[Taxacom] FW: formation of zoological names with Mc, Mac, et

Wed Sep 2 16:53:51 CDT 2009

I have certainly learned a lot from this thread - I always thought
that authority and year were required by the ICZN!

Just looping back into my original question on how Bioinformatics can
contribute to nomenclature. It seems clear that most agree that:

1 - names are not unique identifiers, whether they include
authority+year, initial+authority+year, or even in the extreme case
mentioned about using ten or more fields as identifiers. I do
appreciate the caveat raised that names are not unique identifiers
only for a minority of cases.

2 - bioinformaticians and taxonomists are using names for completely
different reasons, but both profit from standardized databases.

I know that as a taxonomist, I like to see the authority and year and
that is an indication of possible homonymy, where it was possibly
published etc, as Jim Croft points out. But most importantly it tells
me about the context of the organism's description - assuming I have a
good grasp of the relevant literature - and helps me assess biological
questions. So I do like to know exactly who was the person describing
an organism, but this might be just personal as Francisco pointed out,
I can see how it can be irrelevant for many taxonomists. However, when
you get to the historical use of names (which I think is a pivotal
part of taxonomy), things get really complicate, because there are two
types of mistakes: spelling and misidentification.

I have to conclude tentatively, that a currently a name means
different things, when it shouldn't. For nomenclature, name is the
binomial (authority optional), and we have lived happily because
practical taxonomy is made in a small scale, that is, someone
describing a Tandonia would have a good grasp of the literature on
those snails and wouldn't get as confused as we did. For
bioinformaticians, the name needs to be unique given that they are
unifying the names accross the board, and will eventually be as many
fields we agree upon.

I can't conceive that people will follow a standardized amount of
fields for every database that is put together. So is the take home
message that taxonomists should probably start thinking about
modifying current rules to accommodate the problems coming from the
unification of all taxonomies?

