[Taxacom] Does the species name have to change when it moves genus?

[Schindel, David]

This discussion is moving so fast and shifting topics so frequently that it's like trying to hop onto a runaway merry-go-round.



Going back to an earlier topic and connecting it to the discussion of lists...



As Rod and others said, a binomial can be viewed as:



1.       A name that is divided into two parts and concatenated to increase its usability as an indexing tool.  In this capacity it is a label or short-hand for the set of criteria that circumscribe a set of individuals that unite them as members of a coherent set (a species)

2.       A pair of names for two sets - a species name circumscribing a set of individuals as in #1, and a genus name linking the species to other species.  The linkage could be done with cladistic, phenetic, or homespun methods or using rules that no one really understands or believes.  The goal is to create a set of sets that belong together for reasons best (or only) understood by the author and like-minded bystanders.



I've always had a hard time figuring out what a genus is to  Nature, and until we have some consensus then these competing and unregulated usages will produce instability and ambiguity.  Even if two specialists agree on a species under usage 1, they could differ on purely philosophical grounds about #2 which leads to instability.  I understand that Codes are about nomenclature, not taxonomy.  Can any of us imagine a system or laws or patents that considers only form without content?  It adds new meaning to the term 'unresolvable'.



The problem with 'authoritative' lists is that they're meant to provide clean resolution to a very messy reality.  Is the following approach and semantic notation helpful to users (as Rod and all of us would like) but more realistic in light of the way taxonomy is really done?  It focuses on names in the context of publications that act on those names.  Names would appear in print but be linked to underlying publications via dois.  Rather than having an authoritative list, we would have a set of semantic relationships among articles that propose different meanings for a  name, or different names for the same meaning.



Author W describes a new species Aus bus using #1 meaning and possibly #2 meaning as well in an article 123 with a doi to find it).  Subsequently, someone publishes articles related to the new species name based on different interpretations of the name under one or both usages of the name:



A.      Revising the species such that Aus bus (sensu original author W) didn't use the right criteria for circumscribing the set.  This author has a nifty new character (like DNA barcodes - had to get that in somehow) and the new species/set has slightly different members.  In article 456 (different doi), Author X retains the name Aus bus (sensu Author X) but with a different meaning.  It's like styles in a word processor that are based on another style, but with a different font size.  A name resolver could provide the information that Doi(123) revised by doi(456) and Aus bus (sensu Author W) is not equivalent to Aus bus (sensu Author X).

B.      Same as A, but the author wants to propose Aus cus (sensu Author Y).  Different but overlapping set of set members, new name proposed in article 789.  Members of Aus cus overlapping but not equivalent to Aus bus, Doi(123) revised and renamed by doi(789).

C.      Author Z is fine with the species concept in doi(123) but thinks it belongs in genus D, so doi(999) proposes Dus bus.  So the members of doi(999) = members of doi(123) but doi(123) reclassified by doi(999).



Ideally, you could start with a doi or a name and trace where it goes.  It's not pretty but it reflects the way the taxonomy business is conducted.  How close is this to the functionality envisioned for the Global Names Architecture?



David



-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Roderic Page
Sent: Wednesday, June 20, 2012 4:24 AM
To: TAXACOM
Subject: Re: [Taxacom] Does the species name have to change when it moves genus?



Dear Rich,



Thanks for the insightful response. I agree that we are in a transitional period (from analogue to digital), and things will be messy for a while (as we can see by looking at what's happened as the music, newspaper, and movie industries have struggled with this transition). Of course, I want things to go much faster, in part because I'm not convinced that the rest of biology will hang around patiently waiting while taxonomy makes this transition.



As William Gibson wrote "the future is already here - it's just not very evenly distributed" http://en.wikiquote.org/wiki/William_Gibson ZooKeys is one vision of the future, and it's a great journal, it's just a tiny fraction of the current taxonomic output.  In 2010 ION recorded around 18,000 new names, of which a little over 400 were published in ZooKeys. The widely distributed nature of taxonomic publishing means that even the dominant journal (Zootaxa) publishes only 15-20% of all new names. That means there's a lot of publishers to convince to move to new ways of publishing (e.g., XML markup). If we're publishing ~20,000 animal names a year, and the rate of new species description has been relatively constant over the last few years, we still have 50 years to go to double the number of animal names we already have.



