[tcs-lc] Demonstration Dataset

Richard Pyle deepreef at bishopmuseum.org
Sat Mar 5 00:07:37 PST 2005


> You are right, the symbols "represent the full scope of
> individual organisms"
[etc...]

Thanks, and agreed.

> >Slide 3:
> >- Need to be really careful with the words "valid" and
> >"invalid" (side-box
> >for Pyle 1990).
>
> Fair enough. We would hope that the taxonomist - botanical or
> zoological would use the correct relationship for their particular case.
> We merely needed a simple example of a "purely nomenclatural
> change". Sorry if this created additional issues; hope they don't
> distract from what we are trying to show.

Not a distraction -- just a cautionary note about certain words that have
very specific meanings in nomenclature, and (frustratingly) specifically
different meanings in botany vs. zoology (i.e., guaranteed
confusion-causers).

> >Slide 10: The Codes (at least the ICZN code) would not consider the
> >gender-corrected "Aus beus" as a "replacement name" to "Aus
> >bea".  Indeed, I
> >don't think any zoologist would think of these as different
> >"names" -- but
> >rather as different spellings of the same "name". I don't
> >believe the Pyle
> >1990 act of noting the corrected spelling would represent either an
> >"Original" concept, or a "Nominal" concept.  More of a "usage"
> >instance.
>
> we disagree here - if you are making this new name publicly
> available for people to use (in fact actually encouraging people
> to use it from now on...) then it should be a new concept

You call it a "new name".  It may be a new string of text characters (which
I view as a semi-dynamic property of a "name" object), but from my
zoological perspective, it is a corrected spelling of a previously-existing
"name". When people misspell my last name as "Pile" (as they do), nobody
would interpret that as a "different name" -- they would consider it as a
misspelling.  When people substitute the name "Gomer" for my first name (as
they do), they are applying a different first name to me.  It is not always
obvious whether a taxonomic name is a "new name", or a "misspelling of a
previously existing name" -- but it *almost* always is obvious. Of course,
botanists may differ on this.

In any case, I think it would be a mistake to create a new Nominal concept
for every single variation of spelling for a name -- this is why I think
there needs to be a NameVerbatim element to capture the ASCII/Unicode
equivalent of the actual text string used in a particular instance.

Also, I think it will be a grave mistake to treat every such instance of a
nomenclatural alteration *separately* as a "concept".  To me, a concept
(ESPECIALLY a "defined" concept) must say at least *something* about the
size/shape/position of the "circle" of circumscription around a set of
individual "dot" organisms.  As I understand the Pyle 1990 example in the
PPT file, it was intended as a "purely" nomenclatural act.  As such, there
is absolutely NO information concerning the size/shape/position of any
"circle" -- and therefore it is not, by *any* definition, an implied
"concept".

As I understand the point of a "Nominal" concept, it is basically defined as
"the sum of all concept circumscriptions that included the primary type
specimen of this name". I gather it also includes (perhaps pending a user
option) "the sum of all concept circumscriptions misidentified by this name"
(using the word "misidentifed" as I have defined it previously: generically
stated as a case where the identified specimen and the primary type specimen
of the applied name would not, in the indentifiers view, be contained within
the same circumscription). I imagine a suite of variables that a user could
provide for narrowing or expanding the scope of searches (e.g., only
concepts congruent with the corresponding original concept; only homotypic
concepts; etc., etc.)  But the point is, a "Nominal" concept is a "fuzzy" or
"dynamic" definition of the size/shape/position of the concept "circle";
whereas all other types of concept definitions are (presumably) pinned down
to one *specific* size/shape/position circle.

Getting back to the issue at hand, I still fail to see how Pyle 1990 can
represent a non-Nominal "concept", when Pyle 1990 provided absolutely no
information whatsoever about the size/shape/position of the "circle" that
circumscribes any taxon.

> >agree with this), but to me, what distinguishes an "Original"
> >concept from a
> >"Nominal" concept is that the former has a specific implied concept
> >circumscription, whereas the latter is purely nomenclatural.
>
> but the latter still has an implied concpet when it is used by
> someone in the future....

