[Taxacom] Binomial Nomenclature - was: "cataloguing hypotheses & not real things"

Dan Lahr dlahr at ib.usp.br
Sun Sep 1 04:58:55 CDT 2013


Hi Pierre, all,

I think you raise quite an interesting point here:

"- A logical tension comes
from the dual meaning of the modern binominal nomenclature:
the species name is fixed, like a barcode linked to a type specimen;
while the genus name has a hierarchical meaning,
not just a diagnostic or referential one;
but the species is necessarily named by the couple Gus-sus
hence no caution is taken for avoiding synomymy in the species name "sus"

changing "Gus" makes it difficult or impossible
to "track" the species based on "sus" name only"

Not to mention how arbitrary it is. "Let's use two names. Not three, not
four, two. Just because." In my short experience I have never come across a
justification, if someone knows of it, I would love to hear it.

One of the things that I often wonder is why nobody ever suggested a more
logical, parsimonious and I suspect bioinformatics friendlier (not my area,
can someone confirm?) transition to uninomial nomenclature.  There are many
ways in which this can be implemented.  A beautiful world were type
specimens are forever tied to a single non-changing nomen no matter how it
is classified...

cheers,

dan

On Sun, Sep 1, 2013 at 11:44 AM, Pierre Deleporte <
pierre.deleporte at univ-rennes1.fr> wrote:

>
> Dear all,
>
> With all respect due to code-specialists (what I am not),
> and from my limited culture and experience:
>
> - I clearly remember that some scientist colleagues (ecologists and
> ethologists),
> in the seventies, were very crossed against taxonomists
> because "They always change the names of the species"
>
> - If I am well informed, the early nomenclature by Linnaeus
> was plurinominal, not just binominal;
> a series of words could serve as a sketchy description
> of some elementary entity
>
> - A logical tension comes
> from the dual meaning of the modern binominal nomenclature:
> the species name is fixed, like a barcode linked to a type specimen;
> while the genus name has a hierarchical meaning,
> not just a diagnostic or referential one;
> but the species is necessarily named by the couple Gus-sus
> hence no caution is taken for avoiding synomymy in the species name "sus"
>
> changing "Gus" makes it difficult or impossible
> to "track" the species based on "sus" name only
>
> - My colleagues of the time superbly ignored taxonomy (that old stuff),
> they had strictly no interest in systematics/phylogeny
> (I once was named a "guy from planet Mars" in the lab,
> it was in 1988)
> and they had the illusion of their near-completeness
> (...the job must certainly be completed by now),
> they viewed nomenclatural variants as nonsensical arbitrary disputes,
> they just wanted to use "the right species name" fixed once and forever
> (like a "user-friendly barcode" in words?...)
>
> they were professional scientists,
> but regarding nomenclature they were just part of the lay people
>
> best,
> Pierre
> (another old stuff... :-) )
>
>
>
> Le 01/09/2013 09:48, Wulf Schleip a écrit :
> > Dear Michael, dear list,
> >
> > yes, nomenclature and taxonomy are two different things. While
> nomenclature
> > is simply a tool for taxonomy, both canot exist without each other. What
> use
> > would nomenclature do without anything to name? And what chaos would we
> have
> > if we differntiate or classify things without making them clearly
> > identifiable (e.g., by names or numbers)?
> >
> > So, in nomenclature we have names, but these names are usually
> represented
> > by a typ species (generic) or specimen (specific and subspecific). There
> is
> > a concept (maybe a hypothesis) behind each scientific name. Therefore, we
> > use the name as an alias for 1) a label for the type specimen itself, 2)
> for
> > the type specimen as an objective reference with characters on which the
> > concept/hypothesis usually is based on, and 3) for the taxon
> differentiated
> > from others by the concept/hypothesis.
> >
> > A name, therefore, is more than just a name and a catalogue is more than
> a
> > list of names.
> >
> > Cheers,
> > Wulf
> >
> > -----Ursprüngliche Nachricht-----
> > Von: taxacom-bounces at mailman.nhm.ku.edu
> > [mailto:taxacom-bounces at mailman.nhm.ku.edu] Im Auftrag von Ohl, Michael
> > Gesendet: Freitag, 30. August 2013 13:26
> > An: 'Ashley Nicholas'; 'taxacom taxacom'
> > Betreff: Re: [Taxacom] We are cataloguing hypotheses & not real things
> -- I
> > hope everyone appreciates the implications of this. Was Global species
> lists
> > ....
> >
> > I disagree. We are cataloging neither hypotheses nor real things, but
> > linguistic items that may or may not be proper names in a linguistic
> sense
> > and that may or may not label hypotheses on the existence of natural
> things
> > beyond the human mind. Opinions differ on both. This is an important
> > difference, which has been repeatedly been discussed as the difference
> > between nomenclature and taxonomy. Names have no other function than to
> > label information, and cataloging these linguistic labels is important in
> > order to optimize access to the underlying information. The questions of
> the
> > reality and nature of species, whether they are biological species,
> > individuals, relations, or even non-existent, are important, but are not
> a
> > matter of names as linguistic elements, which denote concepts. So
> catalogues
> > are not catalogues of species hypotheses but of names.
> >
> > Cheers, Michael
> >
> >
> >
> > PD Dr. Michael Ohl
> > Curator // Head of Entomological Collections Museum fuer Naturkunde
> > Leibniz-Institut fuer Evolutions- und Biodiversitaetsforschung
> Invalidenstr.
> > 43
> > D-10115 Berlin, Germany
> > Tel: ++49-30-2093-8507
> > Fax: ++49-30-2093-8868
> >
> > E-Mail: michael.ohl(at)mfn-berlin.de
> > URL:
> http://www.naturkundemuseum-berlin.de/institution/mitarbeiter/ohl-micha
> > el/
> >
> > Geschäftsführer der Gesellschaft für Biologische Systematik (GfBS)
> Managing
> > Editor Arthropoda von Zoosystematics and Evolution
> >
> >
> >
> >
> > -----Ursprüngliche Nachricht-----
> > Von: taxacom-bounces at mailman.nhm.ku.edu
> > [mailto:taxacom-bounces at mailman.nhm.ku.edu] Im Auftrag von Ashley
> Nicholas
> > Gesendet: Freitag, 30. August 2013 12:32
> > An: taxacom taxacom
> > Betreff: [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
>
>
> --
> Pierre DELEPORTE
> UMR6552 EthoS
> Université Rennes 1
> CNRS
> Station Biologique
> 35380 PAIMPONT
> tél (+33) 02 99 61 81 63
> fax (+33) 02 99 61 81 88
>
>
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-- 
___________________
Daniel J. G. Lahr, PhD
Assist. Prof., Dept of Zoology,
Univ. of Sao Paulo, Brazil
+ 55 (11) 3091 0948



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