New Abridged Edition of ScienceWeek

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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 3, 2001 -- Vol. 5 Number 31


He who would do good to another must do it in
Minute Particulars: General Good is the plea
of the scoundrel, hypocrite and flatterer; for
Art and Science cannot exist but in minutely
organized Particulars.
-- William Blake (1757-1827)


Section 1

Contents of this Issue (Full reports in Section 2):

Snowball Earth
Carbon dioxide removal by forests
Chemical Systems and Phase Space Trajectories
Crystal structures of a biomolecular motor
Notch signaling and vasculogenesis
Bacterial pathogens and protein secretion
Schizophrenia genetics research
Ancient agriculture in Mexico

An understanding of the weakness of gravitation can be derived
from an understanding of the smallness of the mass of the proton,
and in particular from the constraints imposed by quantum
chromodynamics on the coupling constants between quarks. 


Other reports in this week's Regular Edition of ScienceWeek:

Section 2


The late Proterozoic time-frame marked the first appearance of
multicellular animals, perhaps as early as 1000 to 700 million
years ago, and extensive glaciation may have exerted a
significant stress on living forms during a critical interval
in their evolution. Recent work has focused attention on the
Neoproterozoic time-frame by interpreting new carbon isotope data
to indicate that biological productivity of the oceans virtually
ceased for perhaps millions of years during the glacial era, and
from this work and from other evidence it has been concluded that
the planet entered a "snowball Earth" state, in which it was
completely covered by ice until carbon dioxide outgassing
produced a sufficiently large greenhouse effect to melt the ice.
In this scenario, the sudden warming caused a rapid precipitation
of calcium carbonate, producing certain types of carbonate rocks
often observed in strata of this era. Richard A. Kerr (2001)
reports on discussions of the snowball Earth hypothesis at a
recent meeting of the American Geophysical Union. An alternative
model to snowball Earth that is apparently gaining support, the
model involving cold and permafrost in the tropics, but
temperatures not low enough to freeze over the ocean and threaten
life with extinction. The new model stresses the importance of
the release of methane into shallow seas. Proof will require
finding the isotope signature of methane in carbonate cements.
(SCI 2001 292:2241) (NAT 2000 405:425)

Steven C. Wofsy (2001) discusses the removal of atmospheric
carbon dioxide by forests. Emission rates of carbon dioxide from
combustion of fossil fuel have increased almost 40 percent in the
past 20 years, but the amount of carbon dioxide accumulating in
the atmosphere has remained the same or even declined slightly.
The reason for this discrepancy is that increasing amounts of
anthropogenic carbon dioxide are being removed by forests and
other components of the biosphere. It is estimated that more than
2 billion metric tons of carbon -- equivalent to 25 percent of
the carbon emitted by fossil fuel combustion -- are sequestered
by forests each year. Inverse models for studying atmospheric
concentrations of carbon dioxide suggest that mid-latitude
forests in North America and northern Eurasia are crucial carbon
sinks that remove this carbon dioxide from the atmosphere. But
analyses of forest inventories (which measure forest areas and
timber volume) seem to indicate that forests sequester much
smaller amounts of carbon. Thus we have a mystery. If our forests
have been sequestering billions of tons of carbon annually, why
can't we find it? It appears that most of the carbon dioxide that
is sequestered is in the organic matter of forests that is not
considered valuable and so is not reported in forest inventories:
woody debris, soil, wood products preserved in landfills, and
woody plants that have encroached on grasslands because of the
long-term suppression of natural fires. (SCI 2001 292:2261,2316)

Jullien and Lemarchand (2001) consider the use of the phase space
concept in chemistry. The evolution of various kinds of systems
known to physics, biology, chemistry, and economics can be
approached via the same mathematical model, a nonlinear system of
ordinary differential equations. Although such systems of
equations often have no analytical solutions, geometric theory
provides a powerful tool to describe the qualitative behavior of
a system. The primary concept in this geometric theory of dynamic
systems is the concept of "phase space", which is merely the
space of the dynamic variables that are considered by the
observer to be affected by the evolution of the system. A simple
example of such a phase space involves a mechanical system such
as an oscillating spring (mass (m), stiffness constant (k)). When
the spring is constrained to move along an axis (X), the abscissa
(x) and the corresponding impulsion (p) are sufficient for
describing the system states at any time. The phase space is then
the 2-dimension space (x,p), and differential equations for (x)
and (p) are derived from the laws of mechanics. In chemistry, at
a chosen macroscopic level of description, one often finds
similar components: 1) A set of state variables, such as the
quantities of the species present, is supposed to be sufficient
to describe the state at any time. These variables define the
phase space. 2) Some constraints, e.g., a closed system, fix the
value of certain combinations of the state variables as the total
number of each kind of atom. 3) The dynamic laws can be modeled
by a set of differential equations for the state variables.
(JCE 2001 78:803)

