[Taxacom] Clients for biodiversity informatics

Tony.Rees at csiro.au Tony.Rees at csiro.au
Thu Feb 18 22:39:39 CST 2010

Stephen - well, yes and no... I have had this argument recently with biodiversity managers - they reckon (possibly correctly, possibly not) that want we already know is a pretty good guide to which areas are in need of conserving over others - a bit sub-optimal maybe, but their job *might* be to decide whether to put $$ into conservation or taxonomy - now there's a different tension, maybe.

Cheers - Tony

-----Original Message-----
From: Stephen Thorpe [mailto:s.thorpe at auckland.ac.nz] 
Sent: Friday, 19 February 2010 3:35 PM
To: Rees, Tony (CMAR, Hobart); mesibov at southcom.com.au; taxacom at mailman.nhm.ku.edu
Subject: RE: Clients for biodiversity informatics

A bit of a flaw in your argument Tony! The biodiversity crisis (=taxa disappearing before they can be documented) can only be treated by doing as much descriptive taxonomy as possible as quickly as possible. It seems that the rate of new descriptive taxonomy is actually DECREASING, with money being diverted elsewhere into phylogenetics, molecular stuff, and bioinformatics. Accounting for what has already been described and documented is not of any direct relevance to the biodiversity crisis. Even in N.Z., there are thousands of undescribed/undocumented species sitting in collections, but with little or no prospect of being worked on in the foreseeable future. Another example: Project Wallace found 600 new species of mordellid beetle in Indonesia in the 1980s, only 1 of which has been described to date!
I think your "link" between the biodiversity crisis and bioinformatics is bogus...


From: taxacom-bounces at mailman.nhm.ku.edu [taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Tony.Rees at csiro.au [Tony.Rees at csiro.au]
Sent: Friday, 19 February 2010 5:20 p.m.
To: mesibov at southcom.com.au; taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] Clients for biodiversity informatics

Dear Bob,

Thanks for your comments. Indeed after sending my earlier post at some ungodly hour of the morning (local time), I did wonder whether I had slightly over-simplified my statement of the audience for this "stuff", and considered posting an amplification - but thought I would let it stand, for the following reason in the main:

- A major problem facing the natural world is loss of biodiversity (as has been stated many times on this forum)

- The main players capable of halting this are the managers and planners who control national and international activities (e.g. see Convention on Biological Diversity, http://www.cbd.int/ etc., plus relevant national level initiatives)

- The first thing these managers / policy persons want is to know what biodiversity exists and where. If we (as biodiversity data generators and managers in the broad sense) cannot get our act together to (for example) determine whether the nnn records of species X, under a bewildering variety of names and formats, actually represent one species or lots, we cannot supply that information (or, as an associated task, retrieve all of the relevant information on that taxon because it resides under many labels).

For example: As part of the winding up of the Census of Marine Life program (10 years of new fieldwork, including labour for many taxonomists, plus synthesis of all pre-existing regional information for marine taxa), in my capacity as a Data Manager I have been part of the team trying to assemble a "definitive" (to now) list of marine species for Australia. Guess what is the hardest part (actually 2 parts): (1) finding all of the relevant data in digital form (or digitising it if not), and (2) by far the biggest headache - deduplicating the list - i.e. making sure that the number of entries does not vastly exceed the number of taxa on account of variant names, spellings, ranks (e.g. subgenus <-> genus, infraspecies <-> species), and so on - exactly the type of task that would be hugely simpler with a GNUB or whatever you would like to call it, to do all of the resolution for me. And guess who will (hopefully) be the audience for this:

<quote from Bob:>
- the general public, which relies on WikiXXXX and isn't often disappointed?
- the taxonomic community, which goes to authoritative specialist resources?
- the clueless bureaucrats, who see knowledge as power, confuse data with knowledge and aggregate data for its own sake?

... probably all of the above (once the data plus summary info are available)

And guess who will wield the most power in (just possibly) providing the resources to conserve what is most in need of the same?

Maybe you can come to your own conclusion.

