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ScienceWeek
SCIENCE-WEEK
A Weekly Email Digest of the News of Science
A journal devoted to the improvement of communication
between the scientific disciplines, and between scientists,
science educators, and science policy makers.
January 1, 1999 -- Vol. 3 Number 1
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Science keeps moving us away from the Apes.
Of course, if one wants to be an ape, one
objects to the movement.
-- Anonymous
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Contents of This Issue:
1. On the Uses of Science by Society
2. On Simple Ordering in Complex Fluids
3. Atmospheric Science: El Nino Dynamics
4. Evolution: Jurassic Angiosperm Fossils
5. Molecular Biology: Megaplasmids vs. Minichromosomes
6. On Prions and Prion Diseases: A Nobel Lecture
7. On the Current Status of Tuberculosis
Following the main text: Notices, subscription information,
editorial contacts, etc.
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1. ON THE USES OF SCIENCE BY SOCIETY
Carolyn Shoemaker (US Geological Survey, US) (*Note #1) presents
an essay on the various uses of science by society, the author
making the following points: 1) From the days when humans first
emerged as thinking beings, they have cultivated a curiosity
about the unknown and a desire to explore it. Where did we come
from? Why are we here? Where does our future lie? These are age-
old questions that we are still exploring. 2) Society's
egocentric beliefs were gradually forced to yield to the
realization that Earth was not the center of the Solar System,
that there was more -- a whole universe beyond. 3) Clearly,
science and society are intricately intertwined, and as one
progresses, so does the other. Pure science, the search for
knowledge without knowing where it will lead, is part and parcel
of what will make the world a better place for all mankind. The
more we learn, the more questions we can ask and the more answers
we can obtain. 4) Society may not always look favorable on
science, thinking it too difficult, too technical, or too
abstruse to apply to most people. But as society struggles to
find answers to its problems, it would do well to remember that
science has touched upon and improved almost every aspect of our
lives. We must therefore conquer our fears so that we can
continue to progress on all fronts... The author concludes:
"Science will likely provide the answers for our future and,
indeed, whether we as a species have a future at all. The
challenge awaits us."
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Carolyn Shoemaker: Space -- Where now, and why?
(Science 27 Nov 98 282:1638)
QY: Carolyn Shoemaker, US Geological Survey, 2255 North Gemini
Drive, Flagstaff, AZ 86001 US.
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... ... *Note #1: In 1993, Eugene Shoemaker, Carolyn Shoemaker,
and David Levy discovered the comet Shoemaker-Levy 9, the first
comet to be seen in an orbit around a planet (Jupiter), rather
than in an orbit around the Sun, and the first large object to be
seen impacting another body. The comet was in a 2-year orbit
around Jupiter, having been captured by Jupiter in or before
1929. A close approach to Jupiter (21,000 kilometers) in July
1992 had disrupted the nucleus into at least 21 fragments, and
these fragments hit Jupiter during the week of 16-22 July 1994.
The impacts produced prominent dark spots on Jupiter, visible
even in small amateur telescopes, and these dark spots
subsequently merged into a dark belt that persisted for 8 months.
Eugene Shoemaker died instantly in an automobile accident in
northwest Australia in 1997; his wife Carolyn Shoemaker was badly
injured in the accident but she survived. [SW Note: For more
information, see URL: ]
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Summary & Notes by SCIENCE-WEEK 1Jan99
2. ON SIMPLE ORDERING IN COMPLEX FLUIDS
A colloid is a system of particles 1 to 1000 nanometers in
diameter dispersed in another phase. A colloidal crystal is a
periodic array of suspended colloidal particles, the array
arising spontaneously in a "monodisperse" colloidal system under
proper conditions. A monodisperse colloidal system is simply a
colloidal system in which the suspended particles have identical
size, shape, and interaction. ... ... A.P. Gast and W.B. Russel
(2 installations, US) review current research on ordering in
complex fluids and 2-dimensional crystals, the authors making the
following points: 1) One important feature of colloidal
suspensions is that the sub-micron particles are subject to
constant Brownian motion from the thermal fluctuations in the
surrounding solvent. Thus, to some degree, the particles can be
considered as effective molecules and treated according to the
theories of statistical mechanics. Because the solvents often
contain -- in addition to the colloidal particles -- dissolved
ions, polymer molecules, surface-active molecules, and other
small solutes, colloids are referred to as a general class of
complex fluids. 2) Perhaps one of the most important answers to
the dreams of physicists has been the development of colloidal
particles that interact by means of hard-sphere repulsions...
Entropy is usually thought to bring about disorder. But in a
system of hard spheres, particles gain entropy by arranging
themselves equidistantly from one another to maximize the space
in their vicinity, and thus they are compelled to order. 3) The
addition of a "soft" (i.e., long-range) repulsion to colloidal
particles can keep them sufficiently separated that the *van der
Waals attraction is negligible, rendering the suspension stable
against aggregation under a variety of conditions. Most commonly,
aqueous suspensions are stabilized by the *screened electrostatic
repulsion between charges imparted by the *Debye length, which
scales inversely with the square root of the *ionic strength of
the suspension. 4) The disorder-order transition for particles
having purely repulsive interactions persists when attractive
interactions are added... In aqueous systems, adding electrolytes
to screen the electrostatic repulsion between charged particles
can induce aggregation by means of van der Waals attraction. 5)
The complex structure of proteins can often be deciphered using
the power of crystallography -- but only if the proteins can be
crystallized. Some proteins form 2-dimensional arrays when
attached to a lipid monolayer floating on top of an aqueous
solution, and the monolayer of proteins can then be transferred
to an electron microscope grid for imaging and study by electron
diffraction... Although proteins remain complex in their detailed
structure and interactions, they provide ample opportunity to
study the general phenomenon of crystallization at both colloidal
and molecular scales.
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A.P. Gast and W.B. Russel: Simple ordering in complex fluids.
(Physics Today December 1998)
QY: Alice P. Gast, Stanford University 415-723-3058.
