Bad Language = Bad Science
The language in which a science is framed is all important. Terms
with imprecise or multiple meanings, strong, cathected connotations, or
even those inviting of alliteration (word play in general), have to be avoided
as much as possible. This was evident in Physics already at the time of
Newton, who often resorted to Latin (as does Law) to express himself more
precisely (and in Newton’s case perhaps to think unencumbered by
connotation). It is also one reason (though a minor one now) why so much
of the language of physics is mathematical.
For chemistry to come of age, it had to release itself from the
shackling language-culture of alchemy, a triumph we associate with the
name of Lavoisier. For biology to come of age …. Well it has still to do so,
still to struggle free of its stultifying burden of its anthropomorphisms,
ambiguities, imprecisions and its heavy load of cathected connotations.
[…buys you nothing to invoke it; explains your problem—…away
The root problem in biology is, of course, the language-culture of
Darwinism, which has stood for a century as an enormous boulder in the
path of our proper understanding of evolution—in a proper formulation of the
science of biology, that is, biological organization. Darwinism, however, is a
problem too vast to deal with in the present context. But, the science of
biology has many “teapot versions” of this great one in its language-culture
cabinet. And the one of especial interest to at this point is the continued
useage of the term/concept “Prokaryote”, not simply in microbiology, but
throughout biology. Every time this Trojan Horse of a term is used, in with
it come tacit concepts that staunch creativity, that prevent us from
recognizing, properly interpreting, what lies there before us. The great
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physicist Erwin Schrodinger branded such concepts/explanations as
“guesswork solutions”. “Such a fake” he said, “removes the urge to seek
after a tenable answer.” Moreover, “[s]o efficiently may attention be
diverted that the answer is missed even when, by good luck, it comes close
at hand”. Like it or not, that is the “Prokaryote”. And it is time that
“prokakyote” – the term and embedded concept – be removed from
biology’s lexicon.
The issue behind the issue of the Prokaryote
Uncharacteristically, the concept “prokaryote” had a unique origin.
Neither the term nor its contemporary meaning were in the microbiological
lexicon before 1962-3, and this first usage traces to a single source, the
microbiologist Roger Stainer. In 1962 Stanier and a co-author Cornelius van
Niel invoked the term for the first time (in English), and for the first time
made genuine scientific substance of it. They were not interested in the
prefix “pro-”, however. That had come from an earlier incarnation of
“prokaryote” in its casual useage among certain protozologists to distinguish
the objects of their interest from the bacteria in general; In its early
informal usage the term prokaryote had had evolutionary implications,
vaguely suggesting that bacteria were simpler and/or prior or possibly (some
or all of them ancestral to what then would be called “eukaryotes”, the
nucleated cells that comprise the world of animals, plants, and protests. But
the purpose for which the older informal name was now intended was
different. Stanier and van Niel were to use the term and the
prokaryote/eucaryote couple in their intent to put to rest once and for all
microbiology’s foundational issue. What was at issue here?
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Since the serious study of the microbial world began microbiologists
had struggled to make a basic science of it. It was far more the potpourri of
disease problems, sterility problems, fermentation problems, which had
initiated its investigation. The microbial world obviously presented a major
biological challenge in its own right and, therefore, had to be recast in a
scientifically proper setting. To do so required great improvements in
technique, initially in microscopy, but also in isolation and general handling
of the organisms involved. Enormous problems awaited in the surprisingly
and highly variable physiologies of microscopic organisms and in their
peculiar and varied communal organizations. But to properly study the
microbial world the early pioneers had first and foremost to create the
proper axiomatic base for their new discipline – recognizing the naturally
defined categories, selecting the pertinent facts and key concepts – from
which to bring forth the right “language” in which the discipline could
productively work, could be deeply and broadly explored.
There was, in my opinion, a crucial moment in the development of
microbiology at which the axiomtic foundation began to take concrete form.
Had it continued to do so, microbiology would have been a very different
discipline than it would become during the 20th century; and could have well
changed the course of the biology we know today, instead of standing by as
a passive witness of biology’s conceptual development. But it came and
went with the career of one man, Martinus Beijerinck -- arguably the
greatest microbiologist in the history of the discipline. The crucial moment,
when Beijerinck briefly explained the bases for his study of the microbial
world occurred during his acceptance of the Leeuwenhoek Medal--microbiology's highest honor---in 1905. At the ceremony a member of his
audience had risen to ask his conceptualization of the discipline’s
foundational issue—i.e., asked him his view and practice of microbiology.
