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.

June 22, 2001 -- Vol. 5 Number 25

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The verb "to theorize" is now conjugated as follows:
"I built a model, you formulated a hypothesis, he made
a conjecture."
-- John Ziman

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

1. ASTRONOMY: ON THE SUNSPOT CYCLE
Minor physical changes in the Sun often lead to extreme solar
magnetic activity that can affect the Earth, e.g., by disrupting
radio communications and influencing the weather. Although the
sunspot cycle is of considerable interest, we are far from
understanding its origin and dynamics.

2. THEORETICAL PHYSICS: ON RANDOM WALKS
In general, a "random walk" is a stochastic process presenting
the problem of determining the probable location of a point
subject to random motions. Random walks are involved in a wide
variety of phenomena, from the fluctuation of winnings in games
of chance, to simple Brownian diffusion, to modern studies of
nonlinear dynamics.

3. HISTORY OF CHEMISTRY: ON THE DISCOVERY OF NUCLEAR FISSION
History has its own balance sheet: Until 1997, element 105 was
unofficially known as hahnium. In 1997, the International Union
of Pure and Applied Chemistry adopted the name dubnium for
element 105 and the name meitnerium for element 109. The element
hahnium no longer exists, and behind it all there is a story of
physics, chemistry, politics, and the Nazis.

4. MOLECULAR BIOLOGY: EVOLUTION OF PRION PROTEINS
Prions are a class of poorly understood proteins implicated
in a number of exotic diseases. A new analysis indicates the
existence of a "fossil" of a transmembrane protein in the
sequence of known vertebrate prion proteins, and this suggests
that prion protein was once an integral membrane protein expelled
to the extracellular space by a mutation.

5. MICROBIOLOGY:
PUNCTURE OF EUKARYOTIC CELLS BY BACTERIAL NEEDLES
The bacterium Yersinia enterocolitica polymerizes a 6-kilodalton
protein into needles that are able to puncture the eukaryotic
plasma membrane. These needles apparently form a conduit for the
transport of specific proteins from the bacterial to the
eukaryotic cytoplasm, where they exert their cytotoxic action.

6. EVOLUTIONARY BIOLOGY: VERTEBRATE DISPERSAL OUT OF INDIA
An analysis demonstrates that multiple lineages of frogs survived
Deccan-traps volcanism after millions of years of isolation on
tectonic drifting India. The collision between the Indian and
Eurasian plates was apparently followed by wide dispersal of
several of these lineages, and this "out-of-India" scenario might
reconcile paleontological and molecular data in other vertebrate
groups.

7. IN FOCUS: ON THE NEW ASTRONOMY
The "new astronomy" is a phenomenon of the late 20th century, and
it has completely revolutionized our concept of the Universe.
While traditional astronomy was concerned with studying the light
-- optical radiation -- from objects in space, the new astronomy
encompasses all the radiations emitted by celestial objects.

8. FROM THE SCIENCEWEEK ARCHIVE:
COSMOLOGY: EXPECTATIONS IN THE NEXT CENTURY OF RESEARCH
The great mystery for cosmologists is the series of events that
occurred less than 1 millisecond after the Big Bang, when the
Universe was extraordinarily small, hot, and dense. The laws of
physics with which we are familiar offer little firm guidance for
explaining what happened during this critical period.


