Thursday, 1 August 2013

Phylogenetic clunkiness

Writing a bacterial phylogenetics paper is probably the most agonizing type of paper to write due to the clunkiness of the language. But it's not the jargon that make life hell, it's the missing jargon that make it hard. The quantity of jargon actually make life a bit easier, but the lack of some blatantly useful words makes it painfully clunky and stuffy.
Reading a phylogenetics paper is generally visually painful due to the frequent usage of italics and "quote" marks. A phenomenon that I once read described aptly as a "typographic circus" by someone on a Wikipedia talk page. The italics are for taxa described validly according to the bacteriological code, whereas quotes are reserved for candidate taxa which have not been validated yet —the bugs exist, but nobody has done the paperwork. Nevertheless, the aesthetic problem is trivial compared to the lexal ones…
One such problem is the lack of trivial names (common names).
Only a few groups of  bacteria have trivial names and for some reason in microbiology, unlike botany, scientific names are rarely "trivialised", a process of making an English word for a member of a taxa, for example, a crustacean is a member of the family Crustacea and a bromeliad is a member of the genus Bromelia.
The most notable exceptions are a proteobacterium (a member of the phylum Protobacteria), an enterobacterium (a member of the family Enterobacteriales) and a pseudomonad (a member of the genus Pseudomonas). This is a shame as it circumvents the repetitive clunkiness and stuffiness. Taxonomic names, after all, are labels for the group, which can adopt a metaphorical usage to denote one of its members, primarily due to the quirkiness of the Latin name: for example, a group of sheep is a flock, but calling a single sheep a flock would sound awkward, whereas calling a sheep an Ovis sounds less weird, just technical. However, the phrase "a member of the" becomes really trite really quickly, one alternative is to use the word sp. (species), but it is still a bit weird: is the supposed to be the indefinite article "an" before Ovis sp.? A further perk is that a trivial name often allows adjectives to be formed, which is much nicer to read than a noun used adjectivally or "of the".
This last note is related to another problem with the Latin grammar of the nomenclature: all higher ranked names are plurals in Latin whereas there is only one of them (there are several members). In Latin (and other romance languages) collective nouns are plurals, whereas in English they are generally singulars (grammatical concord), but can be treated as plurals in informal speech (notional concord), e.g. the Alps is a mountain range (grammatical concord), the band are playing (notional concord). It does seem like a minor nuisance, but it gets really knotty when describing relationships and last common ancestors… on the plus side though the pride in the "look at my fancy Latin" is pretty nice.