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ScienceWeek
SCIENCE-WEEK
A Weekly Digest of the News of Science
July 31, 1998
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I believe there is no philosophical high-road in science,
with epistemological signposts. No, we are in a jungle and
find our way by trial and error, building our road behind
us as we proceed.
-- Max Born (1882-1970)
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Contents of This Issue:
1. Nuclear Test Explosions and Scientists in India
2. Dust Disks and Extrasolar Planets
3. Giant Planets vs. Brown Dwarfs
4. On Fusion Research and the Z Machine
5. On Computing with DNA
6. On the Chemistry and Biology of the Oceans
7. Marine Organisms: Acquisition and Use of Transition Metal Ions
8. Evolution: Adaptive Radiation in a Heterogeneous Environment
9. Estrogen: Both a Male and Female Hormone
10. On Photodynamic Therapy in Cancer
-----------------------------------------------
1. NUCLEAR TEST EXPLOSIONS AND SCIENTISTS IN INDIA
G. Padmanaban, Director of the Indian Institute of Science
(Bangalore, IN), in a letter to the journal *Science*, comments
about the Indian science community and the recent nuclear test
explosions in India. The author makes the following points: 1)
The recent nuclear test explosions have created a "tremendous
euphoria" in India. The average Indian does not associate the
test with security concerns or power politics. "Right-thinking
Indians know that our priorities are such things as health,
education, and containment of population." 2) The author says
that India, despite having an ancient culture and a functioning
and stable large democracy, and being a hunting ground for
technically qualified people, has been persistently represented
in the US and the West as the home of poverty, filth, disease,
and backwardness. 3) The author says a feeling of alienation
permeates those segments of Indian society that have anything to
do with the West, and with the US in particular, and that the
general perception among Indian scientists in leading institut-
ions, most of whom are US-trained, is that they are being
discriminated against. Research papers sent to top international
journals from India seem to be reviewed with a bias. "Even if I
manage to publish one of my papers in one of the best journals,
it will seldom be quoted or have an impact, unless I have a US-
Western pedigree or a connection with an inner circle... Even if
I am invited to deliver a lecture at an international research
conference, I am made to feel like an outsider..." 4) The author
says India was denied a Cray computer for more than a decade, and
that Indian scientists "are appalled by how the US, which values
intellectual challenges and academic freedom, can have such a
discriminatory attitude toward a country struggling to develop
its science." 5) The author states: "India has many, many
problems, but we are tired of being depicted in the West as
having negative qualities. Given this treatment, one clutches at
any 'victory' that makes one feel like an entity to be counted.
It can be a win in cricket, a chess match, or a beauty contest,
or even a nuclear blast."
QY: G. Padmanaban
(Science 10 Jul 98 281:175) (Science-Week 31 Jul 98)
2. DUST DISKS AND EXTRASOLAR PLANETS
Paul Kalas (Max-Planck Institute for Astronomy Heidelberg, DE)
reviews current investigations concerning dust disks around stars
and the implications of the data for the existence of planets
around these stars. The author makes the following points: 1) One
of the important discoveries of the 1980s was the existence of
circumstellar disks of dust around some stars, the disks
apparently replenished by unseen parent bodies such as comets and
asteroids. 2) Some of these disks have recently been spatially
resolved by a new generation of ground-based instruments. An
example is the disk surrounding the star HR 4796, discovered in
1991 to have thermal emission from warm circumstellar dust. Two
observing teams have now mapped the emission from this dust disk
and revealed a peanut-shaped disk with the waist of the disk due
to an apparent central cavity (papers by Jayawardhana et al and
Koerner et al, in press). The data are interpreted by the authors
as indicating the existing of planets in formation around the
star, and so announced in news headlines (press releases by US
Harvard-Smithsonian Center for Astrophysics, US Jet Propulsion
Laboratory). Kalas, however, says the interpretation is premature
and not warranted by the data. 3) At about the same time as the
previous reports, maps of dust around the stars Vega, Fomalhaut,
and Beta Pictoris were published (Holland et al, *Nature*,
392:788 1988), and these maps were also interpreted as indicating
the presence of planets, but with differing bases for the
interpretations. Of the four stars, the data from HR 4796 and
Fomalhaut are interpreted as indicating planets creating central
cavities in dust formation, whereas the data from Vega and Beta
Pictoris are interpreted as indicating planets producing local
concentrations in their dust disks. The two interpretations are
apparently inconsistent. 4) Kalas asks: "Could the apparent
discrepancy result from 'planet mania', a bias among astronomers
in which every cavity and blob, even a wiggle, in circumstellar
dust disks is taken as evidence for extrasolar planets? Which
dust-planet relation does theory favor?" 5) Kalas says
theoretical arguments are available for both interpretations: one
can show that gravitational perturbations from a planetary object
will eventually create a cavity in a dust disk, but one can also
show that a planet can create a dust wake that looks like a large
blob following the planet in its orbit. 6) Kalas says: "At
present, therefore, we cannot uniquely identify the cause of the
dust blobs and dust cavities near these four stars. Planet-mass
objects are just one of the physically possible ideas."
