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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.
August 31, 2001 -- Vol. 5 Number 35
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In other words, apart from the known
and the unknown, what else is there?
-- Harold Pinter
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Section 1
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Contents of this Issue (Full reports in Section 2):
1. Comets and the Formation of Our Solar System
2. Physics of Earthquakes
3. Molecular Dynamics/NMR Analysis of Proteins
4. The Rise of Atmospheric Oxygen
5. Chemistry of Bee Venom
6. How Mars Came to Have Canals
7. Structure of the Ribosome
8. Choices in Sequencing Mammalian Genomes
9. African Ancestry of Modern Humans
10. Yellow Fever and the Mosquito
11. Autoimmune Diseases
12. Global AIDS in 2001
13. In Focus: A Cinematic View of Evolution
14. SW Archive: On the Discovery of Electromagnetic Waves
15. PRAXIS Current Issue Contents
16. Sources
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Section 2
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1. COMETS AND THE FORMATION OF OUR SOLAR SYSTEM
Hermann Boehnhardt (European Southern Observatory, CL) discusses
comets and the origin of our solar system. Comets are believed to
be remnants from the birth of our planetary system, which evolved
together with the Sun from a collapsing cloud of dust and gas
approximately 4.6 billion years ago. This formation scenario
predicts that the birthplace of comets was in the outer part of
the disk surrounding the collapsing core (the early Sun) in the
center. Comets are therefore believed to originate from the
region of the major planets Jupiter, Saturn, Uranus, and Neptune.
At that distance, temperatures were low (200 kelvins at Jupiter's
distance and 30 kelvins at Neptune's distance), allowing icy
grains (mostly water and carbon monoxide ices) to survive in the
primordial planetary disk and become the ingredients of cometary
nuclei. The planetary system in our Solar System was apparently
formed in 3 phases: 1) Agglomeration and gentle collisions led to
the growth of stones, rocks, boulders, and mountain-sized bodies
(planetesimals) from dust. 2) This was followed by the runaway
growth of planet-sized bodies through heavy collisions of
planetesimals. 3) The disk was cleaned up through gas dispersion,
accretion, and gravitational scattering of planetesimals by
planets, and destructive collisions of the planetesimals,
boulders, and rocks, followed by the removal of the produced dust
by radiation pressure from the Sun.
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SCI 2001 292:1307
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Related Background:
ASTRONOMY: ON SMALL BODIES OF THE SOLAR SYSTEM
Other than the moons of the various planets, the chief small
bodies of the solar system are comets and asteroids.
In general, a comet is a kilometer-size chunk of ice and
associated dust and debris. The *Oort cloud is an apparent
spherical shell of comets 10,000 to 100,000 *astronomical units
(AU) from the Sun and the proposed source of comets that orbit
the Sun. The cloud is at the extreme edge of the Sun's influence,
halfway to the nearest star, and it is believed that when the
cloud is perturbed by passing stars, comets may be sent into a
solar orbit. The size and structure of the Oort cloud have been
deduced from statistical studies of the orbits of comets; there
is no direct evidence for the cloud's existence. Approximately
900 comets are known.
Asteroids (also called "minor planets") are small rocky
objects, most of which orbit the Sun in a belt between the orbits
of Mars and Jupiter. A few asteroids follow orbits that bring
them into the inner Solar System, and several asteroids
occasionally pass within a few tens of millions of miles of
Earth. Some asteroids are located in the orbit of Jupiter, and
some asteroids have been detected as far away as the orbit of
Saturn. There are approximately 7200 known asteroids, and a
million asteroids are believed resident in the Solar System. The
consensus view is that asteroids are composed of material that
failed to build a planet at a distance of 2.8 astronomical units
from the Sun, perhaps due to the influence of massive Jupiter
just outside the asteroid belt. Until recently, the shapes and
surface features of asteroids were a matter of conjecture; during
the past decade, however, significant direct observations of
asteroids have been relayed back to Earth from spacecraft.
Classical astronomers have categorized comets and asteroids
as distinctly different entities with different histories and
compositions, but recent evidence is blurring the conceptual
boundary between these two groups of small Solar System bodies,
and there are several newly discovered objects that are
considered to be both comets and asteroids on the basis of their
characteristics.
... ... Don Yeomans (California Institute of Technology, US)
presents a review of recent research on comets and asteroids, the
author making the following points:
1) Recent observations have revealed comets in asteroid-like
orbits and asteroids in comet-like orbits. Both comets and
asteroids can evolve from the Oort cloud into highly inclined,
even *retrograde, orbits about the Sun, so orbital behavior is no
better than physical behavior for distinguishing comets from
asteroids. The author suggests that attempts to categorize comets
and asteroids as distinctly separate entities have failed, and
that astronomers should now consider these objects as members of
highly diverse family: the small bodies of the Solar System.
2) If all comets were solid dirty balls of water ice, then
their bulk densities would be approximately 1 gram per cubic
centimeter. But some comets have apparent low-density structures
that are made from several bits held together by little more than
their own self-gravity. This conclusion arose after some comets
were observed to break up as a result of tidal forces from either
the Sun or Jupiter, and more than two dozen other comets have
split apart for no obvious reason at all. In addition, comets
that have apparently transformed from active to quiescent objects
suggest that some cometary bodies do become defunct and join the
ranks of the asteroids. Low-density extinct comets can probably
explain a significant fraction of the near-Earth asteroid
population, "so we cannot assume that all objects that threaten
Earth will have the same composition or structure."
3) Asteroids have been classified according to the light
reflected from their surfaces -- their optical spectra. Although
no two spectra are exactly alike, most asteroids fall into one of
two groups, the C-type (carbonaceous) and S-type (silicaceous).
C-type asteroids have low reflectance (albedo) and may contain
mixtures of hydrated silicates, carbon, and organic compounds. S-
type asteroids have higher albedos and can contain pyroxene
(silicates containing magnesium, iron, and calcium), olivine
(magnesium and iron silicates), and nickel-iron metal. The C-type
asteroids are most common in the outer part of the main asteroid
belt, and the S-type asteroids are mostly found in the inner
asteroid belt.
4) Meteorites are asteroid collision fragments that have
fallen to Earth, and as such are thought to hold clues regarding
the early history of asteroids. Because most asteroid fragments
are rocky, they can survive the passage through the atmosphere of
the Earth. In contrast, debris from comet streams nearly always
burns up in the atmosphere, sometimes producing spectacular
meteor showers in the sky, but leaving little evidence on the
surface of the Earth. The most common meteorite is the ordinary
chondrite, which is composed mostly of rocky silicates, and so
has not experienced the chemical differentiation associated with
melting. Such chondrites are thought to be some of the most
primitive rocks in the Solar System, although their parent
asteroid type is not clear. On 22 March 1998, and ordinary
chondrite was observed to fall to Earth by 7 boys in Monahans,
Texas (US), and within 48 hours the meteorite was under
examination at the Johnson Space Center in Houston, Texas.
Laboratory analysis of the Monahans meteorite detected salt
crystals embedded with water in the form of brine, and the salt
crystals were dated to the very beginning of the Solar System,
approximately 4.6 billion years ago. This suggests the presence
of liquid water on the parent asteroid of this meteorite, and
unless this water derived from a collision with a salt-bearing
icy comet, the parent asteroid itself must have had flowing water
within its interior structure. Far from being the dry rocky
bodies they were once believed to be, it would seem that some
asteroids, along with comets, might be significant sources of
water.
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NAT 2000 404:829
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Text Notes:
... ... *Oort cloud: The cloud is named after Jan Hendrik Oort
(1900-1992). Oort first proposed the existence of the cloud in
1950. In 1927, Oort calculated the mass and size of the Galaxy,
and the distance of the Sun from its center, from the observed
movements of the stars around the center.
... ... *astronomical units (AU): 1 AU = the mean distance from
the Sun to the Earth = approximately 93 million miles, and
exactly 149,597,870 kilometers.
... ... *retrograde: Opposite direction as planets. Prograde =
same direction as planets.
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SW 2000 30 Jun
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SCIENCE-WEEK 31 Aug 2001 http://scienceweek.com
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Related Background:
ON THE ORIGIN OF THE SOLAR SYSTEM
During the past two centuries, astronomers have considered two
types of theories for the origin of our Solar System planets.
Catastrophic theories proposed that these planets formed from
some improbable cataclysm such as the collision of the sun and
another star, while gradualist theories proposed that the planets
formed naturally with the Sun. At the present time, as a result
of evidence accumulated during the past five decades, the
gradualist idea is the consensus idea, and nearly all astronomers
now believe that planets form naturally as a by-product of star
formation. ... ... John A. Wood presents an extensive review of
current ideas concerning the origin of the Solar System, and the
author makes the following points: 1) The current theory is that
the Sun and the planets were born from a rotating disk of cosmic
gas and dust (the "solar nebula"), and the flattened form of the
disk constrained the planets that formed from it to have orbits
lying in the same plane, or nearly so, the planets all moving in
the same direction in which the disk had turned. 2) The idea of a
solar nebula was first formulated in 1755 by *Immanuel Kant.
