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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.
March 30, 2001 -- Vol. 5 Number 13
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-- Emile Duclaux (1840-1904)
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Section 1
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Contents of this Issue (Full reports in Section 2):
1. ASTROBIOLOGY: SELF-ASSEMBLY OF AMPHIPHILIC MOLECULES IN A
MODEL OF INTERSTELLAR/PRECOMETARY ICES
Researchers report the laboratory simulation of an interstellar
ice mixture that upon photolysis produces amphiphilic vesicle-
forming compounds similar to those found in primitive meteorites
such as the *Murchison carbonaceous chondrite. Starting from a
simple but astrophysically relevant ice mixture (water, methanol,
ammonia, and carbon monoxide), a complex mixture of compounds,
including fluorescent molecules and molecules with observed
amphiphile behavior, is generated on low-temperature photolysis.
The authors suggest that the ready formation of these insoluble
compounds from photolyzed ices comprised of simple molecules
indicates not only that this process might be the source of their
origin in meteorites, but that the delivery of such compounds by
comets, meteorites, and interplanetary dust particles during the
heavy bombardment period of early Earth may have played an
influential role in the origin of terrestrial life.
(J.P. Dworkin et al: Proc. Natl. Acad. Sci. US 30 Jan 01 98:815)
2. EXPERIMENTAL PHYSICS: ON THE CASIMIR FORCE IN
MICROELECTROMECHANICAL SYSTEMS
The "Casimir effect" is in general a quantum force that pulls two
parallel electrically conducting plates, placed a short distance
apart in a vacuum, towards one another. The basis of the force is
that the zero-point energy between the plates is reduced compared
to the zero-point energy outside the plates. At present, the
smallest separations between surfaces of micromachined components
are typically on the order of microns, and the operation of
microelectromechanical systems has been well described by
classical mechanics. But as further miniaturization occurs,
quantum effects may become significant in device design and
operation. Researchers now report a demonstration of the Casimir
effect in microelectromechanical systems using a micromachined
torsional device. Attraction between a polysilicon plate and a
spherical metallic surface results in a torque that rotates the
plate about two thin torsional rods. The dependence of the
rotation angle on the separation between the surfaces is in
agreement with calculations of the Casimir force.
(H.B. Chan et al: Science 9 Mar 01 291:1941)
3. HISTORY OF CHEMISTRY: ACIDS AND BASES
The 20th century brought to acid-base chemistry the theories of
Johannes N. Bronsted (1866-1951), Thomas M. Lowry (1874-1936),
and Gilbert N. Lewis (1875-1946), all of whom published their
theories in 1923, with Bronsted and Lowry working independently
but publishing essentially identical ideas. Both the Bronsted-
Lowry theory and the Lewis theory of acids and bases refer to
protons and electrons, thus making use of atomic structure and
producing an important conceptual change in the minds of
chemists. In recent years progress in chemistry has not inspired
new theoretical layers in the study of acids and bases. Acids and
bases are not a spearhead in modern chemical research. One
"acid", however, that is undergoing thorough investigation these
days is deoxyribonucleic acid (DNA). It is ironic that the first
thing that students learn about this acid is that it consists of
four bases.
(W. de Vos and A. Pilot: J. Chem. Educ. 4 Apr 01 78:494)
4. PLANT BIOLOGY: ON THE ARABIDOPSIS GENOME
The recent explosion of interest in Arabidopsis, a weed of
absolutely no economic importance, is unprecedented in the
history of plant biology and provides plant biology with its
first widely adopted model system. Arabidopsis has a rapid life
cycle and has been used in genetic studies for decades, but it
was the discovery that Arabidopsis has a small genome with very
little repeated DNA that provoked its recent popularity. The
widespread adoption of Arabidopsis as an experimental system has
resulted in rapid progress in many areas and has produced the
international effort that led to the sequencing of the
Arabidopsis genome. With 25,000 mostly uncharacterized genes, the
Arabidopsis genome will keep plant biologists busy for a long
time. With a host of interesting problems to study, an unrivalled
set of molecular genetic tools, and now a sequenced genome, for
plant biologists the fun has just begun.
(R. Scott Poethig: Genome Research March 2001 11:313)
5. EVOLUTIONARY BIOLOGY: ON THE ORIGIN OF PLANT LEAVES
The 40-million-year gap between the earliest fossil evidence of
vascular plants and the advent of leaves (megaphylls) is
puzzling. Megaphylls are ubiquitous today, and their
photosynthetic proficiency makes their evolution seem inevitable.
The fossil record indicates that megaphylls evolved from the
photosynthetic branching systems of early vascular plants that
became flattened and later webbed to produce a broad lamina in
several groups by 362.5 million years ago. Researchers now
propose a novel explanation for the long delay in the advent of
leaves. Using a model based on biophysical principles applied to
living plants, and involving details of water use and heat and
gas exchange and anatomical and environmental data from the
fossil record, it is concluded that leaves with a broad lamina
evolved in response to a massive drop in atmospheric carbon
dioxide during the Devonian period (408.5 to 362.5 million years
ago). (Paul Kenrick: Nature 15 Mar 01 410:309)
6. POPULATION GENETICS: ON DISPERSAL OF HUMAN POPULATIONS
From the early work of population geneticists who sought to
discern patterns of historical population movements from the
blood groups, blood serum proteins, and enzymes of a few hundred
donors, we have progressed to megabase sequence comparison from
tens of thousands of individuals with increasingly fine spatial
as well as temporal resolution. Highly informative gene sites,
enzymatically amplified from saliva or hair samples collected
under field conditions, have freed us from a reliance on
population inferences based on acculturated or urbanized groups.
