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.

April 20, 2001 -- Vol. 5 Number 16

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We may or may not be majestic as a species,
but if one considers an astronomer sitting alone
on a cold night at a telescope on a mountain top,
one must conclude we are certainly obsessed with
knowing what and where we are.
-- Anonymous

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=-=-=-=-=-=-=-=-=
Section 1
=-=-=-=-=-=-=-=-=

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

1. CELL BIOLOGY: LIFE IN EXTREME ENVIRONMENTS
The term "extremophiles" refers to organisms, both prokaryotes
and eukaryotes, that live at the relative extreme of some
parameter, e.g., temperature, pressure, acidity, salinity, etc.
Extremes of temperature create challenges to biological
organisms, from the structural devastation produced by ice
crystals at one extreme to the denaturation of biomolecules at
the other extreme. The most hyperthermophilic organism, an
archaean prokaryote named Pyrolobus fumarii, grows at
temperatures up to 113 degrees centigrade. Organisms that can
tolerate extreme desiccation enter "anhydrobiosis", a state
characterized by little intracellular water and no metabolic
activity. Organisms that can become anhydrobiotic and survive
include bacteria, yeast, fungi, plants, insects, tardigrades,
mycophagous nematodes, and the shrimp Artemis salina. Tardigrades
can survive vacuum desiccation. Concerning salinity, some
archaea, cyanobacteria, and the green alga Dunaliella salina can
withstand periods in saturated sodium chloride.
(L.J. Rothschild and R.L. Mancinelli: Nature 22 Feb 01 409:1092)

2. IMMUNOLOGY: ON COMPLEMENT
Complement was first identified as a heat-labile principle in
serum that "complemented" antibodies in the killing of bacteria.
We now know that complement is a system of more than 30 proteins
in plasma and on cell surfaces. Complement proteins in plasma
amount to more than 3 grams per liter and constitute
approximately 15 percent of the globulin fraction. The regulatory
mechanisms of complement are finely balanced: the activation of
complement is focused on the surface of invading microorganisms,
while the deposition of complement on normal host cells is
restricted. When the mechanisms that regulate this delicate
balance go awry, the complement system may cause disease. Many
pathogens take advantage of the complement system to enhance
their virulence. Some viruses and intracellular bacteria use
cell-bound complement-regulatory molecules and receptors as a
means of gaining entry to host cells.
(Mark J. Walport: New England J. Med. 5 Apr 01 344:1058)

3. NEUROBIOLOGY: ON DYSLEXIA AND CULTURAL DIVERSITY
The learning disability called "dyslexia" has a world-wide
incidence. Researchers now report that Italian dyslexics, using a
shallow orthography, performed better on reading tasks than did
English and French dyslexics. However, all dyslexics were equally
impaired relative to their controls on reading and phonological
tasks. Positron emission tomography scans during explicit and
implicit reading showed the same reduced activity in the temporal
lobe region of the left hemisphere in dyslexics from all 3
countries. The authors conclude that a phonological processing
deficit is a universal problem in dyslexia and causes literacy
problems in both shallow and deep orthographies. However, in
languages with shallow orthographies, such as Italian, the impact
is less, and dyslexia has a more hidden existence. By contrast,
deep orthographies like that of English and French may aggravate
the literacy impairments of otherwise mild cases of dyslexia.
(E. Paulesu et al: Science 16 Mar 01 291:2165)

4. CONDENSED-MATTER PHYSICS: ON QUASIPARTICLES AND THE ORBITON
The term "quasiparticle" refers to a propagated perturbation in a
medium (or field) that behaves as a particle, with energy (mass)
and momentum, and that can be treated as such theoretically.
A basic concept in solid-state physics is that when some kind of
symmetry in a solid is spontaneously broken, collective
excitation will arise. For example, phonons are the collective
excitations corresponding to lattice vibrations in a crystal, and
magnons correspond to particle-scale magnetic perturbations
(spin-waves) in a magnetically ordered compound. Thus,
modulations in the relative shape of the electronic "clouds" in
an orbitally ordered state could in principle produce "orbital
waves" (quantized as "orbitons"). This type of elementary
excitation, however, has yet to be observed experimentally.
Researchers now report experimental evidence for orbitons in
LaMnO(sub3), using Raman scattering measurements, the study
involving a model calculation of orbiton resonances which
provides a good fit to the experimental data.
(E. Saitoh et al: Nature 8 Mar 01 410:180)

5. QUANTUM PHYSICS:
AN EXPERIMENTAL DEMONSTRATION OF FERMION VS. BOSON BEHAVIOR
The experimental achievement of Bose-Einstein condensation of
trapped atomic gases in 1995 catalyzed an explosion of research
activity in atoms obeying Bose-Einstein statistics. In contrast,
the pioneering work of DeMarco and Jin (1999) is so far the only
realization of quantum degeneracy in a trapped gas of fermions.
Researchers now report the attainment of simultaneous quantum
degeneracy in a mixed gas of bosons (lithium-7) and fermions
(lithium-6). The Fermi gas was cooled to a temperature of 0.25
times the Fermi temperature by thermal collisions with the
evaporatively-cooled bosons. At this temperature (approximately
200 nanokelvins), the spatial size of the gas is strongly
affected by the Fermi pressure resulting from the Pauli exclusion
principle, providing clear experimental evidence for quantum
degeneracy. (A.G. Truscott et al: Science 30 Mar 01 291:2570)

6. HISTORY OF PHYSICS: ON JOSEPH LOSCHMIDT
Joseph Johann Loschmidt (1821-1895) is claimed by both chemistry
and physics, made important contributions to both sciences, but
received more recognition from physicists than from chemists.
Loschmidt made perhaps the first accurate calculations of the
size of air molecules and of the number of molecules in a gram-
mole (the quantity now commonly called the Avogadro number).
Loschmidt arrived at a size somewhat less than 10^(-7)
centimeters for the diameter of the molecules in air, which is
close to the accepted value of 0.3 x 10^(-7). In German-speaking
countries, what is elsewhere called Avogadro's number is called
"Loschmidt's number". In his eulogy to Loschmidt, Ludwig
Boltzmann said of his good friend: "His work forms a mighty
cornerstone that will be visible as long as science exists...
Loschmidt's excessive modesty prevented his being appreciated as
much as he could and should have been."
(A. Bader and L. Parker: Physics Today March 2001)

