[Taxacom] OMG! DNA only descriptions (with one habitus photo)!

Francisco Welter-Schultes fwelter at gwdg.de
Thu Aug 1 04:40:46 CDT 2019


 > "515" and "648" are numbers
Numbers are also words. 515 is a number, in the same way as an apple is 
a fruit. You can employ words for numbers and for fruits. We can also 
write five hundred fifteen, which we can call three words, or if you 
like it to be one word, fünfhundertfünfzehn.

A "word" can either be a spoken word or a written word. The Code 
Glossary gives no definition as to the sense in which it is meant there.
One can publish a description in a script that uses only symbols, or 
drawings of flags, or photographs of people displaying sign language, 
the meaning of the term "word" in the Code can only be that of a spoken 
word, which represents an idea, a thought or a meaning, and consists of 
units of sound, or expressions of body signs, and which can be 
transformed with some standard conventions to a written form.

T may stand for thymine, or for threonine, or for Tyrannosaurus, 
whatever you like it to represent. The spoken word [ti:] is a word that 
in English language and in this context allows to deduce reliably the 
meaning of thymine.

5.7 cm is also a description in words. In English the words are 
pronounced five point seven centimeters.

Only if you write down something that has no decodable meaning, these 
would be no words and could not represent a description. Even if you 
might be able to pronounce it. It is the meaning that makes a 
description out of these words. "gaba" can ba a baby sound, in which 
case it is not a word because it has no meaning, or it can mean 
Gamma-Aminobutyric acid, in which case it has a meaning and can form 
part of a decription.
"[tu:]" can be a baby sound without meaning, so it is no word, or can be 
equipped with a meaning representing a number, and which can be spelled 
two or 2, in which case it is a word and can form part of a description.

"The" as such is a word, but standing alone such words have no meaning 
that could represent a description. A description is composed of several 
words, forming together a meaning. There are languages such as Quechua 
in which a senseful and complex description can even consist of one 
single word, which contains a combination of several meanings.

We also have that in English. "Bigger" is composed of several meanings, 
representing size, comparison, and reference to a subject of comparison. 
The term "words" in the Code is presented in the plural, but technically 
seen "bigger" is only one word. It would represent a description because 
of it composed nature. We could also write "more big", and then we would 
have two words, or, if we would cover the whole meaning of the statement 
including implicit unexpressed thoughts which are clear by context, 
"bigger in body size than the other species".

If this is really unclear we could add a brief definition for "word" in 
the Glossary in this sense.