What characterizes all the studies is a shift from the discovery
of individual molecular characters to a focus on the population
carrying them. It should continue to humble us that the
technology for detecting variations and extracting once-lost
secrets of population histories is far in advance of the ethical
problems posed by the possession of such knowledge.
(Rebecca L. Cann: Science 2 Mar 01 291:1742)
7. IN FOCUS: ON GIANT MAMMALS AND ROTTING FRUITS
8. FROM THE SCIENCEWEEK ARCHIVE:
MATERIALS SCIENCE: ON EILHARDT MITSCHERLICH
9. ON THE GEOLOGICAL TIME-SCALE: A SIMPLIFICATION
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Section 2
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1. ASTROBIOLOGY: SELF-ASSEMBLY OF AMPHIPHILIC MOLECULES IN A
MODEL OF INTERSTELLAR/PRECOMETARY ICES
In general, the term "interstellar medium" refers to the
matter contained in the region between the stars of our Galaxy,
this matter constituting approximately 10 percent of the Galactic
mass, and consisting of gas and interstellar dust. The
interstellar medium is not uniformly distributed through space,
but contains regions of high-density and low-density clouds. It
is the interstellar medium that provides the material from which
new stars are born.
In this context, the term "molecular cloud" refers to a cool
and dense region of interstellar matter within which atoms tend
to be combined into molecules. Such clouds are composed
principally of molecular hydrogen, with between 300 to 2000
molecules per cubic centimeter. Such clouds also contain an
admixture of "cosmic dust" comprising approximately 1 percent of
the mass, with gas temperatures between 10 and 20 degrees kelvin.
In astrophysics, the term "dust" refers to various entities:
a) interplanetary and cometary dust are found in the Solar
System; b) circumstellar dust is found around stars; c)
interstellar dust is found between stars. Individual dust
particles are usually called "dust grains" and range in size from
approximately 10 nanometers up to the micron range (with an
average size about the size of particles in cigarette smoke).
Interstellar dust extinguishes and reddens starlight, can be
detected by its absorption and emission of infrared radiation,
and can be detected by its polarizing effect on starlight. The
exact composition of interstellar dust is uncertain, but infrared
absorption measurements indicate that a significant fraction of
the material is organic. In general, interstellar dust is
believed to be carbon, iron, and silicates mixed with or coated
with frozen water.
"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.
The permanent solid portion of a comet (its "nucleus") is
believed to be a kilometer-sized solid mixture of dust and ice
("dirty snowball"), a model first suggest by Fred L. Whipple in
1951.
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. Larger aggregates may form vesicles
with diameters in the micron range. Since biological membranes
consist largely of amphiphile lipids, many researchers believe
prebiotic chemical systems may have involved amphiphile vesicles.
... ... J.P. Dworkin et al (4 authors at 3 installations, US)
present a report of self-assembling amphiphilic molecules in a
laboratory model of interstellar dust and cometary ice, the
authors making the following points:
1) The authors point out that interstellar gas and dust are
believed to constitute the primary material from which the Solar
System formed. Near the end of the hot early phase of star and
planet formation, less refractory volatile materials were
transported into the inner Solar System as comets and
interplanetary dust particles. Once the inner planets had
sufficiently cooled, late accretionary infall seeded them with
complex organic compounds, and delivery of such extraterrestrial
compounds may have contributed to the organic inventory necessary
for the origin of life.
2) Interstellar ices, the building blocks of comets, contain
a large fraction of the biogenic elements available in molecular
clouds: infrared observations of molecular clouds, coupled with
laboratory studies, have demonstrated that water, methyl alcohol,
carbon monoxide, carbon dioxide, and ammonia are major components
of ices in such clouds. Energetic in situ processing of
interstellar ices into complex species can be driven by cosmic
ray-induced ultraviolet radiation in dense clouds, by the
significantly enhanced ultraviolet radiation field in star-
forming regions, and by high-energy particle bombardment and
ultraviolet radiation from the earliest stage ("T-Tauri phase")
of stellar birth. Laboratory studies have also demonstrated that
such energetic processing produces many new organic compounds in
these ices, including chemical species far more complex than the
starting materials. Given that this processing occurs wherever
new stars are being created, and that there is isotopic evidence
from meteorites and cosmic dust that these chemical species can
survive incorporation into newly-forming stellar systems and
subsequent delivery to planetary surfaces, this photochemical
processing may have played a significant role in prebiotic
chemistry.
3) The authors report the laboratory simulation of an
interstellar ice mixture that upon photolysis produces
amphiphilic vesicle-forming compounds similar to those found in
primitive meteorites such as the *Murchison carbonaceous
chondrite. Starting from a simple but astrophysically relevant
ice mixture (water, methanol, ammonia, and carbon monoxide), a
complex mixture of compounds, including fluorescent molecules and
molecules with observed amphiphile behavior, is generated on low-
temperature photolysis. The authors suggest that the ready
formation of these insoluble compounds from photolyzed ices
comprised of simple molecules indicates not only that this
process might be the source of their origin in meteorites, but
that the delivery of such compounds by comets, meteorites, and
interplanetary dust particles during the heavy bombardment period
of early Earth may have played an influential role in the origin
of terrestrial life. The authors also suggest that because their
experimental conditions for ice photolysis were designed to
simulate the environments of dense interstellar molecular clouds
(the birth sites of new stars and planetary systems), the
delivery of such compounds to the surfaces of newly-formed
planets may be a universal process.
