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.

February 9, 2001 -- Vol. 5 Number 6

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Our loyalties are to the species and the planet.
We speak for Earth. Our obligation to survive is
owed not just to ourselves but also to that Cosmos,
ancient and vast, from which we spring.
-- Carl Sagan (1934-1996)

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Section 1
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Contents of this Issue (Full reports in Section 2):

1. EVOLUTIONARY BIOLOGY: ON AFROTHERIA
The idea of an Afrotheria group is one of the most remarkable
hypotheses in mammalian evolutionary biology, the hypothesis
proposing that one-third of the orders of placental mammals form
an ancient group that evolved on Africa when that continent was
isolated from other continents by plate tectonics. Although this
hypothesis has been predicted by molecular clock studies,
evidence for it has emerged only in the last 3 years from
phylogenetic analyses of DNA and protein sequence data. Many
mammologists remain baffled and see no support for this idea from
traditional sources of data such as anatomy.
(Proc. Natl. Acad. Sci. US 2 Jan 01: 98:1)

2. ARCHAEOLOGY: CLIMATE AND THE COLLAPSE OF SOCIETIES
Although the consensus among archeologists and historians has
been that societal collapses in prehistory and history resulted
from a combination of social, political, and economic factors, a
new perspective is that the collapse of societies has often been
the result of sudden changes in climate. The accumulation of
high-resolution paleoclimatic data that provide an independent
measure of the timing, amplitude, and duration of past climate
events relevant to societal collapse indicates that these climate
events were abrupt, involved new conditions that were unfamiliar
to the inhabitants of the time, persisted for decades to
centuries, and were highly disruptive.
(Science 26 Jan 01 291:609)

3. MOLECULAR BIOLOGY: NATURAL HISTORY AND PROTEIN FOLDING
Physical chemists have mounted a frontal assault on the problem
of protein folding, using computers to build physical models of
proteins in water, the models involving guesses concerning many
aspects of atomic interactions. The assault has apparently
failed. Biophysicists and chemical biologists may soon discover
that they need to research the history of biomolecules if they
are to understand the physical behaviors they are attempting to
characterize. Since 1990, approximately 30 protein folds have
been predicted using the history of protein families. In many
cases, the prediction provided information about the function as
well as about the form of the protein.
(Nature 25 Jan 01 409:459)

4. HISTORY OF PHYSICS: WOLFGANG PAULI
Much of Pauli's influential work remains unpublished. His proof
of the equivalence of matrix and wave mechanics appears in a
letter to Pascual Jordan, and he wrote down the uncertainty
relation for time and energy in a letter to Heisenberg. Pauli
almost never cared about recognition for his work, although he
took great care in giving credit to other authors. Unlike
Heisenberg and many other physicists, Pauli was not ambitious or
competitive. His principle concern was always to clarify the
greater picture for himself, to obtain a consistent and coherent
description of the totality of the phenomena.
(Physics Today February 2001)

5. INTERSCIENCE: CHAOS AND COMPLEXITY
In common non-scientific usage the term "chaos" is a synonym for
randomness, for completely non-deterministic and irregular
phenomena. In mathematical theory, however, the term "chaos"
refers to a deterministic (i.e., non-random) phenomenon
characterized by special properties that make the predictability
of outcomes very difficult: chaotic behavior is such that
although it does not occur randomly, it has the appearance of a
series of random occurrences. In the research context, complexity
and "chaotic behavior" are not synonymous. If one focuses
attention on the time evolution of an emergent behavior, e.g.,
daily changes in temperature, that behavior may well be
completely deterministic yet indistinguishable from a random
process: the behavior is chaotic. However, although chaos is
often associated with complex systems, not all complex systems
manifest chaotic behavior. (Skeptic 2000 vol.8 No.3)

6. PHYSICAL CHEMISTRY: ON THE STRUCTURE OF WATER
A new quantitative model of liquid water attempts to gain an
understanding of the structure-property relationships of water
through the study of translational and orientational order. Using
molecular dynamics simulations, the authors identify a
structurally anomalous region -- bounded by loci of maximum
orientational order (at low densities) and minimum translational
order (at high densities) -- in which order decreases on
compression, and where orientational and translational order are
strongly coupled. This region encloses the entire range of
temperature and densities for which the anomalous diffusivity and
thermal expansion coefficient of water are observed, and enables
a quantification of the degree of structural order required for
these anomalies to occur. (Nature 18 Jan 01 409:318)

7. IN FOCUS: ON THE INTERACTION OF LIGHT AND MATTER

8. FROM THE SCIENCEWEEK ARCHIVE:
ANTHROPOLOGY: DEFINING THE HUMAN GENUS


=-=-=-=-=-=-=-=-=
Section 2
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1. EVOLUTIONARY BIOLOGY: ON AFROTHERIA
     One of the major current controversies in evolutionary
biology concerns methodology, a conflict between *evolutionary
divergence and groupings as documented by the apparent fossil
record, and divergence and groupings as documented by the
apparent molecular-genetic record. At present, neither record is
complete, and in many cases the records are apparently
contradictory. Down the road there will no doubt be a
rapprochement and the two methodological approaches will be seen
as complementary. Currently, however, there is evidently a
substantive dispute among specialists.
     In particular, the set of relationships within the major
groups of placental mammals as determined by molecules differs
greatly from evolutionary "trees" based on morphological data.
For example, evidence from several independent genes is
interpreted as indicating that one-third of the living orders of
placental mammals now form a well supported group, the
"Afrotheria". This group includes such diverse forms as
elephants, elephant shrews, tenrecs (a group of African shrews),
golden moles, hyracoids (hyraxes), sirenians (sea cows), and
aardvarks. Four members of the group (elephants, elephant shrews,
tenrecs, and aardvarks) have a long snout, and a fifth member
(sirenians) has a mobile snout. The group is believed to also
make geographic sense, since all the members of the group are of
African origin. Fossils and morphology, however, place elephants,
sirenians, and hyracoids with ungulates (horses, cows, etc.).
... ... S. Blair Hedges (Pennsylvania State University, US)
presents a commentary on recent research on Afrotheria, the
author making the following points:
     1) The author points out that the idea of an Afrotheria
group is one of the most remarkable hypotheses in mammalian
evolutionary biology, the hypothesis proposing that one-third of
the orders of placental mammals form an ancient group that
evolved on Africa when that continent was isolated from other
continents by *plate tectonics. Although this hypothesis has been
predicted by *molecular clock studies, evidence for it has
emerged only in the last 3 years from *phylogenetic analyses of
DNA and protein sequence data. Many mammologists remain baffled
and see no support for this idea from traditional sources of data
such as anatomy. The identification of the Afrotheria group
splits apart other established groups of mammals, including
ungulates and insectivores, yet it is the most strongly supported
grouping of mammalian orders in molecular phylogenies.
     2) The 4700 species of living mammals are placed by
taxonomists in approximately 20 orders, including such groups as
rodents (Order Rodentia), primates (Primates), and bats
(Chiroptera). In *systematics, taxonomic names are often treated
as evolutionary hypotheses that imply that members of the group
are more closely related to each other than to other species or
groups. Afrotheria is a superorder that contains 6 orders. Some
of the smallest (Lesser long-tailed tenrec, 5 grams) and largest
(African elephant, 5000 kilograms) species of mammals apparently
belong to this group, and its members fill a diversity of
ecological niches.
     3) The author suggests the discovery of Afrotheria places
more importance on plate tectonics in the early evolution of
placental mammals. However, this is another issue that is hotly
debated. Molecular clocks derived from large numbers of genes
have indicated that placental mammals not only were present deep
in the *Cretaceous period (approximately 100 million years ago),
but were already diverging from one another into groups (*clades)
that eventually led to the present-day orders. Today, Africa is
connected to Europe and Asia, facilitating dispersal of mammals
among the three continents. But in the early Cretaceous period
(approximately 120 million years ago), Africa was apparently
connected to South America, with the two continents separating
approximately 105 million years ago. Africa was relatively
isolated between 105 and 40 million years ago, and during this
time afrotherians were probably evolving and adapting to
different ecological niches. Approximately 30 million years ago,
Africa began to collide with Europe and Asia, and since then
these areas have been closely associated.
-----------
S. Blair Hedges: Afrotheria: Plate tectonics meets genomics.
(Proc. Natl. Acad. Sci. US 2 Jan 01: 98:1)
QY: S. Blair Hedges: sbh1@psu.edu
-----------
Text Notes:
... ... *evolutionary divergence: In this context, the
acquisition of dissimilar characteristics by related organisms in
unlike environments.
... ... *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. 
... ... *molecular clock studies: There are, in general, two
types of "molecular clock" studies: a) In DNA clock studies, it
is postulated that when averaged across the entire genome of a
species, the rate of nucleotide substitutions in DNA remains
constant. Thus, the degree of divergence in nucleotide sequences
between two species can be used to estimate the time of their
divergence in the past (their "divergence node"). b) In protein
clock studies, it is postulated that amino acid substitutions
occur at a constant rate for a given family of proteins, and thus
the degree of divergence between two species in the amino acid
sequences of the protein in question can be used to estimate the
length of time that has elapsed since their divergence from a
common ancestor.
... ... *phylogenetic analyses: In general, the term "phylogeny"
refers to the evolutionary history of a species or group of
species in terms of their derivation and relationships.
... ... *systematics: A classification scheme designed to reflect
evolutionary history. Current systematics in biology tends to
classify living systems in terms of evolutionary history
(phylogeny), and modern taxonomists (systematists) are among the
foremost students of evolution.
... ... *Cretaceous period: The geological period ranging
approximately from 146 million years ago to 65 million years ago.
... ... *clades: A "clade" is a cluster of taxa derived from a
single common ancestor.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 9Feb01
For more information: http://scienceweek.com/swfr.htm

