[Taxacom] LSID versus names

Thu Jun 21 23:18:00 CDT 2012

That is true. Sloppiness in communication on my part. I'm a botanist -
cut me some slack...

Yes, it should have read 'everything of nomenclatural and taxonomic
significance' or similar. Unfortuately the definition of significance
is more than a little subjective.  Basically if The Code is implicated
or involved, then the publication is significant. This ropes in
floras, revisions, monographs, checklist, etc. Popular 'wildflowers of
...' works bleed into this space and we have to make a call.

But in reality the way it woks is that someone complains 'you don't
have this' and it goes on the list. 'Significance' is dealt with by
default as part of the necessary prioritization process as we work
through what are considered to be the most important works first. For
taxonomy all pigs are important - but some are more important tha
others. They will all be done, eventually.

So far we have done all (ok 99.9something%) of the really really
important stuff, the protologues accounting for all the names. We have
also done 'a whole bunch' (this is a precise technical measure of
taxonomic volume) of taxonomic treatments which accounts for 'nearly
all' (another precisely defined metric) of the taxonomic concepts we
want use. In addition we have done 'a lot' (and another) of secondary
references which account for alternative taxonomises and
classifications. You can see a system priorities emerging - there are
others involving taxa, regions and politically and socially squeaky
wheels in need of oil. They might be all important in difference
circumstances; we are just talking about the order in which they get
done. Not a big deal - just time and money.

There is also a bit of an echo chamber in the literature. Having
captured one version of a taxonomic point of view, the pressure to
capture the same view expressed by someone else is not as great as
capturing an entirely different popint of view.  But maybe it is a
extremely important bu unoriginal author. And maybe...

The satisfying thing about this approach, even though one person's
work of of critical importance is another's peripheral trivia, the
data extraction is only done once and part of an immediate prioriory
and is available for a multitude of future uses.  Yes, we will
certainly get the priorities wrong sometime, but in the end it does
not matter - we will get you favourite eventually.

There are some bottom lines here though. If we are to 'resolve' a
taxonomic controversy, or even understand and discuss it sensibly, we
need to have all sides and all aspects and components of the argument
documented. All of them. And if we miss some, and we do, the argument
gets reopened.