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Beijerinck’s answer was: "[My] approach can be concisely stated as the
study of microbial ecology, i.e., of the relation between environmental
conditions and the special forms of life corresponding to them. It is my
conviction that ... this is the most necessary and fruitful direction to guide us
in organizing our knowledge of that part of nature which deals with the
lowest limits of the organic world, and which constantly keeps before our
minds the profound problem of the origin of life itself." What Beijerinck was
sketching here were the foundations for the proper study of the microbial
world, something that would require another century to develop.
He
understood what his successors did not: that organisms cannot be
understood apart from the ecologies and their communal organizations.
Indeed, he understood that the organism does not define the organismal
community, so much as the reverse. And he understood that the microbial
world was and exquisite study in the origin of life and, so, evolution.
Beijerinck was a true biologist who understood that microorganisms must be
studied in their own terms!
Albert Jan Kluyver succeeded to Beijerinck’s post. He was basically a
chemist with an interest in natural products. Microbiology required a lot of
on the job training for him. He never had an abiding interest in bacteria as
organism; and less, it appears, in their community structures and ecological
relationships. But he could and surely did understand them in a
physiological, biochemical sense. Under Kluyver’s guidance microbiology
underwent, in his own words “a change of face”. It became the most
prominent sub-discipline of the burgeoning science of biochemistry. Kluyver
would set sail on the same wind that blew through most of the other 20th
century disciplines, sum-of-the-parts reductionism.
With Kluyver,
microbiology’s foundational issue, which Beijerinck had started to resolve,
returned; and continued to plague the discipline: biochemistry could never
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serve as the axiomatic base for an organismal discipline, especially one as
unique as the microbial world.
The Prokaryote Hypothesis
As microbial biochemistry reached its reductionist apotheosis,
Kluyver’s discovery of the unity of biochemistry and the tour de force that
microbial biochemistry had become, the foundational issue, which had
simmered the while, in Stanier and van Niel’s seminal 1962 article “The
Concept of a Bacterium”, designed to settle it once and for all. The authors
saw the issue as “the abiding intellectual scandal of bacteriology”, which
which they declared to be “the absence of a clear concept of bacterium”.
This, of course, was not the way Beijerinck had seen it -- for it failed to
recognize the interconnectedness of the individual microbe with its ecology,
community structure, or evolution. But the recognition of the invidivual
bacterium as an organismal entity was still a step above the total
reductionism inherent in Kluyver’s “bag of enzymes’ approach to
microorganisms.
Although “the problem of defining these organisms as a group in terms of
their biological organization” had a proper scientific ring to it, the way
Stanier and van Niel went about settling the problem did not. It was lacking
in its logic, which seemed to betray a prejudice in their approaching the
question.
Disproof of the Prokaryote Hypothesis
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-------------------------The beginning of the 21st Century sees institutional biology in a
peculiar place. On one hand, the triumphs of molecular biology and genetics
have given scientists an entirely new understanding of the mechanisms of
cells, and even the power to manipulate the properties of organisms. On the
other hand, the common wisdom and education in deep evolution and
classification is not in a modern state, and indeed is rotten. And
microbiologists stand at the crux of doing something about it. Why do I
assert this? How did it happen? What do microbiologists have to do with it?
The Problem
At issue here is the notion of “prokaryote” and the model of biological
organization and evolution that it elicits.
This model, explicit in most
textbooks and which I term the prokaryote-eukaryote model, posits that
fundamentally there are two kinds of organisms, prokaryotes and
eukaryotes, defined by the presence or absence of a nucleus (more properly
nuclear membrane). Moreover, the model proposes that prokaryotes gave
rise to eukaryotes. The course of evolution promoted by the prokaryoteeukaryote model is diagrammed in the accompanying figure.
The problem, however, is that there isn’t any such thing as a
prokaryote. And therein is the rot. The notion of prokaryote was a logical
fallacy from the beginning because the definition, an “organism without a
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nucleus,” is a negative definition. No one can tell you what a prokaryote is,
they can only tell you what it is not. The course of evolution, from
prokaryote to eukaryote, was a guess – an untested hypothesis. Yet,
institutional biology bit deeply into that hypothesis. The prokaryoteeukaryote model, through the very language, dominates textbooks, journals
and discourse in matters of deep evolution. But it proved wrong.
