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ScienceWeek
SCIENCE-WEEK
A Weekly Email Digest of the News of Science
A journal devoted to the improvement of communication
between the scientific disciplines, and between scientists,
science educators, and science policy-makers.
May 11, 2001 -- Vol. 5 Number 19
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Nowadays our sciences, quick and fickle, wear out
dogmas in 10 years, and axioms take only a little
longer.
-- Erwin Chargaff
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Section 1
=-=-=-=-=-=-=-=-=
Contents of this Issue (Full reports in Section 2):
1. PHYSICAL CHEMISTRY: SOLVATION AT INTERFACES
The bulk properties of solutions depend very much on the ability
of dissimilar molecules to participate in attractive interactions
without forming chemical bonds -- a process known as "solvation".
For example, the solubility of sodium chloride (the solute) in
water (the solvent) can be attributed to favorable interactions
between the surrounding water and each sodium and chloride ion.
But how does solvation change where two different fluids meet?
Such interfaces are found in many biological and industrial
chemical systems and are crucial in creating useful compartments
for different chemical processes and environments. New
experiments using femtosecond spectroscopy to measure the effects
of a biomembrane-like molecular layer on the solvation of a dye
molecule embedded at the water interface indicate that both
equilibrium solvation and solvation dynamics are sensitive to the
presence of a monolayer of protonated fatty acid.
(Peter J. Rossky: Nature 5 Apr 01 410:645)
2. ASTROBIOLOGY: ON THE SEARCH FOR EXTRATERRESTRIAL INTELLIGENCE
N.S. Kardashev, in 1964, classified possible extraterrestrial
civilizations according to the energy at their disposal, the
scheme permitting a determination of whether, in a context of
communication, we would be dealing with a civilization like our
own (type I), a rather advanced civilization (type II), or a
vastly more advanced civilization (type III). The transmission
power of a type I civilization is equal to the power expendable
by all the technological activity on Earth. For a specific
direction, this can be achieved by coupling the output of a 1
megawatt transmitter operating at 10 centimeters to a 100-meter-
diameter telescope. The transmission power of a type II
civilization is the entire output of the Sun, which is equal to
10^(14) times a type I transmission. The transmission power of a
type III civilization is equal to the power from our entire
Galaxy, or 10^(11) times a type II signal.
(T.L. Wilson: Nature 22 Feb 01 409:1110)
3. HISTORY OF CHEMISTRY: ON ERRORS
Why did Priestley maintain the validity of the phlogiston theory
in the face of the evidence and the weight of anti-phlogistic
opinion? Not because he was in some way less objective or less
open-minded than Lavoisier... John Dalton's atomic theory is an
example of a set of mistakes that can be scientifically fruitful.
Dalton's theory pictured chemical compounds much as they are
pictured today, as atoms of different elements bound together,
and the laws of definite proportions and multiple proportions
follow naturally from such an atomistic view of chemical
combination. But as valuable and fruitful as Dalton's work
certainly was, it was equally certainly mistaken in several
details... The chemical periodicity idea of John Newlands
represents a classic case of "incoherent insight", a valid
insight that also contain errors, inconsistencies, or other
shortcomings, and which as a consequence is not fruitful.
(Carmen J. Giunta: J. Chem. Ed. 5 May 01 78:623)
4. PLANT BIOLOGY/EVOLUTIONARY BIOLOGY:
ON THE ORIGIN OF PHOTOSYNTHETIC MEMBRANE ASSEMBLY
Oxygenic photosynthesis is a feature specific to cyanobacteria
and chloroplasts that apparently developed several billion years
ago in an ancestor of present cyanobacteria. The current
consensus view is that an endosymbiotic event, in which a
cyanobacterium was engulfed by an early eukaryote and
subsequently transformed into a cell organelle, transferred this
capacity to plants. During this process many of the genes encoded
by the cyanobacterial genome were transferred to the nucleus of
the host cell or were lost completely. In two cyanobacteria
(Synechocystis and Anabaena) both a thylakoid-protein gene and a
phage shock gene are present, and phylogenetic analysis indicates
that the former originated from a gene duplication of the latter
and thereafter acquired its new function. It also appears that
the C-terminal extension that distinguishes these thylakoid
proteins from phage shock proteins is important for its function
in thylakoid formation.
(S.Westphal et al: Proc. Natl. Acad. Sci. US 27 Mar 01 98:4243)
5. NEUROBIOLOGY: ON THE MOVEMENTS OF NERVE AXONS
In all organisms with a patterned nervous system, one of the
fundamental developmental problems is the achievement of
appropriate connections between neurons, connections essential to
specific functions. The cytoplasmic extension of a nerve cell
primarily responsible for its connections to other nerve cells is
the nerve cell axon (and its branches), and axons in various
parts of the nervous system travel large distances to reach their
target cells. New evidence indicates that the appearance of
responsiveness to a repulsion protein (slit) and a loss of
responsiveness to an attraction protein (netrin) are causally
linked. In the axonal growth cones of embryonic toad (Xenopus)
spinal axons, activation of the slit receptor Robo silences the
attractive effect of netrin-1, but not the growth-stimulatory
effect of netrin-1. This silencing occurs through direct binding
of the cytoplasmic domain of Robo to that of the netrin receptor
DCC. (E. Stein and M. Tessier-Lavigne: Science 9 Mar 01 291:1928)
6. PALEOBIOLOGY: ON THE ORIGINS OF MODERN CORALS
Despite a rich fossil record, the origin of Scleractinia corals
has remained shrouded in controversy. There is a particular
problem with the absence of coral fossils in the first 14 million
years of the Triassic. Now two paleobiologists suggest that many
apparent ambiguities and conflicts in previous analyses can be
reconciled if lineages of corals have lost and redeveloped
skeletons repeatedly through their history in response to
environmental conditions. To test this idea, the authors suggest
that future research should explore biochemical mechanisms of
calcification, establish phylogenetic relationships between
scleractinians and morphologically similar soft-bodied animals,
analyze if and how skeletal structure of scleractinian groups
corresponds with molecular data, and seek evidence of geochemical
changes in geologic history that correlate with changes in the
robustness of coral skeletons and appearances or disappearances
of various coral groups.
(G.D. Stanley and D.G. Fautin: Science 9 Mar 01 291:1913)
7. IN FOCUS: ON THE GREAT BARRIER REEF
8. FROM THE SCIENCEWEEK ARCHIVE:
FOUNDATIONS: 1932 -- THE YEAR OF PHYSICS
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Section 2
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1. PHYSICAL CHEMISTRY: SOLVATION AT INTERFACES
In general, the term "solvation" refers to the association
or combination of a solute unit (e.g., ionic, molecular, or
particulate) with solvent molecules. This association may involve
chemical or physical interactions or both, and may vary in degree
from a loose and indefinite complex to the formation of a
distinct chemical compound, with such an entity containing a
definite number of solvent molecules per solute molecule.
Solvation occurring in aqueous solutions is referred to as
"hydration". In general, solvation is often the key process in
the phenomenon of solubility, since the interaction energy of
solute with solvent must be greater than the interaction energy
of solute molecules with themselves in order for the solute to
dissolve in the solvent. Some textbooks consider solvation to
signify hydration, but this is an error: when a piece of
paraffin, for example, dissolves in benzene, the dissolution of
the paraffin results from the solvation of paraffin molecules by
benzene molecules, the solvation in this case involving only van
der Waals interactions. Hydration is merely a specific type of
solvation, one that involves water molecules as solvent.
The term "femtosecond spectroscopy" refers to a method for
analyzing transition states and intermediates in chemical
reactions, events that occur on the scale of 10 to 100
femtoseconds. Ahmed H. Zewail was awarded the 1999 Nobel Prize
for Chemistry for his invention of the femtosecond spectroscopy
technique. In this method, the molecules being studied are mixed
together, and an ultrafast laser then beams in two pulses, a
"pump pulse" that supplies energy to drive the molecules into a
transition state, and a second and weaker pulse, the "probe
pulse", which is tuned to the wavelength necessary for detecting
the original molecules or an altered form of the molecules. The
pump pulse starts the reaction; the probe pulse examines the
ongoing reaction. By studying characteristic spectra from the
molecules, the structure of the molecules at the transition state
can be determined, as well as the structure of intermediate
products.
In general, "amphiphiles" are molecules with parts (groups)
having diverse affinities for different solvents. For example,
polar groups have an affinity for water, while hydrocarbon groups
have an affinity for oils. Most detergents are amphiphiles,
molecules with a polar head and a long hydrocarbon tail. In this
context, however, possible solvent interactions are only one
aspect of amphiphilic character. The important consideration is
that amphiphiles tend to self-organize: groups of amphiphilic
molecules will form stable domains of polar interactions and
nonpolar interactions. For example, amphiphiles may form
"micelles", spherical or cylindrical arrangements with an
interior forming one interaction domain while the surface forms
another interaction domain. At the air-water interface,
amphiphiles form self-organized monolayers with polar groups
interacting with water molecules and hydrocarbon tails involved
in van der Waals interactions with each other. It is also
possible to produce self-organized amphiphile bilayers that
separate two aqueous compartments, the bilayers stabilized by
amphiphile-solvent interactions and amphiphile-amphiphile
interactions. Such bilayers are of great importance in biology,
since they are the structural basis of various biological
membranes.
... ... Peter J. Rossky (University of Texas Austin, US) presents
a commentary on recent experiments involving ultrafast
observations of amphiphiles at the air-water interface (A.V.
Benderskii and K.B. Eisenthal: J. Phys. Chem. B 104:11723 2000),
with Rossky making the following points:
1) The author (Rossky) points out that the bulk properties
of solutions depend very much on the ability of dissimilar
molecules to participate in attractive interactions without
forming chemical bonds -- a process known as "solvation". For
example, the solubility of sodium chloride (the solute) in water
(the solvent) can be attributed to favorable interactions between
the surrounding water and each sodium and chloride ion. But how
does solvation change where two different fluids meet? Such
interfaces are found in many biological and industrial chemical
systems and are crucial in creating useful compartments for
different chemical processes and environments.
2) The author (Rossky) points out that biological processes
in which solvation plays a crucial role include electron transfer
across membrane-bound proteins, and ion and proton transport
through membranes. Related processes can occur in chemical
environments, such as soap solutions nd microemulsions. Solvation
is important in all of these processes because the movement of
charges needs to be counterbalanced by the rearrangement of the
solvent molecules. To measure the speed at which the solvent
responds to charge migration (solvation dynamics), observations
that are sensitive to molecular movements -- operating on
femtosecond timescales -- are needed.
3) Benderskii and Eisenthal (2000) provide a direct view of
solvation at the air-water interface. By using femtosecond
spectroscopy, these authors are able to measure the effects of a
biomembrane-like molecular layer on the solvation of a dye
molecule embedded at the water interface. The authors find that
both equilibrium solvation and solvation dynamics are sensitive
to the presence of the monolayer of protonated fatty acid.
