Taxacom: paper recommended by Thomas Pape
Stephen Thorpe
stephen_thorpe at yahoo.co.nz
Tue Aug 29 01:07:04 CDT 2023
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
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> -----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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