|
ScienceWeek
SCIENCE-WEEK - December 28, 2001 - Vol. 5 Number 52
An Email Research Digest Published Weekly Since 1997
----------------------------------------------------
SCIENCEWEEK is free on a continuing basis to students worldwide,
a policy made possible by paid non-student personal and library
subscriptions. Information about free student subscriptions is
available at URL: http://www.scienceweek.com/students.htm
Please recommend ScienceWeek for acquisition to your librarian or
information specialist.
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
ANNOUNCEMENT: The new SW Science Discussion List is a moderated
Email forum for the international science community. Details
about this Email discussion list are available at:
http://www.scienceweek.com/swdl.htm
To subscribe to this discussion list, transmit SUB SWLIST to:
swlist@scienceweek.com
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Every great scientific truth goes through three
stages. First, people say it conflicts with the Bible.
Next they say it had been discovered before. Lastly
they say they always believed it.
-- Louis Agassiz (1807-1873)
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
=-=-=-=-=-=-=-=-=
Section 1
=-=-=-=-=-=-=-=-=
Contents of this Issue (Full reports in Section 2):
1. On the Complexity of Information in Biochemistry
2. Modification of Gene Expression by Sensory Experience
3. On the Earliest Humans in Northeast Asia
4. Nickel in Biological Systems
5. Molecular Basis of Immune Recognition
6. On Protein Kinases
7. Chemistry of Embalming Agents in Egyptian Mummies
8. Solvent Interactions and Carbohydrate Conformation
9. Quantum Entanglement and Quantum Optics
10. On the Origin of Water on Earth
11. Trace Gases in Presolar Diamonds
12. Oceanography: Patterns of Arctic Circulation
13. PostDoctoral Fellowship Profiles: Cellular Biochemistry:
Laboratory of Fred Schaufele, Univ. of California San Francisco
14. In Focus: On Mary Somerville and Gravity
15. From PRAXIS (1): Clinical Symptoms: Inhalational Anthrax vs.
Influenza
16. From PRAXIS (2): Epidemiology of Anthrax
17. This Week in PRAXIS
=-=-=-=-=-=-=-=-=
Section 2
=-=-=-=-=-=-=-=-=
1. ON THE COMPLEXITY OF INFORMATION IN BIOCHEMISTRY
Peter D. Karp (SRI International, US) discusses pathway
databases. A biochemical pathway database is a database that
describes biochemical pathways, reactions, and enzymes. The
author poses the question: What happens when a scientific theory
is too large to be grasped by a single mind? Decades of
experimentation by molecular biologists to characterize the
molecular components of single cells, combined with recent
advances in genomics, have thrust biology into the position where
the theoretical understanding of a system such as the biochemical
network of E. coli is too large for a single scientist to grasp.
This situation has a number of disturbing consequences: it
becomes extremely difficult to a) determine whether such theories
are internally consistent or are consistent with external data;
b) to refine theories that are inconsistent or to understand all
of the implications of such large theories. As more details of
such a complex system are elucidated experimentally, it is not so
clear that our understanding of the system as a whole increases
if any new understanding cannot be integrated with the larger
theory it pertains to in a coherent fashion. The authors argues
that as scientific theories reach a certain complexity, it
becomes essential to encode those theories in a symbolic form
within a computer database. The author describes pathway
databases as a case study in encoding scientific theories in
computers. Although the scientific community clearly accepts the
need to encode the ever-expanding quantity of scientific data
within databases, databases of scientific theories, such as a
theory describing the transcriptional regulation of E. coli
genes, are much rarer. Here, the term "theory" refers to
interpretation and synthesis of many experimental results.
-----------
Science 2001 293:2040
-----------
SCIENCE-WEEK 28 Dec 2001 http://scienceweek.com
-------------------
Related Background:
CELL BIOLOGY: FUNCTIONAL MODULES IN BIOLOGICAL ORGANIZATION
The term "phenomenology" has a variety of meanings, but in
this report we are concerned with only one meaning of the term:
we take the term "phenomenology" to refer to a scientific
approach that focuses on explanations based on formal
relationships among observed entities or processes, as opposed to
an approach ("reductionist") that focuses on explanations based
on analysis of the fundamental constituents of such entities or
processes. Using the terms in this way, we have the following
examples: a) Thermodynamics is a phenomenological approach to the
behavior of a gas; statistical mechanics is a reductionist
approach to the behavior of a gas. b) Mendelian genetics is a
phenomenological approach to the inheritance of traits; molecular
genetics is a reductionist approach to the inheritance of traits.
One can think of similar dichotomies in almost every field in
science.
The term "reductionist" has had an unfortunate history in
biology, where it has been used to characterize the idea that any
biological entity or process can be "explained" in terms of the
laws of physics and chemistry. Certainly, the behavior of every
entity or process in the natural world is ultimately totally
dependent on the laws of physics and chemistry (which leads to
the idea that the behavior can "in principle" be derived
["explained"] from such laws), but the actual practical
possibility of any explanations of the behavior of observable
entities or processes in terms of the laws of physics and
chemistry depends on the current state of our knowledge
concerning both the observables and the fundamental laws. In the
practice of science, it can be argued that it does not matter
much which approach is used, phenomenological or reductionist,
provided the approach produces results that are useful, or which
help in understanding the behavior of the entity or process, or
which suggest new and intriguing questions. Beyond this, the
discussion properly belongs in the domain of philosophy and not
science.
The above preamble is necessary in the context of the
present report, since the report concerns a recent article in
which a group of authors (2 molecular biologists, a biophysicist,
and a physiologist) call for a more "phenomenological" approach
to cell biology, an interesting idea, since cell biology is not
one of those areas of biology where such appeals are common.
During the last 50 years, in fact, cell biology has experienced a
remarkable flowering based on the application of fundamental
biochemistry, biophysics, and molecular biology to entities and
processes recognizable at the cellular level (i.e., micron-scale
objects).
... ... L.H. Hartwell et al (4 authors at 3 installations, US)
present an essay calling for a transition from molecular to
"modular" cell biology, the authors making the following points:
1) The authors begin their essay with the following
statement: "Although living systems obey the laws of physics and
chemistry, the notion of function or purpose differentiates
biology from other natural sciences. Organisms exist to
reproduce, whereas, outside religious belief, rocks and stars
have no purpose. Selection for function has produced the living
cell, with a unique set of properties that distinguish it from
inanimate systems of interacting molecules." [Editor's note:
Contrast with this the remarks in the relevant background
material below.]
2) The authors propose that a major challenge for science in
the 21st century is to develop an integrated understanding of how
biological cells and organisms survive and reproduce. The authors
suggest that cell biology is in transition from a science that
was preoccupied with assigning functions to individual proteins
or genes, to a science that is now attempting to cope with the
complex sets of molecules that interact to form "functional
modules".
3) The authors define a "functional module" as a discrete
entity whose function is separable from those of other modules.
This separation depends on chemical isolation, which can
originate from spatial localization or from chemical specificity.
For example, a ribosome, the module that synthesizes proteins,
concentrates the reactions involved in making a polypeptide into
a single particle, thus spatially isolating its function. Modules
can be insulated from or connected to each other. The authors
suggest that in the future, the higher-level properties of cells,
such as their ability to integrate information from multiple
sources, will be described by the pattern of connections among
their functional modules.
4) The authors point out that the number of cellular
functional modules that have been analyzed in detail is very
small, and each of these efforts has required intensive study.