7. IN FOCUS: ON CALCULATING THE CHEMICAL BOND

8. FROM THE SCIENCEWEEK ARCHIVE:
NEURODEVELOPMENTAL DAMAGE IN AUTISM: AN INFECTION-BASED MODEL


=-=-=-=-=-=-=-=-=
Section 2
=-=-=-=-=-=-=-=-=

1. CELL BIOLOGY: LIFE IN EXTREME ENVIRONMENTS
In this context, the term "extremophiles" refers to organisms,
both *prokaryotes and eukaryotes, that live at the relative
extreme of some parameter, e.g., temperature, pressure, acidity,
salinity, etc. Such organisms have been an increasing focus of
research since the 1960s, and intensive study of these organisms
has provided important insights into a number of biological
problems at several levels of biological organization, and has
also yielded some important applications.
... ... L.J. Rothschild and R.L. Mancinelli (NASA Ames Research
Center, US) present a review of current research on
extremophiles, the authors making the following points concerning
the various types of extremophiles:
     1) All biological organisms must either live within certain
conditions, or guard against the environment in order to maintain
these conditions intracellularly: a) In nearly all cases, the
water within a biological system must be liquified. Liquid water
is apparently the _sine qua non_ of life on Earth. b) Life
requires an input of energy, but an organism must also be able to
control energy flow. c) Redox chemistry is apparently universal
in living organisms; any condition that shuts down redox
chemistry is usually lethal. d) Since life is based on organic
chemistry, conditions in general must be such that organic
chemistry is allowed to operate.
     2) The authors point out that extremes of temperature create
challenges to biological organisms, from the structural
devastation produced by ice crystals at one extreme to the
denaturation of biomolecules at the other extreme. The solubility
of gases in water is correlated with temperature, creating
problems at high temperatures for aquatic organisms requiring
oxygen or carbon dioxide. Temperatures approaching 100 degrees
centigrade normally denature proteins and nucleic acids and
increase the fluidity of membranes to lethal levels. Chlorophyll
degrades above 75 degrees centigrade, excluding photosynthesis.
However, despite these restraints, thermal preferences of
biological organisms range from hyperthermophilic (maximum growth
at greater than 80 degrees centigrade) to psychrophilic (maximum
growth at less than 15 degrees centigrade). The most
hyperthermophilic organism, an *archaean prokaryote named
Pyrolobus fumarii, grows at temperatures up to 113 degrees
centigrade. Certain enzymes have high activity up to 142 degrees
centigrade. There are thermophiles among a number of groups of
prokaryotes; in contrast, the upper limit for eukaryotes is
apparently approximately 60 degrees centigrade. Concerning low
temperatures, representatives of all major taxa inhabit
environments with temperatures below 0 degrees centigrade. The
lowest recorded temperatures for active microbial communities is
approximately -18 degrees centigrade. The *nematode worm
Panagrolaimus davidi can apparently withstand the freezing of all
body water, a unique exception to the rule that frozen
intracellular water is lethal.
     3) Concerning the effects of other extremes, the authors
point out the following:
... ... a) The bacterium D. radiodurans is famous for its ability
to withstand radiation up to 20 *kilo-grays of gamma radiation
and UV radiation up to doses of 1000 joules per square meter.
... ... b) The deep sea floor (approximately 11,000 meters) of
the north Pacific Mariana trench harbors organisms that can grow
at standard temperature and pressure, but the trench has also
yielded obligatory "piezophiles" that can grow at 70 to 80
megapascals, but not below 50 megapascals.
... ... c) Organisms that can tolerate extreme desiccation enter
"anhydrobiosis", a state characterized by little intracellular
water and no metabolic activity. Organisms that can become
anhydrobiotic and survive include bacteria, yeast, fungi, plants,
insects, *tardigrades, *mycophagous nematodes, and the shrimp
Artemis salina. Tardigrades can survive vacuum desiccation.
... ... d) Concerning salinity, there are numerous species of
"halophiles", and some archaea, *cyanobacteria, and the green
alga Dunaliella salina can withstand periods in saturated sodium
chloride.
... ... e) Concerning pH, the red alga Cyanidium caldarium grows
at a pH as low as 0.5, although its growth optimum is pH 2 to 3.
The green alga Dunaliella acidophila can survive pH 0, with a
sharp growth maximum at pH 1. There are also various fungi that
grow near pH 0. The organism Ferroplasma acidarmanus has been
described growing at pH 0 in acid mine drainage in Iron Mountain,
California, the organism apparently thriving in a brew of
sulfuric acid and high levels of copper, arsenic, cadmium, and
zinc, with only a cell membrane and no cell wall. Various
archaea, bacteria, *protists, and *rotifers have been described
growing at pH 10.5.
-----------
L.J. Rothschild and R.L. Mancinelli: Life in extreme
environments.
(Nature 22 Feb 01 409:1092)
QY: Lynn J. Rothschild: lrothschild@mail.arc.nasa.gov
-----------
Text Notes:
... ... *prokaryotes and eukaryotes: In general, prokaryotes are
unicellular organisms lacking a membrane-bound cell nucleus;
eukaryotes are unicellular or multicellular organisms in which
cells do contain a membrane=bound nucleus.
... ... *kilo-grays: 1 gray (Gy) = 1 joule of radiation energy
absorbed per kilogram of tissue. 1 rad = 0.01 Gy = 100 ergs per
gram of tissue. An example of magnitude significance: The entire
human body can probably absorb a single dose of up to 2 grays
without death. But as the whole body dose approaches 4.5 grays,
the death rate is approximately 50 percent. In general, the
effect of radiation on biological systems depends on total dose
and dose rate, with biologica effects differing according to the
type of radiation. The sievert (Sv) equals the amount
of energy absorbed by a tissue or substance adjusted by a quality
factor to account for the biologic effects of different types of
radiation. For x-rays and gamma rays, the sievert equals the
gray. The approximate average total whole-body environmental
radiation from all ordinary sources of a human in the US is less
than 2 millisieverts per year.
... ... *archaean prokaryote: In current biotaxonomy, the
prokaryotes are divided into two groups, Archaea and Bacteria,
the groups differing primarily in certain biochemical attributes.
... ... *nematode worm: An abundant and ubiquitous phylum of
unsegmented roundworms.
... ... *tardigrades: An order of minute aquatic arthropods.
... ... *mycophagous nematodes: In general, nematodes that feed
on fungi.
... ... *cyanobacteria: A phylum of bacteria characterized by
blue-green (cyan) photosynthetic pigments, abundant in a variety
of habitats, particularly in fresh water and soil. Cyanobacteria
are responsible for generating a large portion of the free oxygen
in the Earth's atmosphere. They apparently produced stromatolite
limestone deposits, as well as the bulk of modern petroleum
deposits. (Stromatolites are laminated calcareous microbial
fossil deposits formed principally by cyanobacteria and algae.)
... ... *protists: (Proctista) One of the phylogenetic kingdoms,
this category is defined mostly by exclusion and contains all the
eukaryotic nucleated organisms that cannot be classified as
animal, plant, or fungus. Protists include protozoans, algae,
kelps, slime molds, and many obscure eukaryotes.
... ... *rotifers: An abundant and widespread phylum of
microscopic multicellular animals the size of large protozoa but
at the "organ" level of organization.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 20Apr01
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
BIOCHEMISTRY: ON THE PUZZLES OF HYPERTHERMOPHILES
     In this context, the term "geothermal" refers to the escape
of heat from the interior of the Earth into the Earth's surface,
and the term "hydrothermal" refers to hot solutions rising from 
cooling molten rock (magma). "Hydrothermal vents" are hot springs
occurring in volcanic regions of the ocean floor. The heavy-metal
ions and hydrogen sulfide dissolved in the overheated vent fluid
precipitate as metal sulfides as soon as contact with seawater
cools the fluid. This reaction produces the characteristic
underwater black "smoke" plume, with a vent "smoker chimney"
building up from precipitated materials, mostly gypsum and
sulfides.
     "Plate tectonics" is the modern theory that unifies many of
the features and characteristics of continental drift and sea
floor spreading into a coherent model. Continental drift is the
slow movement of the Earth's land masses, a shifting across the
underlying molten material. Sea-floor spreading is the process
whereby sea floor is continuously created as the crustal plates
move apart, and continuously destroyed where the plates push
against each other. The term "mid-ocean(ic) ridge" refers to a
topographic feature of a tectonic spreading center between
diverging oceanic plates. New crustal material is formed by
upswelling magma (molten material from which rock forms) as the
plates diverge.
     In general, bacteria have adapted to a wide range of
temperatures, with the range of temperature over which optimal
growth can occur in any one species spanning approximately 20
degrees centigrade; the range over which any growth at all takes
place usually spans approximately 40 to 50 degrees centigrade.
     Bacteria that grow at temperatures of less than 15 degrees
centigrade are called "psychrophiles". Obligate psychrophiles,
which have been isolated from Arctic and Antarctic ocean waters
and sediments, have optimum growth temperatures of approximately
10 degrees centigrade and do not survive if exposed to 20 degrees
centigrade.
     The term "mesophilic bacteria" refers to those bacteria in
which optimum growth occurs between 20 and 45 degrees centigrade;
such bacteria can usually grow in or survive temperatures between
10 and 50 degrees centigrade, and all animal pathogens are in
this group.
     So-called "thermophilic bacteria" are the only organisms
that can grow at temperatures higher than 60 degrees centigrade.
Such temperatures are encountered in rotting compost piles, hot
springs, and oceanic geothermal vents. In the runoff of a hot
spring, various thermophiles are found near the source where the
temperature has fallen to approximately 70 degrees centigrade. An
example is the species Thermus aquaticus, which has an optimum
temperature for growth of 70 degrees centigrade, and a maximum
temperature for growth of 79 degrees centigrade.
     In the mid-1980s, researchers discovered bacteria in
nutrient-rich, extremely hot hydrothermal vents in the deep sea
floor. For example, the bacteria in the genus Pyrodictium thrive
in the temperature range 80 to 110 degrees centigrade,
temperatures at which the water remains liquid only because of
the extremely high pressure.
... ... R.A. Zierenberg et al (3 authors at 3 installations, US)
