[Taxacom] (no subject)

John Grehan calabar.john at gmail.com
Sat Dec 19 09:26:55 CST 2020


Rich,

Thanks for the detailed scenario. From what I see you have shown that the
boundaries are real, just hard to decide which criterion to use for any
given case.

On Fri, Dec 18, 2020 at 2:40 PM Richard Pyle <deepreef at bishopmuseum.org>
wrote:

> OK, I’ll bite.
>
>
>
> Let’s pick something super basic – like maybe the isthmus joining North
> America and South America.  I’m a fish nerd, so I’ll use a marine example
> (but the same principles apply for terrestrial stuff).
>
>
>
> So we start with an open water pathway between the two Oceans on either
> side of what will eventually become the isthmus.  A single population of
> fish that routinely and freely exchange genes with each other via
> reproductive events exists across both ocean basins.  Any two individuals
> of opposite sex within the population could mate and yield healthy viable
> offspring.  By **any** definition, the population is a single species.
>
>
>
> Geologic conditions change, and the water bridge between the two oceans
> shrinks.  At some point in time, the land bridge is complete.  Shortly
> before that, the last larvae or adult “individual” ( :-) ) traversed from
> one ocean to the other, after which gene-flow between the two oceans fell
> to zero.  The day after that happens, did the two populations in the two
> separate oceans become distinct species?  I’m guessing most of us would
> agree they were not (yet) different species – they were two isolated
> populations of the same species.
>
>
>
> Time passes.  Lots of time passes.  Through genetic drift or founder
> effects or natural selection or whatever processes we want to conjure, gene
> frequencies among the populations in each of the two oceans diverge.  The
> extent to which the gene frequencies diverge is a function of time and gene
> flow.  With the nice, clean, geologic barrier between the two populations,
> we can safely assume gene-flow is zero. At what time/degree of
> gene-frequency divergence do we stop calling them the same species, and
> start calling them different species?  At the moment any measurable
> differences in gene frequencies across the two populations can be
> detected?  At the first sign of any phenotypic (aka morphological)
> difference?  At the point where the morphological difference between he two
> oceans is 100% (e.g., when the last individual with the spot on the fin on
> the Atlantic side has died, and the last individual lacking the spot on the
> fin on the Pacific side has died)?  At the point where viability of
> Atlantic-Pacific cross-bred individuals is lower than the average viability
> of Atlantic-Atlantic or Pacific-Pacific offspring?  At the point in time
> where reproduction between any two individuals on either side of the
> isthmus fails to yield any viable offspring?  There are gazillions of other
> points in time where I could declare that the moment has arrived when we
> should stop calling members of each of the two ocean populations the “same”
> species, and start calling them “different” species.  And, of course,
> different people would (reasonably) disagree on when that threshold has
> been crossed.
>
>
>
> So, my point is this:  even if populations can be split effectively
> instantaneously, evolution is a gradual process, and both opportunity and
> biochemical/genetic compatibility for gene exchange are not absolutes.  The
> transition between one species and two species cannot be easily
> pinpointed.  Therefore, there is always going to be (as Doug nicely noted),
> some “fuzziness” in the boundaries between two sister species.  Our
> nomenclatural system doesn’t accommodate this.  They either are, or are not
> distinct/same species.  So, yes, John, assuming enough time passes with
> zero gene-flow between the two Oceans, we can confidently expect the two
> populations to diverge, and to reflect this divergence through genetics,
> morphology and reproductive viability.  That’s definitely “natural”, and
> the resulting “taxa” exist independently of our (human) interpretation of
> them.  But once we start labelling taxa with names, we emphasize the
> boundaries between them.  And as I’ve hope I’ve illustrated, those
> boundaries are not so natural – they are more in the realm of artificial.
>
>
>
> Darwin said it best:
>
> “We must, however, in many cases, decide by a majority of naturalists, for
> few well-marked and well-known varieties can be named which have not been
> ranked as species by at least some competent judges.”