The authors suggest that biologists need to study more functions
at the modular level and develop methods that make it easier to
determine the relationship of inputs to outputs of modules, their
biochemical connectivity, and the states of key intermediates
within them.
5) The authors suggest that the best test of our
understanding of cells will be to make quantitative predictions
about their behavior and test them. This will require detailed
simulations of the biochemical processes occurring within the
modules. "But making predictions is not synonymous with
understanding. We need to develop simplifying, higher-level
models and find general principles that will allow us to grasp
and manipulate the functions of biological modules."
6) The authors summarize their essay: "Cellular functions,
such as signal transmission, are carried out by 'modules' made up
of many species of interacting molecules. Understanding how
modules work has depended on combining phenomenological analysis
with molecular studies. General principles that govern the
structure and behavior of modules may be discovered with help
from synthetic sciences such as engineering and computer science,
from stronger interactions between experiment and theory in cell
biology, and from an appreciation of evolutionary constraints."
-----------
[Editor's note: The essential idea here can be presented as
follows: Consider a computer, a machine with a "purpose" -- to
compute. A computer operates on its inputs in specific ways to
produce specific outputs. A "flow diagram" of computer dynamics
is a phenomenological description of the behavior of the machine.
A complete "wiring diagram" of electrical entities and events in
the machine is a reductionist description of the behavior of the
machine. (Of course, from the perspective of quantum mechanics,
the wiring diagram is itself phenomenological.) Suppose we are
given a machine and know nothing about it except that it operates
on inputs to produce outputs. If our problem is to predict the
behavior of the machine in response to particular inputs, there
will come a time when a flow diagram, albeit "phenomenological",
will be of immense value in understanding how the machine works.
What the authors propose is that much of the future of cell
biology will lie in the construction of the equivalent of
detailed and predictive flow diagrams for the internal operations
of biological cells.]
-----------
Nature 1999 402supp:C47)
SCIENCE-WEEK 2000 11 Feb
-----------
SCIENCE-WEEK 28 Dec 2001 http://scienceweek.com
-------------------
Related Background:
ON COMPLEXITY IN CHEMISTRY
The term "complexity" is fashionable in science these days, the
interest presumed to indicate a movement away from reductionism,
away from the idea that the behavior of a system is best
understood in terms of how the components of the system behave
and interact. A focus on "complexity", however, is not perforce
anti-reductionist. Indeed, in practice, with real systems, the
behavior of a system is often not predictable from knowledge of
the behavior of its components, but most often this is simply
because that knowledge is incomplete, and not because of any
_principle_ barring prediction of the behavior of the system from
knowledge of its parts. Even systems exhibiting *chaotic
fluctuations are not necessarily non-reductionist, since such
systems are mathematically deterministic. In any case, faced with
an apparent unpredictability of a system given available
information about its parts, one looks for predictive global
methods to understand the system, methods that do not depend upon
a detailed knowledge of the behavior of the components of the
system. Thermodynamics is exactly such a global method of great
utility in chemistry and physics, and since thermodynamics is a
method of analysis that goes back to its originator Carnot in
1824, one can safely say that the idea of special methods to deal
with "complexity" is quite old. In our time, at least for ideal
systems, we can derive the equations of thermodynamics from
statistical mechanics, i.e., derive the global equations from
equations for the behavior of components. But Nicolas Sadi Carnot
(1796-1832) never heard of statistical mechanics, which was
introduced by Boltzmann (1844-1906) in 1871; Carnot founded
thermodynamics as a predictive global method to deal with an
important "complex" system of his time -- the steam engine.
... ... G.M. Whitesides and R.F. Ismagilov (Harvard University,
US) present a review of current ideas in chemistry concerning
"complexity", the authors making the following points:
1) Chemistry has its own understandings of the term
"complexity". In one characterization, a complex system is one
whose evolution is very sensitive to initial conditions or to
small perturbations, one in which the number of independent
interacting components is large, or one in which there are
multiple pathways by which the system can evolve. Analytical
descriptions of such systems typically require nonlinear
differential equations. A second characterization is more
informal; that is, the system is "complicated" by some subjective
judgment and is not amenable to exact description, analytical or
otherwise.
2) Faced with the impossibility of handling many real
systems exactly, chemists have evolved a series of approaches to
the treatment of complex systems. These treatments include
reasoning by analogy, averaging, linearization, drastic
approximation, pure empiricism, and detailed analytical solution.
The emphasis in thinking about complicated systems has been to
find methods that are predictive, even if they are non-
analytical. "Complexity" per se, the study of nonlinear processes
with high sensitivity to conditions, has not been the focus of
major effort.
3) Chemistry has relied heavily on the ability of ensemble
properties that are obtained through thermodynamics and
statistical mechanics to make it unnecessary to consider the
behavior of individual molecules. However, single-molecule
chemistry is now making it possible to inquire about individual
molecular behaviors, and the behavior of macromolecules is a
promising area of research because of the existence of many
possible molecular conformations, each with different properties.
4) At the core of chemical interest in complexity are the
two fundamental problems concerning life: a) how collections of
molecules give rise to the varieties of behaviors that
characterize cells and organisms; and 2) how individual molecules
might have originally assembled into collections that had the
characteristics of life (energy dissipation, self-replication,
and adaptation). Whether the understanding of complexity at the
molecular level will reveal important elements of the structure
of life is unclear.
5) One of the opportunities in fundamental chemical research
is to learn from biology and to use what is learned to design
non-biological systems that dissipate energy, replicate, and
adapt. Whether such systems would model life is not critical;
they would unquestionably be interesting and probably important.
-----------
Science 1999 284:89
-----------
Notes:
... ... *chaotic fluctuations: The term "chaotic", in this
context, is specific. In the study of physical systems, the
term "chaotic behavior" has a specific meaning: the behavior of a
system is said to be "chaotic" if its final state is so sensitive
to the system's precise initial conditions that the behavior of
the system is in effect unpredictable and cannot be distinguished
from a random process, even though the behavior of the system is
strictly determinate in a mathematical sense. In other words, a
deterministic system characterized by extremely sensitive
instabilities, despite the system being determinate, can exhibit
behavior that is unpredictable, and the system is then called
"chaotic". During the past several decades, the analysis of such
chaotic systems has intrigued both physicists and mathematicians.
-----------
SCIENCE-WEEK 1999 2 Jul
-----------
SCIENCE-WEEK 28 Dec 2001 http://scienceweek.com
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
2. MODIFICATION OF GENE EXPRESSION BY SENSORY EXPERIENCE
E.L. Peckol et al (University of California San Francisco, US)
discuss modifications of gene expression. Animals modify their
olfactory behaviors in response to short-term changes in their
environment, and as part of hard-wired developmental programs.
For example, Drosophila temporarily changes its preference for
odors that have been paired with a repellant shock. Drosophila
also demonstrates olfactory preferences that differ from the
larval to the adult stage. Alteration in higher processing
centers underlie some forms of olfactory plasticity, but the
contributions of specific olfactory neurons and their receptors
to short- and long-term behavioral modifications are unknown. The
olfactory systems in flies, mice, and worms contain many
different cell types that can be distinguished by the receptors
they express. Unlike other sensory systems, the olfactory system
uses receptors that are specialized for particular odor stimuli;
therefore, changes in receptor expression have the potential to
alter the stimuli detected by the olfactory system and to also
alter the perception of those stimuli. The small nematode
roundworm worm Caenorhabditis elegans demonstrates behavior
plasticity in response to its environment and as part of its
program of development. C. elegans is exquisitely sensitive to
chemical, thermal, and mechanical stimuli and alters its
responses to those stimuli based on its experience. The authors
demonstrate that in C. elegans specific sensory experiences cause
changes in chemosensory receptor gene expression that may alter
sensory perception. The authors suggest that experience-dependent
changes in chemosensory receptor gene expression may modify
olfactory behavior in this organism.
