Kuhn and Wahl-Jensen [1] if not for its title. (Seriously, read it. Although the note appears in Binomina, it is relevant to scientific nomenclature and terminology in general, not just biological taxonomy.) They write:
When terms get renamed just for the sake of renaming them then outrage at nomenclature experts is justified. But it is a two-way street. Nomenclature without discourse with the scientific community working in laboratories is useless — but science without nomenclature cannot be performed, either.
Conversely, Roderic Page argues that “quite a lot” of biology can be performed without “proper” taxonomic names [2], even though his
definition of “proper” name is a little loose: anything that had two words, second one starting with a lower case letter, was treated as a proper name.
Just imagine the fury of those who are “obsessive-compulsive about terminology” on reading that! Surely not any binomial name is “proper”? However, that is beyond the point. Linnaean names are just the labels. They may be preferable to NCBI tax_id codes because of aesthetic considerations but ultimately they are dispensable. We only cling to them because we believe that these labels have, as Robert M. Pirsig put it, “an intrinsic sacredness” of their own [3]:
One finds that in the Judeo-Christian culture in which the Old Testament ‘Word’ had an intrinsic sacredness of its own, men are willing to sacrifice and live by and die for words.
But what about chemistry? On the one hand, chemistry appears to be in a better position because of superiority of chemical nomenclature over, well, any other known nomenclature. The name constructed according to the rules of systematic chemical nomenclature holds the key to the structure of the entity in question. It does not mean that there could or should be only one “proper” name for one structure. For example, “tetrafluoridolead” (additive nomenclature) and “tetrafluoroplumbane” (substitutive nomenclature) correspond to the same entity, PbF4. You don’t have to know it, because you can figure it out. Compare this with the situation in biology: there is no way to deduce that, say, Prunus dulcis and Amygdalus communis are synonyms.

On the other hand, we chemists often fall into the same trap as anyone else: we tend to believe that “proper” naming of a compound (of known structure) automatically improves our knowledge of it. But why? The terms can change. The nomenclature rules are changing. For a structure of certain complexity, the application of the same rules by different chemists (or different naming software) may result in different systematic names. Some structures as yet cannot be named by any software. So what? It is highly unlikely that a name which takes more than 100 characters will be used in any discourse. I distinctly remember thinking about it a few years ago while reading the draft of IUPAC Recommendations for rotaxane nomenclature [4]. Why not to use the (equally unpronounceable but more useful) InChI string instead?

Still, I wouldn’t dismiss the aesthetics that easily. For me, concise, clear, elegant is good; long, ambiguous, ugly is bad. And coming back to the title of [1]: “being obsessive-compulsive about terminology and nomenclature” is neither a vice nor a virtue. It is a mental condition that some people (myself included) have, for the better or the worse.
  1. Kuhn, J.H. and Wahl-Jensen, V. (2010) Being obsessive-compulsive about terminology and nomenclature is not a vice, but a virtue. Bionomina 1: 11—14.
  2. Page, R. (2011) Dark taxa: GenBank in a post-taxonomic world.
  3. Pirsig, R.M. (1974) Zen and the Art of Motorcycle Maintenance.
  4. Yerin, A., Wilks, E.S., Moss, G.P. and Harada, A. (2008) Nomenclature for rotaxanes and pseudorotaxanes (IUPAC Recommendations 2008). Pure Appl. Chem. 80, 2041—2068.

Friday, April 08, 2011

Amethyst

Last Summer, we bought this crystal-growing kit in Oxfam. It contains ingredients and instructions to grow several types of crystals. Those nicknamed “quartz” and “emerald” in fact are monoammonium phosphate, NH4H2PO4, while “amethyst” and “fluorite” are grown from a solution of potassium aluminium sulphate, KAl(SO4)2. Our latest experiment was to grow an “amethyst” crystal cluster. Timur and I prepared the solution, poured it over two stones from our garden and left to grow for a week. Here’s the result.