[Taxacom] Adl et al. on Protista (was: All levels of organisation...)

Ken Kinman kinman at hotmail.com
Thu Nov 8 21:13:19 CST 2012








Dear All,
             I did a quick read of Adl et al., 2012, and then compared it to my latest classification of Kingdom Protista (posted here on Taxacom in August 2011, and here's a weblink to that):  http://mailman.nhm.ku.edu/pipermail/taxacom/2011-August/073326.html
        Not surprisingly, there are some clear similiarities, but also differences (especially a bit of paraphyly in mine, namely 2 paraphyletic phyla, while the other 14 phyla are believed to be holophyletic).  Having 2 paraphyletic phyla seems reasonable, especially since their exgroups are major Kingdoms.  Of course, paraphylophobia maintains that only 0 paraphyletic taxa are reasonable, but how does one reason with those unwillingly to compromise at all.  I also prefer to encode many of the intermediate clades and simply note them in the footnotes.  Makes for classifications that are less cluttered for the general user and generally more stable as well.      
        I don't really understand why Adl et al. felt compelled to propose new names for two of the major clades.  They replaced Unikonta (which is my clade 3) with the rather nebulous name Amorphea.  Even if they had good reasons to reject the name Unikonta, I would want to at least come up with something less vague than Amorphea.   And an even larger clade is renamed Diaphoretickes, which equals my clade containing clades 4-10.  In the footnotes, I called this the "photokaryote clade", but the formal name Corticata seems perfectly fine (even though I don't think that it included Rhizaria when it was proposed).  The name Corticata has an actual morphological meaning (possession of a cortex), while Diaphoretickes only refers to the general diversity of the group (and therefore seems to be just as vague in meaning as Amorphea).  A neologism like that could make many roll their eyes in the years to come, and I can also imagine it being the butt of a few jokes about sweating ticks.         
                            ------------------Ken   
Date: Thu, 8 Nov 2012 12:52:48 -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: Tony.Rees at csiro.au
CC: kinman at hotmail.com; taxacom at mailman.nhm.ku.edu

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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The Taxacom archive going back to 1992 may be searched with either of these methods:



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(2) a Google search specified as:  site:mailman.nhm.ku.edu/pipermail/taxacom  your search terms here


-- 
___________________________________
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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