Taxacom: demystifying gender agreement ( was Re: Removals of offending scientific names)

Sun Jun 25 02:34:18 CDT 2023

 Rich,At least you are not feeling as much pressure as Stockton Rush! :)You seem to be saying that given enough funding, all problems can be solved. Maybe so, but I'm still wondering how exactly (or even roughly) you intend to validate hundreds of thousands of names. I can sort of see how new names might be handled, but all the historical names are something else entirely. I can sort of see how it might be achieved in a glacially slow bit by bit manner, but what is a realistic timeframe for all historical names to have a unique validated record on Zoobank, or indeed on any database, either online or offline? Ten years, a hundred years, ...? Here in New Zealand, we have this online database called NZOR, which is supposed to be the comprehensive and authoritative database of the N.Z. biota (which is quite small, by global standards), but even it has not only a small but not insignificant amount of errors and omissions, but they can't even seem to keep the functionality of the site working properly, so, for a while now, you can't search for species directly, only genera and then try to find the species you want in the list, which is a pain for big genera like Sagola with over 140 species! My attempts to report the problem have gained no reply. Searches also return results that are near in spelling to the search request, with no easy way to filter out the near misses.Stephen
    On Sunday, 25 June 2023 at 04:00:20 pm NZST, Richard Pyle via Taxacom <taxacom at lists.ku.edu> wrote:  

 I'm just catching up on the Taxacom postings from the past couple of weeks, and just now reading this particular thread.  And...YIKES...I'm definitely feeling the pressure to chime in!

So, first of all, before I address some of the ZooBank and related stuff, I want to say that I wholeheartedly support Doug Yanega's approach to this!  He and I (and, of course, other ICZN Commissioners) have been involved with some pretty intense discussions within the Commission on how to address the gender agreement rules as we continue to draft Code-5.  Note the word "draft"!  The onus is on the Commission (and, specifically, the Code-5 editorial Committee, *superbly* led by Francisco Welter-Schultes) to craft a DRAFT version of Code-5, but that DRAFT then goes out to the public/community for a minimum of one year, and there will be AMPLE opportunity to discuss these things publicly in that context.  As I hope most commentators will come to understand, one of the mantras of the Code (which I first heard expressed by former ICZN Commissioner Philippe Bouchet) is: "the devil hides in the details".  It's super easy to make lofty proclamations about what the Code should or shouldn't do, but it's a LOT harder to "codify" those ideas into actual rules in the Code in such a way that they do not create more problems than they solve.  Even small changes in wording can have a profound impact on how the rules are interpreted; major changes are considerably more challenging (remember: the main function is nomenclatural stability -- a concept which itself is open to a fair bit of interpretation).

But I digress...

The key point here is that within Zoological Nomenclature, we are entering an era of significant potential for change -- and the priority of that change is focuses on simplifying the rules and associated process, minimizing ambiguity, and, a always ana above all, promoting nomenclatural stability.  These are exciting times for zoological name-nerds!

In this broader context (which I'll leverage below);

> So maybe we can now await input from Rich Pyle from the viewpoint of
> ZooBank/GNUB, etc...

My personal feeling about how to deal with the gender agreement has shifted back and forth over the past few years.  I've actually swung from one end of the spectrum of viewpoints to the other, and I have come to understand that there are legitimate arguments being made on both extremes (and, of course, at various points in the middle as well).  I am thoroughly convinced that there is no "right" answer -- it's all a matter of costs & benefits, and different people in different situations assess the magnitudes of those costs and benefits differently.  The only people who are clearly "wrong" in this discussion are the ones who think there is only one obvious correct answer.  But that doesn't mean there aren't pathways that optimize the cost-benefit ratio, and as I said above, the basic concept that Doug described is the best such optimization (and articulation thereof) that I am aware of.

As for the role of ZooBank, I'll quote Stephen:

> Of course, Rich might have some major changes to ZooBank infrastrucure in the pipeline taht 
> I don't know about, but, as it is, I don't think ZooBank is really fit for the task of a 
> comprehensive source of reliable data on ICZN compliant genera.