Where It Came From - The Short History of Prokaryote
It is important to understand that the concept of prokaryote is not
based on scientific results. Rather, it is based on historical conjecture. The
history of the prokaryote concept and its incorporation into the common
wisdom of biologists has been reviewed (###). Prokaryote had its origins in
evolutionary models of the 19th Century. Ernst Haeckel, in his fourkingdoms classification trees in the 1860s, put “monera” at the base of the
eukaryotic kingdoms of plants, animals and protists (microbial eukaryotes).
A century later, in the 1960s, the ecologist ### Whittaker added the
kingdom of fungi to Haeckel’s tree, giving us the popular textbook
organization of biology into five kingdoms, with monera at the origin. Also
in the 1960s, the name “monera” became interchangeable with
“prokaryote,” the name popularized by Roger Stanier and his colleagues M.
Doudoroff and E.A. Adelberg, initially in the 2nd edition of their widely used
textbook “The Microbial World” (###).
The terminology of prokaryote was welcomed by microbiologists and
then was incorporated into the language of biology in general. It is curious
that the nomenclature of “monera” never caught-on among earlier
microbiologists, but “prokaryote” was embraced immediately. I speculate
that the terminology of prokaryote and eukaryote simply sounded scientific,
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as if we finally understood something about the process of evolution, had
gone beyond Haeckel’s monera. But, in fact, prokaryote was not much more
than a name-change from monera. The prokaryote-eukaryote model
remains, after all, a 19th Century notion based on what proved to be bad
guesses.
The Disproof of Prokaryote
The notion of prokaryote was disproved in 1977, with Carl Woese’s
discovery of archaea and the first articulation of a rudimentary molecular
phylogenetic tree that related representatives of the most diverse forms of
life (###). Woese, through comparisons of ribosomal RNA (rRNA)
sequences from different organisms, saw not two relatedness groups, two
kinds of organisms, prokaryote and eukaryote, but three: bacteria,
eukaryotes (which indeed proved monophyletic) and what came to be known
as archaea. Woese originally named the latter group “archaebacteria,” but
this was changed to “archaea” when it became clear they were
fundamentally distinct from bacteria. “Archaebacteria” continues to be seen,
usually perjoratively, as backhanded criticism of the three-domains concept.
Woese’s phylogenetic, three-domains model of relationships and
evolution is experimentally grounded and stands in stark contrast to the
prokaryote-eukaryote model, as diagrammed in the figure. The threedomains pattern shows that eukaryotes constitute a phylogenetically
coherent group, but there is no specific group on which to pin the label
“prokaryote.” Both archaea and bacteria would qualify through their lack of
a nuclear membrane, but these two groups are not specific relatives.
Indeed, one of the two, archaea, is more closely related to eukaryotes than
archaea are to bacteria. This relationship is supported not only by molecular
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phylogeny, but also by many properties of archaeal and eukaryotic cells
compared to bacterial cells (###). I know of no scientifically grounded data
that would call into question the basic pattern of the three-domains
relationships. A substantial and increasing body of scientific evidence
refutes the notion of prokaryote.
Additionally, the phylogenetic model shows no specific group of
organisms that preceded the eukaryotes. The textbook and common
wisdom notion that eukaryotic cells arose late in the history of Earth by
fusion of two prokaryotes are incorrect. Indeed the mitochondria and
chloroplasts were derived by fusion between bacteria, which became
symbionts, and ancestral eukaryotic cells (not shown in the figure). But the
ancestral, eukaryotes must have been already well in place. This history is
seen in the molecular phylogenetic tree as the nuclear line of descent. The
tree shows that the nuclear line of descent is as old as the archaeal line and
was not derived from either archaea or bacteria. The molecular results say
nothing at all about whether or not the earliest eukaryotes possessed
nuclear membranes. In fact, in the light of the sequence comparisons, the
presence or absence of the nuclear membrane or other morphological
property is irrelevant for classification or for deduction of the large scale of
biological organization.
Some Would Argue
Not only did the disproof of prokaryote initially fall on deaf ears, the
result was contested and continues to be denied by many. Prokaryoteeukaryote became solidly entrenched in textbooks and journals, and the
proponents of the concept of prokaryote continue to argue its merits with
religious fervor.