present a review of current research on life in extreme
environments such as hydrothermal vents, the authors making the
following points concerning current puzzles in this area:
     1) The authors point out that eruption of volcanic rocks at
mid-ocean ridges is the major mechanism by which heat is lost
from the interior of the Earth. Approximately one-third of the
heat is removed from the sea-floor spreading centers by
convective circulation of sea water, and the magnitude of this
heat loss requires that the entire volume of the oceans
circulates through the mid-ocean ridges in approximately 10
million years. Seawater interaction with volcanic rocks at near
400 degrees centigrade results in substantial chemical flux and
makes an important contribution to buffering the composition of
some elements in sea water. Sea-floor hydrothermal vents support
ecosystems with enormous biomass and productivity compared with
that observed elsewhere in the deep oceans. What is the energy
source that fuels these oases of life and what adaptations allow
them to exist in these extreme environments?
     2) Although there is a potential abundance of chemical
energy at hydrothermal vents, deep-sea hydrothermal biological
communities have had to adapt to extreme conditions to exploit
this resource. Of particular interest are the hyperthermophiles,
which are defined as microorganisms able to grow at 90 degrees
centigrade and above. Approximately 20 different types of such
organisms are now known. They have been found both within the
walls of black smoker chimneys and where the hydrothermal vent
fluids mix with the surrounding seawater. Classifications of the
hyperthermophiles has provided new insights into the evolution
and the origin of life. All but two of the hyperthermophilic
genera are classified by *ribosomal RNA analysis as "Archaea"
(formerly Archaebacteria), which are the second domain of
prokaryotic life, in addition to the bacteria. By these
phylogenetic analyses, the hyperthermophilic archaea types and
the two hyperthermophilic bacteria types are the most slowly
evolving within their domains, suggesting that life may have
first evolved when the Earth was much hotter than it is now. Such
a thesis is very controversial, the thesis suggesting that extant
life forms are largely the result of temperature adaptations to
lower (below hyperthermophilic) temperatures.
     3) Evolution gives no clue, however, as to how life can
thrive near and above 100 degrees centigrade. Most microbes, and
all *eukaryotic cells, cannot survive at temperatures much above
50 degrees centigrade because of the general instability of
biological molecules. The 3-dimensional structure of most enzymes
and other proteins are lost at temperatures much above 70 degrees
centigrade, and the double-helical structure of DNA has a
comparable lack of stability in _in vitro_ studies. There are
also a wide variety of ubiquitous metabolites that are rapidly
hydrolyzed at temperatures above 90 degrees centigrade. How do
hyperthermophilic cells circumvent these problems?
     4) Although there are some examples of modified pathways and
unusual enzymes in hyperthermophiles, in general the biochemistry
of these organisms closely resembles that of the mesophilic
world. Yet, most enzymes from hyperthermophiles are extremely
stable at high temperatures, showing optimal catalytic activity
above 100 degrees centigrade with virtually no activity at
ambient temperature. These enzymes contain exactly the same 20
amino acids as enzymes from conventional organisms, so why are
they so stable? Sequence comparisons of analogous proteins from
hyperthermophilic and conventional organisms are essentially
identical, so the enormous amount of sequence information now
becoming available will be of little use in elucidating
stabilizing mechanisms. Comparisons must be made at the level of
3-dimensional structures, yet even then, there are no gross
structural differences between hyperthermophilic proteins and
their mesophilic counterparts, and both forms are stabilized by
the same noncovalent interactions. The number and extent of such
interactions is generally only slightly higher in the
hyperthermophilic versions, so extended protein stability at 100
degrees centigrade appears to be the result of very subtle,
synergistic, and cooperative intramolecular interactions.
Moreover, different types of hyperthermophilic proteins seem to
have unique solutions to the problem. A general mechanism by
which any conventional protein could be made stable and
functional at temperatures above 100 degrees centigrade may not
be forthcoming.
-----------
R.A. Zierenberg: Life in extreme environments: Hydrothermal
vents.
(Proc. Natl. Acad. Sci. US 21 Nov 00 97:12961)
QY: Robert A. Zierenberg: Univ. of California Davis 530-752-1863.
-----------
Text Notes:
... ... *ribosomal RNA: A ribosome (not to be confused with
riboZYME) is a small particle, a complex of various ribonucleic
acid component subunits and proteins that functions as the site
of protein synthesis. The tripartite kingdom proposal (Archaea,
Bacteria, Eukarya) of Woese and others is primarily based on gene
sequence analysis of particular ribosomal RNA fractions.
... ... *eukaryotic cells: In general, a eukaryotic cell is any
biological cell containing internal membrane-bound organelles
such as a nucleus.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 19Jan01
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
EVIDENCE AGAINST A HYPERTHERMOPHILIC COMMON LIFE ANCESTOR
An apparent feature of genome sequences is the presence of traces
of extremely ancient evolutionary events, including perhaps the
very first steps of life on Earth. In the late 1970s, by
sequencing small-subunit *ribosomal RNA (rRNA) genes from various
*eukaryotic and prokaryotic species, Woese and colleagues
constructed for the first time a comprehensive picture of the
"universal tree of life". This work gave rise to conjectures
about the nature of the "most recent common ancestor" of extant
life forms. A hot *auxotrophic origin of life was hypothesized,
consistent with conjectures about the former temperature of
Earth. This scenario was later endorsed by numerous authors and
reached the status of a working hypothesis for the early
evolution of life on Earth. Some researchers, however, have
repeatedly criticized this view, arguing that present-day
*hyperthermophily may be a derived state. Resolution of the
question is considered to be dependent on molecular data, but the
molecular data are obscured by numerous nucleotide base
substitution events that have occurred during billions of years
of *diverging evolution. One approach is to construct realistic
models of molecular evolutionary processes in order to
discriminate between molecular evolutionary signals and noise.
... ... N. Galtier et al (3 authors at 3 installations, FR US)
present a modeling approach to the question of the "most recent
common ancestor". The authors consider the fact that the
nucleotide guanine + cytosine (G + C) content of ribosomal RNA
sequences is apparently strongly correlated with the optimal
growth temperature of prokaryotes. The authors propose that this
property allows inference of the environmental temperature of the
common ancestor to all life forms from knowledge of the G + C
content of the ribosomal RNA sequences of the supposed common
ancestor. The authors devised a model of sequence evolution,
assuming varying G + C content among lineages and unequal
substitution rates among genome sites, the purpose of the model
to estimate ancestral nucleotide base compositions. The authors
applied the model to ribosomal RNA sequences of various species
representing the major apparent lineages of life. The authors
report the inferred G + C content of the common ancestor to
extant life forms appears incompatible with survival at high
temperature, and they suggest this finding challenges the widely
accepted hyperthermophilic origin of life hypothesis. Concerning
extant hyperthermophilic species, the authors suggest these forms
evolved from mesophilic organisms via adaptation to high
temperatures. The authors state: "The hypothesis of a hot origin
of life cannot be ruled out (it may have preceded the "most
recent common ancestor"), but no support from rRNA sequences can
be claimed for it."
-----------
N. Galtier et al: A nonhyperthermophilic common ancestor to
extant life forms.
(Science 8 Jan 99 283:220)
QY: Nicolas Galtier, University C. Bernard, Lyon 1, FR.
-----------
Text Notes:
... ... *ribosomal RNA: A ribosome (not to be confused with
riboZYME) is a small particle, a complex of various ribonucleic
acid component subunits and proteins that functions as the site
of protein synthesis.
... ... *eukaryotic and prokaryotic species: Eukaryotes are cells
(and organisms consisting of such cells) that contain
intracellular membrane-bound compartments such as a nucleus
(membrane-bound "organelles"). Prokaryotes are cells (e.g.,
bacteria) without such compartments.
... ... *auxotrophic: An "auxotrophe" is a mutant species
variety, usually a microorganism, that will proliferate only when
its growth medium contains certain specific nutrients not
required by the wild-type (non-mutated) members of the species. 
... ... *hyperthermophily: In general, hyperthermophiles are 
microorganisms whose optimal growth temperature lies above 80
degrees centigrade.
... ... *diverging evolution: In this context, "divergence" is
the acquisition of dissimilar characteristics by related 
organisms in unlike environments.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 2Apr99
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
COMPLETE GENOME OF A HYPERTHERMOPHILIC BACTERIUM
In evolutionary biology, the term "divergence" refers to the
manifestation of new genetic characteristics in a subpopulation
of a species when the subpopulation has become separated from the
larger population by physical barriers -- new genetic
characteristics appearing as the organism adapts to new
conditions. Thermophiles are microorganisms that thrive under
conditions of high temperature such as those in hot springs and
deep ocean vents. "E. coli" refers to the bacterium Escherichia
coli, a rod- shaped intestinal organism that has been used
extensively in research.
... ... Deckert et al (15 authors at 4 installations, US DE)
report the complete genome sequence of Aquifex aeolicus. The
organism is apparently one of the earliest to diverge, and is one
of the most thermophilic bacteria known. It can grow on hydrogen,
oxygen, carbon dioxide, and mineral salts, and at 95 deg C. The
complete genome is one-third the size of the E. coli genome, with
1,551,335 DNA base pairs. The authors suggest that the large
number of diverse genome sequences of various biological
organisms that will become available in the future will allow
more detailed correlation of global genomic properties with
particular physiologies.
QY: Ronald V. Swanson: rswanson@diversa.com
(Nature 26 Mar 98) (Science-Week 10 Apr 98)
For more information: http://scienceweek.com/swfr.htm