4) The author (Rossky) points out that whether the observed
differences in the solvation behavior between membrane-like
interfaces and bulk water play an important role in biological
functions at membranes is not yet clear. In biological systems,
many important factors, such as transmembrane electrochemical
potentials, are governed by processes operating on much longer
timescales and length scales than reflected in these
measurements. "Nonetheless, a successful description of the
molecular mechanisms behind chemical processes at interfaces will
almost certainly include molecular solvation as well as larger-
scale factors."
-----------
Peter J. Rossky: Molecules at the edge.
(Nature 5 Apr 01 410:645)
QY: Peter J. Rossky: rossky@mail.utexas.edu
-------------------
Related Background:
PHYSICAL CHEMISTRY:
DYNAMIC BEHAVIOR OF WATER IN SOLVATION SHELLS
In general, a solute dissolves in a solvent when the
interaction energy between the solvent and solute components is
greater than the interaction energy between the solute components
themselves. In solution, solvent molecules surround each solvent
component in a "solvation shell" whose lifetime is short or long
depending on interactants and conditions.
Water is an excellent solvent because of its highly polar
character and hydrogen-bonding possibilities, which produce
relatively high interaction energies with ions and polar solutes.
When water is a solvent in a system, the solvation shell is
called the "hydration shell", and the character and history of
this shell are of great importance in molecular considerations of
reactions in both biological and non-biological systems.
Consider, for example, the permeation of ions through biological
membranes. What role does the ion hydration shell play in
differential ion permeability through membranes? Are ions
stripped of their hydration shells and then resolvated in the ion
channels? Definitive answers to these questions are not yet
apparent.
In general, with reference to water, the term
"autoionization" refers to the ability of water to behave both as
an acid (a proton donor) and a base (a proton acceptor). The
general schema for this behavior is that expressed by a reaction
equation in which 2 water molecules on one side of the equation
are in equilibrium with a hydrated hydronium ion [H(sub3)O(+)]
and a hydrated hydroxide ion [OH(-)] on the other side of the
equation. At 25 degrees centigrade, the concentration of
hydronium ion in pure water is 1.0 x 10^(-7) moles per liter, and
the concentration of hydroxide ions is the same, producing the
14-unit logarithmic pH scale in which the pH of pure water is 7.
In general, the term "nonlinear spectroscopy" refers to the
study of energy levels not normally accessible with ordinary
optical spectroscopy, the technique involving the use of
nonlinear effects such as multi-photon absorption and ionization.
In general, "ab initio" (from first principles) calculations
utilize experimental data on atomic systems to facilitate the
adjustment of parameters. The excellent performance of ab initio
techniques distinguishes them from their predecessors, the
"semiempirical" methods, with the quantitative predictions of ab
initio techniques usually falling within experimental error when
comparisons are made to experimental measurements.
Two reports advancing our understanding of the physical
chemistry of aqueous solutions have now appeared, one report on
the dynamics of hydration shells, and the other report of the
dynamics of water autoionization.
... ... M.F. Kropman and H.J. Bakker (FOM Institute AMOLF, NL)
present a report on the direct measurement of the dynamics of
water molecules in the solvation shell of an ion in aqueous
solution. The authors report the hydrogen-bond dynamics of water
molecules solvating a chloride, bromide, or iodide anion is slow
compared with pure liquid water, indicating that the aqueous
solvation shells of these ions are rigid. The authors suggest
this rigidity can play an important role in the overall dynamics
of chemical reactions in aqueous solution. The experiments were
performed with femtosecond mid-infrared nonlinear spectroscopy,
since this technique allows the spectral response of the water
molecules in the solvation shell to be distinguished clearly from
that of the other water molecules in the solution.
... ... P.L Geissler et al (5 authors at 3 installations, US DE)
present a report on autoionization in liquid water, the authors
making the following points:
1) The authors point out that the dissociation of the water
molecule in liquid water is the fundamental event in acid-base
chemistry, determining the pH of water. Because of the short time
scales and microscopic length scales involved, the dynamics of
this autoionization have not been directly probed by experiment.
2) The authors report they have revealed the autoionization
mechanism with an ab initio molecular dynamics model. The authors
report they identify the rare fluctuations in solvation energies
that destabilize an oxygen-hydrogen bond. Through the transfer of
protons along a hydrogen-bond "wire", the nascent ions separate
by 3 or more neighbors. If the hydrogen-bond wire connecting the
two ions is subsequently broken, a metastable charge-separated
state occurs, and the ions may then diffuse to large separations.
If, however, the hydrogen-bond wire remains unbroken, the ions
recombine rapidly. Because of the concomitant large electric
fields, the transient ionic species produced by these dynamics
may provide an experimentally detectable signal.
3) The authors conclude that the dynamics of both electric
fields and hydrogen bonding play important roles in the
autoionization mechanism. Rare electric field fluctuations drive
the dissociation of oxygen-hydrogen bonds, and ions produced in
this manner usually recombine quickly because the solvation
fluctuation vanishes within tens of femtoseconds. But when such a
fluctuation is coincident with breaking of the hydrogen-bond wire
(a process normally occurring approximately once every
picosecond), rapid recombination is then not possible. It is with
this coincidence of events that the system crosses a transition
state. The authors suggest this scenario implies the existence of
many short-lived hydronium and hydroxide ions in water, and that
the decay of this transient population over approximately 100
femtoseconds should be observable.
-----------
M.F. Kropman and H.J. Bakker: Dynamics of water molecules in
aqueous solvation shells.
(Science 16 Mar 01 291:2118)
QY: H.J. Bakker: bakker@amolf.nl
-----------
P.L. Geissler et al: Autoionization in liquid water.
(Science 16 Mar 01 291:2121)
QY: David Chandler: chandler@cchem.berkeley.edu
-------------------
Summary by SCIENCE-WEEK http://scienceweek.com 6Apr01
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
USE OF COULOMB EXPLOSION TO OBSERVE FEMTOSECOND REACTIONS
In general, a "Coulomb explosion" is any intense dispersion of
like-charged particles due to Coulomb repulsion. In physics, one
method of producing the phenomenon is to accelerate a molecule to
a high velocity, and then have it strike a solid, which results
in stripping of bonding-electrons in the molecule due to
repulsive collisions with electrons in the solid, and subsequent
explosive repulsive dispersal of like-charged atomic fragments.
In this report, Coulomb explosion in the first femtosecond time-
frame of an initiated chemical reaction was produced by an
intense laser pulse that ionized particles, the resulting
repulsive explosion stopping the reaction instantaneously, with
the masses of the fragments being subsequently measured, and the
measurements used to identify reaction entities and
intermediates. The hydrogen-bonded 7-azaindole dimer is a model
often used to investigate proton transfer between DNA base pairs.
... ... Welford et al (Pennsylvania State University, US) report
the above Coulomb explosion method to arrest chemical reactions
on a femtosecond time scale, with a specific study of the
hydrogen-bonded 7-azaindole dimer. Chemists apparently consider
this new technique an important addition to the tools available
for detection of femtosecond processes and the analysis of
chemical reaction intermediates.
QY: A. Welford Castleman Jr., Pennsylvania State Univ.
814-863-8461
(Chem. Phys. Lett. in press) (Chem. & Eng. News 23 Feb 98)
(ScienceWeek 6 Mar 98).
For more information: http://scienceweek.com/swfr.htm
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2. ASTROBIOLOGY: ON THE SEARCH FOR EXTRATERRESTRIAL INTELLIGENCE
Nearly 30 years ago, Carl Sagan (1934-1996) wrote the
following: "Civilizations hundreds or thousands or millions of
years beyond us should have sciences and technologies so far
beyond our present capabilities as to be indistinguishable from
magic. It is not that what they can do violates the laws of
physics; it is that we will not understand how they are able to
use the laws of physics to do what they do. It is possible that
we are so backward and so uninteresting to such civilizations as
not to be worthy of contact, or at least of much contact. There
may be a few specialists in primitive planetary societies who
receive master's or doctor's degrees in studying Earth or
listening to our raspy radio and television traffic. There may be
amateurs -- Boy Scouts, radio hams, and the equivalent -- who may
be interested in developments on Earth. But a civilization a
million years in our future is unlikely, I believe, to be very
interested in us. There are all those other civilizations a
million years in our future for them to talk to." [*Note #1]
... ... T.L. Wilson (Max Planck Institute for Radio Astronomy,
Bonn, DE) presents a review of some current considerations
concerning the search for extraterrestrial intelligence, the
author making the following points:
1) The author points out that N.S. Kardashev, in 1964,
classified possible extraterrestrial civilizations according to
the energy at their disposal, the scheme permitting a
determination of whether, in a context of communication, we would
be dealing with a civilization like our own (type I), a rather
advanced civilization (type II), or a vastly more advanced
civilization (type III). The transmission power of a type I
civilization is equal to the power expendable by all the
technological activity on Earth. For a specific direction, this
can be achieved by coupling the output of a 1 megawatt
transmitter operating at 10 centimeters to a 100-meter-diameter
telescope. The transmission power of a type II civilization is
the entire output of the Sun, which is equal to 10^(14) times a
type I transmission. The transmission power of a type III
civilization is equal to the power from our entire Galaxy, or
10^(11) times a type II signal.
2) The author points out that humanity has sufficient
resources at present to broadcast messages comparable to a type I
civilization in a specific direction, although in practice the
types of transmission are based on isotropic radiators. A type II
transmission might be transmitted by an extraterrestrial
civilization that had captured all of the power from its central
star. Such extraterrestrial civilizations are often referred to
as "Dyson civilizations". Type III civilizations have captured
the power of an entire galaxy.
3) The author points out that F.D. Drake, in 1965, proposed
what is now called the "Drake equation" as an attempt to quantify
estimates of the number of extraterrestrial civilizations. The
equation takes the form N = RanbcdL, where (N) is the number of
extraterrestrial civilizations in a galaxy communicating at any
given time, (R) is the average rate of galactic star formation,
(a) is the fraction of stars accompanied by planets, (n) is the
number of planets per star system with conditions needed to
support life, (b) is the fraction of habitable planets on which
life actually arises, (c) is the fraction of the life-bearing
planets that develop intelligent life, (d) is the fraction of
intelligent species that develop communication technologies, and
(L) is the "life-span" of the communicating technological
culture.
4) The author points out that stars are concentrated in
galaxies, and there are more than 20 galaxies within 3 million
light years of our own Galaxy. In principle, we should be able to
receive a message from type II or type III extraterrestrial
civilizations in any of these galaxies with technology currently
available. With an average of 10^(10) Sun-like stars per galaxy,
we could detect messages from extraterrestrial civilizations even
if the product of the last 5 terms in the Drake equation were
less than 1 part in 10^(8). The author suggests these
considerations provide a rationale for all-sky untargeted
searches: With the possibility of at least modest numbers of
perhaps readily detectable extraterrestrial civilizations
(especially of type II or type III), the extra sensitivity
conferred by targeted searches would not be an absolute
requirement for success. However, the fact remains that no
confirmed transmissions in the centimeter-wavelength range have
been received, from which it has been claimed that type II and
type III extraterrestrial civilizations do not exist at the
present epoch. The author suggests this claim is overstated: it
may be valid for a sizeable part of our Galaxy, but only if the
extraterrestrial civilizations are broadcasting in the
centimeter-wavelength range without interruption -- and if they
wish their signals to be detectable.