Stephen is 100% correct that ZooBank, as it currently exists, is in absolutely no position to fulfill the dream as articulated by Doug (nor multiple other dreams connected with the utopian promise of a centralized online registration system for zoological nomenclature).  That was pretty obvious back in 2008 when the first ("unofficial") version of ZooBank was launched, and it was even more obvious in 2012 when the second ("official"; informally known as "ZooBank 2.0") version was launched. There are a couple of reasons why this was so obvious.  The first was, no one really knew how the community would react to online registration of works and names/nomenclatural acts.  There was an intentional conflation of introducing mandatory registration and electronic publication within the same Amendment to the Code -- as an effort to encourage people to get engaged.  Even back then, most of us on the Commission knew that ZooBank was largely an experiment -- a prototype, of sorts -- from which we would learn what the community wanted/needed.  Its real purpose was to lay a foundation for the "real" version of ZooBank, which would be developed in conjunction with the next (fifth) edition of the Code. There is a long and detailed history to this, which I won't go into now, but would be happy to share with anyone who is interested.  

The most shocking aspect of ZooBank (to me, anyway) is how few problems there have been.  Don't get me wrong: anyone who uses ZooBank knows there are PLENTY of problems (no one understands this as well as I do -- I promise!!)  But it's also important to understand, that I had expected/predicted FAR more serious problems -- so much so that I was genuinely concerned that it might fail so catastrophically as to set back the very concept of online registration for zoological nomenclature for decades.  If you follow the statistics (https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fzoobank.org%2Fstatistics&data=05%7C01%7Ctaxacom%40lists.ku.edu%7Ce9b9cf93556b455de9ca08db754e98dc%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638232752681206502%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=FYtwS4vct87NcFCkPh6xG8GTebvD1dBqasRlFDNlZlQ%3D&reserved=0), you can look back over time to see that it has remained pretty consistently active (and even growing).

But one key thing to keep in mind is the other reason ZooBank currently has the limitations it does: funding.  Version 1.0 was built as a labor of love on weekends and evenings (and with a bit of support from NBII and GBIF), as an offshoot of one of the chapters of my PhD dissertation.  Version 2.0 (the current and first "official" version) was built with support from two separate projects funded by the U.S. National Science Foundation (NSF).  ZooBank continues to function mostly because Bishop Museum has been extremely generous in supporting it through IT infrastructure, and I continue to spend a lot of my weekends and evenings doing what I can to maintain it (with sincere apologies to those who have to sometimes wait a week or more before I reply to their emails...)

This all leads me to the other part of Stephen's quote above:  "Rich might have some major changes to ZooBank infrastrucure in the pipeline..."  Rich does indeed have some major changes in the pipeline!  As some of you already know, over the course of this (northern) summer, I am slowly putting together a proposal to U.S. NSF to develop the next generation of ZooBank.  I have a VERY clear idea in my head what that proposal will look like, but I need to spend some quiet time over the next couple of months to write down a first draft.  I've already had some preliminary discussions with a few people, but the real discussions will take place later this year.  Suffice it to say that it will not only address all of the issue Stephen correctly articulated, but also a bunch more that he didn't mention (including support for many aspects of what Doug described for a gender agreement solution).  And, perhaps most significantly, it will be very deliberately focused on creating a rock-solid infrastructure and foundation for Code-5.

I'm not going to make any promises for the timeline, and obviously a lot depends on whether we get the funding.  But I'm cautiously optimistic that, one way or another, we will find the funding we need, and we will be able to have a public release in time for people to start using it at the time that Code-5 is out for public review and commentary.

Ok... I just spent way more time writing that overly-long message than I had intended to when I started writing it.  Apologies to everyone who trudged all the way through to the end here.  I think I'll shut-up now, but will gladly entertain any questions. But otherwise, I'll simply advise: "watch this space".