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

2. IMMUNOLOGY: ON COMPLEMENT
     In the history of science, it often happens that important
discoveries result from simple observations. In 1898, Jules
Bordet (1870-1961) noted that if blood serum is heated to 56
degrees centigrade, the *antibodies within the serum are not
destroyed (as evidenced by the fact that the serum still reacts
with antigens), but the ability of the serum to destroy bacteria
is lost. The conclusion was that some fragile heat-labile
component or group of components of serum acts as a "complement"
to antibodies and makes it possible for serum to react with
bacteria. Bordet called the component "alexin", but the eminent
microbiologist Paul Ehrlich (1854-1915) named the mystery
substance "complement", and so it is called today. In 1901,
Bordet demonstrated that when an antibody reacts with an antigen
in serum, complement is depleted, a process called "complement
fixation", and this became of practical importance in immunology,
and is the basis of the Wasserman syphilis test. In 1919, Bordet
received the Nobel Prize in Physiology and Medicine for his work
with complement.
     The "complement system", as it is now called, consists of a
group of more than 30 normally inactive proteins in blood plasma
and in cell membranes. When activated, these proteins enhance
certain immune, allergic, and inflammatory reactions. The
complement system includes 11 proteins named C1 through C9, with
3 forms of C1, cell-surface complement proteins called "factors",
and a number of other proteins that participate in and regulate
complement activation. Complement proteins are synthesized mainly
by the liver and by certain cells of the immune system
(phagocytes; also called "macrophages") that attack and digest
foreign material and debris. Several compliment proteins are
cleaved during activation of the complement system, and the
fragments are designated by lowercase suffixes, e.g., C3a, C3b.
     In general, activation of the complement system involves a
cascade of activations, one complement protein activating another
complement protein in a response chain.
     A key member of the complement system is a plasma protein
called C3, which can be activated in two ways. Activation of C3
by the "classical pathway" is linked to the immune system, the
activation depending on the formation of complexes between
antibodies and the antigenic microbe that triggered the
production of antibodies. Activation of C3 via the "alternative
pathway" involves certain polysaccharides on the surface of a
microbe, the polysaccharides capable of directly activating C3.
The alternative pathway is as important as the classical pathway;
it was merely discovered later. Once C3 is activated, it
activates other complement proteins which attack and destroy
microbes by the following mechanisms:
     1) Activation of inflammation: Certain complement proteins
contribute to the development of *inflammation, dilate
*arterioles (which causes a local increase in blood flow), and
cause the release of histamine from various histamine secreting
cells. Histamine increases the permeability of blood capillaries,
and this enables white blood cells (leukocytes) to more easily
penetrate tissues to combat infection or allergy. Other
complement proteins serve as "chemotactic" agents that attract
microbe-eating cells (phagocytes) to the site of microbial
invasion.
     2) Opsonization: A specific complement fragment (C3b) binds
to the surface of a microbe and then interacts with receptors on
phagocytes to promote phagocytosis. This coating of a microbial
surface is called "opsonization" or "immune adherence".
     3) Cytolysis (lysis): Several complement proteins come
together to form a "membrane attack complex" (MAC) that literally
punches holes in the plasma membrane of the microbe, the holes
causing the microbe to rupture, the process called "cytolysis".
     In biology, the "immunity" of organisms to infection by
various pathogens is functionally characterized into 2 types: The
term "innate immunity" refers to non-specific antimicrobial
systems of response (e.g., phagocytosis: engulfment and digestion
of microbes by "killer" cells) that are innate and not
intrinsically affected by prior contact with the infectious
agent; the term "adaptive immunity" refers to immune responses
which involve an enhanced ability to respond to specific
molecular antigens presented by the invading pathogenic entity,
the enhancement dependent on prior contact with the same
pathogen. In addition, the concept of innate immunity generally
refers to the first-line host defense that serves to limit
infection in the early hours after exposure to microorganisms. 
     The term "immunologic memory" (immune memory) refers in
general to a capability of the immune system to modify and
enhance its responses based on its previous experience with
particular pathogens.
     In general, the term "apoptosis" refers to programmed cell
death, whether as a part of normal tissue differentiation and
development, or as a program activated in a defective cell.
Invasion by pathogens often causes apoptosis in host cells.
     In general, the term "globulin" refers to any simple and
globular protein insoluble or sparingly soluble in water but
soluble in dilute salt solutions. The term "globulins" should not
be confused with "immunoglobulins", which refers specifically to
antibodies. Complement proteins are globulins.
... ... Mark J. Walport (Imperial College of Science, Technology,
and Medicine London, UK) presents a review of current knowledge
of complement, the author making the following points:
     1) The author points out that complement is part of the
innate immune system and underlies one of the main effector
mechanisms of antibody-mediated immunity. The complement system
is involved in 3 main physiological activities:
... ... a) Host defense against infection, which includes
opsonization of bacterial surfaces, chemotaxis and activation of
leukocytes, and lysis of bacteria and other cells.
... ... b) Action at the interface between innate and adaptive
immunity, which includes augmentation of antibody responses and
enhancement of immunologic memory.
... ... c) Disposal of waste, which includes clearance of immune
complexes from tissues and clearance of apoptotic cells.
     2) The author points out that complement was first
identified as a heat-labile principle in serum that
"complemented" antibodies in the killing of bacteria. We now know
that complement is a system of more than 30 proteins in plasma
and on cell surfaces. Complement proteins in plasma amount to
more than 3 grams per liter and constitute approximately 15
percent of the globulin fraction. The nomenclature of the various
proteins of the complement system follows the historical order of
discovery and is rather chaotic.
     3) The author points out that the regulatory mechanisms of
complement are finely balanced: the activation of complement is
focused on the surface of invading microorganisms, while the
deposition of complement on normal host cells is restricted. When
the mechanisms that regulate this delicate balance go awry, the
complement system may cause disease.
     4) The author points out that many pathogens take advantage
of the complement system to enhance their virulence. Some viruses
and intracellular bacteria use cell-bound complement-regulatory
molecules and receptors as a means of gaining entry to host
cells. Some organisms activate host complement, thereby causing
C3b to bind to their surfaces; this process allows the microbe to
use C3 receptors to enter the cell. The human immunodeficiency
virus (HIV) and pathogenic *mycobacteria use this mechanism. In
general, bacteria can evade complement if they have thick outer
layers of extracellular polymer (capsules) that form a physical
barrier against the membrane-attack complex, or if they express
proteins that inhibit the activation of complement. In general,
viruses have 3 ways of evading complement: a) Some viruses, such
as HIV, incorporate complement-regulatory proteins into their
viral envelope. b) Other viruses have proteins that are
structural mimics of complement regulatory proteins. c) Still
other viruses use proteins that have no structural homology to
complement regulatory proteins but that nevertheless have similar
functional properties.
-----------
Mark J. Walport: Complement.
(New England J. Med. 5 Apr 01 344:1058)
QY: Mark J. Walport: m.walport@ic.ac.uk
-----------
Text Notes:
... ... *antibodies: In general, an "antibody" is a protein
molecule produced by the immune system of vertebrate organisms,
the molecule designed to specifically interact with a particular
invading foreign "antigen". In general, an antigen is any
substance or moiety that produces an immune response.
... ... *inflammation: In general, inflammation is a fundamental
pathologic process consisting of a dynamic complex of cellular
and chemical reactions occurring in affected blood vessels and
adjacent tissues in response to an injury or abnormal stimulation
caused by physical, chemical, or biological agents.
... ... *arterioles: Small near-microscope arteries that deliver
blood to capillaries.
... ... *mycobacteria: The mycobacteria (of which there are more
than 50 species) are rod-shaped aerobic bacteria that do not form
spores. The two chief mycobacteria human disease pathogens are M.
tuberculosis (which causes tuberculosis) and M. leprae (which
causes leprosy).
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 20Apr01
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
MEDICAL BIOLOGY: ON THE IMMUNE SYSTEM
Our environment is filled with a variety of infectious agents,
including bacteria, viruses, parasites, and fungi, and the
essential line of defense against these pathogenic invaders is
the "immune system". This system, an evolutionary development in
vertebrates, involves a complex set of dynamic interactions
between various specialized cells, the interactions mediated by
chemistry. An important component is an evolved genomic apparatus
that essentially provides for an "immune memory", which in
general is a capability of the immune system to modify and
enhance its responses based on its previous experience with
particular pathogens. Nowhere is the idea of the human body as a
colony of cells more clear than in consideration of the
cooperative interactions of the various cells of the immune
system functioning to protect the entire organism.
... ... P.J. Delves and I.M. Roitt (University College London,
UK) present an extensive 2-part review of current knowledge
concerning the human immune system, the authors making the
following points:
     1) In humans, there are two fundamentally different types of
responses to invading microbes: a) innate (natural) responses
that occur to the same extent however many times the infectious
agent is encountered; b) acquired (adaptive) responses that
improve after repeated exposure to a given infection.
     2) The innate immune response involves a) various
specialized "phagocytes" (neutrophils, monocytes, macrophages),
cells that "eat" pathogens; b) various cells (basophils, mast
cells, eosinophils) that release *inflammatory mediator
substances; c) *natural "killer" cells. The molecular components
of innate responses include a variety of identified proteins
(e.g., *complement, *cytokines).
     3) The acquired immune response involves the proliferation
of *antigen-specific *B and T cells, which occurs when the
surface receptors of these cells bind to antigen. Specialized
cells, called "antigen-presenting cells", display the antigen to
*lymphocytes and collaborate with them in the response to the
antigen. B cells secrete *immunoglobulins, the antigen-specific
*antibodies responsible for eliminating extracellular
microorganisms. T cells help B cells to make antibody and can
also eradicate intracellular pathogens by activating macrophages
and by killing virally infected host cells. In general, innate
and acquired responses usually work together to eliminate
pathogens.
     4) The various cells of the immune system develop from
*pluripotent stem cells in the fetal liver and in bone marrow and
then circulate throughout the extracellular fluid. B cells reach
maturity within the bone marrow, but T cells must travel to the
thymus gland to complete their development.
     5) Adaptive immune responses are generated in the *lymph
nodes, spleen, and *mucosa-associated lymphoid tissue, all of
which are called "secondary lymphoid tissues": a) In the spleen
and lymph nodes, the activation of lymphocytes by circulating
antigen occurs in distinctive B cell and T cell compartments of
lymphoid tissue. b) The mucosa-associated lymphoid tissues,
including the tonsils, adenoids, and *Peyer's patches, defend
mucosal surfaces. c) Diffuse collections of lymphoid cells are
present throughout the lung and *lamina propria of the intestinal
wall.
     6) To establish an infection, a pathogen must first overcome
numerous surface barriers, such as enzymes and mucus, that are
either directly antimicrobial or that inhibit attachment of the
microbe. Because neither the *keratinized surface of the skin nor
the mucus-lined body cavities are ideal habitats for most
organisms, microbes must breach the *ectoderm. Any organism that
breaks through this first barrier encounters the two further
levels of defense, the innate and acquired immune responses.
-----------
P.J. Delves and I.M. Roitt: The immune system.
(New England J. Med. 6 Jul 00 343:37)
(New England J. Med. 13 Jul 00 343:108)
QY: Peter J. Delves, Dept. of Immunology, University College
London, UK.
-----------
Text Notes:
... ... *inflammatory mediator substances: In general, an
"inflammatory change" is a response of tissues to irritation or
injury. The response involves a dynamic complex of cellular and
chemical reactions that occur in the affected blood vessels and
adjacent tissues.
... ... *natural "killer" cells: Cells of the innate immune
response that recognize and then kill abnormal cells such as
certain infected cells and tumor cells.
... ... *complement: A group of more than 30 interacting serum
proteins, mostly enzymes, which are activated during the immune
response, and which participate in bacterial lysis (destruction
of bacteria by disruption of cell membrane) and macrophage
chemotaxis (chemical attraction of macrophages, immune system
amoeba-like cells active in phagocytosis of bacteria and other
particulates.)
... ... *cytokines: A cytokine is any substance that promotes
cell growth and cell division. Cytokines mediate many functions
of the immune system.
... ... *antigen: In general, an antigen is any entity that
provokes an immune response, and this includes, in certain
disease states, entities that are not "foreign" to the body.
... ... *B and T cells: (B and T lymphocytes) Lymphocytes (lymph
cells, lympho-leukocytes) are a type of leukocyte (white blood
cell) responsible for the immune response. In general, there are
two classes of lymphocytes: 1) the B-cells, when presented with a
foreign chemical entity (antigen), change into antibody producing
plasma cells; 2) the T-cells, which interact directly with
foreign invaders such as bacteria and viruses, and some types of
which assist B-cells in the B-cell response. The general
terminological differentiation between B-cells and T-cells is
based on where the cells mature: B-cells mature in (b)one marrow,
and T-cells mature in the (t)hymus gland.
... ... *lymphocytes: See above note.
... ... *immunoglobulins: (antibody): The immunoglobulins are a
large glycoprotein category that includes antibodies as a subset.
In general, an "antibody" is a protein molecule produced by the
immune system of vertebrate organisms, the molecule designed to
specifically interact with a particular antigen.
... ... *antibodies: See above note.
... ... *pluripotent stem cells: In general, the term "stem"
cells refers to undifferentiated cells that upon differentiation
can give rise to various specialized cell lines such as blood
cells, skin cells, nerve cells, etc. Adult bone marrow, for
example, contains stem cells that are the precursors of the
various specialized types of blood cells. "Pluripotent stem
cells" are stem cells that have the capacity to differentiate
into various cell types.
... ... *lymph nodes: The lymphatic system is a complex network
for the distribution of lymph fluid (which is similar to blood
plasma -- blood without red cells). Lymph is collected by
drainage from the tissues throughout the body, flows in the
lymphatic vessels through the lymph nodes, and is eventually
added to the venous blood circulation. Lymph consists of a clear
liquid portion, varying numbers of white blood cells (chiefly
lymphocytes), and a few red blood cells. The lymph nodes are
small bodies located throughout the lymph system and varying in
diameter from 0.1 to 2.5 centimeters.
... ... *mucosa: In general, a multilayer tissue lining various
tubular structures in the body.
... ... *Peyer's patches: Aggregated lymphoid nodules of the
small intestine.
... ... *lamina propria: The layer of connective tissue
underlying the *epithelial layer of a mucosa. 
... ... *epithelial layer: In animals and humans, epithelial
cells compose the cell layers that form the interface between a
tissue and the external environment, for example, the cells of
the skin, the lining of the intestinal tract, and the lung airway
passages.
... ... *keratinized: Keratin is a protein which helps waterproof
and protect the skin and underlying tissues.
... ... *ectoderm: In the embryos of higher animals, there
occurs the transformation of a single-layer "blastula" into a
3-layered "gastrula" consisting of ectoderm (outermost layer),
mesoderm (middle layer), and endoderm (innermost layer)
surrounding a cavity with one opening. The 3 layers are called
the "germ layer", and these layers, via further cell
differentiation and proliferation, determine the development of
all the major body systems and organs.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 21Jul00
For more information: http://scienceweek.com/swfr.htm

