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

Sat Feb 13 22:46:30 CST 2021

Rich,OK, so we are lurching towards an understanding of the issues here. Let's run with what you have said and examine the consequences for DNA only descriptions. Your view, as I understand it, is that a DNA only description attaches a new name to an individual organism, by way of it's DNA sequence. This is pure nomenclature, with no taxonomy involved, right? It is effectively the same as someone publishing a list of specimens and proposing a new name for each of them, thus forcing future taxonomists to consider those names if they propose a new taxon which includes one of those specimens. I strongly suggest that doing this should be avoided at all costs, because it actually makes the "taxonomic impediment" worse, not better! For a taxonomist revising a group, the simplest scenario is if there are no pre-existing names in the group under revision. Then the taxonomist can simply propose new names without having to consider previous work. Anyone who simply proposes new names for specimens, via DNA sequences, serves only to complicate and slow down the taxonomic revision, forcing the taxonomist to track down and examine all those type specimens based only on DNA sequence. I see this as a very bad thing!Cheers, Stephen    On Sunday, 14 February 2021, 11:15:09 am NZDT, Richard Pyle <deepreef at bishopmuseum.org> wrote:  

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Hi Stephen:

> A DNA sequence is a property of an individual organism, not a species.

Yes, of course!  And under the ICZN Code, a name is linked to a type specimen, not a species.  It’s an issue of taxonomy, not nomenclature, as to how to extend the application of a name beyond the type specimen(s). 

https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2005075 

> I very much doubt that one can set an across the board 

> percentage difference, within which different sequences 

> correspond to the same species

I *completely* agree!  And the exact same thing applies to metrics of morphology when distinguishing species.

> If a species is defined solely by DNA sequence

I was focusing my points in the context of nomenclature, not taxonomy.  The idea of “defining species” is in the realm of taxonomy.

This underpins my problem with Art. 13.1.1 – it’s one of the main points of the Code that dabbles in taxonomy.  Let me give another example of what I’m getting at here:

Suppose that the description/definition stated in words (Art. 13.1.1) is not accurate with respect to the name-bearing type specimen (e.g., states that the elephant’s skin is pink, when in fact the type specimen’s skin is actually grey).  I’m pretty sure that everyone would agree that the type specimen is what the name is associated with, not the words that fulfill Art. 13.1.1.  I’m also pretty sure that in such cases, the name is still regarded as available under the Code (Art. 13.1.1 does not require that the words describing or defining the taxon to differentiate it be accurate – only that they exist – as suggested by the word “purported”).

This is the key point I have been trying to make here:  in the context of the ICZN Code, the objective link between a name and biological reality is the name-bearing type specimen(s).  Once that is understood, the requirement of Art. 13.1.1 serves no legislative function in associating the name with a taxon, as this occurs via the designated type specimen(s).  In effect, the requirement of Art. 13.1.1 is meant to enforce a “convenience” factor in the work establishing a new name for a taxon – that is, saving the reader the trouble of examining the type specimen directly. This is obviously HUGELY important in the history of taxonomy!  But the “bar” for fulfilling Art. 13.1.1 is so low that from a legislative perspective, it has essentially no value (NOT to be confused with the taxonomic value, which again is at least potentially huge).  So, yes:  a robust description or definition that states in words characters purported to differentiate the taxon is a hallmark of good taxonomy.  But it is out of place in the context of nomenclature.

This does NOT mean that I think we should necessarily abandon the requirement.  But at the moment, it does little to help with either the legislative process of nomenclature or the encouragement of “good” taxonomy.  But it does seem to trigger a lot of noise in the form of disagreement and debate.  The cost-benefit ratio of Art. 13.1.1 is very low.  We should either eliminate it entirely from the next edition of the Code, or re-frame it in a way that it serves some meaningful value for either nomenclature, or taxonomy, or (Ideally) both.

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.

