[Taxacom] All levels of organisation and manifestation should be acknowledged for the classificatory and evolutionary value that is inherent in them

David Patterson dpatterson at mbl.edu
Thu Nov 8 13:52:48 CST 2012


My bad

I had intended to point you to the 2012 schema: Adl, S. et al., 'The
Revised Classification of Eukaryotes', Journal of Eukaryotic Microbiology,
2012. doi:10.1111/j.1550-7408.2012.00644.x

The issue of which system to use goes beyond the initial issue of
paraphyly.

Paddy



On Thu, Nov 8, 2012 at 12:22 PM, <Tony.Rees at csiro.au> wrote:

> Hi Paddy,
>
> "Protista" may be gone but the problem is how to replace it in a formal
> classification treatment...
>
> http://en.wikipedia.org/wiki/Eukaryote#Classification details numerous
> alternatives including and since Adl et al. 2005, the paper you cite, with
> not much consensus at this time...
>
> Cheers - Tony
>
> ________________________________________
> From: taxacom-bounces at mailman.nhm.ku.edu [
> taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of David Patterson [
> dpatterson at mbl.edu]
> Sent: Friday, 9 November 2012 5:45 AM
> To: Ken Kinman
> Cc: taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] All levels of organisation and manifestation should
> be acknowledged for the classificatory and evolutionary value that is
> inherent in them
>
> I can comment on protists which I know a little about.
>
> You may wish to look at the most recent global classification of protists
> - J. Eukaryot. Microbiol., 52(5), 2005 pp. 399–451 - 'Protista' has been
> rejected.
>
> Prokaryota is better replaced with the Eubacteria and Archaebacteria.
>
> Perhaps folk with expertise in the other taxa can see if Ken's view is
> consistent with the authoritative perspectives?
>
> David
>
> On Thu, Nov 8, 2012 at 11:11 AM, Ken Kinman <kinman at hotmail.com> wrote:
>
> >  Hi David,
> >
> >      The higher level paraphyletic taxa are probably the most useful,
> > since they have a very wide user pool.  (1)  Kingdom Prokaryota (or rank
> it
> > as Empire or Domain, if you will).  (2) Kingdom Protista is a major
> > example, since trying to get rid of that one has done nothing but create
> > needless confusion.   (3) Phylum Bryophyta.  (4) Class Sarcopterygia.
>  (5)
> > Class Amphibia.   (6) Order or Superorder Dinosauria, for the so-called
> > "non-avian dinosaurs".
> >
> >                    --------------------Ken
> >
> >
> > ------------------------------
> > Date: Thu, 8 Nov 2012 10:23:41 -0700
> > Subject: Re: [Taxacom] All levels of organisation and manifestation
> should
> > be acknowledged for the classificatory and evolutionary value that is
> > inherent in them
> > From: dpatterson at mbl.edu
> > To: kinman at hotmail.com
> > CC: nicholasa at ukzn.ac.za; richard.zander at mobot.org;
> > taxacom at mailman.nhm.ku.edu
> >
> > If 'many other do too', I'd be surprised.  Some, certainly. But the
> > majority see little value in preserving paraphyletic taxa.  But perhaps
> > some of the advocates for retention (nay, adoration) of paraphyly could
> > suggest some 'taxa' that they believe serve us better than holophyletic
> > taxa.
> >
> > David Patterson
> >
> > On Thu, Nov 8, 2012 at 8:58 AM, Ken Kinman <kinman at hotmail.com> wrote:
> >
> >
> > Hi Ashley,
> >       Here, here.  Agree completely, and many others do too.  Not that
> our
> > heads would go on the chopping block, but our heads do get sore banging
> up
> > against that brick wall (of holophyly worship coupled with paraphyly
> > bashing).  You would think branding paraphyletic taxa with a "Scarlet
> > letter" P would satisfy them (Thomas Cavalier-Smith uses a * symbol, and
> I
> > use a % symbol for paraphyletic taxa).  But explicit marking of
> > paraphyletic taxa doesn't satisfy them, and they just want to destroy
> them
> > (not just bash them), no matter how informative and useful such taxa can
> > be.  Few of them seem willing to even discuss possible compromise of any
> > sort on this subject.
> >                      -------------Ken
> >
> >
> >
> >
> -----------------------------------------------------------------------------------------------------------------------------------
> > > From: Nicholasa at ukzn.ac.za
> > > To: Richard.Zander at mobot.org; taxacom at mailman.nhm.ku.edu
> > > Date: Thu, 8 Nov 2012 14:56:50 +0000
> > > Subject: [Taxacom] All levels of organisation and manifestation should
> > be acknowledged for the classificatory and evolutionary value that is
> > inherent in them
> > >
> > > Right - let me put my head on the chopping block!
> > >
> > >
