[Taxacom] We are cataloguing hypotheses & not real things -- I hope everyone appreciates the implications of this. Was Global species lists ....

Schindel, David schindeld at si.edu
Sat Aug 31 11:42:42 CDT 2013


Apropos this discussion of the reality of and relationships among names, hypotheses, classifications and the real world, we (Consortium for the Barcode of Life, CBOL) just held the fourth in a series of workshops on the legal standards for admissibility of DNA barcode data in the courtroom prosecution of wildlife crime.  This application of barcoding couldn't get much more real.  Stopping illegal poaching and trafficking is something taxonomists of all philosophical stripes support, I think.  Kenya's parliament is considering increasing penalties for poaching and trafficking in protected species, including possible mandatory life sentences for possession of their most important species. Other countries are also increasing their penalties for wildlife crime. The taxonomic IDs based on traditional morphology, barcodes or other means will be critical for wild species and criminal defendants alike.

These workshops have been held in South Africa, Kenya, Nigeria and Mexico, four of the six partner countries in the Barcode of Wildlife Project (BWP, see Google+ Page at http://goo.gl/qU8KQ and @BoWProject on Twitter).  BWP is supported by a Google Global Impact Award to CBOL at the Smithsonian.  Barcode data will need to meet admissibility standards in different countries with different national laws covering CITES and other protected species.  Their rules of evidence and courtroom procedures vary along with their laws and regulations concerning endangered species.  BWP (and taxonomy as a whole, for that matter) is about creating a global, interoperable knowledgebase that can be used anywhere, anytime, by anyone (well, almost anyone) to connect features (morphology, DNA, behavior, distributions) with names, and to connect names with features.  Who among us would say that the rules, procedures and practices of taxonomy and nomenclature are standardized enough to stand up in courts in different countries?

After holding these four workshops you may be pleased to hear that taxonomy still has strong standing around the world.  From what prosecutors, lawyers, court officials and even magistrates said in our workshops, the opinions of a taxonomist with proper credentials will be accepted in court in most cases, depending on how well he or she stands up to questioning by defense attorneys.  Up until now, the testimony usually involves qualitative comparisons using identification keys, reference collections, and diagnostic features described and illustrated in the literature.  BWP will be building a reference barcode library for 2,000 endangered species plus 8,000 of their close relatives and look-alikes.  We hope to include at least five exemplars per species for a dataset of 50,000 records.  The evidence and expert opinions generated by the project will all and only be based on this new 'platinum quality' dataset, not GenBank data or even barcode data generated to date.  

We'll be looking for taxonomists with experience in the selected groups who can help clarify species concepts and locate reference material.  The project has funding to support their involvement.  I'll be forwarding an announcement of opportunities through Taxacom and other channels soon.

David

David E. Schindel
Executive Secretary, Consortium for the Barcode of Life
National Museum of Natural History
Smithsonian Institution
Washington, DC

-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Chris Thompson
Sent: Friday, August 30, 2013 9:58 PM
To: Ashley Nicholas; taxacom taxacom
Subject: Re: [Taxacom] We are cataloguing hypotheses & not real things -- I hope everyone appreciates the implications of this. Was Global species lists ....

Thanks, Ashley,

Yes, you are right and that explains why taxonomy is not well supported.

Yes, that mosquito (Anopheles) that carries that parasite (Plasmodium) are 
not REAL THINGS, only hypotheses, but to millions, who suffer from Malaria 
believe otherwise, those are real things.

For them, some of us try to track those names which are the critical 
indexing keys to information which may help those sufferers, who have 
malaria, may well be doing something useful.

Oh, well ...

Sincerely,

Chris

from

-----Original Message----- 
From: Ashley Nicholas
Sent: Friday, August 30, 2013 6:32 AM
To: taxacom taxacom
Subject: [Taxacom] We are cataloguing hypotheses & not real things -- I hope 
everyone appreciates the implications of this. Was Global species lists ....

Dear All,

I just hope that people doing these digital catalogues appreciate that all 
they are doing is cataloguing hypotheses -- in this case species hypotheses 
(species are not real entities -- Popper's World 2)? We measure specimens 
and populations (Popper's World 1). We extrapolate this limited data to 
hypothesise species. If a researcher can claim to have measured every 
specimen and population of a species (maybe possible for species confined to 
small areas esp. islands [maybe this is why vicariance is so easily 
demonstrated in island situation?]). Only then can s/he claim to have 
objectified a species. However, even then this will only hold true for that 
instance because as the gene pool changes over time s/he can no longer claim 
to have objectified that species.

These catalogues are catalogues of species hypotheses. Hypotheses are not 
the "truth" they are suppositions that remain to be verified (a shaky 
premise) or falsified (a better premise). So who is someone doing a 
catalogue to say that one species hypothesis is the correct one -- and 
include it, while rejecting all others? As an empirical scientist that makes 
me feel very uncomfortable.

However, I can see that something needs to be produced for conservationists 
etc. to use. I have no answer. Taxonomy was originally both a science and a 
service (to societies) and we still need to fulfil this role. I was called 
in to identify a plant that had poisoned two young children recently -- and 
thanked my orthodox training because I had the skill to select the one 
"species" in our province from the other 6500 that also occur here in order 
to save their lives. However, the scientist in me also understands the fact 
that we cannot have a dictatorial system that selects some species 
hypotheses over others; science should not be dictatorial -- and these 
catalogues often are.