QY: Paul Kalas
(Science 10 Jul 98 281:182) (Science-Week 31 Jul 98)
3. GIANT PLANETS VS. BROWN DWARFS
Filipe D. Santos (Centro de Fisica da Universidade de Lisboa, PT)
presents a short review of current ideas concerning giant
extrasolar planets and *brown dwarf stars. The author makes the
following points: 1) The recent discoveries of planets orbiting
nearby Sun-like stars have revealed that planetary systems can be
surprisingly diverse. The initial discovery in 1995 of the planet
around the star 51 Pegasi was a surprise because it is apparently
a planet with mass about that of Jupiter (at least 0.44 Jupiter-
mass) and an orbital period of only 4.2 days, which implies that
the planet is 20 times closer to its star than Earth is to the
sun. 2) Seven additional planets around solar-type stars have
since been discovered, with Jupiter-mass values ranging from 0.44
to 6.84. 3) Two critical questions are, a) Where should we set
the dividing line that distinguishes massive planets from brown
dwarfs? and, b) What are the mechanisms leading to the formation
of massive planets and brown dwarfs? 4) Brown dwarfs are expected
to have masses smaller than the hydrogen-burning limit of
approximately 0.075 solar-mass (approximately 75 Jupiter-mass),
but probably larger than the deuterium-burning limit of 0.013
solar-mass (approximately 13 Jupiter-mass). 5) Like the companion
massive planets mentioned, several companion brown dwarfs to
solar-type stars have also been identified. One method of
investigating brown dwarfs involves *astrometric measurements,
and in all cases of brown dwarfs investigated by the astrometric
method, the masses are above or very close to the hydrogen-
burning limit. The extant data thus suggest that the distribution
of mass of brown dwarfs does not extend to masses as small as
giant planets. Also, the new measurements indicate that brown
dwarfs orbiting solar-type stars are very rare. 6) The discovery
of Jupiter-mass planets with orbits very close to their stars
poses a considerable problem, because it is difficult to
understand how such planets could form in place. (Five known
Jupiter-mass planets have orbital radii smaller than the distance
from Mercury to the Sun.) The suggestion has been made that these
planets formed at larger distances and migrated inward, but the
proposed migration mechanisms are not yet empirically
distinguishable. The author concludes: "Clearly the discovery of
planetary systems outside our solar system has opened a Pandora's
box of startling phenomena and new questions."
QY: Filipe D. Santos
(Science 17 Jul 98 281:359) (Science-Week 31 Jul 98)
-------------------
Related Background:
... ... *brown dwarf stars: Brown dwarf stars are formed by the
contraction of a lump of gas with a mass too small for nuclear
reactions to begin in the core. Such a star has a relatively
short-lived luminosity (approximately 100 million years) as the
result of conversion of gravitational energy to radiation. The
surface temperature of a brown dwarf is below 2500 degrees
kelvin. As recently as 1994, brown dwarfs were "theoretical"
stars, with no brown dwarfs considered to be unambiguously
identified.
... ... *astrometric measurements: This method of detection
infers the presence of a companion to a star by measuring the
position of the star as it orbits the center of mass of the
entire system. From the orbital inclination, the real mass of the
companion can be derived.
-------------------
Related Background:
ASTROMETRIC SIGNATURES OF GIANT PLANET FORMATION
The discoveries during the past two years of giant planets
orbiting nearby solar-type stars has raised again the question of
how these planets are formed. Two different models have been
proposed. The gravitational instability model involves formation
of planets directly from the gas in the accretion disk around the
young star. The alternative model is the core-accretion model, in
which rocky cores of about 10 Earth masses form first, with that
followed by hydrodynamical accretion of gas to form the massive
envelopes of the giant planets. ... ... Alan P. Boss (Carnegie
Institution of Washington, US) now proposes, on the basis of
calculations, that these two processes have very different
astrometric signatures, and that it should be observationally
possible to distinguish between them. Planets that form through
gravitational instabilities do so rapidly, so that within just a
few hundred years of the onset of the instability the nascent
planet is making the young stellar object wobble in its orbit.
This can be seen in the youngest stellar objects, with ages as
little as 0.1 million years. If planets form by core accretion,
an observable wobble will not be visible for 10-20 million years.
The author suggests that observations of a suitable ensemble of
optically visible young stellar objects (such as those in the
Taurus molecular cloud) over a period of several decades should
be able to determine which of the two processes is responsible
for the formation of giant planets.
QY: Alan P. Boss <(boss@dtm.ciw.edu>
(Nature 14 May 98 393:141) (Science-Week 5 Jun 98)
-------------------
Related Background:
ON STELLAR PLANETARY SYSTEMS
Extrasolar planetary systems are planetary systems involving one
or more planets in orbit around stars other than our own Sun, and
there is growing evidence that such systems do indeed exist.
The term "Doppler-shift" refers to an observed change in spectrum
frequencies when the source of the spectrum or the observer move
toward or away from each other, and certain perturbations in
Doppler-shifts can be interpreted as indicating the presence of
dark massive objects orbiting stars. The Keck telescopes are a
pair of twin telescopes at the W.M. Keck Observatory on Mauna
Kea, HI US, each with 10 meter mirrors, the pair constructed
1992-1996. The installation is managed by the University of
California (US) and the California Institute of Technology (US).
An optical interferometer is a system involving separate but
linked telescopes whose collection of optical waves is combined
to improve spatial resolution, the resolving power becoming
equivalent to that of a single instrument with an aperture equal
to the largest distance separating the component telescopes.
... ... Marcy and Butler (2 installations, US AU), in a review of
extrasolar planetary systems, note that within the next 5 years
Doppler surveys of nearly a thousand stars will be undertaken,
that the two Keck telescopes will be linked as an optical
interferometer with sufficient precision to detect extrasolar
planets by stellar positional perturbations, and that the US
National and Aeronautics Space Agency's space-borne interfero-
meter, if funded, should be able to obtain actual images of
extrasolar orbiting planets. The authors suggest that by the year
2010 we should have completed the first true census of planets
of nearby stars.