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Text Notes:
... ... *van der Waals attraction: (also spelled Van der Waals)
Considering molecules that have permanent dipoles, and molecules
that can have dipoles induced by the electric fields of other
molecules, there are three possible mechanisms recognized in the
formation of the van der Waals bonds: 1) the orientation effect,
in which molecules rearrange themselves in their mutual
electrical fields, the rearrangements involving reorientations of
whole molecules; 2) the static induction effect, in which
molecules that are static monopoles (ions) or dipoles may induce
a static rearrangement of the electron distribution of other
molecules; 3) the dynamic induction effect, or "dispersion"
effect, in which any molecule, polar or nonpolar, may induce in
other molecules transient electron distribution rearrangements
that are time-variant. All these mechanism involve interaction
energies, and they are "bonds" in the sense that they all involve
energetic couplings between molecules.
... ... *screened: In general, screening is a reduction of the
effective electric field at a point, the reduction due to the
space charge of ambient charged particles of sign opposite to the
source of the field.
... ... *Debye length: (Debye shielding length, Debye-Huckel
screening radius) A characteristic distance in a system of
particles beyond which the electric field of a charged particle
is shielded by particles having charges of the opposite sign.
... ... *ionic strength: A measure of the average electrostatic
interactions among ions in an electrolyte. Quantitatively defined
as one-half the sum of the terms obtained by multiplying the
molality of each ion by its valence squared.
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Summary & Notes by SCIENCE-WEEK 1Jan99
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Related Background:
ATTRACTION BETWEEN LIKE-CHARGED SPHERES IN A CHARGED PORE
A colloid is a system of particles 1 to 1000 nanometers in
diameter dispersed in another phase, and such systems,
particularly systems of electrically charged colloids, have
important practical significance and are also of considerable
theoretical interest. The existence of long-range attractive (as
opposed to the expected repulsive) electrostatic forces between
particles of like charge is one of the current major
controversies of colloid science. The established classical
theory (Derjaguin-Landau-Vervey-Overbeek) of colloidal
interactions predicts that an isolated pair of like-charged
colloidal spheres in an electrolyte should experience a purely
repulsive *screened electrostatic (coulombic) interaction. Direct
measurements of such interactions have shown quantitative
agreement with the classical theory, but recent experiments have
provided evidence that the effective interparticle potential can
have a long-range attractive component in more concentrated
suspensions and for particles confined by charged glass walls.
This long range attraction in concentrated systems is apparently
due to multi-body interactions. Theoretical explanations have
been proposed but remain the subject of controversy.
... ... Bowen and Sharif (University of Wales, UK) now present a
quantitative theoretical explanation of the attractive forces
between confined colloidal particles, the theory based on direct
solutions of the classical nonlinear Poisson-Boltzmann equation
for two like-charged spheres confined in a cylindrical charged
pore. The calculations show that the attraction may be explained
by the redistribution of the electric double layer of ions and
counterions in solution around the spheres, owing to the presence
of the wall. The authors suggest there is thus no need to revise
the established concepts of underlying theories of colloidal
interactions. [Editor's Note: The theoretical result in this
paper is unequivocal: the calculation shows that for the given
boundary conditions, the force between two particles of like
charge dips below zero (i.e., becomes attractive) before
returning to zero at infinite distance.]
QY: W. Richard Bowen
(Nature 18 Jun 98 393:663) (Science-Week 3 Jul 98)
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Related Background:
COLLOIDAL CRYSTAL FILMS AS CHEMICAL SENSORS
In chemistry, a ligand is any molecule that is bound by another
molecule. A colloidal crystal is a periodic array of suspended
colloidal particles, the array arising spontaneously in a
"monodisperse" colloidal system under proper conditions. A
monodisperse colloidal system is simply a colloidal system in
which the suspended particles have identical size, shape, and
interaction. Osmotic pressure is the pressure exerted by a
dissolved material in a solution on a semipermeable membrane or
phase separating the solution from another solution or from pure
solvent. John H. Holtz and Sanford A. Asher (University of
Pittsburgh, US) report the preparation of a material that changes
color in response to selective binding of ligands (analytes). The
material is a crystalline colloidal array of polymer spheres
(approximately 100 nanometers in diameter) polymerized within a
hydrogel that swells and shrinks reversibly in the presence of
certain analytes (for example, ions and glucose). The basis for
the response is the diffraction of light determined by the
crystalline lattice spacing, which changes as the gel swells or
shrinks in response to osmotic pressure changes.
QY: S. Asher
(Nature 23 Oct 97) (Science-Week 14 Nov 97)
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Related Background:
UNEXPECTED SHAPES FORMED BY COLLOIDS IN MICROGRAVITY CONDITIONS
Colloids are extremely small phases (e.g., solid particles) in
the range one nanometer to one micron dispersed in a larger phase
of a different substance, for example in water. They can be
bubbles, globules, microcrystals, etc. In the 1930s, many cell
biologists were excited by the study of colloids because the
interior of the living cell, protoplasm, has many properties of a
colloidal suspension. These days the study of colloids is almost
exclusively the province of the physical chemist. Although
colloidal particles are small, they are much larger than
molecules, large enough to perhaps be affected by gravitational
forces. This week the results of experiments with uniform
colloidal polymer particles carried out in microgravity
conditions aboard the space shuttle Columbia in November 1995
were reported by Jixiang Zhu et al (Princeton University, US;
NASA Lewis Research Center, US; University of Bristol, UK;
Johnson Space Flight Center, US). It was found that the colloidal
crystallization properties of the particles studied are indeed
significantly different under microgravity conditions.
Theoretical models of the behavior of colloidal suspensions
therefore need to take into account the gravitational forces
acting on the particles.
(Nature 26 June) (Science-Week 3 July 97)
3. ATMOSPHERIC SCIENCE: EL NINO DYNAMICS
The term "El Nino" was originally used by Peruvian fishermen for
a warming of coastal waters that begins around Christmas (*El
Nino* is Spanish for "the Christ child"). The term is now used to
refer to the large-scale warming of the entire tropical Pacific
that takes place every 4 years on average and alternates with an
opposite cold phase (sometimes called La Nina).
