ScienceWeek

SCIENCE-WEEK

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science educators, and science policy-makers.

February 2, 2001 -- Vol. 5 Number 5

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Discovery consists of seeing what everybody has
seen and thinking what nobody has thought.
-- Albert Szent-Gyorgyi (1893-1986)

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

1. ASTROPHYSICS: GAMMA-RAY BURSTS STILL A PUZZLE
A striking development in the last several years has been the
measurement and localization of fading x-ray signals from some
gamma-ray bursts, the x-ray signals typically lasting for days
and making possible the optical and radio detection of afterglows
which mark the location of the gamma-ray-burst event. Gamma-ray
bursts appear so bright that their energy output must be on the
order of 10^(51) to 10^(54) ergs per second, larger than that of
any other type of source. Such an energy output is comparable to
burning up the entire mass-energy of the Sun in a few tens of
seconds, or to emit over the same period of time as much energy
as our entire Milky Way Galaxy does in a hundred years. The
progenitors of gamma-ray bursts have not yet been clearly
identified. (Science 5 Jan 01 291:79)

2. EARTH SCIENCES: ON UNIFORMITARIANISM
The concept of uniformitarianism is still influential in
paleoclimatology. The possibility of anthropogenic or natural
climate change affecting societies and ecosystems drives current
researchers attempting to understand and even predict the
behavior of the Earth system. The history of the system is used
in the construction and testing of models, and that history is
written in sea-floor muds, tree rings, cave formations, and other
sedimentary archives. Literally hundreds of physical, chemical,
isotope, and biological paleoclimate indicators are used.
(Nature 18 Jan 01 409:289)

3. EARTH SCIENCES:
SNOWBALL VS. SLUSHBALL EARTH AND PALEOBIOLOGY
Paleomagnetic data suggest that the Neoproterozoic glaciation
involved ice sheets in low latitudes, and this has been explained
by either a global glaciation ("snowball Earth hypothesis") or by
a large obliquity during that era. Since the same era was a
critical time in the evolution of multicellular animals on Earth,
an important question is how early life survived under such
environmental stress. Recently, an alternative to the snowball
Earth hypothesis has been proposed, a so-called "slushball Earth
hypothesis", the essential feature of which is that
Neoproterozoic glaciation was not global but quasi-global,
leaving large areas of open water at Equatorial latitudes. In an
exchange of letters, proponents of the two views argue their
case. (Nature 18 Jan 01 409:306)

4. EVOLUTIONARY BIOLOGY:
RAPID TRANSIT OF MITOCHONDRIAL GENES TO THE NUCLEUS
Given the small genomes of various mitochondria, a central
component of the endosymbiotic theory for the bacterial origin of
the mitochondrion is that many of the mitochondrial genes were
transferred to the nucleus of the host cell. Most of this
transfer is thought to have occurred early in mitochondrial
evolution; functional transfer of mitochondrial genes has ceased
in animals. Researchers now report frequent loss and transfer to
the nucleus of the mitochondrial gene among 277 diverse
angiosperms. The data indicate that many RNA-mediated independent
gene transfers occurred during recent angiosperm evolution.
(Nature 16 Nov 00 408:354)

5. BIOTECHNOLOGY: GENE CHIPS AND FUNCTIONAL GENOMICS
DNA Microarrays are chips containing hundreds or thousands
of gene snippets laid out in precise arrays that when exposed to
active-gene-dependent cellular components can provide rapid
snapshots of the expression of whole suites of genes. The amount
of data that results from DNA-microarray experiments can often be
overwhelming. A single gene chip may generate more than 10,000
data points, the volume of data increasing enormously when one
uses multiple sets of chips, as is the case when replication
experiments are performed. The reams of data pose a considerable
analytical problem, one that many researchers regard as the most
difficult part of the technique.
(American Scientist Nov/Dec 2000 88:508)

6. BIOPHYSICS: ATOMIC FORCE MICROSCOPY IN BIOLOGICAL RESEARCH
Since its introduction in the 1980s, atomic force microscopy
(ATM) has gained acceptance in biological research, where it has
been used to study a broad range of biological questions,
including protein and DNA structure, protein folding and
unfolding, protein-protein and protein-DNA interactions, enzyme
catalysis, and protein crystal growth. Atomic force microscopy
has been used to literally dissect specific segments of DNA for
the generation of genetic probes, and to monitor the development
of new gene therapy delivery particles. (The Scientist 22 Jan 01)

7. IN FOCUS: ON DARWINISM AND AMERICAN SOCIETY

8. FROM THE SW ARCHIVE: ON COMPLEXITY IN CHEMISTRY

9. BOOK NOTICES


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Section 2
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1. ASTROPHYSICS: GAMMA-RAY BURSTS STILL A PUZZLE
     In 1902, Ernest Rutherford (1871-1937) proposed that the
decay of radioactive substances produced 3 different kinds of
radiation, alpha, beta, and gamma rays, with alpha rays the
weakest and gamma rays the strongest in their ability to
penetrate matter. Alpha particles were discovered to be identical
with the nuclei of helium atoms, and beta rays were identified as
electrons. In 1912, it was demonstrated that radioactive-decay
gamma rays are extremely energetic photons, between 10^(4) and
10^(6) times more energetic than the photons of visible light. 
Gamma rays with 10^(12) times higher energy comprise a small
fraction of the *cosmic rays that reach the Earth from supernovae
or galaxies. In general, the origins of the most energetic gamma
rays are not clear.
     Gamma-ray bursts are intense flashes of gamma rays detected
at energies up to 10^(6) *electronvolts. They were discovered by
US Air Force satellites in 1967 but not declassified until 1973.
The detection of these bursts averages approximately 1 per day,
and measurements indicate the distribution of bursts is
isotropic, i.e., they are uniformly distributed across the sky.
... ... P. Meszaros (Pennsylvania State University, US) presents
a review of current research on gamma-ray bursts, the author
making the following points:
     1) The author points out that gamma-ray bursts were first
reported in 1973 on the basis of 1969-1971 observations by the
Vela military satellites monitoring for nuclear explosions in
verification of the Nuclear Test Ban Treaty. When the mysterious
gamma-ray flashes, which apparently did not derive from the
direction of the Earth, were first detected, the initial
suspicion (soon abandoned) was that they might be the product of
an advanced extraterrestrial civilization. It was quickly
realized, however, that these bursts were a new and extremely
puzzling cosmic phenomenon. For the next 20 years, hundreds of
gamma-ray-burst detections were made, but the bursts continued to
vanish too soon for the sources to be accurately positioned by
follow-up observations. In general, the reason for the source-
location problem was that gamma rays are extremely difficult to
focus, so that gamma-ray images are usually not very sharp.
     2) A striking development in the last several years has been
the measurement and localization of fading x-ray signals from
some gamma-ray bursts, the x-ray signals typically lasting for
days and making possible the optical and radio detection of
afterglows which mark the location of the gamma-ray-burst event.
These afterglows in turn have enabled the measurement of
*redshift distances, the identification of gamma-ray-burst host
galaxies, and the confirmation that gamma-ray bursts are at
cosmological distances of the order billions of light years,
similar to those of the most distant galaxies and *quasars. Even
at those distances, gamma-ray bursts appear so bright that their
energy output must be on the order of 10^(51) to 10^(54) ergs per
second, larger than that of any other type of source. Such an
energy output is comparable to burning up the entire mass-energy
of the Sun in a few tens of seconds, or to emit over the same
period of time as much energy as our entire Milky Way Galaxy does
in a hundred years.
     3) The progenitors of gamma-ray bursts have not yet been
clearly identified. The current view is that gamma-ray bursts
arise in only a very small fraction [approximately 10^(-6)] of
stars that undergo a catastrophic energy release event near the
end of their evolution. One class of candidates ("hypernovae";
"collapsars") involves massive stars whose cores collapse,
probably in the course of merging with a companion. Another class
of candidates consists of *neutron-star binaries or neutron-star-
black-hole binaries, which lose orbital angular momentum by
*gravitational wave radiation and undergo a merger. Both of these
progenitor types are expected to lead to the formation of a black
hole whose mass is several times that of the Sun, the black hole
surrounded by a temporary torus of debris whose accretion by the
black hole can provide a sudden release of gravitational energy,
with similar total energies sufficient to power a gamma-ray
burst.
     4) The author concludes: "Our understanding of gamma-ray
bursts has come a long way since their discovery almost 30 years
ago, but these enigmatic sources continue to offer major puzzles
and challenges."
-----------
P. Meszaros: Gamma-ray bursts: Accumulation afterglow
implications, progenitor clues, and prospects.
(Science 5 Jan 01 291:79)
QY: P. Meszaros: pmeszaros@astro.psu.edu
-----------
Text Notes:
... ... *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.
... ... *electronvolts: An electronvolt is defined as the energy
acquired by an electron falling freely through a potential
difference of one volt, and is equal to 1.6022 x 10^(-19) joule.
... ... *redshift distances: Redshift (symbol: z) is a
lengthening of the wavelengths of electromagnetic radiation from
a source caused either by the movement of the source (Doppler
effect) or by the expansion of the universe (cosmological
redshift). Redshift is defined as the change in wavelength of a
particular spectral line divided by the unshifted wavelength of
that line. Large redshifts imply large radial velocities (which
imply large distances, according to current cosmological theory),
but at redshifts greater than about 0.2 there is a relativistic
divergence from a linear relation. A redshift of 4.0 corresponds
to an object receding with a radial velocity 92% that of the
velocity of light.
... ... *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.
... ... *neutron-star binaries or neutron-star-black-hole
binaries: In an ordinary star, the radiation pressure produced by
the burning of the core of the star is enough to counteract the
inward gravitational force and keep the star from collapsing; in
a star that has exhausted its fuel, such radiation pressure is
severely reduced and the star begins a gravitational collapse due
to its enormous mass. But how far will the collapse proceed? If,
following its terminal stages, the remnant mass of a star is
between 1.4 and 2 to 3 solar masses, the star will collapse into
a neutron star, a body with a radius of 10 to 15 kilometers, with
a core so dense that its component protons and electrons have
merged into neutrons. The average density of a neutron star is
10^(15) grams per cubic centimeter, and the weight of an object
on the surface of a neutron star would be 10^(11) its weight on
the surface of the Earth. Neutron stars apparently have an outer
shell of iron, but it is iron like no Earth iron, an iron of 4
orders of magnitude greater density. A "neutron-star binary" is a
binary gravitational system consisting of two neutron stars.
Concerning black holes, if the terminal stages of star death
leave a remnant star mass greater than 3 solar-masses, the
ultimate gravitational collapse will produce a black hole, a
relativistic singularity. A black hole is a localized region of
space from which neither matter nor radiation can escape. The
"trapping" occurs because the requisite escape velocity, which
can be calculated from the relevant equations, exceeds the
velocity of light and is therefore unattainable. A "neutron-star-
black-hole binary" is a gravitational system consisting of a
neutron star and a black hole.
... ... *gravitational wave: In general, this is a wave-like
perturbation in a gravitational field, produced when a mass is
accelerated or otherwise disturbed. According to general
relativity theory, such waves travel through space-time at the
speed of light, with an amplitude proportional to the rate of
acceleration of the body producing the waves. The strongest
sources are the sources with the strongest gravitational fields,
although the gravitational waves produced are comparatively weak.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 2Feb01
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
GAMMA-RAY BURSTS: THE LARGEST EXPLOSIONS IN THE UNIVERSE
... ... Dieter H. Hartmann (Clemson University, US) presents a
review of current research concerning gamma-ray bursts, the
author making the following points:
     1) Gamma-ray bursts are short flashes of almost pure high-
energy emission (x-rays and gamma-rays) that occur randomly on
the sky, and from loci which apparently do not emit more than
once. Typical durations are of the order of seconds, but can
range from a few milliseconds to over 1000 seconds. The bursts
are extremely bright, outshining all other objects on the gamma
ray sky, but their spectra are featureless and reveal little
about the underlying physical processes. Integrating burst
spectra over energy and time yields large fluences (received
energy per unit area), but does not determine the total burst
energy until the distance is known.
     2) Although the statistical properties of gamma-ray bursts
long supported the idea that bursts occur at cosmological
distances, this distance scale was finally established by a burst
on 8 May 1997, for which a faint extended object was optically
identified as the host, the object showing clear evidence of
absorption lines that indicated a lower redshift limit of z =
0.835. On 14 December 1997, another burst showed absorption lines
at z = 3.42, and then a third burst on 3 July 1998 had associated
absorption lines at z = 0.966 -- all of this indicating that
gamma-ray bursts, along with *quasars, are the most distant
objects in the Universe. Such large distances imply large
energies, and in fact the assumption of isotropic emission
implies burst energies in excess of 10^(53) ergs, comparable to
*supernova energies but released predominantly in the gamma-ray
band. The optical afterglows of gamma-ray bursts are much
brighter than supernova, hence the name "hypernova" has been
proposed.
     3) Studies of gamma-ray burst host galaxies suggest they are
normal star-forming galaxies, and not galaxies with *active
nuclei. The estimated star formation rates in these hosts,
together with other evidence from x-ray spectra and photometry of
the gamma-ray burst afterglows suggests that gamma-ray bursts may
be directly associated with star-forming regions. If that turns
out to be correct, astronomers would have a powerful new tool for
the study of structure formation in the Universe, a tool that
could reach further back in time than quasars.
     4) Despite recent breakthroughs in gamma-ray burst
observations, many questions remain about the nature of the
underlying processes and the evolutionary sequences leading up to
the creation of the central engine driving these outbursts. The
ultimate goal of understanding this engine may be accomplished
through simultaneous optical observations, and such is the
objective of dedicated experiments under development throughout
the world.
-----------
Dieter H. Hartmann: Afterglows from the largest explosions in the
Universe.
(Proc. Natl. Acad. Sci. US 27 Apr 99 96:4752)
QY: Dieter H. Hartmann, Clemson University, Clemson SC 29634 US.
-----------
Text Notes:
... ... *electron volts: See main report.
... ... *Redshift: See main report.
... ... *quasars: See main report.
... ... *supernova: A violent explosion in which certain stars
end their lives. The star may become more than 10^(9) times as
bright as the Sun and may outshine its host galaxy for weeks.
... ... *active nuclei: (active galactic nuclei) Central regions
of galaxies in which considerable energy is generated by
processes other than those operating in ordinary stars. The
energy may result from the accretion of material into a massive
black hole situated at the core of the galaxy. (See Report #3
this issue.)
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 16Jul99
For more information: http://scienceweek.com/swfr.htm