"Motor proteins" are mechanico-chemical enzymes involved in
locomotion of cells or transport of materials in cells, and there
are three families of such proteins: kinesins, dyneins, and
myosins. Kinesins and dyneins are microtubule-based motor
proteins, while myosin is a microfilament-based motor protein. 
Kinesin is apparently present in all eukaryotic cells. The form
of kinesin originally discovered is a soluble rod-shaped molecule
composed of two polypeptide chains, the molecule travelling
toward one specific end of microtubules (depending on the type of
kinesin, either the so-called "plus" end or "minus" end. Kinesin
motors apparently power many cellular motile processes by
converting ATP energy into unidirectional motion along
microtubules. Although numerous biochemical and biophysical
studies have accumulated much data that link microtubule-assisted
ATP hydrolysis to kinesin motion, the structural view of kinesin
movement has remained unclarified. A new study of a monomeric
kinesin motor combines x-ray crystallography and cryo-electron
microscopy to allow analysis of force-generating conformational
changes at atomic resolution. The kinesin motor is revealed in
its two functionally critical states -- complexed with adenosine
diphosphate and with a non-hydrolyzable analog of adenosine
triphsophate. The conformational change is apparently modular,
extending to all kinesins, and is similar to the conformational
change used by myosin motors and G proteins. (NAT 2001 411:439)

The construction of an organism from a single egg cell to a
multicellular 3-dimensional structure of characteristic shape and
size is the result of coordinated gene action that directs the
developmental fate of individual cells. So-called "Notch-
signaling", a mechanism conserved in evolution, is used by
multicellular animals to control cell fates through local cell
interactions, and the realization by researchers that this
signaling mechanism controls an unusually broad spectrum of cell
fates and developmental processes (in organisms ranging from sea
urchins to humans) has in the past decade resulted in a large
number of Notch-related studies. Thomas Gridley (2001) discusses
current research on Notch signaling during vascular development.
Formation of the cardiovascular system is one of the earliest and
most important events during embryogenesis in mammals. During the
early stages of vascular development in both the mammalian embryo
and its extra-embryonic membranes (e.g., the yolk sac),
endothelial cell precursors differentiate and proliferate in a
process called "vasculogenesis". These endothelial cells then
coalesce and form the primary vascular plexus, a network of
homogeneously-sized primitive blood vessels. This vascular
network is then remodeled by the process of angiogenesis, which
involves the sprouting, branching, splitting, and differential
growth of vessels in the primary plexus to form the large and
small vessels of the mature vascular system. A number of
different signaling pathways have been implicated in the control
of these processes, and new evidence now adds the Notch signaling
pathway to this list. (PNAS 2001 98:5377,5643)

In general, the term "pathogenicity" describes the ability of a
microbe to cause clinically apparent symptoms. In contrast, the
term "virulence" is used to describe microbes that cause severe
disease. Lee and Schneewind (2001) review the importance of
protein secretion in bacterial pathogenesis. Many bacterial
pathogens have evolved to enter and multiply within blood-
circulated tissues, and the underlying pathogenic strategies are
remarkably diverse and often result in unique disease symptoms.
Nevertheless, all mechanisms of bacterial manipulation of host
organisms can be viewed with respect to three different
categories: microbial adhesion to cell surfaces, secretion of
toxins into the extracellular milieu, and injection of virulence
factors into host cells. All bacterial secretion systems are
apparently highly evolved and efficient, with specificity in the
selection and transport of secretion substrates, the assembly of
the secretion machinery, and the coordinated movement of
macromolecules across one, two, or three lipid bilayers. In
general, protein secretion is a major aspect of successful
bacterial pathogenesis. Bacterial protein secretion is a rapidly
evolving field of research, but most of the work has been
performed with gram-negative organisms. A shift in focus is 
needed, since gram=positive microbes cause many important human
diseases that are still poorly understood. (GD 2001 15:1725)

