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ScienceWeek
SCIENCE-WEEK
A Weekly Email Digest of the News of Science
A journal devoted to the improvement of communication
between the scientific disciplines, and between scientists,
science educators, and science policy-makers.
July 13, 2001 -- Vol. 5 Number 28
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What does it matter to Science if her passionate servants
are rich or poor, happy or unhappy, healthy or ill? She
knows that they have been created to seek and to discover,
and that they will seek and find until their strength dries
up at its source. It is not in a scientist's power to
struggle against his vocation: even on his days of disgust
or rebellion his steps lead him inevitably back to his
laboratory apparatus.
-- Eve Curie (1904-?)
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Section 1
=-=-=-=-=-=-=-=-=
Contents of this Issue (Full reports in Section 2):
1. IN BRIEF:
Xenotransplantation now in clinical trials... Centrosomes and
mitosis... Chelation therapy and children exposed to lead... A
new apoptosis pathway... Quasi-particles and the many-body
problem... Metallic oxygen... Evidence for accelerating cosmic
expansion... A large Kuiper-belt object.
2. PALEOANTHROPOLOGY:
AN APPARENT NEW DIRECT HUMAN ANCESTOR FOSSIL
A fossil recently discovered in the Lukeino Formation of the
Tugen Hills in Kenya, the fossil named Orrorin tugenensis, has
been proposed by its discoverers as another genus of hominin and
a direct ancestor of the Homo group, but classification and
interpretation of this fossil is in dispute.
3. MEDICAL BIOLOGY: ON AMYOTROPHIC LATERAL SCLEROSIS
Amyotrophic lateral sclerosis (ALS) is a disease that affects
only motorneurons in the central nervous system. Genetic analysis
has identified a primary cause of ALS in familial cases:
mutations in a single gene can initiate a process that leads to
the selective degeneration of motorneurons. The clinical and
pathological similarities of familial and sporadic ALS suggest a
common pathogenesis.
4. EARTH SCIENCES: CARBON DIOXIDE AND CLIMATE CHANGE
Although some contradictory data exist, the first order agreement
between the carbon dioxide record and continental glaciation
continues to support the conclusion that carbon dioxide has
played an important role in long-term climate change, and it may
be hazardous to infer that existing discrepancies between models
and data cloud interpretations of future anthropogenic greenhouse
gas projections.
5. PHYSICAL CHEMISTRY: A NEW MODEL OF LIQUID WATER
Coherent patterns in bulk water should be perturbed by the
presence of solute molecules and give rise to characteristic
structures around solute molecules. A new model demonstrates that
such coherent patterns indeed exist and that the structural
ordering provides a perspective for the understanding of
hydration of biomolecules.
6. CHEMISTRY: ON THE SHAPES OF MOLECULES
Molecular orbital calculations indicate that the staggered
conformation of ethane is the result of preferential
stabilization through hyperconjugation. This result contrasts
sharply with the stock explanation presented in almost every
textbook of organic chemistry.
7. IN FOCUS: ON GENES AND NEUROBIOLOGY
It is hard to predict the consequences of the revolution in
genetic techniques for understanding brain function. For example,
although the altered sequences of the Huntington's disease gene
were identified long ago, the function of the protein remains
unknown.
8. FROM THE SCIENCEWEEK ARCHIVE:
ON STATISTICAL PHYSICS AND ITS APPLICATIONS
Statistical physics, and more specifically the theory of
transitions between states of matter, more or less defines what
we know about everyday matter and its transformations.
=-=-=-=-=-=-=-=-=
Section 2
=-=-=-=-=-=-=-=-=
1. IN BRIEF:
... ... XENOTRANSPLANTATION NOW IN CLINICAL TRIALS:
Xenotransplantation is the transplantation of whole or part
organs to humans from other species. The growing disparity
between the number of people who need organ transplants and the
number of available transplantable human organs has made
xenotransplantation an important alternative. Xenotransplantation
products developed from living cells of nonhuman animals are
currently under investigation in clinical trials and active
preclinical studies. The major challenges are to overcome
immunological barriers and prevent transmission of infectious
agents. (J. Amer. Med. Assoc. 2001 285:2304)
... ... CENTROSOMES AND MITOSIS: Successful mitosis is the
generation of two identical daughter cells, which requires the
assembly of a strictly bipolar mitotic apparatus that will ensure
that all daughter chromosomes are segregated to opposite sides of
the cell before completion of mitosis. In higher animal cells,
the agent responsible for this segregation is the pair of
centrosomes that organize the spindle poles during mitosis.
Despite the significant advances that have been made recently in
understanding the control mechanisms governing the centrosomes,
it is becoming evident that the controls for centrosome
duplication are more complex than was expected, and there is not
yet a coherent picture of the process.
(Genes & Development 2001 15:1167)
... ... CHELATION THERAPY AND CHILDREN EXPOSED TO LEAD: Thousands
of children in the US, especially poor children living in
deteriorated urban housing, are exposed to enough lead to produce
neurodevelopmental damage and cognitive impairment. Blood lead
levels as low as 10 micrograms per deciliter are associated with
cognitive deficits. A new study demonstrates that treatment with
succimer, a lead chelator, lowers blood lead levels but does not
improve scores on tests of cognition, behavior, or
neuropsychological function in children with blood lead levels 20
to 44 micrograms per deciliter. Since succimer is as effective as
any lead chelator currently available, chelation therapy is
apparently useless for children with such blood lead levels.
(New Engl. J. Med. 2001 344:1421)
... ... A NEW APOPTOSIS PATHWAY: Programmed cell death
(apoptosis) is an evolutionary conserved property of all
metazoans and essential to development and cellular homeostasis.
It is known that a group of cysteine proteases called "caspases"
are involved in apoptosis. Now a new study demonstrates
physiological evidence for an alternative apoptosis mechanism, a
mechanism involving a mitochondria-localized factor that can
induce apoptosis in mammalian cells in a caspase-independent
manner. This newly discovered apoptosis pathway is apparently
required for early development in the mouse.
(Nature 2001 410:549)
... ... QUASI-PARTICLES AND THE MANY-BODY PROBLEM: A typical
cubic centimeter of a solid contains on the order of 10^(23)
electrons, each of which interacts with [10^(23 - 1] other
electrons and a comparable number of positively charge particles.