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2. ARCHAEOLOGY: CLIMATE AND THE COLLAPSE OF SOCIETIES
The archeological and historical records contain much evidence of
the collapse of prehistoric, ancient, and premodern societies,
with these collapses occurring suddenly and frequently involving
abandonment of the region, replacement of one subsistence base by
another (e.g., replacement of agriculture by livestock-raising
[pastoralism]), or conversion to a lower energy sociopolitical
organization (e.g., conversion to local states from an
interregional empire). Although the consensus among archeologists
and historians has been that such collapses result from a
combination of social, political, and economic factors, a new
perspective is that the collapse of societies in history has
often been the result of sudden changes in climate.
... ... H. Weiss and R.S. Bradley (2 installations, US) present a
review of current research on climate forcing of societal
collapse, the authors making the following points:
     1) The authors point out that the accumulation of high-
resolution paleoclimatic data that provide an independent measure
of the timing, amplitude, and duration of past climate events
relevant to societal collapse indicates that these climate events
were abrupt, involved new conditions that were unfamiliar to the
inhabitants of the time, and persisted for decades to centuries.
These climate events were therefore highly disruptive, leading to
societal collapse, which can be viewed as an adaptive response to
otherwise insurmountable stresses.
     2) Examples of the relationship between paleoclimate and
societal collapse in the Old World suggest that prehistoric and
early historic societies, from villages to states or empires,
were highly vulnerable to climatic disturbances, and many lines
of evidence now point to climate forcing as the primary agent in
repeated social collapse. In the New World, high-resolution
archeological records also point to abrupt climate change as the
proximal cause of repeated social collapse.
     3) Climate during the past 11,000 years was long believed to
have been uneventful, but new evidence increasingly demonstrates
climatic instability. Droughts lasting decades to centuries
started abruptly, were unprecedented in the experience of the
existing societies, and were highly disruptive to the
agricultural foundations of these societies because social and
technological innovations were not available to counter the
rapidity, amplitude, and duration of changing climate conditions.
     4) The authors point out that these past climate changes
were unrelated to human activities. In contrast, future climate
change will involve both natural and anthropogenic forces and
will be increasingly dominated by the latter. Current estimates
suggest changes will be large and rapid. Global temperature will
rise and atmospheric circulation will change, leading to a
redistribution of rainfall difficult to predict. The authors
point out that in spite of technological changes, most of the
world's people will continue to be subsistence or small-scale
market agriculturalists who are as vulnerable to climate
fluctuations as the late prehistoric and early historic
societies. Furthermore, in an increasingly crowded world, change
of habitat ("habitat tracking") as an adaptive response will not
be an option.
     5) In conclusion, the authors suggest we must use current
information "to design strategies that minimize the impact of
climate change on societies that are at greatest risk. This will
require substantial international cooperation, without which the
21st century will likely witness unprecedented social
disruptions."
-----------
H. Weiss and R.S. Bradley: What drives societal collapse?
(Science 26 Jan 01 291:609)
QY: Harvey Weiss: harvey.weiss@yale.edu
-------------------
Summary by SCIENCE-WEEK http://scienceweek.com 9Feb01
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
ON GLOBAL CLIMATE CHANGE
Environmental change involves jumps, fluctuations, and trends,
the environment changing through the operation of the internal
machinery of the *ecosphere (biosphere), and through the external
agencies of cosmic and geological forces. Evidence of past
environmental change, almost always incomplete, derives from
geochemical, physical, biological, historical, and instrumental
sources. In recent years, high-speed computers have allowed
researchers to manipulate complicated and reasonably realistic
models of environmental change, with modelling particularly
useful for studying changes in *sedimentary basins,
biogeochemical cycles, and climate. General circulation models,
run with appropriate boundary conditions, predict climates of the
past, and these predicted climates can be compared with
paleoclimatic indicators.
... ... R.B. Alley et al (3 authors 3 installations, US) present
a review of current research on global climate change, the
authors making the following points:
     1) Prediction of climate change requires observational
constraints on the current climate state, knowledge of the way
the coupled air-ocean-ice-earth-life system behaves, and
information on changing forcings such as solar variability.
Studies of past climate are also required to focus model-building
efforts on climate components that are likely to change, and to
allow testing of the ability of models to predict time-evolution
of the system.
     2) The last few million years have been generally cold and
icy compared with the previous hundred million years but have
alternated between warmer and colder conditions. These
alternations have been linked to changes over tens of thousands
of years in the seasonal and latitudinal distribution of sunlight
on Earth caused by features of Earth's orbit. Globally
synchronous climate change despite some hemispheric asynchrony of
the forcing is explained at least in part by lowering carbon
dioxide during colder times in response to changes in ocean
chemistry. We live in one of the warmer times of these orbital
cycles; the coolest times brought glaciation to nearly one-third
of the modern land area.
     3) Studies of past climate changes indicate that the Earth
system has experienced greater and more rapid changes over larger
areas that was generally believed possible, with jumping between
fundamentally different modes of operation in as little as a few
years. Most of the last 100,000 years or longer has been
characterized by large and abrupt regional-to-global climate
changes, and agriculture and industry have developed during
anomalously stable climatic conditions. New high-resolution
analysis of sediment cores indicates these past changes have been
caused by "*band jumps" between modes of operation of the climate
system. Recurrence of such band jumps is possible and might be
affected by human activities.
-----------
R.B. Alley et al: Global climate change.
(Proc. Natl. Acad. Sci. US 31 Aug 99 96:9987)
QY: Richard B. Alley: ralley@essc.psu.edu
-----------
Text Notes:
... ... *ecosphere (biosphere): In general, the term "biosphere"
refers to the portion of the planet capable of supporting life.
It ranges from elevations of approximately 10,000 meters above
sea level to the deep ocean, and a few hundred meters below the
surface of the soil. The biosphere consists of the hydrosphere,
the lower atmosphere (troposphere), and the surface of the
*lithosphere, all three regions inhabited by metabolically active
organisms.
... ... *lithosphere: In current geology, the lithosphere is the
approximately 100 kilometer rigid upper layer of the crust and
upper mantle of the Earth.
... ... *sedimentary basins: The term "sedimentary basin" refers
to a subsiding area of the Earth's crust, which permits the net
accumulation of sediment, i.e., material derived from pre-
existing rock, from biogenic sources, or precipitated by chemical
processes.
... ... *band jumps: In this context, the term "band jump" refers
to an abrupt change from one range of variation to another.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 1Oct99
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
ON THE POSSIBILITY OF RAPID CLIMATE CHANGE
Over the course of geologic history, the environment on Earth has
been far from static. Geologic evidence suggests that 600 million
years ago the atmosphere lacked sufficient oxygen to support
animal life. More recently, as indicated by sediments recording
conditions over the past 500,000 years, the climate of the planet
varied between at least two different states. The record from the
past 150,000 years is particularly well-preserved, offering
details concerning repeated climate changes. Between
approximately 131,000 and 114,000 years ago, a warm period
similar to the climate of today occurred. This was followed by
what is called the "Wisconsin ice age", which ended approximately
12,000 years ago when the current relatively warm *Holocene
period began. ... ... Kendrick Taylor (Desert Research Institute,
US) presents a review of the research of a large project to
develop a climate record for the past 110,000 years, the author
making the following points:
     1) The layerings of glacial ice record seasonal variations
of temperature, snowfall, concentrations of atmospheric gases,
and atmospheric circulation patterns. In general, the weight of
accumulating snow compresses the snow below it, trapping
atmospheric gases, dust, and chemicals, and a deep ice core thus
provides a sequential record amenable to analysis.
     2) The author reports that by examining ice cores from
Greenland, he and his colleagues have determined that climate
changes large enough to have extensive impacts on our society
have occurred in a time-frame of less than 10 years. The author
suggests that the climate of Earth could change significantly
during a lifetime, that we are still a long way from being able
to predict such a change, but we are getting closer to an
understanding of how it might occur. A pressing concern is
whether anthropogenic changes in the atmosphere of the planet
might perturb climate stability.
     3) The author points out that climate is the result of the
exchange of heat and mass between the land, ocean, atmosphere,
ice sheets, and space. As long as changes to the land, ocean,
atmosphere, and ice sheets stay below certain thresholds, climate
changes will occur slowly. But climate will change rapidly if
those thresholds are crossed. *Greenhouse warming, for example,
by altering ocean circulation and the flow of tropical heat to
the North Atlantic, could lead to rapid cooling in eastern North
America, Europe and Scandinavia. Altered ocean circulation could
lead to much larger changes. We have no experience predicting
climate switches between stable modes.
     4) The author suggests human ingenuity would most likely
allow us to adapt to a rapid change in climate, but we would pay
a larger price than our civilization has ever known. The author
poses a scenario: "Imagine the economic and social cost of
moving, in a 20-year period, most of our agricultural activities
500 miles south of their current locations. Imagine the social
cost and famine if agriculture could not be relocated quickly
enough."
     5) Although we do not know the critical level of greenhouse
gas concentration that would trigger a rapid climate change, we
do know that reducing the rate of greenhouse emissions would help
in two ways. First, the atmospheric concentration of greenhouse
gases would increase more slowly. Second, numerical models
predict that the climate threshold will occur at a higher
concentration of greenhouse gases if the concentration of
greenhouses increases slowly.
     6) The author suggests it will be another 20 years before
the climate changes that are predicted to be associated with the
greenhouse effect becomes large enough to be unambiguously
differentiated from naturally occurring variations in climate.
As a society we have the choice of ignoring the warning signs or
taking some action.
-----------
Kendrick Taylor: Rapid climate change.
(American Scientist Jul/Aug 1999 87:320)
QY: Kendrick Taylor: kendrick@dri.edu
-----------
Text Notes:
... ... *Holocene period: The most recent epoch of the geologic
time scale, from approximately 10,000 years ago to the present.
... ... *Greenhouse warming: See notes to report #1, this issue.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 13Aug99
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
ON CLIMATE FORCINGS IN THE INDUSTRIAL ERA
A "climate forcing" is an imposed perturbation of the Earth's
energy balance with space, for example, a change of the solar
radiation incident on the planet, or a change of carbon dioxide
in the Earth's atmosphere. The unit of measure of climate forcing
is Watts per square meter. Thus, the forcing due to the increase
of atmospheric carbon dioxide since pre-Industrial times is
approximately 1.5 Watts per square meter. Climate change is
combination of deterministic response to forcings and *chaotic
fluctuations -- the chaos a consequence of the nonlinear
equations governing the dynamics of the system. Quantitative
knowledge of all significant climate forcings is needed to
establish the contribution of deterministic factors in observed
climate change and to predict future climate. J.E. Hansen et al,
in a review of current considerations concerning climate forcings
in the Industrial era, make the following points: 1) The forcings
that drive long-term climate change are not known with an
accuracy sufficient to define future climate change. 2)
Anthropogenic greenhouse gases, which are well-measured, cause a
strong positive (warming) force. But other, poorly measured,
anthropogenic forcings, especially changes of atmospheric
aerosols, clouds, and land-use patterns, cause a negative forcing
that tends to offset greenhouse warming. 3) One consequence of
this partial balance is that the natural forcing due to solar
irradiance changes may play a larger role in long-term climate
change than inferred from comparison with greenhouse gases alone.
Current trends in greenhouse gas climate forcings are smaller
than in popular "business as usual" or 1 percent per year carbon
dioxide growth scenarios. The authors suggest that a summary
implication of their considerations is a paradigm change for
long-term climate projections: uncertainties in climate forcings
have supplanted global climate sensitivity as the predominant
issue. The authors further suggest that climate forcing scenarios
are essential for climate predictions, but if only one forcing
scenario is used in climate simulations, as has been a recent
tendency, the scenario itself is likely to be taken as a
prediction, as well as the calculated climate change. The authors
recommend that the use of multiple scenarios will aid objective
analysis of climate change as it unfolds in coming years.
-----------
J.E. Hansen et al (6 authors at National Aeronautics and Space
Administration, US)
Climate forcings in the Industrial era.
(Proc. Natl. Acad. Sci. US 27 Oct 98 95:12753)
QY: James E. Hansen [jhansen@giss.nasa.gov]
-----------
Text Notes:
... ... *chaotic fluctuations: The term "chaotic", in this
context, is specific. In the study of physical systems, the
term "chaotic behavior" has a specific meaning: the behavior of a
system is said to be "chaotic" if its final state is so sensitive
to the system's precise initial conditions that the behavior of
the system is in effect unpredictable and cannot be distinguished
from a random process, even though the behavior of the system is
strictly determinate in a mathematical sense. In other words, a
deterministic system characterized by extremely sensitive
instabilities, despite the system being determinate, can exhibit
behavior that is unpredictable, and the system is then called
"chaotic". During the past several decades, the analysis of such
chaotic systems has intrigued both physicists and mathematicians.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 4Dec98
For more information: http://scienceweek.com/swfr.htm