Although his treatment of the problem was only qualitative, its
precepts were remarkably similar to those considered fundamental
today, and at the present time, Kant's original idea is
considered to be correct: stars and their disks form in much the
same way he pictured, the formation resulting from the
gravitational collapse of huge volumes of thinly dispersed
interstellar gas and dust onto appropriate nuclei. 3) The present
view is that the solar nebula was hot near its center, tapering
off to a cold region, then a very cold region at its outermost
margins. Thus, the falloff of nebula temperature with
heliocentric distance defined 3 radial zones. The innermost zone
was too warm for water to condense as ice; objects forming in the
innermost zone consisted entirely of *silicate minerals and other
*refractory materials, and ultimately became the terrestrial
planets (Mercury, Venus, Earth, and Mars). The next zone of the
solar nebula was colder, water ice was stable, and a vast
blizzard of snowflakes gave rise to the much larger Jovian
planets (Jupiter, Saturn, Uranus, and Neptune). In the outermost
and thus coldest zone of the solar nebula, condensed matter was
also icy, but matter was too sparsely distributed to accrete into
sizable planets; instead matter remained dispersed in small icy
planetesimals -- comet nuclei -- in what is now called the
*Kuiper belt. Evidence suggests the planets assembled themselves
quickly: Although the process differed in detail from zone to
zone, virtually everything was in place within 10 million years,
by which time the solar nebula had largely dissipated. 4) Nearly
four centuries of telescopic observation, combined with four
decades of space exploration, have taught us this essential truth
about the Solar System: While the Sun and its planetary system
surely arose from one grand spiral of gas and dust in a flurry of
collective activity, the results are hardly a homogeneous set of
characterless orbiting entities. Instead this grand scheme of
formation has yielded amazing diversity in the properties of the
various objects in the Solar System.
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Sky and Telescope January 99
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Text Notes:
... ... *Immanuel Kant (1724-1804): Kant is best known as a
philosopher, but he first studied mathematics and physics, and
the year he obtained his doctorate degree (1755) he published his
physical view of the Universe in *General History of Nature and
Theory of the Heavens). In this treatise, Kant described the
solar nebula hypothesis of planet formation, suggested that our
own galaxy is a lens-shaped collection of stars and that other
such "island universes" exist, and suggested that *tidal friction
slows the rotation of the Earth. All three propositions are the
current view in astrophysics.
... ... *tidal friction: A force between the oceans of the Earth
and the ocean floors caused by the gravitational attraction of
the Moon.
... ... *silicate minerals: (silicates) The most important and
abundant group of rock-forming minerals.
... ... *refractory materials: (refractory minerals) Minerals
resistant to decomposition by heat, pressure, or chemical attack.
The term is most commonly applied to heat resistance.
... ... *Kuiper belt: In 1951 the astronomer Gerard P. Kuiper
(1905-1973) postulated the existence of a belt of objects beyond
the orbit of Pluto. Both the existence and nature of the objects
were matters of speculation for decades, and finally in 1992
Jewitt and Luu identified the first Kuiper object. The current
estimate is that as many as 10^(8) objects larger than 10
kilometers in diameter may exist in what is called the "Kuiper
belt", a disc that hugs the plane of the planetary system and
lies between 35 and 1000 AU from the Sun. Observations to date
have yielded some 55 trans-Neptune bodies with radii on the order
of 100 km or larger, and Pluto is considered by some astronomers
to be a member of this population.
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SW 1998 11 Dec
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2. PHYSICS OF EARTHQUAKES
H. Kanamori and E.E. Brodsky (California Institute of Technology)
discuss current research in the physics of earthquakes. The
recent earthquakes in Taiwan, Turkey, and India tragically
demonstrated the abruptness with which earthquakes occur and the
devastation that often accompanies them. In general, earthquakes
are sudden fractures in the Earth's crust followed by ground
shaking, and there are many questions concerning these phenomena.
When do earthquakes occur? What long-term processes and short-
term triggers produce earthquakes? Although *plate tectonics has
provided a successful framework for understanding the long-term
processes, the short-term triggers remain obscure, making
earthquakes unpredictable. An equally important question and a
fundamental challenge to the science of geophysics is, What
happens during an earthquake? What are the forces and motions
during a seismic event? The answer to this question has practical
consequences for mitigating the effects of the expected ground
motion. Most earthquakes occur at depths down to 50 kilometers,
but some earthquakes as deep as 670 kilometers have been observed
in certain regions. Seismologists have never directly observed
ruptures in Earth's interior. Instead, they rely on the
information gleaned from the few available types of data, the
most important of which is the record of seismic waves. During an
earthquake, sudden crustal motion excites elastic waves that
travel through Earth and are observable at seismic stations on
the surface, and these waves carry information about movements at
the source of the earthquake.
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PT 2001 June
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... ... *plate tectonics: The term "lithosphere" refers to the
outer layer of the Earth, comprising the crust and upper mantle,
and extending to a depth of 50 to 70 kilometers. The traditional
view of tectonics (changes in the structure of the Earth's crust)
is that the lithosphere consists of a strong brittle layer
overlying a weak ductile layer. "Plate tectonics" is the current
consensus theory that the Earth's lithosphere is broken into
fairly rigid plates, seven or eight major plates and many smaller
plates, and that convection within the underlying less rigid
"asthenosphere" causes the plates (and the associated continents
and crust) to move relative to each other.
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SCIENCE-WEEK 31 Aug 2001 http://scienceweek.com
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Related Background:
EARTHQUAKES AND FRICTION LAWS
... The traditional view of tectonics is that the lithosphere
consists of a strong brittle layer overlying a weak ductile
layer, the system producing two forms of deformation, namely,
brittle fracture in the upper layer (accompanied by earthquakes),
and aseismic (without earthquakes) ductile flow in the lower
layer. The current consensus is that this view is generally
correct but imprecise, since the accumulated evidence is now
interpreted to indicate that frictional events along fault lines,
rather than new fractures, are the causes of earthquakes. The
essential idea is that fault lines, which are the interfaces
between the crustal plates, build up stresses resulting from the
movements of the plates, and at intervals these stresses are
suddenly relieved by interface slippages the surface manifest-
ations of which are earthquakes. In mechanics, "stick-slip"
friction is friction between two surfaces that are alternately at
rest and in motion with respect to each other, and in recent
years a number of laboratories have conducted model experiments
with stick-slip rock systems with the idea of obtaining a fuller
understanding of the physics of frictional phenomena occurring at
fault lines. C.H. Scholz (Columbia Univ., US), in a review of
current ideas concerning earthquake mechanics, points out that at
present the most precise and predictive model for earthquake
mechanisms is that an earthquake is a frictional rather than a
fractional phenomenon, with brittle fracture of the upper litho-
sphere layer playing a secondary role in the lengthening of
faults and frictional wear. The origin of earthquakes is evid-
ently a stick-slip frictional instability, and many of the
aspects of earthquake phenomena can apparently be explained by
the general laws applying to frictional stability regimes.
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NAT 1998 1 Jan
SW 1998 16 Jan
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Related Background:
THE PREDICTION OF EARTHQUAKES
Earthquake prediction, an aspect of geophysics of obvious
tremendous social and economic importance, demands from
geophysicists more than they are presently able to give.
Seismicity patterns, in conjunction with knowledge of where
historic earthquakes have occurred, permit reasonable judgments
of where future earthquakes are most likely to occur, but at
present it is not possible to predict when an earthquake is
likely to happen in an endangered area. And of course it is the
when that is of great social and economic and even political
importance. A recent published exchange of letters among
seismologists focuses on the problems of earthquake prediction,
the exchange provoked by a previous article which emphasized that
such predictions are not possible (R. J. Geller et al, Science
275:1616 1997). Max Wyss (University of Alaska, US) suggests that
research in the physics of preparation for catastrophic rupture
should not be halted, and that if the lack of funding for
earthquake prediction research continues in the US, the important
discoveries will be made in Japan, Europe, or China. Richard A.
Aceves and Stephen K. Park (University of California Riverside,
US) suggest that the review by Geller et al is "an unduly
negative view of research in a difficult field." But these
authors admit it is time for present earthquake prediction
research to be more honestly identified as earthquake monitoring.
They suggest, however, that considering the large benefit if and
when such research will bear fruit, earthquake prediction
research should definitely continue. Robert J. Geller et al (4
authors at 3 installations in JP, US, IT), the authors of the
review that provoked the letters, respond that they believe
emphasis should be placed on basic research in earthquake
science, real-time seismic warning systems, and long-term
probabilistic earthquake hazard studies.
