[Taxacom] New paper: Ruggiero et al. "A Higher Level Classification of All Living Organisms"
Stephen Thorpe
stephen_thorpe at yahoo.co.nz
Fri Jul 10 18:07:54 CDT 2015
2015
There are certainly big problems with the idea of "consensus". Given that all sorts of people are using all sorts of classifications for all sorts of reasons, isn't a "consensus" just going to deliver some meaningless "one size fits all"? Also, the result will depend on who is included/excluded from the "consensus" group. Theoretically, "consensus" doesn't give due weight to the opinions of the most intelligent people, because (by very definition) they are a minority! Hence "consensus" tends to drag things down to the lowest common denominator. This isn't always a problem, but it certainly can be.
Stephen
--------------------------------------------
On Sat, 11/7/15, John Grehan <calabar.john at gmail.com> wrote:
Subject: Re: [Taxacom] New paper: Ruggiero et al. "A Higher Level Classification of All Living Organisms"
To: "Richard Pyle" <deepreef at bishopmuseum.org>, "taxacom" <taxacom at mailman.nhm.ku.edu>
Received: Saturday, 11 July, 2015, 10:59 AM
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 [...]
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