5) The author points out that there is an advantage in
transmitting signals at short wavelengths, and this explains the
interest in optical searches for extraterrestrial intelligence.
The author suggests the following example illustrates the
advantages of optical searches in regard to effective radiated
power: An extraterrestrial civilization orbiting a Sun-like star
could use a laser to illuminate a 1-meter optical telescope
through narrow-band optical filters. The extraterrestrial
civilization could then produce a short pulse lasting 1
microsecond or less, and this would produce a flash 300,000 times
as bright as their Sun. Even without optical filtering, the flash
would still be 30 times as bright as their Sun, and this factor
would rise to 3000 if the diameter of the telescope were
increased to 10 meters (the diameter of our current Keck
telescopes). Because of the short pulse length, such optical
signals would not be found in conventional optical astronomical
surveys.
6) The author points out that if extraterrestrial
civilizations exist, they are not making their presence obvious.
This in itself suggests that type III and perhaps type II
civilizations are at best extremely rare. There are, however,
many possible reasons why we have not made contact with
extraterrestrial civilizations: a) They may simply be very few.
b) There may be a number of extraterrestrial civilizations, but
these may be sending messages in optical or near-infrared ranges
that we have to explore comprehensively. c) There may be
extraterrestrial civilizations, but these may not be interested
in communicating and choose to keep themselves hidden. This is
more speculative, since it depends on the cultural aspects of
extraterrestrial civilizations. From searches so far, the lack of
contact demonstrates that transmissions, if any, involve weak or
intermittent signals (or both).
7) The author suggests there seems to be no hope for faster-
than-light travel, so actual visits from extraterrestrial
civilization are unlikely. Even with the most efficient
propulsion systems, the energy needed to reach stars at 10 light
years in 20 years would be the equivalent of the present world
consumption for 1000 years. Such expenditure of energy would
hardly deter a type III extraterrestrial civilization, but even
then, broadcasts make more energetic sense than personal
appearances. There have been suggestions that extraterrestrial
civilizations might populate space with self-replicating machines
in space probes. This would allow colonization of large regions
of space in relatively short intervals of time, but it seems
vastly more complex than communicating by means of
electromagnetic radiation.
-----------
T.L. Wilson: The search for extraterrestrial intelligence.
(Nature 22 Feb 01 409:1110)
QY: T.L. Wilson: twilson@as.arizona.edu
-----------
Text Notes:
... ... *Note #1: Carl Sagan: _The Cosmic Connection: An
Extraterrestrial Perspective_, Doubleday, New York 1973, Dell,
New York 1975, p.222.
-------------------
Summary by SCIENCE-WEEK http://scienceweek.com 11May01
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
PROSPECTS FOR THE SEARCH FOR EXTRATERRESTRIAL INTELLIGENCE
The conjured image is poignant: intelligent life sprinkled
throughout our Galaxy, each sprinkle separated from the others by
1000 light years, each sprinkle searching for the others with
radio transmitters and receivers, small robotic spacecraft sent
beeping into empty space between the stars, the beeping like a
faint bleating in the dark as the sprinkles search for each
other. Of course, the conjured image may be wrong: there may be
intelligent life dense in the Galaxy; or we may be alone. It does
not matter. For the human species on this planet Earth, the quest
is part of our destiny, part of what we do as a species, and it
will go on as long as we remain civilized.
... ... J.C. Tarter and C.F. Chyba (SETI Institute, US) present a
review of current and future efforts in the search for
extraterrestrial intelligence, the authors making the following
points:
1) During the past 40 years, researchers have conducted
searches for radio signals from an extraterrestrial technology,
sent spacecraft to all but one of the planets in our Solar
System, and expanded our knowledge of the conditions in which
living systems can survive. The public perception is that we have
looked extensively for signs of life elsewhere. But in reality,
we have hardly begun to search. Assuming our current,
comparatively robust space program continues, by 2050 we may
finally know whether there is, or ever was, life elsewhere in our
Solar System. At a minimum, we will have thoroughly explored the
most likely candidates, a task not yet accomplished. We will have
discovered whether life exists on Jupiter's moon Europa, or on
Mars. And we will have undertaken the systematic exobiological
exploration of planetary systems around other stars, seeking
traces of life in the spectra of planetary atmospheres. These
surveys will be complemented by expanded searches for intelligent
signals.
2) The authors point out that although the current language
is that of a "search for extraterrestrial intelligence" (SETI),
what is being sought is evidence of extraterrestrial
technologies. Until now, researchers have concentrated on only
one specific technology -- radio transmissions at wavelengths
with weak natural backgrounds and little absorption. No verified
evidence of a distant technology has been found, but the null
result may have more to do with limitations in range and
sensitivity than with actual lack of civilization. The most
distant star probed directly is still less than 1 percent of the
distance across our Galaxy.
3) The authors conclude: "If by 2050 we have found no
evidence of an extraterrestrial technology, it may be because
technical intelligence almost never evolves, or because technical
civilizations rapidly bring about their own destruction, or
because we have not yet conducted an adequate search using the
right strategy. If humankind is still here in 2050 and still
capable of doing SETI searches, it will mean that our technology
has not yet been our own undoing -- a hopeful sign for life
generally. By then we may begin considering the active
transmission of a signal for someone else to find, at which point
we will have to tackle the difficult questions of who will speak
for Earth and what they will say."
-----------
J.C. Tarter and C.F. Chyba: Is there life elsewhere in the
Universe?
(Scientific American December 1999)
QY: Jill C. Tarter, SETI Institute, Mountain View, Calif. US.
-------------------
Summary by SCIENCE-WEEK http://scienceweek.com 11Feb00
For more information: http://scienceweek.com/swfr.htm
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3. HISTORY OF CHEMISTRY: ON ERRORS
The non-scientific public often has a distorted view of the
role of "errors" in science. In a closed system of thought, an
admission or discovery of error can be of extreme significance,
since an error in such a system can often cause the entire system
to crash. Science, however, is an open system of thought, one in
which errors, particularly errors of interpretation, are common.
Indeed, an argument can be made that very often the progress of
science depends on the discovery and correction of errors, so
that the existence of errors is part of the fabric of science.
Certainly, examples of important errors and their discovery and
correction are numerous in the history of science. In general, a
conceptual system without errors is dead -- there is nothing more
to be learned.
In this context, the term "phlogiston" refers to a 17th and
18th century chemical theory involving a hypothetical principle
of fire. The idea was that every combustible substance is in part
composed of phlogiston, with the phenomenon of burning caused by
the liberation of phlogiston and the "dephlogistonated" substance
remaining as ash or residue. The phlogiston theory was
experimentally discredited by Antoine Lavoisier (1743-1794)
beginning in 1770, who showed that the newly discovered element
oxygen was always involved in combustion, and by 1800 nearly
every chemist recognized the correctness of Lavoisier's oxygen
theory. One important exception was Joseph Priestley (1733-1804),
the discoverer of oxygen and one of the greatest chemists of his
time.
The phlogiston theory is an example of an erroneous theory
that held sway for nearly 150 years until new facts and new
analyses demolished it. The atomic theory of John Dalton (1766-
1844) is an example of a theory erroneous in detail but correct
in general and extremely fruitful in its effect on the scientific
community. The chemical periodicity idea of John Newlands (1837-
1898) is an example of an erroneous theory without much
foundation but which anticipated a later correct theory. (In
1887, the UK Royal Society awarded Newlands the Davy medal for
his anticipation 24 years earlier.)
... ... Carmen J. Giunta (Le Moyne College, US) presents a review
of certain errors occurring in the history of chemistry, the
author making the following points:
1) The author poses the question: Why did Priestley maintain
the validity of the phlogiston theory in the face of the evidence
and the weight of anti-phlogistic opinion? Not because he was in
some way less objective or less open-minded than Lavoisier. As
Priestley wrote to the leading French chemists at the close of
the 18th century, "no man ought to surrender his own judgment to
any mere _authority_, however respectable." The authority of the
anti-phlogistic theory carried as little weight with Priestley
near the end of his life as the authority of the phlogistic
theory did when it was generally accepted -- or the authority of
the established church or monarchy, for that matter. A
freethinker politically and theologically, Priestley was
caricatured in his day as "Dr. Phlogiston", a radical who
trampled on beliefs held dear to church and state. A Unitarian
minister, Priestley's religious ideas conflicted with those of
the established Church of England. Politically, Priestley's
sympathies for revolutionaries in America and then
revolutionaries in France angered his neighbors, who destroyed
his Birmingham home on Bastille Day 1791. Priestley left England
and settled in the newly independent US, carrying his belief in
phlogiston to his new home.
2) The author points out that John Dalton's atomic theory is
an example of a set of mistakes that can be scientifically
fruitful. Dalton's theory pictured chemical compounds much as
they are pictured today, as atoms of different elements bound
together, and the laws of definite proportions and multiple
proportions follow naturally from such an atomistic view of
chemical combination. But as valuable and fruitful as Dalton's
work certainly was, it was equally certainly mistaken in several
details. Dalton believed that atoms of the same element were
identical. That all atoms of an element were identical was not
simply a default position: Dalton considered the question to be
an important one, and he concluded that if atoms differed in
weight, the difference would have manifest itself in ways that
were detectable in his time. With the discovery of isotopes in
the early years of the 20th century, Dalton's idea of the
identity of all atoms of the same element was proved an error.
Similarly, Dalton's proposed formulas for molecules ("compound
atoms") were also mistaken in many instances. The assumptions on
which his formulas were based were arbitrary, with Dalton
assuming the simplest possible formula if only one compound of a
given pair of elements was known. Thus Dalton proposed HO for
water and NH for ammonia.
3) Concerning the chemical periodicity idea of John
Newlands, the author (Giunta) suggests this represents a classic
case of "incoherent insight". Incoherent insights are, or
contain, valid insights -- sometimes even important or useful
insights. They also contain errors, inconsistencies, or other
shortcomings. As a result, incoherent insights are usually not
actively pursued and are not fruitful. Newlands published some
short notes on the classification of the elements in which he
pointed out several families of elements, the members of each
group resembling each other in chemical properties, and their
atomic weights also seeming to have a discernible pattern. Some
of the groups had gaps, which Newlands predicted would be filled
by elements not yet discovered. A few years later, Newlands
listed all the elements then known in order of increasing atomic
weight. When he did so, he noticed that chemical properties
repeated with a period of 7 elements or a multiple of 7, and he
thus formulated the "law of octaves". This law was not well
received or influential, in contrast with the work of Mendeleev
(1834-1907) on periodicity that appeared only a few years later.
The author (Giunta) suggests that Newlands's work bore no fruit
because its insight of chemical periodicity was not embedded in a
coherent system that had either predictive or explanatory power.
-----------
Carmen J. Giunta: Using history to teach scientific methods: The
role of errors.