Sanders and Gejman (2001) review recent progress in research on
the genetic basis of schizophrenia. Schizophrenia is a
devastating disorder affecting 1 percent of the population
worldwide, and the elucidation of the biology of schizophrenia
will constitute a development of great medical and historic
importance. The study of familial schizophrenia was instrumental
in opening the field of psychiatry to genetic inquiry, and
together with twin and adoption studies helped forge the field of
psychiatric genetics. Over the past century, studies have
consistently demonstrated that both genetic and nongenetic
factors play a significant role in the etiology of schizophrenia.
Currently, a large number of molecular and genomic database
tools, an understanding of complex genetics, and a convergence of
results from genetic mapping of several chromosomal regions all
contribute to optimism that genes involved in the pathogenesis of
schizophrenia will be characterized in the near future.
Identification of susceptibility genes, their products, and
interacting proteins will likely illuminate pathways to illness,
provide more specific pharmacological targets, and lead to
improved understanding of environmental contributions to
susceptibility. The hope is that this knowledge will further
advance clinical progress in treatment and even prevention of
schizophrenia. (JAMA 2001 285:2831)

Dolores R. Piperno discusses the origins of agriculture and
recent evidence for the cultivation of maize more than 7000 years
ago in Mexico. Food surpluses made possible by agricultural
economies have fueled major cultural developments during the past
10,000 years, culminating in the emergence of urban societies and
advanced civilizations around the world. The current consensus is
that agriculture arose independently in 6 to 8 regions of the
world, including both hemispheres of the Americas, after
termination of the last Ice Age 12,000 years ago. Mexico was one
of the primary centers of agriculture with domestication of
maize, and new evidence suggesting that it was also a birthplace
of another important American crop plant, the sunflower
(Helianthus annuus L.). The earliest macrofossils (cobs) of maize
have been found in the arid highland Tchuacan and Oaxaca valleys.
It has been argued on the basis of these macrofossils that corn
was domesticated much later, approximately 6000 years ago, than
other major cereals such as wheat and rice. But recently K. Pope
et al (2001) reported the recovery of 7100-year-old maize pollen
from the San Andres site on the tropical coast of Mexico, the
sample in association with indicators of land-clearance resulting
from slash-and-burn cultivation. This is the oldest evidence for
maize in Mexico, predating the earlier macrofossil evidence by
1000 years. (SCI 2001 292:1370,2260)