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3. MOLECULAR BIOLOGY: NATURAL HISTORY AND PROTEIN FOLDING
Although the term "evolution" is usually applied to the natural
history of entire organisms, another perspective is to consider
the evolution of biological molecules, particularly the protein
biomolecules. The proteins of an organism, the end products of
the working of genes, evolve just as genes evolve, and an
important question is how knowledge of the evolution of proteins
can be used to understand protein dynamics.
... ... Steven A. Benner (University of Florida, US) presents an
essay on the natural history of biomolecules, the author making
the following points concerning natural history and protein
folding:
     1) The author suggests that many chemical biologists and
biophysicists view the future of biology as a metamorphosis in
which understanding of biological phenomena will be replaced by
understanding of the interactions of their underlying
physicochemical components. This metamorphosis is already ongoing
and very productive, but it is unlikely to be the entire story.
The author suggests the surprise will come when biophysicists and
chemical biologists discover that they need to research the
history of biomolecules if they are to understand the physical
behaviors they are attempting to characterize.
     2) One example of the need for natural history is the
problem of protein folding. Physical chemists have mounted a
frontal assault on this problem, using computers to build
physical models of proteins in water, the models involving
guesses concerning many aspects of atomic interactions. The
assault has failed. The only way to make such a computation even
vaguely tractable requires considerable abstraction of the
physical model for the protein, and the same physical theory that
inspired the computation indicates that these abstractions must
compromise the value of the computation as a predictive tool.
     3) Natural history offers an entirely different approach to
protein folding. Divergent evolution creates families of proteins
that have descended from common ancestors. As proteins evolve
from these ancestors, natural selection requires them to remain
"fit". The principal prerequisite for fitness in a protein is a
particular folding of the protein, so proteins that diverge from
a common ancestor generally conserve their folds. This means that
during the evolution of protein sequences, mutations do not
accumulate as they would if proteins were formless and
functionless organic molecules. Instead, amino acids that are
important to the fold experience substitution differently from
those amino acids that are not important to the fold. A signal
should lie in the pattern of protein-sequence divergence -- the
difference between how proteins have divergently evolved in the
past, and they would have evolved had they been formless and
functionless molecules.
     4) At present, the *secondary and tertiary structure of
proteins can reliably be predicted by exploiting the historical
signal embedded in a set of protein sequences related by common
ancestry. Since 1990, approximately 30 protein folds have been
predicted using the history of protein families. In many cases,
the prediction provided information about the function as well as
about the form of the protein.
-----------
Steven A. Benner: Natural progression.
(Nature 25 Jan 01 409:459)
QY: Steven A. Benner: Dept. of Chemistry, Univ. of Florida, PO
Box 117200, Gainesville, FL 32611 (US).
-----------
Text Notes:
... ... *secondary and tertiary structure: In general, the
structures of biopolymers are denoted as follows: 1) Primary
structure: The sequence of subunits that comprise the
macromolecule (e.g., the amino acid sequence of a protein). 2)
Secondary structure: The localized arrangement in space of
regions of a biopolymer (e.g., the alpha-helix). 3) Tertiary
structure: The 3-dimensional configuration of a biopolymer. 4)
Quaternary structure: The 3-dimensional arrangement and
constitution of a multimeric macromolecule (i.e., a substance
containing more than one biopolymer; an entity consisting of
biopolymer subunits. (Also, see related background material
below.)
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 9Feb01
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
BIOCHEMISTRY: PHYSICAL BASIS FOR PROTEIN SECONDARY STRUCTURE
     The term "protein" was first used by the chemist Gerardus
Mulder (1802-1880) to denote the basic building block of the heat
coagulable (albuminous) material found in living systems, but it
was not until the 1920s that proteins were generally recognized
as a special type of macromolecule (a polypeptide) and studied as
polymers. Currently, biochemists and protein chemists distinguish
four orders of polymeric structure in proteins:
     1) The term "primary" structure refers to the linear
structure of the polypeptide as determined solely by the number,
sequence, and type of amino acid residues.
     2) The "secondary structure" of a protein is determined by
interactions between the sequential units, particularly hydrogen
bonding between particular amino acids and nonpolar interactions
between hydrophobic regions, the interactions producing, in
general, three local or global secondary structure variants:
alpha helix, beta sheet, and tight turn. An "alpha helix" is a
spiral configuration of a polypeptide chain in which successive
turns of the helix are held together by hydrogen bonds between
the amide (peptide) links, the carbonyl group of any given
residue being hydrogen-bonded to the imino group of the 3rd
residue behind it in the chain. The term "beta sheet" (beta-
pleated sheet) refers to an array of two or more "beta strands",
with each beta strand consisting of two polypeptide chains in a
so-called "beta configuration", which in turn is a stable
configuration of a polypeptide chain in which the chain is almost
fully extended and hydrogen-bonded to an adjacent polypeptide
chain. The third secondary structure variant, "tight turn" (beta
bend; beta turn) refers to a bending of a short stretch of
polypeptide chain that allows the main direction of the chain to
change. The turn consists of 4 amino acid residues in which the
CO group of residue n is hydrogen-bonded to the NH group of
residue n + 3.
     3) The "tertiary structure" of a polypeptide is a 3-
dimensional configuration, a folding or coiling of the molecule
primarily determined by interactions of hydrophobic regions and
to a lesser extent by hydrogen bonding.
     4) The "quaternary structure" of proteins is characterized
by the interaction of 2 or more individual polypeptides, often
via disulfide bonds, the result a larger functional molecule.
     Although given the above rough categorization of protein
structures, there are many aspects that might be of interest,
there are two salient generalizations concerning proteins which
command attention: a) when, as the result of the expression of a
gene, a specific protein is synthesized in a living system, that
protein rapidly assumes a configuration specific for its type;
and b) whatever it is that a specific protein does in a living
system, that action is dependent primarily and directly on its
configuration rather than on its specific amino acid sequence.
These two generalizations form the basis for much of the research
on protein structure, with two resultant questions: a) What rules
govern the rapid folding into a particular configuration by a
protein? and b) How is the particular configuration of a protein
related to its biochemical actions in the living system? The
first question is currently viewed as a problem in the physical
chemistry of macromolecules, and research on the question has
been heavily theoretical, with models based on a wide range of
quantitative techniques.
     The problem of protein folding is essentially as follows:
Given an ordinary polypeptide, the number of possible
configurations is astronomical. If a particular protein always
assumes the same configuration in a living system (its "native
configuration"), and if that configuration represents some sort
of energy minimum for the polypeptide chain, how does the protein
find that energy minimum within milliseconds? Does the protein
pass through every possible configuration state until the energy-
minimum configuration is "discovered"? Or are there constraints
that reduce the number of possible configurations to a much
smaller number? As easy as it is to state this problem, the
problem is a puzzle that has confounded researchers for 40 years.
... ... R. Srinivasan and G. Rose (Johns Hopkins University, US)
present a physical theory for protein secondary structure, the
authors making the following points:
     1) The authors propose a physical theory for secondary
protein structure based on steric and local interactions, and
suggest their finding demonstrate that local, intrinsic,
sequence-dependent biases toward helix, strand, and turn
configurations are densely dispersed throughout the polypeptide
chain and are unlikely to be merely accidental. The authors
report tests of the theory by *Monte Carlo simulations.
     2) The authors suggest that in essence, secondary structure
bias is largely a consequence of the balance between two opposing
local forces that govern the position of equilibrium between the
two mainchain states of contraction or extension. The competing
forces are attractive local interactions vs. sidechain
conformational restriction.
     3) The authors point out that C.B. Anfinsen (1973) proposed
that proteins attain their native state by folding to a global
minimum of *Gibbs free energy, and that this hypothesis has
usually been interpreted to mean that the native conformation of
individual molecules also corresponds to a global minimum in
internal energy because a fully folded protein will have lost its
*conformational entropy, or almost so. Thus, conformational
entropy is thought to play an insignificant role in the
thermodynamics of protein folding. Specifically, the statistical-
mechanical- (Boltzmann-) weighted populations of any two states
are thought to depend predominantly on their energy difference.
In contrast, the work of the authors suggests the conclusion that
conformational entropy is the main factor that discriminates
between two energetically equivalent (degenerate) ground states,
and in so doing "preorganizes" the protein.
     3) The authors point out that the problem of secondary
structure is intimately related to the Levinthal paradox [C.
Levinthal (1969)], which argues that a folding protein does not
"explore" conformational hyperspace freely; otherwise, the
protein would encounter an insoluble search problem. For
Levinthal, this insight was not a paradox at all, but a
convincing demonstration that some intrinsic constraint limits
the effective size of the conformational space. In this view,
proteins solve the "multiple-minimum problem" not by an extensive
search that identifies the deepest minimum, but by a limited
search that avoids false minima. The existence of intrinsic bias
resolves this paradox by prejudicing the ensemble of available
folding trajectories toward the native minimum. Thus, a folding
protein need not discriminate among an astronomical number of
conformations, because intrinsic bias "steers" the molecule
toward a high degree of preorganization. [*Note #1]
     4) In summary, the authors suggest their analysis has
demonstrated that pronounced biases toward protein secondary
structure are present in natural protein sequences, that these
biases have a discernible physical basis, and that their
existence suggests reinterpretations of current folding models.
-----------
R. Srinivasan and G. Rose: A physical basis for protein secondary
structure.
(Proc. Natl. Acad. Sci. US 7 Dec 99 96:14258)
QY: George D. Rose [rose@grserv.med.jhmi.edu]
-----------
Text Notes:
... ... *Monte Carlo simulations: In general, a "Monte Carlo
method" is any method for obtaining a statistical estimate of a
desired quantity by random sampling. In the most successful
applications, the desired quantity is a statistical parameter,
and the sampling is made from an artificial population that may
be a model of the physical system itself. The method is of
considerable utility in handling certain intractable applied
mathematical problems.
... ... *Gibbs free energy: (Gibbs function; thermodynamic
potential) A thermodynamic function of a system. In the present
context, if a system is considered at constant pressure and
temperature, and the only work done is that caused by changes in
volume, it can be shown that the system is in equilibrium when
the Gibbs free energy has a minimum value.
... ... *conformational entropy: In general, the entropy of a
system is a measure of the unavailability of its internal energy
to do work in a cyclic process. From the standpoint of
statistical mechanics, entropy is in general a measure of the
disorder of a system. The term "conformational entropy" refers to
that part of the total entropy of a system due to specific
orientations of atoms.
... ... *Note #1: In this paragraph, terms such as "hyperspace"
and "trajectory" derive from statistical mechanics and the
following considerations: If the state of a system depends upon N
variables, the state of the system can be viewed as a point
(phase point) in an N-dimensional space (phase space; system
hyperspace), and as the state of the system changes, its phase
point can be viewed as describing a trajectory in its phase
space. There are certain systems for which qualitative analysis
of the phase space trajectories of the system reveals significant
properties of the system otherwise difficult to delineate.
-------------------
Summary & Notes by SCIENCE-WEEK [http://scienceweek.com] 28Jan00
[For more information: http://scienceweek.com/search/search.htm]
-------------------
Related Background:
ON EXPLANATIONS OF PROTEIN FOLDING
Since the 3-dimensional configuration of a protein is an
essential determinant of what the protein does in a biological
system, protein "folding", the process that leads to this
configuration, is a central focus in biophysical chemistry.
... ... William A. Eaton (National Institutes of Health, US)
presents a review of current research in this field, the author
making the following points:
     1) There are two aspects to the problem of protein folding.
The first is predicting the 3-dimensional structure of a protein
from its amino acid sequence; the second is to understand _how_
proteins fold. The problem of protein folding has recently
assumed additional importance as more and more human diseases
(e.g., Alzheimer's and Parkinson's diseases) are believed to be
caused by aggregation of misfolded proteins.
     2) The question of _how_ a protein folds can be phrased more
precisely as follows: What are the sequences of structural
changes that occur in a polypeptide as it finds its way from the
myriad of possible structures in the *denatured state to the
final unique *native structure? How many different folding routes
exist, and what are their relative probabilities?
     3) Until approximately a decade ago, the problem of
understanding how proteins fold was addressed by identifying and
characterizing one or two metastable structures believed to be
obligatory intermediates in a sequential process along a well-
defined protein-folding pathway. The prevailing view was that
structural characterization of such intermediates would give the
clue to the basic underlying mechanism, as in the study of
organic chemical reactions. However, unlike small-molecule
chemical reactions, in which covalent bonds are broken and new
bonds formed in a structurally well-defined transition state, the
many degrees of freedom of a polypeptide chain demand a different
approach. A polypeptide of 100 amino acids has a huge number of
conformations, even if only a tiny fraction of the more than
2^(100) (= 10^(30)) possible conformations are thermally
occupied. Understanding the complexities of protein folding at
the microscopic level, and developing models that make
quantitative predictions, therefore requires a statistical
approach, i.e., the theoretical and computational tools of modern
statistical mechanics.
     4) Nonexponential kinetics have played an important role in
understanding conformational changes in native proteins. They are
particularly interesting for protein folding because they could
arise from a process that is "downhill" in free energy, i.e, one
in which the overall free energy barrier separating the native
from the denatured state is very small or nonexistent. For large
barriers, only the structures of the initial and final states are
observable, because structures along the folding route are too
sparsely populated. If, however, the barrier becomes very small
or disappears altogether, all of the structures can in principle
be detected and characterized by spectroscopy.
     5) At the present time, there exists the exciting prospect
of performing single molecule experiments for direct exploration
of the energy landscape and folding routes. Finding proteins that
fold with a "downhill scenario" is an essential first step in
this quest. That some proteins will exhibit downhill folding,
moreover, is one of the novel theoretical predictions of an
energy landscape analysis of protein folding.
-----------
Editor's note: In addition to the background material below, see
the 8 Aug 99 issue of SW (#32), report #3)
-----------
William A. Eaton: Searching for "downhill scenarios" in protein
folding.
(Proc. Natl. Acad. Sci. US 25 May 99 96:5897)
QY: William A. Eaton [eaton@helix.nih.gov]
-----------
Text Notes:
... ... *denatured state: In biochemistry, the term
"denaturation" refers to the complete unfolding
and loss of catalytic activity of a protein.
... ... *native structure: The "native" structure or
configuration of a biological macromolecule is the functional
state or configuration ordinarily assumed by the molecule in the
biological system in which the molecule occurs.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 3Sep99
For more information: http://scienceweek.com/swfr.htm