(J. Chem. Ed. 5 May 01 78:623)
QY: Carmen J. Giunta: giunta@mail.lemoyne.edu
-------------------
Summary by SCIENCE-WEEK http://scienceweek.com 11May01
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
MATERIALS SCIENCE: ON EILHARDT MITSCHERLICH
At the beginning of the 19th century, the prevailing view of the
nature of crystalline matter was that the fundamental entities
were tiny polyhedra ("integral molecules"), which could not be
further subdivided. This view was the conception of Rene-Just
Hauy (1743-1822), an eminent chemist and mineralogist of the
time, so eminent that the view, although completely erroneous,
was considered an "ipse dixit", a central dogma of mineralogy and
crystallography. Since in science the destruction of central
dogmas, often both common and pervasive, is of singular
importance to conceptual progress, the details of this particular
destruction make an interesting story. For the most part, the
destruction of the "integral molecule" view of crystalline
substances was the result of the work of a young chemist and
amateur mineralogist, Eilhardt Mitscherlich (1794-1863).
Mitscherlich began studying crystals at the age of 24 in 1818,
published what is now called "Mitscherlich's law of isomorphism"
in 1821, was appointed to the Berlin Academy of Sciences in 1821
and to a chair in Berlin in 1825, and then went on to accomplish
the first synthesis of benzene in 1834, and the confirmation, in
1842, of yeast as a microorganism. An interesting sidelight is
that Mitscherlich began as a student of Oriental Languages at
Heidelberg, and then apparently switched to medicine and
chemistry only because the fall of Napoleon precluded continuing
his studies in Paris. Mitscherlich's "law of isomorphism" is
simply stated: Substances that crystallize in isomorphous forms
(i.e., have identical crystalline forms and form mixed crystals)
have similar chemical compositions. The law can be used to
indicate the formulae of compounds. For example, the fact that
chromium oxide is isomorphous with Fe(sub2)O(sub3) and
Al(sub2)O(sub3) implies that the formula of chromium oxide is
Cr(sub2)O(sub3). This law became one of the central
considerations in the atomic weight determinations of the great
chemist J.J. Berzelius (1779-1848), who accurately determined
more than 2000 relative atomic and molecular masses, devised the
system of chemical symbols and formulae now in use, proposed
oxygen as the reference standard for atomic weights, and who was
the foremost proponent of the atomist theory of that time.
... ... Robert W. Cahn (University of Cambridge, UK) presents an
essay on Eilhardt Mitscherlich and the "atomist cause" in the
early 1800s, with Cahn making the following points:
1) The great crystallographer R-J. Hauy had convinced the
mineralogy world of his time that crystals could not be
understood in terms of the regular stacking of spherical atoms,
and therefore there were no such entities as spherical atoms. So
it was not surprising that Hauy attacked with sustained venom the
work of the young Mitscherlich. It was Berzelius who took
Mitscherlich under his wing and who persuaded the German
authorities to appoint Mitscherlich to a chair in Berlin.
Mitscherlich's isomorphism discovery was incompatible with Hauy's
ideas about the fundamental entities in crystals. In his 1821
paper, Mitscherlich also recognized the existence of polymorphs
(quite different crystal forms) of the same substance, and
polymorphism was also incompatible with Hauy's idea of "integral
molecules". Almost simultaneously with Mitscherlich's discovery
of isomorphism, was the discovery by F. Beudant in France and W.
Wollaston in England that isomorphous species can form a series
of solid solutions with each other, the mixed crystals
("Mischkristalle"). This was also incompatible with Hauy's
"integral molecules".
2) Mitscherlich and Berzelius, respectful of Hauy as a great
experimental scientist, attempted for years to persuade Hauy of
the validity of their findings. Hauy, however, was unmovable, and
Berzelius finally decided that "one ought not to expect that a
grey-haired scientist close to the end of an honorable life
should give up a theory he erroneously considered to be the most
important of his discoveries; this is perhaps too much to morally
demand of any man." [*Note #1].
3) Berzelius declared Mitscherlich's discovery and
interpretation of isomorphism, and the P-L. Dulong and A-T. Petit
discovery that the specific heats of solids vary inversely with
their presumed atomic weights, as the most important empirical
proofs of the atomic hypothesis at that time. Yet for another
century there was widespread skepticism about atoms -- until Jean
Perrin's work on Brownian motion in 1926 produced the crucial
experimental evidence that finally established the atomic nature
of matter. [*Note #2].
-----------
Robert W. Cahn: Slaying the crystal homunculus.
(Nature 12 Aug 99 400:625)
QY: Robert W. Cahn, Dept. of Materials Science and Metallurgy,
University of Cambridge, Pembroke Street, Cambridge CB2 3QZ UK.
-----------
Text Notes:
... ... *Note #1: Berzelius, one of the most influential chemists
of his era, had some other words about aging scientists: "God
knows what happens to your time once you have begun to get old.
You are busy all the time, you do important things, you work, and
yet when you sum it all up the result is nothing."
... ... *Note #2: Both Mitscherlich and Berzelius, in
collaboration, had much to do with yeast and fermentation, and it
is an irony that whereas they were right on the mark with respect
to the atomist theory of crystals, they were completely wrong in
their analysis of the role of yeast in fermentation. Berzelius
completely rejected the idea that fermentation required the
intervention of a living organism. And although Mitscherlich
recognized that yeasts were living organisms, he believed
fermentation occurred only on the surface of yeast, the yeast
cells acting only by contact, supporting the view of Berzelius
that fermentation involved a "catalytic force". The eminent
chemist Justus Liebig (1803-1873) also refused to believe that
living yeast had anything to do with fermentation. It was Louis
Pasteur (1822-1895), who started work on yeast fermentation in
1855, who began the modern understanding of the process.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 17Sep99
For more information: http://scienceweek.com/swfr.htm
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
4. PLANT BIOLOGY/EVOLUTIONARY BIOLOGY:
ON THE ORIGIN OF PHOTOSYNTHETIC MEMBRANE ASSEMBLY
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".
The term "oxygenic photosynthesis" refers to photosynthesis
that produces oxygen. Cyanobacteria exhibit oxygenic
photosynthesis, but a number of photosynthetic bacteria (e.g.,
sulfur bacteria) are not oxygenic (nonoxygenic). In addition to
the absence of oxygen production, nonoxygenic photosynthesis
differs from oxygenic photosynthesis in two other ways: a)
nonoxygenic photosynthesis involves absorption of light of longer
wavelengths by pigments called bacteriochlorophylls; b) in
nonoxygenic photosynthesis, reduced compounds other than water
(e.g., hydrogen sulfide or organic molecules) provide the
electrons needed for the reduction of carbon dioxide.
In this context, the term "plastid" refers in general to any
of various types of intracellular organelles found in plant
cells. Chloroplasts are a type of plastid. In general, each
plastid is surrounded by an envelope of two membranes. Plastids
arise either from division of existing plastids or from
protoplastids (proplastids), and plastids are believed to have
originated as endosymbionts in plant cells. Proplastids are
double membrane-bound organelles with little internal structure
that act as precursors for the development of plastids.
The term "granum" refers to the part of the internal
structure of a chloroplast that consists of 5 to 30 membranaceous
disks (thylakoids) 0.25 to 0.8 microns in diameter, with 40 to 80
grana in a typical chloroplast. In this context, the term
"stroma" refers to the interior matrix of the chloroplast, the
matrix within which the grana are embedded. Cyanobacteria have no
chloroplasts, but they do have thylakoids: it is the thylakoid
system that is the basis for oxygenic photosynthesis.
... ... S. Westphal et al (Christian-Albrecht University Kiel,
DE) present a report on the biogenesis of thylakoid protein, the
authors making the following points:
1) The authors point out that oxygenic photosynthesis is a
feature specific to cyanobacteria and chloroplasts that
apparently developed several billion years ago in an ancestor of
present cyanobacteria. The current consensus view is that an
endosymbiotic event, in which a cyanobacterium was engulfed by an
early *eukaryote and subsequently transformed into a cell
organelle, transferred this capacity to plants. During this
process many of the genes encoded by the cyanobacterial genome
were transferred to the nucleus of the host cell or were lost
completely. Many of the features of the cyanobacterium vanished;
other features (e.g., the photosynthetic machinery) remained,
which explains why homologues to many proteins involved in
chloroplast biogenesis and function are found in cyanobacteria.
The photosynthetic machinery is located in a special internal
membrane system, the thylakoids, and the ability to build up and
alter this membrane system appears to be an important feature of
oxygenic photosynthesis.
2) The authors point out that chloroplasts can develop from
proplastids, and it assumed that the thylakoid membranes that are
formed during the chloroplast maturation process are derived from
the inner envelope of the proplastid and chloroplast. No
anatomical connection between thylakoids and inner membranes can
be found in later states of maturation; thylakoids seem to be
maintained by a flux of chloroplast inner membrane vesicles.
Thylakoids consist of a complicated network of protein complexes,
pigments, and other accessory components built into a membrane
support structure. In mature chloroplasts, thylakoids are
continuously altered for adaptation to different environmental
conditions, e.g., variations in light or temperature. Thylakoid
proteins encoded by the chloroplast genome are synthesized on
chloroplast stromal *ribosomes and are *co- or post-
translationally inserted into the chloroplast membrane. Despite
the importance of the thylakoid membrane system for oxygenic
photosynthesis, many questions concerning the processes of
thylakoid formation and maintenance remain unanswered. Even less
is known about how this membrane system originated in the first
place. The photosynthetic machinery of purple bacteria that carry
out nonoxygenic photosynthesis is often located in
intracytoplasmic membranes, but it remains unclear whether these
are a separate entity similar to thylakoids or are a continuum of
the plasma membrane. The authors suggest it is therefore tempting
to speculate that the genesis of the thylakoid membrane system is
directly connected to the development of oxygenic photosynthesis.
3) The authors point out that Vipp1, a vesicle-inducing
protein in plastids, in the garden pea (Pisum sativum) and
*Arabidopsis thaliana, is located in both the inner chloroplast
envelope and the chloroplast thylakoids. In Arabidopsis,
disruption of the VIPP1 gene severely affects the ability of the
plant to form properly structured thylakoids, and as a
consequence severely limits the ability to carry out
photosynthesis. In contrast, the protein Vipp1 in the
cyanobacterium Synechocystis appears to be located exclusively in
the plasma membrane, but as in higher plants, disruption of the
VIPP1 gene locus leads to the complete loss of thylakoid
formation. So far, VIPP1 genes are found only in organisms
carrying out oxygenic photosynthesis. These genes share sequence
homology with a subunit encoded by the bacterial gene PspA
(*phage shock operon), but they differ from PspA by a C-terminal
extension of approximately 30 amino acids.
4) The authors report that in two cyanobacteria
(Synechocystis and Anabaena) both a VIPP1 and a PSPA gene are
present, and phylogenetic analysis indicates that VIPP1
originated from a gene duplication of the latter and thereafter
acquired its new function. It also appears that the C-terminal
extension that distinguishes Vipp1 proteins from Pspa proteins is
important for its function in thylakoid formation.
-----------
S.Westphal et al: Vipp1 deletion mutant of Synechocystis: A
connection between bacterial phage shock and thylakoid
biogenesis.
(Proc. Natl. Acad. Sci. US 27 Mar 01 98:4243)
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.
... ... *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.
... ... *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.
... ... *eukaryote: In general, cells (or organisms composed of
such cells) that contain internal membrane-bound organelles.