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

3. NEUROBIOLOGY: ON DYSLEXIA AND CULTURAL DIVERSITY
     In this context, the term "learning disorder" refers to an
inability to acquire, retain, or generalize specific skills or
sets of information because of deficiencies in attention, memory,
perception, or reasoning. The term "learning disability" refers
to a specific learning disorder, assumes normal cognitive
abilities, and refers specifically to a problem in reading (e.g.,
dyslexia), arithmetic (e.g., dyscalculia), spelling, written
expression, or handwriting (dysgraphia), and in the understanding
and/or use of verbal abilities (e.g., dysphasia, dysnomia) and
nonverbal abilities. 
     What is called "developmental dyslexia" refers to a specific
learning disability, a reading disorder, usually due to
congenital deficiencies in phonologic processing or phoneme
awareness. Other problems with different forms of written
language, such as spelling, reading fluency (rate and accuracy),
and reading comprehension may also be affected. Dyslexics do not
have difficulty understanding spoken language. No definition of
dyslexia is universally accepted, so the incidence is
undetermined. In the US, an estimated 15 percent of public school
children receive special education for reading problems, and it
is believed that 3 to 5 percent of this group are probably
dyslexic. More males than females (approximately 5:1) are
diagnosed with this disability.
     Dyslexia is believed to be due to intrinsic brain factors,
but the underlying cause is unknown. A strong genetic link has
been established, and dyslexia tends to run in families.
Cerebrovascular accidents, prematurity, and intrauterine
complications have been linked to dyslexia. The condition of
"alexia", in which there is almost a complete inability to read,
may also stem from direct insult or trauma to the brain. At the
level of neurobiology, dyslexia is believed to result
predominantly from specific cortical dysfunctions stemming from
congenital neurodevelopmental abnormalities. Many neurobiologists
believe lesions affecting the integration or interactions of
specific brain functions are involved. Asymmetries of the left
and right hemispheres, fewer neurons in specific loci, and
smaller specific language-related gross anatomical regions have
been proposed. Most researchers agree that dyslexia is left-
hemisphere related and associated with deficiencies or
dysfunctions in the areas of the brain responsible for language
association (Wernicke's area) and sound and speech production
(Broca's area), and in the interconnection of these areas via the
fiber tract called the "arcuate fasciculus".
... ... E. Paulesu et al (11 authors at 9 installations, IT, FR,
UK, CA) now report a study of cultural diversity vs. biological
dysfunction in dyslexia, the authors making the following points:
     1) The authors point out that in languages with "transparent
or shallow orthography" (e.g., Italian), the letters of the
alphabet, alone or in combination, are in most instances uniquely
mapped to each of the speech sounds occurring in the language.
Learning to read in such a language is easier than in languages
with "deep orthography" (e.g., English and French), where the
mapping between letters, speech sounds, and whole-word sounds is
often highly ambiguous. Adult skilled readers show a speed
advantage in shallow orthographies, and differences have also
been demonstrated at the physiological level.
     2) The authors point out that developmental dyslexia is
increasingly acknowledged to be a disorder of genetic origin with
a basis in the brain. However, there continues to be doubt about
the universality and specificity of the syndrome because
behavioral studies have demonstrated that the nature and
prevalence of dyslexia differs across languages. The prevalence
estimates of dyslexia in different countries seem to be related
to the shallowness of the orthography. For example, using one of
the most respected behavioral definitions of dyslexia (word
recognition accuracy in relation to IQ), the prevalence of
dyslexia in Italy is apparently half that in the US.
     3) The aim of the study reported by the authors was to
contrast dyslexic and normal adult readers in deep (English and
French) and shallow (Italian) orthographies in order to explore
similarities and differences at both the behavioral and
neurophysiological level. If dyslexia has a universal basis, then
substantial similarities should be found, either at the cognitive
or at the brain level, or both. The authors investigated single-
word reading at explicit and automatic levels, because
differential response to the written word is the most widely
accepted defining behavioral feature of dyslexia. Given that
stimuli differ between different orthographies, and given that
orthographic depth affects reading difficulty, any commonality
found in underlying physiological responses in dyslexics would be
strong evidence for a unitary biological basis.
     4) The authors report that Italian dyslexics, using a
shallow orthography, performed better on reading tasks than did
English and French dyslexics. However, all dyslexics were equally
impaired relative to their controls on reading and phonological
tasks. *Positron emission tomography scans during explicit and
implicit reading showed the same reduced activity in the
*temporal lobe region of the left hemisphere in dyslexics from
all 3 countries, with the maximum reduction in activity compared
to controls in the middle temporal *gyrus and additional
reductions in activity in the inferior and superior temporal
gyri.
     5) The authors conclude: "A phonological processing deficit
is a universal problem in dyslexia and causes literacy problems
in both shallow and deep orthographies. However, in languages
with shallow orthographies, such as Italian, the impact is less,
and dyslexia has a more hidden existence. By contrast, deep
orthographies like that of English and French may aggravate the
literacy impairments of otherwise mild cases of dyslexia."
-----------
E. Paulesu et al: Dyslexia: Cultural diversity and biological
unity.
(Science 16 Mar 01 291:2165)
QY: E. Paulesu: eraldo.paulesu@unimib.it
-----------
Text Notes:
... ... *Positron emission tomography: (PET) Positron emission
tomography is a technique for producing cross-sectional images of
the body after ingestion and systemic distribution of safely
metabolized positron-emitting agents. The images are essentially
functional or metabolic, since the ingested agents are
metabolized in various tissues. Fluoro-deoxyglucose and
H(sub2)O(sup15) are common agents used for cerebral applications,
and in cerebral applications of central importance to the
technique is the fact that changes in the cellular activity of
the brains of normal, awake humans and unanesthetized laboratory
animals are invariably accompanied by changes in local blood flow
and also changes in oxygen consumption.
... ... *temporal lobe: One of the 4 lobes of each hemisphere of
the brain, this lobe situated under the skull at the side of the
head.
... ... *gyrus: In general, the term "gyrus" refers to any of the
visible convoluted ridges of the cerebral hemispheres.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 20Apr01
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
ON DYSLEXIA AND FUNCTIONAL DISRUPTION IN BRAIN ORGANIZATION
Dyslexia is impaired reading ability when the reading competence
is below that expected from the individual's general intelligence
and there is no impairment of vision. It has been proposed that
dyslexic children and adults lack phonologic awareness, an
awareness that strings of letters (orthography) are connected to
corresponding units of speech (phonologic constituents) that they
represent. In biology, magnetic resonance imaging is a technique
involving images produced by mobile protons of a tissue excited
by the application of a magnetic field, and when used in
functional cerebral imaging, the basis of the technique is that
it images very small metabolic, blood-flow, and
perfusion-diffusion changes in vivo, in real time, and with no
risk to the subject, with the essential idea of mapping activity
in the brain in response to external stimuli or during sensory,
perceptual, or cognitive events. ... ... Now Shaywitz et al (15
authors at 2 installations, US) report a study to find the
location and extent of the functional disruption in neural
systems that underlies dyslexia. Functional magnetic resonance
imaging was used to compare brain activation patterns in dyslexic
and nonimpaired subjects as they performed tasks that made
progressively greater demands on phonologic analysis. Brain
activation patterns differed significantly between the groups,
with dyslexic readers showing underactivation in certain specific
brain areas and overactivation in other specific brain areas. The
authors suggest their results support a conclusion that the
impairment in dyslexia is phonologic and that brain activation
patterns may provide a neural signature for this impairment.
-----------
QY: Sally E. Shaywitz: sally.shaywitz@yale.edu
(Proc. Natl. Acad. Sci. US 3 Mar 98) (Science-Week 10 Apr 98)
For more information: http://scienceweek.com/swfr.htm

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

4. CONDENSED-MATTER PHYSICS: ON QUASIPARTICLES AND THE ORBITON
     In this context, the term "quasiparticle" refers to a
propagated perturbation in a medium (or field) that behaves as a
particle, with energy (mass) and momentum, and that can be
treated as such theoretically. Quasiparticles are important
conceptions in condensed-matter physics and nuclear physics, and
in the case of condensed-matter physics, the quasiparticles of
current significance are as follows:
     In crystals, a "hole" is a quasiparticle produced by the
movement of valence electrons through certain metals and
semiconductors, the movement resulting in the creation of a
vacancy in a corresponding energy state. Each vacancy (hole)
represents the absence of an electron from an accessible energy
state in the solid and thus is a center of positive charge.
     An "exciton" is a combination of an electron and a positive
hole, the exciton free to move through a nonmetallic crystal as a
unit. Although it transports energy, the exciton has no net
electrical charge. When an electron in an exciton recombines with
a hole, the original atom is restored and the exciton vanishes.
When this occurs, the energy of the exciton may be converted into
light, or the energy may be transferred to an electron of a
neighboring atom with the production of a new translocatable
exciton.
     A "phonon" is a quantum of crystal-lattice vibration energy,
essentially a wave-packet with particle-like properties. Various
properties of solids can be viewed as determined by the behavior
characteristics of phonons, particularly the thermal conductivity
of insulators and the superconductivity of certain metals. In
most metallic solids, phonons act as electron scatterers; in some
solids at low temperatures, however, phonons may provoke
cooperative phenomena among electrons to produce
superconductivity.
     A "magnon" is a small quantity of propagated energy
corresponding to a specific propagated decrease in magnetic
strength, the perturbation traveling as a unit through a magnetic
substance. In general, as the temperature of a magnetic substance
is increased, its magnetic strength decreases, corresponding to
the presence of a large number of magnons.
     The term "polaron" refers to an electron moving through
constituent atoms in a solid, with the electron causing
neighboring positive charges to shift toward it and neighboring
negative charges to shift away. Thus, a polaron is essentially a
propagated polarization. In general, a polaron behaves as a
negatively charged particle with a mass greater than that of an
isolated electron, the increased mass due to the energy of
interaction with the surrounding atoms of the solid. Polaron
phenomena are most pronounced in ionic solids.
     The term "plasmon" refers in general to a quanta of waves
produced by collective effects of a large number of electrons in
matter when the electrons are disturbed from equilibrium. The
concept arises from the theoretical treatment of free electrons
in metals as an ionized gas (a "plasma"). Plasmons and phonons
are examples of "collective excitation", a quantized mode in a
many-body system produced by cooperative motion of the whole
system as the result of interaction between particles.
     In summary, any traveling energy perturbation can be treated
as a traveling quasiparticle, and in certain cases such treatment
yields new insights into the behavior of various systems. Some
physicists, in fact, have proposed that since every so-called
"actual particle" can be considered a traveling mass-energy
perturbation of a field, every particle is a quasiparticle and
the prefix "quasi-" is superfluous.
     In this context, the term "orbital" refers to a quantum
mechanical wave function that describes properties characteristic
of one electron (or an orbital pair of electrons) in the vicinity
of an atomic nucleus or a system of nuclei. An orbital is often
depicted as a 3-dimensional region within which there is a 95
percent probability of finding a particular electron, the orbital
considered as a "cloud" of electron charge. The term "orbital
order" (cooperative Jahn-Teller order) refers to a regional
ordering of orbitals that apparently occurs in certain solid
compounds below specific temperatures. In this context, the
significance of orbital ordering is that in theory it should
permit the propagation of orbital perturbations.
... ... E. Saitoh et al (9 authors at 3 installations, JP)
present the first experimental observations of propagating
orbital perturbations ("orbitons") in solids, the authors making
the following points:
     1) The authors point out that a basic concept in solid-state
physics is that when some kind of symmetry in a solid is
spontaneously broken, collective excitation will arise. For
example, phonons are the collective excitations corresponding to
lattice vibrations in a crystal, and magnons correspond to
particle-scale magnetic perturbations (*spin-waves) in a
magnetically ordered compound. Thus, modulations in the relative
shape of the electronic "clouds" in an orbitally ordered state
could in principle produce "orbital waves". This type of
elementary excitation, however, has yet to be observed
experimentally.
     2) The authors point out that systems in which the behavior
of electrons is strongly correlated -- such as high-temperature
superconductors and manganites exhibiting *colossal
magnetoresistance -- are promising candidates for supporting
orbital waves, since they contain transition metal ions in which
the orbital degree of freedom is important. Orbitally ordered
states have been found in several transition-metal compounds, and
orbitons have been predicted theoretically for LaMnO(sub3).
     3) The authors now report experimental evidence for orbitons
in LaMnO(sub3), using *Raman scattering measurements, the study
involving a model calculation of orbiton resonances which
provides a good fit to the experimental data. The authors
conclude: "We expect that the present systematic theoretical and
experimental studies of orbital waves and their quantized
equivalents, orbitons, will... help us to understand better the
thermal, electrical, and magnetic properties of orbitally ordered
systems. These properties are all strongly affected by the nature
of the orbital state. It is certainly worthwhile to search for
such orbital waves in other transition-metal compounds with
orbital ordering, in order to ensure the general nature of this
concept."
... ... In a commentary on the above work, P.B. Allen and V.
Perebeinos (State University of New York Stony Brook, US) state:
"[The] identification of the orbiton rests on a theoretical
calculation that agrees nicely with the low-temperature data. But
the case is not airtight. For simplicity, the theory omits the
coupling of orbitons to phonons... It needs to be shown that good
agreement remains when this effect is included, both at low and
room temperature."
-----------
E. Saitoh et al: Observation of orbital waves as elementary
excitations in a solid.
(Nature 8 Mar 01 410:180)
QY: Y. Tokura: tokura@ap.t.u-tokyo.ac.jp
-----------
P.B. Allen and V. Perebeinos: First glimpse of the orbiton.
(Nature 8 Mar 01 410:155)
QY: Philip B. Allen: allen@felix.physics. sunysb.edu
-----------
Text Notes:
... ... *spin-waves: (spin-density waves) In quantum mechanics,
"spin" is the intrinsic angular momentum of a subatomic particle.
Spin states are quantized, multiples of h/2ã, where h = Planck's
constant, and each particle is characterized by a quantum spin
number which is the multiple factor. "Spin density waves", in
general, are 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.
... ... *Raman scattering: The Raman effect, named after C.V.
Raman (1888-1970), is a type of scattering of electromagnetic
radiation in which light exhibits a change in frequency and phase
as it passes through a material medium. In Raman spectroscopy,
light from a laser is passed through a substance and the
scattering is analyzed spectroscopically. The technique is used
to determine molecular structure and in chemical analysis.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 20Apr01
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
CONDENSED-MATTER PHYSICS: ON CORRELATED ELECTRON SYSTEMS
One sure thing in science is that whenever the prevailing
authorities in a field announce that nearly all problems have
been solved and that everyone ought to pack up and go home, that
is the time you need to bet all your capital that within a short
time an important discovery or technological innovation will
suddenly open an entire reservoir of new problems that make the
field young again. In science, "maturity" in a field is usually
doomed to be ephemeral, and every scientist knows examples of
this in his own domain. An instance was the so-called "maturity"
of solid-state physics in the 1970s, when independent electron
approximations worked well for most semiconductors and metals,
the phase transition problem seemed solved, and the fundamentals
of magnetism, ferroelectricity, and superconductivity appeared to
be known. Within a short time, however, as if to slam the
authorities who had pronounced solid-state physics a closed book,
there came discoveries of a variety of new materials whose
behavior could not be understood at all with traditional ideas.
These materials have in common the apparent dominant role played
by electron-electron interaction effects, and such systems are
categorized under the general rubric of "highly correlated
electron systems". Examples of such systems are transition metal
oxides, including copper oxide high-temperature superconductors,
*heavy fermion metals, organic *charge transfer compounds, and
one- and two-dimensional electron gas systems. In addition to
intriguing possible technological applications, the behaviors of
these systems appear to present profound challenges in
fundamental physics.
... ... In a recent group of articles on the new frontier of
correlated electron systems, various authors made the following
points:
     1) R.J. Birgenau and M.A. Kastner (Massachusetts Institute
of Technology, US) point out that correlated electron systems are
typically characterized by the coexistence of various types of
order, including charge and orbital and *spin density waves,
together with superconducting and magnetic order. In such
systems, these different kinds of ordering, which are believed to
compete with each other in conventional systems, are often
synergistic. The authors state: "Clearly, highly correlated
electron systems present us with profound new problems that
almost certainly will represent deep and formidable challenges
well into this new century."
     2) Y. Tokura and N. Nagaosa (University of Tokyo, JP) point
out that in a solid, an electron bound to or nearly localized on
a specific atomic site has three attributes: charge, spin, and
orbital. The orbital represents the shape of the electron cloud
in the solid. In transition-metal oxides with anisotropic d-
orbital electron distributions, the Coulomb interaction between
the electrons ("strong electron correlation effect") is important
for understanding metal-insulator transitions and properties such
as high-temperature superconductivity and *colossal
magnetoresistance. But the orbital degree of freedom occasionally
plays an important role in these phenomena, its correlation
and/or order-disorder transition causing a variety of phenomena
via strong coupling with charge, spin, and lattice dynamics.
     3) Subir Sachdev (Yale University, US) points out that small
changes in an external parameter can often lead to dramatic
qualitative changes in the lowest energy quantum mechanical
ground state of a correlated electron system. In anisotropic
crystals, such as the high-temperature superconductors where
electron motion occurs primarily on a 2-dimensional square
lattice, the quantum critical point between two such lowest
energy states has nontrivial emergent excitations that control
the physics over a significant portion of the phase diagram. The
author concludes: "The availability of a large number of 2-
dimensional correlated electron systems (including the high-
temperature superconductors), along with the highly nontrivial
theoretical framework necessary to describe them, makes this one
of the most exciting research areas in condensed matter
physics... The interplay between theory and experiment promises
to be mutually beneficial, in the best traditions of physics
research."
-----------
R.J. Birgenau and M.A. Kastner: Frontier physics with correlated
electrons.
(Science 21 Apr 00 288:437)
QY: Robert J. Birgenau, Mass. Inst. of Technol. 617-253-1000.
-----------
Y. Tokura and N. Nagaosa: Orbital physics in transition-metal
oxides.
(Science 21 Apr 00 288:462)
QY: Y. Tokura, Dept. of Applied Physics, University of Tokyo,
Bunkyo-ku, Tokyo 113-8656, JP.
-----------
Subir Sachdev: Quantum criticality: Competing ground states in
low dimensions.
(Science 21 Apr 00 288:475)
QY: Subir Sachdev [subir.sachdev@yale.edu]
-----------
Text Notes:
... ... *heavy fermion metals: Fermions (electrons, protons,
neutrons) are particles that obey the Pauli exclusion principle:
i.e., no two fermions of the same kind can occupy the same
quantum state. "Heavy fermion systems" are *intermetallic
compounds whose electrical behavior is theoretically described by
postulating "quasiparticles" whose effective masses at low
temperatures are several hundred times the free-electron mass.
... ... *intermetallic compounds: (electron compounds; Hume-
Rothery compounds) In general, an "intermetallic compound" is an
alloy of two metals in which a progressive change in composition
is accompanied by a progression of phases that differ in crystal
structure.
... ... *charge transfer compounds: In general, a "charge-
transfer compound" is a compound in which electrons move between
molecules.
... ... *colossal magnetoresistance: See main report.
... ... *spin density waves: See main report.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 7Jul00
For more information: http://scienceweek.com/swfr.htm