An exact solution of the resultant many-body problem is hopeless
even with the most advanced computing techniques, but the concept
of the quasi-particle has allowed the complex system of
interacting electrons to be mapped one-to-one onto a system of
non-interacting fictitious particles called "quasi-electrons" --
the result the reduction of the 10^(23)-body problem to 10^(23)
more tractable one-body problems. The quasi-particle concept has
been extremely successful as a basis for describing the bulk
properties of solids. (Science 2001 292:1498)
... ... METALLIC OXYGEN: Researchers at the Lawrence Livermore
National Laboratory (US) report that fluid molecular oxygen
becomes metallic at a pressure of 1.2 megabar and a temperature
of approximately 4500 kelvins. The experiments involved firing a
projectile at a reservoir of liquid oxygen trapped between two
single-crystal sapphire anvils. The multiple reflections of the
resulting shock-wave between the anvils raised the pressure and
compressed the liquid sample. Electrical resistivity measurements
were made during a steady-state that lasted 100 to 200
nanoseconds. The research team notes that the temperatures and
pressures achieved in their experiments are comparable to those
within the gas-giant planets, where oxygen is abundant, which
means these results may help explain the origin of planetary
magnetic fields. (Phys. Rev. Lett. 2001 86:3108)
... ... EVIDENCE FOR ACCELERATING COSMIC EXPANSION: A 10-billion-
year-old stellar explosion accidentally recorded by the Hubble
Space Telescope infrared camera in 1997, the data now analyzed,
apparently demonstrates the cosmic expansion slowing down before
it eventually accelerated. Supernova SN-1997ff is at a redshift
of 1.7, when the expanding cosmos was barely a third of its
present linear size and less than a fourth of its present age.
Almost all theories of the Hubble acceleration conclude that at
large enough redshift we should find a more crowded epoch of
decelerating Hubble expansion in which gravitational attraction
was stronger than the repulsive counterforce of dark energy.
These new measurements apparently provide the first direct
evidence of the transition from the earlier deceleration epoch to
the present accelerating expansion. (Physics Today 2001 June)
... ... A LARGE KUIPER-BELT OBJECT: Pluto and its moon Charon are
apparently members of an ancient belt of icy bodies -- the Kuiper
belt. Now optical and infrared observations of a bright object in
the outer Solar System Kuiper belt reveal the object to be
surprisingly large, almost as large as Pluto's moon, and it is
believed the object could be the first of many such discoveries.
Astronomers D. Jewitt et al report simultaneous measurements of
the thermal emission and reflected optical light of object KBO
(20000) Varuna. The object has an equivalent circular diameter of
900 kilometers, with a surface darker than Pluto's, which
suggests it is largely devoid of fresh ice. (Nature 2001 411:446)
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2. PALEOANTHROPOLOGY:
AN APPARENT NEW DIRECT HUMAN ANCESTOR FOSSIL
The terms "hominoid", "hominid", and "hominin" 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 is currently considered to
comprise both the great ape lineages and human lineages within
the hominoid superfamily; the "homininae" comprise both the human
lineages and the African ape lineages within the hominids, and
the "hominini" comprising only the human lineages. The current
scheme is as follows:
--------------------------------------------------
I. Suborder Hominoids
A. ...
B. Family Hominids
1. ...
2. Subfamily Homininae
a. Tribe Gorillini (African apes)
b. Tribe Hominini
(1) Genus Australopithecus
(2) Genus Homo
(3) Other genera (see below)
--------------------------------------------------
The term "hominins" almost always refers to the tribe
Hominini, and not to the subfamily Homininae.
It is important to note that in the older scheme (before
about 1980), the Hominoids comprised the gibbons (Hylobatidae),
the great apes (Pongidae), and the Hominidae, with the Hominidae
(hominids) consisting only of the two genera Homo and
Australopithecus. The new scheme is therefore considerably
different. For example, under the old scheme, the statement
"modern man is the only living hominid" is correct. Under the new
scheme, that statement is incorrect.
The human lineages (the hominins) are characterized by a
number of features, including bipedalism. In effect, hominins are
the group of fossils more closely related to modern humans than
to any other group. In terms of dating, the hominin group
apparently originated sometime between 5 and 8 million years ago.
Concerning the "apes", there are two categories of relevance
here: The term "great apes" refers to chimpanzees, gorillas, and
orangutans. The term "African apes" refers only to chimpanzees
and gorillas. The distinction is important, since on the basis of
molecular evidence, the African apes are close to humans, while
the orangutans are not that close, and the gibbons are even
further removed.
The classification and interpretation of hominin fossils has
never been free of controversy, partly because hominin fossils
are not that plentiful, and perhaps partly because there are a
number of rival discovery teams, and the significance of a new
hominin fossil discovery is enhanced if the discovery apparently
requires new classifications and/or new interpretations.
At present, 5 genera of hominins are recognized:
Ardipithecus, Australopithecus, Paranthropus, Kenyanthropus, and
Homo. A fossil recently discovered in the Lukeino Formation of
the Tugen Hills in Kenya, the fossil named Orrorin tugenensis,
has now been proposed by its discoverers as another genus of
hominin and a direct ancestor of the Homo group, but
classification and interpretation of this fossil, as indicated
below, is in dispute.
In this context, the term "volcanic tuff" refers to a
compacted volcanic ash deposit.
... ... L.C. Aiello and M. Collard (University College London,
UK) present a commentary on the recent Orrorin tugenensis find
(B. Senut et al: C.R. Acad. Sci. Paris 2001 332:137), the authors
(Aiello and Collard) making the following points:
1) The authors (Aiello and Collard) point out that the
announcement of the Orrorin find has caused considerable stir,
partly because the deposits of the Tugen Hills are being
prospected by two competing groups of researchers, and partly
because Orrorin is claimed to be approximately 6 million years
old. This makes Orrorin 1.5 million years older than Ardipithecus
ramidus, the oldest previously recognized candidate for the
earliest hominin. Orrorin's apparent age falls within the
molecularly determined range of the last common ancestor between
humans and the African apes.
2) Aiello and Collard point out that the great age of
Orrorin does not seem to be in serious question. The geology of
the Lukeino Formation is well known; the volcanic tuffs in this
formation have been securely dated at 6.2 to 5.6 million years
old by radiometric techniques; and there is little doubt that the
specimens come from the Lukeino Formation sediments. But Aiello
and Collard suggest that it is difficult to have the same
confidence in the conclusions of Senut et al about human
evolutionary history, since they adopt a scheme that contrasts
sharply with prevailing ideas and that glosses over many areas of
controversy and uncertainty.
3) Aiello and Collard point out that at least 13 known
hominin species from Africa existed before Homo erectus, and that
currently in consensus among most paleoanthropologists are only
the following ideas concerning the main evolutionary paths: a)
There are 5 hominin genera (Ardipithecus, Australopithecus,
Paranthropus, Kenyanthropus, Homo). b) The large-toothed and
massive-jawed genus Paranthropus represents a dead-end branch.
4) Aiello and Collard conclude: "It... appears that cranial
and dental anatomy does not necessarily mirror molecularly
determined phylogenies in modern primates, which casts
considerable uncertainty on anatomically based evolutionary
trees. For now, at least, it is probably best to avoid naming
ancestors, and maintain a simple division: that between hominins
of archaic aspect (Orrorin, Ardipithecus, Australopithecus --
including Paranthropus -- and Kenyanthropus) and hominins of
modern aspect (Homo sapiens and the remaining species of Homo)."
-----------
L.C. Aiello and M. Collard: Our newest oldest ancestor?