... ... *ribosomes: 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.
... ... *co- or post-translationally: In this context,
translation is protein synthesis, the process during which
polypeptides are synthesized in accordance with RNA code.
... ... *Arabidopsis thaliana: (thale cress) A weed of the
mustard family with a small genome of 120 million base pairs.
Arabidopsis is now an important laboratory species, and it is
presently the model for physiological, biochemical, cell
biological, and developmental studies of over 250,000 plant
species.
... ... *phage shock operon: The term "phage" (bacteriophage)
refers to a type of virus that infects bacteria. In bacteria, an
"operon" is a cluster of functionally interacting genes whose
expression is tightly coordinated. The phage shock operon protein
PspA was originally characterized in the bacterium E. coli, where
it is a peripherally bound inner membrane protein, its expression
strongly induced upon infection of E. coli cells with a
filamentous phage (f1) or upon severe stresses such as heat,
ethanol, or altered osmolarity. Under certain conditions, this
protein also appears to be involved in protein translocation
processes.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 11May01
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
ORIGIN OF A CHLOROPLAST PROTEIN IMPORTER
... 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: See main report.
... ... *endosymbionts: See main report.
... ... *purple bacteria: See main report.
... ... *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:
PALEOBIOLOGY: ON DATING THE EMERGENCE OF PHOTOSYNTHESIS
Although the advent of *photosynthesis is one of the central
events in the early development of life on Earth, the origin and
evolution of photosynthesis is still unresolved. Various studies
have demonstrated that photosynthetic *eukaryotes acquired
photosynthetic properties from *endosymbiosis with
*cyanobacteria, and this observation, coupled with other facts,
supports the idea that photosynthesis is a bacterially derived
process.
... ... David J. Des Marais (NASA Ames Research Center, US)
presents a commentary on recent work in this field, the author
making the following points:
1) Life began very early in Earth's history, perhaps before
3.8 billion years ago, and achieved remarkable levels of
metabolic sophistication before the end of the *Archean epoch
approximately 2.5 billion years ago. Although the great antiquity
of our biosphere may illustrate how easily life can arise on a
habitable planet, this antiquity also poses challenges to our
attempts to delineate our earliest ancestors.
2) The earliest sedimentary rocks have generally undergone
extensive alteration by *metamorphism, which seriously
compromises microfossils, but traces of our distant ancestors are
recorded not only in ancient rocks but also in biological
macromolecules and pathways. The geological and biological
records are highly complementary: The geological record offers
the absolute timing of evolutionary innovations and their
environmental context, while the living biochemical record can
reveal the sequence of development of key pathways and
biomolecules.
3) J. Xiong et al (Science 8 Sep 00 289:1724) have examined
the biological record to study the evolution of photosynthesis,
obtaining new sequence information for genes involved in
photosynthesis, and performing *phylogenetic analyses on the
major groups of photosynthetic bacteria. This work better defines
the molecular origins of these groups and clarifies the great
antiquity of anoxygenic photosynthesis. The report of Xiong et al
adds an important constraint to current perspectives, the authors
demonstrating conclusively for the first time that the major
lineages of pigments involved in anoxygenic photosynthesis arose
before the development of oxygenic photosynthesis. This indicates
that the 6 major bacterial lineages had largely developed by the
mid-Archean, approximately 3.0 to 2.8 billion years ago, and
perhaps much earlier. The study also demonstrates that the early
biosphere passed through a stage during which even its
photosynthetic populations depended exclusively on abiotic
sources of chemical reducing power.
-----------
David J. Des Marais: When did photosynthesis emerge on Earth?
(Science 8 Sep 00 289:1703)
QY: David J. Des Marais: ddesmarais@mail.arc.nasa.gov
-----------
Text Notes:
... ... *photosynthesis: From the standpoint of chemistry,
photosynthesis can be defined as the reductive carboxylation of
organic substrates carried on by chlorophyll-containing
biological cells capable of using light as their energy source.
Fully oxidized carbon atoms in the form of carbon dioxide are
covalently linked ("fixed") to organic acceptor molecules and are
subsequently reduced and rearranged into sugars and other organic
molecules, with light energy used to drive the fixation and
provide the reducing power.
... ... *eukaryotes: In general, biological cells (or systems
composed of such cells) that contain internal membrane-bound
organelles such as a cell nucleus.
... ... *endosymbiosis: 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.
... ... *cyanobacteria: See main report.
... ... *Archean epoch: (Archaean; Archeozoic) In general, the
earliest biotic geological era, from approximately 3.9 billion
years ago to approximately 2.6 billion years ago. This era marked
the first appearance of sedimentary rocks.
... ... *metamorphism: In general, in this context, the process
of changing the characteristics of a rock in response to changes
in temperature, pressure, or volatile content. Most metamorphic
changes do not include bulk chemical changes, but merely the
crystallization of new mineral phases.
... ... *phylogenetic: In general, the term "phylogeny" refers to
the evolutionary history of a species or group of species in
terms of their derivation and relationships.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 6Oct00
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
PLANT BIOLOGY: ON PHOTOSYNTHESIS
Photosynthesis is one of the more important biological
processes on Earth, providing nearly all the oxygen we breathe,
providing (either directly or indirectly) all the food we eat,
and providing the most important net input of energy into the
biosphere.
From the standpoint of chemistry, photosynthesis can be
defined as the reductive carboxylation of organic substrates
carried on by chlorophyll-containing biological cells capable of
using light as their energy source. Fully oxidized carbon atoms
in the form of carbon dioxide are covalently linked ("fixed") to
organic acceptor molecules and are subsequently reduced and
rearranged into sugars and other organic molecules, with light
energy used to drive the fixation and provide the reducing power.
Many differences exist among photosynthetic organisms with
respect to the components and organization of the photosynthetic
apparatus and the end products of photosynthetic energy
transduction. For example, the photosynthetic apparatus of
oxygen-evolving organisms (*eukaryotic plants and
*cyanobacteria), contains two different photosynthetic systems,
whereas nonoxygenic photosynthesis in the *purple photosynthetic
bacteria involves only one system. Nevertheless, there are a
number of features and principles associated with photosynthetic
energy transduction that are common to all organisms:
a) The process is always associated with membranes
(*thylakoids in oxygen-evolving organisms; *chromatophore
membranes in photosynthetic bacteria).
b) The process always involves multi-unit protein complexes.
Initially, light energy must be captured and transferred to a
photochemical reaction center, where it can be used to drive a
reduction-oxidation (redox) reaction. This occurs in complexes,
each complex containing a light-harvesting cluster of chlorophyll
molecules ("antenna complex"; "antenna system") and a
photochemical reaction center. The chemical redox energy
resulting from the photochemical reaction at the reaction center
can then drive a series of redox reactions, commonly termed
"electron transport" reactions, which result in spatial
separation of oxidized and reduced chemical species, and which
provide a source of chemical energy in the form of reducing
equivalents. Coupled with electron transport is the pumping of
protons across the membrane, and the free energy stored in the
resulting electrochemical potential difference of protons across
the membrane is used by an enzyme (ATP synthetase) to
phosphorylate adenosine diphosphate (ADP) and provide *adenosine
triphosphate (ATP) for the cell.
... ... R.J. Cogdell et al (3 authors at University of Glasgow,
UK) present a review of current research on photosynthetic light
harvesting in purple bacteria, the authors making the following
points:
1) The past few years have seen remarkable progress in our
understanding of the very early light reactions in
photosynthesis, and a large part of this research involves the
study of the photosynthetic purple bacteria. These anaerobic
prokaryotes have proved to be excellent model organisms in which
to investigate the basic mechanisms of the primary light
reactions of photosynthesis.
2) The light-absorbing pigments in purple-bacteria
photosynthesis, mainly bacteriochlorophyll-a and carotenoids, are
contained within two types of integral membrane pigment-protein
complexes: light-harvesting complexes and reaction centers. Solar
energy is absorbed by the light-harvesting components before
being rapidly and efficiently transferred to the reaction
centers. These reaction centers "trap" this light energy and
convert it into chemical energy via a series of transmembrane
redox reactions which initiate photosynthetic electron transport
and lead to proton pumping and ATP synthesis.
3) Photosynthesis can occur in the absence of a light-
harvesting system, but only in very bright sunlight. The antenna
system associated with a reaction center increases the effective
cross-sectional area available for photon capture, and this
allows the reaction centers to be supplied with sufficient solar
energy to drive photosynthesis even on dull days. The combination
of light-harvesting complexes with a reaction center is the
"photosynthetic unit". In purple bacteria, the size of this unit
varies with the light intensity at which the bacteria are grown.
In very bright light, the purple-bacteria photosynthetic unit can
be as small as 30 bacteriochlorophyll-a molecules per reaction
center, while at low light intensity the unit can be as large as
several hundred such molecules per reaction center.
-----------
R.J. Cogdell et al: Photosynthetic light harvesting.
(The Biochemist, June 2000)
QY: Richard J. Cogdell [r.cogdell@bio.gla.ac.uk]
-----------
Text Notes:
... ... *eukaryotic plants: In general, plants whose cells
contain nuclei and other intracellular membrane-bound organelles.
(Cells without nuclei are "prokaryote" cells.)
... ... *cyanobacteria: See main report.
... ... *purple photosynthetic bacteria: See main report.
... ... *thylakoids: A sac-like vesicle containing the
photosynthetic pigments in photosynthetic organisms. In
prokaryotes, the thylakoids are of various shapes and are
attached to the plasma membrane; in eukaryotes, the thylakoids
are flattened and located in chloroplasts; in the chloroplasts of
higher plants, the thylakoids form dense stacks called "grana".
Isolated thylakoids preparations can carry out photosynthetic
electron transport and associated phosphorylation.
... ... *chromatophore membranes: In this context, the term
"chromatophore" refers, in general, to any of the particles,
isolated from photosynthetic organisms, that contain
photosynthetic pigments.
... ... *adenosine triphosphate (ATP): 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
various cell components.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 28Jul00
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
PURPLE BACTERIA, QUANTUM PHYSICS, AND PHOTOSYNTHESIS
Purple bacteria are a type of photosynthetic bacteria in which
the photosynthesis apparatus is apparently derived from the
plasma membrane. They are large organisms, about 0.5 microns in
diameter, and several microns in length, and the molecular basis
of the photosynthesis process in these bacteria has been
intensively investigated by molecular biologists. Physicists are
also interested in these organisms as examples of efficient
electron transfer systems. Recently, Xiche Hu and Klaus Schulten
(University of Illinois Urbana-Champaign, US) reviewed the
present structural model of the light harvesting system of purple
bacteria. The authors suggest the physical principles governing
the light harvesting and electron transfer processes of bacteria,
processes that have been selected and optimized over billions of
years of evolution, may one day be applied to the engineering of
solar cells.
-----------
QY: K. Schulten, Univ. Illinois Urbana-Champaign 217-333-3645.
