The New Nominomania

Roger Hyam's blog post Calling time on biological nomenclature and the comments it received, also on Taxacom, makes me wonder if not biodiversity informatics is the enemy rather than the servant of science. What some of my colleagues argue for are empty name lists, including also artificial constructs like barcode species. Then erecting the haplotype as the focal point of taxonomy is apparently to be expected lying in ambush.

For taxonomists, names are abstractions of scientific knowledge, and cannot, consequently, be managed in a formalised top-down system. To call for science to be published in only certain journals, to advocate that certain kinds of "species" should be the only ones permitted, are not friendly proposals to rationalise information flows, but denials of the process of free information gathering. It is plain denying that taxonomic papers are primarily contributions to science in the first place, and name machines only secondarily. Taxonomy must remain a scientific exercise, and cannot be a mechanical process.

The idol project brought forth is the International Code of Nomenclature of Bacteria, where there is a Committee to decide, a single place to register names, and — most importantly, forgotten by the supporters — less than 10 000 diagnosable units are included. Since bacteria are so different from other organisms, and the named units so few (at least that have been admitted by this Committee ...) the ICNB is simply not possible to use as a model for the several million species of multicellular organisms, most of which have not been named yet.

Whereas I am a friend of registration of names, and advocating that scientific names as defined in the Botanical and Zoological Codes are as good markers as can be (human-friendly they are) of scientific processes of elucidating the characteristics, whereabouts, and history of pieces of biodiversity, I cannot be positive to registration replacing the scientific procedure of testing hypotheses of phylogenetic distinctness labelled with scientific names. No committee should certainly be involved here. And whereas barcodes can probably be an interesting tool for the food industry and similar, I don't see much use for it in taxonomy where we have species concepts based on evolutionary theory, type specimens, and diagnoses that are compatible with scientific theory and hypotheses. In taxonomy, contrast to the barcode shop, we also have flexible systems to classify biological units other than "species".

Whereas taxonomists must be more collaborative with biodiversity informatics in, e.g., voluntary registration in ZooBank, and show more effort to make their work and naming visible, it is the task of biodiversity informatics to find the methods to discover, assemble, and present the objects of biodiversity. We must not adapt science to fit the index.

The concerted effort of GBIF and Encyclopedia of Life to build a Global Names Architecture (GNA), providing a Global Names Index (GNI), seems to me to be a way out of the dilemma that biodiversity informatics is entangled in: information about biodiversity cannot be extracted because there are too many names (with misspellings, synonyms, homonyms, etc.) out there and the approximate (can never be exact) meaning of a name may vary from one mention to another. Certain related efforts, such as transparently tagging names with identifiers, as is being done in Zootaxa and ZooKeys, are bridging the gap between computerified and human-mediated names. Thus the technology is there, it is evolving, and taxonomy should be able to continue as a science.

The real difference between the mega-name-consumers and taxonomy is that mega-name-consumers wish to have all in one place, which is probably of zero interest to taxonomy. They are also not interested in metadata such as diagnosis, type specimens, etc., and they do not want taxon concepts to change, which they inevitably must do in science. In taxonomy, only small sets of taxa (and names) are handled at any given time, and of these, all have a definite function in the particular study, may be a revision, a field guide, a phylogeny, or a classification. In such contexts, the name domain is self-contained, and all named units are related to each other by the hypothesis or scope of the study. Everything else is of zero interest. For a study of cichlid fishes, it is of no interest whatsoever if New Zealand Lepidoptera exist. Enter mega-name-consumers, who will need both in the same list because those lists are not based on any scientific criterion and it is absolutely not known what the list is for. If consumers could define their precise needs from study to study, it might be easier to design the tools to extract the names and concepts actually needed. To maintain lists of millions of names, even in a database, for no specific purpose does not make much sense. Indeed, most checklists of smaller scale as well, especially when produced by non-specialists are equally meaningless anachronisms of apparently undefeatable listmania.

So, we must ask from biodiversity informatics:

1. Proper specification of what their taxonomic units (text-names or LSIDs) are going to be used for. Map species occurrences, make phylogenetic hypotheses, sort out homonyms, ...?
   
2. Design systems that can effectively detect, maintain, and trace name usage and relevant metadata, compatible with taxonomic objectives and procedures.
3. Provide voluntary registration systems, and other tools facilitating the exchange of names and metadata between taxonomists and consumers.

Whereas 2 and 3 may be underway, I am beginning to doubt that anyone can give a good answer to 1...

For those who cannot embrace taxonomy fully, I recommend stamp collecting. It has all the flavors of registration, codes, hybridisation, phylogeography, central committees, misidentifications, rare haplotypes, identical reissues, fakes, top-down standards, and stasis. It is a totally unscientific enterprise with no limits to organisational options suitable for old frustrated men obsessed with control. Ooops, does it sound like DNA barcoding ...?

Image: Wikimedia Commons, public domain

8th Indo-Pacific Fish Conference over

The 8th Indo-Pacific Fish Conference is over here in Fremantle, and tonight is the closing banquet. It has all been very well arranged, and organisers must be content. The Swedish delegation of three, slightly outnumbering the Danish, of two, will gradually move back to the other side of the world.

What were the highlights then. Since I have not attended every one of the six concurrent series of sessions, I must be blamed for zooming in on those where I was present. Ralf Britz (Dracula fish) provided strong arguments for and examples of the use of developmental series in homologisations of morphological characters, and Dave Johnson presented a fascinating story of how Mirapinnidae (known only from larvae), Megalomycteridae (known only from males), and Cetomimidae (known only from females) reflect lifestages and sexes of one and the same family, the Cetomimidae (whalefishes).