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SCI 1997 17 Oct
SW 1997 14 Nov
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Related Background:
DEFORMATIONS IN THE SAN ANDREAS FAULT LOWER CRUST
A geophysical fault is a break in rock structure that occurs when
pressures in the Earth's crust are strong enough to cause
fracture and displacement, and earthquakes are common at such
break points. Seismic velocity refers to the propagation velocity
of a seismic disturbance (e.g., an earthquake), and reflectivity
cross-section is a parameter associated with the reflective
properties of a propagated seismic wave. The Mohorovicic
Discontinuity (called "Moho" and named after Andrija Mohorovicic,
who first identified it in 1909) represents the boundary between
the crust and mantle, its depth varying from about 5 kilometers
to as much as 60 to 80 kilometers. A strike-slip fault is a
movement parallel to the fault plane, and the San Andreas fault
of California is of this type. Continental drift is the slow
movement of the Earth's land masses, a shifting across the
underlying molten material, and sea-floor spreading is the
process whereby sea floor is continuously created as the crustal
plates move apart and continuously destroyed where the plates
push against each other. And finally, plate tectonics is the
modern theory that unifies many of the features and character-
istics of continental drift and sea-floor spreading into a
coherent model. Timothy J. Henstock et al (3 authors at 2
installations, US) now report that analysis of a continuous
seismic velocity and reflectivity cross-section of the San
Andreas fault system in northern California reveals offsets in
the lower crust and the Mohorovicic Discontinuity near the San
Andreas and Maacama strike-slip faults, and that the northern
California continental margin to the eastern edge of the Coastal
Ranges is underlain by a high-velocity lowermost crustal layer
that may have been emplaced within 2 million years following the
removal of the plate slab known as the Gorda plate. The authors
suggest that the rapid emplacement and structure within this
layer are difficult to reconcile with existing tectonic models.
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SCI 1997 24 Oct
SW 1997 14 Nov
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3. MOLECULAR DYNAMICS ANALYSIS OF PROTEINS
J.J. Pompers and R. Brueschweiler (Clark University, US) discuss
*relaxation analysis of proteins by combined *molecular dynamics
and *nuclear magnetic resonance (NMR) methods. To perform their
function, proteins often exhibit a significant degree of
flexibility and dynamics, which may occur on a wide range of time
scales from femtoseconds to seconds. Since the flexible parts of
globular proteins, such as loop regions and side chains, are
often involved in mediating specific protein-protein and protein-
DNA interactions, detailed descriptions of the dynamics of these
parts and their changes upon establishment of specific contacts
should help to obtain a better understanding of biologically
important molecular processes. Atoms in biomolecules do not move
independently, but rather in a collective fashion, so a
description that takes motion correlation effects into account is
desirable. Much of what is known about rapid biomolecular
dynamics stems from NMR spin relaxation data and molecular
dynamics computer simulations. The two methods are complementary:
spin relaxation experimentally monitors local reorientational
motions of internuclear vectors and correlation times, while
molecular dynamics provides a detailed theoretical view of
protein dynamics. The authors present an approach for the
interpretation of heteronuclear NMR spin relaxation data in
mobile protein parts, the approach applied to characterize the
dynamics of a loop region of *ubiquitin.
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JACS 2001 123:7305
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... ... *relaxation analysis: In this context, the term
"relaxation" refers to the return of a system to its equilibrium
state after it has experienced a sudden change due to an external
influence.
... ... *molecular dynamics: Contemporary molecular dynamics
simulations, which are extrapolations of statistical mechanics
and which originate in the work of Alder and Wainright in the
1960s, are computer simulations of molecular systems typically
involving hundreds or sometimes thousands of idealized particles
interacting with physically realistic potentials. Such molecular
dynamics simulations can provide time-dependent properties of a
liquid, but most commonly they are used to produce a set of
configurations and forces which can be averaged to give
equilibrium properties of the system.
... ... *nuclear magnetic resonance: The absorption of
electromagnetic radiation at a characteristic precise frequency
by a nucleus with a nonzero magnetic moment in an external
magnetic field. The phenomenon occurs of the nucleus has nonzero
spin, in which case it behaves a small magnet in an external
magnetic field. In quantum mechanics, electrons, protons, and
neutrons have an intrinsic angular momentum known as "spin", and
a magnetic moment parallel or antiparallel to that angular
momentum. When electrons are combined together to form an atom or
ion, there is a resultant angular momentum which is a combination
of the intrinsic spin of the electrons and the angular momentum
due to their motion about the nucleus, and this is the "spin" of
the atom or ion. Atoms or ions with non-zero spin are magnetic
atoms or ions. NMR spectroscopy is the main application of NMR,
the technique widely used for chemical analysis and structure
determination.
... ... *ubiquitin: A small highly-conserved heat-stable protein
of 76 amino-acid residues, the protein widely distributed in
forms ranging from bacteria to mammals.
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4. THE RISE OF ATMOSPHERIC OXYGEN
James F. Kasting (Pennsylvania State University, US) discusses
the rise of oxygen in the atmosphere of ancient Earth. Geologists
and evolutionary biologists have long speculated about when
atmospheric oxygen first became abundant and about how rapidly it
reached its present concentration. The groundbreaking studies by
P.E. Cloud (1972) of reduced and oxidized iron and uranium
minerals, coupled with later studies of microfossils and ancient
soils, convinced most observers that atmospheric oxygen underwent
a dramatic increase in concentration between 2.2 and 2.4 billion
years ago. Some geologists did remain skeptical as late as the
mid-1990s, but recent geochemical evidence has removed much of
the uncertainty. Nevertheless, although the timing of the initial
oxygen rise is now relatively well established, the question of
what triggered the rise remains hotly debated. Researchers agree
that oxygen was produced initially by cyanobacteria, the only
prokaryotic organisms capable of oxygenic photosynthesis. But
cyanobacteria are thought to have emerged by 2.7 billion years
ago, on the basis of evidence from organic biomarkers in well-
preserved sedimentary rocks. (Earlier claims for the existence of
cyanobacteria 3.5 billion years ago have recently been called
into question.) Why was there a gap of at least 400 million years
between the emergence of cyanobacteria and the rise in
atmospheric oxygen?
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SCI 2001 293:819
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Related Background:
ON THE EARLY DEVELOPMENT OF AN OXYGEN-RICH EARTH ATMOSPHERE
It is currently believed that the oxygen concentration in
Earth's atmosphere may have remained at 1 percent of its present
level until approximately 2 billion years ago, after which the
concentration gradually increased to its present value with the
increasing success of photosynthetic life forms. Fossil oxygen-
generating cyanobacteria have been dated as far back as 3.5
billion years ago, but the rate at which oxygen accumulated in
the atmosphere because of photosynthesis is not known.
Although the time-frame of the increase in oxygen
concentration of the atmosphere is uncertain, the consensus among
researchers is that the initiation of an oxygen atmosphere
increased the number and kinds of organisms capable of using
aerobic metabolic pathways. By the start of the Cambrian period
570 million years ago, or somewhat earlier, oxygen levels had
apparently increased enough to permit rapid evolution of large
oxygen-utilizing multicellular organisms.
... ... Norman H. Sleep (Stanford University, US) presents a
commentary on recent research on the early atmosphere of Earth,
the author making the following points:
1) The author points out that although oxygen now
constitutes approximately 20 percent of the gas in the
atmosphere, before approximately 2.5 billion years ago it was
apparently only a trace constituent. The Earth is unique among
the planets in the Solar System in having an oxygenated
atmosphere. The atmospheres of the other planets are anoxic
because oxygen levels are kept relatively low by an equilibrium
system involving chemical processes in crusts, mantles, and
volcanic gases. On the Earth, oxygen levels increased over
geological time apparently mainly as a result of photosynthesis,
which can be expressed as the general reaction carbon dioxide -->
carbon + oxygen.
2) Over the eons, a vast amount of organic carbon has become
locked up in sedimentary rocks, a small part of it in coal and
oil, thus preventing the reverse reaction to equilibrium that
would create carbon dioxide and lower atmospheric levels of
oxygen. However the advent of oxygen-producing photosynthesis
cannot be the entire story of the evolution of Earth's
atmosphere, since photosynthesis apparently existed long before
the well-documented rise in oxygen levels 2.5 billion years ago
(the Archaean-Proterozoic transition).
3) L.R. Kump et al (Geochem. Geophys. Geosyst. 2001) are now
proposing that changes in the deep interior of the Earth affected
the composition of volcanic gases, and that this led to the rise
in atmospheric oxygen levels 2.5 billion years ago. The idea is
that although photosynthesis is presently the main source of
oxygen in Earth's atmosphere, it may have been geological
activity that first allowed an oxygen-rich atmosphere to develop.