You ask



> Why

> not focus on the brave new world of electronic publication, where the

> included information is not limited to what is seen by the human

> eyeballs, and where all this stuff can be harvested seamlessly via

> unambiguous GUIDs (rather than via crude OCR and fuzzy text matching

> of messy text-string names)?  To me, that's where the answer lies going forward.



Partly because the new stuff is relatively easy, in the sense that marked up XML is straightforward to generate and work with (where's the fun in that?), and partly because once the new stuff is marked up, we still have the question "what does it link to?" If I click on a name, I want to see everything about that name, not just the most recent literature. If an article cites a paper that is only available in a digital library like BHL, I want to have a link to that. If the user clicks on that link, I want them to be able to view the BHL content in much the same way as the more recent literature (i.e., names and literature cited also clickable). Our legacy literature will vastly outweigh the newly generated, nicely marked up literature for a while yet.





>> I'm not proposing a change in how we cite names,

>

> Yes, you are.  Since Linnaeus, we have cite species names in the form

> of a species epithet preceded by a genus name, and the genus name is

> selected to reflect the classification of the epithet.  You're

> proposing that we strip the classification information from the

> binomial, and treat it as though it's a single text string that

> happens to include a space within it.  That's a change in how we cite

> names.  Maybe we're operating on different definitions of the word "cite"?





I suspect we are. To me, if I write "Homo sapiens" that's the name. I gather you are saying that actually the name is "sapiens" which I'm citing in the context of the genus "Homo" to indicate its classification. That may well be, but I'd argue it's not how most biologists treat names in practice (i.e., as simple text strings to refer to a taxon).



>

> So in that context

> (if you really believe that's where it's heading), why try to change

> one of the core principles of binomial nomenclature right at the

> twilight of its tenure in science?



That's a very good question.



Regards



Rod



On 19 Jun 2012, at 21:02, Richard Pyle wrote:



>> I'm not actually suggesting we change the code, merely the convention

>> to automatically  change the genus name if a species moves.

>

> I never said anything about changing the Code.  I was talking about

> 250 years of conventional practice.

>

>> Trivial in the sense that if we had all the information on names

>> (synonyms included) linked to types we could resolve synonyms

>> computationally, but we don't, certainly not at the scale of the

>> 10x5 - 10x6 names that databases such as NCBI taxonomy and GBIF deal

>> with. Yes, in principle, it is tractable, but why do we contribute to

>> creating the situation in the first place?

>

> The "situation" is only as such because of the advent of computer systems.

> Prior to computers, people had no issue with it.  Now that we have

> technology that lets us mine vast volumes of historical literature,

> the situation appears problematic because we are now doing at a much

> larger scale something that hasn't really been done before, other than

> by Sherborn, Neave, Linneaus, and a few others.

>

> I've always maintained that this period in history -- starting in the

> mid- to late 1990s and ending probably around 2020-2025 -- is a

> somewhat awkward one because it represents the transition between a

> centuries-long era when paper was the primary mode of information

> dissemination and documentation among humans, and the era when

> information is mostly documented and disseminated via electronic

> signals.  It's awkward in general because not all systems are moving

> in parallel and at the same pace, so various systems get out of phase

> (e.g., the desire by modern taxonomists to publishe new scientific

> names in electronic journals, vs. -- until recently -- the

> requirements of the various Codes).  Specific to this topic, the

> awkwardness relates to the fact that we have computer systems that

> index large numbers of taxonomic name-strings (messy things, that

> don't always make it clear which binomials are homotypic), but don't

> yet have computer systems that index large numbers of taxonomic name

> "objects" (where homotypic binomials are easily identified -- plus much, much more).  By about 2050 or so, this period of awkwardness will warrant only a footnote.

>

>> Personally I suspect the taxon concept issue isn't going to be worth

>> the effort expended, unless tackled with some clever tools for

>> inferring context from citation, etc. it's simply unscalable.

>

> I'm not so sure about that.  Consider that we're rapidly shifting from

> paper-based publication to electronic publication.  To make a major

> change in practice in how we render text strings to human eyeballs

> (i.e., your proposal to stop changing binomial combinations so we can

> maintain more stable text-string labels) seems like using a Ferrari to

> drive down the block to the local grocery store a little faster than

> the Toyota used to get us there.  I imagine a world (not hard to

> imagine, really -- given journals like ZooKeys) where the text string

> name is something just to render on the computer monitor for the

> benefit of human eyeballs.  Behind that text-string name would be the

> necessary electronic link (or links) to the taxonomic object, complete

> with all the metadata any taxonomist would ever want (type specimens,

> concept definitions, literature citations, historical trends in usages, etc., etc., etc.).