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2. EARTH SCIENCES: ON UNIFORMITARIANISM
     The history of modern geology begins in the late 18th
century, a formative period defined by the time-frame 1780 to
1840. The two central figures in the early geological science of
this time were James Hutton (1726-1797) and Charles Lyell (1797-
1875). Hutton studied law, and then medicine, but he soon devoted
himself exclusively to geology. In 1795, Hutton published a two-
volume work, _Theory of the Earth_, which proposed that the
geological processes that had formed the Earth's features could
be observed continuing in the present day, that the heat of the
Earth was the productive power that caused sedimentary rocks to
fuse into the granites and flints, which could be produced in no
other way, and that these forces could also produce the upheaval
of strata, their folding and twisting, and the creation of
mountains. In general, Hutton's idea was that the Earth is
immensely old, and that past geological processes continue in the
present. His famous dictum was that on the face of the Earth, "we
find no vestige of a beginning -- no prospect of an end." His
theory came to be called "uniformitarianism" (the idea of a
uniformity of process through vast geologic time), and although
quickly accepted by many scientists interested in Earth's
history, the idea caused a storm of intellectual protest: a
central establishment thesis of that age was that the Earth was
6000 years old, and that the Earth and everything on it had been
created de novo by a divine being, the Earth created essentially
as a home for Man. The prevailing idea concerning apparent
geologic formations was that such formations had resulted from
various catastrophes ("catastrophism") or from precipitation of
rocks from the sea ("neptunism"). Hutton's work was completely
iconoclastic, and in essence he did for geology something
comparable to what Copernicus (1473-1543) had done for astronomy:
Hutton's evidence and reasoning began the destruction of the
Biblical dogmatism concerning the history of the Earth.
     A generation later, in his _Principles of Geology_ (3 vols.,
1830-1833), the geologist Charles Lyell proposed a uniformitarian
interpretation of geological history, his work much more readable
than Hutton's and much more influential. Lyell's system was based
on two propositions: a) the operating causes of geological change
include all the causes that have acted from the beginning of
geologic time; and b) these causes have always operated at the
same average levels of energy. But Lyell's steady-state theory of
the Earth (and of life on the Earth) was eventually abandoned. It
was Lyell's clear exposition of methodology in geology that
influenced 19th century geologists, and Lyell's _Principles of
Geology_ went through 11 editions and greatly influenced Charles
Darwin (1809-1882).
... ... Richard B. Alley (Pennsylvania State University, US)
presents an essay on uniformitarianism, the author making the
following points:
     1) The author points out that perhaps overreacting to the
persistence of Biblical literalists, Lyell took uniformitarianism
to an extreme, arguing not only that modern processes acted in
the past to shape the Earth, but that those processes have always
occurred at similar rates. Lyell advanced biology by providing
Darwin with the vast ages on which to stage evolution, but Lyell
may have actually delayed the study of the origins and early
evolution of Earth, the environment, and life itself by taking
too literally Hutton's "no vestige of a beginning, no prospect of
an end."
     2) Currently, while "deep-time" geologists have been quietly
moving away from the Lyellian uniformitarianism (i.e., moving
toward the recognition that parameters of a particular geologic
process may alter with time, e.g., due to cooling of the Earth),
the concept of uniformitarianism is still influential in
paleoclimatology. The possibility of anthropogenic or natural
climate change affecting societies and ecosystems drives current
researchers attempting to understand and even predict the
behavior of the Earth system. The history of the system is used
in the construction and testing of models, and that history is
written in sea-floor muds, tree rings, cave formations, and other
sedimentary archives. Literally hundreds of physical, chemical,
isotope, and biological paleoclimate indicators are used. In
general, current paleoclimate research is simple: a) relate some
characteristic(s) of sediment to some characteristic(s) of
climate, by measuring how they vary together at present in
different places, or over the short times of instrumental
records; b) assume that this relation was the same at a place
over different times in the past; c) measure the appropriate
characteristic(s) on older sediment; d) calculate the past
climate characteristic(s). "One needs good instruments, accurate
dating techniques, and the ability to sample the old sediments
and to measure the right things. But with enough money, mass
spectrometers, drill ships and brilliant graduate students, the
procedure is straightforward."
     3) The author concludes: "Until we understand more of past
climates, some of the most modern Earth-science research will
continue to rely heavily on one of the oldest Earth-science
assumptions, that of uniformitarianism."
-----------
Richard B. Alley: The key to the past?
(Nature 18 Jan 01 409:289)
QY: Richard B. Alley: Dept. of Geosciences, Pennsylvania State
University, University Park, PA 16802 (US).
-------------------
Summary by SCIENCE-WEEK http://scienceweek.com 2Feb01
For more information: http://scienceweek.com/swfr.htm