QY: Geoffrey Marcy, San Francisco State Univ. 415-338-2017
(Sky & Telescope March 1998) (Science-Week 30 Jan 98)
-------------------
Related Background:
FURTHER EVIDENCE FOR A PLANET ORBITING STAR 51 PEGASI
Doppler-shift is an observed change in spectrum frequencies when
the source of the spectrum or the observer move either toward or
away from each other. In astronomy, radial velocity is the
velocity of a star along the line of sight of an observer,
determined by measuring the Doppler-shift in the star's spectrum,
and periodic perturbations of an observed stellar Doppler-shift
have in some cases been interpreted as evidence for the existence
of a massive object orbiting the star. A massive planet around
the star 51 Pegasi was reported last year by Mayor and Queloz,
but a subsequent paper by D. Gray challenged their interpretation
of the data on the basis of spectral line-shape oscillations that
would indicate the Doppler-shift perturbations originated in the
stellar surface. ... ... D. Gray (Univ. of Western Ontario, CA)
now reports that recent new monitoring of 51 Pegasi showed an
absence of his previously published spectral line-shape
oscillations that previously called into question the Doppler-
shift data as indicating an orbiting planet. The author suggests
his previous results were noise, and that these new results,
together with other high-precision measurements by other
researchers, indicate the planet hypothesis as the best
explanation for the radial-velocity perturbations. (cf.
contiguous paper by Hatzes et al).
QY: David F. Gray
(Nature 8 Jan 98) (Science-Week 23 Jan 98)
-------------------
Related Background:
A MODEL FOR THE MIGRATION OF MASSIVE PLANETS
Planetesimals are bodies with dimensions of 10^(-3) to 10^(3)
meters that are believed to form planets by a process of
accretion. The term "accretion" refers to an aggregation, an
increase in the mass of a body by the addition of smaller bodies
that collide and adhere to it, provided the relative velocities
are low enough for coalescence. As the mass of the agglomerate
increases, so does the rate of accretion, and this accretion
process is believed to generally occur in the form of a disk. A
stellar accretion disk is a swarm of dust grains that evolve into
planetesimals and then planets. There is now evidence of apparent
massive planets in close orbits around stars, but the formation
of such massive planets in close orbits is unexplained. One
possibility is that these massive planets were formed in a more
distant orbit and then migrated inward. ... ... Murray et al (4
authors at 2 installations, CA) now report a theoretical analysis
of the behavior of planets and planetesimals in a stellar disk.
The calculations predict that gravitational interactions and
collisions between planet and planetesimals, if total
planetesimal surface density exceeds a certain value, may drive
the planet inward a great distance. The authors suggest this
mechanism may explain the presence of Jupiter-mass objects in
small orbits around nearby stars.
QY: N. Murray, Univ. of Toronto, Dept. of Theoretical Astro-
physics, Toronto, ON M5S 3H8 CA.
(Science 2 Jan 98) (Science-Week 16 Jan 98)
-------------------
Related Background:
EVIDENCE OF A PROTOPLANETARY DISK AROUND A YOUNG STAR
The current nebula theory of planet formation proposes that
star-planet systems begin as a contracting cloud of gas and dust
that flattens into a rotating disk. The center of this cloud
becomes the star, and the planets eventually form in the disk of
the nebula. In the inner part of the nebula, the hottest part,
only high density minerals can form solid grains. The outer
regions are cooler, and in those regions icy materials of lower
density are formed. Planets grow from these solid materials,
beginning as dust grains, which grow by condensation and
accretion into planetesimals that range from a few centimeters to
a few kilometers in diameter. These planetesimals settle into a
thin plane around the star and accumulate into larger bodies, the
largest of which grow the fastest and eventually become
protoplanets. Once the star becomes a luminous object, the
remaining nebula is cleared as the star's radiation and the
stellar-wind (powerful streams of charged particles from the
star's surface) push the remnants out of the system. Thus ends
the phase of planet-building. As might be expected, the above
theory is also the current view of the history of our own solar
system. Since the details of disk formation, and the physical
properties of protoplanetary disks, can be modelled by
quantitative theory, the general idea is to investigate such
disks that are apparent around stars to test the theoretical
models. There is no way to do that with our own solar system,
because the protoplanetary disk is long gone. One needs young
stars. ... ... This week Vincent Mannings et al (California
Institute of Technology, CA US) report observations and analysis
of the apparent protoplanetary disk of a star only 6 million
years old, with a mass of 2.3 solar masses. The mass of the disk
is evidently greater than the minimum required to form a
planetary system like our own.
QY: V. Mannings
(Nature 7 Aug 97) (Science-Week 15 Aug 97)
-------------------
Related Background:
A GRAVITATIONAL INSTABILITY MODEL FOR GIANT PLANET FORMATION
Until recently, the consensus theory for the formation of large
planets such as Jupiter was the core accretion model involving
the formation of cores of approximately 10 times Earth mass,
followed by rapid accretion of gas from the primitive solar
nebula. The problem with this model is that the time needed for
accretion (about 1 million years) is of the order of magnitude of
the time during which a young solar-type star's gas dissipates.
The other possible model is one involving a gravitational
instability mechanism in which the solar nebula breaks up into
giant gaseous protoplanets which then contract and collapse to
form giant planets. This model was in the past abandoned because
the extant data concerning the masses of Jupiter and the outer
planets seemed incompatible with the model. But there is now new
data concerning the masses of Jupiter and the outer planets, and
this week Alan P. Boss (Carnegie Institution of Washington, DC
US) reported a revisit to the gravitational instability model,
with computer solutions of the relevant equations of
hydrodynamics coupled with the Poisson equation in a spherical
coordinate system, such solutions providing evidence that the
formation of giant protoplanets in a gaseous nebula disk can
indeed occur. The old gravitational instability model has
therefore apparently been revived.
