[Taxacom] New paper: Ruggiero et al. "A Higher Level Classification of All Living Organisms"

Fri Jul 10 20:21:47 CDT 2015

Semantics!

--------------------------------------------
On Sat, 11/7/15, Richard Pyle <deepreef at bishopmuseum.org> wrote:

 Subject: Re: [Taxacom] New paper: Ruggiero et al. "A Higher Level	Classification of All Living Organisms"
 To: "'John Grehan'" <calabar.john at gmail.com>, "'taxacom'" <taxacom at mailman.nhm.ku.edu>
 Received: Saturday, 11 July, 2015, 12:52 PM

 Hi John,

 I think you would need to read the full paper
 (not just the two lines of text I quoted from the abstract)
 before you could make an assessment as to whether or not
 their work fits within your own personal definition of
 “science”.  Considerably more investigation would be
 required before you could confidently infer whether or not
 the work falls within the authors’ own personal
 definitions of “science”.

 Aloha,

 Rich

 From: John Grehan
 [mailto:calabar.john at gmail.com]

 Sent: Friday, July 10, 2015 1:00 PM
 To: Richard Pyle; taxacom
 Subject: Re: [Taxacom] New paper: Ruggiero et
 al. "A Higher Level Classification of All Living
 Organisms"

 Yes I was implying
 (explicitly) that the authors of the paper appear to have a
 definition of science (assuming that the classification was
 being represented as science) where science is a
 'consensus' of opinion compromising conflicting
 information. When one comes up with a compromise of the sort
 it does not appear to be a process that is attempting to
 reflect reality (whatever that might be), but just a
 compromise between different opinions. A good example of
 this is how so-called ecological areas were defined in New
 Zealand (Under the Protected Natural Areas program, and with
 lots of money to boot) according to compromises over
 different opinions about where the boundaries between the
 areas were to be drawn (said boundaries having no reality
 anyway, hence the ability to 'compromise').

 Perhaps I am being awfully presumptuous, but if
 it is presumptuous to regard consensus opinions as outside
 science then so be it.

 John Grehan

 On Fri, Jul 10, 2015 at 4:06 PM, Richard Pyle
 <deepreef at bishopmuseum.org>
 wrote:

 The “nature of
 reality” is sufficiently vague that it could be
 interpreted just as broadly as “science” can be.

 My only point is that the outer boundaries of
 “science” are not well defined.  Controlled
 experimentation following the scientific method is squarely
 within the realm of science, and most would argue that
 things like Astrology are pretty clearly at the very
 outskirts.  In between those is a very broad range of
 activities, such as phylogenetics, taxonomy, nomenclature,
 informatics, and a whole host of other things that may or
 may not conform to some particular person’s definition of
 “science”.

 Your comment, to which I was
 responding, seemed to imply that we all (including the
 authors of the paper) share a definition of science that
 would unambiguously exclude their paper from “science”
 (i.e., the notion that the authors self-evidently
 “admit” that their work is not science).  That seemed
 awfully presumptuous of you.

 Aloha,

 Rich

 From: John Grehan [mailto:calabar.john at gmail.com]

 Sent: Friday, July 10, 2015 9:52 AM
 To: Richard Pyle

 Subject: Re: [Taxacom] New
 paper: Ruggiero et al. "A Higher Level Classification
 of All Living Organisms"

 Perhaps, but
 what do you think is incorrect about the one I gave? Are you
 saying consensus opinion is science?

 John Grehan

 On Fri, Jul 10, 2015 at
 3:30 PM, Richard Pyle <deepreef at bishopmuseum.org>
 wrote:

 We all like to
 believe our own definition of “science” is the correct
 one.

 Sigh….

 Rich

 From: John
 Grehan [mailto:calabar.john at gmail.com]

 Sent: Friday, July 10, 2015 9:23 AM
 To: Richard Pyle
 Cc: TAXACOM

 Subject: Re:
 [Taxacom] New paper: Ruggiero et al. "A Higher Level
 Classification of All Living Organisms"

 At least the quotes show that the authors admit
 their work not be science (if science is understood to be
 about the nature of reality beyond 'consensus'
 opinion).

 John Grehan

 On Fri, Jul 10, 2015 at 3:07 PM, Richard Pyle
 <deepreef at bishopmuseum.org>
 wrote:

 Hmmm....  I've
 been deliberately quiet on this thread as well.  I
 appreciate the viewpoints of Ken and others in terms of
 holophyly, the value of acknowledging paraphyletic taxa
 through Linnean nomenclature, etc.  This is all good
 philosophical grit, and I enjoy the intellectual stimulation
 as much as anyone.

 However,
 this thread began (and remains?) relevant to the PLoS ONE
 publication of Ruggiero et al., which provides a generalized
 **CONSENSUS CLASSIFICATION**.  Perhaps there is some
 misunderstanding on what is meant by this term (and the
 associated classification)?  Anyone who read as far as the
 abstract of this paper should at least know that:

 "This classification is
 neither phylogenetic nor evolutionary but instead represents
 a consensus view that accommodates taxonomic choices and
 practical compromises among diverse expert opinions, public
 usages, and conflicting evidence about the boundaries
 between taxa and the ranks of major taxa, including
 kingdoms."