... ... J.D. Neelin and M. Latif present a review of current
models of El Nino dynamics, the authors making the following
points: 1) The El Nino/Southern Oscillation phenomenon (called
ENSO) is the strongest source of natural variability in Earth's
climate system. Although ENSO originates in the tropical
latitudes of the Pacific Ocean, its climate impact is felt
globally. Variations in major rainfall systems that are
attributed to ENSO range from droughts in Indonesia and Australia
to storms and flooding in Ecuador and the US. 2) The crucial role
of the interaction between the ocean and the atmosphere in the
tropical Pacific was first postulated in 1969 by *Jacob Bjerknes,
and the development of quantitative models has progressed during
the past 3 decades. The essence of the current Bjerknes
hypothesis, as it is called, is that ENSO arises as a coupled
cycle in which anomalies in sea surface temperature in the
Pacific cause the trade winds to strengthen or slacken and, in
turn, drive the changes in ocean circulation that produce
anomalous sea surface temperatures. Ocean-atmosphere feedback can
amplify perturbations in either the equatorial sea surface
temperature or what is called the Walker Circulation -- the
thermodynamic circulation of air parallel to the equator. 3)
Although the oscillatory aspect of ENSO behavior is now
understood reasonably well, the irregularity of the observed
cycle is a subject of active research. There are currently 3
contending hypotheses for the source of ENSO irregularity: a)
*deterministic chaos within the *nonlinear dynamics of the slow
components of the coupled system; b) uncoupled atmospheric
weather noise; c) long-term variation in the climatic state
affecting ENSO. Since the irregularity of ENSO limits its
predictability, and since these 3 sources of irregularity affect
predictability differently, this particular issue has practical
as well as theoretical importance. The authors conclude: "We must
bear in mind... that only for particular circumstances can we
expect that forecasts will push past the limits to predictability
set by the internal variability of the atmosphere."
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J.D. Neelin and M. Latif: El Nino dynamics.
(Physics Today December 1998)
QY: J. David Neelin, Univ. of Calif. Los Angeles 310-825-4321.
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Text Notes:
... ... *Jacob Bjerknes (1897-1975): Norwegian-American
meteorologist, not to be confused with his father Vilhelm
Bjerknes (1862-1951), the noted Norwegian atmosphere physicist.
... ... *deterministic chaos: See the note on chaotic
fluctuations in the following background report.
... ... *nonlinear dynamics: In general, this refers to any
dynamical system in which some or all of the behavior of the
system is not a linear function of the input to the system.
-------------------
Summary & Notes by SCIENCE-WEEK 1Jan99
-------------------
Related Background:
ON CLIMATE FORCINGS IN THE INDUSTRIAL ERA
A "climate forcing" is an imposed perturbation of the Earth's
energy balance with space, for example, a change of the solar
radiation incident on the planet, or a change of carbon dioxide
in the Earth's atmosphere. The unit of measure of climate forcing
is Watts per square meter. Thus, the forcing due to the increase
of atmospheric carbon dioxide since pre-Industrial times is
approximately 1.5 Watts per square meter. Climate change is
combination of deterministic response to forcings and *chaotic
fluctuations -- the chaos a consequence of the nonlinear
equations governing the dynamics of the system. Quantitative
knowledge of all significant climate forcings is needed to
establish the contribution of deterministic factors in observed
climate change and to predict future climate. J.E. Hansen et al,
in a review of current considerations concerning climate forcings
in the Industrial era, make the following points: 1) The forcings
that drive long-term climate change are not known with an
accuracy sufficient to define future climate change. 2)
Anthropogenic greenhouse gases, which are well-measured, cause a
strong positive (warming) force. But other, poorly measured,
anthropogenic forcings, especially changes of atmospheric
aerosols, clouds, and land-use patterns, cause a negative forcing
that tends to offset greenhouse warming. 3) One consequence of
this partial balance is that the natural forcing due to solar
irradiance changes may play a larger role in long-term climate
change than inferred from comparison with greenhouse gases alone.
Current trends in greenhouse gas climate forcings are smaller
than in popular "business as usual" or 1 percent per year carbon
dioxide growth scenarios. The authors suggest that a summary
implication of their considerations is a paradigm change for
long-term climate projections: uncertainties in climate forcings
have supplanted global climate sensitivity as the predominant
issue. The authors further suggest that climate forcing scenarios
are essential for climate predictions, but if only one forcing
scenario is used in climate simulations, as has been a recent
tendency, the scenario itself is likely to be taken as a
prediction, as well as the calculated climate change. The authors
recommend that the use of multiple scenarios will aid objective
analysis of climate change as it unfolds in coming years.
-----------
J.E. Hansen et al (6 authors at National Aeronautics and Space
Administration, US)
Climate forcings in the Industrial era.
(Proc. Natl. Acad. Sci. US 27 Oct 98 95:12753)
QY: James E. Hansen
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Text Notes:
... ... *chaotic fluctuations: The term "chaotic", in this
context, is specific. In the study of physical systems, the
term "chaotic behavior" has a specific meaning: the behavior of a
system is said to be "chaotic" if its final state is so sensitive
to the system's precise initial conditions that the behavior of
the system is in effect unpredictable and cannot be distinguished
from a random process, even though the behavior of the system is
strictly determinate in a mathematical sense. In other words, a
deterministic system characterized by extremely sensitive
instabilities, despite the system being determinate, can exhibit
behavior that is unpredictable, and the system is then called
"chaotic". During the past several decades, the analysis of such
chaotic systems has intrigued both physicists and mathematicians.
-------------------
Summary & Notes by SCIENCE-WEEK 4Dec98
-------------------
Related Background:
A SCIENTIFIC BASIS FOR CLIMATE FORECASTING
At the beginning of the 20th century it was believed that it
should be possible to predict weather by solving the mathematical
equations that describe the physical laws that govern the motion
of air. It took several decades to develop an appropriate set of
equations and numerical and computational techniques to solve
these equations, and by 1960, routine weather predictions using
global observations, complex mathematical equations, and fast
computers seemed immediately at hand. The promise, however, was
short lived, because in the early 1960s it was discovered that
the mathematical equations for weather forecasting represent a
forced *dissipative nonlinear dynamic system that exhibits
*chaotic behavior, which means that even an infinitesimally small
uncertainty in the initial conditions will grow exponentially to
make the forecast useless after a finite amount of time.