4) Concerning the identities of the chemical species
produced by ultraviolet photolysis, the authors state:
"Unfortunately, there was insufficient material for further
analysis of most of these fractions. It is clear, however, that
each fraction contains numerous compounds, with possibly hundreds
of different molecules contained in the residue."
-----------
J.P. Dworkin et al: Self-assembling amphiphilic molecules:
Synthesis in simulated interstellar/precometary ices.
(Proc. Natl. Acad. Sci. US 30 Jan 01 98:815)
QY: Scott A. Sandford: ssandford@mail.arc.nasa.gov
-----------
Text Notes:
... ... *Murchison carbonaceous chondrite: "Stony" meteorites
(aerolites) are meteorites formed solely of rock-forming
silicates, and chondrites are a type of stony meteorite
consisting of an agglomeration of millimeter-sized globules
(chondrules) that are thought to be unchanged since the original
condensation out of the nebula from which the Sun and
Solar System formed. A "carbonaceous chondrite" is a chondritic
meteorite that contains a relatively large amount of carbon, with
a resultant dark appearance. The "Murchison meteorite" is a
carbonaceous chondrite that fell in 1969 near Murchison,
Australia, the meteorite containing a variety of biologically
relevant molecules.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 30Mar01
For more information: http://scienceweek.com/swfr.htm
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2. EXPERIMENTAL PHYSICS: ON THE CASIMIR FORCE IN
MICROELECTROMECHANICAL SYSTEMS
In general, in physics, the term "zero-point energy" refers
to the energy associated with a particle or system (in addition
to its mass energy) at the absolute zero of temperature. The
zero-point energy cannot be precisely zero because of quantum
uncertainty. Similarly, the lowest energy state of a field (its
"ground state") also cannot be precisely zero.
The "Casimir effect", first predicted by Hendrik B.G.
Casimir [1909- ] in the late 1940s, is in general a quantum
force that pulls two parallel electrically conducting plates,
placed a short distance apart in a vacuum, towards one another.
The basis of the force is that the zero-point energy between the
plates is reduced compared to the zero-point energy outside the
plates. The essential reason for the zero-point energy reduction
between the plates is quantum mechanical: in quantum theory,
electromagnetic fields fluctuate and therefore can never be
exactly zero, and the plates act as boundary conditions on the
vibration mode frequencies of the vacuum electromagnetic field
between the plates. The plates as boundaries, in effect, force
certain vibration modes to drop out, producing a net reduction of
vacuum energy in the volume between the plates compared to the
vacuum electromagnetic field elsewhere. This results in an
effective pressure pushing the plates together. From a classical
perspective the effect seems bizarre, since it involves the
difference between two apparently nonexistent electromagnetic
fields producing an attractive force. All of this is related to
the so-called "active vacuum" of quantum physics, which refers to
the idea that the vacuum state in quantum mechanics has a
zero-point energy (minimum energy) which gives rise to vacuum
fluctuations, so the vacuum state does not mean a state of
nothing, but is instead an active state. This idea is now of
considerable importance in certain cosmological theories.
The Casimir force was first detected experimentally by M.J.
Sparnaay in 1958. Both the sign and magnitude of the effect
depend critically on the geometry of the surfaces. For two
ideally smooth parallel plates, the net attractive force per unit
area between the plates is given by F = k/d^(4), where (k) is a
constant involving only Planck's constant and the speed of light,
and (d) is the distance between the plates. If one surface is
spherical and the other surface a plane, the force becomes
F = k'R/d^(3), where (k') is a different constant involving only
Planck's constant and the speed of light, (R) is the radius of
the spherical surface, and (d) is the shortest distance between
the spherical surface and the plane surface.
... ... H.B. Chan et al (5 authors at Bell Laboratories, US) now
report a study of actuation of microelectromechanical systems by
the Casimir force, the authors making the following points:
1) The authors point out that microelectromechanical systems
are movable structures fabricated on a semiconductor wafer
through the use of integrated circuit technology, and these
systems have become a key technology in the production of sensors
and actuators. So far, the smallest separations between surfaces
of micromachined components are typically on the order of
microns, and the operation of microelectromechanical systems has
been well described by classical mechanics. But as further
miniaturization occurs, quantum effects may become significant in
device design and operation.
2) The authors report a demonstration of the Casimir effect
in microelectromechanical systems using a micromachined torsional
device. Attraction between a polysilicon plate and a spherical
metallic surface results in a torque that rotates the plate about
two thin torsional rods. The dependence of the rotation angle on
the separation between the surfaces is in agreement with
calculations of the Casimir force. The authors suggest their
results demonstrate that quantum electrodynamical effects play a
significant role in such microelectromechanical systems when the
separation between the components is in the nanometer range. The
authors conclude: "This could open up new possibilities for novel
actuation schemes in microelectromechanical systems based on the
Casimir force and may be important in the design of
nanoelectromechanical systems."
-----------
H.B. Chan et al: Quantum mechanical actuation of
microelectromechanical systems by the Casimir force.