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
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> -----Original Message-----
> From: Taxacom <taxacom-bounces at lists.ku.edu> On Behalf Of Tony Rees via
> Taxacom
> Sent: Thursday, June 22, 2023 4:46 PM
> To: Douglas Yanega <dyanega at gmail.com>
> Cc: taxacom at lists.ku.edu
> Subject: Re: Taxacom: demystifying gender agreement ( was Re: Removals of
> offending scientific names)
> 
> Doug Yanega wrote:
> 
> > we are actually not
> >  that far from being able to compile a master list of the genders of all
> >  available genus names - uBio alone has an almost complete list, for
> >  example, though lacking gender designations.
> 
> As I understand it, that was indeed uBio's original vision (see David Patterson,
> "Progressing towards a biological names register", 2003,
> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.nature.com%2Farticles%2F422661a&data=05%7C01%7Ctaxacom%40lists.ku.edu%7Ce9b9cf93556b455de9ca08db754e98dc%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638232752681206502%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=7UgAgUm4XiEaKuhgpjpnzZtMGBPj%2BKr1CKykdaZNAes%3D&reserved=0 ), but like many such projects it
> seems to have foundered in the early 2010s or so for the usual reasons
> (departure of key principals, cessation of funding or institutional support, etc.
> etc.). Also to my knowledge, the uBio Namebank data compilation never did
> really grapple with the issue of deduplication (i.e., multiple namestrings per
> actual taxon "name" depending on the source/s used for data acquisition) and
> in addition may have contained a mix of "clean"
> and "dirty" data (literature misspellings, etc.)
> 
> Meanwhile as some may know, I have had an interest in "all genera index[es]"
> for some time, indeed have been constructing such a resource since 2006 or
> thereabouts, the Interim Register of Marine and Nonmarine Genera, see
> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.irmng.org%2F&data=05%7C01%7Ctaxacom%40lists.ku.edu%7Ce9b9cf93556b455de9ca08db754e98dc%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638232752681206502%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Jb4k6PL8MtvcoecwZOu6UxWeDXgMaWjRXOmZsBA%2FSvo%3D&reserved=0 ... "my" compendium being fairly complete (see 2020
> Megataxa paper entitled "All Genera of the World...") but not an officially
> sanctioned or scrutinized registry of any king. On the other hand ZooBank
> and/or GNUB, the Global Naes Usage Bank, is set up to provide such an
> "official" function so could form the basis of what you envisage, provided it
> were populated to similar degree with relevant genus level content.
> 
> So maybe we can now await input from Rich Pyle from the viewpoint of
> ZooBank/GNUB, etc...
> 
> Regards - Tony
> 
> Tony Rees, New South Wales, Australia
> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fabout.me%2FTonyRees&data=05%7C01%7Ctaxacom%40lists.ku.edu%7Ce9b9cf93556b455de9ca08db754e98dc%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638232752681206502%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=EWOksdV%2B5IfSX4DiaD%2BfT140vfc99kROQ2abEe4qJaQ%3D&reserved=0
> 
> 
> On Fri, 23 Jun 2023 at 07:32, Douglas Yanega via Taxacom <
> taxacom at lists.ku.edu> wrote:
> 
> > I'm back from lunch and have a little more time to respond to George
> > Beccaloni's comment that adhering to gender agreement rules is
> > "irritating".
> >
> > First, I actually agree - but only to a point, and only in a certain
> > context.
> >
> > That context is one which would seem to be what George was describing;
> > one in which an individual taxonomist, operating solely with their own
> > "at hand" resources to guide them, is confronted with a situation
> > where the only way forward is for them to PERSONALLY decide which
> > species names must be changed, and how to change them.
> >
> > In that very specific context, I *absolutely* agree that adhering to
> > gender agreement is not just irritating, but a time-consuming burden,
> > potentially necessitating deep dives into obscure grammatical and
> > linguistic "rabbit holes", and sometimes not even leading to clear and
> > objective answers. This is a terrible and unfair burden for
> > taxonomists, who generally have better things they can be doing with their
> time.
> >
> > That being said, the difficulty is - as I noted before - not something
> > INHERENT in gender agreement. The problem is the concept that every
> > taxonomist has to make these decisions, and do the research, and worry
> > about linguistics, BY THEMSELVES. It does not need to be this way, and
> > I feel it SHOULD not be this way. We can do better, and make it so the
> > process is no longer irritating.
> >
> > There are two things that can free individual taxonomists from the
> > irritation and burden of complying with gender agreement while *still
> > allowing* gender agreement to continue as a practice - a practice
> > which is, in fact, essential to nomenclatural stability.
> >
> > (1) The first thing is, as I said, designing our digital
> > taxonomic/nomenclatural resources so they are "intelligent" enough to
> > be able to perform *one* *incredibly simple task*: matching a gender
> > entry in one field (a genus-linked field) with another gender entry in
> > an "alternative spelling of species name" field. Basically, if the
> > genus entry is listed as "Feminine", e.g., then it links to and
> > displays the "Feminine" spelling variant for any species name linked to that
> genus.
> > We *can* do this, and there are a number of existing resources that
> > *already* do. That's the *easy* part to demystify.
> >
> > (2) The second thing comes naturally to most people's minds when they