(Nature 29 Mar 01 410:526)
QY: Leslie C. Aiello: laiello@ucl.ac.uk
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Summary by SCIENCE-WEEK http://scienceweek.com 13Jul01
For more information: http://scienceweek.com/swfr.htm
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3. MEDICAL BIOLOGY: ON AMYOTROPHIC LATERAL SCLEROSIS
In this context, "motorneurons" are neurons with cell bodies
in the brainstem or spinal cord and extensions that leave the
brainstem or spinal cord to terminate on voluntary muscle
(skeletal muscle) fibers. In this report, the general paradigm
for activation of voluntary muscles is neurons in brain (motor
cortex) to neurons in spinal cord (motor neurons) to peripheral
muscle fibers. (Some authors use the term "motorneurons" for
neurons in the motor cortex of the brain, but this usage is
uncommon.)
"Neurotransmitters" are chemical substances released at the
terminals of nerve axons in response to the propagation of an
impulse to the end of that axon. The neurotransmitter substance
diffuses into the synapse, the junction between the presynaptic
nerve ending and the postsynaptic neuron, and at the membrane of
the postsynaptic neuron the transmitter substance interacts with
a receptor. Depending on the type of receptor, the result may be
an excitatory or an inhibitory effect on the postsynaptic nerve
cell. Glutamate, the anion of glutamic acid (one of the amino
acid components of proteins), is an excitatory neurotransmitter
substance of considerable importance in the brain and spinal
cord.
Amyotrophic lateral sclerosis (ALS) is a disease first
described by J.M. Charcot (1825-1893) in 1874. ALS is a
neurodegenerative disease that attacks only motorneurons in the
brainstem and spinal cord, and eventually neurons in the motor
cortex that provide input to such motorneurons. The disease
affects an estimated 0.05 percent of the population, but this is
an average, and there are known pockets of much higher
prevalence. The disease is also called "Lou Gehrig's disease",
after the New York Yankees baseball player who died of the
disease in 1936. The disease is characterized by the slow but
relentless degeneration of only the motorneurons in the spinal
cord and brainstem, and eventually the neurons of the motor
cortex. Affected individuals exhibit progressive weakness and
wasting of skeletal muscles, and they usually die within 5 years
of disease onset.
Despite its comparatively low prevalence, from a medico-
biological perspective this disease is of considerable
significance: Biologists tend to think of the neurons that
comprise the central nervous system as a "tissue", a system of
differentiated cells derived from certain embryonic precursor
cells. But clearly, a disease that attacks only motorneurons and
not other neurons types in the immediate vicinity indicates that
in the nervous system, as in other tissues, secondary levels of
differentiation can be of extreme clinical importance. The
etiology of ALS is unknown, but whatever the cause of ALS, this
disease is reminding us that motorneurons differ from other nerve
cells in important ways not yet described.
The term "glial cells" refers to cells of the central and
peripheral nervous system that metabolically support neurons.
Such cells also produce the multiple membrane layers called
myelin and enfold nerve cell axons with it. Glial cells of
various types are found everywhere in the brain and spinal cord.
In this context, the term "incidence" refers to the number
of new cases during a specified time period; the term
"prevalence" refers to the total number of existing cases at a
specified time or during a specified time period.
... ... L.P. Rowland and N.A. Shneider (Columbia University, US)
present a review of current progress in clinical research in
amyotrophic lateral sclerosis, the authors making the following
points:
1) The authors point out that "amyotrophic lateral
sclerosis" has two meanings: In one usage, the term refers to
several adult-onset conditions characterized by progressive
degeneration of motorneurons. In the UK, the term "motorneuron
disease" is used for these disorders. In the second usage, ALS
refers to one specific form of motorneuron disease in which there
are both upper (brain and brainstem) and lower (brainstem and
spinal cord) clinical neurological signs of dysfunction.
2) The authors point out that "amyotrophic" refers to the
muscle atrophy, weakness, and involuntary contraction
(fasciculation) that signify disease of brainstem and spinal
motorneurons. The term "lateral sclerosis" refers to the palpable
hardness of the lateral columns of the spinal cord in autopsy
specimens, the hardness resulting from the overgrowth of certain
glial cells (astrocytes) (the process called "gliosis") in
damaged areas of the spinal cord.
3) The authors point out that 5 to 10 percent of cases of
ALS are familial, and that in 1993, D.R. Rosen et al described
mutations in the gene encoding the enzyme superoxide dismutase 1
(SOD1) that account for 20 percent of familial ALS. The remaining
80 percent of familial cases of ALS are apparently caused by
mutations in other genes. Only 5 percent of people with
apparently non-familial (sporadic) ALS also have SOD1 mutations.
Variations in specific amino acid mutations in SOD1 cause
specific variations in onset and course of the disease.
4) The authors point out that considerable evidence suggests
that ALS involves a derangement intracellular free calcium, this
derangement activating a train of events that triggers ultimate
cell death. In patients with ALS, and in mice with mutant SOD1,
the resistance of particular motorneurons (e.g., oculomotor
motorneurons) may be related to the presence of calcium-binding
proteins that protect against the toxic effects of high
intracellular calcium levels. Excessive entry of extracellular
calcium apparently occurs through the inappropriate activation of
glutamate receptors.
5) The incidence and prevalence of ALS vary little
worldwide, but there are notable exceptions, especially in Guam,
where an unusual frequency of ALS, parkinsonism, and dementia has
been noted since the 1940s. The prevalence of ALS in Guam is
currently 50 times the prevalence anywhere else, with the cause
of this high prevalence unknown. Heredity has been discounted as
a factor in Guam because the spouses of many patients are also
affected. No environmental cause or virus has been found
associated with the disease in Guam.
6) There are currently 26 different drugs, including snake
venom, used alone or in combination in the treatment of ALS, but
only one drug is approved by the US Food and Drug Administration
for the treatment of ALS. This drug, Riluzole, a glutamate
antagonist, apparently prolongs survival by 3 to 6 months. Other
glutamate antagonists apparently have no beneficial effects. In
1940, J.S. Wechsler touted the benefits of vitamin E in a series
of patients with ALS. Although Wechsler reported an improvement
in the condition of patient #4, identified on the basis of his
initials and age as Lou Gehrig himself, Gehrig nevertheless died
within a year.
7) The authors (Rowland and Shneider) conclude: "Genetic
analysis has identified a primary cause of ALS. Mutations in a
single gene can initiate a process that leads to the selective
degeneration of motorneurons. The clinical and pathological
similarities of familial and sporadic ALS suggest a common
pathogenesis. The challenge now is to understand how these
mutations cause disease and to use this understanding to develop
a treatment, perhaps a cure."
-----------
L.P. Rowland and N.A. Shneider: Amyotrophic lateral sclerosis.
(New England J. Med. 31 May 01 344:1688)
QY: Lewis P. Rowland: lpr1:columbia.edu
-------------------
Summary by SCIENCE-WEEK http://scienceweek.com 13Jul01
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
ON THE MOLECULAR BASIS OF THE NEURODEGENERATIVE DISEASES
The term "neurodegenerative disorders" is loosely applied to a
group of chronic and progressive diseases of the nervous system,
all of which are characterized by selective and symmetric loss of
neurons in motor, sensory, or cognitive systems. Some
neurodegenerative diseases are extremely cell-specific, causing
loss of only one type of nerve cell, while the neuronal loss
caused by other neurodegenerative diseases is more general,
affecting a wide variety of nerve cells. In all cases, these
diseases primarily affect nerve cells and not other cells.