(Science 9 Mar 01 291:1941)
QY: Federico Capasso: fc@lucent.com
-------------------
Summary by SCIENCE-WEEK http://scienceweek.com 30Mar01
For more information: http://scienceweek.com/swfr.htm
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3. HISTORY OF CHEMISTRY: ACIDS AND BASES
The conceptual division of certain substances into acids and
bases was already evident in the Middle Ages, the terms "acid",
"base", and "salt" occurring in the writing of medieval
alchemists. Acids were probably the first to be recognized,
apparently because of their sour taste: The English word "acid",
the French word "acide", the German "Sauer", and the Russian
"kislota" are all derived from words meaning "sour". Of
particular historical significance was the medieval introduction,
apparently in the 14th century, of acids obtained from minerals,
e.g., sulfuric acid and nitric acid. The discovery of the strong
mineral acids has been considered the most important practical
advance in chemistry after that of the successful production of
iron from its ore approximately 3000 years before. Strong mineral
acids made possible many chemical reactions and dissolutions of
substances previously impossible: vinegar was the strongest acid
known to the Greeks and Arabs. Medieval chemistry began to be
transformed during the 17th century. During the 18th, 19th, and
20th centuries, the study of acid-base chemistry involved a
series of significant conceptual alterations.
... ... W. de Vos and A. Pilot (Utrecht University, NL) present a
review of the history of concepts of acid-base chemistry, the
authors making the following points:
1) The authors point out that sulfuric acid, hydrochloric
acid, nitric acid, and other acids were already known in the
Middle Ages, although by other names. It was also understood that
bases (or "alkalis") such as soda (sodium carbonate), potash
(potassium carbonate), and lime (calcium carbonate), were the
opposites of acids, and that the reaction of an acid and a base
results in mutual neutralization. Litmus, obtained from lichens,
was used to test for acidity or alkalinity of a solution. A
"base" was originally defined as a residue that remained behind
after heating or burning. Potash, obtained from plant ashes, was
such a base. The association with a residue was lost when a base
was redefined as any substance that can neutralize an acid.
Strong and weak acids were already distinguished in the 17th
century, the adjectives "strong" and "weak" referring to the
ability of a strong acid to displace a weaker acid from its
salts.
2) Antoine Lavoisier (1743-1794) proposed that combustion of
nonmetallic elements such as sulfur, phosphorus, and carbon
yields oxides that form acid solutions in water. The name
"oxygen" can be translated as "acid generator", and oxygen was
believed to be the essential ingredient of all acids. Thus the
concept of "acid" became closely linked to the combustion of
nonmetallic elements, and the corresponding oxides were called
"anhydrides". Lavoisier introduced a systematic nomenclature for
inorganic acids, naming each acid after the element from which it
was derived: phosphoric acid, sulfuric acid, carbonic acid, etc.,
and in addition, naming such acids as phosphorous acid and
sulfurous acid, with the suffix (-ous) indicating a lower oxygen
content. As for bases, Lavoisier's view was that bases were
derived from metallic elements via their oxides ("basic
anhydrides"), with acids and bases reacting to form salt and
water. [*Note#1]
3) The ionic theory of acids and bases, as developed in the
early 1880s by Svante A. Arrhenius (1859-1927), stated that in
aqueous solutions acids and bases are ionized, completely ionized
when they are strong and partly ionized when they are weak. Weak
acids and bases in solution were considered to obey the laws of
reaction-equilibrium theory [which holds that when a reaction
system reaches equilibrium, the reactions have not stopped but
are proceeding in their respective directions at equal rates]. An
acid came to be defined in terms of Arrhenius theory as a
hydrogen-containing substance that in aqueous solution ionizes to
produce hydrogen ions, a base as a substance containing the
hydroxyl group (OH), which ionizes as the hydroxide ion. Ionic
equations were written and degrees of ionization were calculated.
[*Note #2]
4) The 20th century brought to acid-base chemistry the
theories of Johannes N. Bronsted (1866-1951), Thomas M. Lowry
(1874-1936), and Gilbert N. Lewis (1875-1946), all of whom
published their theories in 1923, with Bronsted and Lowry working
independently but publishing essentially identical ideas. Both
the Bronsted-Lowry theory and the Lewis theory of acids and bases
refer to protons and electrons, thus making use of atomic
structure and producing an important conceptual change in the
minds of chemists. The Bronsted-Lowry approach gave rise to the
concept of the hydronium ion, since the theory postulates that
water is a proton acceptor as well as a proton donor. An
essential difference with the Arrhenius theory is that acids and
bases are no longer defined in terms of substances but in terms
of particles: not sodium hydroxide, but the hydroxide ion is the
base. An acid-base reaction is now defined in terms of its
apparent reaction mechanism, namely, the reversible transfer of a
proton from the acid to the base. In a general theory of acids
and bases, G.N. Lewis added the concept that an acid is a
substance that can accept an electron pair, and a base is a
substance that can donate a pair of electrons; these are now the
definitions of a "Lewis acid" and a "Lewis base". As the authors
[de Bos and Pilot] point out, these conceptualizations of acids
and bases are not mutually exclusive, but are rather
complimentary, involving a "layering" of concepts.
5) The authors point out that in recent years progress in
chemistry has not inspired new theoretical layers in the study of
acids and bases. Acids and bases are not a spearhead in modern
chemical research: no university has a department of acid-base
chemistry, and there is no _Journal of Acids and Bases_ in
university libraries. One "acid", however, that is undergoing
thorough investigation these days is deoxyribonucleic acid (DNA).
The authors point out that it is ironic that the first thing that
students learn about this acid is that it consists of four bases.
