atom feed130 messages in edu.ku.nhm.mailman.taxacomRe: [Taxacom] validation of taxon names
FromSent OnAttachments
Armand TurpelFeb 14, 2012 12:41 am 
Stephen ThorpeFeb 14, 2012 1:01 pm 
Armand TurpelFeb 15, 2012 12:59 am 
Roderic PageFeb 15, 2012 1:50 am 
Paul KirkFeb 15, 2012 1:55 am 
greg whitbreadFeb 15, 2012 5:05 am 
Chris ThompsonFeb 15, 2012 8:03 am 
David PattersonFeb 15, 2012 8:07 am 
Roderic PageFeb 15, 2012 9:12 am 
Doug YanegaFeb 15, 2012 10:40 am 
Paul KirkFeb 15, 2012 10:51 am 
Roderic PageFeb 15, 2012 11:23 am 
Armand TurpelFeb 15, 2012 11:39 am 
Stephen ThorpeFeb 15, 2012 12:47 pm 
Jim CroftFeb 15, 2012 1:06 pm 
Curtis ClarkFeb 15, 2012 5:49 pm 
Tony...@csiro.auFeb 15, 2012 7:19 pm 
Roderic PageFeb 15, 2012 10:18 pm 
Jim CroftFeb 15, 2012 10:29 pm 
Armand TurpelFeb 16, 2012 5:12 am 
Roderic PageFeb 16, 2012 8:24 am 
Doug YanegaFeb 16, 2012 9:45 am 
Chuck MillerFeb 16, 2012 11:57 am 
Bradley BoyleFeb 16, 2012 2:45 pm 
Richard ZanderFeb 16, 2012 3:10 pm 
Stephen ThorpeFeb 16, 2012 3:24 pm 
Frederick W. SchuelerFeb 16, 2012 3:31 pm 
Chuck MillerFeb 16, 2012 4:14 pm 
Stephen ThorpeFeb 16, 2012 4:28 pm 
Chris ThompsonFeb 16, 2012 7:05 pm 
Kim van der LindeFeb 16, 2012 7:13 pm 
Neal EvenhuisFeb 16, 2012 7:27 pm 
Kim van der LindeFeb 16, 2012 7:38 pm 
Stephen ThorpeFeb 16, 2012 7:40 pm 
muscapaulFeb 17, 2012 12:16 am 
Dr Brian TaylorFeb 17, 2012 12:23 am 
Armand TurpelFeb 17, 2012 1:25 am 
Chris ThompsonFeb 17, 2012 7:03 am 
Chris ThompsonFeb 17, 2012 11:23 am 
Stephen ThorpeFeb 17, 2012 1:09 pm 
Chris ThompsonFeb 17, 2012 2:04 pm 
Tony...@csiro.auFeb 17, 2012 2:32 pm 
Richard PyleFeb 17, 2012 2:51 pm 
Stephen ThorpeFeb 17, 2012 3:16 pm 
Stephen ThorpeFeb 17, 2012 3:18 pm 
Richard PyleFeb 17, 2012 3:22 pm 
Stephen ThorpeFeb 17, 2012 3:37 pm 
Richard PyleFeb 17, 2012 5:06 pm 
Tony...@csiro.auFeb 17, 2012 5:18 pm 
Stephen ThorpeFeb 17, 2012 5:27 pm 
Curtis ClarkFeb 17, 2012 7:39 pm 
Stephen ThorpeFeb 17, 2012 8:04 pm 
Richard ZanderFeb 18, 2012 9:26 am 
Richard ZanderFeb 18, 2012 9:59 am 
Richard PyleFeb 18, 2012 11:33 am 
Curtis ClarkFeb 18, 2012 6:45 pm 
Richard PyleFeb 18, 2012 8:59 pm 
Paul van RijckevorselFeb 19, 2012 12:36 am 
Roderic PageFeb 19, 2012 5:48 am 
Paul van RijckevorselFeb 19, 2012 7:36 am 
Roderic PageFeb 19, 2012 8:09 am 
Paul van RijckevorselFeb 19, 2012 8:58 am 
Curtis ClarkFeb 19, 2012 8:59 am 
Curtis ClarkFeb 19, 2012 9:49 am 
Frederick W. SchuelerFeb 19, 2012 10:29 am 
Richard PyleFeb 19, 2012 12:14 pm 
Stephen ThorpeFeb 19, 2012 12:45 pm 
Bob MesibovFeb 19, 2012 2:23 pm 
Walker, KenFeb 19, 2012 2:36 pm 
Stephen ThorpeFeb 19, 2012 2:38 pm 
Bob MesibovFeb 19, 2012 2:54 pm 
Stephen ThorpeFeb 19, 2012 2:56 pm 
Walker, KenFeb 19, 2012 3:08 pm 
Stephen ThorpeFeb 19, 2012 4:05 pm 
Bob MesibovFeb 19, 2012 4:07 pm 
Stephen ThorpeFeb 19, 2012 4:38 pm 
Stephen ThorpeFeb 19, 2012 5:09 pm 
Curtis ClarkFeb 19, 2012 5:18 pm 
Bob MesibovFeb 19, 2012 5:33 pm 
Stephen ThorpeFeb 19, 2012 5:50 pm 
Kenneth KinmanFeb 19, 2012 7:27 pm 
Weakley, AlanFeb 19, 2012 7:47 pm 
Stephen ThorpeFeb 19, 2012 7:50 pm 
Stephen ThorpeFeb 19, 2012 7:52 pm 
Curtis ClarkFeb 19, 2012 8:13 pm 
Stephen ThorpeFeb 19, 2012 8:22 pm 
Dr.B.J.TindallFeb 19, 2012 11:08 pm 
Paul van RijckevorselFeb 19, 2012 11:52 pm 
Paul van RijckevorselFeb 19, 2012 11:56 pm 
Richard PyleFeb 20, 2012 1:02 am 
Richard PyleFeb 20, 2012 1:24 am 
Richard PyleFeb 20, 2012 1:27 am 
Richard PyleFeb 20, 2012 1:32 am 
Paul van RijckevorselFeb 20, 2012 3:07 am 
Curtis ClarkFeb 20, 2012 7:28 am 
Paul van RijckevorselFeb 20, 2012 8:55 am 
Richard PyleFeb 20, 2012 9:07 am 
Paul van RijckevorselFeb 20, 2012 9:40 am 
Richard ZanderFeb 20, 2012 10:35 am 
31 later messages
Subject:Re: [Taxacom] validation of taxon names
From:Tony...@csiro.au (Tony@csiro.au)
Date:Feb 17, 2012 5:18:48 pm
List:edu.ku.nhm.mailman.taxacom

