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Editorial and replies

Mark Farmer farmer at EMLAB.ZOO.UGA.EDU
Mon May 2 14:12:25 EST 1994

Let me start by stating that I am glad that my editorial has generated some
interest.  For those of you who are not members of the Society of
Protozoologists [shame on you :-)] I will enclose a copy of my original
editorial that appeared in the most recent edition of the Society
Newsletter.  I would also like to draw your attention to a paper that has
recently appeared by John Corliss "An interim utilitarian ("User-friendly")
hierarchical classification and characterization of the protists" Acta
Protozoologica 33:1-51.

As stated in my editorial the problem that I have with Cavalier-Smith's and
Corliss' papers is that they have abandonded the very useful approach of
having a "consensus" taxonomy created by a panel of the world's experts.
Such one-person schemes are almost guaranteed to generate a great deal of
controversy.  With regards to the specific points raised by Andrew Roger of
what is wrong with the scheme, let me elaborate.

First of all, Andrew is correct in stating "...is one supposed to classify an
entire kingdom of eukaryotes using only characters and data that one has
generated oneself?"  Clearly this is NOT what is expected of anyone taking
on so large an undertaking.  One problem with Cavalier-Smith's paper is that
he has based much of it on rRNA sequence data that was generated primarily
in the laboratories of others but has chosen to ignore their suggestions for
how this data should be interpretted and used.  I am not closely enough
involved to comment at length here but some of the concerns that I have
heard raised include the use of entire sequences with little attention being
paid to proper alignment or use of informative vs. non-informative sites.
His statement that "In contrast to most published trees, no parts of the
sequences were masked out and excluded from the phylogenetic analysis except
for a few nucleotides at each end outside the usual PCR amplification
primers because such masking has a subjective element."  is considered to be
highly controversial.

With regards to other particulars, I find his creation of so many new taxa
to be disturbing.  This pertains not only to specific groups (e.g. I see
little justification for his erection of three new euglenid classes: Aphagea,
Peranemea, and Petalomonadea) but also to his use of higher taxa (kingdoms,
subkingdoms, infrakingdoms, and worst of all, parvkingdoms).  What are the
demarcations of these ranks?  By what criteria are new ranks created?

In closing let me reiterate my respect for Dr. Cavalier-Smith and his work.
There are very few researchers who have his command of the literature and a
project such as this one could not have even been attempted by most of us.
Also, it is not as Andrew states "... that the protistological community in
general is displeased with the actual content of Cavalier-Smith's
classification." for we are not.  Most of us accept the wisdom of his
formally grouping together the dinoflagellates, ciliates, and apicomplexans,
and whereas we may disagree with his use of terms such as the "Chromista"
and whether this assemblage warrants its own kingdom, we acknowledge and
respect his reasons for doing so.  Dr. Cavalier-Smith is a gifted researcher
and we would be intellectually impoverished if we were denied exposure to his

My editorial was a chastisement of the Society of Protozoologists and was
primarily geared for the members of that Society (hence its inclustion in
the Newsletter).  Now that it has been brought into the "open" by its
inclusion in this newsgroup I hope that the readers will understand my
reasons for writing it.

-Mark Farmer
Mark A. Farmer
Director, Ctr. Ultrastructural Research
University of Georgia, Athens, GA 30602
(706)542-4080 Voice   (706)542-4271 FAX
farmer at emlab.zoo.uga.edu


New Taxonomy - Old Problems

In a bold and controversial new paper entitled "Kingdom Protozoa
and Its 18 Phyla" (Microbiol. Rev. 57:953-994) Dr. Tom Cavalier-
Smith has erected a new taxonomic scheme that deals with the
Protozoa as he defines them (i.e. exclusion of his Archezoa,
Chromista, Plantae, Fungi, and Anamalia).  He has not only erected
a new taxonomic category (parvkingdom) but has assigned taxa to a
bewildering array of subkingdoms, infrakingdoms, superphyla, and
subphyla.  In doing so he has created a moderate firestorm of
protests from those (including myself) who disagree with a number
of the conclusions that he has reached and/or with his methods of
interpreting data that for the most part were generated by other
researchers.  That being said let me state quite clearly that the
purpose of my editorial is not to criticize Dr. Cavalier-Smith nor
to challenge any of the particulars of his work.  These are matters
that are best dealt with in other ways (e.g. open discussions,
publications, etc.).  Rather, my intent is to draw the Society's
attention to the gauntlet that has essentially been thrown down and
to rally us to meet the challenge that we now face.

