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 12, 1999 -- Vol. 3 Number 11

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There are living systems, there is no "living matter".
-- Jacques Lucien Monod (1910-1976)

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Contents of This Issue:

1. On the Crisis in US Engineering Education
2. On Supersoft X-Ray Stars and Supernovae
3. A Free-Fall Determination of the Newtonian Gravity Constant
4. Assignment of Biochemical Functions of Hypothetical Proteins
5. On Models of Molecular Evolution and Phylogeny
6. 20th Century Trends in US Infectious Disease Mortality

-- In Focus: On the Study of Collective Phenomena in Physics

-- Complete List of SW Focus Reports

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1. ON THE CRISIS IN US ENGINEERING EDUCATION
It is one of the current ironies that in the US, which is perhaps
the most industrialized and technologically advanced nation in
the world, engineers and engineering apparently command little
respect or interest among university students.
... ... Wm. A. Wulf (National Academy of Engineering, US)
presents a short analysis of the problem, the author making the
following points: 1) Enrollment of engineering majors is down 20
percent from its 1983 peak at the same time that overall college
enrollment has increased. 2) The picture is especially grim for
minorities. Whereas overall engineering enrollment has dropped 3
percent since 1992, minority enrollment has fallen 9 percent, and
African-American enrollment has plummeted 17 percent. Enrollment
by women, which had been climbing steadily, has been fixed on a
plateau just below 20 percent of all enrollees for the past few
years. 3) All of this is in spite of high starting salaries. The
author suggests there is something in the perception of
engineering by students: engineering is apparently so repugnant
to students that they are not attracted to it despite the
salaries it offers. The author concludes: "Creativity and
diversity go hand in hand, but engineering seems caught in a
destructive feedback cycle. The profession is perceived as dull,
which is the antithesis of its actual inherent creativity, and
that image repels the diversity that is essential to realize the
full creativity of engineering. We must break that cycle."
-----------
Wm. A. Wulf: The image of engineering.
(Issues in Science and Technology Winter 1998-1999)
QY: Wm. A. Wulf [wwulf@nae.edu]
-------------------
Summary by SCIENCE-WEEK [http://scienceweek.com] 12Mar99