-----------
Proc. Nat. Acad. Sci. 2001 98:11032
-----------
SCIENCE-WEEK 28 Dec 2001 http://scienceweek.com
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
3. ON THE EARLIEST HUMANS IN NORTHEAST ASIA
In this context, the term "geomagnetic polarity reversal" refers
to a change of 180 degrees in the direction of the Earth's
magnetic field. The term "stratigraphy", in general, refers to
the study of stratified rocks in time and space, and the term
"magnetostratigraphy" refers to the branch of stratigraphy based
on geomagnetic polarity reversals. A "magnetozone" is a unit of
rock of the same magnetic polarity, and in this context a "chron"
is a single time interval of constant geomagnetic polarity, with
a "subchron" a subunit of a chron.
... ... R.X. Zhu et al (Chinese Academy of Sciences, CN) discuss
the earliest humans in northeast Asia. The chronology of east
Asian Paleolithic tools is pertinent to both the oldest human
occupation in this region and to the overall framework of human
origin and migration in the Old World. The age of Paleolithic
sites in east Asia has been controversial because of the absence
of suitable material for accurate isotopic dating. In general,
the timing of the earliest habitation and oldest stone
technologies in different regions of the world remains a
contentious topic in the study of human evolution. The authors
contribute to this debate with detailed magnetostratigraphic
results on two exposed parallel sections of lake ("lacustrine")
sediments at Xiaochangliang in the Nihewan Basin, north China.
The authors suggest these results place stringent constraints on
the age of Paleolithic stone artifacts that were originally
reported over two decades ago. The authors suggest their
paleomagnetic findings indicate that the artifact layer resides
in a reverse polarity magnetozone bounded by the Olduvai and
Jaramillo subchrons. The authors suggest that coupled with an
estimated rate of sedimentation, these findings constrain the age
of the layer to approximately 1.36 million years ago. The authors
suggest this result represents the age of the oldest known stone
assemblage comprising recognizable types of Paleolithic tools in
east Asia, and the earliest definite occupation in this region as
far north as 40 degrees N.
-----------
Nature 2001 413:413
-----------
SCIENCE-WEEK 28 Dec 2001 http://scienceweek.com
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
4. ON NICKEL IN BIOLOGICAL SYSTEMS
Rudolf K. Thauer (Max Planck Institute for Terrestrial
Microbiology Marburg, DE) discusses nickel in biological systems.
Nickel was long thought not to be a metal of biological
importance. This changed in 1975, when B. Zerner discovered that
urease is a nickel enzyme. Since then, 5 other important enzymes
that depend on nickel for activity have been identified. The 6
nickel enzymes known to date catalyze different reactions, and
comparison of the available crystal structures demonstrates that
the nickel centers in their active sites also vary widely. The
enzyme CO dehydrogenase contains a nickel-iron-sulfur cluster. In
other nickel enzymes, the metal is coordinated in a tetrapyrrole
complex, a dinuclear nickel-iron complex, and a dinuclear nickel-
nickel complex. Nickel CO dehydrogenase catalyzes the reversible
dehydrogenation of carbon monoxide and water to carbon dioxide.
An iron-sulfur protein serves as both electron acceptor and donor
in the reaction, with both forward and backward reactions of
biological importance. The enzyme is found in many anaerobic
microorganisms, both bacteria and archaea, but it appears to be
absent in aerobic microorganisms. In anaerobic microorganisms,
nickel CO dehydrogenase has many functions. In Carboxydothermus
hydrogenoformans and Rhodospirillum rubrum, the enzyme is
involved in converting carbon monoxide and water to carbon
dioxide and H(sub2). In sulfate-reducing bacteria and archaea,
the enzyme assists the oxidation of acetate to two carbon dioxide
molecules. In methane-producing archaea, the enzyme is involved
in the disproportionation of acetate to carbon dioxide and
methane. And in many acetate-generating bacteria and autotrophic
anaerobes, the enzyme is involved in the total synthesis of
acetate from 2CO(sub2). Up to 10 percent of the organic compounds
generated each year by photosynthesis are estimated to be
remineralized by anaerobic microorganisms in reactions involving
CO dehydrogenase. This enzyme thus plays a quantitatively
important role in the global carbon cycle.
-----------
Science 2001 293:1264
-----------
SCIENCE-WEEK 28 Dec 2001 http://scienceweek.com
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
5. ON THE MOLECULAR BASIS OF IMMUNE RECOGNITION
G.J. Nossal (University of Melbourne, AU) discusses immune
recognition. The mammalian immune system possesses extraordinary
recognition capabilities. On the one hand, it can react to
virtually any molecule in the Universe; on the other hand, it
does not normally attack the body itself. The T (thymus-derived)
and B (bone-marrow-derived) lymphocyte cells, which have the task
of recognition and reaction, somehow seem to know the
immunological self. How do they do it? What prompts them, for
example, to attack a kidney transplant so ferociously that strong
drugs must be administered to keep them at bay, whereas they
leave the individual's own kidney alone? What is the molecular
basis of the immunological self? The issue is rendered more
complex by apparent exceptions to self-recognition. Healthy
people can have antibodies in their serum that react with bodily
components, and some autoreactive T cells are also present.
Indeed, some researchers have questioned the centrality of self-
non-self discrimination. Three key concepts underlie these
apparent paradoxes: 1) The receptors on the surfaces of
lymphocytes have not been created to react with particular
pathogenic microbes or, for that matter, with particular
molecules on foreign kidney cells. Rather, the whole universe of
receptors together constitutes a repertoire, one or more elements
of which are capable of recognizing any foreign molecule. 2) As
lymphocytes mature within the thymus or bone marrow, they pass
through a developmental stage during which specific receptors
first appear on the cell surface. At that particular checkpoint
in the lymphocyte's history, contact with self-antigens may lead
to apoptosis (programmed cell death) of the lymphocyte. This has
been called "negative selection", a process by which the
lymphocyte population is purged of its most dangerous high-
affinity self-reactive constituents. 3) The lower-affinity anti-
self cells will not be triggered into activity simply by meeting
self-antigens: lymphocyte activation requires co-stimulatory
signals delivered by a scavenger cell or by another lymphocyte,
this requirement preventing the mere existence of anti-self cells
from producing autoimmunity.
-----------
Nature 2001 412:685
-----------
SCIENCE-WEEK 28 Dec 2001 http://scienceweek.com
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
6. ON PROTEIN KINASES
D.A. Johnson et al (University of California San Diego, US)
discuss protein kinases in biological systems. Protein
phosphorylation, first elucidated as a regulatory mechanism in
1955, is very likely the most important mechanism for regulation
in mammalian cells. While allosteric regulation allows enzymes to
respond to their immediate environment, protein phosphorylation
provides a mechanism for cells to respond to external stimuli
such as hormones, neurotransmitters, or any type of stress. The
family of enzymes involved in phosphorylation, the kinases, is
large and diverse. On the basis of the C. elegans genome, protein
kinases are predicted to constitute approximately 2 percent of
the human genome, and approximately a third of all proteins in
mammalian cells are phosphorylated. The protein kinases serve as
molecular switches and are thus highly dynamic proteins that can
toggle between different conformational states. Their activation
state also determines who their partners are, whether their
protein-protein interactions are intramolecular or
intermolecular. Most protein kinases are also phosphoproteins,
and these phosphates are an integral determinant for both
structure and function. Phosphorylation sites can serve as
docking sites for other proteins or as organizing points that
lock the kinase itself into a conformation that is optimal either
for catalysis or for inhibition. Correct assembly of the active
kinase often depends on the critical addition of a phosphate.
