Tuesday 04 August 2009
Calling Time on Biological Nomenclature
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I was writing a report on the role of nomenclators in PESI when I realized that (with a little tweaking and injection of dangerous opinions) one section would make a good blog post.
In order to facilitate the accurate exchange of taxonomic information, both within the taxonomic community and more widely in the biological and environmental sciences, the e-infrastructure needs to provide two dictionary functions for scientific names of organisms i.e.
- A recognized list of the names used. To establish that any two studies are actually using the same names whilst accounting for spelling variants and homonyms as well as to facilitate consistency in spelling and presentation.
- A mapping between the names and descriptions of the taxa they are used for. To establish that any two studies are using the names in the same sense or compatible senses.
If the ICBN and ICZN codes required all names to be registered in a single or limited number of places then this would effectively fulfil the first function. Unfortunately neither the ICBN or ICZN codes require names to be registered. Neither do they require names to be published in a particular list of journals. They merely set out the conditions for effective publication. The publications in which new names appear could be published anywhere and deposited in any library. There is no requirement for them to be peer reviewed.
Both codes require that the oldest name be used for a taxon yet provide no mechanism for ascertaining if the oldest name has been found. This means that any revisionary treatment of a group has the potential to destabilise the names in current use by uncovering older publications.
Although continuously updated the codes are still focused on a world of paper publication with a relatively small number of journals in each specialist field. The codes are run on the basis of consensus building and, because the need for registration is not yet universally recognised, no such registers have been established. ICZN is in the process of attempting to establish one in the form of ZooBank. A register for ICBN was proposed, then they fumbled and dropped the ball but may pick it up at some point in the future.
In contrast to these attempts the Bacteriological Code (ICNB) has an effective registration system that has been in place for nearly thirty years. All bacteria names have to either be in the Approved Lists of bacteriological names published in 1980 or published in the Journal of Systematic and Evolutionary Microbiology.
Unless some external body forces, and perhaps funds, the ICBN and ICZN to establish effective registers of names the community is forced to build and maintain separate databases of nomenclatural data – nomenclaturors such as IPNI, uBio, Index Fungorum, etc etc. Multiple databases with multiple versions of how to cite names.
Ultimately scientific names are only human readable strings for referring to biological taxa. As we move to an age where many if not all taxa (even plants!) will be defined in terms of their barcodes* and most biological data is handled by machines then the barcodes become the real identifiers for taxa and scientific names just so much eye-candy. Names are just the display labels for the links. The targets of the links are what is important and they will be defined in terms of barcodes embroidered with morphology.
I am afraid I can see the writing on the wall for old style nomenclature and with it a lot of traditional taxonomy - flame on TAXACOM!
* Before you have a knee jerk reaction to the thought of barcodes defining taxa rather than merely labelling them you might read Identifiers, Indentity and Me where I rather unskillfully advocate that an identifier erects a thing rather than things having identifiers. All we have to do is say "Anything that has this barcode is this thing"