The Next Million Names.

Mark J. Pallen, Andrea Telatin, and Aharon Oren have a paper in Trends in Microbiology (2020) called “The Next Million Names for Archaea and Bacteria“; here’s the opening Highlights section:

Microbiology has entered a golden era of discovery, with exponential growth in the identification of new species, genera, and high-level taxa through culturomics, genomics, and metagenomics. This creates an urgent unmet need for new taxonomic names for Archaea and Bacteria.

Currently, creation of well-formed names relies on time-consuming nomenclatorial quality control by a dwindling pool of experts conversant with classical languages and the International Code of Nomenclature of Prokaryotes. These problems are compounded by the custom of creating names on an as-needed, just-in-time-fashion.

Here, we outline a novel approach with three features: creation of names en masse before they are tied to taxa; combinatorial concatenation of roots from Latin and Greek, drawing on stocks of roots with relevant meanings; computerised automation of the creation of new names.

Latin binomials, popularised in the 18th century by the Swedish naturalist Linnaeus, have stood the test of time in providing a stable, clear, and memorable system of nomenclature across biology. However, relentless and ever-deeper exploration and analysis of the microbial world has created an urgent need for huge numbers of new names for Archaea and Bacteria. Manual creation of such names remains difficult and slow and typically relies on expert-driven nomenclatural quality control. Keen to ensure that the legacy of Linnaeus lives on in the age of microbial genomics and metagenomics, we propose an automated approach, employing combinatorial concatenation of roots from Latin and Greek to create linguistically correct names for genera and species that can be used off the shelf as needed. As proof of principle, we document over a million new names for Bacteria and Archaea. We are confident that our approach provides a road map for how to create new names for decades to come.

I enjoyed this section:

Another pressing problem is that most microbiologists follow Shakespeare in possessing, at best, ‘small Latin, less Greek’ and so are poorly equipped for creating well-formed binomials that comply with the rules of Latin grammar and are presented with clear, plausible etymological justifications (Box 1). Despite the publication of several ‘how-to’ guides, this skills gap has led to propagation of numerous erroneous malformations – a high-profile example is the species epithet pyloridis, which even passed validation in the International Journal of Systematic Bacteriology before it had to be corrected, according to the rules of Latin grammar, to pylori.

Don’t miss that Box 1 link, with its parade of horribles: “Common problems include trying to use poorly Latinised English words (e.g., geesorum instead of anserum for a species associated with geese) or making up nonsensical etymologies.” (Related: Abra cadabra, from 2004.) Thanks, Kobi!

Comments

  1. “International Code of Nomenclature of Prokaryotes” tickles me. I’m imagining an oak-lined chamber with bewigged, humorless prokaryotes pondering names and titles.

    I thought that would be the end of the ridiculousness, and then I got to “geesorum”.

    This discussion makes me think about the far easier problem of proliferating drug nomenclature.

  2. David Marjanović says:

    Huh. Currently, as the paper points out, all new names of prokaryotes must be published in that one journal, and only “species” that have been kept in pure culture are allowed to be named – meaning that there are lots and lots and lots of known “species”, some of them pretty well understood, that can’t be named because nobody has figured out how to grow them in the lab.

    That includes Candidatus Pelagibacter ubique, a major component of seawater.

    Worst part of the paper: the many, many typos in Fig. 1. And then there’s this bit:

    or by adding multiple roots in front of a final element (e.g., merdavium, faecavium, caccavium for species associated with bird faeces).

    No, with shitbirds.

  3. J.W. Brewer says:

    Given the rough job market for newly-minted Ph.D.’s in classics, wouldn’t it be better not to completely automate but to provide some post-doc type jobs for classicists to do quality control on initial proposals?

  4. Viruses get numbers instad of names, like HTVC010P, which infects Pelagibacter ubique and “probably really is the commonest organism on the planet”.

  5. David Marjanović says:

    wouldn’t it be better

    Yes, but good luck convincing any science funder to create any such job.

    (Convincing them to create any job at all is hard enough. There’s so much science to do that nobody funds…)

  6. Why not just go with current trends, and allow corporations to pay for naming rights?

  7. Naming rights for goose-shit bacteria should be quite cheap. I’ll take a dozen, and give them all embarrassing, juvenile-humorous names. Prokaryotes really don’t care.

  8. Indeed, someone with enough money could probably purchase the entire species epithet pylori and change the name back to pyloridis, just to irritate the Latin scholars.