=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

4. HISTORY OF PHYSICS: WOLFGANG PAULI
     Consider an old black-and-white faded photograph: A soccer
ball is flying directly at the camera, almost arrived and large
in view, the soccer ball made fuzzy by its movement, and in the
background, obviously the kicker of the soccer ball, his kicking
foot still raised, is a rather pudgy middle-aged fellow in baggy
trousers, white shirt and tie, grinning with malicious delight at
his aimed kick (the ball actually slammed into the lens of the
expensive Speed Graphic camera), a pudgy fellow with a round face
who might be your uncle, the one who sells real estate, or the
local butcher who chuckles as he chops meat on the chopping
block. But a physiognomy is merely a mask, and the kicker of the
soccer ball, this grinning round-faced fellow facing you with his
foot raised and his back to the shore of Lake Lucerne
(Vierwaldstaetter See) in Switzerland in 1950, the kicker of the
ball is neither your uncle nor the local butcher, but one of
those ephemeral sparks of great genius thrown up by the grinding
gears of history -- the theoretical physicist Wolfgang Pauli
(1900-1958) [*Note #1]. 
     Wolfgang Pauli (Nobel Prize in Physics 1945) [*Note #2]
never published much, certainly not as much as his more
competitive contemporary physicists, but his influence on modern
physics was profound and enduring. He is most remembered for two
major contributions: the *exclusion principle and his prediction
of the existence of the *neutrino, but there were many other
contributions of lasting significance. Pauli exemplifies what
might be called "collegial science": his influence on his
contemporary physicists derived primarily from conversations and
letters.
... ... K. von Meyenn and E. Schucking (2 installations, DE US)
present a biographical essay on Wolfgang Pauli, the authors
making the following points:
     1) The authors point out that Pauli established himself in
the world of physics at the age of 20. When Pauli, 19 years old
and a student of Arnold Sommerfeld (1868-1951), was assigned the
task of writing a report on Einstein's special and general
theories of relativity, Pauli produced a 237 page monograph with
394 footnotes, a monograph soon published in the _Encyclopedia of
the Mathematical Sciences_, and later as a book. This monograph
is still considered one of the best treatments of the relativity
theories, and Albert Einstein (1879-1955), in a review of this
monograph in 1922, wrote as follows: "No one studying this
mature, grandly conceived work would believe that the author is
a man of twenty-one. One wonders what to admire most, the
psychological understanding for the development of the ideas, the
sureness of mathematical deduction, the profound physical
insight, the capacity for lucid, systematic presentation, the
knowledge of the literature, the complete treatment of the
subject matter, or the sureness of critical appraisal."
     2) Sommerfeld introduced Pauli (and Pauli's fellow student
Werner Heisenberg [1901-1976]) to quantum theory, and after the
publication of Pauli's review of relativity theory, Pauli's main
interest shifted to quantum physics. Pauli soon proposed the
atomic "*magneton" and named it after Niels Bohr (1885-1962).
Pauli worked on the *anomalous Zeeman effect and he discovered
nuclear magnetism. In 1925, before the formulations of the new
quantum mechanics by Heisenberg and Erwin Schroedinger (1887-
1961), Pauli proposed his famous exclusion principle, which
explained the structure of atoms in conformity with the periodic
table. By 1929, Pauli had become the world's foremost expert on
the *old Bohr-Sommerfeld quantum theory.
     3) Much of Pauli's influential work remains unpublished. His
proof of the equivalence of matrix and wave mechanics appears in
a letter to Pascual Jordan (1902-1980), and he wrote down the
uncertainty relation for time and energy in a letter to
Heisenberg. Pauli almost never cared about recognition for his
work, although he took great care in giving credit to other
authors. Unlike Heisenberg and many other physicists, Pauli was
not ambitious or competitive. His principle concern was always to
clarify the greater picture for himself, to obtain a consistent
and coherent description of the totality of the phenomena. In
this lifelong endeavor, he wrote thousands of letters analyzing
details and attempting to get things right, and in the 1920s,
Pauli's letters were passed around, copied, and studied by many
physicists. "His contribution of key ideas, and his trenchant
impartial analyses, should have earned him a place as co-author
of many papers on quantum mechanics. Instead, he insisted on the
idea that authorship was unimportant in this collective attempt
to decipher the book of nature."
     4) Pauli and Heisenberg was close friends. The authors (von
Meyenn and Schucking) state: "What clearly emerges from reading
the letters and papers from the incubation period of quantum
mechanics is that, among the score of people creating the new
picture of physics, two protagonists stand out, combining awesome
mathematical power with a global awareness of the experimental
data. These two [were] Pauli and Heisenberg... The main act in
the drama of the new physics is not, as Michael Frayn imagines in
his play _Copenhagen_, the discourse between Bohr and Heisenberg,
but rather the Heisenberg-Pauli dialogue. Bohr, the revered
father figure, no longer had the leading role he played before
1925."
     5) The authors state: "Perhaps we will never know the true
extent of Pauli's contribution to the creation of quantum
mechanics. From the crucial years 1925-1927, we have 34 letters
from Heisenberg to Pauli, but only three of the dozens that Pauli
wrote to Heisenberg have survived. The fate of the others is in
doubt. It was claimed they had been destroyed in a fire. But,
according to another version, they were taken from Heisenberg
when he was arrested by the British in 1945 at the end of the war
in Europe." [Editor's note: Pauli spent the war years in the US
at the Institute for Advanced Study Princeton, and he became a US
citizen in 1946. He later returned to his professorship at the
Federal Institute of Technology Zurich (CH).]
-----------
K. von Meyenn and E. Schucking: Wolfgang Pauli.
(Physics Today February 2001)
QY: Karl von Meyenn: Max Planck-Werner Heisenberg Institute of
Physics Munich, DE.
-----------
Text Notes:
... ... *Note #1: The described photograph can be found in a
remembrance essay by Roy Glauber (Harvard University, US)
(Physics Today February 2001, p.49). It was Roy Glauber who took
the photograph immediately before his camera was hit by the
soccer ball.
... ... *Note #2: There are in physics a Nobel Laureate Wolfgang
Pauli (1900-1958) and a Nobel Laureate Wolfgang Paul (1913-1993).
Wolfgang Paul developed the so-called "Paul trap" for confining
and studying electrons, and for this work he received the Nobel
Prize in Physics in 1989.
... ... *exclusion principle: According to the exclusion
principle as proposed by Pauli, no two electrons in the same
system can share the same quantum numbers, and therefore no two
electrons can share the same quantum state. It is this quantum
exclusion that requires the electrons in an atom to occupy
different energy levels, instead of all electrons congregating at
the lowest energy level. The exclusion principle was later
generalized to constrain "fermions": fermions (electrons,
protons, neutrons) are particles that obey the Pauli exclusion
principle: i.e., no two fermions of the same kind in a closed
system can occupy the same quantum state.
... ... *neutrino: Neutrinos are fundamental particles with zero
charge, possibly zero mass, and an angular momentum factor (spin)
of 1/2. Various natural processes produce neutrinos: stellar
nuclear reactions, reactions occurring during supernova
explosions, cosmic ray collisions with matter, etc. (See related
background material below.)
... ... *magneton: In general, the "magneton" is a unit for
measuring magnetic moments of nuclear, atomic, or molecular
magnets. The "Bohr magneton", introduced by Pauli, has the value
of the classical magnetic moment of an electron.
... ... *anomalous Zeeman effect: (anomalous Zeeman splitting)
The Zeeman effect involves the splitting of a spectral line due
to a magnetic field. Named after Peter Zeeman (1865-1943). In
general, the Zeeman effect occurs when atoms emit or absorb
radiation in the presence of a magnetic field: the field modifies
the energy configuration of the atom with the result that a
spectral line is split into components, with the spacing of the
components a measure of the magnetic field strength. When the
splitting is in accordance with classical theory, the effect is
called the "normal Zeeman effect" (as predicted by Hendrick
Lorentz [1853-1928]); when the splitting is complex, requiring
quantum theory for explanation, it is called the "anomalous
Zeeman effect".
... ... *old Bohr-Sommerfeld quantum theory: The Bohr model of
the atom, first proposed by Bohr in 1913, was the first atomic
model to involve quantum theory. The model essentially involved
the orbiting of electrons in discrete circular orbits around the
atomic nucleus, with a finite number of allowed energy and
occupancy states. The model had great success in predicting the
spectral lines of hydrogen. Sommerfeld, who encouraged Bohr in
his development of the model, introduced the possibility of
elliptical electron orbits. Bohr received the Nobel Prize in
Physics for his work in 1922. Within a few years, the Bohr-
Sommerfeld model of the atom was swept away by the new quantum
mechanics.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 9Feb01
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
HISTORY OF PHYSICS: THE NEUTRINO
     The history of particle physics during the first 30 years of
the 20th century is an excellent example of the intimate
interplay between theory and experiment. One of the central
problems in the physics of matter during this period was to
understand the emissions of radioactive substances first
discovered in 1896 by Henri Becquerel (1852-1908). Spontaneous
radioactive decay is essentially a spontaneous transmutation of
an unstable atomic nucleus (nuclide) A into nuclide B, with
nuclide A initially in a higher energy state and losing energy to
transmute into the "daughter" nuclide B. During the early years
of particle physics, the energy loss was considered to be
accomplished by emission of one of three types, depending on the
nature of nuclide A: positively charged alpha particles (helium
nuclei), negatively charged beta particles (electrons), or
neutral gamma rays (high energy electromagnetic radiation). Since
the energies of decaying nuclides and daughter nuclides are fixed
according to nuclide identity, one would expect the observed
energies of the 3 types of particles to also be fixed for each
species of decaying nuclide. During the period before 1927, this
was known to be true for alpha particles and gamma rays, but
there was intense controversy about whether it was true for beta
particles. Indeed, some early experiments indicated that it was
not true for beta particles, and this posed a problem, since
conservation laws require an accounting for all the energy and
the numbers for beta decay did not add up. The controversy
continued for nearly 30 years, particularly among
experimentalists who disagreed concerning experimental methods
and interpretations of experimental results, until finally in the
late 1920s it was conclusively demonstrated by experiment that
during the beta-decay process high-speed electrons of various
energies are emitted with a continuous beta-emission energy
distribution spectrum (i.e., a plot of the number of electrons
vs. energy of these electrons) over the range of energies.
     Given the experimental evidence of a continuous beta-decay
spectrum, theoreticians tackled the problem of accounting for
beta decay without violating conservation laws. In 1930, 
Wolfgang Pauli (1900-1958) proposed that when a beta particle was
emitted, another particle, without charge, and perhaps without
mass, was also emitted, and that this second particle carried off
the missing energy. Enrico Fermi (1901-1954) suggested the
particle carrying the missing energy be called "neutrino", which
is Italian for "little neutral one", and in 1934 Fermi
incorporated the neutrino into his theory of beta decay.
     Most theoretical and experimental physicists immediately
accepted the proposed existence of the neutrino as the best
solution to an important puzzle, but it was not until 1956 that
Frederick Reines (1918-1998) and Clyde Cowan (1919-1974) managed
to finally obtain experimental evidence for the existence of the
elusive neutrino by means of experiments involving emission beams
from a fission reactor. Enrico Fermi received the Nobel Prize in
Physics in 1938; Wolfgang Pauli received the Nobel Prize in
Physics in 1945; and Frederick Reines received the Nobel Prize in
Physics in 1995. (Clyde Cowan was not eligible for the Nobel
Prize at the time it was awarded to Reines, since the Nobel Prize
is not awarded posthumously.) 
... ... Allan Franklin (University of Colorado Boulder, US)
presents an essay on the history of beta decay and the neutrino
1900-1930. The author points out there were two major responses
to the establishment of the continuous energy spectrum of beta
decay. One idea, favored by Niels Bohr (1885-1962), was that
energy might not be conserved in beta decay. But work on the
*Compton effect provided evidence against this view. The second
major response was Pauli's "desperate way out", Pauli suggesting
that a very light, neutral particle was also emitted in the beta
decay. Pauli originally called this particle the "neutron", but
Fermi christened the particle the "neutrino" and quickly
incorporated the neutrino into a successful theory of beta decay.
During the next few decades, Fermi's theory was strongly
supported by experimental observations, and that success provided
most physicists with sufficient evidence for the existence of the
neutrino. As stated by Frederick Reines, for 26 years before the
existence of the neutrino was experimentally demonstrated, "the
[Fermi] theory was so attractive in its explanation of beta decay
that belief in the neutrino as a 'real' entity was general."
-----------
Editor's note: Although modern views of beta decay and the
neutrino (see related background material below) are more complex
than the views held in the early years of the 20th century, a
remarkable group of early experimental and theoretical particle
physicists (only some of whom are mentioned in this SW brief)
provided the foundation that still supports our understanding of
the atomic nucleus and radioactive decay.
-----------
Allan Franklin: The road to the neutrino.
(Physics Today February 2000)
QY: Allan Franklin, Univ. of Colorado Boulder 303-492-6694.
-----------
Text Notes:
... ... *Compton effect: (Compton scattering) In general, the
reduction in the energy of high energy photons when the photons
are scattered by free electrons, the electrons thereby gaining
energy, with total energy conserved. The effect was discovered in
1923 by A.H. Compton (1892-1962). Compton received the Nobel
Prize in Physics in 1927.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 5May00
For more information: http://scienceweek.com/swfr.htm