Kind regards,

DAn

On Wed, Sep 2, 2009 at 6:49 AM, Jim Croft<jim.croft at gmail.com> wrote:
> Nor, as far as I can tell, does either code dictate how yous should
> cite an author, or a date...
>
> It is just good practice  to do it according to some mutually agreed
> standard if you want to be able to do anything useful with it.
>
> jim
>
> On Wed, Sep 2, 2009 at 9:40 AM, Stephen Thorpe<s.thorpe at auckland.ac.nz> wrote:
>> I was speaking loosely when I said that the authority/date should be thought of as part of the name. My main point was that the original publication is "metadata" over and above the authority/date, the latter of which is not intended to point to a publication, contra AFD style citations of names! Whether you think of authority/date as part of name or not, it is still governed by the Code, whereas "metadata" isn't (the Code can't dictate, for example, how you cite a publication ...)
>>
>> Stephen
>>
>> ________________________________________
>> From: Jim Croft [jim.croft at gmail.com]
>> Sent: Wednesday, 2 September 2009 7:29 p.m.
>> To: Tony.Rees at csiro.au
>> Cc: Stephen Thorpe; fwelter at gwdg.de; taxacom at mailman.nhm.ku.edu
>> Subject: Re: [Taxacom] FW: formation of zoological names with Mc, Mac, et
>>
>> Yes we can agree on the principle and process a far as homonymy resolution goes.
>>
>> In practice I would model all the ancillary stuff you would use to
>> clarify as metadata and not part of the name (as I think both codes
>> describe)
>>
>> On a wry note, if they author/date were part of the name, whtne they
>> would not be homonyms...  ;)
>>
>> On Wed, Sep 2, 2009 at 5:14 PM, <Tony.Rees at csiro.au> wrote:
>>> Hi Jim,
>>>
>>> You have chosen a non-homonym name (so far as we are aware, maybe a cryptic one nevertheless) but what if there were/are multiple taxa called Eucalyptus deglupta? This is where the authority portions come into play, at least for information retrieval/name reconciliation purposes...
>>>
>>> Surely we can agree at least on this much?
>>>
>>> What about (e.g.) Ficus variegatus Blume (our friend once more!), a fig tree, vs. Ficus variegatus Röding, 1798, not a fig tree at all? (Hint: google images will give a clue...)
>>>
>>> You cannot say that the name alone is sufficient without the authority portion, to differentiate these two taxa.
>>>
>>> And in genera, approx. 15% of all names are homonyms, a much bigger problem :(
>>>
>>> - Tony
>>>
>>>
>>> -----Original Message-----
>>> From: Jim Croft [mailto:jim.croft at gmail.com]
>>> Sent: Wednesday, 2 September 2009 5:09 PM
>>> To: Stephen Thorpe
>>> Cc: Rees, Tony (CMAR, Hobart); fwelter at gwdg.de; taxacom at mailman.nhm.ku.edu
>>> Subject: Re: [Taxacom] FW: formation of zoological names with Mc, Mac, et
>>>
>>> We are going to have to differ on this and I guess it is an artefact
>>> of how we each model (or not) our information.
>>>
>>> The only non-Australian eucalypt grows in Indonesia.  It was named as
>>> 'Eucalyptus deglupta' but a Carl Ludwig Blume, aka C.L. Blume, aka
>>> Blume, aka Bl.  He did this in (1849) in a publication commonly, but
>>> not ubiquitously abbreviated to Mus. Bot. Lugd.-Bot. on a page number
>>> I can not find because IPNI is not talking today and nobody else
>>> bother to record this vital piece of information.  Presumably it has a
>>> type which would anchor the name.
>>>
>>> The species does not have any or nomenclatural or taxonomic synonyms,
>>> but is also referred to as Kamarere, Indonesian Gum and Rainbow Gum
>>> and even 'deglupta'.  The names science has chosen to give this
>>> species is Eucalyptus deglupta from which you can deduce it is likely
>>> to be related to other species our Eucalyptus and very little else.
>>>
>>> All else is (pretty vital) metadata of the name taxon name that helps
>>> you clarify what it the name 'most likely' to applies to.  It sum is
>>> not the name.
>>>
>>> We could chose a taxon with ambiguous concepts for the same name, and
>>> then it gets *really* interesting...
>>>
>>> jim
>>>
>>> On Wed, Sep 2, 2009 at 4:23 PM, Stephen Thorpe<s.thorpe at auckland.ac.nz> wrote:
>>>> No way! The authority/date should be thought of as part of the name! The authority is only indirectly about a person. The authority for a taxon is however the surname of the author of that taxon is spelled in the original publication, i.e., it is a "nominal person". If it is Smith, then the authority is just Smith. The name needs to be linked to the original publication is some other (external) way. The only reason for having dates as part of names is because of PRIORITY, NOT to point to a publication. Ideally, in a database, a name needs to be followed by a field pointing to the original publication, maybe like this:
>>>>
>>>> Examplus primus Smith, 1970
>>>> Original publication: J. Smith, 1970a
>>>>
>>>> ________________________________________
>>>> 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: Wednesday, 2 September 2009 6:02 p.m.
>>>> To: jim.croft at gmail.com; fwelter at gwdg.de
>>>> Cc: taxacom at mailman.nhm.ku.edu
>>>> Subject: Re: [Taxacom] FW: formation of zoological names with Mc, Mac, et
>>>>
>>>> Jim Croft wrote:
>>>>
>>>> <snip>
>>>> I am getting quite worried about all this 'sanitization' of authorish
>>>> strings as though it has some sort of nomenclatural, taxonomic or
>>>> operational validity.  The author and date are not part of the name -
>>>> they are attributes of a particular use of the name.
>>>> </snip>
>>>>
>>>> Sounds a lot like operational and taxonomic validity to me. In the cases of homonyms at least, we need to distinguish between usages of a name - different authors/years/publications/pages, different usages, often different taxonomic status (nomen nudum or whatever). If we can't link together authority citations that are not identical but which are variant references to the same published name instance, then they all look like different name usages, which is incorrect.
>>>>
>>>> - Tony
>>>>
>>>> _______________________________________________
>>>>
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>>>>
>>>> The Taxacom archive going back to 1992 may be searched with either of these methods:
>>>>
>>>> (1) http://taxacom.markmail.org
>>>>
>>>> Or (2) a Google search specified as:  site:mailman.nhm.ku.edu/pipermail/taxacom  your search terms here
>>>
>>>
>>>
>>> --
>>> _________________
>>> Jim Croft ~ jim.croft at gmail.com ~ +61-2-62509499 ~
>>> http://www.google.com/profiles/jim.croft
>>> ... in pursuit of the meaning of leaf ...
>>> ... 'All is leaf' ('Alles ist Blatt') - Goethe
>>>
>>
>>
>>
>> --
>> _________________
>> Jim Croft ~ jim.croft at gmail.com ~ +61-2-62509499 ~
>> http://www.google.com/profiles/jim.croft
>> ... in pursuit of the meaning of leaf ...
>> ... 'All is leaf' ('Alles ist Blatt') - Goethe
>
>
>
> --
> _________________
> Jim Croft ~ jim.croft at gmail.com ~ +61-2-62509499 ~
> http://www.google.com/profiles/jim.croft
> ... in pursuit of the meaning of leaf ...
> ... 'All is leaf' ('Alles ist Blatt') - Goethe
>
> _______________________________________________
>
> Taxacom Mailing List
> Taxacom at mailman.nhm.ku.edu
> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>
> The Taxacom archive going back to 1992 may be searched with either of these methods:
>
> (1) http://taxacom.markmail.org
>
> Or (2) a Google search specified as:  site:mailman.nhm.ku.edu/pipermail/taxacom  your search terms here
>

-- 
Daniel Lahr
-------------------------------------------------
PhD candidate
Organismic and Evolutionary Biology
U Massachusetts- Amherst
319 Morrill Science Center, Amherst
Amherst, MA 01003