The name "nucleic acid" expresses the observation of early
biochemists that this material, when isolated from cell nuclei,
was soluble in slightly alkaline solutions and could be
precipitated by adding dilute acid. The name "base", in this
context, refers to specific decomposition products -- purines and
pyrimidines, organic nitrogen compounds known to behave as weak
bases.
-----------
W. de Vos and A. Pilot: Acids and bases in layers: The stratal
structure of an ancient topic.
(J. Chem. Educ. 4 Apr 01 78:494)
QY: Wobbe de Vos: w.devos@chem.uu.nl
-----------
Text Notes:
... ... *Note #1: Antoine Lavoisier, considered the father of
modern chemistry, was no doubt the most eminent scientist to ever
suffer death by the guillotine. In 1780, as a member of the
French Academy of Sciences, Lavoisier was active in rejecting the
application to the Academy of a certain physician Jean-Paul Marat
(1743-1793). Marat apparently did not forget. During the French
Revolution (1787-1799), Marat became a powerful revolutionary
leader, and Marat was instrumental in bringing Lavoisier to trial
for his investments in a much-hated company that collected taxes
for the French government. Lavoisier was guillotined May 8, 1794
and buried in an unmarked grave. (Marat did not live to see this:
Marat himself was assassinated in July 1793.)
... ... *Note #2: During most of the 19th century, atoms were
considered structureless and indivisible, and the idea of a
stable substance like sodium chloride breaking up into ions in
water was inconceivable. Arrhenius developed his ionic theory of
acids and bases while he was still a student, and his ideas were
dismissed by his teachers. In 1884, when Arrhenius (then 25 years
old) presented his theory as part of his PhD dissertation, he
experienced a rigorous 4-hour examination and was then awarded
the lowest possible passing grade by his examiners.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 30Mar01
For more information: http://scienceweek.com/swfr.htm
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
4. PLANT BIOLOGY: ON THE ARABIDOPSIS GENOME
During the past decade, an inconspicuous weed named Arabidopsis
thaliana has moved to the forefront of research in plant
genetics, plant physiology, plant developmental biology, and
plant molecular biology. Arabidopsis is a small plant belonging
to the mustard family, which includes cabbage, broccoli,
cauliflower, rape seed, and bok choy. Because the plant is small,
up to only 30 centimeters in height, it can be grown in large
numbers in small spaces. Its small seeds can be germinated in
quantity in a single petri dish, which makes it easy to screen
for plants with genetic mutations. The Arabidopsis genome, which
was recently completely sequenced, is relatively small at 125
million nucleotide bases, compared with the human genome of
approximately 3 billion nucleotide bases. Arabidopsis thus
presents a simple genome model that allows for the analysis of
defective as well as normal genes with the automated techniques
of modern biotechnology.
... ... R. Scott Poethig (University of Pennsylvania, US)
presents a commentary on current research on Arabidopsis, the
author making the following points:
1) The author points out that the recent explosion of
interest in Arabidopsis, a weed of absolutely no economic
importance, is unprecedented in the history of plant biology and
provides plant biology with its first widely adopted model
system. Arabidopsis has a rapid life cycle and has been used in
genetic studies for decades, but it was the discovery that
Arabidopsis has a small genome with very little repeated DNA that
provoked its recent popularity. The widespread adoption of
Arabidopsis as an experimental system has resulted in rapid
progress in many areas and has produced the international effort
that led to the sequencing of the Arabidopsis genome.
2) The Arabidopsis genome comprises 125 megabases and
encodes approximately 25,000 genes. This plant, therefore, has
significantly more genes that yeast, the nematode worm C.
elegans, or the fruit fly Drosophila. This is primarily because
the genes of Arabidopsis often occur in more than one copy. 17
percent of the genes in Arabidopsis occur as tandem arrays of 2
or more closely related genes, and approximately 60 percent is
segmentally duplicated, albeit in a highly rearranged fashion.
The number of unique types of genes in Arabidopsis (12,000) is
actually approximately equal to the number of gene types in worms
(14,000) and flies (11,000)
3) The types of genes present in Arabidopsis reinforce what
has been learned from previous sequencing projects about the
evolution of *eukaryotes. Genes required for eukaryote cell
function, such as components of the *cytoskeleton, or essential
processes such as DNA replication, repair, and *recombination,
cell division, protein synthesis, and *vesicle trafficking, are
largely conserved between Arabidopsis and other eukaryotes. In
contrast, genes involved in regulatory processes, such as *signal
transduction and *transcription, are quite different in
Arabidopsis, yeast, C. elegans, and Drosophila. Plants have also
evolved a diverse array of *transcription factors not found in
animals. Arabidopsis has approximately 1500 transcription
factors, 1.3 times as many as Drosophila and 1.7 times as many as
C. elegans or yeast. 45 percent of the families of transcription
factors found in Arabidopsis are unique to plants. These
differences are not surprising, given that multicellularity
apparently originated independently in plants and animals, and
given that plants have cell walls and animals do not. The author
suggests the important lesson is that plants are as different
from other organisms as they are the same, and are interesting
for both reasons.
4) The author concludes: "With 25,000 mostly uncharacterized
genes, the Arabidopsis genome will keep plant biologists busy for
a long time. Given the traditional interest in plant diversity,
it will be interesting to see whether this information will be
used primarily to explore the biology of Arabidopsis, or as a
starting point for forays into the far reaches of the plant
kingdom. One thing is clear: With a host of interesting problems
to study, an unrivalled set of molecular genetic tools, and now a
sequenced genome, for plant biologists the fun has just begun."