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5. INTERSCIENCE: CHAOS AND COMPLEXITY
     Ilya Prigogine (Free University Brussels, BE), who received
the Nobel Prize in Chemistry in 1977 for his work in
nonequilibrium thermodynamics, was among the first theoreticians
to deal with the applications of the second law of thermodynamics
to complex systems. The second law of thermodynamics effectively
holds that physical systems tend to slide spontaneously and
irreversibly toward a state of disorder (an increase of entropy).
There is no explanation in classical thermodynamics, however, of
how complex systems can arise spontaneously from less ordered
states and maintain themselves in apparent defiance of the
tendency toward entropy. Prigogine has proposed that as long as
systems receive energy and matter from an external source,
nonlinear systems ("dissipative structures") can pass through
periods of instability and then self-organization, resulting in
more complex systems whose characteristics cannot be predicted
except as statistical probabilities. The work of Prigogine has
been influential in a wide variety of fields, ranging from
physical chemistry to biology, and this work has been fundamental
in the new disciplines of chaos theory and complexity theory.
     What is called "complexity theory" is a theory that proposes
that certain systems manifest behaviors that are completely
inexplicable by any conventional analysis of the constituent
parts of the system. These behaviors, commonly called "emergent
behaviors", apparently occur in many complex systems involving
living organisms. One example is the idea that human
consciousness is an emergent property of a complex network of
neurons in the brain. The major problem of complexity theory is
how to model such emergent behavior: how to devise mathematical
laws that allow emergent behavior to be explained and predicted.
This effort to establish a solid theoretical foundation for the
description of complex systems has attracted mathematicians,
physicists, biologists, economists, and social scientists.
     In the research context, complexity and "chaotic behavior"
are not synonymous. If one focuses attention on the time
evolution of an emergent behavior, e.g., daily changes in
temperature, that behavior may well be completely deterministic
yet indistinguishable from a random process: the behavior is
chaotic. However, although chaos is often associated with complex
systems, not all complex systems manifest chaotic behavior. From
the standpoint of systems theory, it is the interactions of
components that create emergent patterns that are important, and
not any chaotic behavior these may patterns may display.
... ... Massimo Pigliucci (University of Tennessee Knoxville, US)
presents a review of current ideas in chaos and complexity
theory, the author making the following points:
     1) The author points out that in common non-scientific usage
the term "chaos" is a synonym for randomness, for completely non-
deterministic and irregular phenomena. In mathematical theory,
however, the term "chaos" refers to a deterministic (i.e., non-
random) phenomenon characterized by special properties that make
the predictability of outcomes very difficult: chaotic behavior
is such that although it does not occur randomly, it has the
appearance of a series of random occurrences.
     2) Chaotic dynamics are usually (but not always) a property
of nonlinear systems (i.e., systems whose behavior can be
described by sets of nonlinear equations). However, the converse
is not true: not all nonlinear dynamics generate chaotic
behavior. Typically, a given system of equations can produce both
non-chaotic and chaotic outcomes, depending on the range of
values assumed by the parameters of the equations. In many
systems, one can increase the value of a key parameter and obtain
a progression of outcomes from a steady equilibrium state to
regular oscillations with two equilibria, to more complex cycles
with multiple equilibria, to finally producing the chaotic
condition.
     3) Another phenomenon typically associated with chaos is the
so-called "butterfly effect": chaos is analogous to a situation
in which the flapping of a butterfly's wings in Brazil ends up
starting a cascade of events that results in a tornado in Texas.
The term for this is "sensitivity to initial conditions": a small
perturbation of a system can cause a series of effects that
eventually lead to macroscopic consequences later in the time
sequence. Had that perturbation been of a different nature, an
entirely different series of events would have occurred. a more
formal way to describe the butterfly effect is to state that the
predictability of the system decreases exponentially with time:
our predictions of where the system will be are relatively good
for the immediate future, but lose accuracy for slightly longer
intervals of time, and are soon completely useless.
     4) In general, a chaotic system is one whose mathematical
function is characterized by at least one of the following: a)
The system has sensitive dependence on initial conditions on its
domain; and/or b) the system has a positive *Lyapunov exponent at
each point in its domain that is not eventually periodic. A
"Lyapunov exponent" is a convenient measure of how fast the
trajectories of the system diverge in *phase space: if the
exponent is negative, the system actually converges at an
equilibrium point; if the exponent is near zero, the system
behaves with periodic regularity; if the exponent is positive,
the system is either chaotic or (for very large positive
exponents) random.
     5) Chaos theory is a component of a larger but more vague
theoretical framework called "complexity theory". Essentially,
complexity theory is an attempt to study systems that satisfy two
conditions: a) the system is made of many interacting parts; b)
the interactions result in emergent properties that are not
immediately reducible to a simple sum of the properties of the
individual components. In general, complexity theory uses
nonlinear dynamical modeling to account for the behavior of
orderly complex systems. The dynamics manifested by a given
system depend fundamentally on two parameters: the number of
parts (N) that compose the system, and the average number of
connections (K) among the parts within the system. So-called "NK"
systems then fall into 3 types, depending on the relationship
between N and K:
... ... a) K very small compared to N: Number of connections very
small compared to the total number of parts: Each part behaves
essentially independently of other parts, and the properties of
the system are the properties of the individual parts. Such
systems tend to be static or reach simple dynamic equilibria, and
are sometimes called "sub-critical".
... ... b) K increasing compared to N: The dynamics becomes more
complex and emergent properties appear: Local changes propagate
to distant parts of the system as a consequence of connectivity,
but this propagation usually does not cause global change, since
the ratio of K to N is still relatively small. Such systems are
called "edge of chaos" systems, or "critical systems".
... ... c) K approaches N: Most components of the system are
connected to almost every other component: This creates the
determinate but unstable "supercritical" systems described by
chaos theory.
     In terms of Lyapunov exponents: a) subcritical NK systems
have a negative Lyapunov exponent; b) critical NK systems have a
Lyapunov exponent near zero; c) chaotic NK systems are
characterized by a positive Lyapunov exponent.
     Most classical mathematics, physics, and biology deal with
subcritical systems; chaos theory and fractal geometry deal with
supercritical systems; complexity theory focuses on critical
systems and the transition between system types. Alleged examples
of critical systems (i.e., systems on the "edge of chaos")
include the evolution of natural populations, the developmental
biology of plants and animals, the stock market, the global
economy, and the dynamics of galaxy clusters.
-----------
Massimo Pigliucci: Chaos and complexity.
(Skeptic 2000 vol.8 No.3)
QY: Massimo Pigliucci: pigliucci@utk.edu
-----------
Text Notes:
... ... *Lyapunov exponent: See related background material
below.
... ... *phase space: See related background material below.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 9Feb01
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
THEORETICAL PHYSICS: CHAOS AND NONLINEAR DYNAMICS
     In general, a nonlinear dynamical system is a system
described by time-dependent differential equations such that the
rates of change of one or more dependent variables of the system
depend in a nonlinear fashion on the variables themselves.
Certain nonlinear dynamical systems, some of which are of great
scientific interest, exhibit "chaotic dynamics". In this context,
the term "chaos" refers to  unpredictable behavior arising in a
system that obeys deterministic laws but exhibits
unpredictability. The essential idea is that in certain systems
small perturbations may produce a cascade of larger
perturbations, so that eventually the behavior of such systems
cannot be predicted from prior states no matter if the systems
appear simple and obey deterministic laws. Examples of chaotic
nonlinear dynamical systems are the weather and populations of
organisms, and instances of chaotic dynamics have now been
documented in most scientific disciplines.
     Because the differential equations for many nonlinear
systems are often intractable (i.e., no explicit quantitative
solutions are possible), a focus of theoretical research on
nonlinear systems has been on analysis of the qualitative
behavior of such systems, in particular on analysis of the "phase
