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[Taxacom] New paper: Ruggiero et al. "A Higher Level Classification of All Living Organisms"

Robin Leech releech at telus.net
Mon Jul 13 17:52:56 CDT 2015


Stephen, 
I hope, when you write stability in classification, you mean the process.
Nothing else is stable from the subspecies level to the the phylum level. Contents of categories change, concepts for categories change, etc.
New phyla are created when new organisms are found, and frequently the contents of other phyla are depleted and put into the new phyla. 
The concept of what constitutes a particular species changes - think about birds here!
The only think that is stable is(are) the process(es) we use.
Robin

-----Original Message-----
From: Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Stephen Thorpe
Sent: July-13-15 4:36 PM
To: taxacom at mailman.nhm.ku.edu; deepreef at bishopmuseum.org
Subject: Re: [Taxacom] New paper: Ruggiero et al. "A Higher Level Classification of All Living Organisms"

Rich,
Stability in classification is not something that can be imposed for convenience, however convenient it may be. Rather, we hope that stability will result in the long run from convergence of scientific evidence. Of course there is an element of subjectivity (lumping/splitting) in higher classification, which is a further source of classificational "diversity". Most likely, Ruggiero et al. will just contribute further to instability by providing yet another classification that some people will choose to follow and others won't.
Stephen

--------------------------------------------
On Tue, 14/7/15, Richard Pyle <deepreef at bishopmuseum.org> wrote:

 Subject: Re: [Taxacom] New paper: Ruggiero et al. "A	Higher	Level	Classification of All Living Organisms"
 To: taxacom at mailman.nhm.ku.edu
 Received: Tuesday, 14 July, 2015, 10:24 AM
 
 Hi Stephen,
 
 Again, you seem to continue to misunderstand the purpose of
 the CoL Consensus classification.  Yes, it is indeed
 intended to represent a "standard" of sorts (although I'm
 not sure exactly what you mean by "official"), and the POINT
 is that it is STABLE and adopted by a wide array of data
 content providers.  The point is NOT to represent the
 most recent speculation about evolutionary/phylogenetic
 relationships (I chose the word "speculation" here to be
 deliberately provocative, and in line with the gist of
 recent excellent posts by Pierre and Robin, but you can
 substitute the more science-y "hypothesis" if it makes you
 feel better).  
 
 In this context, the only way an alternate classification
 could be "better" is if it is either: 1) MORE stable (i.e.,
 LESS responsive to changes in available
 phylogenetic/evolutionary evidence); or 2) MORE widely
 adopted by biodiversity information content providers. 
 Note that the criteria for "better" in this context does NOT
 include "reflects the most recent evidence concerning
 evolutionary/phylogenetic relationships".  Indeed,
 applying such a criterion to the CoL Consensus
 Classification would actually make it WORSE in this context,
 if doing so caused it to be either 1) less stable, or 2)
 less widely adopted.
 
 Obviously, the "consensus" part is important, and generally
 implies that a majority of contributing experts feels that
 it represents the "least of evils" approach to representing
 roughly the general evolutionary/phylogenetic relationships;
 but I hope by now you will understand that this is not the
 primary purpose of the consensus classification (as
 explicitly stated in the abstract of the Ruggiero et al.
 publication.
 
 I have now made this same point several times on this forum,
 and I honestly cannot think of any other way to make it more
 clear.  If the virtues of a stable, widely adopted
 general classification at ranks of Kingdom to Order are not
 useful to you, then by all means, don't use it!  Those
 of us who need a stable and widely-adopted generalized
 higher (Kingdom through Order) classification to facilitate
 exchanging biodiversity data remain quite pleased that this
 is now in published form!
 
 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: Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu]
 On Behalf
 > Of Stephen Thorpe
 > Sent: Monday, July 13, 2015 11:30 AM
 > 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
 > 
 >  _______________________________________________
 >  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.




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