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

[Richard Pyle]

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

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From: Admin Admin <archilegt at gmail.com> 
Sent: Wednesday, February 10, 2021 4:27 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

 

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