space" and "trajectories" in the phase spaces of such systems.
The idea is essentially as follows: If the state of a system
depends upon N variables, the instantaneous state of the system
can be viewed as a point (phase point) in an N-dimensional space
(phase space; system hyperspace), and as the state of the system
changes, its phase point can be viewed as describing a trajectory
in its phase space. Qualitative analysis of the possible families
of solutions of nonlinear differential equations can provide
information about such phase space trajectories, and there are
certain real systems for which qualitative analysis of the phase
space trajectories of the system has revealed significant
properties of the system otherwise difficult to delineate.
... ... J.P. Gollub and M.C. Cross (2 installations, US) present
a commentary on recent research on chaotic nonlinear dynamics,
the authors making the following points:
     1) The techniques of nonlinear dynamics are well-developed,
but the impact of this field has been largely confined to
phenomena in which there are only a few important time-dependent
quantities. Unfortunately, this excludes a vast range of
important problems in which the behavior of one point in space
can be quite different (though statistically similar) to that at
another location. A particular example is convective behavior.
     2) The traditional approach to studying nonlinear dynamical
behavior is to plot the dynamical variables of the system as a
multidimensional phase space graph indicating how the behavior
changes over time. For example, a simplified model of the Solar
System consisting of the Sun and 9 planets would require a phase
space with as many as 60 dimensions (3 position and 3 momentum
coordinates for each body). In the case of a convecting fluid, a
complete description of the flow pattern requires knowledge of
the velocity and temperature at a very large number of locations,
so the number of dimensions of the phase plot are enormous (from
thousands to millions, depending on the desired spatial
resolution). As a result, the methods of nonlinear dynamics are
cumbersome and progress has been slow, even though many
interesting examples of spatiotemporal chaos have been explored
both experimentally and numerically.
     3) Recent research (D.A. Egolf et al: Nature 404:733 2000)
involving numerical studies of an accepted model of thermal
convection indicates that the origin of unpredictable motion in
chaotic thermal convective systems, at least in one particular
form of spatiotemporal chaos, lies in what occurs in small
regions of space and over short time-scales. These local changes
in the organization of the flow affect the surrounding regions in
such a way that the entire future evolution is affected. The
authors state: "This is something akin to Ed Lorenz's famous
remark [E.N. Lorenz: J. Atmos. Sci. 20:130 1963] that the
localized flapping of a butterfly's wings might change the
weather dramatically over the entire world a few weeks later."
Although such sensitivity to localized fluctuations has never
been confirmed as the source of the unpredictability of the
weather, it is apparently the origin of chaotic dynamics in
thermal convection.
     4) The authors conclude: "The methods used by Egolf et al
should apply to many other forms of chaos in spatially extended
systems (physical, chemical, and biological) for which reliable
model equations are available, so that the key processes leading
to the complex dynamics can be identified. Applications to areas
as diverse as cardiology and atmospheric dynamics might be
expected eventually. Moreover, it is not unreasonable to imagine
that insight into the processes leading to unpredictability will
also lead to progress in modifying or controlling the dynamics of
these systems."
-----------
J.P. Gollub and M.C. Cross: Chaos in space and time.
(Nature 13 Apr 00 404:710)
QY: J.P. Gollub: jgollub@haverford.edu
-------------------
Summary by SCIENCE-WEEK http://scienceweek.com 23Jun00
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
EXPERIMENTAL EVIDENCE FOR MICROSCOPIC CHAOS
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.
In general, in the study of physical systems, the term "phase
space" refers to a multidimensional space, each point of which
(phase point) completely represents the state of the system. For
example, in the study of dynamical systems, each phase point in
the phase space completely represents the values of all the
generalized coordinates and corresponding momenta. As the phase
point of a system moves in the phase space (e.g., changes with
time), the phase point follows a trajectory in the phase space,
and this trajectory is called the "phase point trajectory". In
the mathematical analysis of a particular phase space and its
phase point trajectories, "*Lyapunov exponents" are coefficients
that describe the rates at which nearby phase point trajectories
converge or diverge, and the Lyapunov exponents can be shown to
provide estimates of how long the behavior of a dynamical system
is predictable before chaotic behavior sets in. Chaotic behavior
of a system is characterized by the existence of positive
Lyapunov exponents. ... ... Gaspard et al present the results of
an experimental study of "microscopic chaos". The authors point
out that many macroscopic dynamical phenomena, for example in
hydrodynamics and oscillatory chemical reactions, have been
observed to display erratic or random time evolution, despite the
deterministic character of their dynamics -- a phenomenon known
as "macroscopic chaos". On the other hand, it has been long
supposed that the existence of chaotic behavior in the
microscopic motions of atoms and molecules in fluids or solids is
responsible for their equilibrium  and non-equilibrium
properties. But, the authors state, this hypothesis of
microscopic chaos has never been verified experimentally. The
authors now report direct experimental evidence for microscopic
chaos in fluid systems, the study involving the *observation of
brownian motion of a colloidal particle suspended in water. The
authors report finding a positive lower bound on the sum of
positive Lyapunov exponents of the system composed of the
brownian particle and the surrounding fluid. They suggest their
results and quantitative analysis provide strong experimental
evidence for microscopic chaos. They conclude: "On the assumption
that the system is deterministic, and given our knowledge of the
molecular structure of the fluid, this evidence supports, in
particular, the hypothesis that large systems -- which may be
treated by statistical mechanics -- are typically chaotic. The
result also supports the role of dynamical instability in non-
equilibrium fluids."
-----------
P. Gaspard et al (7 authors at 3 installations, BE US):
Experimental evidence for microscopic chaos.
(Nature 27 Aug 98 394:865)
QY: P. Gaspard: gaspard@ulb.ac.be
-----------
Text Notes:
... ... *Lyapunov: A.M. Lyapunov (1857-1918) developed a general
theory of dynamic stability applicable to both linear and
nonlinear systems. His work was largely buried and forgotten
until it was exhumed nearly 30 years after his death.
... ... *observation of brownian motion: The experiment here
involved a colloidal particle of 2.5 microns diameter moving in
suspension in deionized water at 22 degrees Celsius, with
recorded observations of 145,612 positions over a total time
interval of approximately 2430 seconds, the observations
involving a microscope and video camera, the smallest resolution
stated as 25 nanometers. Particles of this size undergo
sedimentation, which may confound the results with non-Brownian
effects, but the authors report studies of non-sedimenting
smaller particles substantiate their observations, the larger
particle simply allowing tracking observations for a longer time.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 18Sep98
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
ON CHAOS THEORY AND THE STABILITY OF OUR SOLAR SYSTEM
Ordinarily, a physical system is a system in which future states
can be predicted from prior states. But not all physical systems
exhibit such predictability. The term "chaos theory" refers to a
theory of unpredictable behavior arising in a system that obeys
deterministic laws but exhibits unpredictability. The essential
idea is that in certain systems small perturbations may produce a
cascade of larger perturbations, so that eventually the behavior
of such systems cannot be predicted from prior states no matter
if the systems appear simple and obey deterministic laws.
... ... Adam Frank (University of Rochester, US) reviews
considerations of our solar system in terms of chaos theory. The
solar system may have lost several planets, and Mercury or Mars
might be the next planets to be ejected from their orbits.
Mercury has a small but finite chance of being ejected after a
close encounter with Venus. The essential idea is that due to the
gravitational influence of the other planets, the orbit of a
planet may become more and more eccentric over time, finally
cross the orbit of another planet, with the less massive planet
ejected from the solar system. There is a slight possibility that
the orbit of Mars will someday cross the orbit of Earth, with
Mars ejected from the solar system because of its lower mass. The
author suggests that under the influence of chaos theory our
understanding of planetary motion has been considerably trans-
formed, and the solar system is no longer viewed as a stable
clock, but rather as a dynamic and infinitely complex entity.
QY: Adam Frank, Univ. of Rochester, Dept. of Physics 716-275-4356
(Astronomy May 1998)
-------------------
Summary by SCIENCE-WEEK http://scienceweek.com 10Apr98
For more information: http://scienceweek.com/swfr.htm