     According to Newton's law of gravitation, there is a force
of attraction between any two massive particles in the Universe.
This force of attraction, as stated by Newton, may be expressed
as a simple relationship involving the masses of the two
particles and the distance between them. When the two masses are
unit masses and the distance between their centers of mass is
unit distance, then the force of attraction is equal to what is
called the "gravitational constant", usually denoted as "G". The
gravitational constant is usually regarded as a true universal
constant independent of place or time, but in some cosmological
models it is proposed that the gravitational constant decreases
with time as the Universe expands.
... ... Frank Wilczek (Massachusetts Institute of Technology, US)
discusses the relative extreme weakness of gravitational
interactions. Gravity dominates the large-scale structure of the
Universe, but only by default: matter arranges itself to cancel
electromagnetism, and the *strong and weak forces are
intrinsically short range. At a more fundamental level, gravity
is extremely weak: acting between protons, gravitational
attraction is approximately 10^(-36) times weaker than electrical
repulsion. The author asks: "Where does this outlandish disparity
come from? What does it mean?"
     The author points out that these questions greatly disturbed
Richard Feynman (1918-1988). In 1963, in Feynman's famous paper
on quantizing general relativity, the paper in which he first
described his discovery of the "ghost particles" that eventually
played a crucial role in understanding modern *gauge field
theories, Feynman noted that the correct problem is to understand
what determines the size of gravitation.
     Wilczek points out that the same question drove Paul Dirac
(1902-1984) to consider, 30 years before Feynman, the radical
idea that the fundamental "constants" of nature are time
dependent, so that the weakness of gravity could be related to
the great age of the Universe. Dirac's argument was that the
expansion rate of the Universe suggests that it began with a bang
approximately 10^(17) seconds ago. On the other hand, the time it
takes light to cross the diameter of a proton is approximately
10^(-24) seconds, which provides a ratio, 10^(-41), which is not
so far from the mysterious 10^(-36). But the age of the Universe,
of course, changes with time, so if the numerological coincidence
is to abide, something else -- the relative strength of gravity
or the size of protons -- will have to change in proportion.
Since there are powerful experimental constraints on such
effects, Dirac's idea is not easy to reconcile with standard
modern theories of cosmology and fundamental interactions,
theories which are extremely successful.
     Wilczek discusses the dimensionless number N = Gm^(2)/hc,
where (G) is Newton's constant, (m) is the mass of the proton,
(h) is Planck's constant, and (c) is the speed of light.
Substituting measured values, we find N is approximately 3 x
10^(-39), and Wilczek notes: "This is what we mean when we say
gravity is extravagantly feeble." But the real problem, Wilczek
suggests, is to understand the smallness of N.
     Wilczek then proposes that an understanding of the smallness
of N can be derived from an understanding of the smallness of the
mass of the proton, and in particular from the constraints
imposed by the *theory of quantum chromodynamics on the coupling
constants between quarks, the fundamental components of the
proton. Essentially, the inter-quark coupling force increases
with distance between quarks, which provides a powerful
constraint on the size and mass of the proton. The smallness of
N, therefore, is an apparent natural consequence of the theory of
quantum chromodynamics.
Frank Wilczek: Scaling Mount Planck I: A view from the bottom.
(PT 2001 June)
QY: Frank Wilczek: wilczek at
Text Notes:
... ... *strong and weak forces: The weak forces are the
forces responsible for the change of neutrons and protons into
each other in radioactive processes and in the stars. The strong
forces are the forces that hold quarks together inside protons
and neutrons, and that hold protons and neutrons together inside
atomic nuclei.
... ... *gauge field theories: Quantum field theory is the
mathematical fusion of quantum mechanics with special relativity
theory, and there are essentially 2 branches: quantum
electrodynamics (applicable to charged particles involved in
electromagnetic interactions) and quantum chromodynamics
(applicable to nuclear particles involved in strong force
interactions). In this context, a "gauge theory" is any quantum
field theory which has the property of "gauge symmetry", i.e.,
the equations describing the field do not change when some
operation is applied to all particles everywhere in space. In
general, fields with gauge symmetry can be remeasured (regauged)
from different baselines without affecting their properties.
Quantum electrodynamics and quantum chromodynamics are examples
of gauge theories.
... ... *theory of quantum chromodynamics: Quantum chromodynamics
(QCD) is a theory that describes the strong interaction (strong
nuclear force) in terms of quarks and antiquarks and the exchange
of massless "gluons" between them. The "chromo-" in
chromodynamics derives from the use of designated "color"
attributes of quarks, the various "colors" labels for various
quark properties.
Summary & Notes by SCIENCE-WEEK 3Aug01
For more information:
Related Background:
"Gravity is by far the weakest force in the Universe: in the
hydrogen atom, the electromagnetic force between the proton and
electron is about 10^(40) times as great as the gravitational
force between them. This is fairly representative of the
difference in scales between the quantum and gravitational
realms, and accounts for our ability [in cosmology] to separate
the two theories without ambiguity. Yet they must inevitably
meet. Near a singularity, the curvature of space-time must be so
great that the scale of gravity becomes comparable to that of the
other fundamental forces. To describe such a state, we must find
a theory of quantum gravity. Moreover, quantum mechanics has
already been applied to the explanation of the other three
forces, the electromagnetic force and the strong and weak
interactions; should not gravity be similar? It might seem as
though the challenge of developing quantum gravity should not be
so great. After all, special relativity and quantum mechanics
were united in the 1920s by the British physicist Paul A.M.
Dirac. The most significant result of Dirac's theory was its
requirement that antiparticles exist, a prediction that was
confirmed in 1932 by the discovery of the positron (the anti-
electron). The Dirac theory is now well-established as the
special relativistic quantum mechanics. More than 70 years later,
however, general relativity has still not been successfully
incorporated into a consistent quantum formulation."
J.F. Hawley and K.A. Holcomb: Foundations of Modern Cosmology
(Oxford University Press, New York 1998, p.441)
(SW 1999 30 July)


AGP:      Archives of General Psychiatry
APL:      Applied Physics Letters
AS:       American Scientist
CEN:      Chemical & Engineering News
GD:       Genes & Development
GR:       Genome Research
ICAR:     Icarus
JAMA:     Journal of the American Medical Association
JCE:      Journal of Chemical Education
NAT:      Nature
NEJM:     New England Journal of Medicine
NYT:      New York Times
PNAS:     Proceedings of the National Academy of Sciences
PRL:      Physical Review Letters
PT:       Physics Today
SA:       Scientific American
SCI:      Science
SK:       Skeptic
SW:       ScienceWeek
TB:       The Biochemist
TS:       The Scientist



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