IMPORTANT PAPER: SYNOPSIS & TEXT

Ken Kinman kinman at HOTMAIL.COM
Mon Apr 20 07:59:02 CDT 1998


**TITLE: Another Woesian Myth Exposed As Simplistic and Homoplasious,
      Woese's "Stanier Memorial" Self-Serving Authoritarian Sophistry,
      And Finally Regrouping For "A True Renaissance In Bacteriology"
                         by Kenneth E. Kinman
      Citation: Journal of MetaBioSystematics, No. 9 (April 1998)
**SYNOPSIS: (1) Bacterial Diversity and Classification;(2) Mis-
conceptions on the distribution of ester and ether-linked lipids;
(3) Its Implication for the new "HYDROGEN HYPOTHESIS" of eukaryotic
origins; (4) the core of Lake's "Eocyte" theory; (5) Woese's totally
inappropriate choice of occasion ("Stanier Memorial" Lecture) to
criticize Stanier and self-servingly declare a Woesian "Renaissance";
(6) the derived nature of thermophilic life; (7) Whole Genome Sequencing
(what organisms should have higher priority?); and
(8) Trees of Life (Three Domains are simplistic and harmful).
        * * * * * * * * * * * * * * * * * * * * * * * * * *
***FULL TEXT OF ARTICLE:
     Before delving into parallel evolution and the homoplasious nature
of the ether lipid "character" (they actually do occur in Eubacteria,
even the branched-chain type, despite common belief), I would first like
to thank the NCBI taxonomy staff for quickly acting after my paper of
last October (text on my Internet homepage at:
www.geocities.com/CapeCanaveral/5074  ; the text of other relevant
papers are also found there).  Synergistes was not only removed from
Family Clostridiaceae, but from Firmicutes (my Posibacteracea)
altogether, and placed in a "group" of its own.  I was also encouraged
by the January 1998 paper of Hugenholtz et al. (Journal of Bacteriology,
180:366-376) which shows Synergistes branching next to the
Proteobacteria, and thus supports the view of my 1996 and 1997 papers.
These may seem like trivial matters at this point in time, but this
group may prove to be very important in fleshing out a true eubacterial
phylogeny.  Neither "Proteobacteria" (which is probably not holophyletic
anyway), nor Synergistaceae, are nearly as peripheral and unimportant to
bacterial evolution as present gene trees would indicate.  Just more
Woesian distortions that must be addressed.
     More importantly at the present time, however, both NCBI's taxonomy
and the Hugenholtz paper demonstrate a widespread reluctance to adopt a
stable Linnaean classification for bacteria, like the one I presented in
my 1994 book (The Kinman System: Toward A Stable Cladisto-Eclectic
Classification of Organisms; see footnote).  Instead we have a very
uncoordinated conglomeration of "groups", common names, formal names
(some poorly conceived), and "Odyssean" genera (wandering about without
a home).  Do we have to wait for years in a confusing limbo until
another edition of Bergey's Manual finally restores some order?  I think
this would be a mistake (especially since the last edition apparently
made little impact upon molecular biologists anyway), and my formal
classification of 1994 needs relatively little modification (although I
would like to expand it down to family, or even generic level).
     In any case, the genus Synergistes does have a home, namely Family
Synergistaceae Kinman, 1996.  And now that its distinctiveness is being
acknowledged, I here propose that it constitutes a new higher taxon,
Order Synergistales ord. nov.  I would also note that other distinctive
orders were proposed in the 1994 book, including Fibrobacterales,
Thermodesulfobacteriales (which have branched-chain ether-linked lipids,
as will be discussed below), and Verrucomicrobiales.   The latter name
has also been independently proposed by others and is gaining gradual
acceptance, and it is distinctive enough that I placed it in its own
Class Verrucomicrobea (in The Kinman System, 1994).