Thus, this is a group of proteins capable of undergoing multiple
conformational changes, making multiple protein-protein
interactions, and in addition, nucleating the assembly of dynamic
signaling complexes.
-----------
Chem. Revs. 2001 101:2243
-----------
SCIENCE-WEEK 28 Dec 2001 http://scienceweek.com
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
7. CHEMISTRY OF EMBALMING AGENTS IN EGYPTIAN MUMMIES
S.A. Buckley and R.P. Evershed (University of Bristol, UK)
discuss the chemistry of ancient embalming. Chemical treatments
were an essential element of ancient Egyptian mummification.
Although the inorganic salt "natron" (a mineral form of hydrated
sodium carbonate) had a central role as a desiccant, without the
application of organic preservatives the bodies would have
decomposed in the humid environment of the tombs. The nature of
the organic treatments remains obscure, because the ancient
Egyptians left no written record of the process. Secondary
textual evidence for mummification is provided by Herodotus (485-
425 BC), Diodorus Siculus (c. 1st century BC), Strabo (c. 60 BC -
20 AD), and Pliny the Elder (23-79 AD). The most important
account is that of Herodotus (c. 450 BC), although archeological
evidence demonstrates that by this time the process had declined
significantly and the best results had been achieved centuries
before. The account of Herodotus mentions myrrh (an aromatic gum
resin), cassia [oil] (derived from the bark of various chiefly
tropical trees of the genus Cassia), palm wine, "cedar oil"
(still widely disputed) and "gum", but the account is vague with
respect to the specific natural products used. The authors report
the results of chemical investigations of a substantial
collection of samples of tissues, wrappings, and
resinous/bituminous material from provenanced and dated Egyptian
mummies. The authors suggest their results demonstrate that a
mixture of commodities, with a compositional diversity greater
than reported previously, was used. The use of drying oils was
clearly widespread, with coniferous resins and beeswax increasing
in importance with time. The authors suggest that their results
clearly demonstrate that despite statements to the contrary, "we
do not know all there is to know about Egyptian mummification,
and caution needs to be exercised when making assumptions about
the materials that the ancient Egyptian embalmers might have
used."
-----------
Nature 2001 413:837
-----------
SCIENCE-WEEK 28 Dec 2001 http://scienceweek.com
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
8. SOLVENT INTERACTIONS AND CARBOHYDRATE CONFORMATION
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.
The term "rotamer" refers to one of a set of conformational
isomers that differ from each other by restricted rotation about
one or more single bonds.
... ... K.N. Kirschner and R.J. Woods (University of Georgia, US)
discuss carbohydrate conformation, the authors making the
following points.
1) The phenomenon of carbohydrate recognition is critical to
many biological functions, including the response of the immune
system to bacterial pathogens, the attachment of viral influenza
particles to host cells, and the hyperacute rejection of tissue
transplants from nonhuman sources. Understanding the
conformational properties of carbohydrates is essential for the
elucidation of their mechanisms of action, which may aid in the
design of carbohydrate-based vaccines, antiviral drugs, and other
therapeutic agents. For these reasons, much research has involved
the 3-dimensional structures and dynamics of oligosaccharides and
polysaccharides.
2) Unlike polypeptides and proteins, oligosaccharides do not
contain secondary-structural motifs and they do not form well-
organized tertiary structures in solution. Instead,
oligosaccharides often populate multiple conformational families,
thus requiring both temporal and spatial descriptors to quantify
their conformational properties. Experimental methods such as NMR
spectroscopy and x-ray crystallography have a long history of
application to carbohydrates. but these methods generally result
in a single 3-dimensional model for the oligosaccharide, which
fails to adequately describe its dynamic properties.
3) Molecular dynamics simulations applied to
oligosaccharides and oligosaccharide-protein complexes can result
in good agreement with experimental data, and such simulations
offer the advantage of providing insight into the extent and the
influence that internal molecular motions have on the
oligosaccharide, a property difficult to determine
experimentally.
4) Using calculations involving quantum mechanics and
solvated molecular dynamics, the authors demonstrate that correct
reproduction of specific experimental rotamer distributions
(those involving the so-called carbohydrate "omega-angles") is
obtained only after explicit water is included in the molecular
dynamics simulations. The primary role of the water appears to be
to disrupt the hydrogen bonding within the carbohydrate, thereby
allowing the rotamer populations to be determined by internal
electronic and steric repulsions between the oxygen atoms. The
authors suggest their results provide a quantitative explanation
of the conformational behavior of (1-->6)-linked carbohydrates.
-----------
Proc. Nat. Acad. Sci. 2001 98:10541
-----------
SCIENCE-WEEK 28 Dec 2001 http://scienceweek.com
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
9. QUANTUM ENTANGLEMENT AND QUANTUM OPTICS
Paul Kwiat (University of Illinois Urbana-Champaign, US)
discusses quantum entanglement. Quantum entanglement between two
particles means that measuring the behavior of one particle
instantly determines the behavior of the other particle, even
when they are physically far apart. Erwin Schroedinger (1887-
1961) once described this peculiar connection as "_the_
characteristic trait of quantum mechanics, the one that enforces
its entire departure from classical lines of thought."
Entanglement describes a system with several components in which
the individual parts carry no information but nevertheless share
quantum correlations with each other that are stronger than those
allowed by classical physics. For example, photons can be
polarized -- the polarization describes the oscillation direction
of the electric field associated with a light wave. Polarization
filters, such as Polaroid sunglasses, will let through photons
polarized in one plane but block those polarized at right angles,
and so can be used to measure photon polarization. If two photons
have entangled polarizations, each photon individually would
appear completely unpolarized (with no particular oscillation
direction) and yet measuring the polarization of one completely
determines to polarization of the other. It is as if you flipped
two coins, each of which was equally likely to come up heads or
tails, and yet they always gave the same results -- that is,
both heads or both tails. Although normal coins do not behave
like this, it has been known for some time how to produce pairs
of photons that do display such bizarre quantum-mechanical
correlations.