QY: Alan P. Boss
(Science 20 Jun 97) (Science-Week 26 Jun 97)
-------------------
Related Background:
GIANT PLANET EVIDENCE CONFOUNDS SOLAR SYSTEM THEORISTS
Until recently, speculations and theories about planets orbiting
other stars than our sun have depended on our own solar system as
the guiding model. But during the past two years, astronomers
have been able to gather information about nine such planets, and
the evidence is apparently not in harmony with expectations. The
three variables that are evidently making trouble for theorists
are planet size, proximity to the parent star, and orbital
eccentricity. For example, the planet orbiting the star 51 Pegasi
is large enough to have about half the mass of Jupiter, but seems
to be orbiting the star at a radius of one-sixth the radius of
Mercury's to our sun. This is a puzzle, although there appears to
be still controversy about whether this planet is actually a
planet. Others of the discovered planets are apparently in highly
eccentric and unexplained orbits. So the theorists are busy
revising models for planet formation, establishment of orbits,
planetary orbital drift, and so on. The major difficulty is that
there are no direct observations of these discovered planets --
their existence is proposed to explain perturbations in the
behavior of their parent stars. Stephen Lubow of the Space
Telescope Science Institute (Baltimore MD US) says of the recent
observations: "It's been a revolution."
(Science 30 May 97) (Science-Week 5 Jun 97)
4. ON FUSION RESEARCH AND THE Z MACHINE
In general, the idea of nuclear fusion is to combine the nuclei
of two atoms, the result an entity of lower mass than the sum of
the masses of the original atoms, the mass difference released as
energy. Since the energy released is described by E = mc^(2),
where m is the mass converted and c is the velocity of light in a
vacuum, the energy released for a relatively small mass can be
enormous due to the large numerical value of c. The focus of
nuclear fusion engineering research has been on the apparent
simplest fusion, that of the various forms of heavy hydrogen. The
nucleus of deuterium consists of one proton and one neutron, and
one thrust of fusion research is to make two deuterium nuclei
combine. This fusion will produce either a nucleus of helium-3
(two protons and one neutron), which leaves a free neutron, or
alternatively, the fusion will produce tritium (hydrogen-3: two
neutrons and a proton), and leave a free proton spare. In both
cases, several million volts of energy are released from the
nucleus. Another considered approach is the fusion of the two
forms of heavy hydrogen, deuterium and tritium, the essential
idea the same: release of an enormous amount of energy. With a
working fusion process, a thimbleful of liquid deuterium fuel
could produce as much energy as 20 tons of coal. At the moment,
this is the Holy Grail of fuel energy physics, but up to the
present, the only successful method for igniting a man-made
fusion reaction has been that used in exploding a hydrogen bomb.
... ... Gerold Yonas (Sandia National Laboratories, US) reviews
the past several decades of fusion research, and in particular
the new possibilities associated with what is called the "Z
machine". The author makes the following points: 1) Heavy
hydrogen fusion as a practical source of cheap energy has been
pursued for almost 50 years, but the refrain is still that
ignition is "10 years away". Nevertheless, at the moment,
success in generating powerful x-ray pulses using the Z-machine
has restored belief that triggering fusion in the laboratory may
indeed be feasible in a decade. 2) One significant aspect is
that the compression that produces the fusion of nuclei must be
done with almost perfect symmetry so that the hydrogen is
squeezed uniformly to high density. 3) Another important
consideration is that present simulations indicate that almost 5
x 10^(14) watts (500 terawatts) and 2 x 10^(6) joules of
radiation at a temperature of 3 million degrees for 4
nanoseconds are required to ignite the fuel. 4) The author
states that his laboratory will be able to achieve high-yield
fusion with radiation pulses of 1000 terawatts, and that they
have already come within a factor of three of that goal. 5) The
basis of the Z-machine is the Z-pinch: passage of a strong
electric current through deuterium gas both ionizes the gas and
generates a magnetic field that "pinches" the resulting plasma
(the ionized gas) to high temperature and density along the
current path. (The current path is conventionally labelled the
"z" axis, and hence the name Z-pinch.) 6) Although the original
Z-pinch technique proved unable to produce uniform compression
of the plasma, the x-rays generated have energies up to 1000
electronvolts, and the essence of the Z-machine is to use this
energy to ignite fusion: "In the past three years we have shown
that by combining the efficiency and low cost of fast pulsed
power with the simplicity and efficiency of the Z-pinch as a
radiation source, we should reach ignition by using sub-kilo-
electronvolt x-rays to compress a fusion fuel pellet." The
author concludes: "If we can get started soon on design and
construction of the *next big step, we really think we can do
the job in 10 years."
QY: Gerold Yonas, Sandia National Laboratories 505-844-8066.
(Scientific American August 1998) (Science-Week 31 Jul 98)
-------------------
Related Background:
... ... *next big step: The next big step is the so-called "X-1
machine", the proposed successor to the Z-machine. The X-1
machine is expected to provide 16 megajoules of radiation. The
author predicts the cost of the X-1 machine will be in the
neighborhood of US$400 million.
5. ON COMPUTING WITH DNA
In 1936, the mathematician Alan M. Turing (1912-1954) proposed
consideration of an abstract computer that subsequently came to
be known as a "Turing machine". Essentially, the simplest Turing
machine system consists of a movable input tape, a black box (the
Turing machine) that reads the tape according to an internal
algorithm, and an output tape that records the output of the
black box. The machine originally considered by Turing was a bit
more complex, with a single input/output tape demarcated into
discrete small sections, and the machine capable of being in any
one of a set of states (determined by the algorithm or "Rule
Set") according to which section of the tape the machine happened
to be reading, and the output capable of moving the tape backward
or forward. As a mathematician, Turing's interest was to
determine the universe of problems capable of being solved by
such a machine, but to a number of mathematically inclined
biologists the Turing machine in its simplest form has been for
many decades an intriguing model for certain computational
processes in the nervous system, and more recently, in molecular
biology, the Turing machine has been recognized as an analog of
the behavior of nucleic acid polymerases such as DNA polymerase
and RNA polymerase, which sequentially synthesize an output
polymer (output tape) according to the sequential reading of the
individual units of an input polymer (input tape).
... ... Leonard M. Adleman (University of Southern California,
US) presents an essay on a computing ensemble involving DNA, the
ensemble based on the author's recognition of the Turing machine
as an analog of DNA polymerase, and the ensemble applied to the
solution of a mathematical problem known as the "Hamiltonian Path
Problem". As a mathematician and computer scientist, Adleman's
objective is the demonstration that his DNA ensemble can perform
as a powerful computer and solve a posed mathematical problem.