4) The author (Sleep) concludes: "It was over two centuries
ago that Antoine Lavoisier figured out that we breathe oxygen.
But we still don't know how an oxygen-rich atmosphere arose.
Clearly, processes at both the Earth's surface and in its bowels
were involved. Exactly how and by how much each contributed
remain open questions."
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NAT 2001 410:317
SW 2001 29 Jun
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5. CHEMISTRY OF BEE VENOM
A. Niemz and D.A. Tirrell (California Institute of Technology,
US) discuss the chemistry of bee venom. Melittin, the major
component of bee venom, is a 26-amino acid amphiphilic peptide
that inserts into membranes and causes cell lysis. This molecule
has been intensely studied both as a model for peptides with
membrane affinity and to understand the structural bases of its
lytic and antimicrobial activities. In aqueous solution and sub-
millimolar concentration and low ionic strength, melittin exists
as a random coil monomer, mainly due to repulsive interactions
between the highly-charged C-terminal regions. At higher ionic
strength, especially in the presence of divalent anions, melittin
forms a water-soluble tetramer with known crystal structure. Each
monomer assumes the conformation of a bent alpha-helical rod,
with three sections showing distinctive spatial segregation of
hydrophobic and hydrophilic side chains. Insertion into a
phospholipid bilayer also causes melittin to adopt a bent helical
conformation. While the C-terminal section is approximately
parallel to the lipid bilayer, the N-terminal section is inserted
halfway into the membrane, as confirmed by various spectroscopic
methods and computational analysis. The mechanism of cell lysis
caused by melittin is still under debate. One model proposes that
the wedge-like insertion of melittin monomers into one side of
the bilayer disrupts the membrane, causing water penetration and
leakage of small molecules. The authors investigated membrane-
binding behavior of melittins containing trifluoroleucine.
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JACS 2001 123:7407
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6. HOW MARS CAME TO HAVE "CANALS".
K. Zahnle (NASA Ames Research Center, US) discusses the canals of
Mars. Giovanni Schiaparelli (1835-1910) discovered the "canali"
of Mars in 1877 using a modest 22-centimeter refractor in Milan.
Schiaparelli had first won fame by demonstrating that the annual
Perseid meteor shower was due to comet Swift-Tuttle. This fame
earned him his observatory, where he visually measured double
stars to high accuracy. Thus his surprising 1877 map of Mars was
taken seriously. The wonderfully evocative Martian nomenclature
(consider, for example, Tharsis, Chryse, Elysium, Amazonis,
Trivium Charontis, and Syrtis Major) that still survives derives
from this map. The canali were at first depicted mostly as broad
channels, more akin to the Malagasy Strait or the Red Sea than to
the thin blue-green lines they become later. The early
"aerographies" of Schiaparelli and others reflected the theory
that the dark areas on Mars were seas; W.H. Pickering (1858-1938)
and Percival Lowell (1855-1916) later showed the seas to be dry
land. At succeeding and progressively less favorable Martian
oppositions, Schiaparelli's canali hardened into a geometric
network of razor-sharp ruler-straight canals. Many of the canali
also began to appear in pairs, a controversial phenomenon that
Schiaparelli referred to as "germination". Belief in the reality
of the canals spread as ever more observers apparently glimpsed
some of what Schiaparelli had seen. In the late 1880s, apparent
confirmation came from the world's largest refractor telescopes
in Nice and at the Lick Observatory in California. By 1895,
drawings of Mars were interpreted as depicting the Hebrew letters
for the name of God, with the newspaper the _San Francisco
Chronicle_ noting on June 2, 1895 that "the magnitude of the work
of cutting the canals into the shape of the name of God is at
first thought appalling." Sightings of Martian canals by
reputable astronomers were still occurring as late as 1939.
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NAT 2001 412:209
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7. STRUCTURE OF THE RIBOSOME
M.M. Yusupov et al (University of California Santa Cruz, US)
discuss the crystal structure of the ribosome. The large
ribonucleoprotein complexes called "ribosomes" are responsible
for protein synthesis in all cells, with a single bacterium
containing approximately 20,000 of these entities. Unlike other
cellular polymerases, the mechanism of action of ribosomes
appears to be based fundamentally on RNA, which means ribosomes
are essentially "ribozymes", or RNA-enzymes. Understanding the
structural basis for the fundamental capabilities of ribosomal
RNA (rRNA) is essential to explain why these ancient organelles
use RNA instead of protein for the complex and biologically
crucial task of translation. Bacterial ribosomes, which have been
the most extensively investigated, are composed of small (30s)
subunits, containing 16s rRNA and approximately 20 proteins, and
large (50s) subunits, which contain 23s rRNA, 5s rRNA, and over
30 proteins. The complete 70s ribosome is formed by association
of the 30s and 50s subunits via a network of intermolecular
bridges. The intersubunit space is occupied by the transfer RNAs.
The authors describe the crystal structure of the complete
Thermus thermophilus 70s ribosome containing bound messenger RNA
and transfer RNAs at 5.5 angstrom resolution. The authors suggest
that knowledge of the structure of the complete ribosome
complexed with messenger RNA and transfer RNA now provides the
possibility to test various specific molecular models for the
mechanism of translation.
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Related Background:
MOLECULAR BIOLOGY: ON RIBOSOMES
A ribosome is a large ribonucleoprotein particle which is present
in many copies in all biological cells and which is the site of
protein synthesis. All ribosomes consist of 2 subunits of unequal
size, called the "large" and "small" subunits, and the size and
composition of these two subunits differs between *prokaryotic
and *eukaryotic cells (although the overall structure is
similar). Ribosomes from the common bacterium Escherichia coli
have a *sedimentation coefficient of 70s, a total *relative
molecular mass of 2.7 x 10^(6), and a diameter of approximately
200 angstroms. E. coli ribosomes are composed of a large subunit
of 50s and a small subunit of 30s. The 50s subunit consists of 34
different proteins ("ribosomal proteins") and 2 types of
ribosomal RNA. The 30s subunit contains 21 ribosomal proteins and
a 16s RNA. Each ribosomal subunit has been shown to self-assemble
in vitro from its constituent proteins and RNA.
... ... James R. Williamson (Scripps Research Institute, US)
presents a commentary on recent ribosome research, the author
making the following points:
1) The structure of the small subunit of a bacterial
ribosome has now been solved at atomic resolution (B.T. Wimberly
et al: Nature 21 Sep 00 407:327; A.P. Carter et al: Nature 21 Sep
00 407:340). The ribosome is a fundamental cellular component
which synthesizes all of the proteins in the cell, using
*messenger RNA (mRNA) as the template. The ribosome acts in
concert with a variety of smaller entities that help to
orchestrate the process, but the two main functions involve the
ribosome itself: decoding the genetic code in the messenger RNA,
and catalyzing the formation of chemical bonds between amino
acids to result in polypeptide chains of proteins.
2) The 30s subunit has a very different architecture than of
its 50s partner. In the 30s subunit, clear domain boundaries are
evident in crystallographic data, and potentially flexible
regions can be seen in cryo-electron microscope reconstruction.
Large movements, on the scale of tens of angstroms, must occur on
the 30s subunit during translocation of the messenger RNA from
one *codon to the next. In contrast, the 50s subunit is
monolithic, its components being intricately folded and packed
into a rigid structure. These two structurally unlike subunits
work together to carry out, in all biological cells, one of the
most intricate of functions.
3) The author points out that it is perhaps not widely
appreciated that approximately two-thirds of the mass of the
ribosome is composed of RNA. With atomic knowledge of the 30s and
50s structures and how they assemble into the overall 70s
ribosome, one point stands out: the most essential functions of
the ribosome are carried out by RNA.
4) The dogma that nucleic acids are the repository of
information and that proteins catalyze chemical reactions was
overturned only 15 years ago by the demonstration of catalytic
RNAs (ribozymes). Despite increasing support for the "RNA world
hypothesis", which sees RNA-based life forms as the progenitors
of modern biological cells, most biologists did not seriously
consider the possibility that RNA could be playing more than a
minor part in reactions such as protein synthesis. But it has
turned out that in the ribosome most of the important functional
work is done by RNA. The author concludes: "The ribosome is one
colossal RNA enzyme."
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NAT 2000 407:306
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Text Notes:
... ... *prokaryotic: The term "prokaryotes" refers to biological
cells without internal membrane-bound organelles such as a
nucleus.
... ... *eukaryotic: The term "eukaryotes" refers to biological
cells (or organisms consisting of such cells) with internal
membrane-bound organelles such as a nucleus.
... ... *sedimentation coefficient: The sedimentation coefficient
is essentially the rate of sedimentation of a particle in an
ultracentrifuge or other system. The sedimentation coefficients
of macromolecular and cellular particles are often expressed as
Svedberg units, after Theodor Svedberg (1884-1971), the inventor
of the ultracentrifuge, who received the Nobel Prize in Chemistry
in 1926 for his work on disperse systems.