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3. EARTH SCIENCES:
SNOWBALL VS. SLUSHBALL EARTH AND PALEOBIOLOGY
     The Proterozoic era (also called the Algonkian) is the
time-frame 2600 million years ago to 600 million years ago, and
within that time-frame, the Neoproterozoic era is the time-frame
approximately 800 million years ago to 600 million years ago.
     The Earth's magnetic field has been dynamic throughout its
history, and paleomagnetics is the study of the direction and
intensity of the Earth's magnetic field throughout geological
time. Paleomagnetic data suggest that the Earth was glaciated at
low latitudes during the Paleoproterozoic Era (approximately 2.4
to 2.2 billion years ago), and also during the Neoproterozoic
Era, although there is evidently some dispute concerning the
Neoproterozoic data.
     The "obliquity" of the Earth is the angle between the plane
of the equator and the plane of the Earth's orbit, and it is
quite important in determining climate belts around the Earth's
sphere. Any departure of the axial tilt from its present posture
will cause a change in the world climatic zones, and a consequent
change in the seasonal swing of climate, and the climatic
conditions associated with different obliquities have long been a
matter of conjecture. Paleomagnetic data suggest that the
Neoproterozoic glaciation involved ice sheets in low latitudes,
and this has been explained by either a global glaciation
("snowball Earth hypothesis") or by a large obliquity during that
era. Since the same era was a critical time in the evolution of
multicellular animals on Earth, an important question is how
early life survived under such environmental stress.
     Recently, an alternative to the snowball Earth hypothesis
has been proposed (W.T. Hyde et al [2000]; see related background
material below), a so-called "slushball Earth hypothesis", the
essential feature of which is that Neoproterozoic glaciation was
not global but quasi-global, leaving large areas of open water at
Equatorial latitudes.
... ... D.P. Schrag and P.F. Hoffman (Harvard University, US)
present a criticism of the Hyde et al slushball Earth hypothesis,
the authors making the following points:
     1) The authors state they do not believe the slushball Earth
hypothesis is consistent with the most striking geological and
paleomagnetic observations explained by the snowball Earth
hypothesis. Paleomagnetic and geological data from Neoproterozoic
glacial deposits indicate that glaciations were long-lived
(lasting for millions of years) and locally associated with iron
formation. The glacial deposits are covered by extraordinary
sequences of carbonate sediments ("cap carbonates"). The authors
suggest the snowball Earth hypothesis can explain these and other
observations, whereas a semi-frozen (slushball) Earth does not.
     2) The authors suggest that interest in a semi-frozen Earth
explaining the geological observations stems from concern for the
survival of *eukaryotic life in such extreme and extended
glaciations. The critical feature is the survival of groups of
photosynthetic algae that evolved before the glaciations. The
survival of multicellular animals (metazoans) is less of a
problem because such organisms (if they existed) could live
wherever primary producers (photosynthetic or chemosynthetic
biological systems) were still active. The authors suggest
photosynthetic algae could survive a series of glaciations in
refuges near volcanic islands, such as Iceland or Hawaii, or
beneath thin equatorial ice cover. The authors suggest evolution
might well be stimulated by this prolonged genetic isolation, and
by perturbations of biogeochemical cycles during the *post-
glacial ultragreenhouse climate. This is consistent not merely
with the survival of eukaryotic life, but also with the
coincident *evolutionary radiation of metazoa and other groups.
... ... In a reply to the above criticism, W.T. Hyde et al (4
authors at 2 installations, US CA) report the following:
     1) The authors state they are not convinced that the data
discussed by Schrag and Hoffman can be interpreted in only one
way. Concerning the ability of metazoans to survive under the
extreme conditions of a hard snowball Earth, the authors state
they are "not as sanguine as Schrag and Hoffman. Whether life
could survive on a few scattered volcanic islands is a matter of
conjecture." A "thin-ice" scenario is not consistent with results
indicating that such regions have temperatures substantially
colder than those referred to by Schrag and Hoffman. Although
evidence for life extends almost to the oldest rocks, 3 billion
years transpired before the appearance of metazoans, and this
vast time interval suggests that the environmental tolerance of
metazoans is much narrower than that of simpler and hardier
biological systems. If deep waters were anoxic, metazoans could
not survive on deep-sea chemosynthetic communities either, as
these organisms still require free oxygen.
     2) The authors (Hyde et al) conclude: "Future data may call
for the reassessment of our open-water scenario, but we consider
that the hard-snowball scenario is not yet proven. We believe
that the open water solution is much more favorable for the
survival of metazoans, allowing their remote progeny to continue
this discussion."
-----------
D.P. Schrag and P. F. Hoffman: Life, geology, and snowball Earth.
(Nature 18 Jan 01 409:306)
QY: Daniel P. Schrag: schrag@eps.harvard.edu
-----------
W.T. Hyde et al: Reply to "Life, geology, and snowball Earth."
(Nature 18 Jan 01 409:306)
QY: William T. Hyde: hyde@rossby.tamu.edu
-----------
Text Notes:
... ... *eukaryotic: In general, refers to cells which contain a
nucleus.
... ... *post-glacial ultragreenhouse climate: Advocates of the
snowball Earth hypothesis believe that an extremely large and
sudden increase in atmospheric carbon dioxide (and a consequent
"greenhouse effect") terminated Neoproterozoic glaciation. 
... ... *evolutionary radiation: In this context, the term
"radiation" refers to the spread of a group of biological
entities into new environments with consequent diversification.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 2Feb01
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
EARTH SCIENCES:
A NEOPROTEROZOIC "SNOWBALL EARTH" SIMULATION
... ... W.T. Hyde et al (4 authors at 2 installations, US CA)
report computer simulations of the Neoproterozoic climate
stage, the simulations involving a coupled climate/ice-sheet
model. The authors make the following points:
     1) Extant data indicate that some of the most dramatic
events in the history of Earth occurred during the Neoproterozoic
era, including the formation of the supercontinent called
"Rodinia", and the later breakup of this land mass and eventual
reassembly into a different configuration. There were also major
changes in strontium, sulfur, and carbon isotopes, together with
the most extensive glaciation of the past billion years. At least
two main phases of ice advance occurred, with glaciers apparently
extending to the Equator at sea level.
     2) The late Proterozoic also marked the first appearance of
multicellular animals (metazoans), perhaps as early as 1000 to
700 million years ago, and extensive glaciation may have exerted
a significant stress on living forms during a critical interval
in their evolution. Recent work has focused attention on the
Neoproterozoic by interpreting new carbon isotope data to
indicate that biological productivity of the oceans virtually
ceased for perhaps millions of years during the glacial era, and
from this work and from other evidence it has been concluded that
the planet entered a "snowball Earth" state, in which it was
completely covered by ice until carbon dioxide outgassing
produced a sufficiently large greenhouse effect to melt the ice.
In this scenario, the sudden warming caused a rapid precipitation
of calcium carbonate, producing certain types of carbonate rocks
often observed in strata of this era. The repetition of such
formations suggests this sequence of events occurred at least
twice in the Neoproterozoic era.
     3) The authors report that to simulate a snowball Earth in
their computer simulations, they used only a reduction in the
solar luminosity (solar constant) compared to present-day
conditions and kept atmospheric carbon dioxide concentrations
near present levels. Their results indicate rapid transitions
into and out of full glaciation that are consistent with the
geologic evidence. When they combine their results with a general
circulation model, some of the simulations result in an
equatorial belt of open water that may have provided a refuge for
multicellular animals.
     4) The authors conclude: "Although there is clearly a need
for more climate modeling and additional geological data... our
results indicate that inclusion of explicit ice-sheet physics
significantly closes the gap between models and data for the
largest glaciation of the past billion years and for one of the
most critical intervals of evolution in Earth history."
-----------
W.T. Hyde et al: Neoproterozoic "snowball Earth" simulations with
a coupled climate/ice-sheet model.
(Nature 25 May 00 405:425)
QY: William T. Hyde: hyde@rossby.tamu.edu
-------------------
Summary by SCIENCE-WEEK http://scienceweek.com 7Jul00
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
AN EXPLANATION FOR LOW-LATITUDE GLACIATION
... An apparently straightforward explanation for low-latitude
glaciation is that the climate was very cold in *Precambrian
times as a consequence of *reduced solar luminosity uncompensated
by high levels of *greenhouse gases. A problem with this idea
(sometimes called the "snowball Earth" hypothesis) is that it is
difficult to explain how the ice caps could have extended to low
latitudes without causing the extinction of most or all surface
life. An alternative explanation for low-latitude glaciation is
that rather than the polar ice caps extending to the Equator, the
zonation of climate with respect to latitude was reversed. It has
been suggested, for example, that the *obliquity of the Earth may
have been greater than 54 degrees during most of its history,
which would have made the Equator the coldest part of the planet.
But this idea would require a mechanism to bring the obliquity
down to its present value of 23.5 degrees.
... ... D.M. Williams et al (3 installations, US AU) now propose
that "*obliquity-oblateness feedback" could have reduced the
obliquity of the Earth by tens of degrees in less than 100
million years if the continents were situated so as to promote
the formation of large polar ice sheets. The authors suggest a
high obliquity for the early Earth may also provide a natural
explanation for the present inclination of the lunar orbit with
respect to the *ecliptic (5 degrees), which is otherwise
difficult to explain.
-----------
D.M. Williams et al: Low-latitude glaciation and rapid changes in
the Earth's obliquity explained by obliquity-oblateness feedback.
(Nature 3 Dec 98 396:453)
QY: Darren M. Williams 
-----------
Text Notes:
... ... *Paleomagnetic data: In general, paleomagentics is the
study of the direction and intensity of the Earth's magnetic
field throughout geologic time. The essential method of
paleomagnetics is the measurement of *remanent magnetism and the
application of analysis of the data to various questions in 
paleo-geophysics and paleo-geology.
... ... *remanent magnetism: Remanent magnetism is that component
of a rock's magnetization whose direction is fixed relative to
the rock and which is independent of moderate applied magnetic
fields. The significance of remanent magnetization in rocks is
that the polarity fixation occurs during the cooling of molten
rock or the sedimentation of sedimentary rocks in response to the
magnetic field of the Earth at that particular geological time.
Thus, remanent magnetization of rocks provides a history of
Earth's magnetic field.
... ... *Precambrian: In general, the time-frame between the
consolidation of the Earth's crust and the beginning of the
Cambrian period approximately 590 to 550 million years ago. The
Cambrian explosion of life forms, the rather sudden appearance of
numerous invertebrate fossils, has been a long-standing puzzle
for paleobiologists, and at present there is apparently no single
generally accepted explanation. Among the ideas proposed have
been, 1) that the explosion of new forms resulted from a sudden
increase in atmospheric oxygen; 2) that the explosion is only
apparent, and the Precambrian, the period previous to the
Cambrian, lacks fossils because of heat and pressure associated
with important geological changes; 3) that living forms evolved
mostly in freshwater areas, and are therefore absent in
Precambrian sediments, which are primarily marine; 4) that
changes in the shape and extent of shorelines produced by
continental drift dramatically transformed climate and
environment; 5) that the previous evolution of DNA recombination
and regulatory genes culminated in and sparked the diversity and
anatomical complexity manifested in the explosion; 6) that an
exponential increase of species could become significant only
after attaining a threshold value at the start of the Cambrian;
7) that once multicellular organisms appeared, the intrinsic
possibilities for variation increased enormously with a resultant
explosion of evolved forms. Unfortunately, there is no evidence
to suggest a selection of one of these proposals, although some
of them are less convincing than others. And of course the truth
may be that more than one factor was involved. No matter the
origin, the Cambrian explosion is apparently accepted by most
paleobiologists as a real discontinuity, a period that saw the
sudden emergence of dozens of new orders and phyla.  
... ... *reduced solar luminosity: There is apparently good
geophysical evidence that the brightness of the Sun (solar
luminosity; the "solar constant") has increased approximately 25
percent over the lifetime of Earth. The impact on climate of a
Sun supplying only 75 percent of its present heat is considered
by most paleoclimatologists to have been considerable (some
believe the impact would be "spectacular").
... ... *greenhouse gases: The physical basis of the so-called
"*greenhouse effect" is essentially simple: carbon dioxide gas is
transparent to visible light but relatively opaque to infrared
radiation. The same is true of glass. Relatively high-energy
visible light radiation from the sun passes inward through the
atmosphere, warms the surface of the Earth, which then radiates
lower energy in the form of infrared radiation (heat) back to the
atmosphere. But if the atmosphere has a concentration of infrared
impenetrable gases such as carbon dioxide, the infrared radiation
cannot pass out, and the surface of the Earth underlying the
atmosphere cannot cool, and the surface of the Earth thus will
continue to grow hotter.
... ... *obliquity: The "obliquity" of the Earth is the angle
between the plane of the equator and the plane of the Earth's
orbit, and it is quite important in determining climate belts
around the Earth's sphere.
... ... *obliquity-oblateness feedback: The term "oblateness"
refers to the flattening of a star or planet at the poles, caused
by its rotation. Quantitatively, oblateness is measured by
subtracting the polar diameter from the equatorial diameter, then
dividing by the equatorial diameter. The "obliquity-oblateness
feedback" (sometimes called "climate friction") referred to in
this report involves a feedback loop: Earth's obliquity drives
variations in oblateness by changes in continental ice volume and
sea level, and oblateness itself affects the rate at which
obliquity varies.
... ... *ecliptic: The plane of the orbit of the Earth around the
Sun, presently forming an angle of 23.5 degrees with the Earth's
equator.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 8Jan99
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
EARTH'S OBLIQUITY AND THE SHRINKAGE OF THE TROPICS
... ... Rubincam et al (National Aeronautics and Space
Administration, US) review the periodic shrinkage of Earth's
tropical zone. In the past year, the Earth completed one
revolution around the Sun, the Moon went through its phases 13
times, and the tropic of Cancer moved another 14.7 meters south.
The tropic of Cancer is the latitude at which the Sun is overhead
at the June solstice, and that latitude is moving toward the
equator. Similarly, the tropic of Capricorn, where the Sun stands
at the December solstice, moved 14.7 meters northward. Almost
1100 square kilometers move from the tropics into the temperate
zone each year. The reason for the shrinkage is the changing
obliquity of the Earth, which is getting progressively smaller by
approximately 47.5 arc-seconds per century. Various gravitational
torques of the Sun, Moon, and other planets cause the Earth's
obliquity to oscillate with a period of approximately 41,000
years.
-----------
QY: David P. Rubincam, NASA Goddard Space Flight Center,
Greenbelt, MD 20771 US.
(Sky & Telescope June 1998) (Science-Week 8 May 98)
For more information: http://scienceweek.com/swfr.htm