Regards
Ashley

-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu 
[mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Dave Roberts
Sent: 29 August 2013 15:21
To: taxacom taxacom
Subject: Re: [Taxacom] global species lists and taxonomy ( was Re: Draft 
Checklist ...)

Dear all,

I fear that the comparatively greater complexity of the animals will make 
such an approach a considerable amount of work, or more bluntly, will be 
significantly hard.

With the list of names, on which so many people are labouring without, as 
Rich says, sufficient coordination, we also need a classification bank, a 
simple way to find in how many arrangements a given taxon has been placed. 
That was one of the priorities identified in the Biodiversity Informatics 
Decadal Vision [1].

The EU's funding programme H2020 is an opportunity to create a large 
consortium to do exactly that level of coordination.  The problem, though, 
is to link it in some way to either job creation or policy making at an EU 
scale.  The advantage is that international collaboration (i.e. outside 
Europe) is likely to be more tractable in H2020.

Next week's meeting in Rome [2] is a starting point for that kind of 
discussion.

Cheers, Dave

[1] Hardisty, Alex, Dave Roberts, and The Biodiversity Informatics 
Community. "A Decadal View of Biodiversity Informatics: Challenges and 
Priorities." BMC Ecology 13 (2013): 16. doi:10.1186/1472-6785-13-16.
http://www.biomedcentral.com/1472-6785/13/16

[2] http://conference.lifewatch.unisalento.it/index.php/EBIC/BIH2013/

--
On 29 Aug 2013, at 13:08, nicky nicolson <nicky.nicolson at gmail.com> wrote:

> Thanks Karen, yes this is what we are working on in botany and
> mycology - we are using the nomenclators (IPNI and IF) to provide the
> fundamental units (names and the objective relationships between them)
> and then supporting multiple overlapping - even contradictory -
> classifications to be built using these same fundamental units. We are
> storing enough data on the relationships which form the taxonomic
> classifications to do the kind of assessments that Fred suggests -
> e.g. to take into account how recently the hypothesis was published,
> who published it and where (e.g. was it a regional treatment or a 
> globally-scoped monograph).
> I did quite a general talk about this at the Natural History Museum in
> London recently, video here:
> http://www.youtube.com/watch?v=ynFB6DWCBjc and slides here:
> http://www.slideshare.net/nickyn/nicolson-namesbackbonenhm
> We've a funded project to rebuild Kew's taxonomic systems in this
> environment, and we are working on incorporating the World Checklist
> system at the moment, although our communications standard is TCS so
> we should be able to import / export data from many different sources.
> cheers,
> Nicky
>
> PS: I'll be at TDWG along with a few people from the Kew team if
> anybody is interested in having a closer look.
>
>
> On 29 August 2013 12:18, Karen Cranston <karen.cranston at gmail.com> wrote:
>
>> It is not too hard to implement this type of system. Both IPNI and
>> Open Tree of Life are currently implementing a relatively new graph
>> database model (database called neo4j) to load and store multiple
>> hierarchies in the same data structure. Then, you can traverse the
>> graph (which contains all of the nodes and edges, and therefore all
>> of the conflict) in various ways in order to summarize / resolve
>> conflicts / find interesting patterns. You could use algorithmic and
>> / or human-curated approaches to annotate or resolve parts of the
>> hierarchy, while still keeping all of the information from the
>> sources. Visualization libraries like d3 make it easy to create images or 
>> interactive tools to explore the data in the graph.
>>
>>
>>
>> On Thu, Aug 29, 2013 at 7:03 AM, Erik Rijkers <er at xs4all.nl> wrote:
>>
>>> On Thu, August 29, 2013 12:31, Fred Schueler wrote:
>>>>
>>>> Maybe we want to take a lesson from the physicists' ideas of
>>>> infinite parallel universes, and program systems where all
>>>> published classifications are represented, but with some sort of
>>>> combined voting or weighting by the recency of publication, and
>>>> wiki-style comments and discussion, to show users which
>>>> classifications are more currently approved and used.
>>>>
>>>
>>> hear, hear!
>>>
>>> IMHO, this is the only possible way to get usefully stable global lists.
>>>
>>> It amounts to the realisation that the classification business is
>>> producing opinions (however obnoxious this may sound to the
>>> taxonomist).
>>>
>>> So databases should amass these opinions with plenty factual detail
>>> but without implicitly endowing any classification-opinion with the
>>> distinction of being "fact".
>>>
>>> It would seem this obvious way of doing taxonomical databases is not
>>> too hard to implement but I have never seen it done , or even
>>> acknowledged as necessary.
>>>
>>>
>>>
>>> Erikjan Rijkers

-- 
Dr D.McL. Roberts,        Tel: +44 (0)20 7942 5086
ViBRANT Project Manager,
Dept. Life Sciences,
The Natural History Museum,
Cromwell Road,
London        SW7 5BD
Great Britain             Email: dmr at nomencurator dot org
Web page:  http://vbrant.eu
Web page:  http://scratchpads.eu
Web page:  http://www.editwebrevisions.info/
--
"You can't just ask customers what they want and then try and give it to 
them.  By the time you get it built, they'll want something new." [Steve 
Jobs, quoted in The Guardian, Technology Section, 25 June 09].
--





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