Francisco


-----
Francisco Welter-Schultes

Am 29.07.2019 um 09:49 schrieb Thomas Pape via Taxacom:
>>> It is entirely ambiguous between symbol or abbreviation,
>>> so the availability of the work is entirely ambiguous.
>>> Such ambiguity requires a ruling one way or the other
> 
> First of all:
> We are not discussing the availability of the work, which is a different issue. The work appears to be available from its printed version.
> We are discussing the availability of the names in that work, and more specifically if a statement like: "Nucleotides 515 C, 648 T" will fulfill requirements for a description or definition under the current ICodeZN.
> 
> Generally:
> A complex legislation cannot avoid ambiguity. Other examples from the ICodeZN are the requirements that a work, to be regarded as published for the purposes of zoological nomenclature, "must be obtainable", when first issued, and must have been produced in an edition containing "simultaneously obtainable" copies by a method that assures "numerous identical and durable copies" -- or "widely accessible" electronic copies with "fixed content and layout".
> 
> Specifically:
> The issue here is whether, e.g., "Nucleotides 515 C, 648 T", can be considered "a description or definition that states in words characters that are purported to differentiate the taxon".
> There is no doubt that there is a purport to differentiate the taxon.
> Also, "Nucleotides" certainly is a word. "515" and "648" are numbers. "C" and "T" are letters, which can be considered abbreviations or symbols. An abbreviation as defined by the ICodeZN Glossary is "A shortened form of a word".
> 
> A statement like: "Length: 5.7 cm", containing one word, one decimal numeral and one symbol, when given with a purport to differentiate, in my opinion serves as "a description or definition".
> Whether or not such a descriptive statement is "of very dubious value taxonomically" is not an issue in this context.
> 
> /Thomas
> 
> -----Original Message-----
> From: Taxacom <taxacom-bounces at mailman.nhm.ku.edu> On Behalf Of Stephen Thorpe via Taxacom
> Sent: 28. juli 2019 03:46
> To: John Grehan <calabar.john at gmail.com>
> Cc: Taxacom(taxacom at mailman.nhm.ku.edu} <taxacom at mailman.nhm.ku.edu>
> Subject: Re: [Taxacom] OMG! DNA only descriptions (with one habitus photo)!
> 
>   But my "evidence" is fit with the facts. Theories in science and elsewhere are all "speculative" to some extent. They are simply ways of making sense of the facts. In this case, the facts are that Pape is pushing for a reinterpretation of an otherwise straightforward reading of a code article, such that "words", according to him, includes mere strings of symbols. There has been enough comments posted here, in addition my own, to suggest that the DNA-only approach in the work under discussion is not good for taxonomy, yet Pape is resisting straightforward attempts to demonstrate that it is not in fact code compliant! If that don't smell of politics, then I don't know what does!
> Stephen
>      On Sunday, 28 July 2019, 01:35:04 am UTC, John Grehan <calabar.john at gmail.com> wrote:
>   
>   Stephen,
> I don't see how read anything more than what you said. You may feel that your inferences about motives are accurate or fair, but unless backed up by actual evidence (e.g. a person admitting to these motives) then its all irrelevant. For example, years ago Tuxen turned down a paper for his journal and one might impute particular motives that were unrelated to the quality of the paper. As it turned out the editor did put in writing that the reason was his prejudice against Croizat (anything referencing Croizat's  work was not going to be published in that journal as long as he was editor).
> Whether or not decisions are good or not with respect to particular criteria is open for evaluation without considering speculative motives. That's all I am saying.
> John Grehan
> On Sat, Jul 27, 2019 at 9:00 PM Stephen Thorpe <stephen_thorpe at yahoo.co.nz> wrote:
> 
>   John,I think you may be reading too much into what I was trying to say. I was simply suggesting that, regarding the commission, the balance between keeping people happy and ensuring the stability and universality of zoological nomenclature is tilted a bit too much in favour of the former, in my opinion. That's all! As far as "imputing motives" go, it isn't particularly outlandish or suggesting anything shockingly untoward or nefarious. It is just not exactly ideal, that is all. My "evidence" is the way that Pape is reinterpreting the code in order to save this DNA only approach from being deemed non-code compliant. On any straightforward reading of the code, a string of symbols is not "words", but Pape is pushing the argument that T, for example, can be interpreted as an abbreviation (and therefore a word) for thymine, rather than as a symbol (and therefore not a word), and that if it can be so interpreted, then it should be so interpreted, even though the result is to uphold a work that is of very dubious value taxonomically. On the other hand, the commission is less inclined to protect the nomenclature of Ray Hoser, for example, which actually is clearly code compliant! So it seems that the commission is a bit of a "political wind sock".Cheers, Stephen
>      On Saturday, 27 July 2019, 11:00:20 pm UTC, John Grehan <calabar.john at gmail.com> wrote:
>   
>   Stephen, you often make some interesting and even pertinent points, whether or not I may always agree, but please leave out the garbage of imputing motives ( "as they will be more concerned with the politics of not getting off-side with any significant sector of the broadly taxonomic community") unless you have actual hard evidence. I have to put up with certain politicians using that tactic and I would rather not see it adopted in taxonomic discussion.
> John Grehan
> On Sat, Jul 27, 2019 at 6:40 PM Stephen Thorpe via Taxacom <taxacom at mailman.nhm.ku.edu> wrote:
> 
>   Thomas,I didn't say that T has to be interpreted as a symbol for thymine, just that it can reasonably be so interpreted, i.e. there is "wiggle room" to invalidate the work based on lack of descriptions/diagnoses in words. It is entirely ambiguous between symbol or abbreviation, so the availability of the work is entirely ambiguous. Such ambiguity requires a ruling one way or the other (if there is significant disagreement within the taxonomic community on this point, which there may or may not turn out to be). Also, I assume that the journal DEZ still prints hard copy, but if not then the work is unavailable e-only due to the lack of a specified archive on ZooBank.I comes as no surprise to me that the commission is prepared to allow this sort of DNA only pseudo-taxonomy, as they will be more concerned with the politics of not getting off-side with any significant sector of the broadly taxonomic community. Personally, I relegate to the rubbish bin any work which erects new taxa on the basis of*, e.g. "Many specimens of this species were originally identified as Zelomorpha arizonensis by MJS based on morphology. However, p-distances between Z. arizonensis and Z. angelsolisi are greater than 8%", and which fails to even mention a very relevant article from earlier in the year by the same authors, i.e. https://www.mapress.com/j/zt/article/view/zootaxa.4565.1.11Cheers,Stephen
> *The best approach here would have been to simply state that some morphologically indistinguishable specimens of Z. arizonensis have been found to have p-distances up to 8% different from others, which may indicate a cryptic species complex, requiring further research.
>      On Saturday, 27 July 2019, 07:20:39 pm UTC, Richard Zander via Taxacom <taxacom at mailman.nhm.ku.edu> wrote:
> 
>   Possibly SAMPLING is the key to resolving this problem. I've got a book on sampling that requires a huge number of samples to get a true idea of variation, but this is when nothing much is known about a group and the group the group is in.
> 
> We usually know enough to be able to describe a species from a single specimen if we know that related species have little variation, and by extension, so might the new one. Sampling then depends in part on context.
> 
> We sample taxa. Only the most dedicated monographer looks at every specimen. We sample to get a handle on the features of a species. What features? The ones important for other scientists, which nowadays means ecology, evolution, population biology, and the like. Barcoding is unhelpful. Describing in detail every species in a speciose group can be overkill.
> 
> In an era of existential calamity, in my opinion, we want good information to help us deal with evolvability, adaptation, and change of environment without collapse. Relentless taxonomy is useless without those who interpret our product. We need some sort of contract or deal with ecologists and environmentalists that makes the most of what we taxonomists can do in the next 50 years. 30 years? 20 years?
> 
> Take any speciose group. What trends or principles are involved in its evolution, what species die off and what are the correlates if any, what species generate biotypes and descendant species galore, what species are truly different...?  What are the questions you think might be asked of your area of expertise that might incrementally help humans make amends for their hubris? A good revision can provide abundant material for evolutionary and environmental theory. Have you any theories about evolution past and future in your group?
> 
> -------
> Richard H. Zander
> Missouri Botanical Garden – 4344 Shaw Blvd. – St. Louis – Missouri – 63110 – USA richard.zander at mobot.org Ofc: +1 314 577-0276 Web sites: http://www.mobot.org/plantscience/bfna/bfnamenu.htm and http://www.mobot.org/plantscience/resbot/
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