The author considers the following as the tools of a potential
DNA computing system: *Watson-Crick pairing, *polymerases,
*ligases, *nucleases, *gel electrophoresis, DNA synthesis, and
the *polymerase chain reaction. The author presents the
Hamiltonian Path Problem as follows: Given a graph with directed
edges and a specified start vertex and end vertex, one says there
is a Hamiltonian path if and only if there is a path that starts
at the start vertex, ends at the end vertex, and passes through
each remaining vertex exactly once. The Hamiltonian Path Problem
is to decide for any given graph with specified start and end
vertices whether a Hamiltonian path exists or not. The specific
problem chosen by the author involves a 7-vertex graph. Each
vertex is identified by a specific assigned sequence of nucleic
acid bases, and using the repertoire of biochemical tools
indicated above (and an added auxiliary separation technique),
the author demonstrates that this particular problem is easily
solved. Considering molecular computers, the author points out
their advantages: 1) The possibility of extremely dense
information storage. "For example, one gram of DNA, which when
dry would occupy a volume of approximately one cubic centimeter,
can store as much information as approximately 10^(9) CDs." 2)
The possibility for enormous parallelism. In the author's
problem, approximately 10^(14) connection paths were
simultaneously concatenated in about 1 second. 3) Extraordinary
energy efficiency. In principle, 1 joule is sufficient for
approximately 2 x 10^(19) DNA ligation operations. The author
suggests that his experiment "can be viewed as a manifestation of
an emerging new area of science made possible by our rapidly
developing ability to control the molecular world."
QY: Leonard M. Adleman, Univ. of Southern California 213-740-2311
(Scientific American August 1998) (Science-Week 31 Jul 98)
-------------------
Related Background:
... ... *Watson-Crick pairing: Also known as complementary base
pairing. This refers to the specific chemical affinities between
specific base pairs in a nucleic acid: adenine always pairs with
thymine, and guanine always pairs with cytosine. In pairing
between DNA and RNA, the uracil of RNA always pairs with adenine.
Complementary base pairing is not only responsible for the DNA
double helix, but it is also essential for various in vitro
techniques such as PCR (*polymerase chain reaction).
... ... *polymerases: Refers to any enzyme that directs the
synthesis of a polymer by linking individual monomers. Examples
in biological systems are DNA polymerase and RNA polymerase.
... ... *ligases: Ligases are enzymes that catalyze the stitching
together of polymer fragments. DNA ligase, for example,
catalyzes
phosphodiester bond formation between two DNA fragments, and this
enzyme is involved in normal DNA replication, repair of damaged
chromosomes, and various in vitro techniques in genetic
engineering that involve linking DNA fragments.
... ... *nucleases: Refers to any enzyme that acts on nucleic
acids, e.g., DNase, RNase, endonuclease, etc.
... ... *gel electrophoresis: In general, electrophoresis is a
laboratory technique used to separate macromolecules on the basis
of electric charge and size, the technique involving application
of an electric field to a population of macromolecules
dispersing
according to their electric mobilities. In gel electrophoresis,
the porous medium through which the macromolecules move is a gel.
... ... *polymerase chain reaction (PCR): A technique for
isolating and amplifying any specifically desired DNA sequence.
The reaction is facilitated by a heat-stable DNA polymerase
(e.g., Taq, which is obtained from a thermophilic bacterium) that
can withstand the many cycles of heating and cooling involved in
the technique. PCR is considered by many molecular biologists to
be the most important technical advance in molecular biology in
the second half of the 20th century. The inventor of the
technique, Kary Mullis, received the Nobel Prize in Chemistry in
1993 for his discovery.
6. ON THE CHEMISTRY AND BIOLOGY OF THE OCEANS
The combination of vast areas of liquid water on its surface
together with a high concentration of free molecular oxygen in
its atmosphere is unique to Earth in this solar system.
Calculations based on *ultraviolet absorption cross sections
indicate that whereas direct photolysis of water could have
produced small amounts of O(sub2), almost all of the gas was
produced by biological systems through the photobiologically
catalyzed oxidation of the liquid. ... ... Falkowski et al (3
authors at 3 installations, US DE) review the controls and
feedbacks between oceanic *phytoplankton and geochemical
processes with an emphasis on factors that cause a deviation from
the steady state. The authors make the following points: 1)
Changes in oceanic primary production, linked to changes in the
network of global biogeochemical cycles, have profoundly
influenced the geochemistry of Earth for over 3 billion years. 2)
In the contemporary ocean, photosynthetic *carbon fixation by
marine phytoplankton leads to the formation of approximately 45
gigatons of organic carbon per year, of which 16 gigatons are
exported to the ocean interior. 3) Changes in the magnitude of
total and export production can strongly influence atmospheric
CO(sub2) levels (and hence climate) on geological time scales, as
well as set upper bounds for sustainable fisheries harvest. 4)
Because the average turnover time of phytoplankton carbon in the
ocean is on the order of a week or less, total and export
production are extremely sensitive to external forcing, and
consequently are seldom in steady state. 5) Elucidating the
biogeochemical controls and feedbacks on primary production is
essential to understanding how oceanic biota responded to and
affected natural climate variability in the geological past, and
to understanding how oceanic biota will respond in the coming
decades to changes influenced by human activities.
QY: Paul G. Falkowski
(Science 10 Jul 98 281:200) (Science-Week 31 Jul 98)
-------------------
Related Background:
... ... *ultraviolet absorption cross sections: The ratios of the
amount of energy removed from incident UV by absorption to the
total energy of incident UV. In other words, in this context, a
measure of how much energy is (was) actually available for direct
photolysis of liquid water.
