[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 22:14:44 CDT 2015
2015
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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> >
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> > Celebrating
28 years of Taxacom in 2015.
>
>
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