     WARNING:  I am definitely not advocating a mindless or rapid,
wholesale increase in higher taxa of bacteria.  On the contrary, I
believe it is Woese's "Three Domain Theory" which poses the added risk
of massive and unwarranted taxonomic inflation (on top of all the other
problems it is causing).  Hugenholtz et al.'s many "candidate divisions"
provide an unsettling omen that overreaction to newly discovered
bacterial diversity could initiate an excessive taxonomic pendulum
swing, particularly in the most distorted part of Woese's misrooted
phylogenies, namely in my Class Togobacteracea (where most of these
"candidate divisions" are popping up).  These extremes of homeless
genera on the one hand, and numerous candidate divisions on the other,
can only cause a confusing smoke screen that will prevent a stable
taxonomy and delay the inevitable realization of just how distorted and
damaging Woesian bacterial phylogenies actually are.
  >>>The Lipid Misconception---Another Woesian "Simplistication"<<<
     It is clearly not in the interests of Woese et al. to elaborate on
matters than run counter to their paradigm, thus allowing a continuation
of the resulting widespread notion that membrane lipids support a
"monophyletic" (holophyletic) Metabacteria ("Archaebacteria").  I
believe the scientific community at large must take a closer look.
Ether-linked lipids (sometimes even the branched-chain diether types)
actually do occur in Eubacteria (in Aquificales, Thermotogales,
Thermodesulfobacteriales, and no doubt other groups).  Furthermore,
halophilic Metabacteria contain some "ester-linked" lipids and
functional fatty acid synthetases (see Kamekura and Kates, 1988; in the
book Halophilic Bacteria, Rodriques-Valera, ed.).
     This distribution of lipids (along with the homoplasious tendency
of thermophiles to "prefer" ether-linked lipids to the less thermostable
ester-linked types) leads me to believe that many primitive Metabacteria
must have possessed various lipid combinations utilizing two linkage
types and two stereochemistries.  Furthermore, most of the
recently-discovered, non-thermophilic extant members of this group (in
both mesophilic and psychrophilic habitats) are only known from their
rRNA.  Once cultured, some of them could be shown to contain a weak
"ester-linked" composition (like the halophiles) or possibly even
stronger such compositions (especially if some of them lack strong
thermophiles in their ancestry--a possibility worth noting once one
ignores the Woesian myth of a thermophilic origin of life).  I will not
discuss murein here, but I would surmise that there was probably also a
fairly smooth transition between forms containing murein and
pseudomurein (probably no need to invoke convergence for this
character).
     For those who are caught up in 20 years of Woesian circular
reasoning, please do not be tempted to view ether-linked lipids as
"primitive" based upon their distribution in Woese's Three Domain trees.
As a former organic chemist myself, I can assure you that living systems
(and their organic constituents) have a great deal of difficulty
surviving thermophilic conditions.  It took a tremendous amount of
biochemical "pre-adaptation" (including ether lipids in most cases) for
thermophilic life to evolve (the hyperthermophiles in particular).
Years from now scientists will not only chuckle when they look at
Woesian "Trees of Life" (especially the eubacterial parts), but
philosophers of science will wonder why the primitiveness of thermophily
was ever taken seriously at all, much less for decades.
     Although I have not fully evaluated the recent and fascinating
"Hydrogen Hypothesis" for the origin of the eukaryotic cell (Martin and
Muller, 1998; Nature, 392:37-41), I would suggest to others (as I have
already suggested to them) a possible alternative to their solution of
the lipid problem addressed in their Figure 2(d).  In view of what is
related above, I think a more parsimonious solution would be that the
Metabacterial ("Archaebacterial") host of the first eukaryote (assuming
it was the host) may well have had a composite lipid membrane profile
all along.  It is even conceivable it had a predominantly ester-linked
lipid membrane.  The point is that we don't have to invoke reversals and
other unparsimonious explanations every time there are incongruencies
with Woese's ideas.  Once we begin really challenging the underpinnings
of Woesian ideas and phylogenies, many of the incongruencies and
puzzling paradoxes will simply disappear.