... ... Joseph B. Martin (Harvard University, US) presents a
review of the molecular basis of neurodegenerative disorders, the
author making the following points:
1) Delineation of the patterns of cell loss and
identification of disease-specific cellular markers have aided in
the classification of these diseases. For example:
... ... a) *Alzheimer's disease is characterized by *senile
plaques, *neurofibrillary tangles, neuronal loss, and
*acetylcholine deficiency.
... ... b) *Parkinson's disease is characterized by *Lewy bodies
and depletion of *dopamine.
... ... c) *Amyotrophic lateral sclerosis is characterized by
*cellular inclusions and swollen *motor axons.
... ... d) *Huntington's disease is characterized by loss of
*gamma-aminobutyric acid-containing neurons of the *neostriatum.
2) *Mendelian inheritance can be demonstrated in many
neurodegenerative disorders. In some diseases, such as
Huntington's disease, a family history of the disease can be
ascertained in almost every case, whereas in other diseases, such
as Alzheimer's disease, Parkinson's disease, and amyotrophic
lateral sclerosis, about 1 to 10 percent of cases are inherited.
In other conditions, such as *spinocerebellar ataxia, the
syndromes have been difficult to classify because of clinical
overlap, and variants can only be differentiated by genotyping
after the mutant genes have been identified.
3) In families with the above and other neurodegenerative
disorders, *linkage analysis, *positional cloning, and searches
for mutations in candidate genes have been extremely productive.
These efforts, which began in the 1980s with the search for the
gene that causes Huntington's disease, have led to the
identification of mutant genes in more than 50 disorders of the
nervous system.
4) The genetic anomalies that cause neurodegenerative
diseases are varied and complex. In some diseases, several genes
have been found, each of which leads to a similar clinical and
pathological syndrome, with only variations in the age at onset
and the rate of progression to suggest that there are differences
in pathogenic mechanisms. In other disorders, errors in DNA
replication resulting in an increased number of *nucleotide
triplet repeats are associated with selective patterns of
neurodegeneration.
5) In general, the various pathologies of the
neurodegenerative disorders apparently involve abnormalities in
the transport, degradation, and aggregation of proteins that lead
to cell-specific changes and ultimately to neuronal death,
probably by *apoptosis.
-----------
Joseph B. Martin: Molecular basis of the neurodegenerative
diseases.
(New England J. Med. 24 Jun 99 340:1970)
QY: Joseph B. Martin: joseph_martin@hms.harvard.edu
-----------
Text Notes:
... ... *Alzheimer's disease: Alzheimer's disease is
characterized by the presence of large numbers of extracellular
agglomerations (plaques) and intracellular *neurofibril tangles
in the cerebral cortex of the brain. There is also a massive
neuronal cell loss. While plaques and tangles are found in normal
aging brains, they are more numerous and widespread in
Alzheimer's disease. The major protein component of the plaques
is a 39 to 43 amino acid peptide called beta-amyloid, which is
now known to be derived from a much larger protein called the
amyloid precursor protein. This latter protein has been found to
be expressed in every tissue studied.
... ... *neurofibril: A filamentous structure seen with the light
microscope and composed of ultramicroscopic tubular and
filamentous protein arrays (neurotubules and microfilaments). The
function of these structures is unknown.
... ... *senile plaques: In general, the term "plaque" refers to
a deposit. In this context, the deposits are usually
extracellular protein agglomerations.
... ... *neurofibrillary tangles: A neurofibril is a filamentous
structure seen with the light microscope and composed of
ultramicroscopic tubular and filamentous protein arrays
(neurotubules and microfilaments). The function of these
structures is unknown.
... ... *acetylcholine: In general, a neuron has input extensions
(dendrites) and a single but usually branched output extension
(axon). The junction between the terminal of a neuron's axon and
another neuron is called a "synapse". When studying the synapse,
the first neuron is called the "presynaptic" neuron, and the
second neuron is called the "postsynaptic" neuron.
Neurotransmitters are chemical substances released at the
terminals of nerve axons in response to the propagation of an
impulse to the end of that axon. The neurotransmitter substance
diffuses into the synapse, the junction between the presynaptic
nerve ending and the postsynaptic neuron, and at the membrane of
the postsynaptic neuron the transmitter substance interacts with
a receptor. Depending on the type of receptor, the result may be
an excitatory or an inhibitory effect on the postsynaptic nerve
cell. At present acetylcholine, 5 amines, 4 amino acids, 2
purines, and more than 28 peptides are known to be
neurotransmitters.
... ... *Parkinson's disease: A neurological disorder first
described by James Parkinson (1817) and associated with
degeneration of a specific small region of the brain and a
resultant loss of projection to several important brain centers.
... ... *Lewy bodies: Intracytoplasmic neuron inclusions
especially seen in Parkinson's disease.
... ... *dopamine: Dopamine is a neurotransmitter found in
several major areas of the brain, and the degeneration of
so-called dopamine neurons is apparently involved in Parkinson's
disease. Dopamine has also been implicated in the intricate
effects of the psychostimulating drugs associated with drug
abuse. The dietary precursors of dopamine are phenylalanine and
l-tyrosine.
... ... *Amyotrophic lateral sclerosis: A progressive disease of
motor neurons (spinal cord nerve cells that control voluntary
muscles). 50 percent of patients die within 3 years of the first
symptoms.
... ... *cellular inclusions: A general term for residual
entities in cytoplasm produced by metabolism; in this context,
granules or crystals not found in normal cells.
... ... *motor axons: Axons of motor neurons. They can be quite
long: a spinal cord motor neuron controlling muscles in a toe,
for example, has a cell body in the spinal cord and an axon that
runs as a single extension from the spinal cord down to the toe
musculature. Such axons usually propagate impulses at high
velocity (e.g., 100 meters per second).
... ... *Huntington's disease: (Huntington's chorea) First
described by George Huntington (1850-1916), the disease attacks
specific regions of the brain (e.g., caudate nucleus and
putamen), and leads to insanity and eventual death.
... ... *gamma-aminobutyric acid: A widely distributed brain
neurotransmitter.
... ... *neostriatum: This is a term used when considering the
two brain regions, the caudate nucleus and the putamen, as a
single anatomical entity.
... ... *Mendelian inheritance: In general, any inheritance
scenario following the classical Mendelian laws governing the
inheritance of chromosomal genes via the transmission of
chromosomes to subsequent generations, and producing inheritance
of single-chromosome-locus traits.
... ... *spinocerebellar ataxia: In general, an ataxia is an
inability to coordinate muscle activity during voluntary
movement. Spinocerebellar ataxia is the most common hereditary
ataxia. The spinocerebellar degenerative disorders are a group of
diseases involving neurons in several nervous system structures,
including the spinal cord and cerebellum.
... ... *linkage analysis: In general, an analysis of chromosomal
gene location based upon inheritance patterns.
... ... *positional cloning: In general, the identification of a
gene responsible for a disease from a knowledge of its position
in the human genome, and no assumptions about the gene product.