-----------
Nature 2001 412:866
-----------
SCIENCE-WEEK 28 Dec 2001 http://scienceweek.com
-------------------
Related Background:
ENTANGLEMENT, DECOHERENCE, AND THE QUANTUM-CLASSICAL BOUNDARY
Quantum mechanical entanglement is a phenomenon that has caught
the imagination of the public as one of the more bizarre
consequences of fundamental physical theory. Entanglement is
unique to quantum mechanics, and involves a relationship (a
"superposition of states") between the possible quantum states of
two entities such that when the possible states of one entity
collapse to a single state as a result of suddenly imposed
boundary conditions, a similar and related collapse occurs in the
possible states of the entangled entity no matter where or how
far away the entangled entity is located. Entanglement arises
from the wave function equation of quantum mechanics, which has
an array of possible function solutions rather than a single
function solution, with each possible solution describing a set
of possible probabilistic quantum states of the physical system
under consideration. Upon fixation of the appropriate boundary
conditions, the array of possible solutions collapses into a
single solution. For many quantum mechanical physical systems,
the fixation of boundary conditions is a theoretical and
fundamental consequence of some interaction of the physical
system with something outside that system, e.g., an interaction
with the measuring device of an observer. In this context, two
entities that are described by the same array of possible
solutions to the wave function equation are said to be
"coherent", and when events decouple these entities, the
consequence is said to be "decoherence". As a physical
phenomenon, entanglement was discussed many years ago, most
particularly following the publication in 1935 of the often
quoted Einstein-Podolsky-Rosen paper (*Physical Review* 1935
47:777). These discussions have been in the form of "gedanken"
(thought) experiments involving two quantum-mechanical entangled
entities. More recently, however, there have been laboratory
constructions of actual quantum mechanical systems exhibiting
such entanglement phenomena, and the reportage of these
laboratory arrangements by the media have engaged the public
fancy. Essential here is that any purely verbal account of
quantum mechanical phenomena is severely limited by the
constraint that the properties of quantum mechanical systems can
be precisely described only by the equations relevant for those
systems, and all other descriptions usually introduce serious
ambiguities. ... ... Serge Haroche (Ecole Normale Superieure
Paris, FR) reviews quantum mechanical entanglement, decoherence,
and the question of the boundary between the physics of quantum
phenomena and the physics of classical phenomena. Haroche makes
the following points: 1) In quantum mechanics, a particle can be
delocalized (simultaneously occupy various probable positions in
space), can be simultaneously in several energy states, and can
even have several different identities at once. This apparent
"weirdness" behavior is encoded in the wave function of the
particle. 2) Recent decades have witnessed a rash of experiments
designed to test whether nature exhibits implausible nonlocality.
In such experiments, the wave function of a pair of particles
flying apart from each other is entangled into a non-separable
superposition of states. The quantum formalism asserts that
detecting one of the particles has an immediate effect on the
other, even if they are very far apart, even far enough apart to
be out of interaction range. The experiments clearly demonstrate
that the state of one particle is always correlated to the result
of the measurement performed on the other particle, and in just
the strange way predicted by quantum mechanics. 3) An important
question is: Why and how does quantum weirdness disappear
(decoherence) in large systems? In the last 15 years, entirely
solvable models of decoherence have been presented by various
authors (e.g., Leggett, Joos, Omnes, Zeh, Zurek), these models
based on the distinction in large objects between a few relevant
macroscopic observables (e.g., position or momentum) and an
"environment" described by a huge number of variables, such as
positions and velocities of air molecules, number of black-body
radiation photons, etc. The idea of these models, essentially, is
that the environment is "watching" the path followed by the
system (i.e., interacting with the system), and thus effectively
suppressing interference effects and quantum weirdness, and the
result of this process is that for macroscopic systems only
classical physics obtains. 4) In mesoscopic systems, which are
systems between macroscopic and microscopic dimensions,
decoherence may occur slowly enough to be observed. Until
recently, this could only be imagined in a gedanken experiment,
but technological advances have now made such experiments real,
and these experiments have opened this field to practical
investigation.
-----------
Physics Today 1999 July
Science-Week 1998 17 Jul
-----------
SCIENCE-WEEK 28 Dec 2001 http://scienceweek.com
-------------------
Related Background:
EXPERIMENTAL QUANTUM TELEPORTATION
Quantum teleportation is the transmission and reconstruction over
arbitrary distances of the state of a quantum system, an effect
first suggested by Bennett et al in 1993 (Phys. Rev. Lett.
70:1895). The achievement of the effect depends on the phenomenon
of entanglement, an essential feature of quantum mechanics.
Entanglement is unique to quantum mechanics, and involves a
relationship (a "superposition of states") between the possible
quantum states of two entities such that when the possible states
of one entity collapse to a single state as a result of suddenly
imposed boundary conditions, a similar and related collapse
occurs in the possible states of the entangled entity no matter
where or how far away the entangled entity is located.
Polarization is essentially a condition in which the properties
of photons are direction dependent, a condition that can be
achieved by passing light through appropriate media. Bouwmeester
et al (6 authors, Univ. of Innsbruck, AT) now report an
experimental demonstration of quantum teleportation involving an
initial photon carrying a polarization that is transferred to one
of a pair of entangled photons, with the polarization-acquiring
photon an arbitrary distance from the initial one. The authors
suggest quantum teleportation will be a critical ingredient for
quantum computation networks.
-----------
Nature 1997 11 Dec
Science-Week 1998 2 Jan
-----------
SCIENCE-WEEK 28 Dec 2001 http://scienceweek.com
-------------------
Related Background:
REPORT OF FIRST QUANTUM MECHANICAL ENTANGLEMENT OF ATOMS
... In the past, evidence of quantum mechanical entanglement has
been restricted to elementary particles such as protons,
electrons, and photons. Now E. Hagley et al, using rubidium
atoms prepared in circular Rydberg states (which means the outer
electrons of the atom have been excited to very high energy
states and are far from the nucleus in circular orbits), have
shown quantum mechanical entanglement at the level of atoms.
What is involved is that the experimental apparatus produces two
entangled atoms, one atom in a ground state and the other atom
in an excited state, physically separated so that the
entanglement is non-local, and when a measurement is made on one
atom, let us say the atom in a ground state, the other atom
instantaneously presents itself in the excited state -- the
result of the second atom wave function collapse thus determined
by the result of the first atom wave function collapse. There is
talk that before long quantum mechanical entanglement may be
demonstrated for molecules and perhaps even larger entities.
-----------
Phys. Rev. Lett. 1997 79:1
-----------
SCIENCE-WEEK 28 Dec 2001 http://scienceweek.com
-------------------
Related Background:
QUANTUM PHOTON ENTANGLEMENT AT A DISTANCE OF SEVEN MILES
Whether or not the quantum mechanical behavior of elementary
particles is called mysterious depends, more or less, on the
attitude one has. If there is a demand that the behavior of these
particles be explainable with the logistic structure of human
language, then some aspects of their behavior seem mysterious
indeed. On the other hand, if there is a willingness to admit
that the logical structure of human language may not at present
be isomorphic with the logical structure of the laws that govern
the behavior of these particles, then it is probably best to put
off notions of mysteries and take the behavior for what it is.
This week there was announced to the popular press, before
publication, the results of a twin-photon experiment in
Switzerland. Nicolas Gisin et al (University of Geneva, CH)
reported that a pair of twin photons split and sent along two
diverging paths, when arriving at terminals seven miles apart,
exhibit the phenomenon of quantum "entanglement". The gist of it
is that the detection of one of the photons effectively causes
the collapse of the spectrum of its wave-function solutions to a
single solution, and this collapse instantaneously causes the
collapse of the possible quantum states of the other photon, in
this case seven miles away. The melodramatic notion (purveyed by
the press) is that information has somehow travelled from one
photon to the other at a speed greater than the speed of light,
with the result that great canons of thought are thereby
destroyed. But perhaps the more prosaic reality is that any
attempt to describe non-classical events with language based on
classical laws and perceptions cannot succeed.