... ... *relative molecular mass: The unit "relative molecular
mass", often used in biochemistry and denoted by M(subr), is
essentially synonymous with molecular weight, and is the ratio of
the mass of a molecule to the atomic mass constant, which is
taken as one-twelfth of the mass of the nuclide (sup12)C. The
relative molecular mass is a dimensionless number, the magnitude
of which is equivalent to the molecular mass in daltons: A
relative molecular mass of 10,000 is equivalent to 10
kilodaltons.
... ... *messenger RNA (mRNA): The ribonucleic acid molecule
transcribed from DNA that carries the coded information
specifying the sequence of amino acids in a protein.
... ... *codon: A "codon" is the elemental genetic coding unit,
a triplet of 3 consecutive nucleotides that define a specific
amino acid.
-------------------
SW 2000 27 Oct
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Related Background:
MOLECULAR BIOLOGY: ON THE WORKINGS OF THE RIBOSOME
... ... Joachim Frank (State University of New York Albany, US)
presents a review of current understanding of ribosome function
and structure, the author making the following points:
1) Although it is important to know the structure of the
ribosome at atomic resolutions, this goal is still quite remote,
since even one of the simplest ribosomes, that of the bacterium
Escherichia coli, is made up of more than 50 components, mostly
proteins plus 3 large RNA molecules. Ribosomes of higher
organisms are even more complex and have more components.
2) It is now believed that all important functions of the
ribosome actively involve the ribosomal RNAs as major players,
whereas the ribosomal proteins act either as structural "glue" or
as "helpers" that promote specific binding reactions. This
represents a complete reversal of the long-held view that the
proteins of the ribosome perform all the important tasks.
3) The translation from the nucleotides of messenger RNA
(mRNA) to the amino acids in the protein polypeptide chain is
accomplished at the ribosome with the help of an adaptor molecule
called "transfer RNA" (tRNA). The molecule tRNA exists in 20
varieties, each variety specifically designed to accommodate only
one of the 20 amino acids at one end of the tRNA molecule, and
each tRNA molecule also carries a specific *anticodon at the
other end of the molecule that recognizes only the *codon on mRNA
specifying that particular amino acid. Each tRNA molecule thus
acts as a physical code-link between an mRNA codon for an amino
acid and that specific amino acid, the assembly of the protein
polymer involving the sequential selection of amino acids from
the ambient amino acid pool.
4) The author reviews an application of the technique of
cryo-electron microscopy to the determination of ribosome
structure, the application involving methods of "single- particle
reconstruction" developed by the author. Cryo-electron microscopy
provides a means to image macromolecules in a "close- to-native"
conformation by freezing the molecules rapidly in liquid ethane
at -196 degrees Celsius. The technique was first developed in the
1970s by Glaeser et al, and then perfected early in the 1980s by
Dubochet et al. The method of single-particle reconstruction
essentially involves the idea that in principle the 3-dimensional
geometry of a macromolecule can be reconstructed from its
projections on a 2-dimensional surface, provided the molecule
occurs in a range of orientations and provided these orientations
are known. The author reviews in detail what is known concerning
the workings of the ribosome during protein synthesis as
amplified by recent data involving the application of
cryo-electron microscopy coupled with techniques of
single-particle geometric reconstruction.
-----------
AS 1998 86:428
SW 1998 11 Sep
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Text Notes:
... ... *codon and anticodon: A codon is the coding unit of
messenger RNA, comprising a triplet of nucleotides that pairs
with a corresponding triplet (anticodon) of transfer RNA. The
term "codon" is also in more general use as the basic genetic
coding unit, a triplet of nucleotides in DNA.
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8. CHOICES IN SEQUENCING MAMMALIAN GENOMES
S.J. O'Brien et al (National Cancer Institute, US) discuss the
problems of choosing mammalian genomes for sequencing. At
present, approximately 4600 to 4800 species of mammals dominate
the planet, with these species occupying every continent and
diverse ecological niches. The morphological and physiological
differentiation seen among mammals is enormous, ranging from blue
whales to echolocation-driven bats, from blind subterranean naked
mole rats to humans. The richness of mammalian species diversity
and their remarkable adaptations have provided the evolutionary
framework from which the human species evolved. The genomes of
mammalian species encode the script for individual developmental
distinctions, as well as the relict sequence records of
historical genetic events through which the genomes (and the
organisms they prescribe) were sculpted by natural selection.
With the unveiling of draft versions of the human genome earlier
this year, resources are now being harnessed to annotate the
approximately 30,000 human genes that direct our development,
appearance, behavior, talents, and susceptibility to disease. The
interpretation of human genome organization will draw, to a large
extent, from the genomes of other organisms, with other genomes
helping us to infer the function, regulation, and origins of our
own genes. Decisions and priorities regarding the choice of
organisms for whole-genome sequencing will ultimately shape
biology and influence the potential applications of the completed
genome sequences.
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SCI 2001 292:2264
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Related Background:
MOLECULAR BIOLOGY: ON THE NEED FOR A CHIMPANZEE GENOME
The human genome will soon be completely sequenced, a milestone
in the history of biology and medical science. Intensive research
effort is now focused on the next logical biomedically relevant
target -- the mouse. As a mammalian species of importance in
biomedical research, primarily due to economies of research on
this small easily bred animal, the mouse has no equal. And after
the mouse, what next? There have been calls to sequence the
genomes of the rat (Rattus rattus), the African clawed toad
(Xenopus laevis), and the zebra fish (Danio rerio), all
laboratory animals for which there is an enormous literature of
published laboratory experiments. These are certainly species of
great importance to biology. From a biomedical standpoint,
however, a strong argument can be made that the complete
sequencing of the genomes of none of these animals would be as
important as the complete sequencing of the genome of our closest
evolutionary relative, the chimpanzee (Pan troglodytes).
... ... Ajit Varki (University of California San Diego, US)
presents a commentary calling for the sequencing of the
chimpanzee genome, the author making the following points:
1) Chimpanzees and humans share nearly 99 percent of their
genomes. Knowing the complete chimpanzee genome will give us a
window into genes that contribute to "humanness". The emergence
of humans can be regarded as one of the major transitions in
evolution, and the complete explanation of this phenomenon ranks
as one of the greatest unsolved mysteries of science.
2) Extrapolating findings in physiology and pathology from
mice, rats, toads, or fish to humans can be difficult, because of
the physiological and genetic differences between humans and
these species. In contrast, the greater than 99 percent identity
of amino acid sequences of most chimpanzee and human proteins
predict a stronger likelihood of finding genetic explanations for
any disease differences. Studies of the chimpanzee genome could
be considered a logical extension of the current emphasis on
exploiting sequence differences between various human groups to
identify important disease susceptibility genes.
3) Some pathological states in humans seem to represent the
normal situation in chimpanzees, including closure of the skull
sutures around the time of birth (perinatal period)
(craniosynostosis), a high white blood cell count (general
leukocytosis), and hairiness (extensive hypertrichosis). Several
other diseases or physiological states of humans appear to be
rare or markedly attenuated in the chimpanzee. Some of these
diseases can be attributed to anatomic differences between the
species, including protracted, painful, and dangerous childbirth
(resulting from the larger head of the human fetus and the
altered pelvis of the bipedal human female), wisdom tooth
impaction (resulting from reduced jaw size in humans and the lack
of a post-molar gap), and various diseases attributed to gravity
effects on bipedal humans (vertebral osteoarthritis,
intervertebral disc protrusion, varicose veins, and hemorrhoids).
There are also a few anatomically unique diseases of great apes
that do not occur in humans, such as infection of the pharyngeal
air sacs (an organ that is absent in humans). The higher
frequency in humans of anatomical disorders of the central
nervous system (e.g., hydrocephalus) is also intriguing, but
could be explained on the basis of increased perinatal trauma.
4) But many other differences between humans and chimpanzees
cannot be explained on any obvious behavioral, dietary, anatomic,
cellular, or biochemical basis. The author suggests it is these
differences that justify the biomedical imperative of the
sequencing of the chimpanzee genome. The author summarizes these
significant differences as follows:
... ... a) The failure of HIV infection to progress to AIDS in
the chimpanzee. Despite many studies attempting to find the
answer, the mystery remains: the HIV retrovirus seems to live in
a symbiotic state within the chimpanzee immune system, whereas it
almost routinely destroys the helper T cells of humans.