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Section 2
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1. ASTRONOMY: ON THE SUNSPOT CYCLE
     The bright surface layer of the Sun is called the
"photosphere", a region a few hundred kilometers thick at a
temperature that ranges from 5770 kelvins at its innermost part
to 4400 kelvins at its outermost part, the latter the Sun's
temperature minimum. The term "sunspot" refers to a dark area on
the photosphere that is cooler than its surroundings and
associated with strong magnetic fields (on the order of 0.4
tesla). Sunspots generally appear in pairs or groups, the leading
and following spots with opposite magnetic polarities. Sunspot
sizes vary from small pores approximately 300 kilometers in
diameter to groups of sunspots spanning more than 100,000
kilometers. The largest sunspots usually last the longest, up to
6 months; small spots may last for less than an hour. For the
most part, sunspots are confined to belts above and below the
solar equator.
     Since the Sun is not a solid, different parts at the surface
rotate at different rates. The term "solar dynamo" refers to the
action within the Sun whereby the kinetic energy of the hot and
highly ionized gas of the solar interior is converted into the
magnetic field that gives rise to solar activity. The consensus
model, due to H.W. Babcock, is that magnetic field lines under
the photosphere run from pole to pole (the "poloidal field") and
are twisted parallel to the solar equator (the "toroidal field")
by the differential rotation of polar and equatorial regions
     The so-called "sunspot cycle" (solar cycle) is a variation
in the number of sunspots and other forms of solar activity with
an average period of approximately 11 years. In each successive
cycle, the north and south magnetic polarities of the Sun are
reversed, producing a 22-year magnetic cycle. The 11-year
periodicity of the sunspot cycle is believed to arise through the
action of the solar dynamo.
... ... Douglas Gough (University of Cambridge, UK) presents a
commentary on current research on the sunspot cycle, the author
making the following points:
     1) The author points out that minor physical changes in the
Sun often lead to extreme solar magnetic activity that can affect
the Earth, e.g., by disrupting radio communications and
influencing the weather. Although the sunspot cycle is of
considerable interest, we are far from understanding its origin
and dynamics.
     2) The author points out that we are currently experiencing
a peak in the solar cycle and therefore in the number of
sunspots. It is generally believed that the underlying cause of
the sunspot cycle is the interaction between the rotation of the
Sun and the "dynamo" responsible for the Sun's magnetism. In this
model, the dynamo effect creates a magnetic field from the
electric currents caused by convection and large-scale shearing
motions within the Sun. But the outer regions of the Sun tend to
rotate faster near the equator and slower near the poles, and
this results in strong magnetic fields bursting through the
photosphere. These magnetic fields inhibit the convective
transport of heat, permitting material to cool at the surface,
and producing the visibly darker regions called "sunspots".
     3) The author points out that none of the current dynamo
models explain the small observed variation in the luminosity of
the Sun that also follows the sunspot cycle. These small changes
in luminosity (no larger than 0.1 percent) apparently derive from
the release of stored energy somewhere within the Sun. Thus, by
studying the small changes in the radius of the Sun, we might
learn something about the source of this extra energy, and also
ultimately learn something about the process that causes the
luminosity change.
     4) Recent work (M. Emilio et al: Astrophys. J. 543:1007
2000) based on sensitive satellite observations demonstrates
evidence that the energy responsible for variations in the Sun's
radius and luminosity does not come from the inner depths of the
Sun but rather from the outer layers. The author (Gough) states:
"This observation is certainly not the first claimed detection of
a small variation in the Sun's radius, but it may be the first to
survive the test of time."
-----------
Douglas Gough: Sizing up the Sun.
(Nature 15 Mar 01 410:313)
QY: Douglas Gough: douglas@ast.cam.ac.uk
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Summary by SCIENCE-WEEK http://scienceweek.com 22Jun01
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
PRECISION MEASUREMENTS OF BRIGHT RINGS AROUND SUNSPOTS
A "sunspot" is a dark area of the solar surface. The center of
the spot, called the "umbra", is darker than the outer border,
which is called the "penumbra". The average sunspot is
approximately twice the diameter of the Earth and may last for
several weeks. Sunspots tend to form in pairs or groups, and a
large group may contain up to 100 spots and may last as long as 2
months. Sunspots appear dark because they are cooler than the
photosphere (the visible surface of the Sun or a star). The
temperature at the center of a typical sunspot is approximately
4240 kelvins, while the solar photosphere is at
approximately 6000 kelvins. Temperatures of the order of
4000 kelvins, however, are significant: a sunspot emits
enough radiation so that a single sunspot on its own in the
absence of the remainder of the Sun would glow a brilliant
orange-red and would be brighter that the full Moon. Analysis of
the *Zeeman effect in sunspots indicates that the magnetic field
in a typical sunspot is approximately 1000 times stronger than
the average magnetic field of the Sun, and one theory is that
this powerful localized magnetic field inhibits gas motion below
the photosphere, with the result that rising gas cannot deliver
its heat to the surface. Thus, the area cools and a sunspot is
the result. Infrared observations of sunspots have suggested that
the heat that does not emerge through the sunspot is deflected
and produces a slight increase in the temperature of the
photosphere around the sunspot, but so far these measurements
have not been precise and the slight increase has not been
confirmed. The other major theory of sunspots proposes that the
removal of energy from the sunspot location is the result of
enhanced hydromagnetic wave radiation associated with so-called
"*plage fields". Of the two theories, the first theory is
currently favored.
... ... M.P. Rast et al (6 authors at 2 installations, US) now
report high-photometric-precision observations of bright rings
around 8 sunspots. The authors report the rings are approximately
10 kelvins warmer than the surrounding photosphere and
extend at least one sunspot radius out from the penumbra.
Approximately 10 percent of the radiative energy missing from the
sunspots is apparently emitted through these bright rings. The
authors conclude: "Thus, isolated sunspots are seen to be
commonly surrounded by a ring of enhanced radiation, the origin
of which is probably not bright vertical magnetic elements (plage
field), but the re-emergence of heat blocked by magnetic
inhibition of convective transport in the spot itself."
-----------
M.P. Rast et al: Bright rings around sunspots.
(Nature 14 Oct 99 401:678)
QY: M.P. Rast: mprast@ucar.edu
-----------
Text Notes:
... ... *Zeeman effect: (Zeeman splitting) The splitting of a
spectral line due to a magnetic field. Named after Peter Zeeman
(1865-1943). The effect is widely used for the determination of
magnetic fields in astronomical objects, especially concerning
the Sun and sunspots. In general, the Zeeman effect occurs when
atoms emit or absorb radiation in the presence of a magnetic
field: the field modifies the energy configuration of the atom
with the result that a spectral line is split into 2, 3, or more
closely spaced components. The spacing of the components is a
measure of the magnetic field strength.
... ... *plage fields: A "plage" is a brighter, hotter patch in
the *chromosphere of the Sun, and a region of particularly strong
magnetic field.
... ... *chromosphere: The region of the Sun's atmosphere
directly above its photosphere. Visible only immediately before
or after a total solar eclipse.
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Summary & Notes by SCIENCE-WEEK http://scienceweek.com 17Dec99
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
ASTROPHYSICS: THE PHYSICS OF THE SUN AND TERRESTRIAL CLIMATE
     The Sun, a *main-sequence star 1.4 million kilometers in
diameter, is composed predominantly of hydrogen and helium
(approximately 70 percent hydrogen by mass, 28 percent helium by
mass, and 2 percent heavier elements by mass) and it generates
its energy via nuclear fusion processes, particularly via the
*proton-proton chain reaction. As a result, the Sun is losing
mass at a rate of approximately 4 million metric tons per second.
     The generation of energy occurs in the "central core", which
has a temperature of approximately 15 million kelvins, is
approximately 400,000 kilometers in diameter, and contains
approximately 60 percent of the mass of the Sun in 2 percent of
its volume.
     Outside the core is the "radiative zone", an envelope of
unevolved material through which energy from the core is
diffusively transported by successive absorption and emission of
radiation in collisions between atomic particles. It has been
estimated that it may take from 1 million years to as long as 10
to 20 million years for the energy generated in the core to reach
the surface.
     The radiative zone extends to within 200,000 kilometers of
the surface. In the surface layer (the "convective zone"), where
the temperature is only 1 million kelvins, convection is
the most important mode of energy transport.
... ... Eugene N. Parker (University of Chicago, US) presents a
review of the physics of the Sun, the author making the following
points:
     1) The Sun is essentially a thermonuclear core enclosed in
an opaque shroud that insulates the high temperature of the core
from the cold Universe outside. The core is brighter than 10
supernovas at maximum light, but the enclosing shroud turns back
all but one part in 2 x 10^(11) of the thermal radiation. The
outward journey of the energy from the core takes approximately 1
million years, which illustrates the immense opacity and thermal
capacity of the shroud.
     2) Approximately 10^(-5) of the outflowing energy from the
core of the Sun is diverted into magnetic fields that produce a
variety of exotic effects, including *coronal mass ejection,
*solar flares, the million degree corona, the *solar wind, and x-
ray emission. These phenomena are of interest to the physicist
because they represent unanticipated manifestations of classical
physics, extrapolations to astronomical scales of basic
principles traditionally studied in terrestrial laboratories.
     3) The total luminosity of the Sun varies with time, and
systematic monitoring of several Sun-type stars during the past 4
decades reveals magnetic activity cycles comparable to that of
the Sun. The luminosities of some of those stars have been
monitored for approximately 15 years, and the data show
approximately the same variation as the magnetic activity.
     4) The Earth contains a great deal of information about past
solar activity. The rate of production of carbon-14 depends
directly on the intensity of *cosmic rays, and such rays are
partially excluded from the Solar System by the outward sweep of
magnetic fields in the solar wind. Thus the cosmic ray intensity
and carbon-14 production vary oppositely to the general level of
solar activity.
     5) The carbon-14 record indicates that over the last 70
centuries the Sun has been without normal activity for 10
centuries and hyperactive for 8 centuries. The other 52 centuries
were variable but more or less normal. The most recent quiescent
period was from 1645 to 1715, the period called the "Maunder
Minimum". The 12th century "Medieval Maximum" is the most recent
epoch of hyperactivity. The empirical relation between the total
luminosity and magnetic activity, based on many Sun-type stars,
suggests that the Sun was fainter during the *Maunder Minimum by
0.4 +- 0.2 percent, and perhaps brighter by a comparable amount
during the Medieval Maximum. The mean annual temperature in the
northern temperate zone was lower than normal by 1 to 2 degrees
centigrade during the Maunder Minimum and higher by 1 to 2
degrees centigrade during the Medieval Maximum. The fractional
change in temperature is comparable to the fractional change in
solar brightness, with the implication that the Sun is the driver
of the climate. The consequences for agriculture were severe
during both periods, the Maunder Minimum being disastrous in
northern Europe and China, and the Medieval Maximum disastrous in
the semi-arid regions. These periods of abnormal activity of the
Sun are without explanation, as are the variations within the so-
called "normal centuries".
     6) The general level of solar activity doubled or tripled
from 1900 to 1950, an estimate based on sunspot numbers and on
the intensity of geomagnetic activity. This increase suggests an
increase in solar luminosity by perhaps one part in 2000, and the
author suggests it is interesting to note that the mean
temperature in the northern temperate zone, as well as the
surface sea water temperatures, rose during the same period.
"Warmer seas, of course, reduce the rate at which atmospheric
carbon dioxide is absorbed into the oceans. It appears that the
global warming since 1950 is in part a consequence of the
continuing increase in solar brightness, seriously aggravated by
the extravagant burning of fossil fuel. So the mystery of the
variations in the total luminosity of the Sun is part of the
complicated picture of global warming."
[Editor's note: See report #3 in this issue for another approach
to millennial-scale climate changes.]
-----------
Eugene N. Parker: The physics of the Sun and the gateway to the
stars.
(Physics Today June 2000)
QY: Eugene N. Parker, University of Chicago 312-702-9808.
-----------
Text Notes:
... ... *main-sequence star: The Main Sequence is a region on the
*Hertzsprung-Russell diagram where most stars lie, including our
own Sun. The evolution of a star can be diagrammed as a movement
along the Main Sequence and an eventual branching off the Main
Sequence to regions associated with various types of old stars.
... ... *Hertzsprung-Russell diagram: The Hertzsprung-Russell
diagram is a plot of stellar absolute magnitude against spectral
type, and is perhaps the most useful diagrammatic aid in
astrophysics. It allows the portrayal of the evolution of a star
as occurring along various paths in the diagram.
... ... *proton-proton chain reaction: A chain of nuclear
reactions inside a star that converts hydrogen to helium, with
the associated release of energy. In the reaction, 4 hydrogen
nuclei (protons) fuse to form one nucleus of helium, with the
production of a number of intermediate nuclei such as deuterium
and isotopes of lithium, beryllium, and boron. The proton-proton
reaction is the most important stellar reaction at temperatures
below 18 million kelvins, and thus operates chiefly in
stars of less than 2 solar masses.
... ... *coronal mass ejection: The corona is the Sun's faint
outer atmosphere, where the temperature is 2 million degrees
kelvin or more, the corona consisting of a low-density hot gas
that glows with a pale white color.
... ... *solar flares: A solar flare is a sudden release of
energy in the corona of the Sun, the phenomenon usually lasting
up to several hours (in rare cases, up to more than a day).
... ... *solar wind: The solar wind is the steady flow of charged
particles, consisting primarily of protons and electrons, from
the solar corona into interplanetary space. The solar-wind
particles have energies high enough to enable the particles to
escape the Sun's gravitational field, but the wind is influenced
by the Sun's magnetic field, and the particles can be trapped by
planetary magnetic fields.
... ... *cosmic rays: Highly energetic particles moving at close
to the speed of light and continuously bombarding the Earth's
atmosphere from all directions. The energies of the particles are
enormous and range from 10^(8) to over 10^(19) electronvolts.
... ... *Maunder Minimum: Named after the astronomer Edward W.
Maunder (1851-1928), who first noted the absence of reports of
sunspots in the period 1645 to 1715.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 16Jun00
For more information: http://scienceweek.com/swfr.htm