Inherited disease genes identified by positional cloning include
Duchenne muscular dystrophy and Huntington's disease.
... ... *nucleotide triplet repeats: (coding triplet repeats;
codon repeats) In general, a codon is the basic genetic
coding unit, a triplet of nucleotides in DNA. A codon repeat is a
string of identical codons which if expressed produce a string of
identical amino acids in a protein.
... ... *apoptosis: In general, programmed cell death produced by
control mechanisms designed to destroy defective cells.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 2Jul99
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
NEURODEGENERATIVE DISEASE AND SPECIFIC MEMBRANE ION CHANNELS
There are a number of human neurodegenerative diseases that
involve the destruction of specific types of nerve cells, rather
than nerve cells in general (amyotrophic lateral sclerosis, for
example), but the mechanisms for the specificity and the eventual
death of the nerve cells is not known. It has been suggested that
specific gene mutations leading to aberrant ion channels may be
involved. Now Jian Zuo et al (Rockefeller University, US; Johns
Hopkins University, US) report studies of "lurcher" mice, a
mutant that exhibits ataxia associated with death of Purkinje
cells in the cerebellum. What they find is that the mutants have
aberrant glutamate neurotransmitter receptors, which in turn may
result in excess concentrations of calcium ions, enough
intracellular calcium ions to lead to cell death.
-----------
QY: N. Heintz: heintz@rockvax.rockefeller.edu
(Nature 21 Aug 97) (Science-Week 29 Aug 97)
For more information: http://scienceweek.com/swfr.htm
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
4. EARTH SCIENCES: CARBON DIOXIDE AND CLIMATE CHANGE
The term "greenhouse effect" refers to the blockade of
longwave (infrared) radiation from the Earth into space by trace
constituents of the atmosphere, primarily water vapor, carbon
dioxide, ozone, methane, nitrous oxide, and various
chlorofluorocarbons -- gases referred to collectively as the
"greenhouse gases". The sensitivity of the biosphere to the
greenhouse effect has existed throughout the history of life on
Earth: the infrared radiation-blocking gases return radiated heat
to the ground, accounting for approximately 70 percent of the net
input of energy to the Earth's surface.
In this context, the term "radiative forcing" refers in
general to climate changes produced by changes in incoming or
outgoing radiative heat to and from the Earth's surface.
The term "tectonic" refers in general to deformations of the
Earth's crust and consequent structural changes, and "tectonic
timescales" are the long timescales (e.g., tens of millions of
years) over which such deformations occur.
... ... T. J. Crowley and R.A. Berner (2 installations, US)
present a commentary and analysis of current research relating
carbon dioxide and climate change, the authors making the
following points:
1) The authors point out that it has long been known that on
timescales of tens of millions of years, intervals of continental
glaciation were interspersed with intervals of little or no ice.
The magnitude of warmth during these warm intervals is
impressive: for example, at times during the Cretaceous period
(approximately 65 to 145.6 million years ago) duck-billed
dinosaurs roamed the northern slope of Alaska, and deep and
bottom waters of the ocean, now near freezing, could reach a
balmy 15 degrees celsius.
2) The authors point out that in the 1980s, a convergence of
results from paleoclimate data and geochemical and climate models
suggested that such long-term variations in climate were strongly
influenced by natural variations in the carbon dioxide content of
the atmosphere. Recently, some geochemical results have raised
concerns about the validity of this conclusion, since carbon
dioxide concentrations over the past 65 million years appear to
have reached low levels well before the most recent phase (the
past 3 million years) of Northern Hemisphere glaciation. A study
spanning the Phanerozoic time-frame (the past 570 million years)
also suggests some decoupling between times of predicted high
carbon dioxide and some climate indices.
3) In order to reevaluate the validity of the assumed carbon
dioxide-climate link, the authors compared estimates of
Phanerozoic carbon dioxide variations and net radiative forcing
with the continental glaciation record and low-latitude
temperature estimates. The authors report that the first order
agreement between the carbon dioxide record and continental
glaciation continues to support the conclusion that carbon
dioxide has played an important role in long-term climate change.
4) The authors conclude that to weigh the merits of the
carbon dioxide paradigm, it may be necessary to expand the scope
of climate modeling. For factors responsible for the presence or
absence of continental ice, the carbon dioxide model works very
well. In contrast, there are substantial gaps in our
understanding of how climate models distribute heat on the planet
in response to carbon dioxide changes on tectonic time scales.
"Given the need for better confidence in some of the paleoclimate
data, and unanticipated complications arising from altered
tectonic boundary conditions, it may be hazardous to infer that
existing discrepancies between models and data cloud
interpretations of future anthropogenic greenhouse gas
projections."
-----------
T.J. Crowley and R.A. Berner: Carbon dioxide and climate change.
(Science 4 May 01 292:870)
QY: Robert A. Berner: robert.berner@yale.edu
-------------------
Summary by SCIENCE-WEEK http://scienceweek.com 13Jul01
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
EARTH SCIENCES:
AN ALTERNATIVE SCENARIO FOR GLOBAL WARMING
Earth's global surface temperature has increased by
approximately 0.5 degrees centigrade since 1975, a relative
"burst" of warming that has apparently taken the global
temperature to its highest level in the past 1000 years, and
there is a growing consensus that the warming is at least in part
a consequence of increasing anthropogenic *greenhouse gases.
These gases cause a global "climate forcing", i.e., an imposed
perturbation of the energy balance of the Earth with space. There
are many competing natural and anthropogenic climate forcings,
but increased greenhouse gases are estimated to be the largest
forcing and to result in a net positive forcing, especially
during the past few decades. Evidence supporting this
interpretation has been provided by observed heat storage in the
ocean, which is positive and which is of the magnitude of the
energy imbalance estimated from climate forcings for recent
decades.
... ... J. Hansen et al (5 authors at 3 installations, US)
present a discussion of global warming, the authors making the
following points:
1) The authors point out that a common view is that the
current global warming rate will continue or accelerate. The
authors, however, argue that rapid warming in recent decades has
been driven mainly by non-carbon dioxide greenhouse gases such as
chlorofluorocarbons, methane, and N(sub2)O, and not by the
products of fossil fuel burning, carbon dioxide, and *aerosols,
the positive and negative climate forcings of which are partially
offsetting.
2) The authors point out that the growth rate of non-carbon
dioxide greenhouse gases has declined in the past decade. If
sources of methane and O(sub3) precursors were reduced in the
future, the change in climate forcing by non-carbon dioxide
greenhouse gases in the next 50 years could be near zero.
Combined with a reduction of *black carbon emissions and
plausible success in slowing carbon dioxide emissions, this
reduction of non-carbon dioxide greenhouse gases could lead to a
decline in the rate of global warming, reducing the danger of
dramatic climate change.
3) The authors suggest that such a focus on air pollution
has practical benefits that unite the interests of developed and
developing countries, although assessment of ongoing and future
climate change requires composition-specific long-term global
monitoring of aerosol properties.
-----------
[Editor's note: After its publication several weeks ago, this
paper became controversial and received considerable publicity.