     In any case, once we have begun culturing the many "environmental"
members of Euryarchaea and Crenarchaea, we will be in a better position
to deal with the Metabacterial incongruencies more effectively.  This is
especially true for the latter, because Crenarchaea are just another
(but formal) name for Dr. Lake's "eocytes".  Although I disapproved of
his eocyte trees in the 1980's (which made Eubacteria too derived and
metabacterial groups too deep and archaic), his more recent eocyte trees
are much improved.  I still strongly object to viewing Eubacteria as a
"monophyletic" (holophyletic) group, but this is a widespread Woesian
misconception that is rarely challenged (but I continue my research in
trying to set that all straight).  However, I certainly wasn't about to
throw the baby out with the bathwater and have always embraced that part
of Lake's eocyte theory that views Crenarchaea (eocytes) as the
metabacterial (archaebacterial) component of the eukaryotic cell.  I
showed Eukaryota evolving from Crenarchaea in my recent book (The Kinman
System; see footnote) since they were the major component of the
chimaeric eukaryotic cell.  My own continuing studies of Woese's 16S
rRNA data further strengthens my belief in this central tenet of the
"eocyte" theory.
     >>>>Woese's Self-Serving Sermon At Stanier's Expense<<<<
     The Roger Y. Stanier Memorial Lecture of 11 March 1993, given by
Carl Woese, must have been rather uncomfortable (if not shocking) for
many microbiologists.  What a terrible choice of occasion to be branding
the Stanier years as "The Dark Age" and self-servingly declaring a
Woesian "Renaissance".  If I had then been aware of this and other
examples of such poor judgment (both socially and scientifically), I
would have never even begun my attempts to correspond with him in 1994.
This is doubly true in retrospect since I have not received a single
word of correspondence in return, and not even the courtesy of any
reprints.  Perhaps it is fitting that a bully in the pulpit is finally
beginning to get a taste of his own medicine.
     I firmly believe that (1) the lipid misconception discussed above,
(2) the reluctance to embrace the core of Lake's eocyte theory, and (3)
the clumsy, disinformational nature of present bacterial
classifications, are all further cases of prokaryotic evolution being
obscured by an intransigent refusal to let go of a much greater
misconception (namely a thermophilic origin of life and/or a
thermophilic cenancestor of all extant life), and we all know where that
misconception originated!  The discovery in 1977 that we had been
overlooking two important and closely related groups of Metabacteria
(Euryarchaea and Crenarchaea) was unfortunately ladened with a heavy
burden of erroneous notions, including: (1) a fundamental primitiveness
of thermophily, (2) "archaic" primitiveness of Eukaryota and
Metabacteria, and (3) "monophyly" (holophyly) of three simplistic
Urkingdoms.  I have finally concluded that Woese may never let go of his
Three Urkingdoms (a.k.a. Three Domains), in spite of contrary evidence
and criticism.  However, although rRNA sequences are extremely important
(and I rely on them heavily myself), it is foolhardy to view the Woesian
"Tree of RIBOSOMES" as a true "Tree of LIFE".  There are clearly Three
Domains of Ribosomes, but to simplistically declare Three Domains of
Life is not only illogical (as eminent scientists have repeatedly
noted), but also far more damaging than any of them ever imagined.
Eventually the Tree of Ribosomes and the Tree of Life will be one and
the same (but not with Three Domains).
     The reclassification of prokaryotes is progressing in spite of all
this, but we would undoubtedly be much further along without 20 years of
unresolved and unchallenged baggage. Perhaps microbiology would have
experienced a much easier transition if Metabacteria had been discovered
a year or two later by someone else.  I was truly convinced that my 1994
classification (of prokaryotes in particular) would facilitate, perhaps
even invigorate, the process of reevaluation.  Instead I have been very
disappointed by the lack of response to, understanding of, or even
willingness to consider, my contributions thus far.  Whether the
situation in bacteriology is remedied sooner or later, efficiently or
not, we may be shaking our heads 10 years hence in disbelief how clouded
our thinking has been.  The Three Urkingdoms were like boils (in need of
lancing) back in 1990.  Regretfully they were instead bandaged over,
spin-doctored into Three Domains, and allowed to fester ever since.
     And the claims in 1996 that the Methanococcus jannaschii genome
supports the Three Domain Theory seem to be little more than wishful
thinking in the form of nonsensical and unscientific sensationalism,
once again reflective of Woesian authoritarian sophistry.  Complete
genome sequencing is still too expensive to be making such unwise
choices as to which organisms should receive higher priorities.  For
those who think my tone has been too irreverent of late, it was at this
point (August 1996) that my frustration and concern became more like
indignation, especially when my letter to Science was not printed (even
though I expressed my reactions quite diplomatically).  Although never
published, that letter appears on my Internet homepage at:
www.geocities.com/CapeCanaveral/5074    Judge for yourself whether it
was worth printing.