Not in the case of "Pyle 1990"  -- if all he did was say "Hey guys,
according to the rules of nomenclature, if you combine the adjective name
'cea' with the masculine genus 'Aus', you need to spell the species epithet
as 'ceus'."  Pyle is a nomenclatural purist -- he may be an expert in
fishes, when "Aus" is a genus of weevils.  Pyle may not even know what a
"weevil" is (other than a concatenation of "we" and "evil"....sorry,
Nico..couldn't resist) -- so how can we assume that Pyle implied any sort of
"concept" circumscription about "Aus ceus"?

> >Pyle 1990
> >never made any assertions about concept circumscriptions for
> >either name,
> >and therefore should not have an "Original" concept associated
> >with either
> >(by my understanding, anyway).
> >
>
> but then it makes the name unusable if we agree it is meaningless
> to identify something to a name that has no concept.

It only makes the name "unusable" if you assume that names do not exist as
separate objects from concepts.  If Pyle, the fish-nerd, who doesn't even
know what a weevil is, points out to his friend Nico (e.g., via a
publication Pyle edited listing all species known from Hawaii), that the
genus "Aus Linnaeus 1758" is masculine (according to latin rules of
grammar), and that the species epithet of "Aus cea BFry 1989" is an
adjective (again, by rules of latin grammar), and therefore that the proper
spelling of the complete name should be "Aus ceus" -- I would hardly
consider this to be an "unusable" statement.  There in absolutely no
ambiguity about what name object Pyle is referring to (unless someone else
named "BFry" happened to also describe a new species called "cea" in the
genus "Aus", also in 1989) -- even if Pyle didn't know the difference
between a "weevil" and a mountain gorilla.

The point is, Pyle never "identified" any organims as "Aus cea" or as "Aus
ceus".  He never gave any clue whatsoever about the size/shape/position of
any circle circumscribing any dots.  He never even had a concept in his mond
for what a weevil, or an "Aus", or an "Aus cea" is.  But he provided a
valuable contribution to the *nomenclature* nevertheless.

Now, it may be easy to say "So what?", or "Big deal!", or "Do we really need
to track all those concept-less publications dealing with nomenclature?"
Well, according to the LC group, we absolutely do!  It may seem tedious and
trivial -- but by that measure, the entirety of the codes of nomenclature
are tedious and trivial -- so why not abandon them altogether in favor of a
nomenclatural system that *does* anchor names to actual, unambiguously
defined concepts (like Phylocode!)

> >On the other hand, if Franz had discovered that Xus Pargiter 2003 was
> >preoccupied by Xus Smith 1950 (thus Pargiter's "Xus" being a
> >junior homonym
> >of Smith's "Xus"), then published the replacement name "Zus",
> >it *would* be
> >appropriate to create a new "Original" concept and a new
> >"Nominal" concept.
>
> we agree this would be correct but see the previous example in the
> same way...

One major difference (in Zoology, at least) is that the change from "Aus
cea" to "Aus ceus" has absolutely no impact whatsoever on authorship (it
would be retained as "Linnaeus 1758" -- see ICZN Article 34.2), but the
change from the preoccupied, homonymous "Xus" to the homotypic replacement
name "Zus" *does* involve an authorship change (it would be recorded as "Zus
Franz" -- see ICZN Article 60.3 and Recommendation 60A).  Also, it is only a
recommendation in ICZN that a replacement name be established as homotypic
with the name it is replacing.  If this recommendation is not followed, then
"Xus" and its replacement name "Zus" ae subjective synonyms, and therefore
necessarily require separate concepts (which may or may not be congruent
with each other).

> >But this is a special case, and there are botanical/zoological
> >differences
> >here (with respect to basionym treatment).
>
> yes - but when the name is used it will be used with a meaning
> and deserves to have one....

Not in the case of Pyle 1990.  In the PPT file, there was no circumscription
around any set of little symbols connected with Pyle 1990, which to me meant
that the Pyle 1990 statement was purely nomenclatural.