... ... J. Shukla now presents a study involving analyses of
weather observations coupled with model simulations. The author
reports that although the Earth's atmosphere is generally
considered to be an example of a chaotic system that is
sensitively dependent on initial conditions, certain regions of
the atmosphere are an exception, with wind patterns and rainfall
in certain regions of the tropics so strongly determined by the
temperature of the underlying sea surface that they do not show
sensitive dependence on the initial conditions of the atmosphere.
The author suggests it should therefore be possible to predict
the large-scale tropical circulation and rainfall for as long as
the ocean temperature can be predicted, and that if changes in
tropical Pacific sea-surface temperature are quite large, even
the extratropical circulation over some regions, especially over
the Pacific-North American sector, is predictable. In particular,
the author suggests that for all future major *El Nino events, it
should be possible to predict large-scale changes in the winter
season mean circulation over North America several months in
advance, provided we can predict tropical sea surface
temperatures.
-----------
J. Shukla (George Mason University, US)
Predictability in the midst of chaos: A scientific basis for
climate forecasting.
(Science 23 Oct 98 282:728)
QY: J. Shukla, George Mason University 703-993-2400
-----------
Text Notes:
... ... *dissipative: In general, a dissipative system
is a system that loses energy by conversion of energy into heat.
... ... *El Nino: El Nino is an aperiodic intermittent (2 to 10
years) flow of unusually warm surface water along the western
coast of South America, the flow capable of causing abnormally
high rainfall in usually dry areas and severe local ecosystem
dislocations -- what is termed an El Nino "event". El Ninos are
regional phenomena, but they have global consequences. The name
"El Nino" ("The Child") arose because the phenomenon usually
occurs around Christmas. In 1986, M.A. Cane and S.A. Zebiak
proposed a model for making forecasts of El Nino several seasons
ahead by applying Newton's equations of motion and the laws of
thermodynamics to the dynamics of the ocean and atmosphere of the
tropical Pacific.
-------------------
Summary & Notes by SCIENCE-WEEK 20Nov98
4. EVOLUTION: JURASSIC ANGIOSPERM FOSSILS
In botany, an "angiosperm" is a flowering plant whose seeds
develop within ovaries that mature into fruits; an "ovule" is a
structure of a seed plant that contains the female gamete (germ
cell) and can potentially develop into a seed; a "carpel" is a
compartment of a pistil (plant ovary). In general, angiosperms
are defined by carpels enclosing ovules. ... ... G. Sun et al
(Academia Sinica Nanjing, CN) now report that angiosperm
(Archaefructus) fruiting axes (extensions) were discovered from
*Upper Jurassic deposits in *China, and that this fossil features
carpels enclosing ovules, a character lacking in other fossils
reported to be the earliest angiosperms. The authors propose that
for nearly a century many paleobotanists and botanists have
considered the angiosperms to have originated in the tropical
regions of the world, and that the presence of their reported
fossil angiosperm and other fossils of early angiosperms in
northeast China suggests that there were early angiosperms in
China, and that this was one of the areas where early
diversification of the angiosperms took place. The authors point
out that angiosperms and angiosperm-like plants have also been
reported from *Early Cretaceous deposits in Mongolia and Lake
Baikal in eastern Russia, and that these fossils are similar to
the Chinese flora. The authors suggest that angiosperms may have
originated in Asia.
-----------
G. Sun et al: In search of the first flower: A Jurassic
angiosperm, Archaefructus, from northeast China.
(Science 27 Nov 98 282:1692)
QY: Ge Sun
-----------
Text Notes:
... ... *Upper Jurassic: The Jurassic Period is the time-frame
195 to 135 million years ago.
... ... *China: The fossil reported here was found in the
Jianshangou Bed in the lower part of the Yixian Formation in
western Liaoning Province, northeast China. The Yixian Formation
consists of layers of volcanic rocks sandwiched between
sedimentary rocks. "The sedimentary rocks contain abundant
freshwater and terrestrial fossils, including plants, *bivalves,
fish, *conchostracans, *ostracods, *gastropods, insects, turtles,
lizards, shrimps, dinosaurs, birds, and mammals..."
... ... *bivalves: In general, any animal with a shell in two
parts hinged together (e.g., a bivalve mollusc).
... ... *conchostracans: An order of mussel-like crustaceans of
moderate size.
... ... *ostracods: A subclass of Crustacea containing small
bivalved aquatic forms.
... ... *gastropods: A large class of the phylum Mollusca,
containing the snails, slugs, limpets, and conchs.
... ... *Early Cretaceous: The Cretaceous Period is the time-
frame 135 to 70 million years ago.
-------------------
Summary & Notes by SCIENCE-WEEK 1Jan99
5. MOLECULAR BIOLOGY: MEGAPLASMIDS VS. MINICHROMOSOMES
In general, the term "eukaryotes" refers to organisms with
internal membrane-bound compartments, and the term "prokaryotes"
refers to organisms without such compartments. Most biologists
now further dichotomize the prokaryotes into 2 major groups, the
bacteria and the archaebacteria. The bacteria have been studied
extensively, but many of the archaebacteria are difficult to
study in the laboratory (*Note #1). Most prokaryotic genes are
carried on a single circular chromosome containing approximately
4 million base pairs of DNA. But many prokaryotes contain
additional genes on smaller circular or linear molecules of DNA
called "plasmids", which contain from several thousand to 100,000
base pairs of DNA. These DNA entities (chromosomes and plasmids),
which contain genetic information necessary for their own
independent replication, are called "replicons". The classical
dogma concerning prokaryotes has been that they have only a
single circular chromosome, with essentially all smaller
replicons in these cells relegated to the status of plasmids
("extra-chromosomal elements"). In general, the idea has been
that the chromosome contains genes essential for cell viability,
while the plasmids are mainly auxiliary to the genome, containing
genes coding for proteins involved in special functions such as
chemical resistance, toxin-production, symbiosis, etc. But of the
many plasmids that have been characterized, several are
"megaplasmids" from a hundred kilobases to megabase size, and
during the past few years, some of these have been found to
contain genes that are normally thought to be essential for cell
viability. These findings have led to the suggestion that
prokaryotic genomes may be composed of multiple essential
replicons, and that some replicons originally classified as
megaplasmids may in fact be chromosomes. A problem is that at
present there is no apparent consensus concerning the criteria
for chromosomal status, and the criteria could involve essential
genes, size, replication control, evolutionary history, and so
on. ... ... W.V Ng et al (12 authors at 2 installations, US) now
report the complete nucleotide sequence of the plasmid (pNRC100)
of a *halobacterium strain and analysis of its elements and
coding capacity. The authors report this plasmid circle comprises
191,346 base pairs containing a total of 186 likely genes, a
number of which are considered to be genes critically essential
for viability, including a gene for a chromosome replication
initiator protein. The authors suggest the finding of such
essential genes on this plasmid raises the question of the
precise distinction between plasmids and chromosomes, and they
propose that certain replicons could be considered to occupy an
intermediate status between plasmids and chromosomes and may
represent evolutionary intermediates in the formation of new
chromosomes (or the breakdown of old ones).