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6. PHYSICAL CHEMISTRY: ON THE STRUCTURE OF WATER
     Water is the most abundant compound on the surface of the
Earth and the principle constituent of all living organisms. The
oceans alone contain 1.4 x 10^(24) grams, or approximately 3.2 x
10^(7) cubic miles of water. Another 0.8 x 10^(24) grams of water
is held within the rocks of the Earth's crust in the form of
water of hydration. The human body is approximately 65 percent
water by weight, with some tissues (e.g., brain and lung)
composed of nearly 80 percent water.
     The experiments of Henry Cavendish (1731-1810) and Antoine
Lavoisier (1743-1794) in the 1780s established that water is
composed of hydrogen and oxygen. Although the careful data of
Cavendish was sufficient to prove that two volumes of hydrogen
combine with one volume of oxygen, he did not point this out, and
it was left to Joseph-Louis Gay-Lussac (1778-1850) and Friedrich
Humboldt (1769-1859) to make this discovery in 1805. In 1842,
Jean Dumas (1800-1884) found that the ratio of the combining
weights of hydrogen and oxygen in water is very nearly 2 to 16.
     Although water is the most familiar of liquids, it is also a
liquid of peculiar properties. Perhaps the best-known peculiarity
of water is its density maximum at 4 degrees centigrade (at
atmospheric pressure); cooling or heating water from this
temperature reduces its density. An equally striking anomaly is
that as the density of water is increased, water molecules
diffuse more rapidly, but only up to a point known as the
"diffusivity maximum". At higher densities, the diffusivity
decreases with increasing density, similar to what is observed
with normal liquids.
... ... J.R. Errington and P.G. Debenedetti (Princeton
University, US) present a report on the relationship between the
structure of liquid water and its anomalies, the authors making
the following points:
     1) The authors point out that in contrast to crystalline
solids, for which a precise framework exists for describing
structure, quantifying structural order in liquids and *glasses
has proved more difficult because even though such systems
possess *short-range order, they lack *long-range crystalline
order. Some progress has been made using model systems of hard
spheres, but it remains difficult to describe accurately liquids
such as water, where directional attractions (hydrogen bonds)
combine with short-range repulsions to determine the relative
orientation of neighboring molecules as well as their
instantaneous separation. This difficulty is particularly
relevant when discussing the anomalous kinetic and thermodynamic
properties of water, which have long been interpreted
qualitatively in terms of underlying structural causes.
     2) The authors introduce two measures of order in water: a)
the "translational order parameter" measures the tendency of
pairs of molecules to adopt preferential separations; this
parameter vanishes for an ideal gas, and is large for a crystal.
b) the "orientational order parameter" measures the extent to
which a molecule and its four nearest neighbors adopt a
tetrahedral arrangement, such as exists in hexagonal ice; this
parameter vanishes for an ideal gas, and equals 1 in a perfectly
tetrahedral arrangement.
     3) The authors report they have attempted to gain a
quantitative understanding of the structure-property
relationships of water through the study of translational and
orientational order in a model of water. Using *molecular
dynamics simulations, they identify a structurally anomalous
region -- bounded by loci of maximum orientational order (at low
densities) and minimum translational order (at high densities) --
in which order decreases on compression, and where orientational
and translational order are strongly coupled. This region
encloses the entire range of temperature and densities for which
the anomalous diffusivity and thermal expansion coefficient of
water are observed, and enables a quantification of the degree of
structural order required for these anomalies to occur. The
authors also find that these structural, kinetic, and
thermodynamic anomalies constitute a cascade: they occur
consecutively as the degree of order is increased.
     4) The authors summarize: "The physical picture that emerges
from this work is the following: In liquid water there occurs a
cascade of anomalies. Structural anomalies, whereby order
decreases upon compression, occur over the broadest range of
densities and temperatures. Diffusive anomalies, whereby the
diffusion coefficient of water increases by compression, occur
entirely inside the region of structural anomalies. Thermodynamic
anomalies, whereby the density decreases upon cooling at constant
pressure, occur entirely inside the region of diffusive
anomalies. All anomalous states share the topological property
that orientational and translational order are strongly coupled."
... ... In a commentary on this work, Srikanth Sastry (Jawaharlal
Nehru Center for Advanced Scientific Research Bangalore, IN)
states: "Errington and Debenedetti's observations raise
interesting questions and open a new line of investigation. The
characterization of structural anomaly in terms of the strong
coupling between translational order and orientational order may
help to identify precise conditions necessary for anomalous
behavior. But at present it isn't clear why this observed
relationship and the nested pattern of structural, dynamic, and
thermodynamic anomalies hold, and whether we should expect to
find them in other liquids as well."
-----------
J.R. Errington and P.G. Debenedetti: Relationships between
structural order and the anomalies of liquid water.
(Nature 18 Jan 01 409:318)
QY: Pablo G. Debenedetti: pdebene@princeton.edu
-----------
Srikanth Sastry: Order and oddities.
(Nature 18 Jan 01 409:300)
QY: Srikanth Sastry: sastry@jncasr.ac.in
-----------
Text Notes:
... ... *glasses: In this context, the term "glass" refers to an
amorphous solid whose atoms form a random network.
... ... *short-range order: A solid is crystalline if it has
long-range order: once the positions of an atom and its neighbors
are known at one point, the place of each atom is known precisely
throughout the crystal. Most liquids lack long-range order,
although many liquids have short-range order. In this context,
"short range" is defined as the first- or second-nearest
neighbors of a water molecule. However, at distances many
molecules away, the positions of the molecules become
uncorrelated. Fluids such as water have short-range order but
lack long-range order.
... ... *long-range crystalline order: See previous note.
... ... *molecular dynamics simulations: This study was based on
constant temperature and density molecular dynamics simulations
of 256 interacting particles.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 9Feb01
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
ON WATER AND THE STRUCTURES OF BIOLOGICAL MOLECULES
A prominent consideration in the minds of biologists who work at
the level of cells and molecules is that water is the most
prevalent chemical substance in all biological systems, and that
interactions of water with other biological molecules,
particularly with biological macromolecules, are not clearly
understood but are probably of considerable significance.
... ... M. Gerstein and M. Levitt present a review of some
aspects of the physical chemistry of water and an account of
their own computer simulations of biological macromolecules in
aqueous solutions. The authors make the following points: 1) At
the present time it is possible to model proteins and their
associated water molecules on a desktop computer in a few days.
Researchers have now simulated the aqueous structures of more
than 50 proteins and nucleic acids. 2) A single water molecule
has an essentially tetrahedral geometry, with an oxygen atom at
the center of the tetrahedron, hydrogen atoms at 2 of the 4
corners, and clouds of negative charges at the other 2 corners.
Reflecting the tetrahedral geometry of water, each molecule in
liquid water often forms 4 hydrogen bonds: 2 hydrogen bonds
between its hydrogens and the oxygen atoms of 2 other water
molecules, and 2 hydrogen bonds between its oxygen atom and the
hydrogens of other water molecules. The necessity of maintaining
a tetrahedral hydrogen-bonded structure gives water an "open"
loosely packed structure compared with that of most other liquids
[*Note #1]. 3) Present computer simulations are able to reproduce
quantitatively many of the bulk properties of water, such as its
average structure, rate of diffusion, and *heat of vaporization.
4) Biological molecules such as proteins and DNA contain both
hydrophilic and hydrophobic parts arranged in long chains. The 3-
dimensional structures of these molecules are determined by the
way these chains fold into more compact arrangements in which
hydrophilic groups are on the surface where they can interact
with water and hydrophobic groups are buried in the interior away
from water. These local macromolecule solubility considerations
were formulated in 1959 by Walter Kauzman as a "hydrophobic
effect" crucial for protein folding. 4) There are 3 types of
water molecules that must be considered in a computer model of a
biological molecule in aqueous solution: a) the ordered water
surrounding and strongly interacting with the macromolecule; b)
the bulk water beyond the ordered water; and, c) any water
molecules that may be buried within the macromolecule. 5)
Computer simulations of DNA in water have revealed that water
molecules are able to interact with nearly every part of the
double helix of DNA, including the nucleotide base pairs that
constitute the genetic code. In contrast, water is not able to
penetrate deeply into the structure of proteins, whose
hydrophobic regions are arranged on the inside into a close-
fitting core [*Note #2].
-----------
M. Gerstein and M. Levitt (2 installations, US)
Simulating water and the molecules of life.
(Scientific American November 1998)
QY: Mark Gerstein, Yale University, 203-432-4771.
-----------
Text Notes:
... ... *Note #1: In hydrated crystal structures, water molecules
generally donate two hydrogen bonds but may accept either one or
two. When water molecules are 3-coordinated (rather than 4-
coordinated as discussed by the authors in their review), the
geometry can be planar or pyramidal. But examples are known of
coordination as low as 2 and as large as 7.
... ... *heat of vaporization: The quantity of energy required to
evaporate 1 mole (or a unit mass) of a liquid at constant
pressure and temperature.
... ... *Note #2: Concerning the interaction of water molecules
with biological molecules, water molecules hydrogen-bonded to the
functional groups of biological molecules are apparently linked
in chains into extended networks, and some researchers have
suggested the *polarizability of these networks provides a 
mechanism for long-range recognition between biological molecules
in aqueous solution.
... ... *polarizability: The electric dipole moment induced in a
system (such as an atom or molecule) by an electric field of unit
strength.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 13Nov98
For more information: http://scienceweek.com/swfr.htm