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5. QUANTUM PHYSICS:
AN EXPERIMENTAL DEMONSTRATION OF FERMION VS. BOSON BEHAVIOR
     In 1924, Louis de Broglie (1892-1987) suggested that all
particles have wave properties in addition to particle
properties, with the wave properties given by what is now called
the "de Broglie equation": l = h/(mv), where (l) is the
wavelength of the particle, (h) is Planck's constant, (m) is the
mass of the particle, and (v) is the velocity of the particle.
This relationship provided the basis for quantum mechanics as
formulated by Erwin Schroedinger (1897-1961) in 1925-1926. Since
(mv) is defined as the momentum of a particle, the equation can
be described simply as an inverse proportional relationship
between the wavelength and momentum of a particle, with Planck's
constant as the proportionality constant.
     The term "quantum degeneracy" refers in general to any state
involving particles with overlapping wave functions, each wave
function essentially describing the probability of its particle
occupying a particular position with a particular energy at a
particular time. If a gas is at high enough density, the particle
concentration may be so high that ordinary particle statistics
(Maxwell-Boltzmann statistics), derived from classical mechanics,
do not apply and the behavior of the gas is governed by quantum
statistics. For example, electrons that conduct electricity in a
metal form a degenerate gas of high density. Now suppose we have
a gas of atoms and we reduce the kinetic energy of the particles
by cooling the system. As the kinetic energy is reduced, so is
the momentum of the particles reduced, increasing the de Broglie
wavelength of the particles, and at a low enough temperature the
de Broglie wavelength becomes large enough so that the effective
density of particles is substantially increased. When the
effective density of particles is high enough, wave functions
overlap and the gas of atoms is said to be "degenerate".
Extremely low temperatures, therefore, can produce degenerate
systems, and this has been the basis, during the last decade, for
a new focus in condensed-matter physics on the quantum physics of
atoms at low temperatures. In general, experimental access to a
degenerate quantum system offers the promise of insights in new
physics.
     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.
     According to current physics, all particles in nature are
either fermions or bosons, with fermions (always elementary
particles) having half-integer spin (spin-states characterized by
half-integer multiples of Planck's constant divided by 2ã), and
bosons (all other particles) having integer spin (spin-states
characterized by integer multiples of Planck's constant divided
by 2ã). In general, bosons are particles that obey Bose-Einstein
statistics (see below), and they include photons, *pi mesons, all
nuclei having an even number of particles, and all particles with
integer or zero spin.
     The term "Fermi-Dirac statistics" refers to the statistics
of an assembly of identical half-integer spin particles. Such
particles satisfy the Pauli exclusion principle, i.e., no two
particles of the same kind in the system may simultaneously
occupy the same quantum state.
     The term Bose-Einstein statistics refers to the statistical
mechanics of a system of indistinguishable particles for which
there is no restriction on the number of particles that may
simultaneously exist in the same quantum energy state.
     In general, "Bose-Einstein condensation" is a phenomenon
occurring in a macroscopic system consisting of a relatively
large number of bosons at a sufficiently low temperature
(microkelvins down to nanokelvins) in which a significant
fraction of the particles occupy a single quantum state of lowest
energy (the ground state). In an atomic Bose-Einstein condensate,
several thousand atoms essentially become a single atom, a
"superatom", and this effect has been observed experimentally
with atoms of rubidium and lithium, the atoms trapped and cooled
by special methods.
     The term "Fermi gas" (Fermi-Dirac gas) refers to a system of
independent particles that obey Fermi-Dirac statistics, and
therefore obey the Pauli exclusion principle.
     The term "Fermi pressure" (degeneracy pressure) refers to
the pressure exerted by a Fermi gas. This pressure exceeds the
thermal pressure, since according to the Pauli exclusion
principle particles very close together must possess different
momenta, and according to the Heisenberg uncertainty principle,
the difference in momentum is inversely proportional to the
distance between the particles. Thus, in a high-density gas, the
relative momentum of the particles is high, and unlike thermal
pressure, does not tend to zero as the temperature tends to
absolute zero.
     The term "Fermi-Dirac distribution function" refers to a
function specifying the probability that a member of a system of
independent fermions will occupy a certain energy state at
thermal equilibrium. The term "Fermi level" refers to the energy
level at which the Fermi-Dirac distribution function is equal to
0.5. The term "Fermi temperature", which appears as a parameter
in the Fermi-Dirac distribution function, refers to the energy of
the Fermi level of a system of fermions divided by Boltzmann's
constant.
     In general, the term "evaporative cooling" refers to any
method that cools a system of particles by allowing high-speed
particles to escape the system.
     Given the distinction between fermions and bosons in terms
of half-integer and integer spins, composite particles (e.g., 
atoms) composed of an even number of fermions behave as bosons,
whereas particles containing an odd number of fermions behave as
fermions. Lithium-6 contains 3 protons, 3 neutrons, and 3
electrons, and is thus a composite fermion. Adding one more
neutron to make lithium-7 creates a composite boson with
virtually identical chemical properties but dramatically
different behavior in a low-temperature degenerate gas. That is
the subject of this report.
... ... A.G. Truscott et al (5 authors at Rice University, US) 
present a report of observations of Fermi pressure in a gas of
trapped atoms, the authors making the following points:
     1) The authors point out that the experimental achievement
of Bose-Einstein condensation of trapped atomic gases in 1995
catalyzed an explosion of research activity in atoms obeying
Bose-Einstein statistics. In contrast, the pioneering work of
DeMarco and Jin (1999) [see related background material below] is
so far the only realization of quantum degeneracy in a trapped
gas of fermions. Fermions must satisfy the Pauli exclusion
principle, which forbids identical particles from occupying the
same quantum state, and this simple property gives rise to a
number of remarkable effects, including the structure of the
periodic table of the elements and the nature of electrical
conductivity in metals.
     2) The authors report the attainment of simultaneous quantum
degeneracy in a mixed gas of bosons (lithium-7) and fermions
(lithium-6). The Fermi gas was cooled to a temperature of 0.25
times the Fermi temperature by thermal collisions with the
evaporatively-cooled bosons. At this temperature (approximately
200 nanokelvins), the spatial size of the gas is strongly
affected by the Fermi pressure resulting from the Pauli exclusion
principle, providing clear experimental evidence for quantum
degeneracy.
... ... In a commentary on the above work, K.M. O'Hara and J.E.
Thomas (Duke University, US) state: "By comparing the size of
degenerate lithium-6 and lithium-7 clouds in the same container
(a magnetic trap), [Truscott et al] provide a striking
demonstration of the consequences of spin statistics in an
elementary system, an ultracold gas of non-interacting identical
particles."
-----------
A.G. Truscott et al: Observation of Fermi pressure in a gas of
trapped atoms.
(Science 30 Mar 01 291:2570)
QY: Randall G. Hulet: randy@atomcool.rice.edu
-----------
K.M. O'Hara and J.E. Thomas: Standing room only at the quantum
scale.
(Science 30 Mar 01 291:2556)
QY: J.E. Thomas: jet@phy.duke.edu
-----------
Text Notes:
... ... *magnetic moment: (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, the magnitude of the field related to the
magnetic dipole moment of the atom or ion.
... ... *pi mesons: (pions) Pi mesons are subatomic particles
with masses approximately 270 times the mass of the electron.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 20Apr01
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
FERMI DEGENERACY IN A TRAPPED ATOMIC GAS
... In general, an atomic or molecular system is said to exhibit
"quantum degeneracy" when the system has a number of possible
quantized states and two or more distinct states of the set of
possible states have the same energy. A "degenerate gas" is a gas
in which the concentration of particles is sufficiently high for
classical distribution statistics (Maxwell-Boltzmann statistics)
not to hold, with the behavior of the gas controlled by quantum
statistics (e.g., Fermi statistics). In a Fermi-Dirac system, the
"Fermi level" is the energy level at which there is an 0.5
probability of finding an electron, and the "Fermi temperature"
is defined by T(subF) = E(subF)/k, where E(subF) is
the Fermi level energy and k is the Boltzmann constant. In
general, Fermi-Dirac systems (Fermi systems) are dense and
strongly interacting. Until now the only realization of a low-
density Fermi system has been a dilute solution of liquid
helium-3 dissolved in superfluid helium-4.
... ... B. DeMarco and D.S. Jin (University of Colorado, US) now
report the creation of a nearly ideal Fermi gas composed of atoms
(potassium-40) cooled to the regime where the effects of quantum
statistics can be observed. The authors used an evaporative
cooling strategy in which a two-component Fermi gas was used to
cool a magnetically trapped gas of 7 x 10^(5) potassium-40 atoms
to 0.5 of the Fermi temperature. The authors report that in this
temperature regime quantum degeneracy was observed as a barrier
to evaporative cooling and as a modification of the
thermodynamics, and that measurements of the momentum
distribution and the total energy of the confined Fermi gas
directly revealed the quantum statistics. The authors conclude:
"Reaching this quantum regime in the dilute Fermi gas extends the
field of quantum degenerate gases and sets the stage for further
experimental probes of a Fermi sea of atoms."
-----------
B. DeMarco and D.S. Jin: Onset of Fermi degeneracy in a trapped
atomic gas.
(Science 10 Sep 99 285:1703)
QY: D.S. Jin: jin@jilau1.colorado.edu
-----------
Text Notes:
... ... *magnetic moment: See main report.
... ... *Note #1: See main report.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 29Oct99
For more information: http://scienceweek.com/swfr.htm

