Taxacom: paper recommended by Thomas Pape

Tue Aug 29 13:31:36 CDT 2023

Yeah... what Stephen and Francisco said.

[MUCH shorter... :-) ]

Aloha,
Rich

Richard L. Pyle, PhD
Senior Curator of Ichthyology | Director of XCoRE
Bernice Pauahi Bishop Museum
1525 Bernice Street, Honolulu, HI 96817-2704
Office: (808) 848-4115;  Fax: (808) 847-8252
eMail: deepreef at bishopmuseum.org
BishopMuseum.org
Our Mission: Bishop Museum inspires our community and visitors through the exploration and celebration of the extraordinary history, culture, and environment of Hawaiʻi and the Pacific.

> -----Original Message-----
> From: Taxacom <taxacom-bounces at lists.ku.edu> On Behalf Of Francisco
> Welter-Schultes via Taxacom
> Sent: Tuesday, August 29, 2023 2:42 AM
> To: taxacom at lists.ku.edu
> Subject: Re: Taxacom: paper recommended by Thomas Pape
> 
> As almost always in such contexts, Rich's answer was much too short. :-)
> 
> We also have to consider that the French Code is equivalent in force and
> meaning to the English Code, and that the wordings and definitions of the
> regulations and terms associated with Art. 13.1.1 differ substantially between
> the English and French versions.
> Instead of "purported to diffferentiate" the French Code uses the expression
> "permettant de différencier" (allowing to differentiate), and the Glossary
> definitions also deviate.
> So, the Code is not as easy as it may appear when reading the English version
> alone....
> 
> Francisco
> 
> Am 29.08.2023 um 08:07 schrieb Stephen Thorpe via Taxacom:
> >   We are lucky you gave us the short answer! :)
> >      On Tuesday, 29 August 2023 at 05:18:37 pm NZST, Richard Pyle via
> Taxacom <taxacom at lists.ku.edu> wrote:
> >
> >   Hi Thomas,
> >
> >> the concluding section of the referenced paper (Section: "Our
> >> recommendation for future editions of Codes of
> >> bionomenclature") states "We advocate an explicit requirement for
> >> state-specific and contrastive diagnoses."  Doesn't section 13.1.1 of
> >> the ICZN fulfill this requirement?
> >
> > Well... not exactly.  So, let's parse the wording of Art 13.1.1:
> >
> > "[To be available, every new name published after 1930 must satisfy the
> provisions of Article 11 and must] be accompanied by a description or
> definition that states in words characters that are purported to differentiate
> the taxon; or [be accompanied by a bibliographic reference to such; with
> some other stipulations not relevant to the current discussion]"
> >
> > Breaking down the unbracketed text in the above quote:
> >
> > "be accompanied by"
> >
> > I'm not aware of any ambiguity here.  As far as I know, most people
> > interpret this to mean that the elements described in the remaining
> > text of this Article must appear within the relevant work (13.1.2
> > allows for, alternatively, a bibliographic citation to another work
> > containing the elements)
> >
> > "a description or definition"
> >
> > Here's where things get a bit squishy.  First of all, it's not clear whether the
> word "or" here is used in the sense of "A or B", or more in the sense of "A
> (i.e., B)".  In the latter case, "definition" would simply be a word that further
> qualifies "description". In the former case, "description" and "definition" are
> two distinct things, and Art. 13.1.1 requires that at least one of them appear
> within the work.  Most folks interpret this as "A or B", because both words
> ("description" and "definition") appear separately in the Code's glossary:
> >
> > definition, n.
> > A statement in words that purports to give those characters which, in
> combination, uniquely distinguish a taxon [Arts. 12, 13].
> >
> > description, n.
> > A statement in words of taxonomic characters of a specimen or a taxon
> [Arts. 12, 13].
> >
> > The definition of the word "definition" (meta definition?) in the context of
> the Code is interpreted by most people as essentially meaning "diagnosis" as
> used in modern publications.  Essentially, a statement that, in its entirety,
> provides sufficient information on "characters" to distinguish a given taxon
> from all other taxa.  Indeed, the Code does provide a glossary definition of
> "diagnosis":
> >
> > diagnosis, n.
> > A statement in words that purports to give those characters which
> differentiate the taxon from other taxa with which it is likely to be confused.
> >
> > At first glance, this seems entirely synonymous with "definition", but
> different words are used to define each separate term. A definition must
> "uniquely distinguish a taxon", whereas a diagnosis "purports" to
> "differentiate" the taxon from other taxa (specifically, other taxa with which it