... ... *phytoplankton: Also called photoplankton. Small, usually
microscopic, aquatic plants capable of photosynthesis; e.g.,
unicellular algae. Phytoplankton and plankton are not equivalent.
The term "plankton" is a general designation for various
drifting
microscopic aquatic organisms in the upper regions of the oceans,
both photosynthetic and non-photosynthetic.
... ... *carbon fixation: Refers to the process of converting the
carbon in a substance into a form usable by an organism. For
example, the conversion of the carbon in CO(sub2) into organic
carbon (the carbon in organic compounds).
7. MARINE ORGANISMS: ACQUISITION AND USE OF TRANSITION METAL IONS
Metalloproteins comprise a third to a half of all known proteins.
Metals function in catalysis, play structural roles, and activate
biochemical processes. Many essential life processes, including
photosynthesis, respiration, and nitrogen fixation, involve
multi-electron transformations, and the essential steps in all of
these processes are catalyzed by metalloenzymes that contain iron
and other transition metal ions that can exist in multiple
oxidation states.... ... Alison Butler (University of California
Santa Barbara, US) reviews some of the mechanisms by which marine
organisms acquire iron and use other essential metal ions, and
the author makes the following points: 1) Molybdenum is the most
abundant transition metal ion in surface seawater at a
concentration of 100 nM, followed by vanadium at 20 to 35 nM. In
contrast, iron levels in surface seawater are extremely low: 0.02
to 1 nM. 2) Despite its relative scarcity, iron is essential to
marine organisms, and iron levels represent one of the key
limitations in marine ecosystems. 3) Relatively little is known
about marine bioinorganic chemistry, but recent studies are
beginning to unravel some of the mysteries. 4) Marine
microorganisms acquire iron through novel *siderophores, new
siderophore-mediated processes, and other processes. However, in
times of severe iron stress, phytoplankton substitute flavodoxin
for ferrodoxin, replacing the iron-sulfur cluster with an organic
cofactor. The carbonic anhydrases of *diatoms, which have no
homology to other known carbonic anhydrases, are particularly apt
to substitute Co for Zn in the active site, and some even contain
Cd. 5) Iron is arguably the most important transition metal in
the ocean, precisely because of its relatively low abundance. 6)
In addition to phytoplankton, *heterotrophic marine bacteria have
been shown to be limited by the low level of iron in the ocean.
7) In seawater, many of the first-row transition metal ions are
partially or fully complexed by as yet undefined organic ligands.
8) In contrast to the deficit of iron in surface seawater,
vanadium is abundant, and the bioorganic chemistry of vanadium is
diverse. Most marine *tunicates acquire vanadium in large
quantities, but the functional significance of the sequestered
vanadium has eluded researchers since its discovery in seawater
near the turn of the century. The author suggests that detailed
studies into the bioinorganic chemistry of transition metal ions,
together with increased knowledge of the concentration and
speciation of these ions in the oceans, are necessary for a
complete picture of global element cycles involving both
terrestrial and oceanic components.
QY: Alison Butler, Univ. of California Santa Barbara 805-893-8000
(Science 10 Jul 98 281:207) (Science-Week 31 Jul 98)
-------------------
Related Background:
... ... *siderophores: Molecular receptors that bind and
transport iron.
... ... *diatoms: Also called bacillariophytes. Microscopic
unicellular eukaryotic algae; differentiated into approximately
10,000 different species.
... ... *heterotrophic: (syn: organotrophic) Refers to organisms
dependent on external sources of organic compounds as a means of
obtaining energy and/or materials.
... ... *tunicates: Also called urochordates. Subphylum of the
chordates, comprising sea squirts and similar forms.
8. EVOLUTION: ADAPTIVE RADIATION IN A HETEROGENEOUS ENVIRONMENT
The term "adaptive radiation" refers to the rapid evolution of
one or a few forms into many different species that occupy
different habitats within a new geographical area. The marsupial
radiation in Australia illustrates the process: when marsupials
were protected from competition with placental mammals by the
isolation of the continent, the process led to an entire array of
species with widely divergent functions, from herbivores to
carnivores. ... ... Rainey and Travisano (University of Oxford,
UK) report an investigation of the role of ecological opportunity
and competition in driving the genetic diversification associated
with adaptive radiation. The form studied was the common aerobic
bacterium Pseudomonas fluorescens, which evolves rapidly under
novel environmental conditions to generate a large repertoire of
mutants. As bacteria reproduce asexually, identical populations
can be established from a single genotype, and all subsequent
variation is therefore generated de novo by mutation. The authors
report that when provided with ecological opportunity, identical
populations of P. fluorescens diversify morphologically, but when
ecological opportunity is restricted, there is no such
divergence. In spatially structured environments, the evolution
of variant forms follows a predictable sequence, with competition
among the newly evolved niche-specialists apparently maintaining
this variation. The authors suggest their results demonstrate
that the elementary processes of mutation and selection alone are
sufficient to promote rapid proliferation of new designs, and
that their results support the theory that trade-offs in
competitive ability drive adaptive radiation.
QY: Paul B. Rainey
(Nature 2 Jul 98 394:69) (Science-Week 31 Jul 98)
9. ESTROGEN: BOTH A MALE AND FEMALE HORMONE
Hormones are signaling molecules secreted into the blood stream
by endocrine cells and acting on target cells that possess
receptors for the hormone. Estrogen is a collective term for the
female hormones, the most powerful of which is *estradiol. They
control female secondary sexual characteristics, and prepare and
maintain the uterine lining. Estrogen affects the growth,
differentiation, and function of peripheral tissues of the
reproductive system, including the mammary gland, uterus, vagina,
and ovary. Estrogens also play an important role in bone
maintenance and exert cardioprotective effects. In the brain,
estrogens modulate physiological parameters important for
regulating procreation, including reproductive behavior,
*gonadotropin production and release from the pituitary, and
mood. ... ... Kuiper et al (3 installations, SE) review recent
research on estrogen as a hormone, and the authors make the
following points: 1) As the so-called female sex hormone,
estrogen is best known for its critical role in influencing
female secondary sexual characteristics, reproductive cycle,
fertility, and maintenance of pregnancy. Less well known are the
important actions of estrogen in male tissues such as the
prostate, testis, and *epididymis. 2) Estrogens are essential for
the normal development of bone tissue in the male, in addition to
their well-known role in female bone. 3) The recent unexpected
discovery of a second estrogen receptor protein (*ER-beta) has
advanced understanding of the mechanisms underlying estrogen
signaling. The authors suggest the challenge is to use this
knowledge for the development of the next generation of drugs
targeted to the estrogen receptor.
