[Taxacom] New paper: Ruggiero et al. "A Higher Level Classification of All Living Organisms"
Richard Jensen
rjensen at saintmarys.edu
Sun Jul 12 11:30:46 CDT 2015
2015
Stephen,
I didn't miss your point. Anyone who works in taxonomy/systematics is well
aware of the lag time between a taxonomist making a discovery and the rest
of us learning about it. Thus, all classifications are restricted to what
is presently known by those constructing the classification - they cannot
be expected to add caveats or make allowances for information that, while
just discovered a nanosecond before they submitted their final edited copy,
was not available to them.
Let's be realistic about this.
Cheers,
Dick J
On Sat, Jul 11, 2015 at 6:26 PM, Stephen Thorpe <stephen_thorpe at yahoo.co.nz>
wrote:
> Dick J said: ..., 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?
>
> Yes, you did miss something, i.e. the point! My point was that
> classification (particularly when based on phylogenetic analyses) is
> continuously changing with new information coming in all the time. Yet, I
> strongly suspect that it may be something like at least a decade before
> CoL, etc. think about reviewing the results of Ruggiero et al. (2015).
>
> Stephen
>
>
> --------------------------------------------
> On Sun, 12/7/15, Richard Jensen <rjensen at saintmarys.edu> wrote:
>
> Subject: Re: [Taxacom] New paper: Ruggiero et al. "A Higher Level
> Classification of All Living Organisms"
> To: "Stephen Thorpe" <stephen_thorpe at yahoo.co.nz>
> Cc: "Kenneth Kinman" <kinman at hotmail.com>, "Taxacom" <
> taxacom at mailman.nhm.ku.edu>, deepreef at bishopmuseum.org
> Received: Sunday, 12 July, 2015, 1:57 AM
>
> 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 [...]
>
> > >
>
> _______________________________________________
>
> > > 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.
>
>
>
> _______________________________________________
>
> 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.
>
>
>
>
> --
> Richard Jensen, Professor
> Department of Biology
> Saint Mary's College
> Notre Dame, IN 46556
>
>
>
--
Richard Jensen, Professor
Department of Biology
Saint Mary's College
Notre Dame, IN 46556
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