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

4. EVOLUTIONARY BIOLOGY:
RAPID TRANSIT OF MITOCHONDRIAL GENES TO THE NUCLEUS
     In biology, the term "symbiosis" refers in general to an
intimate and protracted association of individuals of different
species, and "endosymbiosis" refers to a symbiotic association
between cells of two or more different species in which a smaller
cell inhabits a larger host cell.
     The term "eukaryotes" refers to biological cells containing
internal membrane-bound organelles, particularly a bounded cell
nucleus. Cells without such internal organelles are called
"prokaryotes". Mitochondria (singular = mitochondrion) are a type
of intracellular organelle, and they are involved with several
important biochemical pathways, including electron transport and
oxidative metabolism. Various types of eukaryotic cells may
contain from none to a few to several thousand mitochondria in
each cell type, and in general, wherever they occur, mitochondria
are critically essential for energy metabolism. In form, the
mitochondria are relatively large cylindrical structures up to 10
microns long and up to 2 microns in diameter, and when a
eukaryotic cell undergoes cell division, the mitochondria present
inside the cell undergo division at the same time. In the 1960s,
biologists were startled to discover that mitochondria contain
their own DNA, the mitochondrial DNA (mtDNA) constituting a
separate mitochondrial genome, and it now generally believed that
mitochondria originated as prokaryotic organisms (bacteria) that
became endosymbiotic with larger cells, presumably cells that
already contained a cell nucleus.
     In botany, an "angiosperm" is a flowering plant whose seeds
develop within ovaries that mature into fruits.
... ... K.L. Adams et al (5 authors at 2 installations, US AU)
present a report of apparent repeated transfers of a
mitochondrial gene to the nucleus of cells in angiosperms, the
authors making the following points:
     1) The authors point out that, given the small genomes of
various mitochondria, a central component of the endosymbiotic
theory for the bacterial origin of the mitochondrion is that many
of the mitochondrial genes were transferred to the nucleus of the
host cell. Most of this transfer is thought to have occurred
early in mitochondrial evolution; functional transfer of
mitochondrial genes has ceased in animals. Although mitochondrial
gene transfer continues to occur in plants, no comprehensive
study of the frequency and timing of such transfers during plant
evolution has been reported.
     2) The authors report frequent loss (26 times) and transfer
to the nucleus of the mitochondrial gene _rps10_ among 277
diverse angiosperms. The data indicate that many independent RNA-
mediated _rps10_ gene transfers occurred during recent angiosperm
evolution, and this gene has apparently been transferred to the
angiosperm cell nucleus at a surprising high rate during
angiosperm evolution. The structure of several nuclear _rps10_
genes reveal diverse mechanisms by which transferred genes become
activated, including parasitism of pre-existing genes for
mitochondrial or cytoplasmic proteins.
... ... In a commentary on the this report, Michael W. Gray
(Dalhousie University, CA) concludes: "We could hardly have
imagined the relative ease with which angiosperms seem to be able
to shuttle mitochondrial genes into the nucleus and activate them
there. Unravelling the genetic and biochemical workings of this
highly-efficient rapid-transit system will undoubtedly provide
further surprises down the road."
-----------
K.L. Adams et al: Repeated, recent and diverse transfers of a
mitochondrial gene to the nucleus in flowering plants.
(Nature 16 Nov 00 408:354)
QY: Jeffrey D. Palmer: jpalmer@bio.indiana.edu
-----------
Michael W. Gray: Mitochondrial genes on the move.
(Nature 16 Nov 00 408:302)
QY: Michael W. Gray: m.w.gray@dal.ca
-------------------
Summary by SCIENCE-WEEK http://scienceweek.com 2Feb01
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
MITOCHONDRIAL EVOLUTION
The classification schemes devised by biologists to bring some
conceptual order to the tremendous variety of living organisms
must depend upon what is known about the various living
organisms, both in general and in detail. Classification schemes,
therefore, can be expected to change as the science changes. At
the present time, all biological cells are classified into 2
broad categories, prokaryotes and eukaryotes. Prokaryotes are
defined as cells without internal membrane-bound organelles such
as a nucleus, and eukaryotes are defined as cells that do have
such internal membrane-bound organelles. (The prefix "eu-" means
"true", and "karyon" means nucleus; "eukaryote" literally means
possessing a true nucleus). One type of internal membrane-bound
organelle of great importance is the mitochondrion (plural:
mitochondria), often present in large numbers inside certain
eukaryotic cells. In general, mitochondria are found in all
eukaryotic cells in which aerobic respiration (the direct
utilization of oxygen) and energy production take place. Almost
all the adenosine triphosphate (ATP) in non-photosynthetic cells
is produced in mitochondria. Each mitochondrion is surrounded by
two phospholipid bilayer membranes similar to the plasma membrane
of the host cell. Apart from their role in cellular energy
production, what is most interesting about mitochondria is that
they are self-replicating entities, containing their own DNA-
based genome, and although their existence is dependent on the
viability of the host cell, the mitochondria have very much the
elements of integral living organisms. All the evidence, in fact,
suggests that mitochondria are indeed the substantial remnants of
independent living organisms that were somehow co-opted by
evolution into becoming part of the internal metabolic apparatus
of eukaryotic cells. The term "endosymbiosis" refers to an
arrangement in which one organism lives inside another organism,
but the term is usually restricted to arrangements of mutual
benefit, thus not including parasite-host relationships. A number
of eukaryotic cell organelles in addition to mitochondria are
believed to have originated from endosymbiotic relationships
between eukaryotic cells and simpler cells. Finally, we must note
the existence of the terms "eubacteria" and "proteobacteria". All
eubacteria are prokaryotes, i.e., they do not possess internal
membrane-bound organelles of any kind (again, the prefix "eu-"
means "true": the eubacteria are _not_ eukaryotes, but "true"
bacteria or prokaryotes). The term "proteobacteria" is a rather
loosely used rubric bringing together a large variety of
eubacteria subtypes into one group based on details of metabolic
energy sources. Most organisms in the world are classified as
"proteobacteria" (also called "purple bacteria"). Concerning
mitochondria, an important question is where do they come from?
If mitochondria were originally endosymbionts, from which
primitive life form do they derive? ... ... M.W. Gray et al (3
authors at 2 installations, CA) present an extensive review of
current research concerning the evolution of mitochondria, the
authors making the following points:
     1) The "serial endosymbiosis" theory is the favored model
for explaining the origin of mitochondria, a defining event in
the evolution of eukaryotic cells. As usually described, this
theory postulates that mitochondria are the direct descendants of
a bacterial endosymbiont that became established at an early
stage in a nucleus-containing host cell without mitochondria.
     2) Analysis of gene sequence data strongly supports a
single-species origin of the mitochondrion from a eubacterial
ancestor in the proteobacteria subgroup known as "alpha-
proteobacteria". Members of the rickettsial subdivision of the
alpha-proteobacteria are obligate intracellular parasites that
are considered to be among the closest known eubacterial
relatives of mitochondria.
     3) However, recent studies of unicellular eukaryotes
(*protists), some of these species little known, have provided
insights that challenge the traditional serial endosymbiosis view
of how the eukaryotic cell and its mitochondria came to exist.
These new data indicate that the mitochondrion arose in a common
ancestor of all extant eukaryotes, and the data raise the
possibility that mitochondria originated at essentially the same
time as the nucleus of the eukaryotic cell, rather than in a
separate subsequent event as is commonly believed.
-----------
M.W. Gray et al: Mitochondrial evolution.
(Science 5 Mar 99 283:1476)
QY: Michael W. Gray: m.w.gray@dal.ca
-----------
Text Notes:
... ... *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.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 18Jun99
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
GENOME OF THE TYPHUS PARASITE AND THE ORIGIN OF MITOCHONDRIA
The Rickettsia are small bacteria (600 x 300 nanometers, or
spherical as "cocci"), classified as a type of proteobacteria
(i.e., "purple" bacteria, a huge phylum including many common
bacteria). The Rickettsia are obligate intracellular parasites
(i.e., they can replicate only inside living cells), and one of
the most notorious of these parasites is R. prowazekii, the agent
of epidemic louse-born typhus in humans. R. prowazekii is
estimated to have infected 20 to 30 million humans in the wake of
the First World War and killed another few million humans
following the Second World War. Because it is apparently the
descendent of free-living organisms, the genome of R. prowazekii
may provide insight into the adaptations producing an obligate
intracellular lifestyle. Also, phylogenetic analyses based on
sequences of *ribosomal RNA and *heat-shock proteins indicate
that *mitochondria may be derived from the proteobacteria, and
indeed the closest extant relatives of the ancestor to
mitochondria seem to be the Rickettsia. Finally, the genome of R.
prowazekii is a small one, making it amenable to genome analysis.
... ... S.G.E. Andersson et al now report the complete genome
sequence (1,111,523 *base pairs) of R. prowazekii. The authors
report this genome contains 834 protein-coding genes, the
functional profiles of which show similarities to those of
mitochondrial genes: no genes required for anaerobic glycolysis
are found in either R. prowazekii or mitochondrial genomes, but a
complete set of genes encoding components of the *tricarboxylic
acid cycle and the *respiratory-chain complex is found in R.
prowazekii (and in mitochondria). In effect, *ATP production in
Rickettsia is the same as that in mitochondria. Many genes
involved in the biosynthesis and regulation of biosynthesis of
amino acids and *nucleosides in free-living bacteria are absent
from R. prowazekii and mitochondria, and such genes have
apparently been replaced by homologues in the host genome. The R.
prowazekii genome contains the highest proportion of non-coding
DNA (24 percent) detected so far in a microbial genome, and the
authors suggest such non-coding sequences may be *degraded
remnants of "neutralized" genes that await elimination from the
genome. The authors finally suggest that phylogenetic analyses
indicate that R. prowazekii is more closely related to
mitochondria than is any other microbe studied thus far.
-----------
S.G.E. Andersson et al (10 authors at 2 installations, SE US)
The genome sequence of Rickettsia prowazekii and the origin of
mitochondria.
(Nature 12 Nov 98 396:133)
QY: Charles G. Kurland chuck@xray.bmc.uu.se
-----------
Text Notes:
... ... *ribosomal RNA: A class of RNA molecules that have an
important role in the structure of ribosomes, the large molecular
entities that carry out protein synthesis in all cells.
... ... *heat-shock proteins: A group of specific proteins
apparently synthesized by both prokaryotes (cells without
membrane-bound organelles) and eukaryotes (cells with membrane-
bound organelles) in response to a sudden elevation of ambient
temperature.
... ... *mitochondria: Mitochondria are double-membrane enclosed
organelles of cells that are involved with several important
biochemical pathways, including electron transport and oxidative
metabolism. Various types of eukaryotic cells may contain from a
few to several thousand mitochondria in each cell type. The
mitochondria are relatively large cylindrical structures up to 10
microns long and up to 2 microns in diameter, and most biologists
believe mitochondria are cell organelles that may have originated
as separate organisms that became resident in eukaryotic cells.
Mitochondrial DNA is independent of nuclear DNA. It consists of a
circular molecule, 16,569 base pairs long in humans, with a known
nucleotide sequence.
... ... *base pairs: The term "base pair" refers to the bases
(nucleotides) always found chemically bonded together in the DNA
double helix (adenine, for example, always bonds with thymine,
and guanine with cytosine).
... ... *tricarboxylic acid cycle: (Krebs cycle, citric acid
cycle) In aerobic respiration, the set of oxidative reactions
occurring after *glycolysis.
... ... *glycolysis: One of the 2 main energy-producing pathways
of the cell, this involves the anaerobic breakdown of glucose
with the generation of 2 molecules of adenosine triphosphate
(*ATP).
... ... *respiratory-chain complex: (electron transport chain)
Refers to a sequence of steps in the final stage of the aerobic
respiration biochemical pathway in which high energy electrons
are effectively passed through a series of membrane-bound carrier
molecules to support a proton gradient involved in energy
storage. The term "transport" here refers essentially to a
chemical flow diagram and not necessarily to an actual spatial
translocation of electrons.
... ... *ATP: (adenosine triphosphate) ATP is the most important
chemical energy source in all living cells, intimately involved
in various cell functions and cell metabolism, and an entity in
numerous cyclic chemical pathways involved in the synthesis of
components.
... ... *nucleosides: The base-sugar moieties of nucleotides.
... ... *degraded remnants: In this context, the idea is that the
Rickettsia are descendents of bacteria with substantially larger
genomes, and that both Rickettsia and mitochondria are the
products of several types of reductive evolution.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 18Dec98
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
ORIGIN OF A CHLOROPLAST PROTEIN IMPORTER
In general, photosynthesis is the utilization of light energy to
power biosynthesis, and chloroplasts are the plant cell
organelles in which photosynthesis occurs, the chloroplasts
containing several photosynthetic pigments (chlorophylls).
Chloroplasts are found in all photosynthetic plant cells, but not
in photosynthetic prokaryotes (i.e., not in cells without
membrane-bound organelles). The typical higher plant chloroplast
is lens-shaped, approximately 5 microns across the larger
dimension, and the number of chloroplasts per cell can vary from
1 to 100 depending on the type of cell. A mature chloroplast is
typically bounded by two membranes, an inner membrane and an
outer membrane, the membranes possessing significantly different
chemical constituents. In addition to a number of enzymes
involved in photosynthesis, chloroplasts also contain in their
interior a circular DNA molecule and protein synthetic machinery
typical of prokaryotes. The current consensus is that
chloroplasts may have originated from *cyanobacteria that became
*endosymbionts, an origin similar to that of mitochondria, which
are believed to have originated from so-called "*purple
bacteria". During evolution, chloroplasts (like mitochondria)
have apparently relinquished the majority of their genes to the
host nucleus, since chloroplast DNA codes only for some of the
proteins required by chloroplasts. The protein products of such
transferred genes are evidently imported into chloroplasts with
the help of biochemical import machinery distributed across the
inner and outer chloroplast membranes. The evolutionary origin of
this machinery is considered a puzzle, since the two bounding
membranes of the cyanobacteria have exhibited no functionally
similar protein import system. Recently, however, in the genome
of a species of cyanobacteria (Synechocystis), an apparent gene
(an "*open reading frame") has been identified that codes for an
amino acid sequence that shares an approximate 22 percent amino
acid identity with a protein-transporting channel in the outer
envelope of pea chloroplasts. ... ... B. Bolter et al (5 authors
at 2 installations, DE) now report that the protein coded by the
open reading frame of the Synechocystis cyanobacterium is located
in the outer membrane of that organism (the lipopolysaccharide
layer), and apparently transports polyamines and peptides. The
authors suggest their results indicate that a component of the
chloroplast protein import system may have been recruited from a
preexisting channel-forming protein of the cyanobacterial outer
membrane, and that in addition the presence of a protein in the
chloroplast outer envelope which is *homologous to a
cyanobacterial protein provides support for the general
prokaryotic nature of the outer membrane of chloroplasts.
-----------
B. Bolter et al: Origin of a chloroplast protein importer.
(Proc. Natl. Acad. Sci. US 22 Dec 98 95:15831)
QY: Jurgen Soll: jsoll@bot.uni-kiel.de
-----------
Text Notes:
... ... *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.)
... ... *endosymbionts: Endosymbiosis is an arrangement in which
one organism lives inside another organism, but the term is
usually restricted to arrangements of mutual benefit, thus not
including parasite-host relationships. A number of eukaryotic
cell organelles (including mitochondria) are believed to have
originated from endosymbiotic relationships between eukaryotic
cells and simpler cells.
... ... *purple bacteria: Specifically, any of the various
photosynthetic bacteria that contain bacteriochlorophyll, and are
thus distinguished by purplish or reddish-brown pigments. But the
term "purple bacteria" is sometimes used as a synonym for the
phylum Proteobacteria, a general category comprising a large
number of diverse forms.
... ... *open reading frame: The term "reading frame" refers to a
specific permutation of nucleotide triplets in DNA as "framed" by
a preceding start triplet (start codon), and an open reading
frame is any DNA sequence of triplets that potentially encodes a
protein.
... ... *homologous: In this context, the term refers to similar
sequences of amino acids in two proteins.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 26Mar99
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
A HYDROGENOSOME WITH A GENOME
Certain *anaerobic *protozoa and *fungi possess membrane-bound
organelles known as "hydrogenosomes". These organelles are
approximately 1 micron in diameter and are so called because they
produce molecular hydrogen. The anaerobic *ciliate protozoan
Nyctotherus ovalis, found in the hindgut of several species of
cockroach, has numerous hydrogenosomes that are intimately
associated with *endosymbiotic methane-producing *Archaea, the
latter using the hydrogen produced by the hydrogenosomes. Like
*mitochondria, the hydrogenosomes are bound by distinct double
membranes and have an inner membrane with *cristae-like
projections. The matrix contains *ribosome-like particles of the
same size as a numerous type of ribosome (70s) of the
endosymbiotic methanogenic Archaea. It has been postulated that
hydrogenosomes evolved from mitochondria by the concomitant loss
of their respiration and organellar genomes, and indeed so far no
hydrogenosome has been found that has a genome.
... ... A. Akhmanova et al (8 authors at 2 installations, NL) now
report evidence of a hydrogenosomal genome of apparent
mitochondrial descent, and also evidence that the protozoan N.
ovalis possesses a new type of nucleus-encoded "iron-only"
*hydrogenase. The authors suggest their results indicate that N.
ovalis hydrogenosomes evolved from mitochondria, but that
contrary to what has been proposed by others, the hydrogenosomes
have not relinquished their genomes. The authors further suggest
that the evolutionary origin of the N. ovalis nuclear hydrogenase
gene remains puzzling.
-----------
A. Akhmanova et al: A hydrogenosome with a genome.
(Nature 10 Dec 98 396:527)
QY: Johannes H.P. Hackstein: hack@sci.kun.nl
-----------
Text Notes:
... ... *anaerobic: Refers to a life form or process sustained in
the absence of free (gaseous or dissolved) oxygen.
... ... *protozoa: A phylum (or subkingdom) comprising
unicellular and colonial animals of varied form, cells ranging
from simple to extremely complex macro-structures.
... ... *fungi: A kingdom of primarily multicellular organisms
lacking chlorophyll and existing as parasites, symbionts, or
saprophytes. In general, "symbionts" are organisms that live in
close association (symbiosis) with other organisms; saprophytes
are organisms that feed on dead or decaying life forms.
... ... *ciliate: Cilia are short threadlike extensions, hundreds
usually present on an individual ciliated cell, the cilia
undergoing synchronized movements to produce locomotion of the
protozoan.
... ... *endosymbiotic: Endosymbiosis is an arrangement in which
one organism lives inside another organism, but the term is
usually restricted to arrangements of mutual benefit, thus not
including parasite-host relationships. A number of eukaryotic
cell organelles (including mitochondria) are believed to have
originated from endosymbiotic relationships between eukaryotic
cells and simpler cells.
... ... *Archaea: The archaebacteria (also called the Archaea)
are a subkingdom of bacteria considered to be ancient compared to
other bacterial kingdoms, and possibly the most ancient life
forms and the ancestors of all eukaryotes (cells and organisms
with intracellular membrane-bound organelles). They typically
exist in extreme environments, and include the methane-producing
bacteria (methanogens), the "salt-loving" bacteria (halophilic
bacteria), and the sulfur-acid tolerant thermoacidophilic
bacteria.
... ... *mitochondria: Mitochondria are double-membrane enclosed
organelles of cells that are involved with several important
biochemical pathways, including electron transport and oxidative
metabolism.
... ... *cristae: The folds of the inner mitochondrial membrane.
They contain the enzymes and other proteins involved in
mitochondrial metabolism.
... ... *ribosome: 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.
... ... *hydrogenase: (hydrogenlyase) An enzyme that catalyzes
the interaction of reduced *ferredoxin with ionic hydrogen to
produce oxidized ferredoxin and molecular hydrogen. 
... ... *ferredoxin: In general, a simple non-enzymic iron-sulfur
protein. Such proteins act as electron carriers in a variety of
oxidation-reduction systems and are found in a wide range of
microorganisms, in chloroplasts, and in some types of
mitochondria.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 12Feb99
For more information: http://scienceweek.com/swfr.htm