-----------
W.V. Ng et al: Snapshot of a large dynamic replicon in a
halophilic archaeon: Megaplasmid or minichromosome?
(Genome Research November 1998 8:1131)
QY: Shiladitya DasSarma
-----------
Text Notes:
... ... *Note #1: Some archaebacteria, for example, are killed by
contact with oxygen; others grow at temperatures exceeding that
of boiling water; the methanogens carry out an anaerobic
respiration that gives rise to methane; the halophiles demand
extremely high salt concentrations for growth; the thermo-
acidophiles require high temperature or acidity or both. It has
now been established that these archaebacteria prokaryotes share
biochemical traits that set the group entirely apart from all
other living organisms. (See below for background material on the
controversy concerning the classification of archaebacteria.)
... ... *halobacterium strain: The halobacterium strain (NRC-1)
involved in this study grows optimally at a nearly saturated (4.5
molar) sodium chloride concentration.
-------------------
Summary & Notes by SCIENCE-WEEK 1Jan99
-------------------
Related Background:
BIO-TAXONOMY: EMERGENCE OF A SHARP PERSONAL CONTROVERSY
In a recent report (see Related Background material below) we
briefed a proposal by Ernst Mayr for a return to the *prokaryote-
eukaryote domain dichotomy from the present *archaea-eubacteria-
eukaryote domain trichotomy that has come to be used by many
biologists during the past decade. The details of the distinction
are provided in the report attached below, so we will not repeat
them. The controversy is of some interest in biology, as perhaps
a possible controversy concerning the present standard model
classification scheme of fundamental particles and forces in
physics would be to physicists. The domain trichotomy idea in
bio-taxonomy was first proposed in the 1980s by Carl Woese, who
like Ernst Mayr, is a member of the US National Academy of
Sciences. Writing in the same journal in which Mayr's proposal
appeared a few weeks ago, Woese now attempts to rebut Mayr's
ideas with an apparent singular vehemence, proposing that the
issue is more profound than that of merely assessing the utility
of a classification scheme. Woese writes: "If there were ever an
issue in biological classification that cannot be settled by
pedantry, it is this one." [Editor's note: This is not completely
gratuitous, since in his paper Mayr states, "Here it must be
remembered that Woese was not trained as a biologist and quite
naturally does not have an extensive familiarity with the
principles of classification."] And again from Woese: "To Mayr,
the issue is one of whether we should define two or three domains
and what the classificatory precedents or rules for deciding this
are. However, the *universal phylogenetic tree tells us that the
domains are unique among taxa and that their number and their
composition are not subject to classificatory fiat, but are
naturally defined." Woese's idea, apparently, is that the
trichotomous classification scheme is discovered rather than
constructed, which implies a significant problematic
philosophical subtext that is not amplified in his paper. In
summary, Woese makes the following points concerning his
position: 1) Mayr's article is not a taxonomic quibble but a "de
facto pronouncement on the nature of biology." A biological
classification is in effect an overarching evolutionary theory
that guides our thinking and experimentation, and it must be
structured to reflect evolutionary reality. 2) The prokaryote-
eukaryote dichotomy, which Mayr proposes to reinstitute, is a
failed taxonomic theory that was never recognized as theory and
therefore never tested in a timely fashion, with the consequence
that it has adversely affected the development of biology,
especially microbiology, in the latter half of this century. 3)
The scientifically perceived importance of a group of organisms
must reflect the natural importance of the group. 4) Microbial
diversity is far more than a listing of distinguishable microbial
species. We need to understand the quality of microbial
diversity, for it is the diversity that defines the biosphere of
this planet. 5) Evolution must be integrated into the fabric of
molecular biology... Any comprehensive understanding of a
biological entity, be it an organism or a molecule, necessarily
has an evolutionary component. Woese concludes: "The disagreement
between Dr. Mayr and myself is not actually about classification.
It concerns the nature of Biology itself. Dr. Mayr's biology
reflects the last billion years of evolution; mine, the first
three billion. His biology is centered on multicellular organisms
and their evolutions; mine on the *universal ancestor and its
immediate descendants. His is the biology of visual experience,
of direct observation. Mine cannot be directly seen or touched;
it is the biology of molecules, of genes and their inferred
histories. Evolution for Dr. Mayr is an "affair of phenotypes".
For me, evolution is primarily the evolutionary _process_, not
its outcomes. The science of biology is very different from these
two perspectives, and its future even more so." [Editor's note:
Ignoring the personalized undercurrents, the essential
controversy here is apparently between a classification system
based on utility criteria and observed similarities and
differences among entities (Mayr), and a classification scheme
based on theoretical and experimental molecular-genetic
relationships (Woese). The question of why there must be only one
classification scheme in use by working biologists is not
addressed by either Mayr or Woese.]
-----------
C.R. Woese (University of Illinois Urbana-Champaign)
Default taxonomy: Ernst Mayr's view of the microbial world.
(Proc. Natl. Acad. Sci. US 15 Sep 98 95:11043)
QY: Carl R. Woese
-----------
Text Notes:
... ... *prokaryote-eukaryote domain dichotomy: See reports
attached below.