(Physics Today August 1997) (Science-Week 10 Oct 97)
For more information: http://scienceweek.com/swfr.htm
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
5. NEUROBIOLOGY: ON THE MOVEMENTS OF NERVE AXONS
In all organisms with a patterned nervous system, one of the
fundamental developmental problems is the achievement of
appropriate connections between neurons, connections essential to
specific functions. The cytoplasmic extension of a nerve cell
primarily responsible for its connections to other nerve cells is
the nerve cell axon (and its branches), and axons in various
parts of the nervous system travel large distances to reach their
target cells.
The term "axonal growth cone" refers to a specialized
structure at the tip of the extending axon. Growth cones are
highly motile structures that explore the extracellular
environment and respond to local cues by changing the speed or
direction of growth.
In neurobiology, the term "commissure" refers to a nerve
tissue tract that joins two bilaterally symmetrical parts of the
nervous system. In arthropods and annelids, commissures connect
ganglia of the paired ventral nerve cords, and connect the brain
ganglia (supraoesophageal ganglia) with lower ganglia. In
vertebrates, commissures unite the two hemispheres of the brain.
In this context, the term "floor plate" refers to the
ventral midline portion of the developing neural tube, the
embryonic hollow tube of neural tissue that eventually forms the
brain and spinal cord.
The term "netrin" refers to a long-range chemoattraction
protein released by cells of the embryonic floor plate; netrin
binds to so-called "DCC" receptors on commissural neurons,
causing attraction of their growth cones. In this context, the
term "slit" refers to a short-range chemorepulsion protein that
binds to so-called "Robo" receptors on commissural axons. Slit-
based short-range chemorepulsion apparently prevents axons from
recrossing the floor-plate once they have crossed it.
In this context, the term "midline" refers to the imaginary
line that separates two bilaterally symmetrical parts of the
nervous system.
... ... E. Stein and M. Tessier-Lavigne (University of California
San Francisco, US) present a report of the interaction of netrin
and slit functions in guiding commissural axons. The authors make
the following points:
1) The authors point out that in the developing nervous
system, many axons find their final targets by navigating a
series of intermediate targets: in general, axons are attracted
to each successive intermediate target. This presents an apparent
paradox: If the cells that form the intermediate target are
initially perceived as attractive, how can the axons move on from
this target to the next target? The answer appears to lie in the
ability of axonal growth cones to change their response to the
guidance molecules presented by intermediate target cells, so
that what was initially perceived as an attractive cellular
environment is now interpreted as repulsive.
2) This changing preference of migrating axons is well
documented for the guidance of commissural axons at the midline
of the nervous system. In vertebrates, insects, and nematode
round worms, commissural axons are attracted to the midline by
chemoattractants of the phylogenetically conserved netrin family
of proteins, these proteins signaling attraction by activating
receptors of the DCC family of guidance receptors on axonal
growth cones. Commissural axons then cross the midline and
project alongside it, never recrossing. This failure to recross
is explained, at least in the fruit fly Drosophila, by the fact
that midline cells, in addition to expressing attractive netrin
proteins, also express the repellant protein "slit", which
signals repulsion by activating the Robo (Roundabout) receptor.
The axonal growth cones can cross once because they do not
initially express Robo protein on their surface, but upon
crossing, via a mechanism that is still poorly understood, axon
growth cones then express Robo protein on their surface and
become responsive to slit proteins, which prevents them from
recrossing the midline.
3) The authors report evidence that the appearance of
responsiveness to slit and a loss of responsiveness to netrin are
causally linked. In the axonal growth cones of embryonic toad
(Xenopus) spinal axons, activation of the slit receptor Robo
silences the attractive effect of netrin-1, but not the growth-
stimulatory effect of netrin-1. This silencing occurs through
direct binding of the cytoplasmic domain of Robo to that of the
netrin receptor DCC. The authors suggest that from a biological
perspective, this hierarchical silencing mechanism helps to
prevent a tug-of-war between attractive and repulsive signals in
the axonal growth cone that might cause confusion. The authors
suggest that at the molecular level, silencing is enabled by a
modular and interlocking design of the cytoplasmic domains of
these potentially antagonistic receptors, a design that
predetermines the outcome of their simultaneous activation.
... ... In a commentary on this work, Barry J. Dickson (Research
Institute of Molecular Pathology Vienna, AT) states: "The studies
of the Tessier-Lavigne laboratory force us to revise our view of
how axons respond to multiple guidance cues. In vivo, axons are
simultaneously exposed to a number of different attractive and
repulsive forces. It has generally been thought that the axon
integrates all of these signals in order to calculate its next
move. But, as Stein and Tessier-Lavigne show, multiple guidance
signals can also be combined in a hierarchical fashion, with one
signal silencing the response to another."
-----------
E. Stein and M. Tessier-Lavigne: Hierarchical organization of
guidance receptors: Silencing of netrin attraction by slit
through a Robo/DCC receptor complex.
(Science 9 Mar 01 291:1928)
QY: Marc Tessier-Lavigne: marctl@itsa.ucsf.edu
-----------
Barry J. Dickson: Moving on.
(Science 9 Mar 01 291:1910)
QY: Barry J. Dickson: dickson@nt.imp.univie.ac.at
-------------------
Summary by SCIENCE-WEEK http://scienceweek.com 11May01
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
NEUROBIOLOGY:
SYNAPTIC ASSEMBLY WITHOUT NEUROTRANSMITTER SECRETION
One of the major essential challenges of the embryonic phase
of the development of the vertebrate nervous system is the
construction of accurate "hard-wiring" -- the formation of
anatomical connections between various nerve cell groups that
must physiologically work together. What are the mechanisms that
control the directed growth of neuron extensions (axons) to make
contact with target cells, both target cells that are close by
and target cells that are often at relatively enormous distances?
And once primary connections are made, to what extent are
secondary connections dependent on the activity of those primary
connections?
In general, nerve cells have a single long extension (the
"axon") that propagates the electrical output (the action
potential) of the cell. The term "synapse" refers to the junction
between the terminal of a neuron's axon and another neuron. When
studying the synapse, the first neuron is called the
"presynaptic" neuron, and the second neuron is called the
"postsynaptic" neuron. The term "neurotransmission" refers to all
the events at a synapse, particularly the release of
neurotransmitters and their action on the postsynaptic neuron.
Neurotransmitters are chemical substances released at the
terminals of nerve axons in response to the propagation of an
impulse to the end of that axon. The neurotransmitters are
contained in membrane-bound vesicles in the terminal of the axon,
and release of neurotransmitter substance involves fusion of
vesicles with the surface membrane of the axon terminal -- each
vesicle essentially releasing a "packet" of neurotransmitter
substance. The neurotransmitter substance diffuses into the
synapse, the junction between the presynaptic nerve ending and
the postsynaptic neuron, and at the membrane of the postsynaptic
neuron the transmitter substance interacts with a receptor. In
general, depending on the type of receptor, the result may be an
excitatory or an inhibitory effect on the postsynaptic nerve
cell.
A important question concerning the development of the
nervous system, and in particular the development of the
mammalian brain, is to what extent are the migrations of axons to
make new connections dependent on the activity of those axons and
the consequent release of neurotransmitter substances at the axon
terminals? To establish the synaptic network in the brain,
outgrowing axons are apparently precisely directed to their
targets by means of a variety of guidance cues and recognition
signals involving the outgrowing axon and the target cell. Fusion
of neurotransmitter vesicles at the axon tip has been proposed as
a mechanism to supply the surface membrane required for axon
outgrowth, and the concomitant neurotransmitter release has been
thought to have a *trophic role and to provide essential signals
for the correct targeting of axons and synapse formation.
... ... M. Verhage et al (12 authors at 5 installations, NL US)
now present a report of experiments that apparently overturn
prevailing ideas concerning the role of neurotransmitter release
in the hard-wiring of the embryonic mammalian brain. The authors
report the following:
1) Genetic-engineering deletion of a single protein (Munc
18-1) in mice leads to a complete loss of neurotransmitter
secretion from synaptic vesicles throughout development, but this
deletion does not prevent normal brain assembly, including the
formation of layered structures, fiber pathways, and
morphologically defined synapses. After assembly is completed,
these neurons undergo classical programmed cell death
(apoptosis), producing widespread neurodegeneration. (These
mutant mice with this gene deletion (Munc 18-1 knockout mice) are
paralyzed at birth and die immediately after birth, apparently
because they cannot breathe.)
2) The authors point out that despite the general, complete,
and permanent loss of synaptic transmission in these knockout
mice, their brains were assembled correctly. Neuronal
proliferation, migration, and differentiation into specific brain
areas were unaffected, and brains from mutant and control
littermates were morphologically indistinguishable. At birth,
late-forming brain areas such as the *neocortex appeared
identical in mutant and control littermates, including a
distinctive segregation of neurons into cortical layers.
Furthermore, fiber pathways were targeted correctly in mutants.
3) The authors conclude: "Our data indicate that the
neuronal networks are synaptically assembled and reach the
*selection stage without synaptic transmission, but cannot
persist without it. When synaptic transmission is absent in newly
established synaptic connections, these synapses degenerate and
neurons go into apoptosis. Finally, our data indicate that the
distribution of [surface] membrane to the growing axon tip and
the release of signals that allow correct axon targeting depend
[on molecular mechanisms different from] neurotransmitter release
by regulated exocytosis of synaptic vesicles."
-----------
M. Verhage et al: Synaptic assembly of the brain in the absence
of neurotransmitter secretion.
(Science 4 Feb 00 287:864)
QY: Matthijs Verhage [m.verhage@med.uu.nl]
-----------
Text Notes:
... ... *trophic: In general, the term "trophic" refers to
nutrition or food. (The term should not be confused with "tropic"
[from "tropism"; e.g., a "tropic" response], which refers to an
involuntary or reflex turning by a cell, plant, or animal in
response to a stimulus.)
... ... *neocortex: In general, the most recently evolved part of
the cerebral cortex.
... ... *selection stage: The stage when certain networks are
selected to be retained and other networks are degraded and
eventually obliterated. After normal synaptic assembly of the
brain, activity-dependent selection is thought to maintain
certain synaptic connections for adult life, whereas other
connections are discarded.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 26May00
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
NEUROBIOLOGY:
INTRACELLULAR CALCIUM IONS AND NERVE GROWTH CONES
After neurons have differentiated and migrated to their intended
specific destinations, they extend *axons that select connection
targets from an enormous number of possibilities, and eventually
these axons form *synapses with appropriate cells in the target
region. These events depend on a complex of cellular and
molecular signals that guide axons and facilitate correct
connections. The signals involve *cell adhesion molecules that
regulate the interactions between axons and the surfaces upon
which they grow, diffusible molecules that attract growing axons,
and a family of molecules called "*neurotrophins" that promotes
and maintains stable synapses between axons and their targets.
The circuitry of the developing nervous system is thus gradually
constructed by means of such intricate interactions. The local
dynamics of growing axons are now known to involve the properties
of the "growth cone", a specialized structure at the tip of the
extending axon. Growth cones are highly motile structures that
explore the extracellular environment and respond to local cues
by changing the speed or direction of growth. Experiments
indicate that in vitro the intracellular calcium ion
concentration of growth cones is correlated with their motility,
but the links between environmental cues and axon growth in vivo
are unknown.