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2. THEORETICAL PHYSICS: ON RANDOM WALKS
     The term "stochastic process" (random process) refers to a
process described by a set of random variables. One type of
stochastic process is a so-called "Markov process", named after
the mathematician Andrei A. Markov (1856-1922). In general, a
Markov process is a stochastic process whose future history
depends on its present state but not on its past history.
     There are many types of Markov processes, and one of these
types is the so-called "symmetric random walk". In general, a
"random walk" is a stochastic process presenting the problem of
determining the probable location of a point subject to random
motions, given the probabilities (the same at each step) of
moving some distance in some direction. A typical example is the
so-called "drunkard's walk", in which a point beginning at the
origin of the Euclidean plane moves a distance of one unit for
each unit of time, the direction of motion, however, being random
at each step. The problem is to find, after some fixed time, the
probability distribution of the distance of the point from the
origin.
     If the system is perfectly isotropic, with no forbidden
directions and no probability biases in any direction, the random
walk is called "symmetric" and is a Markov process. Symmetric
random walks have intriguing properties, for it can be shown that
for a 1-dimensional or 2-dimensional symmetric random walk, the
point returns with probability 1 to its initial position in
infinite time, and hence to every possible position infinitely
many times in infinite time. However, if the random walk is in 3
dimensions, the probability of reaching the starting point again,
as the number of steps approaches infinity, is given by the
constant 0.3405373296. Physical applications of random walk
analysis include diffusion, Brownian motion, and certain problems
in disordered solids and the structures of polymers.
... ... Michael F. Schlesinger (Office of Naval Research, US)
presents a commentary on the history of random walk analysis, the
author making the following points:
     1) The author points out that random walks are involved in a
wide variety of phenomena, from the fluctuation of winnings in
games of chance, to simple Brownian diffusion, to modern studies
of nonlinear dynamics. In 1785, Jan Ingenhausz (1730-1799), a
physician and plant physiologist, placed charcoal powder on an
alcohol film and observed the grains move randomly. In 1828, the
botanist Robert Brown (1773-1858) reported erratic dancing of
small particles in fluids at rest. In 1905, Albert Einstein
(1879-1955) considered such fluids to be composed of discrete
molecules whose many collisions with a Brownian particle caused
the particle to jump in random directions -- a random walk.
Einstein's analysis not only explained Brownian motion, but also
bolstered the case for the existence of atoms, which at that time
was not universally accepted.
     2) The author points out that Einstein's approach to
Brownian motion was based on the principal that noise, like other
natural phenomena, is an expression of physical law. Einstein
demonstrated that the Brownian particle obeys the diffusion
equation, and his formula for the mean-squared displacement
involved Avogadro's number as a factor in the diffusion constant.
Jean Perrin (1870-1942) made careful observations of Brownian
motion, observations that allowed him to calculate Avogadro's
number, and Perrin won the Nobel Prize in Physics in 1926 for his
work.
     3) The author (Schlesinger) points out that, as is often the
case, once Einstein's and Perrin's work was recognized as
important, precursors were identified. In the 1700s, Jacob
Bernouilli (1654-1705) and Abraham DeMoivre (1667-1754) studied
the random walk of a gambler's stake as it changed with the
outcome of a fair game of chance. In 1880, John Rayleigh (1842-
1919) made the connection between diffusive heat flow and random
scattering. In 1900, Louis Bachelier (?-?) introduced the random
walk theory of market fluctuations, finding that bond prices
could diffuse in the same manner as heat. The author
(Schlesinger) points out that all these cases, including
Einstein's, describe a sequence of uncorrelated random changes of
a quantity (position, price, or winnings). Even though each
change is random, a probability distribution can be derived,
allowing the formulation of equations that predict the
probability of future behavior. The underlying equation is the
diffusion equation; it's solution is the bell-shaped Gaussian
curve, which widens linearly with time (e.g., with the number of
collisions, market trades, or games played).
     4) The author (Schlesinger) points out that certain types of
random walks (e.g., "Levy walks") appear in dynamic systems that
are deterministic without a hint of probability in the equations
of motion. The key is that seemingly random-like behavior can
arise through nonlinearity. This is the famous "chaos paradigm".
In certain nonlinear systems, solution trajectories can diffuse
in a chaotic sea, diffusion alternating with trapping on almost
closed and nested nonlinear orbits. These systems have nonlinear
sensitivities that produce solution trajectories reminiscent of
random walks (Levy walks).
-----------
Michael F. Schlesinger: Physics in the noise.
(Nature 7 Jun 01 411:641)
QY: Michael F. Schlesinger: Office of Naval Research, 800 Quincy
St., Arlington, VA 22217 US.
-------------------
Summary by SCIENCE-WEEK http://scienceweek.com 22Jun01
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
EXPERIMENTAL EVIDENCE FOR MICROSCOPIC CHAOS
In the study of physical systems, the term "chaotic behavior" has
a specific meaning: the behavior of a system is said to be
"chaotic" if its final state is so sensitive to the system's
precise initial conditions that the behavior of the system is in
effect unpredictable and cannot be distinguished from a random
process, even though the behavior of the system is strictly
determinate in a mathematical sense. In other words, a
deterministic system characterized by extremely sensitive
instabilities, despite the system being determinate, can exhibit
behavior that is unpredictable, and the system is then called
"chaotic". During the past several decades, the analysis of such
chaotic systems has intrigued both physicists and mathematicians.
In general, in the study of physical systems, the term "phase
space" refers to a multidimensional space, each point of which
(phase point) completely represents the state of the system. For
example, in the study of dynamical systems, each phase point in
the phase space completely represents the values of all the
generalized coordinates and corresponding momenta. As the phase
point of a system moves in the phase space (e.g., changes with
time), the phase point follows a trajectory in the phase space,
and this trajectory is called the "phase point trajectory". In
the mathematical analysis of a particular phase space and its
phase point trajectories, "*Lyapunov exponents" are coefficients
that describe the rates at which nearby phase point trajectories
converge or diverge, and the Lyapunov exponents can be shown to
provide estimates of how long the behavior of a dynamical system
is predictable before chaotic behavior sets in. Chaotic behavior
of a system is characterized by the existence of positive
Lyapunov exponents. ... ... Gaspard et al present the results of
an experimental study of "microscopic chaos". The authors point
out that many macroscopic dynamical phenomena, for example in
hydrodynamics and oscillatory chemical reactions, have been
observed to display erratic or random time evolution, despite the
deterministic character of their dynamics -- a phenomenon known
as "macroscopic chaos". On the other hand, it has been long
supposed that the existence of chaotic behavior in the
microscopic motions of atoms and molecules in fluids or solids is
responsible for their equilibrium  and non-equilibrium
properties. But, the authors state, this hypothesis of
microscopic chaos has never been verified experimentally. The
authors now report direct experimental evidence for microscopic
chaos in fluid systems, the study involving the *observation of
brownian motion of a colloidal particle suspended in water. The
authors report finding a positive lower bound on the sum of
positive Lyapunov exponents of the system composed of the
brownian particle and the surrounding fluid. They suggest their
results and quantitative analysis provide strong experimental
evidence for microscopic chaos. They conclude: "On the assumption
that the system is deterministic, and given our knowledge of the
molecular structure of the fluid, this evidence supports, in
particular, the hypothesis that large systems -- which may be
treated by statistical mechanics -- are typically chaotic. The
result also supports the role of dynamical instability in non-
equilibrium fluids."
-----------
P. Gaspard et al (7 authors at 3 installations, BE US):
Experimental evidence for microscopic chaos.
(Nature 27 Aug 98 394:865)
QY: P. Gaspard 
-----------
Text Notes:
... ... *Lyapunov: A.M. Lyapunov (1857-1918) developed a general
theory of dynamic stability applicable to both linear and
nonlinear systems. His work was largely buried and forgotten
until it was exhumed nearly 30 years after his death.
... ... *observation of brownian motion: The experiment here
involved a colloidal particle of 2.5 microns diameter moving in
suspension in deionized water at 22 degrees Celsius, with
recorded observations of 145,612 positions over a total time
interval of approximately 2430 seconds, the observations
involving a microscope and video camera, the smallest resolution
stated as 25 nanometers. Particles of this size undergo
sedimentation, which may confound the results with non-Brownian
effects, but the authors report studies of non-sedimenting
smaller particles substantiate their observations, the larger
particle simply allowing tracking observations for a longer time.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 18Sep98
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
BROWNIAN DYNAMICS SIMULATIONS OF PROTEIN FOLDING
Protein folding occurs on a time scale ranging from milliseconds
to minutes for a majority of proteins. Computer simulation of
protein folding, from a random configuration to the native
structure, is nontrivial due to the large disparity between the
simulation and folding time scales. In order to overcome this
limitation, simple models with idealized protein subdomains,
e.g., the diffusion-collision model, have gained some popularity.
The diffusion-collision protein-folding mechanism postulates the
early-stage formation of fluctuating quasiparticles (micro-
domains), which may be incipient secondary structures (alpha-
helices and beta-sheets) or hydrophobic clusters. These micro-
domains move via diffusion, and their coalescence leads to the
formation of folded proteins. Thus, the diffusion-collision model
reduces the complexity of the folding process from a
consideration of individual amino acids to that of the properties
-----------
QY: Sangtae Kim: kim01@aa.wi.com
(Proc. Natl. Acad. Sci. US 14 Apr 98 95:4288)
(Science-Week 15 May 98)
For more information: http://scienceweek.com/swfr.htm