-----------
R. Scott Poethig: Life with 25,000 genes.
(Genome Research March 2001 11:313)
QY: R. Scott Poethig: University of Pennsylvania 215-898-5000.
-----------
Text Notes:
... ... *eukaryotes: The term "eukaryotes" refers to biological
cells containing internal membrane-bound organelles, particularly
a bounded cell nucleus. Cells without such internal organelles
are called "prokaryotes".
... ... *cytoskeleton: The quasi-rigid matrix that among other
things determines cell shape and acts as a scaffold for various
intracellular translocations.
... ... *recombination: In general, integration of DNA fragments
into a particular site in a genome.
... ... *vesicle trafficking: In this context, "vesicles" are
small intracellular spherules that sequester various substances,
and by translocation processes effectively transport these
substances from on part of the cell to another.
... ... *signal transduction: The term "signal", in this context,
refers to a chemical-signal input to a cell, the input transduced
by a cell-surface receptor into a cascade of intracellular events
that produce a response of the cell to the input signal.
... ... *transcription: In this context, the process by which
genetic information in DNA is converted into RNA, with the RNA
ultimately "translated" into protein.
... ... *transcription factors: A class of DNA-binding proteins
that regulate RNA transcription.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 30Mar01
For more information: http://scienceweek.com/swfr.htm
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5. EVOLUTIONARY BIOLOGY: ON THE ORIGIN OF PLANT LEAVES
The plant kingdom includes organisms that range in size from
a tiny moss to a giant tree. All plants are multicellular and
eukaryotic, each plant cell possessing a membrane-bound nucleus
that contains the chromosomes. Most plants contain photoreactive
pigments (e.g., chlorophylls a and b, and carotenoids), which
play a central role in converting solar radiation into chemical
energy (photosynthesis), the process involving reduction of
carbon dioxide.
The evolutionary history of plants is recorded in fossils,
with some fossils showing the external forms of plant parts,
other fossils showing cellular features, and still other fossils
consisting of microfossils of pollen and spores. The fossil
record reveals a pattern of accelerating rates of evolution
coupled with increasing diversity and complexity of biological
communities. This diversity and complexity increased enormously
with the invasion of land and the progressive colonization of the
continents. At present, fossil evidence for the first land plants
dates to the Ordovician time-frame (510 to 439 million years
ago).
The term "vascular plants" (tracheophyta) refers to plants
that have vascular tissues (xylem and phloem) through which water
and nutrients are transported.
One of the most important organs of contemporary plants is
the leaf, a thin and usually green expanded tissue borne on a
node on the stem of the plant. Leaves typically have a stalk and
blade (lamina), and they are the main site of solar radiation
input and carbon dioxide absorption and photosynthesis. The
fossil record indicates that for the first 40 million years of
their invasion of land, land plants had no leaves, merely small
spine-like appendages, and an important question in evolutionary
biology is, How did leaves evolve?
... ... Paul Kenrick (Natural History Museum London, UK) presents
a commentary on a recent report on the evolution of plant leaves
(D.J. Beerling et al: Nature 15 Mar 01 410:352), the author
(Kenrick) making the following points:
1) The author points out that vascular plants have leaves of
two main types. The "microphyll" is usually a short spine-like
leaf and is characteristic of clubmosses; the "megaphyll" is
generally larger, with a substantial lamina and a complex pattern
of veins like the leaves of ferns and flowering plants. Almost
all living plants have megaphylls or their derivatives.
2) The 40-million-year gap between the earliest fossil
evidence of vascular plants and the advent of megaphylls is
puzzling. Megaphylls are ubiquitous today, and their
photosynthetic proficiency makes their evolution seem inevitable.
The structural framework necessary to assemble the primitive leaf
was in place approximately 408.5 million years ago. The fossil
record indicates that megaphylls evolved from the photosynthetic
branching systems of early vascular plants that became flattened
and later webbed to produce a broad lamina in several groups by
362.5 million years ago (the end of the Devonian).
3) Beerling et al propose a novel explanation for the long
delay in the advent of leaves. They use a model based on
biophysical principles applied to living plants and involving
details of water use and heat and gas exchange. They also draw on
anatomical and environmental data from the fossil record. They
conclude that leaves with a broad lamina evolved in response to a
massive drop in atmospheric carbon dioxide during the Devonian
period (408.5 to 362.5 million years ago).
4) The author (Kenrick) asks: "If Beerling et al are right,
and leaf evolution was driven by a large fall in atmospheric
carbon dioxide, what then drove that fall in carbon dioxide?
Remarkably, the answer appears to be plants." The scheme is as
follows: The physical and chemical effects of root systems on
rocks and soils increase rates of weathering, which is thought to
have been responsible for removing enormous quantities of carbon
dioxide from the Devonian atmosphere. Thus, roots may have played
a key role in the evolution of leaves by way of the *carbon
cycle.
5) The author (Kenrick) states: "The results of modeling
systems that are so remote from the modern world have to be
treated with skepticism. How can one be confident in a result for
which so many parameters have to be estimated? This is a genuine
concern, but Beerling and colleagues' calculations are based on
independent biochemical, paleobotanical, and geochemical
evidence, and seem reasonable."
-----------
Paul Kenrick: Turning over a new leaf.
