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

Sun Sep 1 08:01:30 CDT 2013

> When the taxonomy is stable, so too is the nomenclature.

As our understanding of organisms increases and new methods and data become
available, existing taxa will be revised and new ones will be described.
This is the work of taxonomists. Or as Padial and de la Riva (2006) put it,
If the inventory of living species is far from finished then arresting any
change in lists composition could only come from a similar arrest of
taxonomic work. There is no stable taxonomy per se, as long as we have not
found the one and only real and final "tree-of-life"!

-----Ursprüngliche Nachricht-----
Von: taxacom-bounces at mailman.nhm.ku.edu
[mailto:taxacom-bounces at mailman.nhm.ku.edu] Im Auftrag von Raymond Hoser -
The Snakeman
Gesendet: Sonntag, 1. September 2013 13:19
An: Dan Lahr; Pierre Deleporte
Cc: taxacom at mailman.nhm.ku.edu
Betreff: Re: [Taxacom] Binomial Nomenclature - was: "cataloguing hypotheses
& not real things"

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-mi
> > cha
> > > 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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> >
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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
> _______________________________________________
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(2) a Google search specified as:  site:mailman.nhm.ku.edu/pipermail/taxacom
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Celebrating 26 years of Taxacom in 2013.