[Taxacom] People and databases - an example

[Stephen Thorpe]

Just a quickie comment to Bob's post below: the LESS well studied a  
taxon is, the EASIER it is to deal with in a bioinformatics sense!  
Bioinformatics people must make a huge sigh of relief when a taxon has  
only been mentioned once in the literature (the original description).  
One mention = no disagreement!

Stephen

Quoting Bob Mesibov <mesibov at southcom.com.au>:

> In an earlier post I contrasted the naming and classification of two  
> gigantic sets of natural entities: organic molecules and species. I  
> pointed out that taxonomy might look chaotic to an outsider, and  
> suggested that an important difference was that the entities being  
> named and classified in taxonomy did not have fixed boundaries.
>
> I don't think this point is adequately appreciated by many database  
> builders, although Roger Hyam in his nice draft chapter and Rich  
> Pyle in many places have emphasised the plasticity and ephemerality  
> of linkages between names, types, taxon circumscriptions, specimens,  
> PUTNIs, etc. There are many, many examples of taxonomic complexities  
> known to taxonomists on this list. Such complexities might be  
> unfamiliar to some in the biodiversity informatics world, some of  
> whom - I stress 'some' - think that a species is a natural entity  
> waiting to be discovered and pigeon-holed, and all the taxonomic  
> blather surrounding this fundamental truth only needs to be recorded  
> for historical purposes. Once you've got the primary key - the  
> species - all the rest sorts itself out in the linked tables in the  
> database.
>
> The following arbitrarily chosen example shows why this approach is  
> misguided.
>
> The latest synonymy for the millipede Ophyiulus targionii Silvestri,  
> 1898 contains 45 entries and is incomplete. Ignoring spelling  
> variants, it shows that the original name has accreted 1 species  
> synonym, 8 subspecies and 2 varieties, and that at various times one  
> of the subspecies names has been elevated to species and synonymised  
> with targionii. There is a 110-year history of splitting and  
> lumping, and of shuffling of types between different names. There  
> have been numerous misidentifications, and many innocent uses of  
> non-diagnostic characters in diagnoses.
>
> No one has yet sat down with every specimen from the synonymy, plus  
> an adequately broad sampling of possible O. targionii from across a  
> very large range, which now includes introductions in Australia and  
> New Zealand. It is unclear whether these animals exist as a  
> geographical mosaic of potentially interbreeding forms specialised  
> for life in different regions, or as a cline of such forms, or  
> whether there are reproductive barriers in different parts of the  
> range. It might be possible to answer these some of these questions.  
> In other words, a human taxonomist in 2009 might decide to  
> re-examine all the data, get new data (e.g., mtDNA sequences) and  
> come up with a plausible taxonomic scheme, valid for 2009, which  
> reassigns names to the hypothetical entities we call species.
>
> But there is no way a machine can sort out this mess. And "O.  
> targionii" is a relatively *well-studied* entity. The vast majority  
> of arthropod species haven't had anywhere near this much attention.  
> A biodiversity informatician might be satisfied that a taxonomic  
> database satisfactorily represents what's known about biodiversity,  
> but from a taxonomist's point of view all that's happened is that a  
> gigantic mess has been stuffed into a box out of which  
> non-taxonomists plan to serve out portions of 'fact' to anyone  
> interested.
>
> The more traditional and pragmatic approach is to encourage humans  
> to become experts. Anyone interested can then go to an expert for  
> answers, one of which will always be 'We don't know yet', and that's  
> a response very difficult to program into a database interface.
> --
> Dr Robert Mesibov
> Honorary Research Associate
> Queen Victoria Museum and Art Gallery, and
> School of Zoology, University of Tasmania
> Home contact: PO Box 101, Penguin, Tasmania, Australia 7316
> (03) 64371195; 61 3 64371195
> Website: http://www.qvmag.tas.gov.au/mesibov.html
>
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