-----------
New York Times 1997 22 Jul
-----------
SCIENCE-WEEK 28 Dec 2001 http://scienceweek.com
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
10. ON THE ORIGIN OF WATER ON EARTH
Francois Robert (CNRS, FR) discusses the origin of water on
Earth. Approximately 4.55 billion years ago, the Sun and planets
formed from the protosolar nebula, a rotating disk of gas and
grains largely made of molecular hydrogen and helium. This disk
is believed to have had a homogeneous isotopic composition from
its center to its edge. However, the hydrogen isotopic
composition of water on Earth differs widely from that of the
primitive Sun. A deuterium/hydrogen ratio of (149 +- 3) x 10^(-6)
has been estimated for the bulk Earth, compared with a solar
ratio of (20 +- 4) x 10^(-6) deduced from solar wind implanted
into lunar soils. This raises the problem of where the water on
Earth originated. A clue comes from carbonaceous meteorites, the
most primitive objects of the Solar System available for
laboratory study. These meteorites contain two distinct hydrogen
carriers: water, present in clay minerals, and organic hydrogen,
present mostly in macromolecular structures. Chemically extracted
organic matter has shown a systematic enrichment in deuterium
relative to Earth, with deuterium/hydrogen ratios up to (380 +-
10) x 10^(-6). In contrast, the clays, which are associated at a
submicron scale with the organic hydrogen, had a
deuterium/hydrogen ratio close to the terrestrial ratio. The
deuterium enrichment in organic matter from meteorites has been
interpreted as a relic of interstellar chemical reactions that
occurred shortly before the planets formed. It appears that
terrestrial water must have been imported from the coldest
regions of the Solar System after Earth had formed, but the exact
conditions under which this addition was realized are unknown.
-----------
Science 2001 293:1056
-----------
SCIENCE-WEEK 28 Dec 2001 http://scienceweek.com
-------------------
Related Background:
ON THE ORIGIN OF WATER ON EARTH
James F. Kasting presents a review of current ideas concerning
the origin of water on Earth, the author making the following
points: 1) Life exists on Earth because Earth has a surface that
supports liquid water, which is required by all living things...
The long molecular chains and complex branching structures of
carbon make carbon the ideal chemical backbone for life, and
water is the ideal solvent in which carbon-based chemistry can
proceed. 2) Dating of meteorites indicates that the Solar System
is approximately 4.6 billion years old, and Earth appears to be
approximately the same age. Yet the oldest sedimentary rocks --
those that formed by processes requiring liquid water -- are only
approximately 3.9 billion years old. This observation suggests
that at least some water was present on the surface of the Earth
by that time, but the early conditions remain unclear. Recently,
there has been intense interest in the discovery that one of
Jupiter's moons, Europa, apparently has an ocean of liquid water
beneath its crust of water ice. 3) If the aggregating
*planetesimals that formed the Earth resembled the most abundant
type of meteorites, the ordinary *chondrites, they contained
approximately 0.1 percent water by weight. An early Earth
consisting of 0.1 percent water would contain 4 times the amount
of water now held in the oceans. 4) The evidence indicates that
Earth (as well as the Moon) underwent relatively heavy meteorite
bombardment from approximately 4.5 billion years ago until
approximately 3.8 billion years ago. If those meteorites also
resembled ordinary chondrites, this would also provide for more
than enough water for the oceans. 5) Comets have been proposed as
another possible source of water, but recent analysis of the 3
comets Halley, Hyakutake, and Hale-Bopp indicates these comets
have a relatively high percentage of deuterium -- twice as much
in the comets as in sea water, which poses a problem for any
model involving comets as a source of early Earth's water. More
recently, it has been proposed that Earth has been continually
bombarded by small house-sized comets, enough to fill the oceans
with water over the lifetime of the Earth, but this hypothesis
remains in sharp controversy.
-----------
Scientific American Presents 1998 Autumn
-----------
Notes:
... ... *planetesimals: Planetesimals are bodies with dimensions
of 10^(-3) to 10^(3) meters that are believed to form planets by
a process of accretion.
... ... *chondrites: Chondrites are a type of stony meteorite
consisting of an agglomeration of millimeter-sized globules
(chondrules) that are thought to be unchanged since the original
condensation out of the nebula from which the sun and solar
system formed.
-----------
SCIENCE-WEEK 1998 18 Dec
-----------
SCIENCE-WEEK 28 Dec 2001 http://scienceweek.com
-------------------
Related Background:
MESOSPHERIC WATER DATA SUPPORTS SMALL-COMET THEORY
Our current conceptions of the physics of the Earth's atmosphere
may be on the verge of change. The first rumbles began last May
with the report of Louis Frank (University of Iowa, US) of dark
spots in the outer atmosphere interpreted to be the result of
bombardment by house-sized water-containing small comets striking
the atmosphere at the rate of 1000 comets per hour. Many
geophysicists were dubious, but a few did support Frank's
explanation for the dark spots. Now an orbiting instrument of the
Naval Research Laboratory, a high resolution spectrograph, has
detected abundant hydroxyl radicals, a breakdown product of
water, in the mesosphere above northern latitudes. The mesosphere
is the layer from 50 to 80 kilometers out, part of the
ionosphere, and according to current views it is supposed to have
much less water than what the new measurements indicate. Many
geophysicists are still resistant to Frank's explanation, but
this new data certainly requires attention, and some
geophysicists are saying it is time to take the idea of small
comets seriously and rethink current assumptions.
-----------
Science 1997 22 August
Science-Week 1997 5 Sep
-----------
SCIENCE-WEEK 28 Dec 2001 http://scienceweek.com
-------------------
Related Background:
EVIDENCE FOR CONTINUAL BOMBARDMENT OF EARTH WITH WATER SOURCES
The water on the Earth has always been thought of as here from
the beginning, a result of the process of planetary cooling, the
seas produced by condensation of water vapor originating from
the Earth itself. Today came the startling news of evidence that
the Earth is being constantly showered with miniature comet ice
balls of 20 to 40 tons in mass at the astonishing rate of over
40,000 per day. The evidence is provided by the NASA Polar
orbiting spacecraft, the research team led by Louis A. Frank
(University of Iowa, US), who in fact first suggested this
bombardment 11 years ago to explain markings in photographs
received by NASA's Dynamics Explorer I. At that time, Frank was
heavily criticized by his colleagues and his idea called
outlandish. At this moment Frank has apparently been vindicated,
his report presented in a crowded hall yesterday at a meeting of
the American Geophysical Union convention. Calculations show
that the incoming water could account for the oceans on Earth,
and if the assessment continues to be supported, it opens new
possibilities for the understanding of early conditions on the
planet.
-----------
New York Times 1997 29 May
Science-Week 1997 29 May
-----------
SCIENCE-WEEK 28 Dec 2001 http://scienceweek.com
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
11. ON TRACE GASES IN PRESOLAR DIAMONDS
A.P. Koscheev et al (Karpov Institute of Physical Chemistry, RU)
discuss presolar diamonds. Diamond grains are the most abundant
presolar grains found in primitive meteorites. They apparently
formed before the Solar System, and therefore provide a record of
nuclear and chemical processes in stars and in the interstellar
medium. Their origins are inferred from the unusual isotopic
compositions of trace elements -- mainly xenon -- which suggest
that they came from supernovae. But the exact nature of the
sources has been enigmatic, as has the method by which noble
gases were incorporated into the grains. One observation is that
different isotopic components are released at different
temperatures when the grains are heated, and it has been
suggested that these components have different origins. The
authors report results of a laboratory study that demonstrates
that ion implantation (previously suggested on other grounds) is
a viable mechanism for trapping noble gases. Moreover, the
authors find that ion implantation of a single isotopic
composition can produce both low- and high-temperature release
peaks from the same grains. The authors conclude that both
isotopically normal and anomalous gases may have been implanted
by multiple events separated in space and/or time, with thermal
processing producing an apparent enrichment of the anomalous
component in the high-temperature release peak. The previous
assumption that the low- and high-temperature components were not
correlated may therefore have led to an overestimate of the
abundance of anomalous argon and krypton, while obscuring an
enhancement of the light -- in addition to the heavy -- krypton
isotopes.
