[Taxacom] New paper: Ruggiero et al. "A Higher Level Classification of All Living Organisms"
Stephen Thorpe
stephen_thorpe at yahoo.co.nz
Sun Jul 12 15:39:33 CDT 2015
2015
Dick,
Yes, but how long is a piece of string? Five years is too long! Problems arise trying to fit new species into classifications which don't yet recognise the relevant higher taxa. Do we really want a 5 year time lag for new species??
Stephen
--------------------------------------------
On Mon, 13/7/15, 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>, "Richard Pyle" <deepreef at bishopmuseum.org>
Received: Monday, 13 July, 2015, 4:30 AM
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 [...]
> >
_______________________________________________
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> > The Taxacom Archive back to 1992 may
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> > http://taxacom.markmail.org
> >
> > Celebrating
28 years of Taxacom in 2015.
> >
_______________________________________________
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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.
>
>
_______________________________________________
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> The Taxacom Archive back to 1992 may be
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>
> Celebrating 28 years
of Taxacom in 2015.
>
>
>
>
>
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>
>
_______________________________________________
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>
> Celebrating 28 years
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_______________________________________________
Taxacom Mailing List
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The Taxacom Archive back to 1992 may be
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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.
--
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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