Tatsuya Kaga gave a nice, concise presentation of the phylogeny of the Sillaginidae, and Tan Heok Hui presented new data on the systematically and biologically fascinating miniature peat swamp fishes, Paedocypris and Sundadanio.

Bill Eschmeyer received the Bleeker Award in Taxonomy, well deserved for his long-term work on the Catalog of Fishes, a tool ichthyologists refer to daily or at least weekly or they are not ichthyologists.

Yes, that was perhaps the biased view of a morphological systematist. I gave a presentation of a molecular phylogeny of South American cichlids, Te Yu Liao a snapshot of his PhD dissertation on the systematics of Rasbora, which was very nice, and Fang presented the first molecular outcome of the continuing analysis of danionin interrelationships.

I obtained from Martien van Oijen, Naturalis Museum in Leiden, a new, very heavy book: A translation to English of Bleeker's Ichthyologiae Archipelagi Indici Prodromus. Volumen 1. Siluri. I am personally quite content with the Latin and Dutch version, but this is an important work making Bleeker's text generally available to the majority of ichthyologists working on Indonesian catfishes. I was informed that the cyprinids are next.

Darwinius masillae available

Finally, not letting the news fade too quickly, PloS have earned one more publicity score by adhering to the International Code of Zoological Nomenclature, by making prints available of its article on Darwinius masillae, as reported to The Loom.

If it is so difficult for e-only journals to publish taxonomic papers following the simple rules applying, no wonder that the International Commission of Zoological Nomenclature is working so hard to make it possible, and possible for everyone, not just PloS, to publish nomenclatural acts e-only.

The Commission has opened a consultation with the community about an amendment to the Code to permit e-only publishing of nomenclatural acts, posted on their website. A first round of comments has already been published.

With more than 1.8 million species named, and scientific names being the only index to this diversity, it is evident that the stability of names within the botanical and zoological nomenclatural systems is a priority for all. In its strive to take nomenclature to digital dimensions while still maintaining a system supporting stability in the short and long term, the Commission needs all advice and comments it can get from experts and practitioners.

Today's buzz

Da buzz of today and the day before is a long-tailed almost-monkey hitting the book shelves, TV screens, all other media, and the scientific press in one sweep. If it costs USD 1 million on the fossil market, there are consequences.

Ida, also known as Darwinius masillae, a 47 million year old fossil of a
primate mammal. From Franzen et al. (2009), slightly modified.

So, where to go with taxonomy? Play show, or play low? Whereas on the one hand it is fascinating that taxonomy can be so pervasive and so hypeable, and should nourish hopes of more appreciation for this discipline which underlies all biology but also is a science on its own; the other hand is raised in warning that we can't do science only in the headlines.

Although the article in question, about a 47 million year old primate fossil from Germany, is very nicely done, and has a fascinating history to tell, the most telling indication that things are not coming out as intended is the complete misunderstanding expressed in all headlines, "missing link between monkey and Man". For what I understand it is more something that went extinct between lemurs and monkeys. But I see Sir David hugging a lemur in promoting the research on .... aw, yes, that's where we are. The crucial piece in taxonomy. The scientific name. The index. The one item that is needed to find back the information about this species.

PlosOne, the publisher of the study of dear almost-monkey is an e-only journal, where authors pay to publish, but it is free to read online. There is no paper edition. For a scientific name to be available it has to be in a publication printed on paper, with simultaneously available more than one identical copies (or on other more or less durable media provided some special conditions, but web publication is not permitted). The International Code of Zoological Nomenclature is quite clear on this in its Article 8. The Code is there to keep track of the names of more than 1.5 million animal species on Earth, and thus a very important instrument in Zoology.

There is no evidence yet that this paper publication exists, and thus the intended name of the fossil, Darwinius masillae, as it appears in the online article, is reproduced here only to attract search engines to this blog.

This is somewhat embarrassing, but also sign of the times, times when roads cross at different levels and communication has glitches in changing traditions. We are going digital. Not only our toys and tools are binary and glowing like Swatch watches, but our minds have drifted away with the circuits. I was fascinated by the digital displays and remote controls on the vacuum cleaners when looking for replacement for the one that died; seems, however, the analogue version eventually purchased sucks dust with sufficient energy without displays.

I have no intention of not being absorbed by the digital tsunami. I will survive surfing. It will take some adjustments, however. E-only publishing of taxonomic matter is still counter to stability. But we have to find ways for e-only to come forth. Not to promote hype, but so we can get more papers published and more papers (read: information) more widely accessible, than is possible by paper publication. My office, my home office, are both like libraries. And still every day there is some paper-only publication that I need and cannot get. But I am immensely grateful for AnimalBase and the Biodiversity Heritage Library, and of course the Internet Archive and Google Books, for frequently saving my day.

I want all of the fishes I publish on to be on TV, and in the newspapers. I want TV personalities to enthusiastically comment on the fishes I study. But first of all, I would like to see this information society come together a little bit better, with open access, GUIDs, e-only publishing, the Global Names Architecture (GNI) and more from the informatics side, and names, descriptions, diagnoses, images, data and interpretations from the taxonomists's side. In that context, we shall not forget to make the names nomenclaturally available.

Blog links
Ed Young
Brian Switek
Carl Zimmer

Article link

Franzen JL, Gingerich PD, Habersetzer J, Hurum JH, von Koenigswald W, et al. 2009 Complete Primate Skeleton from the Middle Eocene of Messel in Germany: Morphology and Paleobiology. PLoS ONE 4(5): e5723. doi:10.1371/journal.pone.0005723