-----------
Nature 2001 412:615
-----------
SCIENCE-WEEK 28 Dec 2001 http://scienceweek.com
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
12. OCEANOGRAPHY: PATTERNS OF ARCTIC CIRCULATION
Lawrence A. Mysak (McGill University, CA) discusses Arctic
circulation patterns. The North Atlantic Oscillation (NAO) is
perhaps the best known mode of atmospheric variability outside
the tropics. It consists of a north-south fluctuation of air mass
over the North Atlantic sector whose time evolution is
characterized by the NAO index: the standardized winter sea level
pressure difference between the Azores High and the Icelandic
Low. When the NAO index is in a positive mode, a deepened
Icelandic Low causes strong westerlies over the eastern North
Atlantic, strong southerly winds over the Norwegian Sea, and
strong northerly winds over the Labrador Sea. In the negative
mode, the Icelandic Low and the Azores High tend to be weak and
the winds are reduced in the above areas. Another wintertime
oscillation closely associated with the NAO is the Arctic
Oscillation (AO), which consists of fluctuations in air mass
between middle and high latitudes all around the Northern
Hemisphere. The AO index is highly correlated with the NAO Index,
and because the largest north-south air mass exchanges associated
with the AO occur over the North Atlantic sector, the NAO is
regarded as the regional representative of the AO. On decadal and
longer time scales, the NAO and AO indices over the past 50 years
closely resemble a third index -- the vorticity index. This index
characterizes the wind patterns over the central Arctic. When the
vorticity index is positive (corresponding to both the NAO and AO
indices being positive), there is a weak Arctic High, and the
associated winds tend to produce anti-clockwise ice drift motion
in the eastern Arctic (the European Basin). Conversely, when the
vorticity index is negative (corresponding to negative NAO and AO
indices), there is a strong Arctic High and the ice drift motion
is clockwise in the European Basin. In general, it is clear that
i response to atmospheric circulation fluctuations, the Arctic
Ocean current and sea-ice drift patterns vary on a wide range of
time scales.
-----------
Science 2001 293:1269
-----------
SCIENCE-WEEK 28 Dec 2001 http://scienceweek.com
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
13. POSTDOCTORAL FELLOWSHIPS PROFILE:
Laboratory of Fred Schaufele, Univ. of California San Francisco
---------------------------------------------------------------
DEPARTMENT: Metabolic Research Unit, Diabetes Center,
Department of Medicine
GENERAL RESEARCH AREA: Cellular biochemistry
HEAD OF THIS SPECIFIC LABORATORY: Fred Schaufele
POSTDOCTORAL FELLOWSHIPS AVAILABLE IN THE FOLLOWING SPECIFIC
RESEARCH PROBLEMS:
a) Intracellular structure and function of nuclear
receptors: There has been a recent realization that subcellular
and subnuclear distribution of nuclear receptors and their
interacting cofactors likely govern their function. We study the
intracellular locations of nuclear receptors and interacting
cofactors by fluorescence microscopy. Fluorescence resonance
energy transfer between fluorophores attached to the receptors
and their cofactors defines the direct interactions between
receptor dimers and with the cofactors. Mapping FRET, and the
efficiency of FRET, at small (100 nm by 100 nm) sections of each
nucleus identifies local variations in the dimer conformations
and interactions. We determine how those interactions change in
space and with time following ligand addition to the cell.
Together with collaborators in the UCSF Pharmaceutical Chemistry
Department, we are determining the effects of existing and novel
nuclear receptor ligands on the spatial and temporal interactions
and locations of a variety of nuclear receptors and cofactors.
Other collaborators within the Metabolic Research Unit and UCSF
Department of Biochemistry provide structural and functional
information on the molecular actions of nuclear receptors. Our
goal is to correlate nuclear receptor structure and function with
a precise definition of the interactions of wild-type and mutant
receptors that occur in space and time following the addition of
physiologic and more selective ligands. By doing so, we will
better understand the nuances of divergent nuclear receptor
actions. We may even develop ligands that affect only subsets of
those activities. Those highly selective ligands might be useful
for more targeted clinical actions and thus reduce the side
effects of some current therapies.
b) Intranuclear organization of transcription factors and
co-factors during differentiation: We similarly study the role of
the subnuclear distribution, conformations, and interactions of
transcription factors and their cofactors that regulate cellular
differentiation. Two progenitor cell models are particularly
used: one for pituitary cell differentiation and the other for
adipocyte differentiation. We identify how the intracellular
positions of the factors change and how this may affect the roles
of those factors in changing patterns of gene expression and in
blocking cellular proliferation. This involves the fluorescence
imaging techniques discussed for the nuclear receptors, as well
as more traditional biochemical, molecular and cellular
approaches to studying gene activation. Collaborations with other
laboratories at the University of Virginia and the University of
Michigan help the successful completion of this project.
PREVIOUS RESEARCH EXPERIENCE AND DEGREES REQUIRED: The
postdoc is expected to have obtained an advanced degree in which
she/he has published at least one, and preferably more,
manuscripts in internationally recognized journals. A solid
background in molecular biology is preferred. Most important is
some demonstration of independent thinking, background in an
appropriate field, and knowledge of and enthusiasm for the
scientific process.
USUAL STARTING STIPEND: The starting stipend for someone
immediately finished graduate school is $32,000 per year plus
health benefits. This increases with years of experience.
SPECIAL REQUIREMENTS: Citizenship and residency status are
only important for the ability to obtain fellowship funding.
APPROXIMATE NUMBER OF PEOPLE CURRENTLY WORKING IN THIS
SPECIFIC LABORATORY (FACULTY, STAFF, STUDENTS, POSTDOCS): 5 in
the specific laboratory, but there are extensive collaborations
and contacts with others
CONTACT FOR MORE INFORMATION: Fred Schaufele at Email:
freds@diabetes.ucsf.edu
FURTHER RELEVANT INFORMATION: We try to maintain a fairly
small laboratory in which the principal investigator remains
active and has enough time to spend with the investigators. The
principal investigator recognizes that the postdoctoral
experience is for the benefit of the postdoc and that future
career prospects depend upon the research success, and the
development, of a research program during the postdoctoral
period. In order to maintain a critical mass of knowledge and
expertise, we therefore emphasize our collaborations with other
groups and laboratories. The laboratory maintains an open
environment in which the researchers are encouraged to work
together and with others.
----------------------------------------------------------
ScienceWeek welcomes submission of postdoctoral fellowship
profiles by heads of laboratories. There is no publication
charge. Query: request@scienceweek.com
----------------------------------------------------------
SCIENCE-WEEK 28 Dec 2001 http://scienceweek.com
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
14. IN FOCUS: ON MARY SOMERVILLE AND GRAVITY
"Mary Fairfax Somerville (1780-1872) was a mathematician,
scientist, and translator who in a most serious and significant
sense popularized the Newtonian universe, in particular as
expounded by Laplace. The story is told of Laplace, over dinner
in Paris, remarking to Somerville that 'only two women have ever
read the Mecanique Celeste; both are Scotch women: Mrs. Greig and
yourself.' (During her first marriage, Somerville was known as
Mrs. Greig.) In fact, Somerville not only had read it but also
had translated it into English -- and 'into common language' --
under the title _The Mechanism of the Heavens_. The success of
her second book, _On the Connection of the Physical Sciences_,
excerpted here, led to her election to the Royal Astronomical
Society, of which she and Caroline Herschel became the first
women members..." [D.R. Danielson].