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They argue for instance that bacteria and archaea are united by their
very small size. But they ignore that many microbial eukaryotes overlap the
bacterial and archaeal size ranges. They argue that bacteria and archaea
are united in use of coupled transcription and translation. This is not
meaningful, rather, is just another twist on the presence or absence of the
nuclear membrane. The barrier of the nuclear membrane precludes
eukaryotes from participation in the comparison. At the last resort, the
proponents of prokaryote insist, “You have to call them something.” But
that’s the problem: there isn’t any “them.” The molecular phylogenetic
results, bolstered by decades of biochemical corroboration, show that there
is no natural grouping that would correspond to prokaryote.
Some might argue that the prokaryote terminology is a convenient
classification (for what?) and that historical usage justifies continued usage.
These rationalizations are scientifically inappropriate, however. A critical
point here, one usually missed by proponents of the prokaryote concept, is
that scientific classification is not a convenience. As scientists we must
observe nature and classify accordingly. As Darwin insisted, “Our
classifications will come to be, as far as they can be so made, genealogies.”
“Prokaryote” doesn’t fit the observed genealogy. It needs to be retired from
the language of biology. It has become a distraction, another example of
Intelligent Design that didn’t work out.
Why It Matters
Any scientific field rests on two foundations of understanding, both of
which must be grounded on experiment, not conjecture.
One foundation
requires understanding of the order, the organization, of the subjects of
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study. Thus, the chemist would refer to the periodic table to understand
chemical reactivities; biologists look to phylogenetic relationships to
understand properties of organisms. The other foundation of any scientific
field is how those subjects of study change. Chemists study reaction
mechanisms and radioactive decay; astronomers study the HertsprungRussell series for the evolution of stars; biologists reflect on phylogenetic
trees, maps of the course of evolution. Critical foundational issues for
progress in biology, therefore, are proper perceptions of phylogenetic groups
and relationships, and consequently the path of evolution. The prokaryoteeukaryote notion fails in both these regards. In contrast, the three-domains
pattern of life’s organization and large-scale path of evolution is scientifically
grounded.
What To Do about It and Why Microbiologists are Critical
Institutional biology is now heavily invested in the prokaryote concept.
The language permeates our literature and thereby pollutes understanding
of foundational issues in biology. One problem that faces efforts to rectify
matters is that most students, biologists and authors of general textbooks
don’t think very much about microbes. Their world is generally that of large
organisms. They, unlike microbiologists, are not faced with trying to make
sense of a vast diversity of life with comparatively little variation that we can
observe without resort to biochemistry and gene sequences. So most
biologists ignore, or pay only lip service, to recent discoveries in deep
phylogeny; the classification of “prokaryote” sweeps microbial diversity
under the rug. The three-domains phylogenetic model is beginning to
appear in textbooks, but usually as just another method of classification,
along with the Five-Kingdoms scheme. The implications of the three-domain
pattern of evolution are seldom broached. What to do about it?
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The retirement of prokaryote from the lexicon of biology will be slow
because it is now so deeply entrenched into institutional biology.
Consequently, movement toward the retirement of prokaryote needs to be
catalyzed. Microbiologists and teachers of microbiology are in the best
position to effect change. Their organisms span the three domains and the
phylogenetic perspective is evident and necessary. Proper treatment of
these issues by microbiological journals and textbooks will lead to
modernized general texts. An early challenge to microbiologists is to stop
using the term “prokaryote.” This is hard to do because of long
conditioning. Those tempted still to use it must realize, however, that they
saddle their students with misconception and muddy their thinking about
foundational issues in biology.
How can teachers broach this issue in the face of the currently
pervasive reference to prokaryotes in journals and textbooks? One way is to
use the discordance between recently emerging data and the textbook
notions as a wonderful example of how science, biology in this case, is an
ongoing, living process. Bringing the subject to students shows them how
new information based on experimental evidence can fundamentally change
understanding. Dealing with the prokaryote issue provides a good example
of testing specific hypotheses with experimental data, with results important
for biology. Phylogenetic trees, maps of evolutionary relationships, are
straightforward metaphors for the course of evolution and are not hard for
students to understand in essence. The three domains concept of course
poses many questions, but it also provides a solid foundation for progress
toward answering those questions.
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