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3. HISTORY OF CHEMISTRY: ON THE DISCOVERY OF NUCLEAR FISSION
     The story of the discovery of nuclear fission can be briefly
summarized as follows: In 1932, James Chadwick (1891-1974)
discovered that beryllium, when exposed to bombardment by *alpha
particles, released an unknown radiation that in turn ejected
protons from the nuclei of various substances. Chadwick
interpreted the radiation as consisting of particles of mass
approximately equal to that of the proton, but without electrical
charge, and these particles were named "neutrons". In 1934,
Enrico Fermi (1901-1954) and his associates, in a systematic
project involving the bombardment of various elements with
neutrons, discovered that at least four different radioactive
species resulted from the bombardment of uranium with neutrons.
In 1939, Otto Hahn (1879-1968) and Fritz Strassman (1902-1980)
demonstrated that these radioactive species produced by the
bombardment of uranium atoms were barium, lanthanum, and other
elements. Immediately afterward, also in 1939, Lisa Meitner
(1878-1968) (a former long-time collaborator with Hahn and
Strassman) and Otto Frisch (1904-1979) demonstrated that the
liquid-drop model of the nucleus proposed earlier by Niels Bohr
((1885-1962) provided a qualitative theoretical interpretation of
the Hahn-Strassman observations, suggested that the uranium atoms
subjected to neutron bombardment split approximately in half,
named the process "nuclear fission", and showed that a large
energy release should accompany the event. Finally, and also in
the year 1939, Frederic Joliot-Curie (1900-1958) and others
demonstrated that several neutrons were emitted in the fission of
uranium-235, which immediately suggested the possibility of a
self-sustaining chain reaction producing enormous energy. In
1942, Enrico Fermi and his group at the University of Chicago
demonstrated this chain reaction in a laboratory under the
university athletic field, and this led to the construction of
the first atomic bomb.
     Much has been written about the role of Lisa Meitner in the
history of nuclear fission. She was Otto Hahn's close scientific
collaborator for 30 years, and it is generally agreed that
Meitner's realization (with her nephew Frisch) that neutron
bombardment of uranium split the uranium atom into two parts of
nearly equal mass was as important as the experimental work of
Hahn and Strassman. It was Hahn alone, however, who received the
Nobel Prize in 1945 for his work on nuclear fission. Apart from
the recurrent apparent errors made by Nobel award committees, one
reason for Meitner's neglect was certainly the fact that in 1938,
although a highly respected professor of physics, she had to
abandon her close collaboration with Hahn and flee Germany. It
was in 1938 that Nazi Germany annexed Austria, and all Austrian
citizens such as Lisa Meitner automatically became German
citizens and subject to the laws of Germany. Lisa Meitner had
been baptized as an infant and raised as a Protestant, but she
had one grandparent who was Jewish, and because of that her post
at the Kaiser Wilhelm Institute in Berlin was terminated in 1938,
and friends fearful for her life quickly smuggled her out of
Germany to Sweden. Hahn and Strassman remained in Germany and
continued their work on uranium fission; Meitner was abruptly
relegated to a long-distance theoretical counselor.
     History has its own balance sheet: Until 1997, element 105
was unofficially known as hahnium. In 1997, the International
Union of Pure and Applied Chemistry adopted the name dubnium for
element 105 and the name meitnerium for element 109. The element
hahnium no longer exists.
... ... E. Wiesner and F. Settle Jr. (Washington and Lee
University, US) present a review of the history of the discovery
of nuclear fission, the authors making the following points:
     1) The authors point out that while the history of nuclear
fission is a testament to the powers of scientific investigation,
the history and the subsequent recognition for the discovery
provide examples of human fallibility. The political environment
in Nazi Germany that surrounded the discovery, personal
prejudices among scientists, and the power of the discovery
itself brought fame to Otto Hahn while relegating his
collaborators to relative obscurity. The neglect of Lisa Meitner,
in particular, reveals shortcomings of judgment in the scientific
community. Although she was a driving force in nuclear physics
and intimately involved in the discovery of nuclear fission, her
contributions were almost lost in the aftermath of World War II
when the Nobel Prize in Chemistry was awarded in 1945 to Hahn.
     2) The authors point out that when Hitler completed the
takeover of the German government in 1933, one of the many
"reforms" enacted that year was the Reestablishment of the
Professional Civil Service Act. This law removed Jews from any
government-related jobs and resulted in the decimation of German
universities and research institutes [*Note #1]. At the Kaiser
Wilhelm Institute for Chemistry in Berlin, Lisa Meitner, who was
one-quarter Jewish, became subject to this new policy. As an
Austrian citizen, she had received a temporary respite, but with
Germany's annexation of Austria in March 1938, Meitner became by
law a citizen of the German Reich and many of her colleagues
feared for her safety. In July 1938, with the help of friends,
Meitner escaped from Germany to Stockholm, where she was given a
position in the Nobel Institute of Physics, a new institute
directed by Karl Manne Siegbahn (1886-1978).
     3) The authors point out that Otto Hahn's ambiguous role in
Meitner's escape from Germany reflects his later attitudes toward
her role in the discovery of nuclear fission. Immediately after
the annexation of Austria, Hahn became disturbed by Meitner's
presence at the Kaiser Wilhelm Institute of Chemistry and its
possible implications for the institute. He apparently discussed
the situation with one of the institute's sponsors, thereby
bringing Meitner's situation to the attention of the Ministry of
Education. On a personal level, however, Hahn apparently provided
Meitner with a great deal of support. When Meitner left Germany
quickly with little preparation, Hahn took care of her belongings
and other personal affairs. The authors state: "Thus while Hahn
cared for Meitner, he lacked the integrity to take any risks on
her behalf."
     4) The authors point out that while Meitner's contributions
to the discovery of nuclear fission were real and substantial,
her absence from Berlin during the actual discovery was a
significant factor in her neglect. Hahn and Strassman could not
admit to any collaborative work with an exiled Jewish scientist.
Although Hahn included a reference to the interpretations of
Meitner and Frisch in his February 1939 paper on the verification
of barium and other products from the neutron irradiation of
uranium, his words minimized the importance of the Meitner-Frisch
contribution. But even after the war, when Hahn was free of the
restraints of the Nazi regime, there is evidence that Hahn was
unwilling to admit the contributions of Meitner and Frisch to his
work on nuclear fission. The authors state: "Although [Hahn]
acknowledges the contributions of Meitner and Frisch in his
autobiography, there are also indications that he simply did not
understand Meitner's later theoretical contributions and
therefore felt she had contributed little to the discovery."
-----------
[Editor's note: In addition to her experience with the Nazi
regime in Germany, Lisa Meitner had life-long experience of
discrimination against women in science. After she obtained her
doctorate, the great chemist and Nobel laureate Emil Fischer
(1852-1919) allowed Meitner to work in his institute provided she
never stepped into any laboratory in which males were present.
Meitner was given space in an old carpentry shop. Also, appended
below is a brief report concerning Marietta Blau, an Austrian
female physicist and contemporary of Lisa Meitner, who also had
to flee the Nazis. Blau was not as fortunate as Meitner in
recovering some of her life.]
-----------
E. Wiesner and F. Settle Jr.: Politics, chemistry, and the
discovery of nuclear fission.
(J. Chem. Educ. July 2001 78:889)
QY: Frank Settle Jr.: fsettle@wlu.edu
-----------
Text Notes:
... ... *alpha particles: These particles are identical to
helium-4 nuclei: each particle contains two protons and two
neutrons.
... ... *Note #1: In 1933, when the chemist Carl Bosch (1874-
1940) cautioned Hitler against the policy of dismissing non-Aryan
scientists, pointing out to Hitler the severe damage which this
policy threatened to inflict on the pursuit of chemistry and
physics in Germany. Hitler responded: "Then we'll just get along
without physics and chemistry for a hundred years!"
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 22Jun01
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
REVELATIONS CONCERNING LISA MEITNER AND THE NOBEL PRIZE
Science is a human activity, and the prizes that are awarded to
individuals in science are perhaps a necessary element in
scientific progress. Nearly everyone wants approval and accolades
for one's work, and if there is not that motive, there is always
the rationalization that receiving an important prize is an aid
to getting more funds for research, more equipment, more time,
and so on. One of the most prestigious prizes is the Nobel Prize
in the various sciences, and now an article has appeared in the
journal Physics Today that tells a sad story. Based on recently
available documents of the Royal Swedish Academy of Sciences,
official records of Nobel Prize deliberations, Elizabeth Crawford
et al (3 installations, FR and US) review the details of the
Nobel Prize awards in physics and chemistry in the years 1945 and
1946, in particular the long-puzzling failure of the physicist
Lise Meitner (1878-1968), acknowledged as one of the central
discoverers of atomic fission, to win either the prize in physics
or the prize in chemistry for those years. Meitner was a long-
time collaborator of Otto Hahn (who received the 1945 Nobel Prize
in Chemistry); she barely escaped the Nazis in 1938 to work in
Sweden. The conclusions of the authors: Meitner did not share the
chemistry prize in 1945 because of "a mixture of disciplinary
bias, political obtuseness, ignorance and haste." As for the
physics prize of 1946, for which Meitner was also nominated, the
authors conclude the failure to then award her the prize was "a
rare instance in which personal negative opinions apparently led
to the exclusion of a deserving scientist." Meitner received the
U.S. Atomic Energy Commission Fermi Award in 1966.
-----------
QY: E. Crawford, CNRS, Pasteur Univ., Strasbourg FR.
(Physics Today Sep 97) (Science-Week 17 Oct 97)
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
MARIETTA BLAU: THE DESTRUCTION OF A CAREER IN PHYSICS
A nuclear emulsion is a photographic emulsion specifically
designed to register individual tracks of ionizing particles. The
emulsion technique, so important in the early history of 20th
century particle physics, was developed in the 1930s primarily by
Marietta Blau (1894-1969), an Austrian physicist. Blau was a
Jew, and she was forced to flee her laboratory when the Nazis
occupied Austria in 1938. The other people in the laboratory,
including Blau's assistant, the physicist Hertha Wambacher, were
in fact Nazis themselves, and they immediately assumed control of
the laboratory and may have ordered the seizure of Blau's
notebooks, which were confiscated as she exited Germany from
Hamburg. Although the chemists and physicists of the nuclear
emulsion group who remained in Germany and Austria for the most
part continued their work and after the war moved into important
professorships in those countries, Marietta Blau, the prime
force in the early development of nuclear emulsion technology,
wandered from country to country as a lost experimental physicist
without a laboratory. She died poor and unemployed 20 years after
the war ended. Peter Galison, a physicist and historian of
science, recently published a book entitled _Image and Logic: A
Material Culture of Microphysics_ (University of Chicago Press,
1997), and in a recent issue of the journal Physics Today he
presents an excerpt from that book that details the Blau story.
He says, "the fate of Marietta Blau signifies what it meant to be
a woman, a Jew, and a solitary physicist fleeing the convulsing
world of Nazi Austria."
-----------
(Physics Today November 97) (Science-Week 21 Nov 97)
For more information: http://scienceweek.com/swfr.htm