... ... *archaea-eubacteria-eukaryote domain trichotomy: See
reports attached below.
... ... *universal phylogenetic tree: Refers to the present
taxonomic-evolutionary classification scheme for all life on
Earth.
... ... *universal ancestor: Refers to the common ancestor from
which all life on Earth is considered to have derived. See
Related Background report attached below of SW 3 Jul 98).
-------------------
Summary & Notes by SCIENCE-WEEK 16Oct98
-------------------
Related Background:
BIO-TAXONOMY: A PROPOSAL FOR ONLY TWO EMPIRES
The physicist confronting bio-taxonomy for the first time may
experience bewilderment: there are in excess of 30 million
species of life forms, the classification system is far from
simple, the system has some historically based confusions, and
the system is frequently redefined. Perhaps only the organic
chemist can feel a full empathy here, since organic chemistry is
faced with the similar problem of classifying millions of organic
chemical entities. A fundamental consideration is that in the
context of such a diversity of objects, a self-consistent
classification scheme is of extreme importance. At the present
time, in biology, there is a significant controversy concerning
primary categories, and that is the subject of this report. Two
main groups of life forms have been recognized for some time,
prokaryotes and eukaryotes. Prokaryotes are cells without a cell
nucleus and other membrane-bound organelles, and eukaryotes are
cells with a cell nucleus and other membrane-bound organelles.
(Organisms composed of eukaryote cells are also called
"eukaryotes"). For example, all bacteria are prokaryotes; all
complex animals, plants, etc., are eukaryotes. Fifteen years ago,
C.R. Woese (University of Illinois Urbana-Champaign, US) proposed
that the prokaryotes actually consist of two main groups, the
eubacteria and the archaebacteria, and that the differences
between these two groups are as great as the differences between
prokaryotes and eukaryotes, and that as a consequence a
tripartite primary scheme should be used, the primary categories
(kingdoms or empires) consisting of Eubacteria, Archaebacteria,
and Eukaryotes. Woese's differentiation of eubacteria and
archaebacteria was based on *habitats, cell wall constituents,
genome organization, and various aspects of protein synthesis
biochemical machinery, and during the past decade most biologists
have apparently accepted his categorization scheme. ... ... Now
Ernst Mayr (1904- ), a prominent biologist, proposes a rejection
of the Woese categorization and a return to a scheme involving
only 2 primary categories (empires), the Prokaryotes and
Eukaryotes. Mayr makes the following points: 1) A classification
scheme is essentially an information storage and retrieval
system, permitting the location of an entity with a minimum of
effort and loss of time, the objective optimally achieved by
arranging entities in a hierarchy of classes, ranked by degree of
similarity. 2) Evidence indicates that the archaebacteria are so
much more similar to the eubacteria than to the eukaryotes, that
their removal from the prokaryotes is not justified. The
eukaryotes differ from the prokaryotes (including the
archaebacteria) not only by the possession of a nucleus and
*mitosis but also by individual protein-rich chromosomes,
*meiotic sexuality (including viable regular cell fusions),
cellular organelles, highly complex sets of regulatory genes, and
all those genes that permit biodiversity... When a biologist
speaks of eukaryotes, he or she has in mind palms, oaks, and
orchids; mice, bats, and whales; and hummingbirds, chickens, and
ostriches. And this world of highly evolved eukaryotes is simply
an entirely different world from the world of the two kinds of
bacteria, the Prokaryotes. 3) Ranking, in any scheme of
classification of items (living or not), is by necessity based on
degree of difference. The two kinds of bacteria, in the vast
majority of their characteristics, are exceedingly similar to
each other and fundamentally so different from the eukaryotes
that they have to be ranked as a single *taxon, the prokaryotes,
different from the only other taxon of this rank, the eukaryotes.
Mayr suggests that only a two-empire classification correctly
reflects this structure of the living world.
-----------
E. Mayr (Harvard University, US)
Two empires of three?
(Proc. Natl. Acad. Sci. US 18 Aug 98 95:9720)
QY: Ernst Mayr
-----------
Text Notes:
... ... *habitats: Many species of archaebacteria live in hot
acidic conditions, growing best at temperatures approaching 100
degrees centigrade. Because of this, it has been suggested the
lineage is more ancient than eubacteria, arising during
primordial conditions on Earth.
... ... *mitosis: In this context, division of the cell nucleus.
... ... *meiotic sexuality: A reduction division process whereby
a nucleus divides by 2 divisions into 4 nuclei, each containing
half the original number of chromosomes.
... ... *taxon: The organisms comprising a particular taxonomic
entity.
-------------------
Summary & Notes by SCIENCE-WEEK 25Sep98
6. ON PRIONS AND PRION DISEASES: A NOBEL LECTURE
Prions are defined as proteinaceous infectious particles that
lack nucleic acid, and in 1997 Stanley B. Prusiner was awarded
the Nobel Prize in Physiology and Medicine for his discovery of
prions, an entirely new genre of disease-causing agents.
... ... In a recently published abbreviated version of Prusiner's
Nobel Lecture (the lecture comprising an extensive review of
prion research), Prusiner makes the following points: 1) Prions
are unprecedented infectious pathogens that cause a group of
invariably fatal neurodegenerative diseases by an entirely novel
mechanism. 2) Prion diseases may appear as genetic, infectious,
or sporadic (i.e., non-familial) disorders, all of which involve
modifications of the prion protein. Bovine spongiform
encephalopathy ("mad cow disease"), scrapie of sheep, and
Creutzfeldt-Jakob disease of humans are among the most notable
prion diseases. 3) Prions are transmissible particles that are
devoid of nucleic acid and seem to be composed exclusively of a
modified protein. The normal cellular prion protein is converted
into modified protein through a *post-translational process
during which it acquires a high *beta-sheet content. The variety
of a particular prion is determined by the sequence of the
chromosomal prion protein gene of the mammals in which the prion
protein last replicated. 4) In contrast to pathogens carrying a
nucleic acid genome, prions appear to encode strain-specific
properties in the *tertiary structure of the modified prion
protein. *Transgenetic studies suggest that modified (pathogenic)
prion protein acts as a template upon which normal prion protein
is refolded into a nascent modified protein through a process
facilitated by another protein. 5) While knowledge about prions
has profound implications for studies of the structural
plasticity of proteins, investigations of prion diseases suggest
that new strategies for the prevention and treatment of these
disorders may also find application in the more common
degenerative diseases. The author concludes: "The discovery of
prions and their eventual acceptance by the community of scholars
represents a triumph of the scientific process over prejudice.