The senior author, James Hansen, is noted for helping to alert
the world to global warming in 1988, and this recent paper has
been interpreted as a reversal of his ideas concerning the
dangers of fossil fuel, carbon dioxide, and aerosol emissions,
and publicized by those opposed to the Kyoto Protocol on climate
change. For an account of reaction to this paper, see:
Nature 7 Sep 00 407:7.]
-----------
J. Hansen et al: Global warming in the 21st century: An
alternative scenario.
(Proc. Natl. Acad. Sci. US 29 Aug 00 97:9875)
QY: James Hansen: jhansen@giss.nasa.gov
-----------
Text Notes:
... ... *greenhouse gases: The physical basis of the so-called
"*greenhouse effect" is essentially simple: carbon dioxide gas is
transparent to visible light but relatively opaque to infrared
radiation. The same is true of glass. Relatively high-energy
visible light radiation from the sun passes inward through the
atmosphere, warms the surface of the Earth, which then radiates
lower energy in the form of infrared radiation (heat) back to the
atmosphere. But if the atmosphere has a concentration of infrared
impenetrable gases such as carbon dioxide, the infrared radiation
cannot pass out, and the surface of the Earth underlying the
atmosphere cannot cool, and the surface of the Earth thus will
continue to grow hotter.
... ... *aerosols: The term "aerosol" refers to a dispersion in
which a finely divided solid is suspended in air and the
particles are of colloidal dimensions. The term "colloidal
dimensions" refers to the range approximately 1 nanometer to 100
nanometers in diameter.
... ... *black carbon: (carbon black) Amorphous (i.e., non-
crystalline) carbon.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 6Oct00
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
CLIMATOLOGY:
ANTHROPOGENIC ATMOSPHERIC AEROSOLS AND GLOBAL CLIMATE CHANGE
... Aerosols are an important component of atmospheric chemical
dynamics, with the contributions of aerosols to global and
regional climate far from simple.
... ... S.E. Schwartz and P.R. Buseck (2 installations, US)
present a commentary on recent research on anthropogenic
atmospheric aerosols, the authors making the following points:
1) Most considerations of global climate change caused by
human activities have focused on the warming influence of
greenhouse gases. However, aerosols are another important
atmospheric constituent that influences climate and that has been
affected by human activities. In general, aerosol particles
increase scattering and absorption of shortwave (solar)
radiation, increase cloud reflectance, enhance cloud lifetimes,
and suppress precipitation. These phenomena are all thought to
exert a cooling influence on climate. Recent data indicate that
anthropogenic aerosols reduce cloud droplet size and suppress
precipitation downward of major urban areas and industrial
facilities, which is consistent with earlier hypotheses.
2) The influences of aerosols on climate are more complex
than those of greenhouse gases. Bulk aerosol composition is
highly variable spatially and temporally because of different
sources and production mechanisms and short atmospheric residence
times (from less than a day to more than a month). Particles
sizes range from nanometers to microns, and within the same size
class, particles can exhibit widely different compositions and
morphologies, with different constituents present within the same
particle (e.g., 10 nanometer carbon spherules can be found
embedded within much larger sulfate particles). The
inhomogeneities in properties and geographical distribution of
aerosols make it difficult to characterize their influences on
climate and to represent these influences in models.
3) Recent analysis of the consequence of absorption of
shortwave radiation by aerosols indicates that the heating of the
atmosphere can evaporate clouds. Clouds exert both cooling and
warming influences on climate: cooling in the shortwave (because
of their reflectance), and warming in the longwave (because of
absorption and re-emission of thermal infrared radiation). The
shortwave component dominates, so a reduction in cloud coverage
would result in a net warming influence.
5) The authors conclude: "Recent studies demonstrate both
the importance of aerosol effects on climate and the complexity
of aerosol-cloud interactions. Unfortunately for those would like
a quick and accurate assessment of anthropogenic climate forcing
over the industrial period, the studies also demonstrate that
there is much to be learned before such an assessment can
confidently be given."
-----------
S.E. Schwartz and P.R. Buseck: Absorbing phenomena
(Science 12 May 00 288:989)
QY: S.E. Schwartz: ses@bnl.gov
-------------------
Summary by SCIENCE-WEEK http://scienceweek.com 23Jun00
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
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
5. PHYSICAL CHEMISTRY: A NEW MODEL OF LIQUID WATER
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
defined but are probably of considerable significance.
Of importance in understanding the role of water, not only
in biological interactions, but also in all solute-solute
interactions in aqueous systems, is the unique structure of water
produced by the short-term and long-term interactions of water
molecules with other water molecules, these interactions caused
primarily by a) hydrogen bonding, and b) polar interactions due
to electrostatic asymmetry.
Contemporary "molecular dynamics simulations", which are
extrapolations of statistical mechanics and which originate in
the work of Alder and Wainright in the 1960s, are computer
simulations of molecular systems typically involving hundreds or
sometimes thousands of idealized particles interacting with
physically realistic potentials. Such molecular dynamics
simulations can provide time-dependent properties of a liquid,
but most commonly they are used to produce a set of
configurations and forces which can be averaged to give
equilibrium properties of the system.
... ... J. Higo et al (5 authors at 2 installations, JP) present
a new model of liquid water, the authors making the following
points:
1) The authors point out that in order to understand the
dynamics of solute molecules and biomolecules functioning in
aqueous solutions, it is important to describe the cooperative
motions of solvent water molecules. Although molecular dynamics
analyses have focused on the statistical laws of motions of water
molecules, and on the collective dynamics of hydrogen-bond
network rearrangements, a clear theoretical picture of these
complex motions has not yet been obtained.
2) The authors point out that the study of the structure and
dynamics of the liquid state must involve both cooperative
motions of molecules and random motions of individual molecules.
Cooperativity of motions of water molecules is manifested in the
observed correlation between orientations of neighboring
molecules. On the other hand, each water molecule rapidly
translates and rotates with a 5 to 10 picosecond timescale, which
produces rapid randomization of orientations.
3) The authors propose a framework to describe the two
aspects of water molecule behavior in a unified way, the
framework involving the introduction of a new quantity, "site-
dipole field". The "site dipole" is defined at each spatial
position by the averaged orientation of water molecules that pass
through that position. Although each water molecule randomly
moves and quickly passes through each spatial site, it is
expected that the site-dipole field shows a coherent pattern
because of cooperativity among water molecules. Such coherent
patterns in bulk water should be perturbed by the presence of
solute molecules and give rise to a characteristic site-dipole
structure around solute molecules. The authors demonstrate that
such coherent patterns indeed exist and that the structural
ordering of site dipoles provides a perspective for the
understanding of hydration of biomolecules.
4) The authors report their simulations reveal the presence
of large vortex-like structures of more than 10 angstroms in
size, with such coherent patterns persisting more than 300
picoseconds, although the orientational memory of individual
molecules is quickly lost. A 1 nanosecond molecular dynamics
simulation of systems consisting of two amino acids shows that
the fluctuations of site-dipole field of solvent are pinned
around the amino acids, resulting in a stable dipole bridge
between side chains of amino acids. The dipole bridge forms even
for a side-chain separation of 14 angstroms, which corresponds to
5 layers of water molecules. The formation of the dipole bridge
is sensitive to the side-chain orientations, and thereby suggests
an explanation for specificity in solvent-mediated interactions
between biomolecules.
