[Taxacom] [iczn-list] GENERAL CALL TO BATTLE

Thu Feb 11 23:36:27 CST 2021

Hi Carlos,

Thanks for the thoughtful reply.  I guess we’re at the “agree to disagree” stage.  I already answered your specific question in a previous post.

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

 <http://hbs.bishopmuseum.org/staff/pylerichard.html> 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.

From: Admin Admin <archilegt at gmail.com> 
Sent: Wednesday, February 10, 2021 11:48 PM
To: Richard Pyle <deepreef at bishopmuseum.org>
Cc: Mallet, James <jmallet at oeb.harvard.edu>; iczn-list at afriherp.org; Thomas Pape <tpape at snm.ku.dk>; Taxacom <taxacom at mailman.nhm.ku.edu>
Subject: Re: [iczn-list] GENERAL CALL TO BATTLE

Hi Rich,

"As you noted in an earlier post, diagnoses are useful for differentiating a new taxon from previously existing taxa."

Read both diagnoses and descriptions, because they are meant to achieve the same, with a different length. And they are not meant to be "useful", they are meant to be methodologically sound, DIFFERENTIAL from the previous, and SUFFICIENT.

"They are somewhat less useful with respect to as-yet unnamed taxa."

That depends on how detailed the diagnoses/description is. And they do NOT have to be differential and sufficient (even less "useful") from yet-unnamed taxa, because that does not affect the core Principle of Priority. It is not previous taxa which should be demonstrably different, but new taxa which should be demonstrably new. Additionally, remember that we already have molecular species with equal barcodes that got finally diagnosed and splitted into two on the basis of non-molecular characters. So, barcodes are also not the universal panacea and morphology continues to play a role, especially for authors with apparent "hyperdiversity goals".

"One could easily argue that an image or a barcode is vastly more useful than a text diagnosis because both are more likely to contain information about characters that will help distinguish the new species from both previously known *and* as-yet unknown species."

You continue to use "vastly", which is a particular judgement of value from your side. The word "vastly" is mentioned ZERO times in the Code. You continue to use "useful", which is not a qualifier that we are discussing here. The word "useful" is mentioned ONCE in the Code, in the preface to the Fourth Edition, which is NOT part of the Code proper. What we are discussing here is the methodological obligation to diagnose differentially and sufficiently from the previous. That is not achieved by CHARACTERIZING with pictures and barcodes. That is achieved by practicing the methodological exercise of DIAGNOSING, i. e., COMPARING. A methodologically sound comparison contains equal, shared elements among the taxa compared. This is achieved, for two species, by making reference to the genus. A methodologically sound comparison contains differential elements which are not shared among the taxa compared. This is achieved, for two species, by presenting the sufficient diagnostic character state of the new species, or the combination of characters which combined provide a sufficient, differential diagnosis. Regarding "yet-unknown" species, again I remind you that the Code is framed with the Principle of Priority and not with a "Principle of Futurity".

"One could easily argue"

As per the explanation above, your easy argument has been easily nullified.

"What is more powerful: a text description that my new species has a longer snout than that other species?  Or an image of both snouts, without any text commentary?" 

Apply the same reasoning that I applied to "useful". You can use it as a particular judgement of value from your side, but it is mentioned ZERO times in the Code. Apply the rest of my previous argument. This is not about "useful" and "powerful". This is about the methodological obligation to diagnose differentially and sufficiently from the previous. 

"Or in the case of DNA barcodes, which is more powerful:  a text description that “my new species differs from that other species on the basis of 27 differences in the barcode sequence”; or simply providing the two barcode sequences without any commentary on the differences?"

The former will give you both the barcodes AND the comparison, and it will achieve SUFFICIENCY and DIFFERENTIATION FROM THE PREVIOUS. The latter is inadmissible on methodological grounds, because it fails to exercise COMPARISON and therefore DIAGNOSIS. You continue equate CHARACTERIZING with DIAGNOSING, but it is only the latter which methodologically satisfies the PURPOSE OF DIFFERENTIATING.