> > >
> > > One of the disturbing things about modern classificatory paradigms is
> > that a whole level of organisation (organismal morphology) is being
> written
> > off as scientifically worthless. Am I the only one who is scared by
> > empirical scientific implications of this?
> > >
> > >
> > >
> > > I personally think this is bad science. Biodiversity presents us with
> > information at the molecular, genetic, organismal, physiological and
> > ecological levels and data from all level gives us important information
> > about how organisms manifest and change with time. The acceptance of
> strict
> > monophyly is allowing scientists to discount groups of organisms defined
> by
> > unique morphologies. These groups are valid and could easily be accepted
> > under a paraphyletic classification. This is possibly arguable, but if we
> > are to create classifications in which data from all levels of
> organisation
> > are acknowledged for the value that is inherent in them, then we must
> > accept paraphyly. Besides all new major evolutionary lines start off as
> > paraphyletic side branches -- and paraphyly says a great deal about the
> way
> > in which organisms and groups evolve. By removing paraphyly we remove the
> > possibility of investigating some very intriguing evolutionary questions
> -
> > that I feel need to explored rathe
> >  r than ignored.
> > >
> > >
> > >
> > > Everyone seems focused on the morphological versus molecular and
> > monophyletic versus paraphyletic battlefields. There are other levels of
> > organization which we neglect at our scientific peril.
> > >
> > >
> > >
> > > At the end no matter the evidence used (morphological or molecular)
> > classifications that are extrapolated from this evidence only hypotheses.
> > Hypotheses are merely concepts out there for further verification or
> > falsification. They are not the truth. Despite what outsiders may think
> > scientists live in a world of uncertainty and all good scientists will
> > embrace this fact.  As a professional taxonomist I live (in my head) in a
> > world of multiple taxonomies and classifications base on the same
> > organisms. Why are we so fixated on having only one classification? I
> wish
> > other scientists and funders would stop trying to put me into either the
> > morphological or molecular box. As a scientist I refuse to limit myself
> > like this -- the organismal diversity I walk through when I am in the
> bush
> > is more than just morphology and molecules. I do not see any good
> > scientific reason to abandon information from other levels of
> manifestation.
> > >
> > >
> > >
> > > Ashley
> > >
> > > ---------------------------------------------------
> > >
> > > Ashley Nicholas (PhD)
> > >
> > > Associate Professor & Curator Ward Herbarium
> > >
> > > School of Life Science,  Westville Campus
> > >
> > > University of KwaZulu-Natal,
> > >
> > > Private Bag X54001,
> > >
> > > Durban, 4000, South Africa
> > >
> > > Tel.:+27-31-260 7719 Fax.: +27-31-260 2029
> > >
> > > nicholasa at ukzn.ac.za
> > >
> > > ----------------------------------------------------
> > >
> > > Let's not continue to fool ourselves, we are no longer sititing at the
> > edge of the cliff of "environmental disaster", we have gone over that
> edge.
> > - Ashley Nicholas (at the moment six cities the size of Johannesburg are
> > added to the world every year)
> > >
> > > --------------------------------------------------------------------
> > >
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> >
> >
> > --
> > ___________________________________
> > David J Patterson
> >
> >
> >
>
>
> --
> ___________________________________
> David J Patterson
>
> Senior Scientist, Marine Biological Laboratory
> 7 MBL Street, Woods Hole, MASS 02543, USA.
>
> Research Professor
> School of Life Sciences, Arizona State University
> Tempe, AZ 85287-4501
>
> Professor (MBL) Ecology and Evolutionary Biology
> Brown University, Providence, Rhode Island
>
> Life Sciences Lead, Data Conservancy dataconservancy.org
>
> globalnames.org
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-- 
___________________________________
David J Patterson

Senior Scientist, Marine Biological Laboratory
7 MBL Street, Woods Hole, MASS 02543, USA.

Research Professor
School of Life Sciences, Arizona State University
Tempe, AZ 85287-4501

Professor (MBL) Ecology and Evolutionary Biology
Brown University, Providence, Rhode Island

Life Sciences Lead, Data Conservancy dataconservancy.org

globalnames.org



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