Further to my message below, and at the risk of minor self promotion, he/one
could also use my global genera compilation (not 100% complete but not too bad)
to discover that Stilbospora is a fungus in the first place...

http://www.marine.csiro.au/mirrorsearch/ir_search.go?searchtxt=Stilbospora&hlevel=genus

Or for example if it is misspelled (e.g. Stibospora for Stilbospora):

http://www.marine.csiro.au/mirrorsearch/ir_search.go?searchtxt=Stibospora&hlevel=genus

Hopefully this is a useful product as a first step towards, or a component of, a
global TNRS (taxonomic name resolution service) as previously mentioned.

Regards - Tony

________________________________________ From: taxa@mailman.nhm.ku.edu [taxa@mailman.nhm.ku.edu] On
Behalf Of Tony@csiro.au [Tony@csiro.au] Sent: Saturday, 18 February 2012 9:32 AM To: step@yahoo.co.nz; arma@gmail.com;
taxa@mailman.nhm.ku.edu Subject: [ExternalEmail] Re: [Taxacom] validation of taxon names

Dear all,

Of course I agree with Stephen and Chris that the work needs to be done, funded,
and by relevant specialists. However where that work has been done, the issue is
then how to access it. For example Armand asked:

Stilbospora angustata Pers. 1801 > Is it a synonym and if yes of what?

The answer is here (providing you accept MycoBank's opinion):

http://www.mycobank.org/MycoTaxo.aspx?Link=T&Rec=194690

Species: Stilbospora angustata Pers. 1801

MycoBank's opinion: this name is a synonym of Truncatella angustata (Pers.) S. Hughes 1958
(MB307155) ... Obligate synonym(s): Truncatella angustata (Pers.) S. Hughes 1958 [LEG; MB307155] Pestalotia angustata (Pers.) Arx 1981 [LEG; MB115996] Sporidesmium angustatum (Pers.) Corda 1829 [LEG; MB229553] ... Taxonomic synonym(s): Pestalotia affinis Sacc. & Voglino 1885 [LEG; MB201735] Phragmotrichum lignicola Corda 1838 [LEG; MB178084] Alternaria lignicola (Corda) Fr. 1849 [LEG; MB507274] Pestalotia lignicola Cooke 1871 [LEG; MB208762] Seiridium lignicola (Corda) Sacc. 1884 [LEG; MB182142] Pestalotia truncata var. lignicola (Cooke) Grove 1937 [LEG; MB255200] Pestalotia truncata Lév. 1846 [LEG; MB357321] Truncatella truncata (Lév.) Steyaert 1949 [LEG; MB291629]

So the question is really, has someone you can trust placed such opinions
online, and if so where, and how can these be addressed in any integrated
manner.