> ok we are trying to be consisten in the modelling approach the actual
> relationships (i.e. what they are called - still to be agreed on
> but good list for starters by Nico) can capture these semantic
> differences between the codes.

I'd recommend starting with the folks involved with the "BioCode"
(http://www.rom.on.ca/biodiversity/biocode/intro.html).

MAN, our job would be so much easier if we could somehow all conform to a
single Code of nomenclature...but alas....well...'nuff said.

> >Slide 14: I had been under the impression that "Original" concept was
> >restricted to Basionyms, true "replacement names", and *perhaps* new
> >combinations (if the botanists win) -- but not alternate
> >spellings. However,
> >I get the impression that here a new "Original" concept is
> >created whenever
> >there is a novel "NameString" (specific string of characters).
>
> yes they are created for all novel Namestrings - but only new
> strings that are in a taxon definition or a nomenclatural act (if
> that's what its called), not just some usage in say the New York
> Times..... ;-)

...and of course, we all recognze that there is an essentially smooth
continuum of circumstances between the NY Times and, say, the journal
"Nature".  Citation of two extremes of a continuum do not a
fundamental/objective difference make...

> >Also, I
> >thought they were created only in cases where an actual concept
> >(circumscription of specimens) was asserted -- not for purely
> >nomenclatural
> >acts (without any concept implications).
>
> no

Well--they should be!  If there is no circumscription, how can you say there
is a concept?  I'm willing to accomodate the idea of a special-case
"Nominal" concept, which can be ascribed to a
calculated/algorithmically-derrived concept (based on examinations of
homotypic concepts, etc.).  But if you tell me that other kinds of concepts
sometimes have a circumscription, and sometimes do not (i.e., sometimes are
a concept, and sometimes are not), then I'm getting VERY uneasy about
things.  It's almost as if you're trying to force-fit information about
nomenclatural objects into a structure intended for concept objects... ;-)

> >Slide 15: Because Pyle never made any statements about the
> >shape/size/position of the concept circumscriptions associated
> >with the two
> >names he was correcting, I don't see why there should be any "SEC Pyle"
> >instances.
>
> because the corrected the name - deosn't he deserve a SEC. for this?

Not in my mind.  To me, the attribution of a "SEC." is the distinction
between a "Name" (anchored to a single "dot" that is the primary type
specimen), and a "Concept" circumscription (information describing the
size/shape/position of a circle that circumscribes many other dots in
addition to the primary type specimen of the applied name).  If you don't
have any information relating to the size/shape/position of the circle, you
don't have a concept circumscription, and therefore you don't have a "SEC."

If you mean to say that "SEC." sometimes means "in the nomenclatural sense
of...", and sometimes means "according to the concept circumscription
of...", then  I think we might need to make sure we all agree with more or
less the same definitions of "Concept" and "Name".  I'm beginning to think
that maybe we do not.

> >- Also, I think there is an error in the box for TCrev19 --
> >shouldn't that
> >be "Aus cea Fry 1989", instead of "Aus cea Archer 1965"?
> yes there is a mistake sorry it should be "Aus cea BFry 1989"
> >Also,
> >what's with
> >the "BFry"?  Is that a botanical author code?
> >
> it was just to show that the author Fry could also  be abreviated
> as BFry (Linnaeus, L. Linn. etc) i.e. differently in the name and
> in the publication.

ok

> There were a couple of other little typos on that slide....The
> lower TCori14 should've been TCori16 and "Aus ceus Archer 1965"
> should be "Aus ceus BFry 1989" just like in real life ;-)

got it -- just wanted to be sure I wasn't misunderstanding something.

> >Regarding the "Demo_v2.xml" file:
> >
> >- Why don't any of the Species-rank names have Relationships?
> >Are there no
> >reciprocal "is type of" or "is child of" relationships?
> >
>
> we represetned the XML to match the scenario and the genera were
> defined in terms of the species as in this example this is what
> we said the taxonomists did. You can back-track the speciifed
> relationships if you want - but we don't represent explicitly.