From: Stephen Thorpe <stephen_thorpe at yahoo.co.nz> 
Sent: Friday, February 12, 2021 5:52 PM
To: 'Francisco Welter-Schultes' <fwelter at gwdg.de>; iczn-list at afriherp.org; Richard Pyle <deepreef at bishopmuseum.org>
Subject: Re: [iczn-list] GENERAL CALL TO BATTLE

Rich,

There are serious potential problems here. A DNA sequence is a property of an individual organism, not a species. Theoretically at least, a mutation can change a base at any location (or at least many locations), but it doesn't change the species. I very much doubt that one can set an across the board percentage difference, within which different sequences correspond to the same species. At best, DNA sequences can be used to help to identify species, but should not be used as the defining basis for a species. If a species is defined solely by DNA sequence, then it is useless for further studies into its ecology, behaviour, etc., until somebody links the sequence to a differential morphological diagnosis, so nothing is gained by naming the species based solely on DNA sequence. Define it by morphology and by all means chuck in the DNA sequence, but the latter, by itself, is useless for most practical purposes.

Cheers, Stephen

On Saturday, 13 February 2021, 04:17:07 pm NZDT, Richard Pyle <deepreef at bishopmuseum.org> wrote: 

Just a couple of additional points here:

First, it's important to note that Art., 13.1.1. calls for "...a description or definition..." [emphasis added].

As Francisco notes, the definitions of both these terms are in the glossary:

definition, n.

A statement in words that purports to give those characters which, in combination, uniquely distinguish a taxon

description, n.

A statement in words of taxonomic characters of a specimen or a taxon

I raise this because sometimes people focus only on the definition of what constitutes a “description”, and ignore the fact that an alternative to providing a “description” that states in words characters that are purported to differentiate the taxon, Art. 13.1.1 is to instead provide a “definition”.

So, consider the following example of a published work attempting to establish two new species-group names:

Aus bus, n.sp.

Diagnosis: Consensus barcode: “AGTCAGTC…[etc.]”

Aus cus, n.sp.

Diagnosis: Consensus barcode: “AGTCAGTT…[etc.]”

In the above two treatments, I would interpret “Consensus barcode” as a character, and the sequences themselves (AGTC…etc.) as the character state. Or, alternatively, one could argue that each position in the sequence is a different character, and one of “A”, “G”, “T”, C” would represent the possible character states.

I’m fairly persuaded that the requirement of “in words” is met in these examples. One might be able to argue that neither represents a “description”, but I believe that legitimate argument can be made that a “definition” (sensu Code glossary) has been provided.

But I think the real ambiguity is, how much is required in order to be interpreted as “purported to differentiate the taxon”?  If the above example included a statement somewhere in the published work, “the consensus barcode values for these two species are different from each other” – is that enough?  Or is that even necessary – could it be self-evident that the presentation of the two sequences are different, and as presented therefore purport to differentiate the taxon?  Or, would the statement need to explicitly say “Aus bus can be differentiated from Aus cus on the basis of different barcode sequences”?  Or maybe even that would not be enough – perhaps the statement would need to explicitly say “the consensus barcode of Aus bus differs from that of Aus cus in positions 8, x, x, [etc.]”?  Or maybe even that is not enough – perhaps the statement would need to be “the consensus barcode of Aus bus differs from that of Aus cus in that position 8 of the former is C, and the latter is T [etc.]”?  Or, maybe even that is not enough, and the only way for Art. 13.1.1 to be fulfilled would be to compare consensus barcodes for every other known species in the genus?

Anyone who claims to have the “right” answer in the sense of the ICZN Code reveals a misunderstanding of the Code.  There is no “right” answer, because the word “purport” is not defined in the Code.  How explicit does a statement need to be in order to “purport” to differentiate a new taxon?  Moreover, does it require a comparison with specific other taxa (e.g., “Aus bus differs from Aus cus…”), or is it sufficient to say “Aus bus differs from all other known taxa…”?  Or is such an explicit statement not even necessary, because it’s clearly implied?