(Nature 15 Mar 01 410:309)
QY: Paul Kenrick: p.kenrick@nhm.ac.uk
-----------
Text Notes:
... ... *carbon cycle: In its most general outline, the term
"carbon cycle", in geochemistry and Earth science, refers to the
movement of carbon from an atmospheric inorganic state to a
biospheric organic state and then back to an atmospheric
inorganic state.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 30Mar01
For more information: http://scienceweek.com/swfr.htm
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6. POPULATION GENETICS: ON DISPERSAL OF HUMAN POPULATIONS
In this context, the term "macroevolution" refers to a large
evolutionary pattern viewed from the perspective of geologic
time, e.g., the evolution of the horse from the ancestral
Eohippus to the modern Equus. In contrast, the term
"microevolution" refers to an evolutionary pattern usually viewed
over a short period of time, e.g., changes in gene frequency
within a population over relatively few generations.
In genetics, the term "allele" (allelomorph) refers to any
one of two or more genes that may occur alternatively at a given
site (locus) on a chromosome. Alleles may occur in pairs, or
there may be multiple alleles affecting the expression
(phenotype) of a particular trait. Most traits are determined by
more than two alleles; all genetic traits are the result of the
interaction of alleles. Mutation, exchange of genetic material
between chromosome ("crossing over"), and environmental
conditions selectively change the frequency of phenotypes (and
thus their alleles) within a population.
In humans, the "ABO blood group system" is a system of
alleles residing on chromosome 9, the system specifying certain
red blood cell *antigens responsible for agglutination of red
blood cells. Blood groups are inherited according to the
Mendelian laws governing the transmission of chromosomes to
subsequent generations ("Mendelian genetics").
In this context, the term "assortive mating" refers to
sexual reproduction in which the pairing of male and female is
not random, but involves a tendency for males of a particular
kind to breed with females of a particular kind.
The term "genetic drift" refers to a statistically
significant change in population gene frequencies resulting not
from selection, emigration or immigration, but from causes
operating randomly with respect to the fitnesses of the genes
concerned. For example, external events suddenly impacting a
population can result in an abrupt shift in gene frequencies in
that population.
A genetic "polymorphism" is a naturally occurring variation
in the normal nucleotide sequence of the genome within
individuals in a population. Variations are denoted as
polymorphisms only if they cannot be accounted for by recurrent
mutation and occur with a frequency of at least approximately 1
percent. In humans, studies of single-nucleotide polymorphisms,
as molecular genetic markers for mapping common disease genes,
have reconfirmed the importance of human population structure.
Recent evidence indicates that for protein-coding regions of the
human genome, there is one difference for every 1200 nucleotide
base pairs. Some of these differences are common around the
world, but others are associated with local populations, and such
differences are now being used to study historical human
population dispersals.
... ... Rebecca L. Cann (University of Hawaii Manoa, US) presents
a review of current research on human population genetics applied
to the study of human population dispersal, the author making the
following points:
1) The author suggests that time has usually been a
contentious factor in the study of human populations,
particularly in the popular press, because of the bias to reward
studies that highlight the oldest, the newest, the largest, or
the most distinctive. In the past, anthropologists and
evolutionary biologists concentrated on investigating human
population diversity over space and time by using variability in
skull shape, facial features, skin color, stature, and body form.
Charles Darwin (1809-1882) and Thomas H. Huxley (1825-1895),
founders of evolutionary theory, looked forward to an era when a
full appreciation of human evolution would incorporate the global
perspective of geographically distinct humans from different
homelands, reasoning that migration, colonization, and isolation,
along with adaptation, hold the clues to resolving apparent
discrepancies between macro- and microevolution evolutionary
patterns seen in the human fossil record.
2) From the early work of population geneticists who sought
to discern patterns of historical population movements from the
blood groups, blood serum proteins, and enzymes of a few hundred
donors, we have progressed to megabase sequence comparison from
tens of thousands of individuals with increasingly fine spatial
as well as temporal resolution. Highly informative gene sites
("loci"), enzymatically amplified from saliva or hair samples
collected under field conditions, have freed us from a reliance
on population inferences based on acculturated or urbanized
groups. What characterizes all the studies is a shift from the
discovery of individual molecular characters to a focus on the
population carrying them.
3) Molecular medical genetics has rediscovered a basic
feature of our species, the structured population, which was
first quantified in 1901 by Karl Landsteiner (1868-1943) with the
discovery of ABO blood groups. Population structure is caused by
assortive mating, variation in reproductive success, and limited
dispersal. In response to new selective forces, populations
either restrict their ranges, go extinct, or adapt. Two
consequences of these facts are a) common alleles increase in
frequency, and b) rare alleles arise through mutation, and, if
adaptive, may be spread throughout the larger gene pool if time
and gene flow are sufficient. But new alleles can also spread by
genetic drift, making definitive statements concerning past
forces speculative. Although it follows that frequencies and
distributions of genetic polymorphisms can reveal the past
selective forces our direct ancestors faced, estimating the
duration and strength of those forces is still a challenge.
4) The author concludes: "Knowledge about the past, as
reconstructed with population genetic principles, will come
directly from the screening for human mutations. It should
continue to humble us that the technology for detecting
variations and extracting once-lost secrets is far in advance of
the ethical problems posed by the possession of such knowledge."
-----------
Rebecca L. Cann: Genetic clues to dispersal in human populations:
Retracing the past from the present.