O.K. -- probably a topic of discussion for another day... :-)

> >- Does <Relationship type="has type"> mean "Has type
> >species."?  If so, I
> >understand why cl1 has this relationship, but why is it
> >repeated for ca1,
> >cf1, ct1, etc.  Is this only because these are "Revision"
> >concepts, and in
> >each case the author re-affirmed the type species of the
> >genus?
>
> yes htat's how we interpretted it.

O.K., because there is something governed by the Codes called
"typification" -- that is, the actual published act that established the
primary type of a name (not always the original description in zoology for
names published prior to 2000).  To a nomenclaturalist, these definitely
need to be distinguished from other publications (e.g., revisions) that
"reaffirmed" that the type was such & such specimen, but otherwise have no
nomenclatural standing.

> > Or will
> >*all* concept instances of Aus L. 1758 contain a copy of this
> >connection
> >with the type species?
>
> not if in the definition it doesn't reaffirm it.

O.K.  Again, may need to discuss this a bit more, but we'll save it for
another day...

> > This is an example of something that
> >is a property
> >of the *name* "Aus", not of every single Concept instances of "Aus".
> >
> This could also be inferred  by navigating to the orignal concept.

...or to the Revision concept that serves as the Code-compliant type
fixation event of the name.

> >General question about "Original" vs. "Nominal" concept:
> >Intuitively, it makes sense to me that if you're going to go
> >to the trouble
> >of automatically creating a Nominal Concept for every Original
> >Concept, then
> >the Nomenclatural information should be embedded within the "Nominal"
> >version, and that should be the unit of exchange for
> >nomenclators.
>
> well that gives some definition to it

How so?  If it only includes purely nomenclatural information (without any
statements about the size/shape/position of the circle circumscribing a set
of dots), then I see no concept definition asserted.

> and we're trying to say use
> the nominal concept where you don't know what the name means.

Yes, and including nomenclatural stuff gives you no information at all about
what the name means (beyond the primary type specimen).

> > It seems
> >intuitive to me that a "Nominal" concept would be a container
> >for "all the
> >name stuff".  I think an "Original Concept" should be used for a true
> >concept -- the concept that was asserted by the Author(s) of
> >the original
> >description of the name.
>
> we've discussed this before I think and are saying that an
> original concept will always hold the nomenclautraul information
> ralted to that name.

That's how I do it in Taxonomer, but that's not how I think it ought to be
done in the global standard (and believe me -- it PAINS me to spend so much
of my precious time arguing for something that will ultimately consume more
of my precious time further down the road when I try to output Taxonomer
data to TCS....!)

> >Also, we need more discussion about what sorts of "name changes" should
> >warrant the creation of a new "Original" concept and/or
> >"Nominal" concept.
> >
> yes - see earlier discussion - any name that has a published
> definition and any name change that is intended to be followed
> and therefore has an implied definition.

In the LC group, we forbade unqualified use of the word "name" in any
discussion. See:
http://wiki.cs.umb.edu/twiki/bin/view/UBIF/LinneanCoreDefinitions

So, it's not clear what you mean by a "name change".  To me, "Aus cea" -->
"Aus ceus" may represent a change of "Name-literal" and/or "Name-String",
but not a "Name Object" (not defined on the LC page, but I can define it
here, if you like).

> >If the TCS group would find it useful, I could offer a
> >real-world set of
> >examples in fishes that offer a set of particularly thorny
> >nomenclatural
> >issues.  I would begin with a PPT file similar to the abstract one in
> >"TimeLine", except I would replace it with real values. Would that be
> >worthwhile?
>
> yes we were always asking for real data .......
> we can always see if how you would do it would be how we thought
> it could be done.

O.K., I'll try to find some time this weekend.

G'night for now...

Rich

P.S. Thank you SO MUCH, Jessie, for taking the time to read and respond to
my long diatribes -- and for not giving up on me.  These past few days of
concversation have certainly helped me understand the TCS approach (mostly
in the form of revealing new aspects of it that I disagree with!! ;-) ).





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