[Taxacom] New paper: Ruggiero et al. "A Higher Level Classification of All Living Organisms"
Richard Jensen
rjensen at saintmarys.edu
Sat Jul 11 08:57:04 CDT 2015
2015
Hi all,
A couple of observations:
First, as Richard Pyle noted, consensus does not necessarily mean
unanimity. If so, then most political bills would never be passed. Think
of 'consensus trees"; these reflect areas of agreement among competing
views and leave the differences largely unresolved.
Second, perhaps I missed something in Stephen's last note; isn't any
classification (except for those that are purely fanciful) limited by what
is presently known?
Third, I haven't read the paper, but comments made by several participants
certainly come close to reflecting the thinking of numerical taxonomists,
whose classifications were based on overall patterns of agreement among all
characters available (or all characters used in the particular analysis).
These classifications were intended, in keeping with ideas expressed by
Gilmour, to be useful and, perhaps, serve as the basis for inferring
components of evolutionary relationships (although this was not the goal).
Based on what I've read here, the new classification attempts to provide a
useful consensus.
Cheers,
Dick J
On Fri, Jul 10, 2015 at 11:14 PM, Stephen Thorpe <stephen_thorpe at yahoo.co.nz
> wrote:
> I have no problem with alphabetical sequencing of taxa at each level, in
> fact I prefer it. My only gripe is that the paper be seen for what it
> really is, i.e. simply a choice of classification, based in part on
> PRESENTLY available evidence. Also, classifications should really be
> specified from the bottom up. Top down approaches just push a lot of
> unresolved rubbish down to the lower levels and ignore it.
>
> Stephen
>
>
> --------------------------------------------
> 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: "'Kenneth Kinman'" <kinman at hotmail.com>, taxacom at mailman.nhm.ku.edu
> Received: Saturday, 11 July, 2015, 2:37 PM
>
> 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 [...]
> > >
> _______________________________________________
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> > >
> > > Celebrating
> 28 years of Taxacom in 2015.
> > >
> _______________________________________________
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> > > http://taxacom.markmail.org
> > >
> > > Celebrating
> 28 years of Taxacom in 2015.
> >
> >
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> > Taxacom Mailing List
> >
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> > 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
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> searched at:
> http://taxacom.markmail.org
> >
> > Celebrating 28 years
> of Taxacom in 2015.
>
> _______________________________________________
> Taxacom Mailing List
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>
> 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:
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>
> Celebrating 28 years of Taxacom in 2015.
>
--
Richard Jensen, Professor
Department of Biology
Saint Mary's College
Notre Dame, IN 46556
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