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6. HISTORY OF PHYSICS: ON JOSEPH LOSCHMIDT
     Joseph Johann Loschmidt (1821-1895) is claimed by both
chemistry and physics, made important contributions to both
sciences, but received more recognition from physicists than from
chemists. A child of poor peasants, Loschmidt was educated by
local clergy who recognized his brilliance, and in 1839 he was
admitted to the German University in Prague. He completed his
university studies in Vienna in 1843, but he was unable to obtain
a teaching post. So Loschmidt went into the chemical business,
was not successful, and after 10 years of it declared bankruptcy.
He then decided to return to science, and in 1856 he qualified as
a teacher and obtained a post teaching chemistry in a high
school, the Vienna Realschule. He began research in chemistry and
theoretical physics and started publishing scientific papers.
Before long, at the age of 47, he became an assistant professor
of physical chemistry at the University of Vienna.
     Loschmidt was the first to use double and triple lines to
represent the double and triple bonds in organic molecules. He
recognized that most "aromatic compounds" (so-called because they
were obtained from fragrant substances) could be derived from
benzene by replacing one or more hydrogen atoms by other atoms or
groups. The term "aromatic" thus came to be applied to any
hydrocarbon that has the benzene ring as part of its structure
(although the definition of "aromatic" in chemistry is now
expanded: see *Note #1). Loschmidt was the first to state that in
alcohols containing several OH groups, each OH group is attached
to a different carbon atom. He published partial explanations of
the structures of several organic and inorganic compounds,
including benzene, toluene, and ozone, and he also recognized
that an element could have several valences. Loschmidt
anticipated the ring structure of benzene, so that some
historians claim that the assertion of Friedrich Kekule (1829-
1896) that idea of the benzene ring came to him in a dream is
probably fallacious, since Kekule most likely read Loschmidt's
published paper on benzene and benzene derivatives.
     All this chemistry aside, what Loschmidt is most famous for
is his work in physics: he made perhaps the first accurate
calculations of the size of air molecules and of the number of
molecules in a gram-mole (the quantity now commonly called the
Avogadro number). Loschmidt arrived at a size somewhat less than
10^(-7) centimeters for the diameter of the molecules in air,
which is close to the accepted value of 0.3 x 10^(-7). In German-
speaking countries, what is elsewhere called Avogadro's number is
called "Loschmidt's number".
... ... A. Bader and L. Parker (2 installations, US) present an
essay on Loschmidt, the authors making the following points:
     1) The molecular size determinations made by Loschmidt
quickly brought him recognition, and were the basis for his
professorship at the University of Vienna. In 1870, moving to
another area of research, Loschmidt published the most accurate
measurements yet made of the interdiffusion of two gases. James
Clerk Maxwell (1831-1879), following Loschmidt's lead, used these
data to calculate the molecular diameters of various gases.
Loschmidt rose rapidly at the University of Vienna, becoming a
full professor in 1872. Loschmidt and his younger university
colleague, Ludwig Boltzmann (1844-1906), a future giant of 19th
century physics) became good friends, and Loschmidt's critique of
Boltzmann's attempt to derive the second law of thermodynamics
from kinetic theory became famous as the "*reversibility
paradox". This led Boltzmann to his statistical concept of
entropy as a logarithmic tally of the number of microscopic
states corresponding to a given thermodynamic state.
     2) In an era when atoms and molecules were not yet fully
confirmed as entities, an estimate of their size was of profound
importance. By 1808, Joseph-Louis Gay-Lussac (1778-1850) had
established that when different gases combine chemically, the
combining volumes of the gases are in the ratio of simple
integers. In 1811, Amadeo Avogadro (1776-1856) interpreted this
observation as implying that the number of molecules in a liter
of gas at a given temperature and pressure is the same for all
gases. But Avogadro was never able to determine that number:
before it could be calculated, one would need to know the
characteristic size and mass of a molecule. An immediate
consequence of Loschmidt's calculation of the diameter of a
molecule was a reasonably good estimate of molecular mass and of
the number of molecules per unit volume of a gas at standard
temperature and pressure (STP). Loschmidt was the first to
publish corrections to the ideal gas law, corrections due to both
finite molecular size and time delays during collision, that were
compared with experiment. The inclusion of collisional time delay
allowed Loschmidt to fit the experimental data, but his modified
gas law missed an important correction discovered years later --
the weak attractive force between molecules first proposed by
Johannes van der Waals (1837-1923).
     3) Loschmidt's estimate of approximately 1 nanometer for the
typical diameter of an air molecule was too high, but only by a
factor of 3. At present, the "Loschmidt number" has come to mean
simply Avogadro's number, the number of molecules in a mole, but
Boltzmann originally coined the term "Loschmidt's number" to
signify the number of molecules per cubic centimeter for an ideal
gas at standard temperature and pressure. The modern value for
this is approximately 2.7 x 10^(19) per cubic centimeter.
     4) The main source of errors in Loschmidt's estimate of the
molecular diameter were errors in the measurements of the mean
free path and in the estimate of the density of liquid air. These
uncertainties may have been on Loschmidt's mind when he devised a
very accurate experimental method for measuring another quantity
closely related to molecular size, namely the diffusion
coefficient governing the rate interdiffusion of one gas into
another. His experimental diffusion results were published in
1870. In Loschmidt's experiments, two gases were initially
separated by a horizontal partition in a vertical cylindrical
container, with the lighter gas on top. The partition was removed
and the two gases were permitted to diffuse into each other for a
certain time, after which the fraction of mixing was carefully
measured. By comparing the experimental results with Maxwell's
mathematical solution for the time dependence of interdiffusion
in such a setup, Loschmidt was able to determine diffusion
coefficients with greater accuracy than any previous measurements
had achieved.
     5) The authors point out that the prominent chemists of
Loschmidt's time rejected or ignored his pioneering work on
chemical structures. In contrast, Josef Stefan (1835-1893), James
Clerk Maxwell, Ludwig Boltzmann, and other leading physicists
were very receptive to Loschmidt's determinations of molecular
size and mass, and to his later work in physics. In his eulogy to
Loschmidt, Boltzmann said of his good friend: "His work forms a
mighty cornerstone that will be visible as long as science
exists... Loschmidt's excessive modesty prevented his being
appreciated as much as he could and should have been." [*Note #2]
-----------
A. Bader and L. Parker: Joseph Loschmidt, physicist and chemist.
(Physics Today March 2001)
QY: Alfred Bader: Aldrich Chemical Company, Milwaukee, WI (US)
-----------
Text Notes:
... ... *Note #1: In chemistry, the term "aromaticity" currently
refers to stability. A compound is aromatic if it is
significantly more stable than would be predicted on the basis of
the most stable Lewis structural formula written for it. This
special stability is related to the number of electrons contained
in a cyclic conjugated system. All compounds that possess benzene
rings possess special stability and are classified as "benzenoid
aromatic compounds". Certain other compounds lack a benzene ring
yet satisfy the criterion of special stability, and these
compounds are classified as "nonbenzenoid aromatic compounds".
... ... *reversibility paradox: The reversibility paradox is most
simply stated as follows: Let us assume that an isolated system
does indeed evolve from an initial state to a final state of
higher entropy. But it is a given that the microscopic laws of
mechanics are invariant under time reversal. Therefore, there
must also exist an entropy-decreasing evolution which is set in
motion simply by taking the final state of the previous evolution
as the new initial state and then reversing all the individual
molecular velocities. This time-reversed evolution would seem to
violate the 2nd law of thermodynamics. Boltzmann evidently took
the reversibility paradox very seriously, and it led him to the
realization that a statistical interpretation of the 2nd law of
thermodynamics was essential. Boltzmann ultimately proposed the
his famous expression for entropy (carved into his gravestone at
the Vienna Central Cemetery): S = klogW, where (S) is entropy;
(W) is the number of microstates compatible with the values of
the thermodynamic variables characterizing the macroscopic state
of a system; and (k) is what we call "Boltzmann's constant".
... ... *Note #2: Presently, 135 years after Loschmidt's
determination of molecular size, some relevant approximate
numerical magnitudes ranges for gases at ordinary temperature and
pressure are as follows:
... ... molecular diameter: 10^(-8) to 10^(-7) centimeters.
... ... molecular number density: 10^(19) molecules per cubic
centimeter
... ... average molecular speed: 10^(4) to 10^(5) centimeters per
second.
... ... average distance between molecules: 10^(-7) 10^(-6)
centimeters.
... ... collision rate per molecule: 10^(9) to 10^(10) collisions
per second.
... ... average time between collisions: 10^(-10) to 10^(-9)
seconds.
... ... average distance traveled between collisions (mean free
path): 10^(-5) to 10^(-4) centimeters.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 20Apr01
For more information: http://scienceweek.com/swfr.htm