     Ironically it was Woese himself who complained in 1993-94 that this
"is the way of paradigms"---that challenges to them are ignored and/or
scoffed at.  It seems to me this is a flagrant case of the pot calling
the kettle black, ignoring Mayr, Lake, myself, and others.  Microbiology
had every right (even a duty) to question Woese's paradigm, for he
appears to have used his good fortune (to be the first to discover
Metabacteria) to promote a lot of damaging nonsense and stubbornly
refuse to accept evidence to the contrary.  And it is not just Stanier
who has been unjustly criticized in this process, but also C.B. van
Niel, Ernst Mayr, and others.  Unfortunately when a significant portion
of his house of cards finally begins to crumble, it will be others who
will have to pick up the pieces.  The circular reasoning alone may have
done so much damage that it will probably take decades to assess its
scope.
     Recognition for my own work (much less funding for it) may never
come (especially for the bacteriological aspects).  In which case, I may
well continue to live impoverished and struggling to continue my
research.  But I will never regret having stood up for what I believe
and practice real scientific thinking.  It has been suggested to me that
I should give up this stressful and financially draining crusade and
redirect my talents elsewhere.  It may eventually come to that, but I
wouldn't feel right if I abandoned the effort when there seems to be at
least some progress being made.  If funding should eventually be found,
the spark would remain, but the ability to publish in peer-reviewed
("real") journals could temper my polemic, reduce the frustration, and I
might even become positively diplomatic once again.  Those who know me
realize that this is my natural inclination.  But if for some reason
this is that last of my papers on bacteriology, I wish you all luck in
the difficult period ahead.  Someone has to clean up the mess, and if
you kill or starve the messenger, he can't be around to help set things
right.
     Finally, although none of us knows for certain what tomorrow will
bring, the nature of my own work leaves me even more uncertain than most
what the future holds.  With that in mind, I would like to note that one
of the most often quoted papers in bacteriology is Woese, 1987, but I
wonder how many biologists have read it carefully.  As time goes on,
many of the assumptions and conclusions in that paper, look more and
more erroneously circular (if not outright fanciful).  If I don't get a
chance to expose the many other fallacies in that paper, I hope others
will do so, and that there will be less tendency in the future to quote
that paper as being so authoritative.  Viewing it as a firm foundation
on which to build seems ill-advised.  The real evolutionary story of
life has often taken twists and turns that fool those whose notions are
too simplistic, and whose minds are not open enough to accept credible
challenges.  Intransigence is unacceptable and is eventually exposed,
but unfortunately it is too often neither a timely nor efficient
process.  Biology, and bacteriology in particular, needs to take a hard
look at what has actually happened in the last 20 years, and make some
changes that will improve its future prospects.
                                           Kenneth E. Kinman
                                           P.O. Box 1377
                                           Hays, Kansas  67601
*****FOOTNOTE:  Kinman, K.E. 1994.  The Kinman System: Toward A Stable
Cladisto-Eclectic Classification of Organisms (Living and Extinct; 48
Phyla, 269 Classes, 1,719 Orders).  Published September 1994.
     Many libraries do not yet have this book.  However, it is available
(to libraries and individuals) from the author for $38.00 U.S. postpaid
(outside the U.S. add $5.00).  Libraries can access bibliographic
information about the book through OCLC/WorldCat.  An 8-page extract is
also available, describing and illustrating the new system, including
the cladisto-eclectic classification of the 48 phyla of organisms (cost
of book extract is $5.00 U.S. postpaid; $6.00 elsewhere).  The proceeds
help to fund further research.
Kenneth E. Kinman, P.O. Box 1377, Hays, Kansas  67601-8377
e-mail:   kinman at hotmail.com
      or  kinman at scientist.com
      or  kinman at usa.net
homepage:  www.geocities.com/CapeCanaveral/5074
     Feedback (positive or negative) on the above paper is encouraged
and welcome.  Thanks.  [Please forward this paper to any of your
colleagues who you think might find it of interest.]


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