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

Sun Sep 1 06:18:45 CDT 2013

Dan, may I state that the ideal world you seek actually already exists - provided people stick the rules of Zoological nomenclature.  These are the rules of homonymity, priority and stability and limit the number of correct names available for a taxon.  When the taxonomy is stable, so too is the nomenclature.
Problems arise when people create unnecessary synonyms - see me next post here that follows this one ....

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> Date: Sun, 1 Sep 2013 11:58:55 +0200
> From: dlahr at ib.usp.br
> To: pierre.deleporte at univ-rennes1.fr
> CC: taxacom at mailman.nhm.ku.edu
> Subject: [Taxacom] Binomial Nomenclature - was: "cataloguing hypotheses &	not real things"
> 
> 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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> > Celebrating 26 years of Taxacom in 2013.
> >
> 
> 
> 
> -- 
> ___________________
> Daniel J. G. Lahr, PhD
> Assist. Prof., Dept of Zoology,
> Univ. of Sao Paulo, Brazil
> + 55 (11) 3091 0948
> _______________________________________________
> Taxacom Mailing List
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> The Taxacom Archive back to 1992 may be searched with either of these methods:
> 
> (1) by visiting http://taxacom.markmail.org
> 
> (2) a Google search specified as:  site:mailman.nhm.ku.edu/pipermail/taxacom  your search terms here
> 
> Celebrating 26 years of Taxacom in 2013.