... ... b) Alzheimer's disease is a common and devastating
disease causing dementia in elderly humans, the human brain
pathology characterized by the accumulation of amyloid plaques
together with neurofibrillary tangles. The pathological lesion,
including the neurofibrillary tangles, has never been observed in
the brains of elderly chimpanzees. In contrast, age-matched
samples from human brain specimens show a significant rate of
these classic lesions, often well before symptoms of dementia
have become evident. Neurofibrillary tangles can even exist in
human brains independent of plaques, beginning virtually at birth
and reaching a 50 percent prevalence by age 48. The fact that the
full-blown lesion of Alzheimer's disease has also not been
observed in other long-lived animals (e.g., elderly elephants),
increases the significance of this finding, and makes a
comparison between humans and the corresponding chimpanzee genes
of great potential benefit.
... ... c) Of all the different forms of malaria, that caused by
the pathogen Plasmodium falciparum is the most aggressive and
acutely life-threatening; it is a major cause of mortality
worldwide. Chimpanzees are apparently immune to infection by this
parasite, and instead get infected by its close relative
Plasmodium reichnowii, which evidently does not make the
chimpanzee very ill. The knowledge gleaned from comparative
studies of the relevant parasite genomes as well as the human and
chimpanzee genomes could be of great importance.
... ... d) The most common human cancers, epithelial neoplasms
such as carcinomas of the breast, ovary, lung, stomach, colon,
pancreas, and prostate, cause more than 20 percent of deaths in
modern human populations. In contrast, the cancer incidence rates
for non-human primates is only approximately 2 to 4 percent and
seems to be even lower in the great apes. It is of interest that
a cell-surface sugar modification that is lost in the human
lineage due to genomic mutation is reported to reappear in human
cancers.
... ... e) Several aspects of female reproductive biology appear
to be different between great apes and humans. For example,
menopause has not been observed in long-lived captive female
chimpanzees. Compared to chimpanzees, human females are unusual
in having a high frequency of breast diseases such as fibrocystic
disease and cancer. Also, the absence of external signs of
ovulation in human females may result in fertilization taking
place at suboptimal times with regard to the condition of the
ovum. Thus, the question arises whether fertilization of
deteriorating eggs may explain -- at least partly -- the
relatively high rate of gross chromosomal and other genetic
abnormalities in human fetuses.
... ... f) In addition to the above examples, anecdotal evidence
suggests that some other common human conditions are rare in
great apes in captivity: i) Despite a high frequency of atopic
rhinitis and polyps, bronchial asthma is rarely diagnosed in
chimpanzees. ii) Acne vulgaris, the common skin affliction of
human teenagers, also appears to be uncommon in the adolescent
chimpanzee. iii) Rheumatoid arthritis has not been detected in
chimpanzees.
-----------
GR 2000 10:1065
SW 2000 15 Sep
-------------------
Related Background:
MOLECULAR BIOLOGY:
ON THE RAT AS A MODEL SYSTEM IN FUNCTIONAL GENOMICS
In a few years, the complete sequence of nucleotide bases in the
human genome will be determined. But that is only the first phase
of the new human biology of the 21st century: after specification
of the complete sequence will come years of arduous work
identifying specific new genes and relating the proteins encoded
by these genes to specific sets of events in health and disease.
This second phase of genome research, the "functional genomics
era", will be carried out, for the most part, on animals, using
animal models to formulate hypotheses concerning the role played
by various parts of the human genome in human biology. The basis
for the use of animal models in this undertaking is the strong
apparent similarity of the genomes and physiology of certain
mammalian species to the human genome and human physiology. The
mouse, a small mammal easily maintained and easily bred, is
currently the favorite animal model used in mammalian genetics
research, but there are a number of candidates for future
functional genomics, and researchers, as always, will need to
make important strategic decisions concerning the focus of their
laboratory work. Intrinsic to the use of an animal model in
functional genomics is the complete sequencing of the genome of
that animal.
... ... Howard J. Jacob (Medical College of Wisconsin, US)
presents a review of the role the rat will play in annotating the
human genome in the functional genomics era. The author makes the
following points:
1) The author points out that the laboratory rat, _Rattus
norvegicus_, was the first mammalian species domesticated for
scientific research, with work dating back to before 1850. From
this beginning, the rat has become the most widely studied
experimental animal model for biomedical research. Since 1966,
nearly 500,000 research articles reporting the use of rats have
been published, with most of these articles focused on evaluating
the biology and/or pathobiology of the rat. In contrast to its
central role in the study of behavior, biochemistry,
neurobiology, physiology, and pharmacology, the rat has lagged
far behind the mouse as a genetic model organism.
2) The author points out that although research on rat
genetics and mouse genetics historically had a parallel
beginning, the mouse soon became the model of choice for
mammalian geneticists, whereas the rat became the model of choice
for physiologists, nutritionists, and other biomedical
researchers. Geneticists preferred the mouse because of its
smaller size, which simplified housing requirements, and the
availability of many coat-color and other mutants exhibiting
Mendelian patterns of inheritance. In contrast, physiologists and
other biomedical researchers favored the rat because its larger
size facilitated experimental interventions, and over time a
large number of rat models were used to develop disease models by
selective breeding that fixed natural disease *alleles in
particular strains or colonies.
3) The author concludes: "The rat offers many advantages for
identification of gene functions that relate to common human
diseases, because of the existing body of knowledge of
physiological mechanisms, the availability of models that mimic
these diseases, the ease of breeding, and the ability to generate
new and better models that match subsets of patients at both the
*phenotypic and genomic levels... Once genes and their functions
are identified in rats, pathophysiologic mechanisms can be
elucidated, and human genetic counterparts can be more easily
identified."
-----------
GR 1999 9:1013
-----------
Text Notes:
... ... *alleles: An allele is one of two or more forms of a
given gene that control a particular characteristic, with the
alternative forms occupying corresponding loci on homologous
chromosomes.
... ... *phenotypic and genomic levels: In general, the term
"phenotype" refers to the total appearance of an organism as
determined by the interaction during development between its
genetic constitution (genotype) and the environment.
-----------
SW 2000 24 Mar
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9. AFRICAN ANCESTRY OF MODERN HUMANS
Y. Ke et al (Fudan University, CN) discuss the African origin of
modern humans in East Asia. The "Out-of-Africa" hypothesis
suggests that anatomically modern humans originated in Africa
approximately 100,000 years ago and then spread outward and
completely replaced local archaic populations outside Africa.
This proposition has been supported by genetic evidence and
archaeological findings. The proposed replacement in Europe was
supported by recent ancient DNA analyses, which ruled out the
contribution of Neanderthals to modern Europeans. However, it has
been argued that the abundant hominid fossils found in China and
other regions in East Asia (e.g., Peking man and Java man)
demonstrate continuity, not only in morphological characters but
also in spatial and temporal distributions. The authors sampled
12,127 male individuals from 163 populations and typed for 3 Y
chromosome bi-allelic markers (YAP, M89, and M130). All the
individuals carried a mutation at one of the 3 sites. These 3
mutations (YAP+, M89T, M130T) coalesce to another mutation
(M168T), which originated in Africa approximately 35,000 to
89,000 years ago. Therefore, the authors suggest, the data do not
support even a minimal in situ hominid contribution in the origin
of anatomically modern humans in East Asia: The results indicate
that modern humans of African origin completely replaced earlier
populations in East Asia.
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Related Background:
ANTHROPOLOGY: ANCIENT DNA AND THE ORIGIN OF MODERN HUMANS
Mitochondria are double-membrane enclosed organelles of
cells, the mitochondria involved with several important
biochemical pathways, including electron transport and oxidative
metabolism. Various types of cells containing internal membrane-
bound organelles (eukaryotic cells) may contain from a few to
several thousand mitochondria in each cell type. The mitochondria
are relatively large cylindrical structures up to 10 microns long
and up to 2 microns in diameter, and most biologists believe
mitochondria are cell organelles that may have originated as
separate organisms that became resident in eukaryotic cells.
Mitochondrial DNA is independent of nuclear DNA, consisting of a
circular molecule, 16,569 base pairs long in humans, with a known
nucleotide sequence.
Investigations of human mitochondrial DNA have revealed two
facts relevant to questions of human origins: a) the variation
among modern human populations is small compared, for example, to
that between apes and monkeys, which has been interpreted to
indicate the recency of human origins; b) there is a distinction
between African and other human mitochondrial types, which has
been interpreted to indicate the relative antiquity of the
African peoples and the relative recency of other human
populations.
Interpretations of mitochondrial DNA evidence have been much
debated in anthropology. Such evidence is a crucial part of the
"single origin" model of human origins, which proposes that one
early population of modern humans spread out of Africa
approximately 60,000 to 100,000 years ago and eventually replaced
all less modern populations of the genus Homo worldwide. Thus,
the difference between "African" and "non-African" mitochondrial
DNA is explained by the idea that small "founder" populations
left Africa, carrying with them only a small sample of the
genetic variation found in Africa as a whole, and that such
founder populations then expanded as they occupied Eurasia,
growing into a large population with a distinctly non-African
mitochondrial DNA structure. This idea became popular in the late
1980s, when it was called the "Mitochondrial Eve" or "Out of
Africa" hypothesis. Although since then this hypothesis has lost
some support, it is still one of the major ideas concerning human
origins.