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5. BIOTECHNOLOGY: GENE CHIPS AND FUNCTIONAL GENOMICS
     In an animal or human, every cell carries the entire animal
or human genome, but cell types differ from each other according
to which genes are active or inactive, and for any particular
cell type, the profile of active genes may change with time and
circumstance or disease.
     The term "messenger RNA" (mRNA) refers to the ribonucleic
acid molecule normally transcribed from DNA, the mRNA carrying
the coded information specifying the sequence of amino acids in a
protein. Present in each cell at any time are mRNA molecules
specific for each active gene.
     Complementary DNA (cDNA) is a single-stranded DNA molecule
that has a particular complementary base sequence to a particular
molecule of messenger RNA. In general, a "complementary base
sequence" is a sequence in a polynucleotide chain in which all
the bases are able to form base pairs with a sequence of bases in
another polynucleotide chain. Complementary DNA is synthesized in
vitro from an RNA template using the enzyme reverse
transcriptase, and cDNA can be used to investigate the presence
of various genes. Essentially, the idea is that if the RNA
template is active messenger RNA in a particular cell type, the
cDNA derived from that RNA can demarcate the active (operational)
genes in that cell type -- the original genes that produced the
active messenger RNA.
     DNA Microarrays are chips containing hundreds or thousands
of gene snippets laid out in precise arrays that provide rapid
snapshots of the expression of whole suites of genes. The general
method in microarray analysis is to a) isolate messenger RNAs
(mRNAs) produced by a genome; b) convert mRNA into complementary
DNA (cDNA); c) add a fluorescent tag to the cDNA for tracking
purposes; d) wash a solution of tagged cDNAs over a DNA
microarray chip. Each DNA snippet on the chip will bind the cDNA
from the corresponding gene, and by measuring the fluorescences
arrayed on the chip, the profile of gene expression is revealed. 
... ... H. Hamadeh and C.A. Afshari (National Institute of
Environmental Health Sciences, US) present a review of gene-chip
technology, the authors making the following points concerning
only some of the aspects of DNA microarray technology:
     1) Ordinarily, gene chips do not carry copies of the entire
genome, but carry only a portion of the total number of genes in
a cell. The DNA is removed from the cell by several methods, then
isolated and fragmented into segments corresponding to individual
genes or large fragments of genes. These segments are then
amplified into higher concentrations, and then each gene is
placed in a solution, after which small amounts of each solution
are placed into an array of wells in a plate. 
     2) A DNA chip is made by using a glass microscope slide,
7.62 centimeters by 2.54 centimeters, and approximately 1.2
millimeters thick. Samples of DNA, in the form of spots, are
"printed" on the slide, using a procedure similar to the
procedure used to print computer chips. The DNA spots adhere to
the slide, each spot being a cloned DNA sequence that represents
a gene. Printing or spotting is accomplished with a machine
called an "arrayer". At present, most arrayers are custom-built
instruments featuring a high-speed robotic arm fitted with a
number of pins. The arm is controlled by software that allows the
user to place genes in select areas and configurations on the
glass slide. The pins resemble the tips of quill pens. By
capillary action, each pin draws up a small amount of a solution
containing the DNA for a single gene and deposits it in a precise
location on a glass slide. Since the robotic arm holds many such
pins, many genes are deposited on the slide at a time, and
computers keep track of each gene on the gene chip.
     4) The amount of data that results from DNA-microarray
experiments can often be overwhelming. A single gene chip may
generate more than 10,000 data points, the volume of data
increasing enormously when one uses multiple sets of chips, as is
the case when replication experiments are performed. In addition,
for certain biological studies it may be necessary to examine
changes in gene expression over multiple time-points. The reams
of data pose a considerable analytical problem, one that many
researchers regard as the most difficult part of the technique,
and the emerging science of "bioinformatics" has been helpful. In
general, what is called "bioinformatics" involves the sorting of
large amounts of data into databases which are then analyzed and
presented in an understandable form.
-----------
H. Hamadeh and C.A. Afshari: Gene chips and function genomics.
(American Scientist Nov/Dec 2000 88:508)
QY: H. Hamadeh: Laboratory of Molecular Carcinogenesis, PO Box
12233, National Institutes of Environmental Health Sciences,
Research Triangle Park, NC 27709 (US).
-------------------
Summary by SCIENCE-WEEK http://scienceweek.com 2Feb01
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
BIOTECHNOLOGY: DNA MICROARRAYS IN MEDICINE
... ... M. Diehn et al (3 authors at Stanford University, US)
present a review of the use of microarrays in medicine, the
authors making the following points:
     1) All of the genes in a genome can be arrayed in an area no
larger than a standard microscope slide. At present, the largest
DNA microarrays contain elements representing almost 40,000
genes, roughly half the predicted number of genes in the human
genome. In the near future, when the complete human genome is
determined, DNA microarrays will allow a complete profile of all
expressed genes in a particular cell type.
     2) The important consideration is that gene expression
patterns reflect the internal state and microenvironment of a
cell, creating a molecular picture of the state of the cell. DNA
microarrays can be used to capture these molecular pictures and
thus to deduce the condition of cells. Also, systematic
microarray studies of global gene expression can provide detailed
clues to the functions of specific genes. This is an important
advance, since we currently know the functions of fewer than 5
percent of the genes in the human genome.
     3) DNA microarrays have already had various applications:
messenger RNA expression profiling for improved disease
classification; genotyping of *polymorphisms affecting disease
susceptibility; identification of genetic lesions within
malignancies; design and discovery of new therapeutic drugs;
sequencing of DNA. In general, the ability to use a DNA sequence
directly as a reagent for detecting and assaying copies of that
sequence in a biological sample provides a valuable route to
assays for the protein products of every gene.
     4) Most disease processes are accompanied not only by
characteristic macroscopic or histological changes, but also by
systematic changes in gene expression patterns. For some
pathological processes such as cancer, inappropriate gene
expression is a fundamental aspect of pathogenesis. For other
pathological processes, the gene expression programs both in
cells directly affect by a disease and in healthy cells
responding to the local and systemic effects of a disease can
provide a detailed molecular picture of the pathogenic process.
     5) The authors suggest that the detailed molecular pictures
provided by genomic expression analysis will revolutionize
molecular medicine just as high-resolution radiographic imaging
methods have revolutionized diagnosis and treatment at the gross
anatomic level.
-----------
M. Diehn et al: Examining the living genome in health and disease
with DNA microarrays.
(J. Amer. Med. Assoc. 3 May 00 283:2298)
QY: Maximilian Diehn, Stanford University 415-723-3058.
-----------
Text Notes:
... ... *polymorphisms: A genetic polymorphism is a naturally
occurring variation in the normal nucleotide sequence of the
genome within individuals in a population. Variations are denoted
as polymorphisms only if they cannot be accounted for by
recurrent mutation and occur with a frequency of at least about 1
percent.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 26May00
For more information: http://scienceweek.com/swfr.htm