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7. IN FOCUS: ON THE INTERACTION OF LIGHT AND MATTER
"The principle governing the interaction of light and matter may
be stated in simple terms: matter interferes with radiation when
the atomic or sub-atomic dimensions (such as the distance between
the atoms in a crystal, or the wavelength characterizing the
motion of an extra-nuclear electron) are commensurate with the
wavelength of the incident radiation. We may compare the surface
of a crystalline solid to a series of turnstiles, spaced at equal
distances, and leading, let us say, from one enclosure to
another. The incident light may be compared to an orderly army
advancing towards them. If the soldiers were Lilliputians, they
would pass through the turnstiles without turning them, or
affecting them in any other way; if they were giants, they would
pass over and ignore them. But if the advancing host consisted of
human beings, for the hindrance of whom the gates were erected,
there would clearly be interference with their march at the
boundary; some would be let through, some would not, while others
would come out having turned round once inside the revolving
gates. The gamma-rays emitted by radioactive elements will pass
through several centimeters of lead; and cosmic rays, which have
even shorter wavelengths (possibly of a different kind), will
penetrate the Earth to depths of hundreds of feet. Wireless
waves, which are of great length, ignore material interference,
unless provoked. We owe to [Max] von Laue [1879-1960] the
suggestion that x-rays have a wavelength of the same order of
magnitude as the distance between atoms in crystals, and the
first demonstration that this distance can be calculated from the
interference produced."
-----------
E.A. Moelwyn-Hughes: _Physical Chemistry_ (2nd edition)
(Pergamon Press, 1961, p.18)
-----------
[Editor's note: Max von Laue (1879-1960), who essentially founded
x-ray crystallography, first studied the interaction of x-rays
and crystals in order to establish the wavelengths of x-rays.
There were no techniques available to manufacture the fine
grating required for such a measurement, and Laue hit on the idea
of using a crystal of zinc sulfide as a grating. He was awarded
the Nobel Prize in Physics in 1914 for his work on x-ray
diffraction in crystals. Subsequently, by using x-rays of known
wavelength, it became possible to study the atomic structure of
various crystals, including polymers, where such structure was
unknown. The metaphor used by Moelwyn-Hughes in his classic text,
the image of an advancing army, is apt: Max von Laue was the son
of an army official and spent his youth moving from one army post
to another. Laue obtained his PhD in theoretical physics in 1903.
Between 1905 and 1909, Laue worked as assistant to Max Planck
(1858-1947), and they evidently established a close friendship.]
-------------------
SCIENCE-WEEK http://scienceweek.com 9Feb01
For more information: http://scienceweek.com/swfr.htm

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8. FROM THE SCIENCEWEEK ARCHIVE:
ANTHROPOLOGY: DEFINING THE HUMAN GENUS
Taxonomy is the field in biology devoted to the classification of
living organisms, and the term "taxon" is used to indicate the
members of any particular group in the classification scheme:
class, family, genus, etc [*Note #1]. The general problem is how
to incorporate information about evolutionary history and
adaptation into taxonomic classification schemes, with the
problem exemplified by attempts to define our own genus, Homo.
The definition of the genus Homo has always been somewhat
contentious, not least because it is tied, implicitly or
explicitly, to the state of "being human". A series of anatomical
characteristics is found to be apparently unique in Homo -- for
example, an increase in cranial vault height and cranial
thickness, reduced lower facial prognathism (i.e., reduced
projection of the jaw), and in dentition reduction in the size of
the premolars and molars and the length of the molar row -- but
what has always been emphasized by taxonomic definitions is the
size of the Homo brain as revealed by the size of the cranium.
According to the classical scheme, to be Homo is to be a large-
brained *hominine (the apparent human-related fossil group), a
hominine presumably more technologically accomplished than the
ancestor group, the *Australopithecines. At the present time, as
is evident in this report, the taxonomic categorizations related
to the human genus are far from fixed. ... ... B. Wood and M.
Collard (2 installations, US UK) present an extensive review of
the taxonomic situation concerning the genus Homo, the authors
making the following points:
     1) The authors suggest that recent data, fresh
interpretations of the existing evidence, and the limitations of
the paleoanthropological record invalidate existing criteria for
allocating fossil species to Homo.
     2) The authors suggest that regardless of any formal
definitions, in current practice fossil hominin species are
assigned to Homo on the basis of one or more out of 4 criteria:
a) absolute brain size at least 600 cubic centimeters; b)
possession of language as inferred from *endocranial casts; c)
possession of a modern human-like precision grip involving a
well-developed and opposable thumb (pollex); d) the ability to
manufacture stone tools. The authors state: "It is now evident,
however, that none of these criteria is satisfactory."
     3) The authors present a revised definition for the genus
Homo based on criteria considered verifiable and conclude that
two species, *Homo habilis and *Homo rudolfensis, do not belong
in the genus. The authors suggest the earliest taxon to satisfy
the criteria is *Homo ergaster, or early African *Homo erectus,
which currently appears in the fossil record at about 1.9 million
years ago.
     4) The authors suggest that a fossil species should be
included in Homo only if the following can be demonstrated:
... ... a) the species is more closely related to H. sapiens than
it is to the australopiths;
... ... b) the species has an estimated body mass more similar to
that of H. sapiens than to that of the australopiths;
... ... c) the species has reconstructed body proportions that
match those of H. sapiens more closely than those of the
australopiths;
... ... d) the species has a *postcranial skeleton whose
functional morphology is consistent with modern human-like
obligate bipedalism and limited facility for climbing;
... ... e) the species is equipped with teeth and jaws that are
more similar in terms of relative size to those of modern humans
than to those of the australopiths;
... ... f) the species shows evidence for a modern human-like
extended period of childhood growth and development.
     5) The authors conclude by suggesting that the adoption of
the above criteria would mean the genus Homo would have both
phylogenetic and adaptive significance. "Researchers can then
explore whether this adaptive shift in hominin evolution
corresponds with changes in climate, analogous evolutionary
changes in other large mammal groups, particular innovations in
the hominin cultural record, substantial expansions in geographic
range, or changes in ecological tolerance as reflected in
reconstructions of hominin habitats."
-----------
B. Wood and M. Collard: The human genus.
(Science 2 Apr 99 284:65)
QY: Bernard Wood [bwood@gwu.edu]
-----------
Text Notes:
... ... *Note #1: The conventional hierarchy of classification in
biology is Kingdom, Phylum, Class, Order, Family, Genus, and
Species. In the literature, organisms are usually referred to by
genus and species in binomial nomenclature, with the genus
capitalized. Human beings are genus Homo, species sapiens,
binomially Homo sapiens. The convention in binomial nomenclature
is to initialize the genus; thus: H. sapiens.
... ... *hominine: The terms hominine, hominin, hominoid,
hominid, are not interchangeable, but their classification
criteria are variously in a state of flux. In general, the
hominoids are a primate superfamily, the hominid family comprises
the great apes within the hominoid superfamily, the hominini are
a "tribe" within the hominids characterized by a number of
features including bipedalism, and the hominini are further
partitioned into the genera Homo and Australopithecus. Concerning
research in human evolution, most paleoanthropologists agree that
what is important is to achieve an understanding of the
evolutionary transitions and transformations, and any
classification scheme must be secondary to this objective. In
other words, in this context, classification must ultimately
reflect phylogeny (the actual evolutionary relationships), and as
knowledge of phylogeny changes, so must the extant classification
schemes.
... ... *Australopithecines: Members of the now extinct genus
Australopithecus, believed to exist between 4.4 and 1 million
years ago, and believed to be precursors of the genus Homo. All
australopithecines are apparently characterized by an ape-like
form, rather than the human-like form of the Homo genus.
... ... *endocranial casts: In general, an "endocast" (steinkern)
is any fossil formed after dissolution of an interior molding
substance. An "endocranial cast" is an endocast involving the
cranium. The interior of the endocast can often reveal details
concerning the absent soft interior substance (in this case, the
brain).
... ... *Homo habilis: In 1964, an early fossil hominin (1.9 to
1.6 million years before the present) was found in Olduvai,
Tanzania, the brain apparently intermediate in size between the
earliest known Homo fossil *Homo erectus and the Australopithecus
group. This new fossil was denoted as a new species by its
discoverers and named Homo habilis. The original set of H.
habilis fossils included a relatively complete hand, its
structure apparently compatible with an ability to make and use
tools. (Homo habilis literally means "handy-man") Considerable
controversy in the paleoanthropology community concerning H.
habilis has continued from 1964 until the present.
... ... *Homo rudolfensis: The original H. habilis species has
more recently been divided into H. habilis and H. rudolfensis,
after a fossil of the latter group was discovered in 1993 and
related to an earlier find in 1967, both dating at approximately
2.4 million years ago. One view is that Homo habilis/rudolfensis
evolved in Africa approximately 2 million years ago and quickly
expanded into Asia to become *Homo erectus/ergaster.
... ... *Homo ergaster: H. ergaster and *H. erectus are the two
immediate precursors of H. sapiens, with H. ergaster believed to
have originated in Africa and to have given rise to H. erectus in
Asia. But as with other hominid fossil groups, precise
evolutionary sequences and geographical loci continue to be
debated.
... ... *Homo erectus: First discovered by Eugene Dubois in 1891
in Indonesia, this fossil group is currently viewed as the
closest precursor to H. sapiens. Formerly called "Anthropithecus
erectus" and "Pithecanthropus erectus". Pithecanthropus erectus
and Sinanthropus erectus ("Peking man", discovered in 1927) were
in 1951 subsumed under the single category Homo erectus, which
was then recognized as a widespread species exhibiting
significant geographical variation.
... ... *postcranial skeleton: In general, this refers to the
skeleton behind the cranium in a quadruped and below the cranium
in a biped.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 9Jul99
For more information: http://scienceweek.com/swfr.htm


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