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4. MOLECULAR BIOLOGY: EVOLUTION OF PRION PROTEINS
     Prions are a class of poorly understood proteins implicated
in a number of exotic human neurological diseases and in some
common animal diseases such as sheep scrapie and bovine
spongiform encephalopathy in cattle ("mad cow disease").
Spongiform encephalopathies are a type of brain disease found in
humans and animals and are characterized by macroscopic vacancies
produced by the disease process (the brain has a sponge-like
appearance). What is remarkable about prions is that they behave
as infectious agents, but they are 100 times smaller than viruses
and their mechanism of replication is unclear. One human disease
in which prions have been strongly implicated is *Creutzfeldt-
Jakob disease (CJD), which appears to have a genetic basis in
about 15% of the cases. All the prion diseases are apparently
associated with the accumulation in the brain of an abnormal
*protease-resistant isoform of the prion protein. In other words,
an abnormal variant of the normal prion protein is somehow copied
or produced by the disease process, which can be initiated by
introducing infectious prion into the system.
     The term "membrane protein" refers to any protein that is
ordinarily closely associated with a cell membrane. Such an
association results from a variety of properties of the protein.
So-called "integral membrane proteins" are membrane proteins
containing hydrophobic regions that traverse the membrane lipid
bilayer. In some cases such a protein has only one hydrophobic
region, with hydrophilic domains on either side of the membrane;
in other cases, several hydrophobic regions are present, so that
a single polypeptide chain may traverse the membrane several
times.
     In general, the term "globular protein" refers to any
protein whose polypeptide chain(s) are folded so as to give the
whole molecule an approximate spherical shape.
     In this context, the term "energy landscape" refers to the
contours of what is essentially a classical energy/entropy
diagram for a protein, with the native configuration state of the
protein positioned at the bottom of a deep potential well.
... ... P. Tompa et al (4 authors at 2 installations, HU UK)
present an analysis and hypothesis concerning prion protein, the
authors making the following points:
     1) The authors point out that the existence of prion protein
in at least two extremely different structural states -- the
benign cellular form of unknown function (Prp) and the pathogenic
scrapie state (PrP-sc) -- is incompatible with the current energy
landscape theory of protein folding, which states that globular
proteins possess a rather smooth and funnel-like conformational
energy landscape that ensures their efficient folding into a
unique and stable native state. There are various lines of
evidence to suggest that prion protein has the genuine structural
capacity to attain distinct conformations without aggregation,
and thus represents a structural conundrum, the existence of
which raises serious questions.
     2) The authors suggest that the answer to the conundrum lies
in the evolutionary history of prion protein. Their analysis
reveals the existence of a "fossil" of a transmembrane protein in
the sequence of known vertebrate prion proteins, and this
suggests that prion protein was once an integral membrane protein
probably expelled to the extracellular space by a mutation.
Apparently, this environmental change gave rise to other stable
conformations of comparable free energy, but did not create an
evolutionary pressure sufficient to select against all but one of
these conformations.
     3) The authors conclude: "In a structural sense, the prion
protein links foldable proteins that have a single low energy
conformation and nonfoldable polypeptides that possess a
practically unlimited number of 3-dimensional structures of
comparable energies. In our view, the emergence of this
structural peculiarity can be explained by assuming that a
radical change in the cellular environment of this protein
occurred some time during evolution."
-----------
P. Tompa et al: Prion protein: Evolution caught en route.
(Proc. Natl. Acad. Sci. US 10 Apr 01 98:4431)
QY: I. Simon: simon@enzim.hu
-----------
Text Notes:
... ... *Creutzfeldt-Jakob disease (CJD): Until 30 years ago,
Creutzfeldt-Jakob disease was an obscure form of dementia unknown
to most physicians. The name is now familiar to the medical
community as the major prion disease in humans.
... ... *protease: In general, any enzyme that cleaves proteins,
usually by hydrolysis.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 22Jun01
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
ON PRIONS AND PRION DISEASES: A NOBEL LECTURE
Prions are defined as proteinaceous infectious particles that
lack nucleic acid, and in 1997 Stanley B. Prusiner was awarded
the Nobel Prize in Physiology or Medicine for his discovery of
prions, an entirely new genre of disease-causing agents.
... ... In a recently published abbreviated version of Prusiner's
Nobel Lecture (the lecture comprising an extensive review of
prion research), Prusiner makes the following points: 1) Prions
are unprecedented infectious pathogens that cause a group of
invariably fatal neurodegenerative diseases by an entirely novel
mechanism. 2) Prion diseases may appear as genetic, infectious,
or sporadic (i.e., non-familial) disorders, all of which involve
modifications of the prion protein. Bovine spongiform
encephalopathy ("mad cow disease"), scrapie of sheep, and
Creutzfeldt-Jakob disease of humans are among the most notable
prion diseases. 3) Prions are transmissible particles that are
devoid of nucleic acid and seem to be composed exclusively of a
modified protein. The normal cellular prion protein is converted
into modified protein through a *post-translational process
during which it acquires a high *beta-sheet content. The variety
of a particular prion is determined by the sequence of the
chromosomal prion protein gene of the mammals in which the prion
protein last replicated. 4) In contrast to pathogens carrying a
nucleic acid genome, prions appear to encode strain-specific
properties in the *tertiary structure of the modified prion
protein. *Transgenetic studies suggest that modified (pathogenic)
prion protein acts as a template upon which normal prion protein
is refolded into a nascent modified protein through a process
facilitated by another protein. 5) While knowledge about prions
has profound implications for studies of the structural
plasticity of proteins, investigations of prion diseases suggest
that new strategies for the prevention and treatment of these
disorders may also find application in the more common
degenerative diseases. The author concludes: "The discovery of
prions and their eventual acceptance by the community of scholars
represents a triumph of the scientific process over prejudice.
The future of this new and evolving area of biology should prove
even more interesting and productive as a multitude of
unpredicted discoveries emerge."
-----------
Stanley B. Prusiner: Prions
(Proc. Natl. Acad. Sci. US 10 Nov 98 95:13363)
QY: S. B. Prusiner, Univ. of Calif. San Francisco 415-476-4044.
-----------
Text Notes:
... ... *post-translational process: Translation is protein
synthesis, the process during which polypeptides are synthesized
in accordance with RNA code.
... ... *beta-sheet: In general, protein chains fold into
alpha-helices or beta-sheet structures. The beta-sheet is a
protein structure where the peptide is extended and stabilized by
hydrogen bonding between NH and CO groups of different
polypeptide chains or of separate regions of the same chain.
... ... *tertiary structure: In general, the structures of
biopolymers are denoted as follows: 1) Primary structure: The
sequence of subunits that comprise the macromolecule (e.g., the
amino acid sequence of a protein). 2) Secondary structure: The
localized arrangement in space of regions of a biopolymer (e.g.,
the alpha-helix). 3) Tertiary structure: The 3-dimensional
configuration of a biopolymer. 4) Quaternary structure: The 3-
dimensional arrangement and constitution of a multimeric
macromolecule (i.e., a substance containing more than one
biopolymer; an entity consisting of biopolymer subunits.
... ... *Transgenetic studies: (transgenic) In general, studies
involving the transfer of genetic material from one organism to
another, and subsequently the second organism expressing the
transferred genes with a resultant production of specific
proteins.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 1Jan99
For more information: http://scienceweek.com/swfr.htm