-----------
J. Higo et al: Large vortex-like structure of dipole field in
computer models of liquid water and dipole-bridge between
biomolecules.
(Proc. Natl. Acad. Sci. US 22 May 01 98:5961)
QY: Junichi Higo: higo@ls.toyaku.ac.jp
-------------------
Summary by SCIENCE-WEEK http://scienceweek.com 13Jul01
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
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
... ... 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
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
6. CHEMISTRY: ON THE SHAPES OF MOLECULES
The conformation of molecules in space (and the factors that
determine those confirmations) are important aspects of the
reactivity of molecules and the subject of intensive research in
theoretical chemistry.
The Schroedinger wave equation is the equation that serves
as the mathematical model for electrons in molecules, but this
equation unfortunately can be solved exactly only for one-
electron systems such as the hydrogen atom. If the equation could
be solved exactly for molecules containing two or more electrons,
we would have precise quantum-mechanical pictures of the shapes
of electron density distributions (electron orbitals) and
numerical values for the energy of each orbital.
Since exact solutions to the wave equation are not available
for many-electron systems, various approximations have been made,
some requiring more computational power than others. One class of
approximations of the wave equation is the class of molecular
orbital (MO) methods, and of these there are several subtypes.
The simplest molecular orbital calculation method is the Hueckel
Molecular Orbital method (HMO). A class of more advanced methods
is the group of "self-consistent field" (SCF) orbital computation
methods, one of which methods is the Hartree-Fock (HF) method
(which takes into account the Pauli exclusion principle for
electrons). A recent variation of the Hartree-Fock method, made
practical by the advent of modern computers, is the "natural
bonding orbital" (NBO) method, and it is this latter method that
is used in the report below [*Note #1].
Although it is certainly true that all current molecular
orbital computational methods for many-electron systems involve
severe approximations of the mathematics in quantum theory, it is
also true that these approximations often produce experimentally
verifiable numerical results that provide confidence in the
applicability of computations where verifying experiments are not
yet possible.
In this context, the term "hyperconjugation" refers to the
interaction of sigma bonds with pi bonds in a molecule, as in,
for example, the interaction of the methyl group with the benzene
ring in toluene. Hyperconjugation is often considered as a
contribution of resonance structures in which a sigma bond is
broken to give ions, and it has been called "no-bond resonance".
... ... V. Pophristic and L. Goodman (Rutgers University, US)
present a theoretical study of the structure of ethane, the
authors making the following points:
1) The authors point out that the parts of many molecules
can rotate internally around one or more bonds, so that during a
full 360 degree rotation, the molecule will change between
unstable and relatively stable conformations. Ethane is the
textbook example of a molecule exhibiting such behavior: as one
of the two methyl groups rotates once around the central carbon-
carbon bond, the molecule will alternate 3 times between an
unstable "eclipsed conformation" and the preferred "staggered
conformation". This structural preference is usually attributed
to steric effects involving repulsions and rotation barriers that
destabilize the eclipsed structure. Stabilization of the
staggered structure through weakening of the central C-C bond and
hyperconjugation have been considered to be involved, but
evaluation of the contributions of these effects to ethane's
internal rotation and conformational preference has been
difficult.
2) The authors report a series of ethane structure
optimization calculations, the calculations involving successive
removal of different interactions. The authors report their
results indicate that the staggered conformation of ethane is the
result of preferential stabilization through hyperconjugation.
Removal of hyperconjugation interactions yields the eclipsed
structure as the preferred conformation, whereas repulsive
forces, either present or absent, have no influence on the
preference for a staggered conformation.
... ... In a commentary on this work, Frank Weinhold (University
of Wisconsin, US) states: "What causes the internal energy [for
ethane] to rise in passing from the stable staggered conformation
to the unstable eclipsed conformation? The emerging answer, as
pointed out by Pophristic and Goodman (2001), contrasts sharply
with the stock explanation presented in almost every textbook of
organic chemistry... When will chemistry textbooks begin to serve
as aids, rather than barriers, to [the] enriched quantum-
mechanical perspective on how molecular [conformations] work?"
-----------
V. Pophristic and L. Goodman: Hyperconjugation not steric
repulsion leads to the staggered structure of ethane.
(Nature 31 May 01 411:565)
QY: Lionel Goodman: goodman@rutchem.rutgers.edu
-----------
Frank Weinhold: A new twist on molecular shape.
(Nature 31 May 01 411:539)
QY: Frand Weinhold: weinhold@chem.wisc.edu
-----------
Text Notes:
... ... *Note #1: In the Hueckel approximation, the sigma
orbitals are treated separately from the pi orbitals, the shape
of the molecule being determined by the sigma orbitals, with
interactions between neighboring atoms neglected. In self-
consistent field approximations, an approximate solution for the
wave equation is obtained using the average interaction of an
electron with the rest of the molecule, and that solution is used
to calculate a new average interaction, which is used in turn to
recompute the wave equation, and so on, The iterative procedure
ends when no further change in the wave function is evident, the
calculation thus becoming "self-consistent".
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 13Jul01
For more information: http://scienceweek.com/swfr.htm
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7. IN FOCUS: ON GENES AND NEUROBIOLOGY
"It is hard to predict the consequences of the revolution in
genetic techniques for understanding brain function. The present
use of transgenic animals in which identified genes have been
altered or deleted provides a powerful tool, but one still
hampered by difficulties of interpretation owing to redundancy of
function and unexpected side effects. With the completion of the
Human Genome Project, candidate genes and molecules that are
altered in disease and development will be known. To analyze this
large array of information and separate the important from the
incidental constitutes an immense task. The scope of the problem
is illustrated by the study of inherited diseases, such as
Huntington's disease, in which the altered gene can be identified
by linkage analysis of the affected families. Yet, although the
altered sequences of the Huntington's disease gene were
identified long ago, the function of the protein remains unknown.
Similarly, mutations in genes coding for voltage-gated calcium
channels are associated with familial hemiplegic migraine and
cerebellar ataxia. But again there is no clear link in terms of
mechanisms. A long term hope is that genetic therapies will be
developed for such conditions. Possibly the way to devise
treatments will become clearer with better means of delivery, as
well as better temporal and spatial control of [gene] expression.
It is perhaps worth commenting that this paragraph deals with
techniques and information in search of questions."
-----------
J.G. Nicholls et al: _From Neuron to Brain_ 4th Edition
(Sinauer Assoc., Sunderland MA US 2001, p.577)
http://www.amazon.com/exec/obidos/ASIN/0878934391/scienceweek
-------------------
SCIENCE-WEEK http://scienceweek.com 13Jul01
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8. FROM THE SCIENCEWEEK ARCHIVE:
ON STATISTICAL PHYSICS AND ITS APPLICATIONS
Statistical physics (statistical mechanics) is the branch of
physics that attempts to explain the macroscopic properties of a
system on the basis of the properties of its microscopic
constituents. Usually the number of constituents is extremely
large, and all the characteristics of the constituents and their
interactions are presumed to be known. Although as a distinct
research area statistical physics dates back to James Clerk
Maxwell (1831-1879) and Ludwig Boltzmann (1844-1906) and their
work on probability distributions in the kinetic theory of gases,
the field was substantially transformed in the 20th century, and
it has now been fruitfully applied to nearly all states of matter
including biological systems.