> is likely to be confused). However, the word "diagnosis" is not part of Art
> 13.1.1, so it is not really relevant here.
> >
> > The definition of the word "description" is slightly more relaxed than
> "definition", because it does not include a provision for uniquely
> distinguishing a taxon -- it only requires a statement of characters for a
> specimen or a taxon.  It also can apply to a specimen, whereas "definition"
> only applies to a taxon.
> >
> > Note that both of these terms involve "a statement in words" (i.e., not
> illustrations or other means of non-word documentation of characters), and
> both involve "characters" that have something to do with taxa.
> >
> > Moving on...
> >
> > "that states in words"
> >
> > In some ways this is redundant, because already both "A" and "B"
> ("description" or "definition") require a "statement in words", so we already
> know just from those two words that "words" must be the basis of the
> description or definition.  This opens up a separate line of ambiguity
> regarding what a "word" is.  The Code Glossary offers no definition to help us
> here, but the most basic interpretation is that it can't be an illustration or
> image or drawing or photo or anything like that.  However, there is ongoing
> disagreement among "Code Warriors" as to whether or not a statement along
> the lines of "AGTCGAC..." etc. count as "words".  Each of these letters
> represents a well-understood abbreviation for words (Adenine, Guanine,
> etc.).  Some argue that abbreviations count as words, and some argue that
> they don't.  A similar ambiguity involves numerals.  For example, is "3" a
> word?  This discussion alone could fill an entire thread, so I won't dwell on it
> -- just underscoring that it represents part of the ambiguity of the meaning
> of Art. 13.1.1.
> >
> > Next...
> >
> > "characters"
> >
> > This one also comes with a definition in the glossary:
> >
> > character, n.
> > Any attribute of organisms used for recognizing, differentiating, or
> classifying taxa.
> >
> > Despite what some have argued, I think it's difficult to exclude "molecular"
> attributes from the scope of "characters".
> >
> > And, finally...
> >
> > "purported to differentiate the taxon"
> >
> > The word "purported" here is generally interpreted to mean "asserted".
> > In other words, even if the author of a word presents a character that
> > doesn't actually exist on the taxon, or if the character does not
> > differentiate the taxon, it still counts for fulfillment of the
> > requirement of Art. 13.1.1 as long as the work "purports" it to be
> > true.  There are some other interpretations (especially when you
> > consider this Article in the Code represented in other languages), but
> > I don't want to go overboard here (too late?)
> >
> > Fortunately, the word "differentiate" is defined for us in the Glossary:
> >
> > differentiate, v.
> > To distinguish something (e.g. a taxon) from others [Art. 13]. See also
> definition.
> >
> > I probably don't need to dwell on this one, so I won't.
> >
> > Now, to tie all this together with your original question above, let's examine
> the quoted text:
> >
> > "We advocate an explicit requirement for state-specific and contrastive
> diagnoses."
> >
> > The key terms here are "state-specific" and "contrastive".  Suppose
> someone proposes a new species name with a sentence like this:
> >
> > "My new species differs from all other species in the color of its head."
> >
> > This is "a statement in words of taxonomic characters of a specimen or
> > a taxon" (i.e., it meets the definition of "description" in the sense
> > of the Code), and it purports to differentiate the taxon.  So strictly
> > speaking, it fulfills the requirements of Art. 13.1.1. However, unless
> > you really stretch the definitions of those terms, such a description
> > is neither "state-specific" (i.e., what color is the head?), nor
> > "contrastive" (i.e., how is the color different from other taxa?)
> >
> > Now consider this version:
> >
> > "My new species differs from all other species in that it has a green head."
> >
> > This is "state-specific", because it actually represents a character state
> (green head), rather than just a character (color of the head).  But it's not
> contrastive.
> >
> > Now another version:
> >
> > "My new species differs from all other species in that it has a green head,
> whereas all other species of the genus has a red head."
> >
> > This one is both state-specific and contrastive.
> >
> > The problem that this proposal (i.e., the next Code requiring
> descriptions/definitions that are both state-specific and contrastive) means