Support for the opposing "regional-continuity" model is
based primarily on evidence of gradual morphological change,
mainly of the skull, from ancient to modern inhabitants in
different parts of the world. In this scenario, modern humans
developed almost simultaneously in various geographical regions
around the world, replacing less evolved Homo species beginning
approximately 1.5 million years ago.
These are only the general outlines of a hotly debated
complex area of research in human evolution.
... ... G.J. Adcock et al (7 authors at 3 installations, AU)
present a report of a study of mitochondrial DNA sequences in
ancient Australians of modern morphology, the authors making the
following points:
1) The authors point out that since its beginning more than
25 years ago, the debate over recent human origins has focused on
two models. The regional-continuity hypothesis postulates that
ever since humans began to migrate out of Africa more than 1.5
million years ago, there has been a single evolving species, Homo
sapiens, distributed throughout the Old World, with all regional
populations connected, as they are today, by gene flow. Some
skeletal features developed and persisted for varying periods in
the different regions, so that recognizable regional morphologies
have developed in Africa, Europe, and Asia.
2) The other view, the "recent out of Africa" model, argues
that over the period since humans began to leave Africa, there
have been several species of Homo. In this model, H. sapiens
emerged in Africa approximately 100,000 years ago and then spread
globally, replacing other species of Homo that it encountered
during the expansion. This model proposes that all current
regional morphologies, especially those outside Africa, developed
within the last 100,000 years.
3) These alternative models arose from interpretations of
morphological evidence. During the last 15 years, molecular data,
particularly nucleotide sequences drawn from populations of
living humans, have made an increasing contribution to the
debate. Analysis has demonstrated that humans have remarkably
little mitochondrial DNA sequence variation, and that the
earliest branching lineages are found in East Africa. These
findings were interpreted as strongly supporting the "recent out
of Africa" model. The authors suggest, however, that this
interpretation fails to recognize that the demographic history of
a species cannot be inferred from the pattern of variation of a
single nucleotide segment. Patterns of variation in different
regions of the genome must be considered and interpreted in the
context of paleontological and archeological evidence.
4) The authors report mitochondrial DNA sequence evidence
from 10 fossils, all agreed to be anatomically modern, rather
than archaic, Homo sapiens (4 "*gracile" and 6 "*robust"
specimens). The 10 fossils range in age from less than 10,000
years ago to approximately 60,000 years ago. The authors report
that in one fossil (Lake Mungo 3, dated at 60,000 years ago), the
mitochondrial DNA sequence is the most divergent of all of the
Australian fossils analyzed, and this is evidently an example of
a mitochondrial DNA lineage that existed in an ancient modern
human but is absent in living human mitochondria. The authors
state: "Our data present a serious challenge to interpretation of
contemporary human mitochondrial DNA variation as supporting the
'recent out of Africa' model. A separate mitochondrial DNA
lineage in an individual whose morphology is within the
contemporary range and who lived in Australia would imply [from
the out of Africa model and its usage of mitochondrial DNA data]
both that anatomically modern humans were among those that were
replaced and that part of the replacement occurred in Australia."
... ... In a commentary on this work, John H. Relethford (State
University of New York College of Oneonta, US) states: "If the
mitochondrial DNA present in a modern human (Lake Mungo 3) can
become extinct, then perhaps something similar happened to the
mitochondrial DNA of *Neanderthals. If so, then the absence of
Neanderthal mitochondrial DNA in living humans does not reject
the possibility of _some_ genetic continuity with modern
humans... The modern human origins debate can be informed by
genetic data, both living and ancient, but can only be resolved
by also considering the fossil and archeological evidence. The
picture presented by Adcock et al suggests that modern human
origins were more complicated than once envisioned."
-----------
PNAS 2001 98:390,537
-----------
Text Notes:
... ... *gracile: In general, a Homo fossil with a lightly built
skull. The Lake Mungo 3 fossil is a gracile specimen.
... ... *robust: In general, a Homo fossil with a heavily built
skull.
... ... *Neanderthals: The human group we call the "Neanderthals"
lived in much of Europe, part of Asia, and the Middle East
between 150,000 to probably less than 30,000 years ago.
Neanderthals were the first fossil humans to be discovered, and
they have long been the focus of anthropological investigation.
More bones of Neanderthals are known than for any other
human-related (hominine) fossil group, including 30 nearly
complete skeletons, so the preoccupation of the anthropology
community with the Neanderthals is perhaps understandable.
-----------
SW 2001 16 Feb
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SCIENCE-WEEK 31 Aug 2001 http://scienceweek.com
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10. YELLOW FEVER AND THE MOSQUITO
Richard Horton (Lancet) discusses yellow fever and the mosquito.
No other disease did more to shape the evolution of American life
than yellow fever. HIV-AIDS may, in a century or so, come to be
regarded as an equal influence, but it was yellow fever that set
the modern rules of engagement -- emotional, political,
scientific, and medical -- in confrontations between disease and
humankind. As is often the way with pathologies suppressed and
illnesses prevented, the threat that yellow fever posed to
society is now largely and happily forgotten, at least in the US.
Yellow fever is caused by a virus transmitted to humans in
villages and towns by a delicate-looking mosquito called Aedes
aegypti, but the connection between mosquitoes and the fever was
not established until 1900. When the yellow-fever infected
mosquito enters a human settlement, outbreaks of disease tend to
be explosive and fatal. An epidemic in Ethiopia between 1960 and
1962 killed as many as 30,000 people. The disease itself is
particularly horrible: illness begins abruptly with fever,
headache, and muscle pain; the victim is extremely ill with
bleeding and violent episodes of vomiting; within a few days, the
pulse slows, blood pressure falls, and the kidneys fail; blood
oozes from every tissue surface. When the infection is severe,
half of those affected die.
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NYR 2001 9 August
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SCIENCE-WEEK 31 Aug 2001 http://scienceweek.com
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11. AUTOIMMUNE DISEASES
A. Davidson and B. Diamond (Albert Einstein College of Medicine,
US) discuss current research in autoimmune diseases. These
diseases, with the exception of rheumatoid arthritis and
autoimmune thyroiditis, are individually rare, but together they
affect approximately 5 percent of the population in Western
countries. Currently, an "autoimmune disease" is defined as a
clinical syndrome caused by the activation of T cells or B cells
or both, the activation in the absence of an ongoing infection or
other discernible cause. For many years the central dogma of
immunology focused on the idea that the clonal deletion of
autoreactive cells leaves a repertoire of T cells and B cells
that recognize specific foreign antigens. The current consensus,
however, is that a low level of autoreactivity of the immune
system is physiologic and crucial to normal immune function.
Autoantigen helps to form the repertoire of mature lymphocytes,
and the survival of naive T cells and B cells in the periphery
requires continuous exposure to autoantigens. Since there is no
fundamental difference between the chemical structure of self-
antigens (autoantigens) and that of foreign antigens, lymphocytes
apparently evolved not to distinguish self from foreign, as some
have speculated, but to respond to antigens only in certain
microenvironments, generally in the presence of inflammatory
cytokines. Since autoreactivity is physiologic, the challenge in
the context of autoimmune diseases is to understand how it
becomes a pathologic process and how T cells and B cells
contribute to tissue injury.
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NEJM 2001 345:340
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SCIENCE-WEEK 31 Aug 2001 http://scienceweek.com
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12. GLOBAL AIDS IN 2001
The US Centers for Disease Control discusses the global HIV and
AIDS epidemic in the year 2001. Sub-Saharan Africa is currently
the region of the world most affected by HIV and AIDS. Uganda,
Kenya, and Tanzania were among the countries where the HIV
epidemic was first recognized during the early 1980s. In the year
2000, an estimated 25.3 millions people in sub-Saharan Africa
were infected with HIV, and the average national prevalence of
HIV infection among persons aged 15 to 49 years was 8.8 percent.
Approximately 4 million new infections occurred during the year
2000. In Botswana, the country with the highest prevalence, 36
percent of the adult population is infected with HIV. The
epidemic continues to spread in Asia. In China, HIV prevalence
was as high as 82 percent among injection drug users and 6
percent among commercial sex workers during 1998-1999. In India,
the estimated HIV infection rate among persons aged 15 to 49
years is 0.7 percent, and as of mid-1998, an estimated 3.5
million persons were infected with HIV. In contrast with other
Asian countries, the prevalence of HIV in Thailand has been
declining due to government-sponsored education and regulatory
programs. Eastern Europe has had recent and rapid growth of HIV
infection among injection drug users, with 70,000 cumulative
cases in the Russian Federation by December 2000. In Western
Europe and the US, deaths attributed to HIV have declined
substantially since the introduction of highly active anti-
retroviral therapies. In Latin America and the Caribbean, the
leading modes of HIV transmission are sex between men, sex
between men and women, and injection drug use. By December 2000,
an estimated 1.4 million adults and children were infected with
HIV/AIDS in Latin America and the Caribbean. The Caribbean, with
an adult prevalence of 2.1 percent, is the second most affected
world region. In Brazil, reported HIV-related deaths have
declined by 40 percent, in large part because of the government
policy of providing universal free access to anti-retroviral
therapies.
