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 
37 later messages
Subject:Re: [Taxacom] validation of taxon names
From:Richard Pyle (deep@bishopmuseum.org)
Date:Feb 17, 2012 2:51:20 pm
List:edu.ku.nhm.mailman.taxacom

I SO don't have time to engage on this (apologies to all who have sent me emails to which I have not yet responded), but as this is a topic that is near & dear to me, I can no longer resist. A few random comments:

Doug wrote:

Second, if one has a master list of all published names, simply annotating that name X was, in year N, synonymized with name Y by author Z does NOT tell you whether name X is *presently* treated as valid.

Absolutely! But I'll take it a step further: the question: "Is name X presently treated as valid?" has no answer, as such. Without qualification of what is meant by "presently", and without some indication of by whom a name is treated as valid or not, this is a question that can only be answered in shades of gray (or spectra of RGB, if you prefer).

This relates to Chuck's comment:

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.

I think the only realistic path forward for taxonomic professionals is a graphic representation of the history of how names are treated, along the lines of what Ryan Schenk has put together (http://synynyms.no.de/). For the non-taxonomist who wants a single answer, I think there are only two options:

1) select a specific "meta-authority" (e.g., Catalogue of Life) to represent the "whom".; or

2) Develop an "I'm Feeling Lucky" algorithm (analogous to Google's feature of the same name) that can essentially review a broad spectrum of criteria (how the name has been treated over time, influenced by various objective "quality" metrics related to the published works and authors of such, etc.) that effectively produces two results: a) The name that rises to the top of the "I'm Feeling Lucky" algorithm; and b) Some sort of confidence value that indicates whether the name is essentially stable and universal (e.g., Homo sapiens), or is the subject of recent and un-settled debate (many examples)

Richard Zander wrote:

Yes, deciding which name is "correct" ("valid" for botanists) is a problem for those not familiar with the subject matter.

I think the parenthetical should have been '("valid" for zoologists)' ... "valid" in botany is more akin to "available" in zoology (i.e., "validly published").

And further:

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?

But only one of these questions has scope only in the context of human brains....the others are questions that exist outside the existence of humans. But maybe we'd best not go there....again....

Stephen wrote:

bioinformaticians like Jim Croft are somewhat stuck between a rock and a hard place, for they just want to list all taxonomic opinions on a taxon objectively, but what are they going to call the taxon??

I don't think that Jim "just" wants this (index of existing taxonomic opinions). Rather, he (correctly!) recognizes that this is a critical component in the right direction, and one that is far more tractable informatically than most of the passionate debates that pass through this email forum.

Note that I agree that the publications of Hoser or whoever should be noted in relation to the taxon, but I am denying that there is any compulsion to accept as the "currently valid name" one of Hoser's opinions just because it was published 5 minutes *after* some reputable scientist made a different call ...

This sounds a bit like a straw man. I've not yet met anyone who actually thinks that the most recent assertion about a taxon is, by default, the "correct" one.

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 ...

YES!! This is the KEY point, I think, for this entire discussion. The trick is: how do we make the outside world understand (first) the importance of biodiversity, and (second) the importance good taxonomy within that realm?

And, saving the best for last....

Rod wrote:

But if you have LOTS of names then having a local of the data copy is great. CouchDB is a wonderful tool, especially for semi-structured data. It excels at some things, but bulk checking of names probably isn't one of them (you'd probably get more joy doing an SQL join in a relational database then handing the names that don't match).

YES! THANK YOU! This is *exactly* the point I have believed and (to a lesser extent) have been preaching for years now. My vision for the architecture of data components of GNA is, and has been, EXACTLY along these lines. I only hope it's feasible to implement (I already know it's feasible from a technical perspective; but it's not clear yet whether it will be feasible from a socio-political perspective...)

Aloha, Rich

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