[Taxacom] LSID versus names

Stephen Thorpe stephen_thorpe at yahoo.co.nz
Fri Jun 22 02:18:45 CDT 2012


I doubt that (m)any botanists, nevermind bacteriologists, fully grasp the gigantic mess that is zoological nomenclature/taxonomy. LSIDs, ZooBank, etc. do little or nothing to improve that mess. There are far more important things to be done first, like just sorting out and linking together names and literature, something along these lines (http://species.wikimedia.org/wiki/Category:Publications_of_M.C._Miller), but for *all groups/authors*. This is a task so huge that it may never be completed, and yet it must take priority over LSIDs, etc....

Stephen



________________________________
 From: Dr.B.J.Tindall <bti at dsmz.de>
To: Jim Croft <jim.croft at gmail.com> 
Cc: TAXACOM <taxacom at mailman.nhm.ku.edu> 
Sent: Friday, 22 June 2012 7:03 PM
Subject: Re: [Taxacom] LSID versus names
 
Jim,
I know a lot of the background and from where I stand there is a big  
difference between the discussions I have heard and what has actually  
been implmented elsewhere. You summarised the benefits nicely:

"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 is why ZooBank and MycoBank are following the lead made under  
the Bacteriological Code. No its not perfect, but it is a start and it  
can be improved upon.

LSIDs - an interesting statement. I haven't heard anyone questioning  
who issues IP addresses or DOIs for publications.

Brian

Quoting Jim Croft <jim.croft at gmail.com>:

> The last time a centralized system was seriously proposed for plants,
> the botanical community freaked and started torching the code and
> burning effigies in the streets. The suggestion is still there, but I
> am not sure we are ready for it yet. A lot will depend on the
> implementation mechanisms.
>
> As with LSIDS, the idea is one thing, but who gets to implement it and
> call the shots is another thing entirely.
>
> jim
>
> On Fri, Jun 22, 2012 at 4:35 PM, Dr.B.J.Tindall <bti at dsmz.de> wrote:
>> Jim,
>> Actually you seem to have covered a lot of the relevant points in your
>> reply. Perhaps the only major difference is the fact that since I work with
>> prokaryotes I have become used to dealing with a centralised system, which
>> is anchored in the Bacteriological Code. The system operates with all the
>> potential problems you list, but this is not the fault of the system, rather
>> whether the correct information is supplied in the first place. It depends
>> on the rigour of those who maintain the system along with the willingness of
>> those who should comply to do so.
>>
>> Brian
>>
>> Quoting Jim Croft <jim.croft at gmail.com>:
>>
>>> 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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>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> 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)
>>>>>>
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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
>>>
>>
>>
>>
>> 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
>



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)

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