> > are told they could automate gender agreement: "That doesn't tell me
> > which names to enter in the database as having variable spellings, and
> > which names only can ever have one spelling, nor does it tell me which
> > genus names are which genders." This is a more significant issue, and
> > I freely admit that an actual solution is not going to be simple.
> > However, a solution is possible, and I think it is highly desirable,
> > and maybe even necessary. Namely, we create two resources: a single
> > master registry of all available genus-rank names *that includes their
> > genders *(as established by the rules in the Code), plus a single
> > standard adjectival lexicon that indicates which species names (or
> > name suffixes) are ALWAYS adjectival with variant spellings, and which
> > names are in the very small subset that can be *either* nouns or
> > adjectives depending on whether the coining author explicitly
> > specified the etymology (with, for each such name, an appropriate
> > default). Any name *not* listed in the lexicon would be treated as having
> invariant spelling.
> >
> > The rationale for having a single master registry of genus names is to
> > prevent disputes and debates and - most importantly - redundancy of
> > effort. There is no reason for hundreds of taxonomists to have to
> > independently research the gender of a genus name. The sensible thing
> > to do is to compile a list from existing resources, and have a small
> > group of Code-conversant people review all of the disputable names on
> > the list, and resolve all those disputes permanently. Make the list
> > public, and permanent.
> >
> > The rationale for a single standard lexicon is basically the same: to
> > put an end to confusion, indecision, and controversy, as well as
> > redundancy of effort. For example, in Latin, the word "alba" is both a
> > noun and an adjective, but in the history of nomenclature, it has only
> > ever been used as an adjective (to my knowledge). This should not be
> > subject to debate or revisionism: "alba", "albus", and "album" should
> > all be treated as adjectives EVEN IF the coining author happened, by
> > some miracle, to have explicitly stated otherwise. Otherwise, things
> > would be too confusing, given how common these epithets are in both
> > plants and animals. This decision should only need to be made once,
> > not subject to "second-guessing", and made fully public and adhered to
> > by all taxonomists. It's a burden for an individual taxonomist to have
> > to look through two books and five online resources to figure out
> > whether "alba" is a noun or an adjective, but it's trivial if they
> > only need to look at a SINGLE resource, type in the name "alba", and
> > be told
> > *unambiguously* that for nomenclature it is an adjective, and ONLY an
> > adjective, AND what the alternative spellings are.
> >
> > The important point I would like to make, for those of you who are
> > rolling your eyes or shaking your heads, is that we are actually not
> > that far from being able to compile a master list of the genders of
> > all available genus names - uBio alone has an almost complete list,
> > for example, though lacking gender designations - and the number of
> > disputable cases is a very small subset of that total, so assigning
> > each genus name a definitive *and irrevocable* gender is entirely feasible.
> > The overwhelming majority of genus names are unambiguously assignable
> > under the Code. We are, admittedly, not as close to having a list of
> > all existing adjectival species names, but there *are* exhaustive
> > digital lexicons of Latin and Greek adjectives that could be adapted
> > to our needs. The subset of those terms that are disputable under the
> > Code is perhaps a bit larger, but still not entirely unmanageable.
> > I've spent over 10 years going over the names of insects, and out of
> > over 200,000 valid insect species-rank names, only about 8% are
> > disputable, and a
> > *very* high percentage of those are duplicates (e.g., 1100 of the
> > 16000 disputable names I have recorded are those ending in "-cola",
> > "-colus", or "-colum"). So, even this particular task, of an "official
> > list" of species names, is attainable.
> >
> > The bottom line is that I would ask people to reconsider their
> > opposition to gender agreement, if the only reasons you oppose it are
> > the issues that would be resolved by having access to the resources
> > described above.
> >
> > Specifically, if the scenario I describe were to become reality -
> > having smarter databases, and being provided with official lists - are
> > there people here who would *still* advocate that we reject gender
> agreement?
> > If so, why?
> >
> > Sincerely,
> >
> > --
> > Doug Yanega      Dept. of Entomology      Entomology Research Museum
> > Univ. of California, Riverside, CA 92521-0314    skype: dyanega
> > phone: (951) 827-4315 (disclaimer: opinions are mine, not UCR's)
> >              https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Ffaculty.ucr.edu%2F~heraty%2Fyanega.html&data=05%7C01%7Ctaxacom%40lists.ku.edu%7Ce9b9cf93556b455de9ca08db754e98dc%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638232752681206502%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=wjCoIkoSYl1YGoPJlbkgGuQqvSvbzfWwcNblu7OXG2Q%3D&reserved=0
> >    "There are some enterprises in which a careful disorderliness
> >          is the true method" - Herman Melville, Moby Dick, Chap. 82
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> > Nurturing nuance while assailing ambiguity and admiring alliteration
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Nurturing nuance while assailing ambiguity and admiring alliteration for about 36 years, 1987-2023.