(Science 2 Mar 01 291:1742)
-----------
Text Notes:
... ... *antigens: In general, any chemical entity that activates
an immune response, especially an entity originating outside the
body. Antibodies are specific proteins synthesized by the immune
system which interact with specific antigens. In the present
context, the agglutination of "foreign" red blood cells is caused
by an antigen carried by those blood cells, the antigen provoking
an immune response in the host, the response resulting in the
agglutination of the foreign red blood cells.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 30Mar01
For more information: http://scienceweek.com/swfr.htm
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7. IN FOCUS: ON GIANT MAMMALS AND ROTTING FRUITS
"The Age of Great Mammals ended long before chainsaws and
internal combustion engines evolved. In Europe and nontropical
regions of Asia, it petered out in steps between 50 and 15
thousand years ago, when the straight-tusked elephants, woolly
mammoths, rhinos, and other great beasts of the Pleistocene epoch
vanished. Throughout that vast continental mass, a quarter of all
genera of animals regarded as megafauna -- those weighing more
than a 100 pounds, or 45 kilograms -- were lost to extinction.
Europe lost all 6 species of herbivores weighing more than 1000
kilograms. In Australia, the Age of Great Mammals ended sometime
between 40,000 and 30,000 years ago, when giant kangaroos,
enormous wombats, and rhino-like marsupials (as well as the most
formidable crocodiles, lizards, and snakes) were purged from the
landscape. This extinction catastrophe stripped Australia of all
but one of its 16 genera of megafauna. In the Western Hemisphere,
the Age of Great Mammals came to an abrupt end 13,000 years ago,
when the mastodons and mammoths, the ground sloths and
glyptodonts, the native horses and large camels, and a beaver and
an armadillo both as big as a bear all disappeared forever. North
America lost 68 percent of its generic richness of Pleistocene
megafauna (32 of 47 genera), and South America lost 80 percent
(47 of 59 genera). Outlying islands were hit even harder, though
several thousand years later, following advances in sailing
technologies. Not until 7000 years ago, for example, did Cuba
lose its half dozen species of sloth, including a ground dweller
as big as a black bear. Just 4000 years ago, while the Egyptians
were building pyramids, the last mammoths on Earth expired on an
island off Siberia. Madagascar lost all of its biggest lemurs
within the past 2000 years, along with both native species of
hippopotamus, a strange carnivore, and the giant elephant birds
unique to that island... The Age of Great Mammals may be over,
but the plants have not yet caught on. Those that depended upon
mammals to swallow big fruits, as well as those that deployed
armaments to deter soft snouts from stripping foliage, are still
doing what they have always done. Fruit rotting on the ground is
the most obvious sign... The big beasts are gone, but the fruits
remain. Year after year in the American tropics (and temperate
climes too), trees and vines produce fruits that make little
sense today. Some fruits simply rot on the ground beneath the
parent plant. Others are raided by seed predators or plundered by
pulp thieves. Whether rotted, raided, or plundered, viable seeds
are rarely dispersed. The plants not only remember the great
mammals of the Pleistocene and before, they expect gomphotheres,
ground sloths, toxodons, and their ilk to show up any day now.
Thirteen thousand years is not enough time for plants to notice
and genetically respond to the loss."
-----------
Connie Barlow: _The Ghosts of Evolution: Nonsensical Fruit,
Missing Partners, and other Ecological Anachronisms_
(Basic Books, New York 2000, p.3)
-------------------
SCIENCE-WEEK http://scienceweek.com 30Mar01
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8. FROM THE SCIENCEWEEK ARCHIVE:
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
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9. ON THE GEOLOGICAL TIME-SCALE: A SIMPLIFICATION
From the Editors: The identification of geological time-frames,
because of the hierarchical nomenclature currently in use, is
often confusing for people outside the geology/paleontology
community. As a convenience, therefore, we are adopting the
following continuous and non-overlapping time-scale for use in
ScienceWeek, and we hope presenting the entire time-scale in one
place will be useful. In the tabulation below, any given time-
frame runs from the given starting date to the next starting date
below it. Although this time-scale omits certain other currently
used hierarchical subdivisions, the time-scale is continuous, and
the names and starting dates of the time-frames are those now in
most frequent general use.
Time-Frame Starting Date (Millions of Years Ago)
---------- -------------------------------------
Hadean 4600
Archaean 4000
Proterozoic 2500
Cambrian 570
Ordovician 510
Silurian 439
Devonian 408.5
Carboniferous 362.5
Permian 290
Triassic 245
Jurassic 208
Cretaceous 145.6
Paleocene 65
Eocene 56.5
Oligocene 35.4
Miocene 23.3
Pliocene 5.2
Pleistocene 1.64
Holocene 0.01
In the geology/paleontology community, the scheme in general use
is more complex. For example, from the Hadean through the
Proterozoic constitutes the "Precambrian" time-frame; from the
Cambrian through the Permian constitutes the "Paleozoic Era";
from the Paleocene through the Pliocene constitutes the "Tertiary
sub-Era"; from the Paleocene through the Holocene constitutes the
"Cenozoic Era". The continuous time-scale presented above is a
simplification, but any wider time-frame in use can be
conveniently represented by a doublet from the above time-scale.
The so-called "Quaternary" sub-Era, for example, is the time-
frame Pleistocene-Holocene inclusive. We hope that geologists and
paleontologists will not be too annoyed and will understand that
our objective is that our readers be able to easily place a
particular time-frame in the entire geological time-scale.
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