The future of this new and evolving area of biology should prove
even more interesting and productive as a multitude of
unpredicted discoveries emerge."
-----------
Stanley B. Prusiner: Prions
(Proc. Natl. Acad. Sci. US 10 Nov 98 95:13363)
QY: S. B. Prusiner, Univ. of Calif. San Francisco 415-476-4044.
-----------
Text Notes:
... ... *post-translational process: Translation is protein
synthesis, the process during which polypeptides are synthesized
in accordance with RNA code.
... ... *beta-sheet: In general, protein chains fold into
alpha-helices or beta-sheet structures. The beta-sheet is a
protein structure where the peptide is extended and stabilized by
hydrogen bonding between NH and CO groups of different
polypeptide chains or of separate regions of the same chain.
... ... *tertiary structure: In general, the structures of
biopolymers are denoted as follows: 1) Primary structure: The
sequence of subunits that comprise the macromolecule (e.g., the
amino acid sequence of a protein). 2) Secondary structure: The
localized arrangement in space of regions of a biopolymer (e.g.,
the alpha-helix). 3) Tertiary structure: The 3-dimensional
configuration of a biopolymer. 4) Quaternary structure: The 3-
dimensional arrangement and constitution of a multimeric
macromolecule (i.e., a substance containing more than one
biopolymer; an entity consisting of biopolymer subunits.
... ... *Transgenetic studies: (transgenic) In general, studies
involving the transfer of genetic material from one organism to
another, and subsequently the second organism expressing the
transferred genes with a resultant production of specific
proteins.
-------------------
Summary & Notes by SCIENCE-WEEK 1Jan99
7. ON THE CURRENT STATUS OF TUBERCULOSIS
Roy M. Anderson (University of Oxford, UK) presents a review of
the growing domestic and international problem of tuberculosis,
the author making the following points: 1) In New York City, from
1985 to 1992, reported cases of tuberculosis rose by more than 20
percent. This followed a 30-year period of decline in the
incidence of the disease. 2) The reasons for the reversal include
the role of *HIV-1 infection in enhancing disease progression and
transmission, homelessness in the city, the emergence of multi-
drug resistant strains of the etiological agent (*Mycobacterium
tuberculosis), and a failing public health infrastructure. 3)
Globally, the scale of the tuberculosis problem is enormous, with
the World Health Organization estimating that a third of the
population of the world is infected with the bacterium and
predicting 90 million new cases in the decade up to the year
2000. 4) As the magnitude of the problem continues to grow, the
dream of eradication of tuberculosis fades into the distant
future, despite the fact that the treatment of the disease by
mass chemotherapy is a very cost-effective public health
intervention. 5) Tuberculosis is likely to remain one of the 10
most important causes of premature mortality worldwide in the
coming 2 decades. ... ... In an paper in the same issue of the
journal (the article the subject of a commentary by the Anderson
review), C.J.L. Murray and J.A. Salomon (Harvard University, US)
present the results of a mathematical epidemiological modeling
study of tuberculosis, the model applied to 5 regions of the
world. The authors report that 6.7 million new cases of
tuberculosis and 2.4 million deaths from tuberculosis are
estimated for 1998. Based on current trends in international
treatment strategy, the authors report they expect a total of 225
million new cases and 79 million deaths from tuberculosis between
1998 and 2030. The authors propose that active case-finding could
save 23 million lives over this period. A single contact
treatment of tuberculosis could avert 24 million cases and 11
million deaths, and combined with active screening could reduce
mortality by nearly 40 percent. A new vaccine with 50 percent
efficacy could lower incidence by 36 million cases and mortality
by 9 million deaths. The authors suggest that support for major
extensions to global tuberculosis control strategies will occur
only if the size of the problem and the potential for action are
recognized more widely.
-----------
Roy M. Anderson: Tuberculosis: Old problems and new approaches.
(Proc. Natl. Acad. Sci. US 10 Nov 98 95:13352)
QY: Roy M. Anderson, Wellcome Trust Centre for the Epidemiology
of Infectious Diseases, University of Oxford, UK.
-------------------
C.J.L. Murray and J.A. Salomon: Modeling the impact of global
tuberculosis control strategies.
(Proc. Natl. Acad. Sci. US 10 Nov 98 95:13881)
QY: Joshua A. Salomon
-----------
Text Notes:
... ... *HIV-1: HIV-1 is the subtype of HIV (human immune-
deficiency virus) that causes most cases of AIDS in the Western
Hemisphere, Europe, and Central, South, and East Africa.
... ... *Mycobacterium tuberculosis: The mycobacteria (of which
there are more than 50 species) are rod-shaped aerobic bacteria
that do not form spores. The two chief mycobacteria human disease
pathogens are M. tuberculosis (which causes tuberculosis) and M.
leprae (which causes leprosy). The form of the tuberculosis
bacterium actually varies, since on artificial media spherical
and filamentous forms are seen, while in tissue the tubercle
bacilli are thin straight rods measuring approximately 0.4 x 3
microns.
-------------------
Summary & Notes by SCIENCE-WEEK 1Jan99
-------------------
Related Background:
ANTI-TUBERCULOSIS DRUG RESISTANCE 1994-1997
In the past 50 years, the proliferation of anti-microbial agents
for use in humans and animals has placed enormous selective
pressure on microorganisms. Drug resistance in patients with
Mycobacterium tuberculosis infection became apparent soon after
the introduction of effective antituberculosis agents in the
1940s, but it was not until the early 1990s, when outbreaks of
multi-drug-resistant tuberculosis were reported in patients with
human immunodeficiency virus (HIV) infection in the US and
Europe, that the problem received international attention.
