[Taxacom] New paper: Ruggiero et al. "A Higher Level Classification of All Living Organisms"
Robin Leech
releech at telus.net
Mon Jul 13 16:57:01 CDT 2015
2015
Stephen,
Like I said, I do not agree with everyone, and yes, there are some out
there, somewhere,
who disagree with me, or who think I am full of it. If I couldn't handle
the heat,
I wouldn't stay in the kitche.
In Taxacom, you can stand on your box and thump your chest, and the next
person
coming along may strongly agree, strongly disagree, or be neutral to your
comments.
Thus, you have no fear of "official standard" being created and followed -
some sort
of dogma. Because this is an open forum, no cluster of individuals "sticks
too rigidly".
That is how we find "better" (or if not better, perhaps something different
and new),
by listening to and reading the comments of others - no matter how far out
to right or
left field (political comment, not a baseball comment).
If your comments regularly strike people positively, you will develop a
following.
If not, then you may find yourself being argued with by everyone.
Most know when I am being an agent provocateur, and when I assume that role,
it is
for positive purposes.
Nuff said.
Robin
-----Original Message-----
From: Stephen Thorpe [mailto:stephen_thorpe at yahoo.co.nz]
Sent: July-13-15 3:30 PM
To: 'Pierre Deleporte'; taxacom at mailman.nhm.ku.edu; Robin Leech
Subject: Re: [Taxacom] New paper: Ruggiero et al. "A Higher Level
Classification of All Living Organisms"
Not that well said, actually! The term "natural classification" refers to a
classification based on evolutionary/phylogenetic relationships rather than
on subjective judgements of similarity and/or "groups of convenience". As I
said earlier in this thread, one is free to choose a classification, and
that of Ruggiero et al. is a choice one may choose, but there could be
problems resulting from sticking too rigidly to it for too long, that's all.
There may be better alternatives. I would really hate to see it adopted as
some kind of "official standard", when all it is is one suggestion.
Stephen
--------------------------------------------
On Tue, 14/7/15, Robin Leech <releech at telus.net> wrote:
Subject: Re: [Taxacom] New paper: Ruggiero et al. "A Higher Level
Classification of All Living Organisms"
To: "'Pierre Deleporte'" <pierre.deleporte at univ-rennes1.fr>,
taxacom at mailman.nhm.ku.edu
Received: Tuesday, 14 July, 2015, 9:16 AM
Well said, Pierre.
Robin
-----Original Message-----
From: Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu]
On Behalf Of Pierre Deleporte
Sent: July-13-15 2:16 PM
To: taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] New paper: Ruggiero et al. "A Higher Level
Classification of All Living Organisms"
all classifications are concepts - there is no classification without a
classifier - there is no "natural"
classification standing in itself out there in the natural wild
(proponents of "natural" classifications should meticulously explain what
they mean)
useful classifications serve communication purposes (talking of things or
'objects' by meaningful classes rather than on by
one)
many classifications can be useful, provided that they fit their goals
(what kind of information do we want to convey
?) and their specification (what are the desired properties of such a
classification, given its goals ?)
in the present case, the classification of Ruggiero et al.
should be evaluated according to its specific goals (some kind of informal
"majority rule consensus" for practical purposes of stability on a 5-years
basis)
criticisms in terms of "scientificity" or "naturalness" are largely
missing the point
Best,
Pierre
Le 13/07/2015 19:45, Richard Pyle wrote :
> Hi Stephen,
>
> A piece of string is as long as it needs to be to perform a specified
task.
> In this case, you still seem to be having trouble understanding what >
the specific task of the CoL consensus taxonomy is. Tony Rees > answered
much more effectively than I could have; but the key point to > understand
is that a consensus taxonomy of this sort is established > explicitly to
facilitate harmony among disparate datasets, to more > effectively allow
cross-dataset comparisons, and to dramatically > simplify activities that
benefit from a general organization of > biological names into a
rough/approximate SHARED classification. In > this context, the
importance of stability and shared use of the > consensus classification
across multiple data-providing constituents > VASTLY exceeds the
importance of reflecting the evolutionary > speculation du jour. We have
plenty of information streams to provide > dynamic/evolutionary
classifications as new information becomes > available in real time. What
we've been lacking (prior to the > establishment of this CoL consensus
taxonomy), is a community-oriented classification "flag-pole" around which
data content providers can collectively rally.
>
> Also, your reference to a "new species" further reveals your >
misunderstanding of what this consensus classification is intended > for.
If you had read the paper, and downloaded the classification, you > would
see that it only goes down as far as the rank of Order. More > granular
changes to taxonomy (e.g., families, genera, species, etc.) > are not
included (those are in the realm of the much-more dynamically updated CoL
itself).
> Personally, I think a consensus classification at the rank of Order >
and higher probably does not need to be updated more than once a > decade,
but I suppose that revisiting it every five years is a reasonable
frequency.
>
> In any case, I agree with Tony that the discussion has gotten a bit >
off track.
>
> Aloha,
> Rich
>
> Richard L. Pyle, PhD
> Database Coordinator for Natural Sciences | Associate Zoologist in >
Ichthyology | Dive Safety Officer Department of Natural Sciences, > Bishop
Museum, 1525 Bernice St., Honolulu, HI 96817 > Ph: (808)848-4115, Fax:
(808)847-8252 email: deepreef at bishopmuseum.org
> http://hbs.bishopmuseum.org/staff/pylerichard.html
>
>
>
>> -----Original Message-----
>> From: Stephen Thorpe [mailto:stephen_thorpe at yahoo.co.nz]
>> Sent: Sunday, July 12, 2015 10:40 AM >> To: Richard Jensen >> Cc:
Kenneth Kinman; Taxacom; Richard Pyle >> Subject: Re: [Taxacom] New paper:
Ruggiero et al.
"A Higher Level
>> Classification of All Living Organisms"
>>
>> 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.0118
>> 247
>>
>>
>>
>> > > 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
>>
>>
> _______________________________________________
> 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.
--
Pierre DELEPORTE
UMR6552 EthoS
Université Rennes 1
CNRS
Station Biologique
35380 PAIMPONT
tél (+33) 02 99 61 81 63
fax (+33) 02 99 61 81 88
_______________________________________________
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The Taxacom Archive back to 1992 may be searched at:
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Celebrating 28 years of Taxacom in 2015.
_______________________________________________
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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.
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