Of course there are associated questions - which sources do you trust the most,
which have been updated most recently and on what evidence, what do do when
equally trusted sources give diverging opinions, and so on, but where the "work"
has been done it hopefully does not have to be repeated from scratch for every
enquiry. In essence we are using the nomenclators and taxonomic specialists as
our proxy to the original literature, and for their expertise in wighing and
assessing the available evidence and coming to appropriate conclusions (at least
for today).

If Armand would care to give a few more cases one could presumably look for
patterns and see which resources are the most appropriate to answer his
questions. He could even then construct an automated distributed search (similar
to the ING portal described earlier) which would query a chosen set of resources
and see what they hold. For example if I know something is an extant fish I
would try Eschmeyer's Catalog, for an alga AlgaeBase, for a fly Systema
Dipterororum (except that just now you can't), and so on...

Cheers - Tony

________________________________________ From: taxa@mailman.nhm.ku.edu [taxa@mailman.nhm.ku.edu] On
Behalf Of Stephen Thorpe [step@yahoo.co.nz] Sent: Saturday, 18 February 2012 8:10 AM To: Armand Turpel; taxa@mailman.nhm.ku.edu Subject: Re: [Taxacom] validation of taxon names

to answer these sorts of questions requires a *vast* amount of work, checking
names against the original primary literature, work that is increasingly
difficult to get funded ...

________________________________ From: Armand Turpel <arma@gmail.com> To: taxa@mailman.nhm.ku.edu Sent: Friday, 17 February 2012 10:25 PM Subject: Re: [Taxacom] validation of taxon names

I'm not a taxonomist or a biologist but a simple computer scientist who have to fight nightmares when taxonomy hits his door.

There are different levels of validation of taxons in our database or species observation files we receive. Here a few examples:

Crouan{?} ex Nyl. > ????

SULZER > Sulzer

Schmitt > Schmit, Schmith, Schmidt, Schmitd, Schmid : we need the right Schmi*

Muller > Müller, Mueller: Some one couldn't find ü on his keyboard

1903 > 1907, 1902 or no year

(Schrank, 1789) > Schrank, 1789

Bombasta testosterosa (Schwarzeneggerii, 1971) > Family of Bodyaceae or Brainaceae or, hey, what's this?

Stilbospora angustata Pers. 1801 > Is it a synonym and if yes of what?

Onthophagus somalicus > Is it a homonym?

Then there are lsids, genetics and quantic effects ...., next week as promised!

Nevertheless I enjoy this discussion which, in my opinion, is really necessary.

a+ arm

On 17/02/2012 00:10, Richard Zander wrote:

It seems to be best that informatics deals best with as objective, factual information, minimizing the gray area.

Regarding "subjective," however, taxonomists wrestle mightily with decisions every day, trying to make reasonable and fact-based name changes of benefit to all users of taxonomy. They use discursive logic based on examination of dozens or hundreds of specimens in the context of evolutionary theory, and this is not particularly subjective to me.

Yes, deciding which name is "correct" ("valid" for botanists) is a problem for those not familiar with the subject matter. Using the latest name is a good rule of thumb, although I've argued against the newest molecular phylogenetic names interminably in the past.

One might make an analogy with scientific theorization in other fields. Which theory is right, photon or wave? Is the world round or flat? Is the red shift a property of an expanding universe or a function of decreasing energy associated with intervening gravity wells? Is the value of pi different if you have a large enough circle, like one around the whole universe? Is the black maple a species or only a variety of the sugar maple?

Note that the above are, however some are strange, scientific questions. Scientific intuition helps solve them. Each question in valid/correct names needs a FermiLab of scientists to do the molecular, growth, ethology, allozyme, biogeography, cytology, population, and etc. studies needed to get a definitive answer.

This is why it is easy to say decisions are subjective when they are merely poorly funded. If every informatics person spent half his/her time in biosystematics work, these problems would be less "subjective."

* * * * * * * * * * * * Richard H. Zander Missouri Botanical Garden, PO Box 299, St. Louis, MO 63166-0299 USA Web sites: http://www.mobot.org/plantscience/resbot/ and http://www.mobot.org/plantscience/bfna/bfnamenu.htm Modern Evolutionary Systematics Web site: http://www.mobot.org/plantscience/resbot/21EvSy.htm

-----Original Message----- From: taxa@mailman.nhm.ku.edu [mailto:taxa@mailman.nhm.ku.edu] On Behalf Of Chuck Miller Sent: Thursday, February 16, 2012 1:58 PM To: Roderic Page; taxacom Subject: Re: [Taxacom] validation of taxon names

Dear Rod,

I would propose to extend your phrase to "person(s) x in publication y asserted that two names are synonyms or lexical variants of each other" The assertion of related names occurs in a publication by that/those person(s). Publication y's assertion should just be an objective fact and immutable.

But, the sticky wicket comes when point 6 is posed: "Which of all the related names is the best one to use to refer to the organism right now"? The issue of best is invariably subjective.

Chuck

here

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