... ... Pablos-Mendez et al (12 authors at 7 installations, US FR
CA NL KR and the World Health Organization) report a study of the
prevalence of resistance to 4 first-line drugs (isoniazid,
rifampin, ethambutol, streptomycin) in 35 countries participating
in an international collaborative study of the problem between
1994 and 1997. Among patients with no prior treatment, a median
of 9.9 percent of M. tuberculosis strains were resistant to at
least one drug. The prevalence of primary multi-drug resistance
(resistance to at least isoniazid and rifampin) in this group was
1.4 percent. Among patients with histories of treatment for one
month or less, the prevalence of resistance to any of the four
drugs was 36 percent, and the prevalence of multi-drug resistance
was 13 percent. Particularly high prevalences of multi-drug
resistance were found in the former Soviet Union, Asia, the
Dominican Republic, and Argentina. The authors conclude that
resistance to antituberculosis drugs exists in all 35 countries
and regions surveyed, and they suggest that it is a global
problem. In an editorial in the same issue of the journal, D.E.
Snider and K.G. Castro (Centers for Disease Control, US) warn
that a greater commitment by the developed countries is needed
"if we are to ward off what could become a global health
disaster."
QY: Ariel Pablos-Mendez, Columbia University (US) 212-854-1754.
QY: Dixie E. Snyder, Centers for Disease Control and Prevention,
Atlanta, GA 30333 US.
(New England J. Med. 4 Jun 98 338:1641,1689)
(Science-Week 26 Jun 98)
-------------------
Related Background:
EVIDENCE OF HUMAN GENETIC SUSCEPTIBILITY TO TUBERCULOSIS
A genetic polymorphism is a naturally occurring variation in the
normal nucleotide sequence of the genome within individuals in a
population. Variations are denoted as polymorphisms only if they
cannot be accounted for by recurrent mutation and occur with a
frequency of at least about 1%. Macrophages, of which there are
many varieties, are large, mononuclear cells of the immune system
that usually engage in phagocytosis (physical incorporation and
digestion) of foreign material such as bacteria, particularly in
the lung, but may also be involved with immune system signaling.
Tuberculosis kills more people in the world than any other
disease caused by an infectious pathogen. ... ... Bellamy et al
(6 authors at 2 installations, UK GM) report the use of molecular
genetic techniques in a study of human polymorphisms in the
macrophage protein gene in 410 adults with pulmonary
tuberculosis (and 417 ethnically matched healthy controls) in the
Gambia, West Africa, and that 4 polymorphisms were each
significantly associated with tuberculosis. The authors suggest
that genetic variation in affects susceptibility to
tuberculosis in West Africans, and that the results support the
strategy of mapping and identifying genes for resistance to
infectious disease in mice and then testing their human homo-
logues as candidate genes for susceptibility to related infect-
ions in humans. QY: Adrian V.S. Hill, Wellcome Trust Center for
Human Genetics, Windmill Rd., Oxford OX3 7BN UK.
(New England J. Med. 5 Mar 98)
-------------------
Related Background:
MECHANISM OF MACROPHAGE INVASION BY TUBERCULOSIS PATHOGEN
The mycobacteria include bacterial species in the genus
Mycobacterium. They are a group of rod-shaped bacteria with large
amounts of mycolic acid in their cell walls. Many mycobacteria
are free-living, but two notorious pathogens are in this group:
M. tuberculosis, the cause of tuberculosis in humans and cattle;
and M. leprae, the cause of leprosy in humans. Tuberculosis was
recently under control in the U.S. (25,000 cases in 1990), but
the combination of immunodeficiency disease and drug-resistant
mutant variants of M. tuberculosis has alarmed epidemiologists,
and the incidence of tuberculosis among certain sub-populations
appears to be rising markedly. The fact is tuberculosis worldwide
is the leading cause of death due to an infectious organism, with
an estimated 3 million deaths annually. Pathogenic mycobacteria
evidently require entry into host macrophages (large ameboid
leukocytes that are part of the vertebrate immunological defense
system) in order to begin the disease process. Now Jeffrey S.
Schorey et al (Washington University School of Medicine, US;
Harvard Medical School, US) have presented evidence that
pathogenic mycobacteria, as opposed to non-pathogenic myco-
bacteria, are able to utilize cleavage products (C2a) of
complement proteins (plasma proteins specifically involved with
immune responses) to achieve invasion of macrophages. The authors
suggest this invasion mechanism is crucial in mycobacterial
pathogenesis, and that the mycobacterial cell wall component
required for this invasion process may provide a new target for
therapeutic intervention.
QY: Eric J. Brown, Washington Univ.
School of Medicine (314) 889-6000 (Science 22 Aug 97)
(Science-Week 5 Sep 97)
-------------------
Related Background:
DISCOVERY OF TUBERCULOSIS-ANTAGONIST BODY CHEMICAL
Although one-third to one-half the world's population is infected
with tuberculosis, only a fraction of those who are infected
actually get the life-threatening disease. This has always been a
medical mystery. Now the mystery may be solved, and with it we
may have a new technique for treating tuberculosis that does not
involve antibiotics. Richard A. Young and Gerald J. Nau
(Whitehead Institute for Biomedical Research, Cambridge MA US;
Massachusetts General Hospital, Boston MA US) report the
discovery of a substance called osteopontin that is produced by
the body when the lungs are infected with the tuberculosis
bacillus. Osteopontin, which is produced by macrophages after
they fail to eliminate the infection, acts as a signal for other
defense cells to form a mass of tissue around the invader and
imprison it. These small granulomas are characteristic of
tuberculosis, and are also found in healthy people whose
tuberculosis infection has not become virulent. Young and Nau
believe it may be osteopontin production and the formation of
granulomas that prevent worse infections, and they suggest
osteopontin as a candidate for tuberculosis therapy. Osteopontin
was discovered by comparing thousands of genes operating in
tuberculosis infected tissues with those operating in uninfected
tissues. Apparently, the only noticeable difference is that
infected tissue produces osteopontin.
(Proceedings of the U.S. National Academy of Sciences 10 Jun 97)
(Science-Week 12 Jun 97)
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