>
>
>
> We can certainly discuss the naturalness of phylogenies – especially when
> we represent them as tidy cladograms with clean bifurcations at nodes among
> the branches.  But I’ve rambled on enough already that I’ll save the
> dissection of that particular illusion for another rant.  But for now, at
> least, I hope I’ve adequately explained my deliberately cryptic and
> intentionally snarky remark that taxa may be “natural”, but the boundaries
> between them not so much.
>
>
>
> 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 <http://hbs.bishopmuseum.org/staff/pylerichard.html>
>
> *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:* John Grehan <calabar.john at gmail.com>
> *Sent:* Friday, December 18, 2020 9:04 AM
> *To:* Richard Pyle <deepreef at bishopmuseum.org>
> *Cc:* Kipling (Kip) W Will <kipwill at berkeley.edu>; Taxacom <
> taxacom at mailman.nhm.ku.edu>
> *Subject:* Re: [Taxacom] (no subject)
>
>
>
> Perhaps one can philosophically argue that taxa are natural while the
> boundaries between them are not. I'm not much of a philosopher so I cannot
> argue that. But there are cases of allopatric taxa having geographic
> boundaries corresponding to tectonic zones. This would seem to me to imply
> that the taxon boundary has some kind of natural existence or this would
> not be possible to recognize.
>
>
>
> On Fri, Dec 18, 2020 at 1:56 PM Richard Pyle <deepreef at bishopmuseum.org>
> wrote:
>
> I like Doug’s reply (I’m a closet physics nerd).  But I guess I would put
> it this way:
>
>
>
> Taxa are natural.  The boundaries between them are not.  Our nomenclature
> over-emphasizes the boundaries, so through our nomenclatural way of
> thinking about taxa, we also over-emphasize the boundaries.
>
>
>
> Aloha,
>
> Rich
>
>
>
> P.S. Kip:  I got a fair degree of bombardment off-list (not as bad as I
> was expecting).  Doug perfectly captured my reason for putting the scare
> quotes around “individual”:  if we can’t even define truly discrete units
> at the subatomic level, even atoms and molecules get hard to pin down.  And
> if we think of individual organisms as collections of atoms and molecules
> that (more or less) begin when a sperm fertilizes an egg (or replicated
> cells disconnect), and ends when … I don’t know… a heart stops beating or
> brain neurons stop firing or however we want to define “death” (more or
> less – and is a preserved dead specimen the same “individual” as it was
> when it was alive? How much of the matter comprising the living organism
> needs to decay and disperse before we stop thinking of it as the same
> “individual”?), then a whole lot of turnover happens between those two
> points in time.  By some metrics, I’m not the same individual now that I
> was when I started typing this email (some parts of my skin have
> undoubtedly found their way among the keys of my keyboard).  There is no
> spoon.
>
>
>
> 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 <http://hbs.bishopmuseum.org/staff/pylerichard.html>
>
> *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:* John Grehan <calabar.john at gmail.com>
> *Sent:* Friday, December 18, 2020 7:26 AM
> *To:* Kipling (Kip) W Will <kipwill at berkeley.edu>
> *Cc:* Richard Pyle <deepreef at bishopmuseum.org>; Taxacom <
> taxacom at mailman.nhm.ku.edu>
> *Subject:* Re: [Taxacom] (no subject)
>
>
>
> I do wonder about that assertion of taxa not being natural phenomena. What
> phenomena are 'natural'? If taxa are not natural phenomena and am not sure
> anything could qualify as it could be excluded by some
> philosophical argument or other. From a pragmatic point of view it seems
> interesting that the use of taxa can lead to
> empirically verifiable predictions of 'phenomena' that were not
> previously known. I refer to the famous case of the composite tectonic
> structure of North America which was first predicted from biogeography that
> used taxa, as then characterized, to identify a composite
> biogeography which was predicted to correspond to a composite geological
> origin - and this was later corroborated by geologists who also
> acknowledged that the biogeographers got to that discovery first. If all of
> this is just in the mind of humans then there would seem to be no science -
> just one delusion or another (and Trump did win the election of course).