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5. MICROBIOLOGY:
PUNCTURE OF EUKARYOTIC CELLS BY BACTERIAL NEEDLES
     Biologists classify living systems into two distinct types,
cells without an internal membrane-bound genome-carrying nucleus
(prokaryotes), and cells (or organisms composed of such cells)
that do have an internal membrane-bound genome-carrying nucleus
(eukaryotes). Prokaryotes consist of two types of bacteria, the
archaebacteria and the eubacteria, with continuing controversy
concerning the early evolution of these groups.
     The prefix "eu-" means "true". In the first instance above,
"eukaryotes" means "true kernel" i.e., "true nucleus". In the
second instance above, "eubacteria" means "true bacteria", which
is more confusing than useful.
     Bacteria are indeed "primitive" organisms. But consider the
vital statistics: Each bacterium contain 4000 or 5000 distinctly
different proteins, each protein type a separate functional
entity, and most of these proteins are precisely and dynamically
arranged in space in a system that completely replicates itself
approximately every 20 minutes. There are no trivialities when
confronting such an apparatus, and the nontriviality is amplified
when considering that minute quantities of some of these
organisms are capable of killing other organisms a million times
their size.
     Most bacteria can be classified into two types, depending on
the chemistry of their outer coat, which chemistry determines
whether a bacterium will admit certain dyes into the interior.
The classification, according to the differential staining
technique, is "gram-negative" vs. "gram-positive", named after
the bacteriologist H.C. Gram (1853-1938). Gram-positive bacteria
take up a crystal violet stain and turn purple, while gram-
negative bacteria exclude the crystal violet and counterstain
instead with stains such as safranin, eosin red, or brilliant
green. As might be expected, since the technique differentiates
the outer coats of bacteria, some antibiotics are effective
against one type and not the other type, and vice versa.
     In general, gram-positive bacteria have a structure
consisting of a cytoplasmic core, a plasma membrane, and a rigid
external capsule. Gram-negative bacteria, however, have two
plasma membranes between the inner cytoplasmic core and the
external capsule: the two plasma membranes are separated by a
"periplasmic space" packed with various enzymes.
     Depending on the species, bacteria have various types of
extensions protruding through the external capsule and into the
ambient medium. One or more "flagella" may be present, long
filamentous and flexible structures whose mechanical motions
provide the bacterium with motility. Two types of rigid
extensions are common, "pili" (Latin for "hairs") and "fimbriae"
(Latin for "fringes") (singular: pilus, fimbrium), both much
shorter than flagella, and fimbriae much shorter than pili. These
structures are 7 nanometers in diameter, and much thinner than
flagellae (which are 25 nanometers in diameter). Both pili and
fimbriae are believed to be involved in the adhesion of
pathogenic bacteria to the surfaces of host cells. The report
below concerns a new and third type of external extension --
penetrating "needles" that come into existence only upon contact
with a host cell.
     The bacterial species Yersinia enterocolitica is a pathogen
related to Yersinia pestis, the cause of plague. Yersinia
enterocolitica is found in the intestinal tract of a variety of
animals, the bacterium usually causing disease in these animals.
Like Y. pestis, this pathogen is transmissible from animals to
humans, in whom it can produce a variety of clinical syndromes.
Both Y. pestis and Y. enterocolitica are gram-negative rods.
     Among the distinguishing characteristics of prokaryotes is
their ability to exchange small packets of genetic information.
In many cases, this genetic information is carried on "plasmids",
small and specialized extrachromosomal genetic elements that are
capable of replication within at least one prokaryotic cell line.
In some cases, plasmids may be transferred from one bacterial
cell to another via a "sex pilus" that serves as a conduit for
the transfer of genetic material -- thus effecting the
transmission of specialized genetic information (including
virulence characteristics) through a bacterial population.
... ... E. Hoiczyk and G. Blobel (Rockefeller University, US)
present a report on "needle" punctures of eukaryotic cells by Y.
enterocolitica, the authors making the following points.
     1) The authors point out that a number of pathogenic gram-
negative bacteria are able to secrete specific proteins across
three membranes: the inner and outer gram-negative bacterial
membrane and the eukaryotic plasma membrane. In the pathogen Y.
enterocolitica, the primary structure of the secreted proteins,
as well as the components of the secretion machinery, both
plasmid-encoded, is known. But the mechanism of protein
translocation from bacterium to host cell is largely unknown.
     2) The authors report that Y. enterocolitica polymerizes a
6-kilodalton protein of the secretion machinery into needles that
are able to puncture the eukaryotic plasma membrane. These
needles apparently form a conduit for the transport of specific
proteins from the bacterial to the eukaryotic cytoplasm, where
they exert their cytotoxic action. Electron microscopy
demonstrates the needles are 60 to 80 nanometers long, 6 to 7
nanometers wide, and contain a hollow center of approximately 2
nanometers in diameter. The authors state their data indicate
that it is the polymerization of the 6-kilodalton protein into
these needles that provides the force to perforate the eukaryotic
plasma membrane. The authors conclude: "Surprisingly, the basic
principle of such an injection mechanism is widespread among life
forms and is found in organisms as diverse as insects, snails,
and fish."
-----------
E. Hoiczyk and G. Blobel: Polymerization of a single protein of
the pathogen Yersinia enterocolitica into needles punctures
eukaryotic cells.
(Proc. Natl. Acad. Sci. US 10 Apr 01 98:4669)
QY: Egbert Hoiczyk: hoiczye@rockvax.rockefeller.edu
-------------------
Summary by SCIENCE-WEEK http://scienceweek.com 22Jun01
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
IN FOCUS: ON THE WORKINGS OF THE BACTERIAL CELL
"A few years ago a well-known physical chemist interested in
bacterial physiology wrote this remarkable sentence: 'The
structure of the bacterial cell is simple.' This is true of
course from the bacterial point of view. The bacterial machine
works, synthesizes, grows, and divides. And, as the bacterium is
devoid of brain, it has no problems. But for us, the suffering
human beings who try to penetrate the intimate nature of life,
the bacterial cell, despite being small, is far from simple. In
this machine of around 1 micron diameter, corresponding to a
volume of 10^(-12) milliliters, a few thousand specific molecular
species are at work, manufacturing more of their specific kind.
And we would rather be inclined to say with Anton van Leewenhoek,
who in 1676 discovered the bacterial world, 'Dear God, what
marvels there are in so small a creature'... At first sight the
problem seems formidable and the situation hopeless. A cell
contains some 2000 to 5000 species of macromolecules. Moreover,
nature has produced an immense variety of categories of different
organisms. Yet, when the living world is considered at the
cellular level, one discovers unity. Unity of plan: each cell
possesses a [genome] embedded in protoplasm. Unity of function:
the metabolism is essentially the same in each cell. Unity of
composition: the main macromolecules of all living beings are
composed of the same small molecules. For, in order to build the
immense diversity of the living systems, nature has made use of a
strictly limited number of building blocks. The problem of
diversity of structures and functions, the problem of heredity,
and the problem of diversification of species have been solved by
the elegant use of a small number of building blocks organized
into specific macromolecules... Each macromolecule is endowed
with a specific function. The machine is built for doing
precisely what it does. We may admire it, but we should not lose
our heads. If the living system did not perform its task, it
would not exist. We have simply to learn how it performs its
task."
-----------
Andre Lwoff: _Biological Order_
(MIT Press, Cambridge MA 1962)
[Microbiologist Andre Lwoff (1902-1994) demonstrated that enzymes
produced by some genes regulate the function of other genes.
Lwoff shared the 1965 Nobel Prize in Physiology and Medicine with
Jacques Monod and Francois Jacob.]
-------------------
SCIENCE-WEEK http://scienceweek.com 1Sep00
For more information: http://scienceweek.com/swfr.htm