  9. Just lump ’em all together as the Lumpenprokaryotes.

  10. You guys are no doubt aware of The Holotypic Occlupanid Research Group : A Database of Synthetic Taxonomy (http://www.horg.com/horg/)? Quote: “[The] Holotypic Occlupanid Research Group[‘s] site contains several years of research in the classification of occlupanids. These small objects are everywhere, dotting supermarket aisles and sidewalks with an impressive array of form and color. The Holotypic Occlupanid Research Group has taken on the mantle of classifying this most common, yet most puzzling, member of phylum Plasticae.”

    What we need is a generator for all the forms that plastic takes on the seas, on the land, and in the air. Just naming all the stringiforms (angling threads, nets, tows) could keep people busy for a while.

  11. Athel Cornish-Bowden says:

    Why was I not surprised by this sentence:

    However, the practice continues, with the most salient example being the use of Massilia (the Latin name for Marseille) by the IHU Méditerranée Infection – a term that has found its way into over 260 species or genus names

    That must be Didier Raoult’s doing, I thought, and sure enough it is. When he’s not busy promoting the use of hydroxychloroquine for treating Covid-19 he’s busy writing papers that describe new microorganisms. I think I probably won’t catch Covid-19, but if I do they’ll take me to the Hôpital La Timone, where Didier Raoult has his institute.

  12. You guys are no doubt aware of The Holotypic Occlupanid Research Group : A Database of Synthetic Taxonomy

    I wasn’t, so thanks — that’s great!

  13. So… Chaos chaos is an indie synthpop band, but its Wikipedia article

    https://en.wikipedia.org/wiki/Chaos_Chaos

    begins with a disambiguation from ‘the amoeba formerly known as Chaos chaos’.

  14. “Occlupanid” – I do not know why but I remembered the time when Chinese schoolkids spoke English worse than me rather than better, and I received spam like: “good glass beads from China 95% spherical 90% float in xylene”.
    This usage of ‘good’ is really cute.

  15. David Eddyshaw says:

    I remembered the time when Chinese schoolkids spoke English worse than me

    Older Kusaasi still describe some piece of poorly-made junk liable to break down at any moment as Zapan “Japanese”, despite it being a lifetime since Japan was the world’s leading provider of cheap tat. The Kusaasi may simply have been taken in by Brit propaganda in the first place, come to that. It was probably cheap British tat all along, masquerading as Japanese.

    I once came across a report from the early twentieth century by some especially imperceptive colonialist Brit administrator, which declared that the people of Canton Province would never amount to anything because they were intrinsically idle and improvident.

  16. From Back to the Future, Part III:

    Doc: No wonder this circuit failed. It says, “Made in Japan.”
    Marty: What do you mean, Doc? All the best stuff is made in Japan.
    Doc: Unbelievable.

  17. John Emerson says:

    I knew of a carpenter who refused to use Jap tools into the 70s. I think WWII had something to do with it.

  18. David Eddyshaw says:

    The actual proposal reminds me of Charles Moore’s idea when he became editor of the Daily Telegraph, that human cryptic-crossword setters could be dispensed with, as crosswords could be automatically generated from the existing database of clues.

    It was then that I first realised that Tories were not simply mistaken, but actively evil.

  19. John Cowan says:

    I have had similar notions of rap songs “performed” by a speech synthesizer hooked to a drum machine. There is also a Spider Robinson story “Half an Oaf” in which a not-too-clever time traveler’s time-belt has malfunctioned, leaving his upper half in the 1950s and his lower half uptime where he started (though somehow blood circulation continues unimpeded[*]). The local who is trying to help him refers to “that Jap belt of yours”, to which the oaf replies “Jap! I wish it was.”

    occlupanids

    See Lehmer et al, “Plastic bag clip discovered in partial colectomy accompanying proposal for phylogenic plastic bag clip classification”, BMJ Case Rep. 2011; 2011: bcr0220113869. There is a later report linked from that page on the discovery of an occlupanid infesting a patient’s subglottic airway: remarkably, it was removed under local anaesthetic only.

    [*] This reflects one of Niven’s Laws: time travel stories are fantasies, not science fiction. His Svetz stories are evidence of this: in “Get a Horse!”, the first of them, a 30C time traveler is charged with obtaining a specimen of the extinct species Equus caballus, but the one he finds, though matching the records otherwise, has a mysterious and inexplicable horn in the center of its forehead….

  20. I knew of a carpenter who refused to use Jap tools into the 70s. I think WWII had something to do with it.

    I think it was in the 1980s that I spoke to an Australian farming acquaintance (1950s born) who apologetically referred to his pick-up truck as “Japanese” (I don’t remember his exact wording; it may have involved “cheap”, “junk”, or “rubbish”).

  21. Bathrobe:

    Did he have a ute or a pick-up truck?

  22. It was a light truck. Not a ute, at least not in my terminology.

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