QY: George G.J.M Kuiper, Karolinska Institute Huddinge, SE.
(Science & Medicine Jul/Aug 1998) (Science-Week 31 Jul 98)
-------------------
Related Background:
... ... *estradiol: 1,3,5(10)-estratriene-3,17beta-diol.
C(sub18)H(sub24)O(sub2). This is the natural hormone -- present
in pure form in the urine of pregnant mares and in the ovaries of
pigs.
... ... *gonadotropin: (gonadotrophin, gonadotrophic hormone)
Refers to a group of hormones capable of promoting growth and
function of the gonads.
... ... *epididymis: An elongated structure connected to the
surface of the testis, it stores and matures sperm cells.
... ... *ER-beta: The first discovered estrogen receptor (ER) has
now been renamed ER-alpha. Both receptors apparently consist of
several functional domains: a transcription activation domain, a
central DNA-binding domain, an estrogen-binding domain. The
second estrogen receptor was first cloned in 1995.
-------------------
Related Background:
A ROLE FOR ESTROGENS IN THE MALE REPRODUCTIVE SYSTEM
Estrogen is a collective term for the female hormones, the most
powerful of which is estradiol. These hormones control female
secondary sexual characteristics, and prepare and maintain the
uterine lining. There are a number of environmental contaminants
that have weak estrogenic properties, the most noted being the
polychlorinated biphenyls (PCBs), the insecticide DDT, and its
breakdown product DDE. Both PCBs and DDE exist in the global
ecosystem in fish, wildlife, human tissue, blood, and milk, and
it has been suggested that these organochlorine "xenoestrogens"
and related compounds contribute to the increased incidence of
breast cancer in women, decreases in sperm counts in men, and
neurodevelopmental deficits in children. Luminal fluid refers to
tubular fluid, and the epididymis is one of a pair of long
tightly coiled tubes that in the male carry sperm from the
testicles to the tip of the penis. Hess et al (7 authors at 3
installations, US) report evidence for a physiological role of
estrogen in male reproductive organs, their data indicating that
estrogen regulates the reabsorption of luminal fluid in the head
of the epididymis, and that disruption of this function causes a
dilution of sperm with a resultant infertility. The authors
suggest their findings raise further concern over the potential
direct effects of environmental estrogens on male reproduction
and reported declines in human sperm counts.
QY: Rex A. Hess
(Nature 4 Dec 97) (Science-Week 26 Dec 97)
-------------------
Related Background:
STRUCTURAL DIFFERENCES OF ANTI-ESTROGENS
Tamoxifen, the trans isomer of a substituted triphenylethylene,
is a non-steroidal anti-estrogen that has been widely used for
the treatment of breast cancer and also for the prevention of
breast cancer in women considered at risk because of apparent
cellular changes in breast tissue. One of the adverse effects of
tamoxifen is that it can produce a loss of bone density, and such
loss can lead to debilitating osteoporosis. Raloxifene, a non-
steroidal benzothiophene, is stereochemically similar to
tamoxifen, also has an apparent high affinity for the estrogen
receptor, also acts as an anti-estrogen and weak anti-tumor
agent, but unlike tamoxifen it does not produce a loss of bone
density. In addition, Raloxifene has the positive effect of
lowering serum cholesterol levels. Grese et al (Eli Lilly and
Co., US) report that structural differences between tamoxifen and
raloxifene are responsible for the differences in the anti-
estrogenic effect of these compounds. The degree of flexibility
of the raloxifene side chain is apparently critical, with a rigid
side-chain necessary for the unique biological profile of this
compound.
QY: Timothy A. Grese, Eli Lilly and Co. 212-854-1754
(Proc. Natl. Acad. Sci. US 94:14105 1997)
(Science-Week 26 Dec 97)
-------------------
Related Background:
EVIDENCE FOR DIFFERING ROLES OF THE TWO ESTROGEN RECEPTORS
Estrogen is a collective term for a class of steroid hormones,
the most important of which is estradiol, the strongest naturally
occurring estrogen. The estrogens are produced in the ovaries,
and in small amounts in the testes and adrenal glands, and in
women they control the development of secondary sexual character-
istics, regulate the menstrual cycle, and prepare and maintain
the uterine lining for pregnancy. The estrogens have also been
implicated in various cancers, particularly breast cancer. As a
lipid soluble steroid, estrogen easily passes through the cell
membrane. Like all hormones, estrogen acts as a ligand and binds
to a receptor, a protein that has a specific docking site for the
estrogen molecule. For many years it was thought that estrogen
binds to a receptor in the cytoplasm, but it is now known that
the estrogen receptor is in the cell nucleus. Understanding the
exact nature of the receptor is of some importance not only to
our understanding the action of this hormone, but also to our
understanding the pharmacological mechanisms that might be used
to block estrogen action when it would be clinically useful. In
this latter area, there has been much confusion, since certain
drugs like tamoxifen do block estrogen in some tissues, but they
apparently act otherwise in other tissues. Last year the first
piece of the solution to the puzzle came into place when the
Gustafson group in Sweden reported the existence of two different
receptors for estrogen. Now Kolja Paech et al (University of
California San Francisco, US; Karolinska Institute, SE) report an
analysis of ligand activation of the two estrogen receptors
ER(alpha) and ER(beta), and apparently these estrogen receptors
are quite different from each other, can produce different
consequences, even act antagonistically, and the differences may
be the beginning of an explanation for the puzzling experimental
and clinical results that have been obtained with various
estrogen analogs and blockers. The estrogen receptor is at the
moment the only known member of the steroidal subfamily of
nuclear receptors to have different subtypes. These observations
are undoubtedly important. QY: Thomas S. Scanlon, Dept. Cell.