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6. EVOLUTIONARY BIOLOGY: VERTEBRATE DISPERSAL OUT OF INDIA
     The time-frame known as the "Cretaceous period" extends from
145.6 million years ago to 65 million years ago; the time-frame
known as the "Tertiary era" extends from 65 million years ago to
1.64 million years ago.
     The largest mass extinction of the past 200 million years
occurred 65 million years ago, when approximately half of the
genera of multicellular organisms on Earth, including all of the
dinosaurs, suddenly died off. The geological record indicates
that a layer of impact-produced minerals and the element iridium
(an element rare in the crust of the Earth but more abundant in
primitive meteorites) was deposited at the time the dinosaurs
vanished -- the so-called Cretaceous/Tertiary or K/T boundary. In
addition to this, the largest known crater on Earth to be dated
at less than 1 billion years old was apparently formed at this
time. Taken together, many researchers believe these data imply
that the K/T mass extinction was caused by the impact into the
Yucatan peninsula of an asteroid or comet of approximately 10
kilometers in radius.
     Igneous rocks are rocks that have congealed from a molten
mass. Basalt is a dark gray to black igneous rock of volcanic
origin that cools rapidly. It is found as basement rock on land,
and on sea floor spreading from mid-ocean ridges. The term "flood
basalt" refers to very fluid basaltic lava that flows over large
areas, in some cases with a series of flows occurring one after
the other. The largest known area (the "Deccan traps") of flood
basalt covers 250,000 square kilometers of the Deccan plateau on
the Indian subcontinent.
     In this context, the term "adaptive radiation" refers to the
rapid evolution of one or a few biological forms into many
different species that occupy different habitats within a new
geographical area.
     The term "molecular clock" (evolutionary clock) refers to
the hypothesis that the rate at which mutational changes in DNA
or proteins accumulate is constant over time. The idea is in
dispute, and also in dispute is to which genes or genomes the
clock may apply.
     The term "phylogeny" refers to the evolutionary history of a
species or group of species in terms of their derivation and
relationships, and the term "molecular phylogeny" refers to a
phylogeny based on molecular analysis of genes and/or proteins.
     The term "lithosphere" refers to the outer layer of the
Earth, comprising the crust and upper mantle, and extending to a
depth of 50 to 70 kilometers. The traditional view of tectonics
(changes in the structure of the Earth's crust) is that the
lithosphere consists of a strong brittle layer overlying a weak
ductile layer. "Plate tectonics" is the current consensus theory
that the Earth's lithosphere is broken into fairly rigid plates,
seven or eight major plates and many smaller plates, and that
convection within the underlying less rigid "asthenosphere"
causes the plates (and the associated continents and crust) to
move relative to each other.
     Plate tectonics 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.
     Evidence indicates that the Madagascar-Seychelles-Indian
landmass became isolated from Africa approximately 130 million
years ago, that India drifted toward Eurasia, and that India
connected to Eurasia 65 to 56 million years ago. (The present
Himalayan mountain range is apparently the "seam" of that
connection.) In this context, the term "drifting India" refers to
the continental drift of India from Africa to Eurasia.
... ... F. Bossuyt and M.C. Milinkovich (University of Brussels,
BE) present an analysis of early Tertiary dispersal of amphibians
from India, the authors making the following points:
     1) The authors point out that the mass extinction of the K/T
boundary coincided both with a well-documented asteroid or comet
impact on the Yucatan coast of Mexico and with massive flood
basalt volcanism that produced on the Indian-Seychelles land mass
the largest continental lava deposit (the "Deccan traps") of the
past 200 million years. It has been suggested that one or both of
these events caused a global bottleneck of biodiversity, which
was followed by a period of intense biodiversification through
adaptive radiations (especially in birds and mammals) during the
early Tertiary era. However, some aspects of this theory have
been challenged by molecular evidence suggesting that many
lineages of birds and mammals survived the K/T transition.
     2) The authors report that using an approach independent of
any molecular-clock hypothesis for inferring dating information
from molecular phylogenies, an analysis demonstrates that
multiple lineages of frogs survived Deccan-traps volcanism after
millions of years of isolation on drifting India. The collision
between the Indian and Eurasian plates was apparently followed by
wide dispersal of several of these lineages, and this "out-of-
India" scenario reveals a zoogeographical pattern that might
reconcile paleontological and molecular data in other vertebrate
groups.
     3) The authors conclude: "Krause and Maas (1990) suggested
that 'among early Tertiary large landmasses, the Indian
subcontinent is unique in its combination of having been in the
right place at the right time to provide for the development and
the subsequent disembarking of several new higher taxa of
mammals.' Our analyses provide molecular evidence extending this
zoogeographical perception to amphibians and suggest that the
origin of other vertebrate lineages might need to be sought in
India, despite [its] extensive isolation and massive volcanism."
-----------
F. Bossuyt and M.C. Milinkovich: Amphibians as indicators of
early Tertiary "Out-of-India" dispersal of vertebrates.
(Science 6 Apr 01 292:93)
QY: Michel C. Milinkovich: mcmilink@ulb.ac.be
-------------------
Summary by SCIENCE-WEEK http://scienceweek.com 22Jun01
For more information: http://scienceweek.com/swfr.htm