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MMWR 2001 50:434
JAMA 2001 285:3081
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SCIENCE-WEEK 31 Aug 2001 http://scienceweek.com
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13. IN FOCUS: A CINEMATIC VIEW OF EVOLUTION
"Fifty years ago, James Rettie (Coronet 1951 29:21) proposed a
graphic imagery that made the geological time-frame of biological
evolution more comprehensible. Rettie imagined a time-lapse
motion picture of Earth taken from space, beginning 757 million
years ago, with one image being photographed each year. Projected
at the normal speed of 24 images per second, the resulting movie
would take a year to view, with each day representing 2.1 million
years. Here is what the movie would show: From January to March,
there is little sign of life, then the first unicellular microbes
appear in early April, giving rise to small multicellular
aggregates later that month. In May the vertebrates emerge, and
by July land plants have begun to cover the globe. In mid-
September early reptiles preview the dawn of the dinosaur era,
which continues through late November, dominating the world for
70 days. Birds and small mammals first appear in early November,
but are overshadowed by reptilian species until 1 December, when
the dinosaurs disappear abruptly. By late December, the
recognizable ancestors of modern families of mammals make their
debut, but not until midday on New Year's Eve do our first
ancestors appear. Between 9:30 and 10:00 pm, Homo sapiens
migrates out of Africa to populate Eurasia and the Americas. At
11:54 pm, recorded human history and civilization as we know it
begin."
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S.J. O'Brien et al: SCI 2001 292:2264
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SCIENCE-WEEK 31 Aug 2001 http://scienceweek.com
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14. FROM THE SW ARCHIVE:
ON THE DISCOVERY OF ELECTROMAGNETIC WAVES
Sometime around the mid 1880s, the noted physicist Hermann
Helmholtz (1821-1894) suggested to one of his accomplished former
students that the student compete for a prize being offered by
the Berlin Academy of Science for work in the field of
electromagnetics. James Clerk Maxwell (1831-1879), the chief
theoretical architect of electromagnetics, was no longer on the
scene, and the field was in the doldrums. The former student of
Helmholtz had some interest in Maxwell's theoretical equations,
but not much interest in the Berlin Academy prize. Nevertheless,
he went to work to compete for the prize, and in 1888 the former
student of Helmholtz (the student now Professor of Physics at
Karlsruhe), Heinrich Hertz (1857-1894), presented to the world
the first theoretical prediction and experimental demonstration
of what later came to be called "radio waves". Hertz's
experimental demonstration was essentially as follows: If an
oscillating electrical potential is produced in an appropriate
circuit located at point A, that oscillation is propagated
through space and can be detected by an appropriate independent
electrical circuit located at point B, the two circuits having no
direct electrical connection (e.g., no wires) between them. Hertz
was 31 years old at the time of his presentation; what else he
might have done in physics in a full life was never to be known,
for he died before his 37th birthday of a blood disease. Thus
came into being one of the most important technological advances
of modern times -- the physics underlying radio communications,
microwave radiation, radar, satellite telecommunications, and so
on [*Note #1].
... ... Dominique Pestre (Ecole des Hautes Etudes en Sciences
Sociales Paris, FR) presents a biographical essay on Heinrich
Hertz and the discovery of radio waves and the controversy
surrounding the discovery, the author making the following
points:
1) The European physics community of the 1880s was divided
into two camps concerning the physics of electromagnetics. In one
camp were the British "Maxwellians", followers of James Clerk
Maxwell, who supported the idea of electromagnetic radiation
through an ether; in the other camp were the Continental
physicists such as Ernst Mach (1838-1916) and Hermann Helmholtz,
who viewed electromagnetics as an action-at-a-distance
phenomenon. "The first to seize upon Hertz's publications were,
of course, the British Maxwellians, as they were already
convinced that Maxwell was right. They welcomed the news that the
physics professor at Karlsruhe had found ways to produce
electromagnetic waves, to have them interfere, and to measure
their speed of propagation in air, which he found to be the
predicted 300,000 kilometers per second. They announced the
result everywhere and began mounting public demonstrations of the
marvel of the sparks induced at a distance by a Hertzian
generator."
2) In the following months, many physicists throughout the
Western world examined the issues. Studies of the various
parameters of the phenomenon were made, detectors and generators
constructed all over Europe, and new setups and diverse
interpretations conceived and put forward to explain the
phenomenon and certain apparent problems in the measurement of
wave propagation velocity. Many physicists quickly performed
experiments inspired by Hertz, all were able to generate sparks,
and Hertz came to be considered a true genius. "On the other
hand, most people were finally convinced by their own
experiments, their own devices and calculations, their own way of
adjusting proofs and expectations..."
3) The author concludes by noting the accounts of the
phenomenon in textbooks published 1888 to 1890 by Hertz, J.J.
Thomson (1856-1940), and Henri Poincare (1854-1912), with each
author providing a different proof and interpretation of the
observed phenomenon. "Hertz had made a major discovery, no doubt,
but what he had proved, and who had decisively improved our
understanding of this complex phenomenon, remained a matter of
opinion."
-----------
NAT 1999 401:745
-----------
Text Notes:
... ... *Note #1: In 1896, the first patent for wireless
telegraphy, i.e., the transmission of messages without wires, was
granted to Gugliemo Marconi in the UK. By the following year, the
Wireless Telegraphy Company had been formed to exploit the
invention, and in 1899, the Marconi Wireless Company of America
was set up. American Marconi, as it was called, soon began the
manufacture of wireless equipment for commercial and military
markets. Although Marconi's original invention (based on Hertz's
radio waves) was designed for fixed (point-to-point) and ship-to-
shore message communication, the idea of wireless as a one-way
medium to transmit speech to many people (i.e., "broadcasting")
was quick to follow. On Christmas Eve 1906, 18 years after the
discovery of radio waves by Hertz, Reginald Fessenden made the
first documented broadcast of speech and music from Brant Rock,
Massachusetts. His transmitter was a 1 kilowatt 50 hertz
alternator built by the General Electric Company. The signal was
received clearly in many locations and even on ships at sea. Lee
de Forest made some experimental broadcasts from New York in 1907
and from Paris in 1910. but his 500 watt transmitters were
inherently noisy. However, in 1906 one of de Forest's associates,
Henry Dunwoody, patented a solid-state detector using the newly
invented material carborundum. These crystal detectors soon
became the heart of early radio receivers. Used with headphones
which drew very little power, crystal sets had the great
advantage of not requiring any external source of electricity. In
summary, within a few decades of the discovery by Hertz of radio
waves, practical applications that would dramatically change
society were in place -- all of it an early part of the ongoing
technological upheaval to be witnessed by the 20th century.
-----------
SW 1999 10 Dec
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SCIENCE-WEEK 31 Aug 2001 http://scienceweek.com
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15. PRAXIS Current Issue Contents (September 3, 2001)
1. On Optimization Theory
2. A New Colloid Stabilization Mechanism
3. On Energy Landscapes
4. Solar Cells by Self-Assembly
5. Molecular and Supramolecular Photoactive Switches
6. Container Molecules
7. Laboratory-Engineered Genomes
8. Positron Emission Tomography in Molecular Biology
9. DNA Chips and Cancer Diagnostics
10. Brain Pacemakers
11. Treatment of Cancer With a Virus
12. Peptide Nanotubes as Antibiotics
13. SW Archive: On the Uses of Science by Society
For information about PRAXIS: www.scienceweek.com/praxis/
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16. SOURCES:
APL: Applied Physics Letters; AS: American Scientist; CEN:
Chemical & Engineering News; GD: Genes & Development; GR: Genome
Research; ICAR: Icarus; JACS: Journal of the American Chemical
Society; JAMA: Journal of the American Medical Association; JCE:
Journal of Chemical Education; MMWR: CDC Morbidity and Mortality
Weekly Report; NAT: Nature; NEJM: New England Journal of
Medicine; NYT: New York Times; NYR: New York Review; PNAS:
Proceedings of the National Academy of Sciences; PRL: Physical
Review Letters; PT: Physics Today; SA: Scientific American; SCI:
Science; SW: ScienceWeek; TS: The Scientist.
In the text, the affiliation following the author's name is the
affiliation of the lead author. The indication (na) signifies no
known research affiliation.
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