Mol. Pharmacol., Univ. Calif., San Francisco CA 94143-0446
(Science 5 Sep 97) (Science-Week 19 Sep 97)
-------------------
Related Background:
POSTMENOPAUSAL ESTROGEN THERAPY BENEFITS HYPERCHOLESTEROLEMIA
Coronary heart disease is the leading cause of death among women
in industrialized countries, and high serum levels of high-
density lipoprotein have been shown to be protective. It is known
that postmenopausal estrogen therapy has favorable effects on
serum lipoproteins in women with normal lipid levels, and now
Giselle M. Darling et al (Jean Hailes Foundation, AU; Monash
University, AU) report that in postmenopausal women with
hypercholesterolemia, therapy with estrogen plus progestin has
beneficial effects on lipoprotein levels, and that hormone
therapy may be an effective alternative to treatment of
hypercholesterolemia with drugs such as simvastatin.
QY: G. M. Darling, Jean Hailes Foundation, 291 Clayton Rd.,
Clayton, Victoria 3168, AU.
(New England J. Med. 28 Aug 97) (Science-Week 29 Aug 97)
-------------------
Related Background:
RETRACTION OF IMPORTANT ESTROGENIC PESTICIDE SYNERGIES PAPER
... In its action, each steroid hormone crosses the cell membrane
and binds to a specific receptor in the cytoplasm or nucleus of
the cell, and the receptor-hormone complex then causes either
stimulation or inhibition of the activity of specific genes. So
these are substances of prime significance in the workings of the
cell, and of great importance in clinical medicine. There is
evidence that a number of pesticides (endosulfan, dieldrin,
toxaphene, chlordane) bind to the human estrogen receptor, and
from that there have been suggestions that these pesticides may
be implicated in the incidence of human breast cancer in
geographical areas with high pesticide pollution. In 1996, S. F.
Arnold et al reported a study of estrogenic activity of these
chemicals, both singly and in combination, on yeast cells
engineered to contain the gene for the human estrogen receptor.
The substances in combination, as opposed to singly, were found
to be demonstrably effective in binding to and switching on the
estrogen receptor in yeast cells. This study, as one would
expect, generated considerable discussion among environmentalist
groups and government health policy people everywhere in the
world. The senior author of the paper by S. F. Arnold et al was
John A. McLachlan (Tulane Univ., US). This week, in a letter to
the journal *Science*, McLachlan has retracted the paper, stating
that his laboratory and other laboratories have been unable to
replicate the results, and also stating that the five other
authors of the original paper concur in the retraction.
QY: J. McLachlan, Tulane Univ. (504) 865-5731.
(Science 25 Jul 97) (Science-Week 1 Aug 97)
10. ON PHOTODYNAMIC THERAPY IN CANCER
David Kessel (Wayne State University, US), in a review of the
biochemical basis of photodynamic therapy, makes the following
points: 1) The first report of the phototoxic effects of dyes on
living cells was by Raab in 1900, who observed that paramecia
exposed to *eosin in a well-lighted room tended to stop moving, a
sign of death in that organism. More recently, in the 1960s,
Schwartz and Lipson reported that systemic administration of a
crude preparation of *hematoporphyrin to cancer patients
scheduled for surgery resulted in the appearance of red
fluorescence at thoracic tumor sites when these were exposed to
ultraviolet light. 2) When a porphyrin molecule absorbs light, it
either emits a photon at a longer wavelength or it transforms an
oxygen molecule to an activated state. 3) Suitably prepared
porphyrin derivatives tend to concentrate in tissues where
metabolic activity is high, including tumors and tumor blood
vessels. 4) The fluorescence effect permits endoscopic
localization of tumors, and the oxidizing effect has the
potential to damage and kill cancer cells. These are the
principles of photodynamic therapy, which is being used with
success in the treatment of tumors in the esophagus, lung, and
bladder, and which may find applications outside the field of
oncology as well. 5) The future of photodynamic therapy has
several apparent paths. One path is the development of safe,
effective, and readily formulated agents that are rapidly cleared
from the skin, to minimize the need for protection of patients
from sunlight after therapy. Another path is the development and
use of radiation sensitizers that absorb light in the far red and
near-infrared to promote photodamage to pigmented or deep
tumors.
QY: David Kessel, Wayne State University 313-577-3577.
(Science & Medicine Jul/Aug 1998) (Science-Week 31 Jul 98)
-------------------
Related Background:
... ... *eosin: (eosine, bromoeosin) A red fluorescent dye. Its
sodium or potassium salt is used in organic pigments, biological
stains, and in pharmaceuticals. C(sub20)H(sub8)O(sub5)Br(sub4).
... ... *hematoporphyrin: The porphyrins are cyclic organic
molecules that form the basis for many important biochemical
compounds. They form complexes with metal ions, iron in the case
of hemoglobin and magnesium in the case of chlorophylls, and this
property is essential to their function. Hematoporphyrin
C(sub34)H(sub38)N(sub4)O(sub6) is obtained from heme, the
*prosthetic group of hemoglobin.
... ... *prosthetic group: The non-protein group of a *conjugated
protein. It may be another organic molecule or an inorganic
metal
ion.
... ... *conjugated protein: A protein to which a non-protein
component (prosthetic group) is attached. This should not be
confused with "conjugated" as a term referring to alternating
single and double bonds in a chemical structure.
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