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7. IN FOCUS: ON THE NEW ASTRONOMY
"The "new astronomy" is a phenomenon of the late 20th century,
and it has completely revolutionized our concept of the Universe.
While traditional astronomy was concerned with studying the light
-- optical radiation -- from objects in space, the new astronomy
encompasses all the radiations emitted by celestial objects:
gamma rays, x-rays, ultraviolet, optical, infrared, and radio
waves. The range of light is surprisingly limited. It includes
only radiation with wavelengths 30 percent shorter to 30 percent
longer than the wavelengths to which our eyes are most sensitive.
The new astronomy covers radiation from extremes which have
wavelengths less than 10^(-9) as long, in the case of the
shortest gamma rays, to over 10^(8) times longer for the longest
radio waves. To make an analogy with sound, traditional astronomy
was an effort to understand the symphony of the Universe with
ears which could hear only middle C and two notes immediately
adjacent. The rapid growth of the new astronomy is due partly to
the accidental discovery in the 1930s of radio waves from beyond
the Earth, which showed that there are non-optical radiations
from space. But there have been two major barriers, overcome only
in recent decades. First there are technological problems. We
must build new types of telescopes to gather other kinds of
radiation, and focus them into an image. We must also develop new
detectors to record the image and show it to us in a way we can
comprehend. The other is a natural barrier. Earth's atmosphere
absorbs most of the radiations from space before they reach the
ground, and the new detectors for many wavelengths must be flown
well above the atmosphere. These branches of the new astronomy
could not be pursued until telescopes could be launched by the
rockets, and carried on the satellites, of the 'space age'".
-----------
N. Henbest and M. Marten: _The New Astronomy_, 2nd Edition.
(Cambridge University Press, Cambridge UK 1996, p.6)
-------------------
SCIENCE-WEEK http://scienceweek.com 22Jun01
For more information: http://scienceweek.com/swfr.htm

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8. FROM THE SCIENCEWEEK ARCHIVE:
COSMOLOGY: EXPECTATIONS IN THE NEXT CENTURY OF RESEARCH
Cosmology is one of the grand sciences, a domain of research
whose results have enormous intellectual consequences, at least
for people who care about what they are and where they are.
Martin Rees (Cambridge University, UK) presents an essay on the
near-future research expectations of cosmologists, the author
making the following points:
     1) Astronomers still do not know what the Universe is made
of. Observable radiation-emitting objects -- such as stars,
*quasars, and galaxies -- apparently constitute only a small
fraction of the matter in the Universe. The vast bulk of matter
is dark and unaccounted for, and most cosmologists believe this
dark matter is composed of weakly interacting particles left over
from the *Big Bang. But dark matter could be something more
exotic. "Whatever the case, it is clear that galaxies, stars and
planets are a mere afterthought in a Cosmos dominated by quite
different stuff." The author suggests that intensive searches for
dark matter, mainly via sensitive underground experiments
designed to detect elusive subatomic particles, will continue in
the coming decade, and that within the next decade both the
amount and nature of dark matter will be clarified.
     2) The author suggests that research in the near-future is
also likely to focus on the evolution of the large-scale
structure of the Universe. The current view is that ever since
the Big Bang, gravity has been amplifying inhomogeneities,
building up structures and enhancing temperature contrasts -- "a
prerequisite for the emergence of the complexity that lies around
us now and of which we're a part." The author suggests that
astronomers are now learning more about the 10 billion year
process of Cosmic evolution by creating virtual universes on
computers, and that in the coming years researchers will be able
to simulate the history of the Universe with ever improving
realism and then compare the results with astronomical
observations.
     3) The author suggests that the great mystery for
cosmologists is the series of events that occurred less than 1
millisecond after the Big Bang, when the Universe was
extraordinarily small, hot, and dense. "The laws of physics with
which we are familiar offer little firm guidance for explaining
what happened during this critical period." To solve this
problem, it will necessary to improve and refine current
observations in order to understand the characteristics of the
Universe when it was only one second old: its expansion rate, the
size of its density fluctuations, and its proportions of ordinary
atoms, dark matter, and radiation.
     4) The author suggests the following Cosmic timeline for the
evolution of the Universe from the Big Bang to the present:
... ... a) 10^(-43) seconds after the Big Bang: the *Quantum
Gravity Era.
... ... b) 10^(-36) seconds after the Big Bang: Probable *Era of
Inflation.
... ... c) 10^(-5) seconds after the Big Bang: Formation of
protons and neutrons from *quarks.
... ... d) 3 minutes after the Big Bang: Synthesis of atomic
nuclei.
... ... e) 300,000 years after the Big Bang: First atoms form.
... ... f) 1 billion years after the Big Bang: Appearance of
first stars, galaxies, and quasars.
... ... g) 10 to 15 billion years after the Big Bang: Appearance
of modern galaxies.
     5) The author concludes: "How did a hot amorphous fireball
evolve, over 10 to 15 billion years, into our complex Cosmos of
galaxies, stars, and planets? How did atoms assemble -- here on
Earth and perhaps on other worlds -- into living beings intricate
enough to ponder their own origins? These questions are a
challenge for the new millennium. Answering them may well be an
unending quest."
-----------
Martin Rees: Exploring our Universe and others.
(Scientific American December 1999)
QY: Martin Rees: Cambridge University, UK.
-----------
Text Notes:
... ... *quasars: (quasi-stellar objects). Extremely luminous
sources radiating energy over the entire spectrum from x-rays to
radio waves, and which are apparently the oldest and most distant
objects in the universe. They are believed to involve massive
black holes.
... ... *Big Bang: The Big Bang theory is the general
cosmological model that proposes that all matter and radiation in
the universe originated in an explosion at a finite time in the
past.
... ... *Quantum Gravity Era: Quantum field theory is the
mathematical fusion of quantum mechanics with special relativity
theory, and the term "quantum gravity" refers to the fusion of
quantum mechanics with general relativity theory. The essential
basis for these fusions is the so-called "equivalence principle",
which identifies the mass involved in the gravitational force
equation with the inertial mass in the equation that relates any
force to the product of inertial mass and acceleration. The
"quantum gravity era" is the time-frame during which both quantum
effects and gravity determined the behavior of particles.
... ... *Era of Inflation: The inflationary model, first
proposed by Alan Guth in 1980, proposes that quantum
fluctuations in the time period 10^(-35) to 10^(-32) seconds
after time zero were quickly amplified into large density
variations during the "inflationary" 10^(50) expansion of the
universe in that time frame.
... ... *quarks: A quark is a hypothetical fundamental particle,
having charges whose magnitudes are one-third or two-thirds of
the electron charge, and from which the elementary particles may
in theory be constructed.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 28Jan00
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
IN FOCUS: ON COSMIC HISTORY
"The history of our Universe divides into three parts. 1) The
first millisecond, a brief but eventful era spanning 40 powers of
10 in time, starting at the Planck era [10^(-43) seconds]. This
is the intellectual habitat of mathematical physicists and
quantum cosmologists. The relevant physics is still speculative
-- indeed, one motive for studying cosmology is that the early
Universe may offer the only real clues to the laws of nature at
extreme energies. 2) The second stage runs from a millisecond to
about 1 million years. It's an era where cautious empiricists
feel more at home. The densities are far below nuclear density,
but everything is still expanding quite smoothly. There is good
quantitative evidence -- the cosmic helium and deuterium
abundances, the background radiation, and so on -- and the
relevant physics is well tested in the lab. Part two of cosmic
history, though it lies in the remote past, is the easiest to
understand. 3) But the tractability lasts only so long as the
Universe remains amorphous and structureless. When the first
gravitationally bound structures condense out -- when the first
stars, galaxies, and quasars have formed and lit up -- the era
studied by traditional astronomers begins. We then witness
complex manifestations of well-known basic laws. Part three of
cosmic history is difficult for the same reason as all
environmental sciences -- from meteorology to ecology -- are
difficult: they involve ultracomplex manifestations of simple
laws."
-----------
Martin Rees: _Before the Beginning_
(Helix Books, Reading 1997, p.160)
[Sir Martin Rees is Astronomer Royal of the UK and former
Director of the Cambridge University Institute of Astronomy.]
-------------------
SCIENCE-WEEK http://scienceweek.com 16Jul99
For more information: http://scienceweek.com/swfr.htm


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