... ... James Q. Zheng (Univ. of Medicine and Dentistry of New
Jersey, US) now reports new evidence concerning the role of
calcium ion in nerve growth cone directionality, the author
making the following points:
1) Although guidance of developing axons involves turning of
the growth cone in response to a variety of extracellular cues,
little is known concerning the intracellular mechanism by which
the directional signal is transduced. Calcium ion is apparently a
key "*second messenger" in growth cone extension and has been
implicated in growth-cone turning.
2) The author reports that with cultured amphibian neurons
(Xenopus laevis; African clawed toad) a direct spatially
restricted elevation of intracellular calcium ion concentration
on one side of the growth cone by focal laser-induced photolysis
(FLIP) of caged calcium ions consistently induced turning of the
growth cone to the side with elevated calcium ion concentration.
Furthermore, when the resting intracellular calcium ion
concentration at the growth cone was decreased by the removal of
extracellular calcium ion concentration, the same focal elevation
of intracellular calcium ion concentration by FLIP induced
repulsion.
3) The authors suggests these results provide direct
evidence that a localized calcium ion signal in the growth cone
can constitute the intracellular directional cue for extension,
and this cue is sufficient to initiate either attraction or
repulsion, depending on ambient conditions. By integrating local
and global calcium ion signals, a growth cone could thus generate
different turning responses under different environmental
conditions during guidance. The author concludes: "Such diversity
of regulation along the signal transduction pathway... could
provide the potential for the specific and accurate wiring of
millions of axons through a limited number of cues available
during development."
-----------
James Q. Zheng: Turning of nerve growth cones induced by
localized increases in intracellular ions.
(Nature 6 Jan 00 403:89)
QY: James Q. Zheng [zhengiq@umdnj.edu]
-----------
Text Notes:
... ... *axons: In those animals that have nervous systems, one
task of embryological development is to ensure the proper
functional connections between nerve cells and other nerve cells,
and between nerve cells and muscle cells. The innervation must be
exact, in the sense that the growing nerve cell extension (the
axon), which will ultimately serve to propagate information, must
reach a specific and often distant target. In humans, for
example, there are nerve cells whose growing axons reach specific
targets as much as a meter distant from the cell body.
... ... *synapses: The junction between the terminal of the axon
of one neuron and another neuron is called a "synapse".
... ... *cell adhesion molecules: In general, substances that
regulate the interactions between axons and the surfaces upon
which they grow.
... ... *neurotrophins: In general, neurons in the central
nervous system apparently depend for their survival on a number
of secreted substances called neurotrophins (neurotrophic
factors). These substances are polypeptides of 200 to 300 amino
acids, and at least 4 different neurotrophins have been
identified.
... ... *second messenger: In general, the "second messenger" is
an intermediary compound that couples extracellular signals to
intracellular processes with amplification of the transduced
signal.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 28Apr00
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
NEUROTROPHIC FACTORS AND LONG-DISTANCE AXON DEVELOPMENT
... Classic studies in neurobiology have demonstrated that many
neuronal populations in vertebrates are initially generated in
excess numbers during embryonic development, and that excess
neurons are subsequently eliminated by naturally occurring
neuronal cell death. This massive death of excess neurons usually
occurs soon after the axons of these neurons reach their targets,
and appears to result from a dependence of the neurons on
"trophic substances" (*neurotrophic factors) secreted by their
target cells. The trophic substances are present in limited
amounts, and the incoming axons evidently compete for these
limited amounts. This competition is thought to provide a
mechanism for matching the size of the presynaptic neuronal
population to the size of the target population, and has also
been suggested to provide a mechanism for eliminating
misprojecting neurons (axons that have extended to the wrong
location), the misprojecting axons not having access to the
target-derived trophic support. With the identification of many
neurotrophic factors in recent years, evidence has started to
accumulate that neurons that have reached their targets may
receive trophic support not just from their target cells, but
also from other cellular sources such as those located near their
cell bodies or axons. There is also evidence that some
differentiated neurons may have trophic requirements before they
reach their target fields.
... ... H. Wang and M. Tessier-Lavigne (University of California
San Francisco, US) now report that rat spinal commissural
neurons, a group of long-projection neurons in the central
nervous system, in addition to trophic support from final
targets, are also dependent for their survival on trophic support
from one of their intermediate targets, the "*floor plate" of the
spinal cord. The authors report this dependence occurs during a
period of several days when the axons extend along the floor
plate, following which period they develop additional trophic
requirements. The authors suggest that a dependence of neuron
axon growth on trophic support derived "en passant" from their
intermediate targets provides a mechanism for rapidly eliminating
misprojecting neurons, which may help to prevent the formation of
aberrant neuronal circuits during the development of the nervous
system.
-----------
H. Wang and M. Tessier-Lavigne: En passant neurotrophic action of
an intermediate axonal target in the developing mammalian CNS.
(Nature 21 Oct 99 401:765)
QY: Marc Tessier-Lavigne [marctl@itsa.ucsf.edu]
-----------
Text Notes:
... ... *neurotrophic factors: See main report notes.
... ... *floor plate: A small well-defined area at the ventral
margin of the developing neral tube (brain and spinal cord). (The
"ventral margin" is the margin toward the abdomen.)
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 10Dec99
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
NEURON PATHFINDING AND GROWTH-CONE CALCIUM ION TRANSIENTS
... T.M. Gomez and N.C. Spitzer (University of California San
Diego, US) now report a study of the development of axonal
projections of various types of nerve cells in the spinal cord of
the embryo of the toad (Xenopus). The authors report that axon
growth cones generate transient elevations of intracellular
calcium ion concentration as they migrate within the embryonic
spinal cord, and that the rate of axon outgrowth is inversely
proportional to the frequency of transients. Suppression of
calcium ion transients by photorelease of a calcium ion chelator
accelerates axon extension, whereas mimicking transients with
photorelease of calcium ion slows otherwise rapid axonal growth.
The authors report that the frequency of calcium ion transients
is cell-type specific and depends on the position of growth cones
along their pathway. The authors further report that growth-cone
stalling and axon retraction, which are two important aspects of
pathfinding, are associated with high frequencies of calcium ion
transients. The authors suggest their results indicate that
environmentally regulated growth-cone calcium transients control
axon growth in the developing spinal cord.
-----------
T.M. Gomez and N.C. Spitzer: In vivo regulation of axon extension
and pathfinding by growth-cone calcium transients.
(Nature 28 Jan 99 397:350)
QY: Timothy M. Gomez [tgomez@biomail.ucsd.edu]
-----------
Text Notes:
... ... *axons: See previous report(s).
... ... *synapses: See previous report(s).
... ... *cell adhesion molecules: See previous report(s).
... ... *neurotrophins: See previous report(s).
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 23Apr99
-------------------
Related Background:
ACTIVITY-DEPENDENT CORTICAL TARGET SELECTION BY GROWING AXONS
Many of the connections between nerve cells (the "wiring" of the
nervous system) are programmed in mammals during development.
This is particularly true of the pathway connections of the
sensory systems and the basic motor output systems. During the
wiring of the connections between the *thalamus and *cortex in
mammals, there is an intermediate step in which thalamic axons
grow and interact with a special population of neurons (so-called
subplate neurons) before they contact their ultimate target
neurons within the cerebral cortex (cortical plate). Such
connections in the developing nervous system are thought to be
formed initially by a process not dependent on activity, the axon
pathfinding process and target selection only afterward refined
by neural activity. ... ... Now Catalano and Shatz (University of
California Berkeley, US) report that blockade of *sodium action
potentials by *intracranial infusion of *tetrodotoxin in cats
during the early period when axons from the *lateral geniculate
nucleus were in the process of selecting visual cortex as their
target altered the pattern and precision of this thalamo-cortical
projection. The majority of these neurons, rather than projecting
to visual cortex, elaborated a significant projection within the
subplate of cortical areas normally bypassed. Those axons that
did project to their correct target were *topographically
disorganized. The authors suggest that neural activity is thus
required for initial targeting decisions made by thalamic axons
as they cross the subplate, and that whatever the mechanisms, the
formation of connections between thalamus and *neocortex in
mammals be a special exception to the general rule that target
selection by developing axons is independent of neural activity.
QY: Carla J. Shatz
(Science 24 Jul 98) (Science-Week 14 Aug 98)
-------------------
Related Background:
... ... *thalamus: The thalamus is a deep brain structure that
consists of groups of nerve cells that project to various other
regions of the brain. In general, these groups of nerve cells are
specific relay stations for sensory information (e.g., visual,
auditory, pain, temperature, etc.)
... ... *cortex: The term "cortex" is often used as the short
form for "cerebral cortex", but there are other anatomical
structures also called "cortex", so the meaning is context-
dependent.
... ... *sodium action potentials: In vertebrates, most action
potentials are "sodium action potentials", due to a transient
increase in sodium ion permeability that is propagated down the
axon to the axon terminal(s).
... ... *intracranial infusion: In general, the introduction of
any solution into the brain within the skull.
... ... *tetrodotoxin: A neurotoxin that specifically blocks the
change in sodium ion permeability necessary for the production of
an action potential. Tetrodotoxin acts on sodium ion channels in
the axon membrane.
... ... *lateral geniculate nucleus: A thalamic cell group that
acts as a relay station in the visual pathway from the retina to
the primary visual area of the cerebral cortex.
... ... *topographically disorganized: Ordinarily, the
topographical organization of visual (photon) input to the retina
is for the most part projected isomorphically to the primary
visual area of the brain for analysis. Any topographical
disorganization of information in the pathway or at its terminus
(a disruption of the "mapping") can thus have devastating effects
on the ability of the system to analyze visual inputs.
... ... *neocortex: The most recently evolved part of the
cerebral cortex.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 14Aug98
For more information: http://scienceweek.com/swfr.htm
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
6. PALEOBIOLOGY: ON THE ORIGINS OF MODERN CORALS
The term "coral" refers to any of a variety of invertebrate
marine organisms of the class Anthozoa (phylum Cnidaria) that are
characterized by skeletons (external or internal) of a stonelike,
horny, or leathery consistency. The term "coral" is also applied
to the skeletons of these animals, particularly to the skeletons
of the stonelike corals. Stony corals (order Madreporararia or
Scleractinia) number approximately 1000 species; black corals and
thorny corals (Antipatharia) number approximately 100 species;
horny corals (Gorgonacea) number approximately 1200 species; and
blue corals (Coenothecalia) number one living species. The body
of a coral animal consists of a polyp, a hollow cylindrical
structure attached at one end to a surface. At the free end is a
mouth surrounded by tentacles which gather food and which are
extensible to varying degrees, and which are armed with
specialized stinging structures (nematocysts) that paralyze prey.
The skeleton of a stony coral is almost pure calcium carbonate
and is deposited in a cup-shaped form with the polyp inside. The
growth rate of the skeleton varies with age, food supply, water
temperature, and species. Atolls and coral reefs are composed of
stony coral, with such formations growing at an average rate of
approximately 0.5 to 2.8 centimeters per year.