Now Rich, as I provided the context of Meierotto et al. (2019), and as I have provided profuse methodological explanations, I am going to repeat my direct question to you (and to all the Commissioners): Can anyone claim that 15 species in one genus (Zelomorpha) are new when they know that there are 52 other species but they only diagnosed the 15 "new" among them and from the type species, while neglecting other 51 species on purpose? Can someone claim that those 15 species are new? Do you support that claim? Was letting that claim pass a reviewer and an editorial mistake or not?

Please, do not attempt to dodge my direct question this time. Not you, not the other Commissioners. I am very much looking forward to your answers.

I will proceed by explaining what is going to happen if the Commission fails to stop the ongoing nomenclatural vandalism and if it fails to declare the recent fallacious claims of novelty unavailable under article 13.1.1 of the Code.

First, the Commission will be failing in securing an organized transition from one diagnostic character set to another. Second, the Commission will be failing to recognize the necessary role of integrative taxonomy during the transition time, which is meant to secure that 250+ years of morphological knowledge for 10% of the species is integrated into the upcoming, molecularly diagnosed 90% of species.

As the Commission will fail to the broader taxonomic community, those particular taxonomic communities who disagree on having their morphological knowledge overwritten by a parallel molecular nomenclatural system will split apart from the current ZooCode. I will assist those communities myself, and I am sure that many more taxonomists with good knowledge of the Code will respond to the call of duty. Community after community, we will abandon consensus and we will regroup together. The Commission and the molecular taxonomists who want to stay will be left with the "Molecular Code of Zoological Nomenclature", and the rest of us will build consensus about the same Code, the "Integrative Code of Zoological Nomenclature". We will form a new Commission, arbitrarily set the publication date of Meierotto et al. (2019) as 31 December 2019, and arbitrarily set 30 December 2019 as the date of the split of the broader taxonomic community. We will adopt the current Code, we will declare unavailable those molecular works which fail to differentiate from the previous, and we will strengthen Article 13.1.1 and secure a period of integrative taxonomy and a smooth transition to molecular diagnoses. The Integrative Code will rule over 100% of the described species, except for ca. 500 molecular Hymenoptera species.

If the Commission thinks that the broader taxonomic community is going to sit and watch how our names are overwritten and how our corpus of knowledge disregarded, you are very much mistaken.

Kind regards,

Carlos

On Thu, Feb 11, 2021 at 8:14 AM Richard Pyle <deepreef at bishopmuseum.org <mailto:deepreef at bishopmuseum.org> > wrote:

Hi Carlos,

Thank you for the expanded explanation of where you are coming from on this.  What you say makes sense, even though I disagree with some of your positions. Also, I think I was not clear in the point I was trying to make.  I’ll continuing playing the role of devil’s advocate.

As you noted in an earlier post, diagnoses are useful for differentiating a new taxon from previously existing taxa. They are somewhat less useful with respect to as-yet unnamed taxa. With something like 90% of biodiversity in the latter category (i.e., as-yet unnamed), we’re kidding ourselves if we think that some sort of textual word-based assertion of character differences with the already-known 10% of taxa someone improves the “robustness” of a new species description.

One could easily argue that an image or a barcode is vastly more useful than a text diagnosis because both are more likely to contain information about characters that will help distinguish the new species from both previously known *and* as-yet unknown species.  Sure, the text diagnosis might accidentally include characters or combinations of characters that hep distinguish from future new species.  But there’s a reason I was always taught to examine the types of known species – to make sure that the suite of characters I’m using to distinguish my new species are legit (and not missing from the previous text diagnosis of the previous species, or based on differences in measurement techniques, or whatever).

What is more powerful:  a text description that my new species has a longer snout than that other species?  Or an image of both snouts, without any text commentary?  Having only the words tells us only about the relative snout length. Having the images shows us that, in a potentially quantifiable way, and probably shows us a whole bunch of additional characters that might prove useful for distinguishing my new species from future as-yet unknown species.  Or in the case of DNA bar codes, which is more powerful:  a text description that “my new species differs from that other species on the basis of 27 differences in the barcode sequence”; or simply providing the two barcode sequences without any commentary on the differences?  In the latter case, the differences are self-evident from simply comparing the two sequences. And so are he positions of the differences.  And so are all the other positions in the entire barcode for comparing to as-yet unknown future species.