That is not to say that the taxonomists too cannot benefit (a little / a lot) as per Rich's posts. Here's another instance, just from yesterday/today's activities here as it happens:

- A team of 13 experts have just (late last year) published the "be all and end all", most up-to-date, authoritative systematic treatment of decapod crustaceans down to genus level. I have just been looking through the 2726 genera they list (with relevant higher classification etc.) and comparing these names with names presently on my "IRMNG" master genus list for everything - in principle looking to upgrade my own classification, also add in any names not previously held. In doing this, I discovered 31 potential preoccupied names, potentially of interest to the authors, viz:

Alcockia, Allogalathea, Arcotheres, Boreas, Duncania, Eoplax, Euclosia, Feldmannia, Forestia, Forsteria, Laurentiella, Lissopsis, Loerentheya, Meriola, Mithrax, Naxia, Noetlingia, Odhneria, Oxythyreus, Pelagopenaeus, Psaumis, Pseudomicippe, Quadrella, Rathbunella, Stratiotes, Syphax, Thia, Villalobosus, Wanga, Xandaros, Zehntneria

Now not all of these will actually be preoccupied (for example the earlier instance of Pelagopenaeus is a nomen nudum), but I am reasonably sure that a good swag of them are (e.g. Alcockia is a valid genus of fish). Also 6 (or possibly 8) misspelled genera too - I will not list them here but again, hopefully of interest to the authors of that paper. Here I should point out that I am by no means an expert on this group, but applying the dreaded "database" approach allows me to rapidly find things that even an expert might have missed.

Anyway you can see that I do stand by my original statement, even though in reality there is no doubt that the true applicability of this "stuff" is wider than I stated in fact...

Regards from the south of the island,


-----Original Message-----
From: Bob Mesibov [mailto:mesibov at southcom.com.au]
Sent: Friday, 19 February 2010 2:48 PM
Cc: Rees, Tony (CMAR, Hobart)
Subject: Clients for biodiversity informatics

Tony Rees wrote:

"The above is just to point out that Rich is over-simplifying if anything: this is the real world situation (of names used as pointers to information) that "Biodiversity informatics" and its clients (generally managers and policy makers who know nothing about taxonomy, and care even less) is making at least some efforts to come to grips with."

Was this the GOTCHA! moment? Have the principal beneficiaries of these enormous effort been - at last - revealed? Namely taxonomically clueless bureaucrats?

I'm kidding - a little. I've been asking who's going to use the Gigantic All-Species Distributed Database, and for what purposes, for several years on Taxacom, and not getting a clear answer. My main explanation (to myself) has been that the workers in this enterprise really aren't too sure. As with Rich Pyle, it's obvious to them that what they're working toward is better than what we have now, so the projects have a lot of well-founded progressive momentum.

Occasionally we get a 'sell' of the enterprise from highly cluey taxonomists like Rich, who can see benefits and use them in his daily work. But a 'sell' is necessary because there is no International Union of Taxonomists which voted unanimously to Go Go Go...Databasing! Not all taxonomists want it, or want to use it, and some (like Stephen Thorpe) are vocally grumbling.

I can say without much fear of being stomped on what taxonomists *do* want. They want human-digested and human-processed biodiversity information. They want expert summaries and compilations, not the ability to gather every tidbit of information *de novo* from the entire biodiversity literature. Where these expert summaries and compilations don't exist yet, taxonomists are building them, bottom up, in their own specialised areas or (as in Wikipedia and Wikispecies) in general. There are some really great specialist sites on the Web. No matter how much money gets poured into EoL or GBIF, the acronyms are highly unlikely to achieve the passionate focus, the wise perspective and the high data quality you can find on those specialist sites.

Will "managers and policy makers who know nothing about taxonomy, and care even less" visit those sites? I doubt it. Not when they've spent millions on the huge IT projects. So do we finish up with 3 classes of biodiversity information user?:

- the general public, which relies on WikiXXXX and isn't often disappointed?
- the taxonomic community, which goes to authoritative specialist resources?
- the clueless bureaucrats, who see knowledge as power, confuse data with knowledge and aggregate data for its own sake?
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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