Search the Taxacom archive · Browse by month · Mirror of the former lists.ku.edu archive (1992–2025)

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

Richard Pyle deepreef at bishopmuseum.org
Fri Jul 10 21:37:14 CDT 2015 

Sure, one could argue indefinitely about how to contruct a "better"
consensus classification.  But these LITERALLY endless arguments are exactly
why no such comprehensive classification has previously been presented FOR
THE PURPOSES INTENDED BY THIS classification.  The value of this listing is
not the "classification" part, so much as it is the "consensus" part.
Consensus is not the same thing as unanimity.  You can certainly convey your
personal opinions (as listed below) to the architects of the list, and maybe
a future version will be altered to reflect them (assuming your opinions
resonate with the broader consensus).

 

In any case, sequencing of names in a list is an incredibly BAD way to
represent phylogenetic information; ESPECIALLY in the context of that this
particular list is intended for.  If you want to represent affinities of
taxa, there are three basic ways to do it:

1)      Come up with a mark-up scheme (like yours)

2)      Acknowledge names at ever finer units of intermediate ranks, so that
relationships can be represented within nested sets

3)      Draw a cladogram

 

For the purposes of this list, any sequence other than alphabetical
(particularly if some sort of information is intended to be conveyed by the
particular sequence) would have been a very silly thing to do.

 

Aloha,

Rich

 

 

 

From: Kenneth Kinman [mailto:kinman at hotmail.com] 
Sent: Friday, July 10, 2015 3:39 PM
To: deepreef at bishopmuseum.org; taxacom at mailman.nhm.ku.edu
Subject: RE: [Taxacom] New paper: Ruggiero et al. "A Higher Level
Classification of All Living Organisms"

 

Hi Rich,

        I think John is being overly harsh.  Overall, it's not a bad
classification, but I think it certainly could be made better.  The protist
classification is very good, thanks to the work of Thomas Cavalier-Smith.
It's too bad he couldn't get his co-authors to classify Posibacteria and
Archaebacteria together in one Kingdom (and Negibacteria in another).  I
still think alphabetizing the lists is still a sad loss of information.  It
may be a bit more convenient for some, but I'm sure many others will find
the loss of information more than just an inconvenience.     

          I don't understand why they didn't subdivide the list of orders of
eutherian mammals (and splitting Pilosa and Cingulata as separate orders
unfortunately eliminated the more familiar name Xenarthra, as well as being
separated alphabetically).  And of course, I would raise Aves back to Class
status, and add an {{Aves}} marker within Reptilia.  Anyway, even if they
insist on retaining the alphabetical "convention" for the convenience of
some, there is still plenty of room for improvement in my opinion.


                    ---------------Ken                    

P.S.  Hexapoda is probably polyphyletic.  Collembola almost certainly
evolved hexapody independently from one group of crustaceans, and the
insects from a different group of crustaceans

.
----------------------------------------------------------------------------
---------------------------------------------

> From: deepreef at bishopmuseum.org
> To: calabar.john at gmail.com; taxacom at mailman.nhm.ku.edu
> Date: Fri, 10 Jul 2015 14:52:03 -1000
> Subject: Re: [Taxacom] New paper: Ruggiero et al. "A Higher Level
Classification of All Living Organisms"
> 
> 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.

More information about the Taxacom mailing list