... ... Philip Ball (_Nature_, UK) presents a commentary on the
history and applications of statistical physics, the author
making the following points:
1) Statistical physics, and more specifically the theory of
transitions between states of matter, more or less defines what
we know about everyday matter and its transformations. In
addition, statistical physics provides a conceptual apparatus for
dealing with complex collective quantum phenomena of current
intense interest, particularly: a) Bose-Einstein condensation (in
which a collection of particles all occupy the same quantum
ground state); and b) high-temperature superconductivity (i.e.,
superconductivity above 35 degrees kelvin). Many of the states of
condensed matter that promise new technological applications,
ranging from *block copolymers to magnetic multilayers, can be
understood as the consequence of the kind of collective behavior
that statistical physics describes.
2) From the 1960s to the 1980s, statistical physicists were
primarily concerned with "critical points", the points in
thermodynamic phase diagrams at which two or more phases become
identical. The reasons for this interest are twofold: a) the
behavior of a system at its critical point also determines its
behavior in the broad vicinity of the critical point (within a
so-called "critical region"; b) the behavior of a system at a
critical point reveals kinships between different systems. For
example, liquid-gas criticality and the behavior of some magnets
at their Curie point (the temperature above which they lose their
*ferromagnetism) have numerically equal *critical exponents, and
both can be modeled by the so-called "*Ising model", a model
based on a lattice of two-state *spins. Commonality of critical
exponents gives rise to the idea of universality, the idea that
there are generic models in statistical physics that describe a
variety of apparently different many-body systems. This means
that solving one problem in statistical physics generally
delivers solutions for several other problems at the same time.
In addition, there is an implication that many-body behavior is
fundamentally determined only by global aspects such as the range
of interparticle forces, the dimensionality of the system, and
the nature of the "*order parameter" (whose abrupt change from a
zero to a non-zero value defines the transition from one state to
another).
3) A fruitful present area of research is the intersection
of statistical physics with quantum mechanics, in particular, the
many-body behavior of electrons in condensed matter. Correlated
behavior of electrons, in which electrons display a degree of
collective or coherent dynamics, produces superconductivity, the
*integer and fractional quantum Hall effect, so-called "*heavy-
fermion" behavior, *spin density waves, and *colossal
magnetoresistance. All of these collective phenomena have in
recent years been shown to underlie unexpected and potentially
useful properties of novel materials. Colossal magnetoresistance,
for example, may lead to the development of highly-sensitive
read-out heads for magnetic memories.
4) The author suggests that despite the proven value to cell
biology of some concepts from the study of phase transitions (for
example, the entropic effect of fluctuations on interactions of
lipid membranes), there remains much skepticism as to whether
biological phenomena can be approached as arising from collective
emergent behavior of statistical interacting ensembles rather
than from the closely controlled protein relays to which cell
biologists are accustomed. Yet statistical physics must
inevitably provide the baseline even in the cell: proteins may
phase-separate and membranes may adopt equilibrium conformations
unless actively opposed by cell processes.
-----------
Philip Ball: Transitions still to be made.
(Nature 2 Dec 99 402supp:C73)
QY: Philip Ball: p.ball@nature.com
-----------
Text Notes:
... ... *block copolymers: A copolymer in which a number of units
of the same monomer are located adjacent to one another (in
"blocks" of monomers).
... ... *ferromagnetism: A "ferromagnet" is a material (such as
iron) in which there may be a permanent *magnetic moment, and in
which the *spins of the atoms are aligned parallel to each other.
... ... *magnetic moments: (magnetic dipole moment) The intrinsic
spins of the electrons in an atom, together with the motion of
the electrons around the nucleus, give rise to a magnetic field
around the atom, and the magnitude of this field is related to
the magnetic dipole moment of the atom or ion.
... ... *critical exponents: In this context, a "critical
exponent" is a parameter that characterizes the temperature
dependence of a thermodynamic property of a substance near its
critical point. The temperature dependence has the form
|T-T(subc)|^(n), where T is the temperature, T(subc) is the
critical temperature, and (n) is the critical exponent.
... ... *Ising model: In general, a simplified model in which the
atomic *spins are assumed to be aligned parallel or antiparallel
in a given direction.
... ... *spins: In quantum mechanics, electrons, protons, and
neutrons have an intrinsic angular momentum known as "spin", and
a magnetic moment parallel or antiparallel to that angular
momentum. When electrons are combined together to form an atom or
ion, there is a resultant angular momentum which is a combination
of the intrinsic spin of the electrons and the angular momentum
due to their motion about the nucleus, and this is the "spin" of
the atom or ion. Atoms or ions with non-zero spin are magnetic
atoms or ions. The idea of electron spin was first proposed by
Goudsmit and Uhlenbeck in 1925 to explain the splitting of atomic
spectroscopic emission lines in the presence of a magnetic field.
Elementary particle spin involves a virtual rotation about the
axis of the particle, which means only two spin states are
possible, one clockwise and one counterclockwise.
... ... *order parameter: In general, a quantity that
characterizes the phase of a system below its transition
temperature, the parameter having a nonzero value below the
transition temperature and a zero value above the transition
temperature. If the phase transition is continuous, the order
parameter falls to zero continuously as the transition
temperature is approached.
... ... *integer and fractional quantum Hall effect: In classical
physics, the Hall effect is the development of a transverse
voltage across a current-carrying conductor in a magnetic field,
the voltage being perpendicular to both the direction of the
current and the direction of the magnetic field. In quantum
physics, there are two other Hall effects, an integer charge
quantum Hall effect, and a fractional charge quantum Hall effect,
these quantum Hall effects being observed at extremely low
temperatures (a few degrees Kelvin) and extremely intense
magnetic fields (at least several tesla). Both quantum Hall
effects were first noted in the 1980s, and the fractional quantum
Hall effect, although experimentally observed, has not been
theoretically resolved.
... ... *heavy-fermion: "Heavy-fermion systems" are solids in
which electrons behave as if they have masses several hundred
times their normal masses. Substances containing such electrons
have unusual thermodynamic, magnetic, and superconducting
properties that are not completely understood.
... ... *spin density waves: In general, propagating collective
spin-variation excitations associated with certain magnetic
systems.
... ... *colossal magnetoresistance: (giant magnetoresistance)
The term "magnetoresistance" refers to a change in the electrical
resistance of a conductor or semiconductor upon the application
of a magnetic field, a property of certain systems. Giant
magnetoresistance is a quantum mechanical effect observed in
magnetic thin-film structures composed of alternating
ferromagnetic and nonmagnetic layers.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 3Mar00
For more information: http://scienceweek.com/swfr.htm
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