[Taxacom] validation of taxon names

Richard Pyle deepreef at bishopmuseum.org
Fri Feb 17 16:51:43 CST 2012


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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