Paradigm Shifts, Paradigm Drifts
As microbiology advances in a number of directions, our perspectives
on what has gone before and where it is going are bound to change
Moselio Schaechter
n 1962, Thomas Kuhn wrote a book of
I seminal importance, The Structure of
Scientific Revolution, wherein he intro-
duced the concept of “paradigm shift.”
Kuhn proposed that science advances
through a “series of peaceful interludes punctu-
ated by intellectually violent revolutions,” revo-
lutions in which “one conceptual world view
is replaced by another.” Paradigm shifts occur
rapidly; other significant insights take their time
in developing and are the stuff of “regular”
science. Borrowing from the language of influ-
enza virology, I will call the latter “paradigm
drifts.” How do these concepts apply to the
microbial sciences?
A paradigm shift, in the Kuhnian view, must
have some of these attributes: unprecedented,
open-ended, broad, simple, and fruitful. The
definition does not readily lend itself to quanti-
tative analysis, and I will use a personal reading
of Kuhn’s terms. I present here examples of
what in my mind constitute paradigm shifts in
microbiology. Each of them can be reduced to a
Moselio Schaechter
generalization that is both gracefully simple and
is Chair of the Mi-
exceedingly far-reaching. I realize that making
crobe Editorial
such choices may be audacious, but it is meant
Board and Distin-
to be merely a personal statement. My purpose
guished Professor,
here is primarily to elicit discussion.
Emeritus, Tufts Uni-
The Planetary Prevalence of Microbes. It has
versity School of
Medicine, Boston,
been known for centuries that massive rock
Mass.; Adjunct Pro-
deposits such as limestone, biogenic silica, and
fessor Emeritus,
coal are of biological origin, much of it micro-
Department of Biol- bial in nature. Still, it came as a surprise some
ogy, San Diego years ago when it was calculated that the Earth’s
State University, extant biomass is hugely microbial, the mi-
San Diego, Calif.; crobes perhaps comprising as much as half the
and Visiting total weight of living things. Much of this enor-
Scholar, University mous global cargo is found in the underground
of California at San water occupying the spaces within the rocks.
Diego. Here, metabolism is thought to be slow and
538 Y Microbe / Volume 4, Number 12, 2009
unhurried, yet the total flux contributes mean-
ingfully to geochemical activities. In the oceans,
microbes carry out about as much photosynthe-
sis as all land plants combined. Prokaryotic and
eukaryotic microbes share the work, perhaps
equally. Metagenomic techniques even allow
some measure of a census of the microbes
present in many habitats. We can securely con-
tend that geologic and atmospheric transactions
cannot be considered without including the ac-
tivities of microbes. Both quantitatively and
qualitatively, much of the planet’s metabolism is
microbial. And I haven’t even mentioned the
viruses!
Evolution. Two radical findings characterize
the modern view of evolution: the existence of
three domains of life and the lateral transfer of
genes between species. Both are fundamental
concepts, and both arose abruptly. Conceptu-
ally, both leave key questions open. Thus, what
is the origin of the three domains? Discussions
abound, especially about the ancestry of eukary-
otic cells. Of equal concern is the extent and
importance of lateral gene transfer. To what
degree does it inconvenience the very concept of
the Tree of Life? Or is it mainly relevant to the
lower taxa? Strongly held views exist on all
these questions. Are today’s tools adequate to
resolve them? Will more genome sequencing
and informatics analysis further our under-
standing of how microbes, and indeed all of life,
have evolved? Or must we await a new method-
ology?
Microbial Sociology (or Sociomicrobiology).
For most of the history of bacteriology, bacteria
were thought to perform as individuals, with
only a few significant interactions between
them. The few celebrated instances of collective
behavior, such as seen in certain differentiating
bacteria, were considered to be special cases. We
now know that bacteria and archaea build com-
plex and interactive communities, the result of
intricate conversations between them. But be-
yond that, even “planktonic” prokaryotic cells
communicate with one another. Much like in-
sects, they use specific chemical compounds as
their community organizers. These act to turn
on and off genes, direct the making of biofilms,
and trigger a response to inimical influences
such as antibiotics. Generally speaking, bacteria
and archaea act like the social insects. They are
indeed “superorganisms.” Not only must we
treat microbes with greater regard in general, we
may also presume that the behavior of all living
things evolved from that of the “simple forms of
life.”
Cellular Microbiology. (I consider this a
thorny term, as all microbiology is cellular,
but it seems to have traction, so I will use it
here.) Previously, hosts and symbionts, bene-
ficial or otherwise, were believed to go their
own separate way. The exception to this had
always been the viruses, while pathogenic bac-
teria, fungi, and protists were thought not to
have such a close interdependence with their
hosts. We now know that hosts and parasites
interact extensively at a molecular level, each
using molecular and structural constituents of
the other for their own apparent purposes.
The kinds of mutual appropriations and em-
bezzlements of course differ between specific
pairings, reflecting the skills and competency
of each member, but, in each case, the give and
take is extensive and has profound conse-
quence. Our thinking has shifted from viewing
symbiosis and parasitism in terms of pairs of
organisms engaged in a complex choreogra-
phy to a more unitary view in which the two
constitute a new whole.
Surely, readers will want to add to or subtract
from this list of paradigm shifts since, as I im-
plied above, there is considerable room for opin-
ions. Here I will posit that many of the most
exciting current developments in microbiology
qualify rather as paradigm drifts because they
are distinctly work in progress. I have no doubt
but that eventually they will lead to important
generalizations, but not quite yet. This view
does not diminish their grandeur and luster. I
present one example.
Microbial Cell Structure. Ours is the Age of
Imaging. Biology has rendezvoused with its vi-
sual origins. For much of its recent history, the
chemical way of looking at things biological
prevailed. Enormously contributory as it was,
visual it was not. How things have changed!
Now, every aspect of biology has benefited from
methodological developments in microscopy,
from the ability to visualize single molecules,
often within living cells, to the discovery of
bacterial cytoskeleton-like structures, to the
chance to “crawl” inside cells to see what they
are made of. Optical tweezers technology per-
mits the study of single molecules in action—
polymerizing, stretching, pulling, twisting. The
optical microscope is now transcending the bar-
rier of physical resolution, thanks to an array
of fancy methods with acronyms such as SI,
PALM, STORM. The electron microscope is not
left out, with progress in cryotomography and
other techniques, and neither are various scan-
ning probe microscopes. New views are gradu-
ally replacing old ones with regard to the behav-
ior of individual molecules and the structure of
cells and viruses. But, despite all these magnifi-
cent development, few generalizations are yet
possible in this field.
Now, how about the advances in such areas
as the regulation of gene expression, the animal
microbiome, the evolution of symbioses, and
many, many more? I would like to leave their
status as being open to discussion. You might
add to this list or argue about individual choices.
A suitable venue may be our blog, Small Things
Considered. Whether my choice of shifts and
drifts matches yours or not, no matter. Let us
rejoice in living at a time when the list of micro-
biological nominees is growing at such a rapid
pace.
Volume 4, Number 12, 2009 / Microbe Y 539