[Excerpt from Somerville's _On the Connection of the
Physical Sciences_ (1840)]: "Astronomy affords the most extensive
example of the connection of the physical sciences. In it are
combined the sciences of number and quantity, of rest and motion.
In it we perceive the operation of a force which is mixed up with
every thing that exists in the heavens or on Earth; which
pervades every atom, rules the motions of animate and inanimate
beings, and is as sensible in the descent of a rain drop as in
the falls of Niagara; in the weight of the air, as in the periods
of the Moon. Gravitation not only binds satellites to their
planet, and planets to the Sun, but it connects sun with sun
throughout the wide extent of creation, and is the cause of the
disturbances, as well as of the order, of nature: since every
tremor it excites in any one planet is immediately transmitted to
the farthest limits of the system, in oscillations, which
correspond in their periods with the cause of producing them,
like sympathetic notes in music, or vibrations from the deep
tones of an organ."
-----------
Dennis R. Danielson (ed.): _The Book of the Cosmos: Imagining the
Universe from Heraclitus to Hawking_
(Perseus Publishing, Cambridge MA 2000, p.298)
http://www.amazon.com/exec/obidos/ASIN/0738204986/scienceweek
-----------
SCIENCE-WEEK 28 Dec 2001 http://scienceweek.com
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
15. FROM PRAXIS (1):
CLINICAL SYMPTOMS: INHALATIONAL ANTHRAX VS. INFLUENZA
The Weekly Morbidity and Mortality Report (Centers for Disease
Control and Prevention, US) discusses differences in symptoms and
signs of inhalational anthrax and influenza with the following
tabulation of percentage of cases showing a symptom/sign in each
disease category. The inhalational anthrax percentages are based
on 10 recent confirmed cases of inhalational anthrax that have
been identified as caused by bioterrorism:
Symptom/Sign Inhalational Anthrax Influenza
------------ -------------------- ---------
Elevated temperature 70 percent 68-77 percent
Fever or chills 100 83-90
Fatigue/malaise 100 75-94
Unproductive cough 90 84-93
Shortness of breath 80 6
Chest discomfort/pain 60 35
Headache 50 84-91
Myalgias 50 67-94
Sore throat 20 64-84
Rhinorrhea 10 79
Nausea or vomiting 80 12
Abdominal pain 30 22
-----------
Morb. Mort. Weekly Rep. 2001 50:984
J. Am. Med. Assoc. 2001 286:2536
-----------
PRAXIS 24 Dec 2001 http://scienceweek.com/praxis
-----------
SCIENCE-WEEK 28 Dec 2001 http://scienceweek.com
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
16. FROM PRAXIS (2):
EPIDEMIOLOGY OF ANTHRAX
Morton N. Swartz (Massachusetts General Hospital Boston, US)
discusses the epidemiology of anthrax, the authors making the
following points:
1) Bacillus anthracis has a nearly worldwide distribution,
existing in the soil in the form of extremely resistant spores
and causing infection in humans and in farm and wild animals who
have grazed on contaminated land or ingested contaminated feed.
Under natural conditions, humans acquire anthrax infection
(usually the cutaneous form) from contact with infected animals
or contaminated animal products such as hides, wool, hair, and
ivory tusks. Rarely, gastrointestinal (or oropharyngeal) anthrax
has followed the ingestion of poorly cooked infected meat. Cases
of inhalational anthrax (also known as "woolsorters' disease")
have been linked to the large scale processing of hides and wool
in enclosed factory spaces, where aerosolized anthrax spores may
be inhaled.
2) Between 1979 and 1985, in association with war and the
interruption of veterinary public health practices, Zimbabwe was
the site of the largest outbreak of anthrax, with about 10,000
cases, almost all of which were cutaneous infections. This human
epidemic was directly related to a major animal epidemic
(epizootic) in cattle. Several lessons were learned from this
outbreak: a) it is important to vaccinate livestock in such
endemic areas regularly to control and prevent outbreaks of
anthrax in humans; b) direct contact with infected livestock and
meat has a major role in the acquisition of infection, and biting
flies may have a minor role; c) there seems to be little danger
of cross infection of other hospitalized patients or nursing
staff; d) complications (such as bacteremia, sepsis syndrome, and
meningitis) and death can be prevented by treatment with
penicillin.
3) Between 20,000 and 100,000 cases of anthrax have been
estimated to occur worldwide annually, but in the US, the annual
incidence was only 127 in the early part of the 20th century, and
it subsequently declined to less than 1 case per year -- a rate
maintained for the past 20 years. Until now, there had not been a
case of inhalational anthrax in the US in more than 20 years.
Thus, the recent occurrence of 12 cases of anthrax, 6 involving
inhalation and none with the conventional exposure to infected
animals or animal products, has spotlighted the current
consideration of anthrax as a weapon of bioterrorism.
4) We were forced to recognize the possibility that anthrax
may be used as a biologic weapon in 1979, when at least 66 people
in Sverdlovsk (USSR) died in the largest known epidemic of
inhalational anthrax. This epidemic followed the accidental
release of anthrax spores into the atmosphere by a research
facility involved in "weaponizing" anthrax by preparing finely
milled nonclumping (electrostatically neutral) spores that are
optimal for dissemination and inhalation and that produce toxins
when they germinate. After the Gulf War, Iraq admitted producing
and deploying such weaponized anthrax in missiles, so a clear
threat remains.
-----------
New Engl. J. Med. 2001 345:1621
-----------
PRAXIS 24 Dec 2001 http://scienceweek.com/praxis
-----------
SCIENCE-WEEK 28 Dec 2001 http://scienceweek.com
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
17. THIS WEEK IN PRAXIS (24 Dec 01):
-------------------------------
1. On Noise and Quantum Information Processing
2. Conductance Properties of Conjugated Molecular Wires
3. Health Benefits of Greenhouse Gas Reduction
4. On the Surfaces of Inorganic Nanocrystals
5. Clinical Symptoms: Inhalational Anthrax vs. Influenza
6. Epidemiology of Anthrax
7. Economics: On Predicting Rational Behavior
8. Beyond Proteomics
9. On Cancer Prevention
10. On Synthesis of Oligonucleotide Arrays
11. Humans as the World's Greatest Evolutionary Force
12. Approaches to Stroke Therapy
13. From SW: Neurobiology of Emotions and Feelings
14. This Week in ScienceWeek
For information about PRAXIS, see:
http://www.scienceweek.com/praxis
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
In the text, the affiliation following the names of authors is
the affiliation of the lead author.
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
NOTICES
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
CHANGE OF EMAIL ADDRESS:
If at any time you need to change the Email address at which you
receive SW, please send the information to:
request@scienceweek.com
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
SCIENCE-WEEK SUBSCRIPTIONS:
Any student in any country can request a continuing free
subscription at: http://www.scienceweek.com/students.htm
Information concerning other subscriptions is available at:
http://www.scienceweek.com/subinfo.htm
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
We welcome comments, suggestions, and criticisms from our
subscribers. Public letters relevant to any report are also
welcome. Editorial contact: editors@scienceweek.com
Editor/Publisher: Dan Agin
Managing Editor: Claire Haller
Associate Editor: Joan Oliner
Copyright (c) 1997-2001 SCIENCE-WEEK
All Rights Reserved
US Library of Congress ISSN 1529-1472
---------------------------------------------
ScienceWeek/Spectrum Press Inc.
3023 N. Clark Street #109
Chicago, 60657-5205 IL, USA.
---------------------------------------------
-----end file
|