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6. BIOPHYSICS: ATOMIC FORCE MICROSCOPY IN BIOLOGICAL RESEARCH
The new technology of scanning probe microscopy has created a
revolution in microscopy, with applications ranging from
condensed matter physics to biology. The first scanning probe
microscope, the scanning tunneling microscope, was invented by G.
Binnig and H. Rohrer in the 1980s (they received the Nobel Prize
in Physics in 1986), and the invention has been the catalyst of a
technological revolution. Scanning probe microscopes have no
lenses. Instead, a "probe" tip is brought very close to the
specimen surface, and the interaction of the tip with the region
of the specimen immediately below it is measured. The type of
interaction measured essentially defines the type of scanning
probe microscopy. When the interaction measured is the force
between atoms at the end of the tip and atoms in the specimen,
the technique is called "atomic force microscopy". When the
*quantum mechanical tunneling current is measured, the technique
is called "scanning tunneling microscopy". These two techniques,
atomic force microscopy (AFM) and scanning tunneling microscopy
(STM) have been the parents of a variety of scanning probe
microscopy techniques investigating a number of physical
properties. 
... ... C. Wright-Smith and C.M. Smith (San Diego State College,
US) present a review of the use of atomic force microscopy in
biology, the authors making the following points:
     1) Since its introduction in the 1980s, atomic force
microscopy (ATM) has gained acceptance in biological research,
where it has been used to study a broad range of biological
questions, including protein and DNA structure, protein folding
and unfolding, protein-protein and protein-DNA interactions,
enzyme catalysis, and protein crystal growth. Atomic force
microscopy has been used to literally dissect specific segments
of DNA for the generation of genetic probes, and to monitor the
development of new gene therapy delivery particles.
     2) Atomic force microscopy is just one of a number of novel
microscopy techniques collectively known as "scanning probe
microscopy (SPM). In principle, all SPM technologies are based on
the interaction between a submicroscopic probe and the surface of
some material. What differentiates SPM technologies is the nature
of the interaction and the means by which the interaction is
monitored.
     3) Atomic force microscopy produces a topographic map of the
sample as the probe moves over the sample surface. Unlike most
other SPM technologies, atomic force microscopy is not dependent
on the electrical conductivity of the product being scanned, and
ATM can therefore in ambient air or in a liquid environment, a
critical feature for biological research. The basic atomic force
microscope is composed of a stylus-cantilever probe attached to
the probe stage, a laser focused on the cantilever, a photodiode
sensor (recording light reflected from the cantilever), a digital
translator recorder, and a data processor and monitor.
     4) Atomic force microscopy is unlike other SPM technologies
in that the probe makes physical (albeit gentle) contact with the
sample. The cornerstone of this technology is the probe, which is
composed of a surface-contacting stylus attached to an elastic
cantilever mounted on a probe stage. As the probe is dragged
across the sample, the stylus moves up and down in response to
surface features. This vertical movement is reflected in the
bending of the cantilever, and the movement is measured as
changes in the light intensity from a laser beam bouncing off the
cantilever and recorded by a photodiode sensor. The data from the
photodiode is translated into digital form, processed by
specialized software on a computer, and then visualized as a
topological 3-dimensional shape.
-----------
C. Wright-Smith and C.M. Smith: Atomic Force Microscopy.
(The Scientist 22 Jan 01)
QY: Carol Wright-Smith: csmith@sdsc.edu
-------------------
Summary by SCIENCE-WEEK http://scienceweek.com 2Feb01
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
ON SCANNING PROBE MICROSCOPY
... ... A. Yazdani and C.M. Lieber (2 installations,
US) present a review of recent developments in scanning probe
microscopy, the authors making the following points:
     1) The invention and development of scanning probe
microscopy has taken the ability to image matter to the atomic
scale and opened fresh perspectives on everything from
semiconductors to biomolecules, and new methods are being devised
to modify and measure the microscopic landscape in order to
explore its physical, chemical, and biological features.
     2) In scanning tunneling microscopy, electrons quantum
mechanically "tunnel" between the tip and the surface of the
sample. This tunneling process is sensitive to any overlap
between the electronic wave functions of the tip and sample, and
depends exponentially on their separation. The scanning tunneling
microscope makes of this extreme sensitivity to distance. In
practice, the tip is scanned across the surface, while a feedback
circuit continuously adjusts the height of the tip above the
sample to maintain a constant tunneling current. The recorded
trajectory of the tip creates an image that maps the electronic
wave functions at the surface, revealing the atomic landscape in
fine detail.
     2) The most widely used scanning probe microscopy technique,
one which can operate in air and liquids, is atomic force
microscopy. In this technique, a tip is mounted at the end of a
soft cantilever that bends when the sample exerts a force on the
tip. By optically monitoring the cantilever motion it is possible
to detect extremely small chemical, electrostatic, or magnetic
forces which are only a fraction of those required to break a
single chemical bond or to change the direction of magnetization
of a small magnetic grain. Applications of atomic force
microscopy have included in vitro imaging of biological
processes.
     3) In general, the various techniques of scanning probe
microscopy have now been applied to high-resolution spectroscopy,
the probing of nanostructures, measurements of forces in
chemistry and biology, the production of deliberate movements of
small numbers of atoms, and the use of precision lithography as a
tool for making nanometric-sized electronic devices.
     4) The authors conclude: The scanning probe microscope has
evolved from a passive imaging tool into a sophisticated probe of
the nanometer scale. These advances point to exciting
opportunities in many areas of physics and biology, where
scanning probe microscopes can complement macroscopically
averaged measurement techniques and enable more direct
investigations. More importantly, these tools should inspire new
approaches to experiments in which controlled measurements of
individual molecules, molecular assemblies, and nanostructures
are possible."
-----------
A. Yazdani and C.M. Lieber: Up close and personal to atoms.
(Nature 16 Sep 99 401:227)
QY: Ali Yazdani [ayazdani@uiuc.edu]
-----------
Text Notes:
... ... *quantum mechanical tunneling current: In general,
quantum mechanical tunneling is a quantum mechanical phenomenon
involving an effective penetration of an energy barrier by a
particle resulting from the width of the barrier being less than
the wavelength of the particle.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 29Oct99
For more information: http://scienceweek.com/swfr.htm