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7. IN FOCUS: ON CALCULATING THE CHEMICAL BOND
"Our understanding of why atoms combine together to form
molecules and why the most stable molecules satisfy the rules of
valence was unclear until the development of quantum mechanics.
Theoretical chemists now have available many computer packages
(prepared after huge efforts at writing software) that allow them
to obtain approximate solutions to the Schroedinger equation for
the electrons and to deduce the structure, stability, and other
properties of a molecule. It has, however, been very difficult to
obtain results that provide confident predictions for the
experimentalist, except for rather simple (few-electron)
molecules. Even today there are many calculations for which
theoretical chemists will happily call on the maximum computer
power available; so, it is necessary to explain why the
calculations are so difficult. The energy of a molecule is a
balance between the attractive forces between electrons and
nuclei and the repulsive forces acting between nuclei and between
electrons. Multiply-charged molecules, either positive or
negative, are rarely stable with respect to dissociation in the
gas phase because the repulsive forces win (in solution there are
other factors that affect the stability). Because nuclei are so
much heavier than electrons, one can obtain an energy for
electrons moving in a potential from fixed nuclei and then use
this to determine the nuclear motion; this is called the Born-
Oppenheimer approximation. It is the first of these tasks, that
of calculating the energy of the electrons, that is particularly
difficult, because the repulsion between the electrons is an
important part of the chemical bond energy and, for many
molecules, unless it is calculated with high accuracy, the
results are poor. The role of computers for chemical bond
calculations was mapped out in a landmark paper in _Nature_,
published in 1956 by Boys, Cook, Reeves, and Shavitt, under the
title 'Automatic fundamental calculations of molecular
structure'. They not only proposed a method that is still the
basis of many current calculations but also performed
calculations on what was then quite a complicated system, namely
the water molecule. They used the first University of Cambridge
computer, EDSAC, which carried out 1000 operations per second and
had a 1000-word store. A single calculation took 40 hours (how
did they keep it running?). Such a calculation today might take 4
seconds."
-----------
John N. Murrell: Bonding and the Theory of Atoms and Molecules.
in: Nina Hall (ed.): _The New Chemistry_
(Cambridge University Press, Cambridge UK 2000, p.33
-------------------
SCIENCE-WEEK http://scienceweek.com 20Apr01

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8. FROM THE SCIENCEWEEK ARCHIVE:
NEURODEVELOPMENTAL DAMAGE IN AUTISM: AN INFECTION-BASED MODEL
     Exposure of the fetus and newborn infant around the time of
birth ("perinatal exposure") to infectious agents and toxins has
been linked to the pathogenesis of certain human neuropsychiatric
disorders, particularly *autism. But the mechanisms by which
environmental factors such as infectious agents and toxins
interact with developing immune and neural systems to create
neurodevelopmental disturbances are only poorly understood.
     Autism disorders occur as frequently as 1 in 500 children, a
rate that may be increasing in some geographical regions. A
neurodevelopmental hypothesis for autism is supported by various
approaches: brain imaging, anatomic and *cytoarchitectonic
evidence, and epidemiologic evidence. The view among many
researchers is that autism has likely perinatal origins; a
linkage to microbial or immune factors; an association with
dysfunction of the *hippocampus, *amygdala, and *cerebellum; and
a connection with disturbances of certain *neurotransmitters
(e.g., *dopamine and *serotonin). Of significance are the various
neurobehavioral dysfunctions characteristic of autism: motor,
postural, and sensory deficits; *hypotonia; *stereotypies; poor
eye contact; mental retardation, and so on.
     "Borna disease" is a central nervous disease of horses and
certain other vertebrate species. The disease is caused by Borna
disease virus, an RNA virus similar to *rhabdoviruses and
*paramyxoviruses, but with a number of unique features. The virus
has a high affinity for nerve cells, and there is data to
associate the virus with neuropsychiatric disorders in humans:
Borna disease virus *antibodies have been detected in
approximately one-third of patients with certain mental
illnesses, including depression, schizophrenia, and obsessive-
compulsive disorder. In addition, Borna disease virus RNA and
*antigen have been detected in peripheral blood *monocytes and in
autopsy brain samples of psychiatric patients. Nevertheless, it
remains to be established whether Borna disease virus is
etiologically involved in the pathophysiology of certain human
mental disorders.
... ... M. Hornig et al (4 authors at 3 installations, US AT) now
present an animal model for investigating disorders of central
nervous system development, the model based on neonatal rat
infection with Borna disease virus. The authors report infection
by inoculation of neonate rats with the virus results in abnormal
righting reflexes, hyperactivity, inhibition of open-field
exploration, and stereotypic behaviors. Neuronal architecture is
markedly disrupted in the hippocampus and cerebellum, with
reduction in the numbers of certain types of nerve cells (granule
cells and Purkinje cells). Neurons are apparently lost
predominantly by *apoptosis, and a variety of *inflammatory
changes in the brain occur. The authors suggest that the
resemblance of these functional and neuropathologic abnormalities
to human neurodevelopmental disorders indicates the utility of
this model for defining cellular, biochemical, histologic, and
functional outcomes of interactions of environmental influences
with the developing central nervous system. In particular, the
authors suggest that the disturbances of central nervous system
architecture produced by Borna disease virus infection in rats
parallel the structural and behavioral abnormalities observed in
human autism.
-----------
M. Hornig et al: An infection-based model of neurodevelopmental
damage.
(Proc. Natl. Acad. Sci. US 12 Oct 99 96:12012)
QY: Ian Lipkin [ilipkin@uci.edu]
-----------
Text Notes:
... ... *autism: Autism is a behaviorally defined syndrome of
unknown etiology associated with poor social interaction,
disordered language, and atypical responses to people, objects,
and events. The syndrome is classically manifested by severe
disturbances in cognition, language, and behavior that appear
before the age of 30 months. In some cases, there is an apparent
hyperarousal state. Autistic children often exhibit ritualized
body movements, repeated touching and sniffing of objects,
ritualistic ordering, checking, and collecting, and insistence on
precisely following routines. The ratio of male to female cases
ranges from 2:1 to 4:1, and studies of monozygotic and dizygotic
twins indicate an important role for genetic factors. There is
presently a controversy over whether movement disorders play a
central role in the phenomenon of autism and even whether such
movement disorders exist in autism at all.
... ... *cytoarchitectonic: In the central nervous system,
particularly in the brain, nerve cells arrange themselves during
development in consistent patterns, e.g., the layers of the
cerebral cortex. The same patterns are found in all individuals
without evident neural dysfunctions, and the presence of various
patterns of nerve cell arrangements has come to be called
"architecture". In this context, the term "cytoarchitectonic"
refers to various patterns of neuron arrangement in distinct
central nervous system locations: cytoarchitectonic areas are
distinct regions of the cerebral cortex identified by differences
in cell size, packing density, and laminar arrangement.
... ... *hippocampus: A brain cortex structure in the medial part
of the temporal lobe. In humans, among other functions, the
hippocampus is apparently involved in short-term memory. Analysis
of the neurological correlates of learning behavior in the rat
indicates that the hippocampus is also involved in memory in that
species.
... ... *amygdala: a cluster of nerve cell bodies (the cluster
called a "nucleus") in the temporal lobe of the brain, the
cluster with major involvements in autonomic, emotional, and
sexual behavior.
... ... *cerebellum: A large neural structure at the base of the
brain involved in motor coordination, posture, and balance.
... ... *neurotransmitters: 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.
... ... *dopamine: A neurotransmitter substance of critical
importance in certain areas of the brain involved in movement
control.
... ... *serotonin: A neurotransmitter substance involved in
nearly everything occurring in the brain, including psychological
states such as anxiety and depression, and dysfunctions producing
migraine and epilepsy.
... ... *hypotonia: In this context, a loss of the tension of
relaxed muscle (loss of muscle tone.)
... ... *stereotypies: In this context, a "stereotypy" is a
persistent repetition of gestures or movements that do not appear
to be goal-directed.
... ... *rhabdoviruses: Rhabdoviruses are rod- or bullet-shaped
single-stranded RNA viruses 75 x 180 nanometers, each particle
surrounded by a membranous envelope with protruding spikes 10
nanometers long. The rabies virus is an example of a rhabdovirus.
... ... *paramyxoviruses: These viruses include the most
important agents of respiratory infections of infants and young
children, as well as the causative agents of mumps and measles.
In general, paramyxoviruses are 150 to 300 nanometers in
diameter, the viral genome a linear single-stranded RNA molecule
of 16 to 20 kilobases.
... ... *antibodies: In general, an antibody is a protein
molecule produced by the immune system of vertebrate organisms,
the molecule designed to specifically interact with a particular
chemical entity called an antigen, the antigen usually a
particular surface component of a foreign organism.
... ... *antigen: See previous note.
... ... *monocytes: The monocytes are the largest of the
leukocytes (white blood cells).
... ... *apoptosis: In general, programmed cell death produced by
control mechanisms designed to destroy defective cells.
... ... *inflammatory changes: In general, an "inflammatory
change" is a response of tissues to irritation or injury. The
response involves a dynamic complex of cellular and chemical
reactions that occur in the affected blood vessels and adjacent
tissues.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 17Dec99
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
INFANT AUTISM: USE OF MOVEMENT ANALYSIS IN DIAGNOSIS
... ... P. Teitelelbaum et al (5 authors at University of Florida
Gainesville, US) now report that a study of 17 autistic children
showed disturbances of movement that could be detected at the age
of 4 to 6 months and sometimes even at birth. The authors used a
standard movement analysis system (the Eshkol-Wachman system) in
combination with still-frame videodisc analysis to study videos
obtained from parents of children who had been diagnosed as
autistic by conventional methods, the diagnosis usually occurring
at about age 3 years. The videos showed the behaviors of the
children when they were infants, long before they had been
diagnosed as autistic. The authors report that movement disorders
varied from child to child, with disturbances revealed in the
shape of the mouth and in some or all of the milestones of
development, including lying, righting, sitting, crawling, and
walking. The authors suggest their findings support the view that
movement disturbances play an intrinsic part in the phenomenon of
autism, that movement disturbances in autistic children are
present at birth, and that such movement disturbances can be used
to diagnose the presence of autism in the first few months of
life. The authors further suggest these results indicate the need
for the development of methods of therapy to be applied from the
first few months of life in autistic children.
-----------
P. Teitelbaum et al: Movement analysis in infancy may be useful
for early diagnosis of autism. (Proc. Natl. Acad. Sci. US 10 Nov
98 95:13982) QY: Philip Teitelbaum 
-------------------
Summary by SCIENCE-WEEK http://scienceweek.com 15Jan99 
For more information: http://scienceweek.com/swfr.htm


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