 And:

 "Beyond its immediate use
 as a management tool for the CoL and ITIS (Integrated
 Taxonomic Information System), it is immediately valuable as
 a reference for taxonomic and biodiversity research, as a
 tool for societal communication, and as a classificatory
 “backbone” for biodiversity databases, museum
 collections, libraries, and textbooks."

 In this context, it is
 ABSOLUTELY CORRECT that the subtaxa within a taxon are
 alphabetically arranged!  It is absolutely NOT intended to
 reflect any sort of "naturalness" in patterns of
 evolution.  Yes, it probably does kinda- sorta- happen to
 reflect modern views of evolutionary relationships
 (otherwise there wouldn't be much consensus behind
 it).  But its function is to serve as a tool for
 informatics and generalized (i.e., highly simplified)
 organizational representation of life on Earth.  As such,
 it is overwhelmingly valuable to the people for whom it was
 intended (see second quote above).

 Aloha,
 Rich

 > -----Original
 Message-----
 > From: Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu]
 On Behalf
 > Of Richard Zander
 > Sent: Friday, July 10, 2015 7:51 AM
 > To: TAXACOM
 > Subject:
 Re: [Taxacom] New paper: Ruggiero et al. "A Higher
 Level
 > Classification of All Living
 Organisms"
 >
 >
 Maybe now is the time to add my perspective, backing up that
 of Ken.
 >
 >
 Phylogenetic classification is artificial. Artificial
 classifications use one set of
 > traits
 to group taxa, e.g., molecular races, shared traits (only).
 Artificial
 > classifications are
 repeatable, yet repeatability is not the only requirement
 of
 > science. Alphabetization is
 repeatable.
 >
 >
 Principles of phylogenetic classification are artificial.
 Some principles include
 > strict
 monophyly (so long Aves), putting known taxa at the top of a
 tree of
 > relationships
 ("tree-thinking") rather than in the tree when
 known (stem-
 > thinking), ignoring the
 probability of extinct paraphyly that casts doubt on
 > molecular trees, ignoring the evolutionary
 importance of autapomorphies,
 > asserting
 that only zero length branches imply a surviving ancestral
 taxon,
 > pretending that a cladogram is
 "the evidence" (when it is only some
 > evidence) and evolutionary theory is mere
 narrative . . . you can probably
 > think
 of more phylogenetic principles of classification that do
 violence to
 > evolutionary theory
 developed only after long struggle with artificial
 > classifiers of the past.
 >
 > Classification by
 phylogenetic principles is actually quite unprincipled,
 and
 > serves only to preserve a
 modification of older methods of numerical
 > taxonomy.
 >
 > Richard
 >
 >
 > -------
 > Richard H. Zander
 >
 Missouri Botanical Garden – 4344 Shaw Blvd. – St. Louis
 – Missouri – 63110 –
 > USA richard.zander at mobot.org
 Web sites:
 > http://www.mobot.org/plantscience/bfna/bfnamenu.htm
 and
 > http://www.mobot.org/plantscience/resbot/
 >
 >
 >
 -----Original Message-----
 > From:
 Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu]
 On Behalf
 > Of Nico Franz
 > Sent: Friday, July 10, 2015 12:16 PM
 > To: TAXACOM
 > Subject:
 Re: [Taxacom] New paper: Ruggiero et al. "A Higher
 Level
 > Classification of All Living
 Organisms"
 >
 >
 Computational logic? Nico
 >
 > Reasoning over taxonomic change:
 > http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0118247
 > Taxonomy - for computers:
 > http://biorxiv.org/content/early/2015/07/09/022145
 >
 > -----
 > Date: Thu, 9 Jul 2015
 >
 From: Kenneth Kinman
 >
 > Hi Stephen,
 >     
   Logically, we must remember that [...]
 >
 _______________________________________________
 > Taxacom Mailing List
 >
 Taxacom at mailman.nhm.ku.edu
 > http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
 > The Taxacom Archive back to 1992 may be
 searched at:
 > http://taxacom.markmail.org
 >
 > Celebrating 28 years
 of Taxacom in 2015.
 >
 _______________________________________________
 > Taxacom Mailing List
 >
 Taxacom at mailman.nhm.ku.edu
 > http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
 > The Taxacom Archive back to 1992 may be
 searched at:
 > http://taxacom.markmail.org
 >
 > Celebrating 28 years
 of Taxacom in 2015.

 _______________________________________________
 Taxacom Mailing List
 Taxacom at mailman.nhm.ku.edu
 http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
 The Taxacom Archive back to 1992 may be
 searched at: http://taxacom.markmail.org

 Celebrating 28 years of
 Taxacom in 2015.

 _______________________________________________
 Taxacom Mailing List
 Taxacom at mailman.nhm.ku.edu
 http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
 The Taxacom Archive back to 1992 may be
 searched at: http://taxacom.markmail.org

 Celebrating 28 years of
 Taxacom in 2015.