The geological period known as the Cambrian is the time
frame from approximately 570 million years ago to 510 million
years ago. Its most outstanding aspect is the rather sudden
appearance of numerous invertebrate fossils, so numerous that
some have termed it an explosion of evolutionary processes. Many
of the life forms that existed during the Cambrian are long
extinct, but their fossils are numerous, and through their
fossils the various Cambrian species have been the subject of
much study by paleobiologists. The Cambrian explosion of life
forms 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; and, 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.
The "Permian period" comprises the approximate time-frame
290 to 245 million years ago, and the "Triassic period" comprises
the approximate time-frame 245 to 208 million years ago. At the
end of the Permian period, many groups of animals and plants
apparently vanished in the greatest known crisis in the history
of life on Earth. This extinction event was the most severe in
the past 540 million years, killing off over 90 percent of all
marine species, approximately 70 percent of terrestrial
vertebrate genera, and most land plants. Proposed catastrophic
hypotheses for the Permian/Triassic boundary extinction include
an exploding meteor (bolide) (asteroidal or cometary) and massive
volcanic lava flows (flood basalt volcanism). Other extinction
mechanisms involving ocean anoxia, as well as changes in sea
level and climate, have also been proposed.
The so-called "Paleozoic era" comprises the time-frame 570
million to 245 million years ago, thus beginning with the
Cambrian period and terminating at the end of the Permian period.
... ... G.D. Stanley Jr. and D.G. Fautin (2 installations, US)
present a commentary on recent research on the origins of modern
corals, the authors making the following points:
1) The authors point out that most calcifying multicellular
animals made their debut approximately 540 million years ago
during the Cambrian period, soon after the explosion of
biological diversity in the sea. Molecular evidence indicates
that most Paleozoic multicellular animals (metazoans) originated
much earlier, in the Precambrian. Scleractinian corals are
relative latecomers, appearing in the fossil record during the
Triassic period approximately 237 million years ago -- 14 million
years after the Permian extinction.
2) The authors point out that despite a rich fossil record,
the origin of Scleractinia corals has remained shrouded in
controversy. The absence of coral fossils in the first 14 million
years of the Triassic coincides with a time when carbonate
deposition was apparently suppressed globally, long after most
marine life had been extinguished at the end of the Permian. This
gap is a problem for the old theory that scleractinians were
derived from Paleozoic corals. It has been postulated that some
survived but that post-extinction abundances were low, and the
resulting fossils so rare that they have eluded detection.
Another theory is that these corals survived the 14-million-year
gap in as yet undiscovered refuges. The authors suggest both
ideas seem tenuous in light of the intense global scrutiny by
researchers of lower Triassic rocks.
3) The authors suggest that many apparent ambiguities and
conflicts in previous analyses can be reconciled if lineages of
corals have lost and redeveloped skeletons repeatedly through
their history in response to environmental conditions. To test
this idea, the authors suggest that future research should
explore biochemical mechanisms of calcification, establish
phylogenetic relationships between scleractinians and
morphologically similar soft-bodied animals, analyze if and how
skeletal structure of scleractinian groups corresponds with
molecular data, and seek evidence of geochemical changes in
geologic history that correlate with changes in the robustness of
coral skeletons and appearances or disappearances of various
coral groups.
-----------
G.D. Stanley and D.G. Fautin: The origins of modern corals.
(Science 9 Mar 01 291:1913)
QY: George D. Stanley: fossil@selway.umt.edu
-------------------
Summary by SCIENCE-WEEK http://scienceweek.com 11May01
For more information: http://scienceweek.com/swfr.htm
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7. IN FOCUS: ON THE GREAT BARRIER REEF
"On a trip to the Great Barrier Reef early in 1999 I went
into a dive shop to hire some dive gear. 'Have a good holiday.
Enjoy the reef while you can,' said the shop assistant. I thought
then that he meant 'Enjoy it while you can,' in the 'life is
fleeting' sense. Later I realized he meant 'Enjoy it while it's
still here.' In 1998 a dramatic wave of coral bleaching spread
across the tropical oceans of the world. Corals from most species
bleached to white, suddenly and within weeks. First noticed in
December 1997 in the Galapagos Islands, the bleaching swept
across the Pacific Ocean to the Great Barrier Reef and onward,
ultimately affecting corals in the Caribbean some nine months
later. The colors of corals bring pleasure; their widespread
bleaching brought dismay. While some corals have recovered,
others have since died. The situation is disturbing. The Great
Barrier Reef has existed in its present form for roughly 6000
years, which is only a moment in geological time, but the reef's
moment may be passing...
"The 1998 International Year of the Oceans was the hottest
year on record for a thousand years; it was also the year of
death of corals on a scale never seen before, through coral
bleaching. In bleaching, coral loses its color and much more. The
brilliant colors of corals come from tiny single-celled algae,
the zooxanthellae or symbiotic dinoflagellates, which live in the
tissues of the corals in great numbers; between 6 million and 12
million organisms to a square inch of coral tissue. When the
zooxanthellae get stressed, they collect together in the hollow
column of the coral polyp and leave their host. They bail out
into the ocean to take up an independent life. The coral skeleton
becomes visible through the now transparent polyp. Normally, the
algae live in symbiosis with the polyps and produce up to 60
percent of their energy; when they bail out, ill health and often
death of corals follow.
"Coral bleaching is relatively new as a cause of massive
death and destruction of corals. It was observed on the Great
Barrier Reef before 1998 but on isolated reefs in isolated
patches. There have been five similar if less serious outbreaks
since 1979, though, curiously, few reports before then. The
bleaching effect was linked to a number of causes, both increased
sea temperature and decreased water salinity caused by heavy rain
can prompt corals to release large numbers of algae. Laboratory
studies in the 1980s showed that other stresses such as increased
ultraviolet light, sedimentation, and toxic chemicals also may
cause bleaching..."
-----------
Rosaleen Love: _Reefscape: Reflections on the Great Barrier Reef_
(Joseph Henry Press, Washington 2001, p.4,175.)
http://www.amazon.com/exec/obidos/ASIN/0309072603/scienceweek
-------------------
SCIENCE-WEEK http://scienceweek.com 11May01
For more information: http://scienceweek.com/swfr.htm
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8. FROM THE SCIENCEWEEK ARCHIVE:
FOUNDATIONS: 1932 -- THE YEAR OF PHYSICS
Identification of important discoveries in science is easier in
the long-run than in the short-term, principally because
consequences and influences of a discovery accumulate over
decades, and the most important discoveries acquire obvious
accumulations. The 20th century has been a phenomenal time for
physics, with important discoveries made nearly every year. In an
essay, H.G.B. Casimir (b. 1909), whose career in physics spans
almost the entire 20th century, chooses 1932 as an "annus
mirabilis" in physics. Casimir identifies four major discoveries
by physicists in 1932: the neutron, heavy hydrogen, nuclear
reactions, and the positron. But heavy hydrogen, in fact, was
discovered by a chemist, Harold C. Urey (1893-1981), who never
called himself other than a chemist, and who received the Nobel
Prize for Chemistry in 1934 for his discovery. Casimir implies
that the discovery of heavy hydrogen (and the "deuteron" nucleus)
followed easily from the discovery of the neutron by James
Chadwick (1891-1974), but Urey actually made his discovery of
heavy hydrogen in late 1931, before the results of Chadwick's
famous experiment were obtained. Leaving aside these historical
refinements, we note the following points made by Casimir:
1) Ernest Rutherford (1871-1937) postulated the existence of
the neutron, a particle without electric charge and approximately
the same mass as the proton. The neutron was discovered in 1932
by James Chadwick, who created beams of neutrons by irradiating
beryllium with alpha particles. The result of this experiment was
that it quickly became clear that atomic nuclei were composed of
protons and neutrons, and were not a medley of protons, "nuclear
electrons", alpha particles, etc., the medley that was considered
the consensus model of the atomic nucleus between 1920 and 1932.
The Chadwick experiment was indeed a major breakthrough in atomic
physics. Chadwick received the Nobel Prize for Physics in 1935.
2) Casimir says only the following about the discovery of
heavy hydrogen: "[After Chadwick's experiment] nuclei were
henceforth regarded as compounds of protons and neutrons. The
simplest case is one proton and one neutron. This particle was
called deuteron, D. Its oxide, D(sub2)O is the molecule of heavy
water. It was found in 1932 that about one part in six thousand
of normal water is heavy water." [Editor's note: Strangely,
Casimir does not mention Urey at all. Urey's discovery of heavy
hydrogen is a classic illustration of how a simple experiment can
yield extraordinarily important results. Urey began working on
heavy hydrogen in 1931, when it was already suspected by chemists
that hydrogen had a heavy isotope. Reasoning that liquid hydrogen
composed of the lighter hydrogen should evaporate before liquid
hydrogen composed of the more massive heavy hydrogen, Urey slowly
evaporated 4 liters of liquid hydrogen down to 1 cubic centimeter
and then investigated the spectrum of the remnant. He found the
ordinary absorption lines of hydrogen were accompanied by faint
lines in the exact positions later predicted by theory for heavy
hydrogen. The name "deuterium" was given to the heavy isotope.
After Urey's discovery, Chadwick and others in his laboratory
investigated the structure of the deuteron and demonstrated that
it consisted of one proton and one neutron.]
3) In 1932, John Cockcroft (1897-1967) and Ernest Walton
(1903-1995) used a 700-kilovolt high-voltage generator to
accelerate protons against lithium atoms and demonstrate that
these lithium atoms "broke in two". Cockcroft and Walton
announced they had "split the atom", and "so began the era of big
machines." Casimir states: "The high voltage generators were
succeeded by cyclotrons, the cyclotrons by even more powerful
apparatus." Cockcroft and Walton received the Nobel Prize for
Physics in 1951. [Editor's note: Here again, Casimir's account
requires some modification: The first "cyclotron" was built and
used experimentally and named in 1930 by Ernest O. Lawrence
(1901-1958), well before the Cockcroft-Walton experiment. Larger
and larger cyclotrons were indeed built during the following
decades. Concerning the "splitting of atoms", an argument can be
made that Rutherford had already done so before 1920. Rutherford
had certainly driven protons out of nitrogen atoms by bombarding
the atoms with alpha particles.]
4) In 1932, Carl D. Anderson (1905-1991) discovered the
positron, whose existence was predicted by the theoretical
physicist Paul A.M. Dirac (1902-1984). The positron is the
antiparticle of the electron. It has a charge identical but
opposite to that of the electron, and a rest mass identical to
that of the electron. Anderson received the Nobel Prize for
Physics in 1936. Casimir points out that the positron was the
first short-lived particle to be "created out of empty space" --
a prelude to the high-energy physics that blossomed beginning in
1950, and the powerful machines that now reveal the existence of
"whole families of short-lived particles, many of them predicted
by theory." Casimir concludes: "Sometimes it almost appears that
the theories are not a description of a nearly inaccessible
reality, but that so-called reality is a result of the theory."
-----------
H.B.G. Casimir: Annus physicalis 1932.
(Nature 2 Dec 99 402:463)
QY: H.B.G. Casimir, De Zegge 7, 5591 TT Heeze, NL.
-------------------
Summary by SCIENCE-WEEK http://scienceweek.com 7Jan00
For more information: http://scienceweek.com/swfr.htm
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