>

> You're talking about changing how we do things going forward, right?

> Why not focus on the brave new world of electronic publication, where

> the included information is not limited to what is seen by the human

> eyeballs, and where all this stuff can be harvested seamlessly via

> unambiguous GUIDs (rather than via crude OCR and fuzzy text matching

> of messy text-string names)?  To me, that's where the answer lies

> going forward.  Not putting a band-aid on a centuries-old practice

> that is still trying to use text-string names as unique identifiers.

>

>> Why not focus on what is tractable and will add immediate value?

>

> It would appear that you and I have different ideas about what is

> tractable (or maybe we define the word differently?)

>

>> I'm not proposing a change in how we cite names,

>

> Yes, you are.  Since Linnaeus, we have cite species names in the form

> of a species epithet preceded by a genus name, and the genus name is

> selected to reflect the classification of the epithet.  You're

> proposing that we strip the classification information from the

> binomial, and treat it as though it's a single text string that

> happens to include a space within it.  That's a change in how we cite

> names.  Maybe we're operating on different definitions of the word "cite"?

>

>> and suggestions that embed more semantics in names (such as author,

>> date,

> first name)

>> are just asking for trouble http://bit.ly/KQ6o46

>

> Perhaps.  But why not instead leverage the move towards electronically

> published works by embedding GUIDs (which are themselves hidden from

> human eyeballs), rather than continue to overload the feeble text

> string with more information than it's capable of representing?

>

>> Citing a reference for "what I mean by" is useful, but I'd be happier

>> if that was linked to actual data.

>

> We're in agreement on this one -- the key word being "linked".

>

>> Ironically, if you read the tea leaves the way I do, we are moving to

>> a biodiversity science without names, where specimens will be the

>> unit of choice, and taxa will be computational inferences, not vague

>> assertions supported by a citation at best. But that's another

>> story...

>

> ...and I wouldn't necessarily disagree with that story.  So in that

> context (if you really believe that's where it's heading), why try to

> change one of the core principles of binomial nomenclature right at

> the twilight of its tenure in science?

>

> Aloha,

> Rich

>

>

> Richard L. Pyle, PhD

> Database Coordinator for Natural Sciences Associate Zoologist in

> Ichthyology Dive Safety Officer Department of Natural Sciences, Bishop

> Museum

> 1525 Bernice St., Honolulu, HI 96817

> Ph: (808)848-4115, Fax: (808)847-8252

> email: deepreef at bishopmuseum.org<mailto:deepreef at bishopmuseum.org>

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

>

> Note: This disclaimer formally apologizes for the disclaimer below,

> over which I have no control.

>

>

>

>

> This message is only intended for the addressee named above.  Its contents may be privileged or otherwise protected.  Any unauthorized use, disclosure or copying of this message or its contents is prohibited.  If you have received this message by mistake, please notify us immediately by reply mail or by collect telephone call.  Any personal opinions expressed in this message do not necessarily represent the views of the Bishop Museum.

>



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

Roderic Page

Professor of Taxonomy

Institute of Biodiversity, Animal Health and Comparative Medicine College of Medical, Veterinary and Life Sciences Graham Kerr Building University of Glasgow Glasgow G12 8QQ, UK



Email: r.page at bio.gla.ac.uk<mailto:r.page at bio.gla.ac.uk>

Tel: +44 141 330 4778

Fax: +44 141 330 2792

Skype: rdmpage

AIM: rodpage1962 at aim.com<mailto:rodpage1962 at aim.com>

Facebook: http://www.facebook.com/profile.php?id=1112517192

Twitter: http://twitter.com/rdmpage

Blog: http://iphylo.blogspot.com

Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html



_______________________________________________



Taxacom Mailing List

Taxacom at mailman.nhm.ku.edu<mailto:Taxacom at mailman.nhm.ku.edu>

http://mailman.nhm.ku.edu/mailman/listinfo/taxacom



The Taxacom archive going back to 1992 may be searched with either of these methods:



(1) by visiting http://taxacom.markmail.org



(2) a Google search specified as:  site:mailman.nhm.ku.edu/pipermail/taxacom  your search terms here