There may be those who feel that such a debate about the
classification of organisms is without much merit.  However even as
we contemplate the beginning of the 21st century, the field of
taxonomy remains one of the most contentious and lively topics of
discussion.  The value of taxonomy rests in its ability to provide
new insights into the evolutionary relationships among organisms.
More importantly, an understanding of these evolutionary
relationships allows one to think in new ways.  For example, the
recent recognition of ciliates, dinoflagellates, and apicomplexans
as members of a monophyletic assemblage may lead to new approaches
in the study and treatment of human diseases such as malaria.  

Taxonomy also remains the primary and in some cases the only,
exposure that many people have to a particular group of organisms. 
As protozoologists we must be keenly aware of this because fewer
people can relate to protists than can recognize an animal, a
fungus, a bacterium or a plant.  It is these "casual" followers of
our field who are most likely to be influenced by papers such as
Dr. Cavalier-Smith's and others.  Those of us who are well informed
on the issues can form our own opinions, but those who either lack
the knowledge or the initiative are likely to accept such schemes
as dogma.

The creation of taxonomic schemes is a time honored tradition in
our field.  Beginning with M!ller, Ehrenberg, Dujardin, B!tschli,
and Stein, and continuing into modern times protozoologists have
sought to organize organisms into higher taxa.  In a dramatic break
with the past, the Society of Protozoologists embarked on a
innovative approach, namely to put forward a new taxonomy that was
arrived at by a consensus of a group of leading experts in the
field.  First under the leadership of R.P. Hall (1954) and later
chaired by B.M. Honigberg (1959) the Committee on Taxonomy and
Taxonomic Problems first published "A Revised Classification of the
Phylum Protozoa" in 1964 (J. Protozool. 11:7-20).  With the
publication of this paper any interested scientist could learn what
the latest thinking was regarding the evolutionary relationships
among different protists.  

Taxonomy is, by its very nature, an artificial construct and as our
knowledge of the protists changed so did our ideas concerning their
interrelatedness.  Once again, the Society rose to the occasion
with the publication "A Newly Revised Classification of the
Protozoa" by Levine et al. in 1980 (J. Protozool. 27:37-58).

Now we find ourselves in 1994.  In the years since Levine et al.
our knowledge has fairly exploded as the fields of electron
microscopy and molecular biology have provided us with a nearly
overwhelming amount of new data and ideas.  For several years now
the time has been ripe for us to share these new ideas in an
authoritative and definitive manner.  As the experts in the field
it is up to us to reach the best consensus that we can and to
disseminate this thinking to our colleagues in other disciplines. 
Towards this end a Committee on Systematics and Evolution headed by
John Corliss has tried to forge a unified taxonomic scheme.  It has
met with opposition, infighting, and even name calling.  This has
created a void which many have predicted would soon be filled.  Now
Dr. Cavalier-Smith has filled it and doubtless others are soon to

Clearly, passions run deep and new data appear every day that force
us to rethink our positions but despite these facts it is high time
that we as a Society of Protozoologists unite around a new
taxonomic scheme.  Granted it will not be perfect, no taxonomic
scheme ever can be, and not everyone will accept it in its
entirety.  Still, with the formation of a new Committee now headed
by David Patterson we once again have the opportunity to take the
lead and offer to the scientific community a compilation of our
best ideas as of 1994.  This should be an ongoing process and once
this new committee has completed its mission we should not wait too
many years before convening a new one to continue its work.  If we
do not support the scheme of any one individual then it is up to us
to offer something tangible in its place.  Until we do so we should
not criticize those who offer alternatives nor fault those who
blindly follow them.

---     Mark Farmer

[Editor's note: I invite all those who have an opinion on this
issue to submit their comments to the Newsletter]

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