>
>
>
> John Grehan
>
>
>
> On Fri, Dec 18, 2020 at 12:13 PM Kipling (Kip) W Will via Taxacom <
> taxacom at mailman.nhm.ku.edu> wrote:
>
> Hey Richard,
> I don't think we can let you put scare quotes around individual and leave
> there. You need to provide your definition of the term so you may be
> properly bombarded. :)
>
> Kip
>
>
> On Wed, Dec 9, 2020 at 4:24 PM Richard Pyle via Taxacom <
> taxacom at mailman.nhm.ku.edu> wrote:
>
> > > any opinions, especially most critical and provocative, are very
> > interesting.
> >
> > Biological taxa are not "natural phenomena" -- they only exist in the
> > minds of humans. Thus, there is no "thing" to which scientific names are
> > actually applied (except maybe neurological patterns inside human
> brains).
> > The only meaningful "individual" associated with scientific names is a
> type
> > specimen, but one could argue that even type specimens/individual
> organisms
> > have imprecise boundaries (and thus, again, ultimately exist as
> > "individuals" only through neurological patterns inside human brains).
> >
> > There is no spoon.
> >
> > Aloha,
> > Rich
> >
> > P.S. Provocative enough? (running for shelter to hide from the inevitable
> > bombardment to follow...)
> >
> > 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: Taxacom <taxacom-bounces at mailman.nhm.ku.edu> On Behalf Of igor
> > > pavlinov via Taxacom
> > > Sent: Wednesday, December 9, 2020 8:15 AM
> > > To: Richard Jensen <rjensen at saintmarys.edu>
> > > Cc: Taxacom <taxacom at mailman.nhm.ku.edu>
> > > Subject: Re: [Taxacom] (no subject)
> > >
> > >
> > > Well, Dick’s concern about “proper” and “true” names is seemingly based
> > on
> > > their nominalistic treatment. It’s ok as far as current professional
> > > nomenclature systems are discussed.
> > >
> > > My concern is about looking at the names from another,
> > natural-philosophical
> > > standpoint. Suppose, each particular natural phenomenon is a particular
> > > “thing”. Then, any its consideration as a “natural kind” or anything
> else
> > > “collective” becomes irrelevant: it is an “individual». So its calling
> > in a
> > > particular manner is its “proper name”, i.e., it is (logically) a
> > referentative and
> > > not an attributive name. So, natural-philosophically, to be “proper”,
> > its name
> > > is to be just the “true”.
> > >
> > > PS Actually, my concern is about historical roots of the current
> > nomenclature
> > > systems. This is because I’m going to write and publish a book on the
> > history
> > > and theory of nomenclature, so any opinions, especially most critical
> and
> > > provocative, are very interesting.
> > >
> > > Cheers, I
> > >
> > >
> > > - - -
> > > Igor Ya. Pavlinov, DrS
> > > Zoological Museum of Lomonosov Moscow State University ul. Bol'shaya
> > > Nikitskaya 6
> > > 125009 Moscow
> > > Russia
> > > http://zmmu.msu.ru/personal/pavlinov/pavlinov1.htm
> > > http://zmmu.msu.ru/personal/pavlinov/pavlinov_eng1.htm
> > >
> > >
> > > >Среда, 9 декабря 2020, 19:53 +03:00 от Richard Jensen
> > > <rjensen at saintmarys.edu>:
> > > >
> > > >Igor's bit of philosophy brings up a point I have made before:
> > > >scientific names are not "proper names" as the latter are generally
> > > understood.  The philosophers quoted were wrong with respect to proper
> > > names.  Proper names do not define anything; a thing and its proper
> name
> > are
> > > not the same; there are no true names for us to search for.  Proper
> names
> > > have few, if any, "rules" for their application and use.  In conducting
> > > genealogical research, I have found hundreds of individuals named Hans
> > > Christian Andersen and probably many more named, very simply, Jens
> > > Jensen.  The same holds for proper names of places: there are numerous
> > > counties, cities and towns (in the US) named Washington, or Madison -
> the
> > > people of each locality were free to choose whatever name they wished
> to
> > > use.  If I tell you that someone lives in Washington, what do you know
> > for
> > > sure?  Essentially, nothing.