jim

On Fri, Jun 22, 2012 at 1:34 PM, Stephen Thorpe
<stephen_thorpe at yahoo.co.nz> wrote:
> Jim,
>
> There are several problematical issues with such an approach. For one, you
> say:
>
>>Our 'list', APNI, aims to record and document everything that was ever
>> said, by anyone, about the nomenclature and taxononomy of an Australian
>> plant<
>
> the problem here is that there is no clearly demarcated line dividing the
> relevant from the irrelevant, so you really end up having to record and
> document everything anybody has ever said about *any* plant, Australian or
> not (OK, so some things are clearly irrelevant, but it is all one big
> system)
>
> what we really want to know about taxa are the "important things", but by
> trying to account for *everything* said about them, you spend 99% of the
> time and effort on unimportant things ...
>
> Stephen
>
> From: Jim Croft <jim.croft at gmail.com>
> To: Dr.B.J.Tindall <bti at dsmz.de>
> Cc: TAXACOM <taxacom at mailman.nhm.ku.edu>
> Sent: Friday, 22 June 2012 3:07 PM
> Subject: Re: [Taxacom] LSID versus names
>
> Sorry Brian - I am having difficulty in keeping up... :)
>
> At the moment a 'list' is, in botany at least, an index, a tool to
> stop you having to scour through the literature for tke killer fact
> that will make or break a decision. Someone, bless their souls, has
> already done that work for us.
>
> With registration, the game changes. A list will or could become the
> list. What hapens to the point of truth? Is it the type? The
> publication? the list? Or a murky combination? What if the publication
> contains different information to the type (shock!)? Or the the list
> contains different information to both (horror!). Or all three are
> different (oh the humanity!). Which ones can or should get
> 'corrected'? Of course, things like this will never happen...
>
> Our 'list', APNI, aims to record and document everything that was ever
> said, by anyone, about the nomenclature and taxononomy of an
> Australian plant, even ambiguity and errors - the good the bad and the
> downright ugly (you want ugly Rich, we'll give you ugly!). Essentially
> your a) through d). But it is still, when you break it down, as
> rigourous, perfect and useful as we like to imagine it could be, just
> a list of names and list of assertions about those names, with no
> legal standing under The Code at all.
>
> Obviously this task will never be completed  in my life time, or at
> all when you think about it. But the journey of a thousand miles,
> etc...
>
> Back to the purpose of a/the list? To make our collective lives
> easier, to make taxonomy more efficient and productive, but most
> importantly, it is a shit tedious but essential job and we do not want
> to have people do it more than once and be freed up to do more
> taxonomy... which creates more names and more assertions which... you
> get the picture... :)
>
> jim
>
> On Thu, Jun 21, 2012 at 9:52 PM, Dr.B.J.Tindall <bti at dsmz.de> wrote:
>> Jim,
>> which begs the question what is the purpose of the list? As far as I am
>> concerened the list (which is not necessarily simply limited to "names")
>> does not replace the main information concerning the properties of the
>> taxon
>> in question etc. It summarises critical information, which in the case of
>> the Bacteriological Code would be:
>> a) the name and where it was published (in our case in a Code compliant
>> fashion).
>> b) where one finds the description
>> c) where the types are located
>> d) given the relevance of specialist databases for data such as
>> gene/protein
>> sequences the links to the relevant sequence accession numbers.
>> e) documenting assertions of synonym (without determining whether such
>> assertions are to be followed), or rulings affecting the use of names made
>> by appropriate authorities that deal with such matters.
>>
>> That is a good start. Both ZooBank and MycoBank look like that they would
>> like to head for being far more than being just lists of names.
>>
>> Brian
>>
>>
>> Quoting Jim Croft <jim.croft at gmail.com>:
>>
>>> Absolutely... which is why as a community we invest in things like
>>> IPNI, APNI, etc.
>>>
>>> But I think there is a risk, if not a problem, in assigning the point
>>> of authority to an abstracted list rather the publication.
>>>
>>> Having said that, the crystal ball and bat entrails are insisting that
>>> time and technology will inevitably take us to a place where 'the list
>>> is the thing'. They don't tell me when or how it is going to work, but
>>> they are pretty sure it is going to happen.
>>>
>>> jim
>>>
>>> On Wed, Jun 20, 2012 at 10:57 PM, Dr.B.J.Tindall <bti at dsmz.de> wrote:
>>>>
>>>> Jim,
>>>> Well, if anything is going to be "authoritative" it would have to be the
>>>> fact that certain nomenclatural and taxonomic events/acts have taken
>>>> place.
>>>> There is no better way of doing this than to make sure that these
>>>> acts/events are properly documented. In bacteriology and virology this
>>>> is
>>>> via a centralised system. To my knowledge the virologists maintain an
>>>> authoritative list of names on the ICTV website and there were
>>>> suggestions
>>>> that bacteriologists should do the same - the only issue being who pays
>>>> the
>>>> bills.
>>>>
>>>> The only issue that is problematic is when there is an "authoritative"
>>>> list
>>>> (which in bacteriology would document new names and new combinations)
>>>> and
>>>> other lists surface which are misleading/erroneous and undermine the
>>>> work
>>>> of
>>>> those who try to make sure that the "authoritative lists" are accurate.
>>>>
>>>> Brian
>>>>
>>>> Quoting Jim Croft <jim.croft at gmail.com>:
>>>>
>>>>> This kind of thinking is a big problem and one of the reasons we get
>>>>> into messes like this. NONE of these databases is authoritative.  They
>>>>> are not mentioned in the Code, they have not legislated priority and
>>>>> have no official standing in nomenclature or taxonomy at all. They are
>>>>> at best useful and reliable indices to the literature (with the type
>>>>> and cited specimens, the real authority), at worst, incomplete
>>>>> perpetuators of falsehoods.
>>>>>
>>>>> There is no point looking for a single point of truth when there isn't
>>>>> one. Well ok, it might be core business for religion and politics. But
>>>>> it is not going to work for nomenclature and taxonomy, unless we
>>>>> change the Code radically and create one (ducks quickly, to avoid the
>>>>> ugly reg* word).
>>>>>
>>>>> jim
>>>>>
>>>>> On Wed, Jun 20, 2012 at 5:42 PM, Roderic Page <r.page at bio.gla.ac.uk>
>>>>> wrote:
>>>>>>
>>>>>>
>>>>>> Plant people are
>>>>>> somewhat better off with IPNI, although one could argue whether we
>>>>>> should
>>>>>> regard IPNI, Tropics, or the Plant List as the definitive authority.
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>>
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>>>>>
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>>>>>
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>>>>>
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>>>>>
>>>>
>>>>
>>>>
>>>> Dr.B.J.Tindall
>>>> Leibniz-Institut DSMZ-Deutsche Sammlung von
>>>> Mikroorganismen und Zellkulturen GmbH
>>>> Inhoffenstraße 7B
>>>> 38124 Braunschweig
>>>> Germany
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>>>>
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>>>>
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>>>
>>>
>>>
>>>
>>> --
>>> _________________
>>> Jim Croft ~ jim.croft at gmail.com ~ +61-2-62509499 ~ http://about.me/jrc
>>> 'Whenever you find yourself on the side of the majority, it's time to
>>> pause and reflect.'
>>> - Mark Twain
>>> 'A civilized society is one which tolerates eccentricity to the point
>>> of doubtful sanity.'
>>>  - Robert Frost
>>>
>>> Please send URLs, not attachments:
>>> http://www.gnu.org/philosophy/no-word-attachments.html
>>>
>>
>>
>>
>> Dr.B.J.Tindall
>> Leibniz-Institut DSMZ-Deutsche Sammlung von
>> Mikroorganismen und Zellkulturen GmbH
>> Inhoffenstraße 7B
>> 38124 Braunschweig
>> Germany
>> Tel. ++49 531-2616-224
>> Fax  ++49 531-2616-418
>> http://www.dsmz.de/
>> Director: Prof. Dr. J. Overmann
>> Local court: Braunschweig HRB 2570
>> Chairman of the management board: MR Dr. Axel Kollatschny
>>
>> DSMZ - A member of the Leibniz Association (WGL)
>>
>> ----------------------------------------------------------------
>> This message was sent using IMP, the Internet Messaging Program.
>
>
>
> --
> _________________
> Jim Croft ~ jim.croft at gmail.com ~ +61-2-62509499 ~ http://about.me/jrc
> 'Without the freedom to criticize, there is no true praise.
> - Pierre Beaumarchais
> 'Whenever you find yourself on the side of the majority, it's time to
> pause and reflect.'
> - Mark Twain
> 'A civilized society is one which tolerates eccentricity to the point
> of doubtful sanity.'
>  - Robert Frost
>
> _______________________________________________
>
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> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>
> The Taxacom archive going back to 1992 may be searched with either of these
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>
> (1) by visiting http://taxacom.markmail.org/
>
> (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://about.me/jrc
'Without the freedom to criticize, there is no true praise.
- Pierre Beaumarchais
'Whenever you find yourself on the side of the majority, it's time to
pause and reflect.'
- Mark Twain
'A civilized society is one which tolerates eccentricity to the point
of doubtful sanity.'
 - Robert Frost