Sure, the best thing to do would be to show the pictures *and* point out the differences *and* provide the sequences *and* identify, using words, which positions of the sequence differs.  That’s good (better) taxonomy, of course.  But the point is that, a compelling case can be made that providing the raw data (hence allowing for comparisons with future species) is superior than explicit statements about specific characters that happen to distinguish a new species from previously described species.

I hope it’s clear that I’m not trying to say your wrong.  In fact, I personally agree with a lot of what you say (though not all).  I just want to illustrate that a “call to battle” might be a bit overkill on this issue; and instead a reasoned discussion about alternative approaches to establishing new species.

Above all, I do not want to discourage these debates – quite the opposite!  Now is *exactly* the time to be having these discussions, because the ICZN very much wants to get input on what the community would like to see in the next (5th Edition) of the Code.  The Code is not for the benefit of the Commission; it is for the benefit of all taxonomy, biology, science, humanity, etc.  It’s important to come up with a Code that both respects historical practice and accommodates trends that apply to the future (and the other ~90% of the world’s species that are yet to be named…)

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 <mailto:deepreef at bishopmuseum.org> 

 <http://hbs.bishopmuseum.org/staff/pylerichard.html> 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.

From: Admin Admin <archilegt at gmail.com <mailto:archilegt at gmail.com> > 
Sent: Wednesday, February 10, 2021 4:27 PM
To: Richard Pyle <deepreef at bishopmuseum.org <mailto:deepreef at bishopmuseum.org> >
Cc: Mallet, James <jmallet at oeb.harvard.edu <mailto:jmallet at oeb.harvard.edu> >; iczn-list at afriherp.org <mailto:iczn-list at afriherp.org> ; Thomas Pape <tpape at snm.ku.dk <mailto:tpape at snm.ku.dk> >; Taxacom <taxacom at mailman.nhm.ku.edu <mailto:taxacom at mailman.nhm.ku.edu> >
Subject: Re: [iczn-list] GENERAL CALL TO BATTLE

Uppercase letter used for stylization of text and not for shouting

So here came Rich with a "one-line morphological diagnosis":

Rich: “my new taxon differs from that other existing taxon in that mine has a longer snout” 

Well, yes, that is a methodologically correct DIFFERENTIAL DIAGNOSIS, which hopefully is also SUFFICIENT to differentiate both taxa in question. And it does fulfill "the requirement that authors must describe in words the characters purported to differentiate the taxon when proposing new names". And it also fulfills the logical requirement of "differentiating from the previous", in this example the previous taxon with the shorter snout.

WHAT IS NOT A DIFFERENTIAL DIAGNOSIS:

1) A "high-resolution photograph of the type" per se

2) A "DNA barcode of the type", when there are no barcodes for the vast majority of congeneric species and a comparison with the previous species is not made

THIS IS A PROBLEM OF DEFINITION:

<Rich>"the latter two are"</Rich>   NOT   <Rich>"VASTLY more useful in diagnosing the taxon"</Rich>   because CHARACTERIZING IS NOT DIAGNOSING.

More about diagnoses:

1) Morphological diagnoses do NOT stand in the air. They stand within a classification, and they inherit the characters of the upper hierarchies. So, Scolopendra morsitans inherits the characters of Arthropoda, Myriapoda, Chilopoda, Scolopendromorpha, Scolopendridae and Scolopendra, unless otherwise stated at the species rank or above. That is ANCHORING.

2) Authors are meant to create a SUFFICIENT diagnosis for a given taxon, shorter or longer, which purports to differentiate that taxon from the closely related taxa. In the case of a species, it can be differentiated from other species in the genus, or subgenus, or from a smaller aggregate of species. That is PURPOSE TO DIFFERENTIATE. Differentiation can be achieved by means of just one character state of one character, the so-called SUFFICIENT CHARACTER STATE, or it can be achieved by CHARACTER STATES WHICH COMBINED ARE SUFFICIENT to differentiate the taxon

This is a one-line diagnosis for Scolopendropsis duplicata: With 39 or 43 leg-bearing segments. The binomen provides ANCHORING to a genus in which all known species have 21 or 23 leg-bearing segments and PURPORTS TO DIFFERENTIATE the new species by using the character state “39 or 43 leg-bearing segments”, which is SUFFICIENT for separating the new species from all previously known species in that genus. This can be done because the full set of character states of a character has been scored for all species in the genus. 

