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

Stephen Thorpe stephen_thorpe at yahoo.co.nz
Tue Jul 14 17:37:36 CDT 2015


No Robin, it is a clear case of a careless mistake, and I can only wonder how many others are in the paper.

Stephen

--------------------------------------------
On Wed, 15/7/15, Robin Leech <releech at telus.net> wrote:

 Subject: RE: [Taxacom] New paper: Ruggiero et al. "A Higher Level	Classification of All Living Organisms"
 To: "'Stephen Thorpe'" <stephen_thorpe at yahoo.co.nz>, "'Richard Jensen'" <rjensen at saintmarys.edu>, "'Richard Zander'" <Richard.Zander at mobot.org>
 Cc: "'Taxacom'" <taxacom at mailman.nhm.ku.edu>
 Received: Wednesday, 15 July, 2015, 10:35 AM
 
 Hmmm. Stephen,
 
 You'd do that without listening or reading about it? 
 That is tantamount to "My head is made up.  Don't 
 bother me with the facts."
 
 The Neuropterida is a natural group, so whether you consider
 it on a par with Holometabola, or as a subgroup, it 
 doesn't matter.  As you know what is a subfamily today
 is a family in the making tomorrow (e.g., Family Thomisidae,
 
 with the subfamilies Thomisinae and Philodrominae about 10
 years ago).  Today we have Thomisidae and
 Philodromidae,
 and I have not seen any dissention among the troops on
 this.
 
 Often what happens is that with more work done, the
 distinctions between two subfamilies become more distinct. 
 I can cite other examples of this for the family
 Amaurobiidae.  What was once considered 1 family with a
 number 
 of subfamilies is now a whole bunch of erections to family
 level.
 Robin
 
 
 -----Original Message-----
 From: Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu]
 On Behalf Of Stephen Thorpe
 Sent: July-14-15 4:16 PM
 To: Richard Jensen; Richard Zander
 Cc: Taxacom
 Subject: Re: [Taxacom] New paper: Ruggiero et al. "A Higher
 Level Classification of All Living Organisms"
 
 Well at any rate, any classification which pulls
 Neuropterida out of Holometabola goes straight into my
 rubbish bin!
 
 Stephen
 
 --------------------------------------------
 On Wed, 15/7/15, Richard Zander <Richard.Zander at mobot.org>
 wrote:
 
  Subject: RE: [Taxacom] New paper: Ruggiero et al. "A Higher
 Level Classification of All Living Organisms"
  To: "Richard Jensen" <rjensen at saintmarys.edu>,
 "Stephen Thorpe" <stephen_thorpe at yahoo.co.nz>
  Cc: "Taxacom" <taxacom at mailman.nhm.ku.edu>
  Received: Wednesday, 15 July, 2015, 2:40 AM
  
  This thread seems to consider
  classification either as a non-theoretic pattern of
 evidence
  or a subjective art form. I think that there are
 objective,
  scientific criteria for judging a "best" classification,
  e.g. the dissilient species/genus/family concept in:
  http://www.mobot.org/plantscience/ResBot/Repr/Zander-Framework.pdf
  
  
  Stephen suggests that " The term "natural classification"
  refers to a classification based on
  evolutionary/phylogenetic relationships"
  Which is it? Phylogenetic relationships minimize
 paraphyly,
  evolutionary relationships maximize paraphyly. The
  classifications are commonly different.
  
  -------
  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 Richard Jensen
  Sent: Tuesday, July 14, 2015 8:46 AM
  To: Stephen Thorpe
  Cc: Taxacom
  Subject: Re: [Taxacom] New paper: Ruggiero et al. "A
 Higher
  Level Classification of All Living Organisms"
  
  Stephen,
  
  Isn't ant classification simply one of a set of
 alternative
  classifications?
  
  And, you have your interpretation of what a "natural"
  classification is, but this is not something that has been
  accepted by all.  The history of the concept of
 natural
  classification is fraught with disagreements, sometimes
  quite heated, about this idea.
  
  
  Cheers,
  
  Dick J
  
  On Mon, Jul 13, 2015 at 5:30 PM, Stephen Thorpe <stephen_thorpe at yahoo.co.nz>
  wrote:
  
  > 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
  [...]
  >  >>
  >  >>
  >  >>
  >  >>     > >
  >  >>
  >  >>
  >  >>
  >  >>
  > 
    
 _______________________________________________
  >  >>
  >  >>
  >  >>
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  Taxacom Mailing
  >  List
  >  >>
  >  >>
  >  >>
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  >  >>
  >  >>
  >  >>
  >  >>     > > 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
  >  >>
  >  >>
  >  >>
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  >  >>
  >  >>
  >  >>
  >  >>     > > http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
  >  >>
  >  >>
  >  >>
  >  >>     > > The
  Taxacom
  >  Archive back to 1992 may
  >  >>
  >  >>
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  >  >>     be searched
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  >  >>
  >  >>
  >  >>
  >  >>     > > http://taxacom.markmail.org
  >  >>
  >  >>
  >  >>
  >  >>     > >
  >  >>
  >  >>
  >  >>
  >  >>     > >
  Celebrating
  >  >>
  >  >>
  >  >>
  >  >>     28 years of
  Taxacom in
  >  2015.
  >  >>
  >  >>
  >  >>
  >  >>     >
  >  >>
  >  >>
  >  >>
  >  >>     >
  >  >>
  >  >>
  >  >>
  >  >>
  > 
    
 _______________________________________________
  >  >>
  >  >>
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  >  >>     > Taxacom
  Mailing List
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  >  >>
  >  >>
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  >  >>     > http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
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  >  >>
  >  >>
  >  >>
  >  >>     >
  >  >>
  >  >>
  >  >>
  >  >>     >
 Celebrating
  28 years
  >  >>
  >  >>
  >  >>
  >  >>     of Taxacom in
  2015.
  >  >>
  >  >>
  >  >>
  >  >>     >
  >  >>
  >  >>
  >  >>
  >  >>     >
  >  >>
  >  >>
  >  >>
  >  >>     >
  >  >>
  >  >>
  >  >>
  >  >>     >
  >  >>
  >  >>
  >  >>
  >  >>     >
  >  >>
  >  >>
  >  >>
  >  >>     >
  >  >>
  >  >>
  >  >>
  >  >>     >
  >  >>
  >  >>
  >  >>
  >  >>     >
  >  >>
  >  >>
  >  >>
  >  >>
  > 
    
 _______________________________________________
  >  >>
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  Mailing List
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  >  >>
  >  >>
  >  >>
  >  >>     > 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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 Mailing
  List
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  >  >>
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  >  >>
  >  >>     The Taxacom
  Archive back to
  >  1992 may be
  >  >>
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  >  >>
  >  >>     searched at: http://taxacom.markmail.org
  >  >>
  >  >>
  >  >>
  >  >>
  >  >>
  >  >>
  >  >>
  >  >>     Celebrating 28
  years of
  >  >>
  >  >>
  >  >>
  >  >>     Taxacom in
  2015.
  >  >>
  >  >>
  >  >>
  >  >>
  >  >>
  >  >>
  >  >>
  >  >>
  >  _______________________________________________
  >  >>
  >  >>
  >  >>
  >  >>    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
  >  >>
  >  >>
  >  >
  _______________________________________________
  >  > 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.
  >
  
  
  
  --
  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.
  
 _______________________________________________
 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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