I think we have two challenges in dealing with this in the next Edition to the Code:

   - Deciding what the rule should be; and
   - Crafting language that unambiguously articulates that rule.

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: iczn-list <iczn-list-bounces at afriherp.org> On Behalf Of Francisco Welter-

> Schultes

> Sent: Friday, February 12, 2021 4:19 PM

> To: Stephen Thorpe <stephen_thorpe at yahoo.co.nz>; iczn-list at afriherp.org

> Subject: Re: [iczn-list] GENERAL CALL TO BATTLE

> 

> Stephen,

> I did not say more than that the definition for the term "description"

> should not be contained in Art. 13.1.1, but in the Glossary. This action as such

> would not change the content.

> 

> A description in the sense of a description of a new zoological nominal taxon is

> a differential description. Saying "the new elephant species is grey" is not a

> description in this sense, because previously described elephant species are

> also known to be grey, this would not distinguish the taxon. A statement "the

> new elephant species is pink" is a description in this sense because taxonomists

> with expertise in the concerned group will know that all previously described

> elephant species were not pink, this would be the first one known.

> 

> The Code cannot demand "that the description actually does differentiate the

> species adequately". The Code can only demand the presence of such a

> description. The content of the description is taxonomy. The attribute

> "differential" must be judged by the community. Names with insufficient

> descriptions - if subsequent authors provide evidence for it - are not available.

> 

> The splitter (actually any zoologist who discovers cryptic species, distinguished

> only by DNA) has indeed a problem. Usually they would discover cryptic

> species in the DNA record and then look again more closely on the taxa and

> discover differences.

> 

> There will be a public review period of one year where comments to the

> Code-5 draft and suggestions for improvements will be solicited.

> 

> Cheers

> Francisco

> 

> Am 13.02.2021 um 01:32 schrieb Stephen Thorpe:

> >   Francisco,It is presumably obvious, but just in case, I feel that I must point

> out that the consequences would be disastrous if there were a requirement on

> the availability of names that the description actually does differentiate the

> species adequately! That would mean that for any species which a taxonomic

> splitter considers to be more than one species (based on "cryptic species

> complexes", for example), the existing name would be thereby rendered

> retrospectivelt unavailable!!Cheers,Stephen

> >      On Saturday, 13 February 2021, 01:04:33 pm NZDT, Francisco Welter-

> Schultes <fwelter at gwdg.de> wrote:

> >

> >   Just a short response to this thought expressed by Rich:

> >

> > Am 12.02.2021 um 19:27 schrieb Richard Pyle:

> >> I think you perfectly captured my own concern about Art. 13.1.1 in that, as

> currently written, it’s effectively toothless and empty.  I guess I would put it

> this way:  it is incredibly easy to fulfill this requirement in a taxonomically

> useless way, yet by some interpretations, it is also incredibly easy to fail this

> criterion while still providing and incredibly robust description of a new taxon.

> >>

> >>

> >>

> >> My feeling is that the next edition of the Code should either make this

> requirement much more specific and explicit, or abandon it entirely.

> >

> > This problem has been detected earlier in the course of the ongoing

> > work on the Code revision. The term "description" should be defined in

> > the Glossary, and in Art. 13.1.1 we would only need to say that a new

> > name needs a description. I we intend to retain that.

> >

> > This procedure would, of course, just forward the basic problem

> > discussed here to the definition in the Glossary.

> >

> > The term "purported" is not very well understood in the community. The

> > French Code (which is equivalent to the English Code) does not use

> > this term, there the Code just says "characters that allow to

> > differentiate the taxon". One of the objects of the Code revision is

> > to align the English and the French Code.

> >

> > Best wishes

> > Francisco

> > _______________________________________________

> > iczn-list mailing list

> > iczn-list at afriherp.org

> > http://list.afriherp.org/mailman/listinfo/iczn-list

> >

> >

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