What the enthusiasts of barcoding are trying to do is to use an incomplete set of character states for one character which has not been scored for all species in one genus. And they still pretend to claim priority under the Code over the names of new species proposed using that method, even when they recognize that additional species exist which have not been molecularly surveyed. That means that the purpose of "differentiating from the previous" and Article 13.1.1 cannot be considered as satisfied, unless that we all suddenly become blind to logical fallacies. Something cannot be claimed to be "new" and "differentiated" when a comparison has not been made. Amusing that I have to explain this.

If and only if a full set of barcodes is completed for a given group, the logical fallacy will exist no more, as all species would have a full set of barcodes, and new species could be DIFFERENTIALLY AND SUFFICIENTLY DIAGNOSED FROM THE PREVIOUS ONES. Taxa with full sets of barcodes could migrate to barcode diagnoses.

Differential barcode diagnoses do not pose a major methodological problem. In Myriapodology, we used the methodology already EIGHTEEN YEARS AGO, for mitochondrial 16S RNA, because yes, not everything in this world is COI. Undoubtedly, this is just one of many options. And I very much encourage everyone to read that paper and see how the diagnostic nucleotide changes for each species were summarized in figure 5, page 520.

-----------------------

Molecular diagnosis of putative Anadenobolus species
Nucleotide substitutions that are diagnostic for each species were determined using the character trace function in the computer program MacClade (Maddison and Maddison 2000). Because we are only interested in three nodes that are found in all recovered trees (see Results), tree choice was unimportant. Therefore one of the most parsimonious trees was chosen at random from the set of all equally parsimonious trees reported in Bond and Sierwald (2002b, fig. 2). All nucleotide substitutions were plotted onto this tree using the ‘Trace All Changes’ function with the ‘Unambiguous Changes Only’ option selected. Only those character-state changes that were non-homoplasious above the node of interest are used to diagnose species.
However, substitutions that appear in other regions of the phylogeny are considered (we differentiate between the two below).
Each species diagnosis lists the character state (nucleotide) followed parenthetically by the nucleotide position number. The position number refers to the nucleotide position in the fully aligned data set used in this study. A reference alignment of all three species is available in electronic form on request from the first author and for download at http://core.ecu.edu/biol/bondja and is also available as Accessory Material from the journal’s website. We adopt this approach because the region of 16S sequenced is highly variable and is not easily aligned to commonly cited model arthropod genomes (e.g. Drosophila yakuba, Clary and Wolstenholme 1985).

Reference: Bond, J. & P. Sierwald. 2003. Molecular taxonomy of the Anadenobolus excisus (Diplopoda:Spirobolida:Rhinocricidae) species-group on the Caribbean island of Jamaica. Invertebrate Systematics 17 (4):515-528. https://www.researchgate.net/publication/253260124

----------------------- 

And before someone brings up the topic, diagnoses are short descriptions and descriptions are expanded diagnoses. However, given the apparent lack of logic and methodology that has brought us to this historically low point, it would be advisable that SUFFICIENT, DIFFERENTIAL DIAGNOSES are made mandatory as soon as possible, in an Amendment to the Code, to prevent that the purpose of differentiating from the previous continues to be vandalized. It would also be most advisable to set an example by declaring recent fallacious claims of novelty unavailable under article 13.1.1 of the Code.

Kind regards,

Carlos

On Thu, Feb 11, 2021 at 3:19 AM Admin Admin <archilegt at gmail.com <mailto:archilegt at gmail.com> > wrote:

The phrase means nothing else to me than its literal meaning. And as I cannot sleep, I will proceed to explain one of the methodological problems that is causing all this and that is also present in the previous email by Rich.

On Thu, Feb 11, 2021 at 3:07 AM Richard Pyle <deepreef at bishopmuseum.org <mailto:deepreef at bishopmuseum.org> > wrote:

> “Good people on both sides!” Now where have I heard that before?

Yup... hence my comment about it being "a very notorious statement in another context"...

Aloha,
Rich