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7. IN FOCUS: ON DARWINISM AND AMERICAN SOCIETY
[Editor's note: The following was written by an eminent biologist
more than 40 years ago, and the fact that nothing much has
changed on this question since then, considering all the
stupendous technological and socio-political changes that have
occurred, is perhaps a most extraordinary and unexpected aspect.]
-----------
"One hundred years ago, Charles Darwin, in what was undoubtedly
the greatest scientific book of all time, presented the evidence
that he had gathered and developed during the previous twenty
years for the theory of evolution by natural selection. His
treatment was so unprecedented, so comprehensive, and so masterly
as first to stagger and then to convince all whose minds were
mobile enough to follow his arguments adequately. Since that
time, the whole matter has been subjected to the most copious and
exacting criticism, and to ever more searching exploration and
testing. The result has been that this revolutionary view of life
now stands as one of the most firmly established generalizations
of science, and that far more is now understood about the manner
by which evolution operates than was ever imagined a century ago.
It ill befits the American people, four generations after Darwin
published his epochal discovery, to turn their backs on it, to
pretend that it is unimportant or uncertain, to adopt euphemistic
expressions to hide and soften its impact, to teach it only as
one alternative theory, to leave it for advanced courses in
universities, where the multitudes cannot encounter it, or, if it
is dealt with at all in a school biology course, to present it as
unobtrusively and near the end of the course as possible, so that
the student will fail to appreciate how every other feature and
principle found in living things is in reality an outgrowth of
its universal operation. The failure of our people to take
evolution seriously can be traced to the slighting of the subject
in our schools, although, of course, beneath this neglect there
lurks a still deeper cause: our domination by antiquated
religious traditions... We need, in these decisive days of world
tension, when free men will stand or fall according to how fully
they recognize and act upon the most honest views of the truth
that they can glean, to execute a complete about-face in this
critical area."
-----------
Hermann J. Muller: "One Hundred Years Without Darwin Are Enough."
(The Humanist, 1959 19:139)
-----------
[Editor's note: Hermann J. Muller (1890-1967) received the Nobel
Prize in Physiology or Medicine in 1946 for his work on the
induction of mutations by x-rays. Muller is considered by many to
be the most influential geneticist of the 20th century.]

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8. FROM THE SW ARCHIVE:
ON COMPLEXITY IN CHEMISTRY
The term "complexity" is fashionable in science these days, the
interest presumed to indicate a movement away from reductionism,
away from the idea that the behavior of a system is best
understood in terms of how the components of the system behave
and interact. A focus on "complexity", however, is not perforce
anti-reductionist. Indeed, in practice, with real systems, the
behavior of a system is often not predictable from knowledge of
the behavior of its components, but most often this is simply
because that knowledge is incomplete, and not because of any
_principle_ barring prediction of the behavior of the system from
knowledge of its parts. Even systems exhibiting *chaotic
fluctuations are not necessarily non-reductionist, since such
systems are mathematically deterministic. In any case, faced with
an apparent unpredictability of a system given available
information about its parts, one looks for predictive global
methods to understand the system, methods that do not depend upon
a detailed knowledge of the behavior of the components of the
system. Thermodynamics is exactly such a global method of great
utility in chemistry and physics, and since thermodynamics is a
method of analysis that goes back to its originator Carnot in
1824, one can safely say that the idea of special methods to deal
with "complexity" is quite old. In our time, at least for ideal
systems, we can derive the equations of thermodynamics from
statistical mechanics, i.e., derive the global equations from
equations for the behavior of components. But Nicolas Sadi Carnot
(1796-1832) never heard of statistical mechanics, which was
introduced by Boltzmann (1844-1906) in 1871; Carnot founded
thermodynamics as a predictive global method to deal with an
important "complex" system of his time -- the steam engine.
... ... G.M. Whitesides and R.F. Ismagilov (Harvard University,
US) present a review of current ideas in chemistry concerning
"complexity", the authors making the following points:
     1) Chemistry has its own understandings of the term
"complexity". In one characterization, a complex system is one
whose evolution is very sensitive to initial conditions or to
small perturbations, one in which the number of independent
interacting components is large, or one in which there are
multiple pathways by which the system can evolve. Analytical
descriptions of such systems typically require nonlinear
differential equations. A second characterization is more
informal; that is, the system is "complicated" by some subjective
judgment and is not amenable to exact description, analytical or
otherwise.
     2) Faced with the impossibility of handling many real
systems exactly, chemists have evolved a series of approaches to
the treatment of complex systems. These treatments include
reasoning by analogy, averaging, linearization, drastic
approximation, pure empiricism, and detailed analytical solution.
The emphasis in thinking about complicated systems has been to
find methods that are predictive, even if they are non-
analytical. "Complexity" per se, the study of nonlinear processes
with high sensitivity to conditions, has not been the focus of
major effort.
     3) Chemistry has relied heavily on the ability of ensemble
properties that are obtained through thermodynamics and
statistical mechanics to make it unnecessary to consider the
behavior of individual molecules. However, single-molecule
chemistry is now making it possible to inquire about individual
molecular behaviors, and the behavior of macromolecules is a
promising area of research because of the existence of many
possible molecular conformations, each with different properties.
     4) At the core of chemical interest in complexity are the
two fundamental problems concerning life: a) how collections of
molecules give rise to the varieties of behaviors that
characterize cells and organisms; and 2) how individual molecules
might have originally assembled into collections that had the
characteristics of life (energy dissipation, self-replication,
and adaptation). Whether the understanding of complexity at the
molecular level will reveal important elements of the structure
of life is unclear.
     5) One of the opportunities in fundamental chemical research
is to learn from biology and to use what is learned to design
non-biological systems that dissipate energy, replicate, and
adapt. Whether such systems would model life is not critical;
they would unquestionably be interesting and probably important.
-----------
G.M. Whitesides and R.F. Ismagilov: Complexity in chemistry.
(Science 2 Apr 99 284:89)
QY: George M. Whitesides [gwhitesides@gmwgroup.harvard.edu]
-----------
Text Notes:
... ... *chaotic fluctuations: The term "chaotic", in this
context, is specific, and in the study of physical systems, the
term "chaotic behavior" has a specific meaning: the behavior of a
system is said to be "chaotic" if its final state is so sensitive
to the system's precise initial conditions that the behavior of
the system is in effect unpredictable and cannot be distinguished
from a random process, even though the behavior of the system is
strictly determinate in a mathematical sense. In other words, a
deterministic system characterized by extremely sensitive
instabilities, despite the system being determinate, can exhibit
behavior that is unpredictable, and the system is then called
"chaotic". During the past several decades, the analysis of such
chaotic systems has intrigued both physicists and mathematicians.
-------------------
Summary & Notes by SCIENCE-WEEK [http://scienceweek.com] 2Jul99

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9. BOOK NOTICES:

J.G. Nichols et al: From Neuron to Brain (4th edition)
Sinauer Associates, 2001, 704pp., Hardcover, US$75.95
"A readable and coherent account of how cellular and molecular
approaches can provide insights into the workings of the brain."
For more information or to order this book:
http://www.amazon.com/exec/obidos/ASIN/0878934391/scienceweek

C. Daly and N. Rao: Scalar Diffraction from a Circular Aperture
Kluwer Academic, 2000, 175pp., Hardcover, US$125
For physicists working in optics, acoustics, antenna design,
biomedical engineering, and astronomy.
For more information or to order this book:
http://www.amazon.com/exec/obidos/ASIN/0792378105/scienceweek

M. Denny and S. Gaines: Chance in Biology: Using Probability to
Explore Nature.
Princeton University Press, 2000, 424 pp., Hardcover, US$39.50
An introduction to the application of probability theory in
biology. Mathematical requirements limited to calculus.
For more information or to order this book:
http://www.amazon.com/exec/obidos/ASIN/0691005214/scienceweek

J. Billingham and A. King: Wave Motion
Cambridge University Press, 2000, 475pp., Paperback, US$37.95
An introduction to the mathematics of wave phenomena. Includes
advanced material on both linear and nonlinear waves.
For more information or to order this book:
http://www.amazon.com/exec/obidos/ASIN/0521634504/scienceweek

P. Machamer et al: Scientific Controversies: Philosophical and
Historical Aspects.
Oxford University Press, 2000, 278pp., Hardcover, US$45
For more information or to order this book:
http://www.amazon.com/exec/obidos/ASIN/0195119878/scienceweek

G. Fraser: Antimatter: The Ultimate Mirror
Cambridge U. Press, 2000, 213pp., Hardcover, US$24.95
For more information or to order this book:
http://www.amazon.com/exec/obidos/ASIN/0521652529/scienceweek

J.C. Wheeler: Cosmic Catastrophes: Supernovae, Gamma-Ray Bursts,
and Adventures in Hyperspace.
Cambridge U. Press, 2000, 288pp., Hardcover, US$24.95
For more information or to order this book:
http://www.amazon.com/exec/obidos/ASIN/0521651956/scienceweek

R.M. Barnett et al: The Charm of Strange Quarks: Mysteries and
Revolutions of Particle Physics.
Springer-Verlag, 2000, 302pp., Hardcover, US$39.95
For more information or to order this book:
http://www.amazon.com/exec/obidos/ASIN/0387988971/scienceweek

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The first issue of SCIENCE-WEEK appeared May 1, 1997, and it has
been published regularly each week since that date. SW is
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