> > > >
> > > >Our binomials are different.  They are (within the bounds of the
> > different
> > > codes) unique names that apply to specific entities recognized by
> > > taxonomists.  These names cannot be freely applied to other entities
> and
> > > these names have a very important quality not found in proper names -
> > they
> > > tell us a great deal about the "thing" bearing the name.  If you are
> > told that
> > > there is a plant in my backyard that is a representative of  Quercus
> > palustris
> > > Muenchh., you can immediately (if you are a reasonably knowledgeable
> > > botanist) provide a list of many characteristics of this plant, from
> > general
> > > features (e.g., life form, anatomy, physiology) down to "specific"
> > characters
> > > (e.g., size and shape of fruits, floral structure, leaf shape, etc.).
> > Our scientific
> > > names are not the same as proper names because they do define the
> "thing"
> > > bearing the name, they are unique, and they cannot be changed, except
> > > within the context of the appropriate code.  Proper names do not have
> > these
> > > qualities.
> > > >
> > > >Cheers,
> > > >
> > > >Dick
> > > >
> > > >
> > > >On Tue, Dec 8, 2020 at 11:11 PM igor pavlinov via Taxacom <
> > > taxacom at mailman.nhm.ku.edu > wrote:
> > > >
> > > >>With regard to the indigenous names, one serious issue is that they
> > are, in
> > > many cases, nature-philosophically sound. Actually, as Chuang Tzu
> said, a
> > > thing becomes what it is when named/called. According to Plato, a thing
> > and
> > > its name are the same, as far as express the same eidos. From this,
> > > Tournefort’s idea of by giving true names to God's creatures echoed
> > > subsequently by Linne with his “proper names”. Such a mysterious
> > attitude to
> > > the “true names” is evidently expressed, in many indigenous tribes, in
> a
> > > prohibition to use the names given to people at their born in everyday
> > life,
> > > which to be replace by respective “nick names” (the “vulgar names” of
> > Linne
> > > are analogies of the latter).
> > > >>Understanding of this seems to yield quite different accent in
> > consideration
> > > of an aspiration of people to “get back to roots” that agrees
> > fundamentally
> > > with Confucius’ call to “restore the true names”.
> > > >>However, this attitude contradicts fundamentally to the leading
> > principle of
> > > contemporary taxonomic nomenclature “a name is just a name” set by
> > > Adanson.
> > > >>All this, of course, a “philosophy”, but is helps sometime to see
> “the
> > other
> > > side of the Moon”
> > > >>Igor
> > > >>
> > > >>
> > > >>- - -
> > > >>Igor Ya. Pavlinov, DrS
> > > >>Zoological Museum of Lomonosov Moscow State University ul. Bol'shaya
> > > >>Nikitskaya 6
> > > >>125009 Moscow
> > > >>Russia
> > > >>http://zmmu.msu.ru/personal/pavlinov/pavlinov1.htm
> > > >>http://zmmu.msu.ru/personal/pavlinov/pavlinov_eng1.htm
> > > >>_______________________________________________
> > > >>Taxacom Mailing List
> > > >>
> > > >>Send Taxacom mailing list submissions to:
> taxacom at mailman.nhm.ku.edu
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> > > >>You can reach the person managing the list at:
> > > >>taxacom-owner at mailman.nhm.ku.edu The Taxacom email archive back to
> > > >>1992 can be searched at:  http://taxacom.markmail.org
> > > >>
> > > >>Nurturing nuance while assaulting ambiguity for about 33 years,
> > 1987-2020.
> > > >
> > > >  --
> > > >Richard Jensen, Professor Emeritus Department of Biology Saint Mary's
> > > >College Notre Dame, IN 46556
> > >
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> > >
> > > Nurturing nuance while assaulting ambiguity for about 33 years,
> > 1987-2020.
> >
> > _______________________________________________
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> >
> > Nurturing nuance while assaulting ambiguity for about 33 years,
> 1987-2020.
> >
>
>
> --
> --
> https://nature.berkeley.edu/willlab/
>
> Contact info:
>
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>
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