> that only the last version of the examples above would fulfill the
> requirement.  However, under the current wording of the Code, any of these
> (including "My new species differs from all other species in the color of its
> head.") could be argued to meet the requirement of Art. 13.1.1.
> >
> > Here's a similar example using molecular characters:
> >
> > "My new species differs from all other species in the sequence of base pairs
> of the COI gene."
> >
> > "My new species differs from all other species in having a sequence of base
> pairs of the COI gene as follows: AGTCAG[etc...]"
> >
> > "My new species differs from all other species in base pairs of the COI gene
> at positions 32 (A instead of G), 48 (C instead of T), 82 (G instead of A) and
> 113 (T instead of C)."
> >
> > I realize this was an exceedingly long and detailed reply (we Commissioners
> are noting if not pedantic), but I wanted to answer your question as
> thoroughly as possible.  I hope I accomplished that goal, at least somewhat.
> >
> > Aloha,
> > Rich
> >
> > Richard L. Pyle, PhD
> > Senior Curator of Ichthyology | Director of XCoRE Bernice Pauahi
> > Bishop Museum
> > 1525 Bernice Street, Honolulu, HI 96817-2704
> > Office: (808) 848-4115;  Fax: (808) 847-8252
> > eMail: deepreef at bishopmuseum.org
> > BishopMuseum.org
> > Our Mission: Bishop Museum inspires our community and visitors through
> the exploration and celebration of the extraordinary history, culture, and
> environment of Hawaiʻi and the Pacific.
> >
> >> -----Original Message-----
> >> From: Taxacom <taxacom-bounces at lists.ku.edu> On Behalf Of Thomas
> >> McCabe via Taxacom
> >> Sent: Monday, August 28, 2023 3:13 PM
> >> To: taxacom at lists.ku.edu
> >> Subject: Taxacom: paper recommended by Thomas Pape
> >>
> >> Hello. Thanks to  Scott Thomson, Stephen Thorpe, Richard Pyle, and
> >> John Grehan, who gave their answers here to my August 25 posted
> >> questions about the paper ("Tightening the requirements for species
> >> diagnoses would help integrate DNA-based descriptions in taxonomic
> >> practice", *PLoS Biol*
> >> 21(8):
> >> e3002251) recommended on August 24 by Thomas Pape.
> >>
> >> Richard, in his response, noted that section 13.1.1 of the current
> >> International Code of Zoological Nomenclature stipulates that
> >> "...every new name published after 1930 must... be accompanied by a
> >> description or definition that states in words characters that are
> >> purported to differentiate the taxon…." On the other hand, the
> >> concluding section of the referenced paper (Section: "Our
> >> recommendation for future editions of Codes of
> >> bionomenclature") states "We advocate an explicit requirement for
> >> state-specific and contrastive diagnoses."  Doesn't section 13.1.1 of
> >> the ICZN fulfill this requirement? I do not have access to the other
> >> codes, but I wonder if they too contain such stipulations.
> >>
> >> I am not a producer but a user of biological taxonomy, especially
> >> microbiological species definitions. So I appreciate section 13.1.1 of the
> ICZN.
> >>
> >> Respectfully,
> >>
> >>      Thomas McCabe
> >> _______________________________________________
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> >>
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> >> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Ftaxacom.markmail.org%2F&data=05%7C01%7Ctaxacom%40lists.ku.edu%7C661559da775f4826653808dba8be32b1%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638289307073228638%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=CPTgA4DgxHV2lsD2KebAkAeMQMX2RfwttipX8FOYnlI%3D&reserved=0
> >>
> >> Nurturing nuance while assailing ambiguity and admiring alliteration
> >> for about 36 years, 1987-2023.
> >
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> >
> > Nurturing nuance while assailing ambiguity and admiring alliteration for
> about 36 years, 1987-2023.
> >
> > _______________________________________________
> > Taxacom Mailing List
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> >
> > Nurturing nuance while assailing ambiguity and admiring alliteration for
> about 36 years, 1987-2023.
> >
> _______________________________________________
> Taxacom Mailing List
> 
> Send Taxacom mailing list submissions to: taxacom at lists.ku.edu For list
> information; to subscribe or unsubscribe, visit:
> https://lists.ku.edu/listinfo/taxacom
> You can reach the person managing the list at: taxacom-owner at lists.ku.edu
> The Taxacom email archive back to 1992 can be searched at:
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> 
> Nurturing nuance while assailing ambiguity and admiring alliteration for
> about 36 years, 1987-2023.