2. ON SUPERSOFT X-RAY STARS AND SUPERNOVAE
In recent years, astronomers have discovered a new type of star
that apparently emits x-rays of unusually low energy. These so-
called "supersoft sources" are now thought to be *white dwarf
stars in a *binary system that absorb mass from their stellar
companions and then in many cases ultimately explode.
... ... P. Kahabka et al (3 authors at 2 installations, NL US)
present a review of recent work concerning supersoft x-ray stars,
the authors making the following points: 1) Since the 1930s,
astronomers have known that ordinary stars shine because of
nuclear fusion deep in their interiors. In the core of the Sun,
for example, 600 million tons of hydrogen fuse into helium every
second. This process releases energy in the form of x-rays and
gamma rays, and this radiation slowly wends its way outward
through the thick layers of gas. By the time the radiation
reaches the surface of the star, the radiation has degraded into
visible light. 2) Researchers recently have discovered a new
class of stars in which the nuclear fusion occurs not in the deep
interior of the star but in the outer layers just below the
surface. These stars appear to be white dwarfs in orbit around
ordinary stars. The white dwarfs apparently acquire hydrogen gas
from their companions, accumulate the hydrogen gas on their
surfaces, and resume fusion. The result is a torrent of x-rays
with a distinctive "soft" range of wavelengths, and such stars
are known as "supersoft x-ray sources". As the white dwarfs gain
mass, they eventually become unstable, at which point they can
collapse into an even denser *neutron star or explode. 3) The
disruption of white dwarfs has long been conjectured as the cause
of one type of supernova explosion called *type Ia. With the
discovery of the supersoft sources, observers have identified for
the first time a class of star system that can detonate in the
manner of type Ia supernovae. Such supernovae have become
important as bright "*standard candles" for measuring distances,
and much of the uncertainty concerning such estimates of
distances is connected to ignorance of the determinants of these
supernovae. The supersoft sources may be the long sought missing
link... Their death-rate roughly matches the observed supernova
frequency, and at present the luminous supersoft binary x-ray
sources are the first firmly identified class of objects that can
realistically be expected to end their lives in type Ia
explosions. The authors conclude: "Now it is clear that a once
bewildering assortment of variable stars, novae and supernovae
are all variants on the same basic system: an ordinary star in
orbit around a reanimated white dwarf. The universe seems that
much more comprehensible."
-----------
P. Kahabka et al: Supersoft x-ray stars and supernovae.
(Scientific American February 1999)
QY: Peter Kahabka, Astronomical Institute, University of
Amsterdam, NL.
-----------
Text Notes:
... ... *white dwarf stars: These are extremely dense and compact
stars that have undergone gravitational collapse after nuclear
fusion burn-out in their centers. They are the final stage in the
evolution of low-mass stars after such stars have lost their
outer layers. The white dwarfs are about the size of Earth, but
with a mass about that of the Sun. The evolution of a star into a
white dwarf depends on its terminal mass. The remnant mass after
the blow-off of mass that occurs during the terminal stage of the
life of a star determines the ultimate fate of the star. If the
remnant mass is less than 1.44 solar masses (the Chandrasekhar
limit for a star with no hydrogen content), the star collapses
into a white dwarf. If the remnant mass is greater than 1.44
solar masses, depending on the remnant mass, the star collapses
into either a *neutron star or a *black hole. [The Chandrasekhar
limit is named after Subrahmanyan Chandrasekhar (1910-1995), who
first proposed the modern theory of stellar gravitational
collapse, and who received the Nobel Prize in Physics 1983.]
... ... *binary system: Binary stars are a pair of stars
revolving around a common center of mass under the influence of
their mutual gravitational attraction, and apparently the
majority of stars in the universe are binaries and not singlets.
In some cases the binary system is resolvable into two
components, and in other cases the presence of a second star is
inferred by perturbations in the motion or emitted radiation of
the first star. If the binaries are close enough, they may share
stellar material, and this results in a particular kind of
stellar evolution.
... ... *neutron star: If, following its terminal stages, the
remnant mass of a star is between 1.44 and 2 to 3 solar masses,
the star will collapse into a neutron star, a body with a radius
of 10 to 15 kilometers, and with a core so dense that its
component protons and electrons have merged into neutrons. ...
... ... *black hole: If the terminal stages of star death leave a
remnant star mass greater than 3 solar masses, the ultimate
gravitational collapse will produce a black hole, a relativistic
singularity. A black hole is a localized region of space from
which neither matter nor radiation can escape. The "trapping"
occurs because the requisite escape velocity, which can be
calculated from the relevant equations, exceeds the velocity of
light and is therefore unattainable. Another view of a black hole
is that it is a mass that has collapsed to such a small volume
that its gravity prevents the escape of all radiation.
... ... *standard candles: In general, in this context, the term
"standard candles" refers to astronomical objects whose intrinsic
brightness is known and whose distance can therefore be
calculated from apparent brightness.
-------------------
Summary & Notes by SCIENCE-WEEK [http://scienceweek.com] 12Mar99
-------------------
Related Background:
NEW EVIDENCE FOR A COSMIC ANTIGRAVITY FORCE
Type 1a supernovas are believed to be white dwarf stars that have
accreted enough matter from another star to be pushed over a mass
threshold (the Chandresekhar threshold) and into a thermonuclear
explosion. Since most supernovas of this type have similar
spectral emission curves and absolute magnitudes at maximum, they
can be used as "standard candles" for distance determinations,
i.e., their apparent luminosity becomes a measure of their
distance. At a recent astrophysics meeting (3rd International
Symposium on Sources and Detection of Dark Matter in the
Universe, 18-20 February 1998, Marina del Rey, Calif., US),
Alexei Filippenko (University of California Berkeley, US)
presented a report that 14 distant type Ia supernovas are on the
average 10% to 15% further away than expected, and these results,
coupled with previous independent observations by others on other
type 1a supernovas, are pushing astrophysicists to a consensus
that cosmic expansion is accelerating, rather than decelerating
due to gravitational forces, and that a repulsive antigravity
force may be counteracting gravity on large scales. One
theoretical result has been a renewed interest in Einstein's
"cosmological constant", an intrinsic space-time background
energy that would produce such a force, and which for many years
has been disregarded as an ad hoc theoretical improvisation.
Apparently, astrophysicists are all accepting the new supernova
data, and the question is what to make of it -- and whether some
serious theoretical reformulations are necessary.
QY: James Glanz [science_editors@aaas.org]
(Science 27 Feb 98) (Science-Week 13 Mar 98)


3. A FREE-FALL DETERMINATION OF THE NEWTONIAN GRAVITY CONSTANT
According to Newton's law of gravitation, there is a force of
attraction between any two massive particles in the Universe.
This force of attraction, as stated by Newton, may be expressed
as a simple relationship involving the masses of the two
particles and the distance between them. When the two masses are
unit masses and the distance between their centers of mass is
unit distance, then the force of attraction is equal to what is
called the "gravitational constant", usually denoted as "G". The
gravitational constant is usually regarded as a true universal
constant independent of place or time, but in some cosmological
models it is proposed that the gravitational constant decreases
with time as the Universe expands. A precise knowledge of the
gravitational constant is of considerable interest, since it
provides a unique and valuable measurement challenge. But despite
two centuries of experimental effort, the exact value of the
gravitational constant remains poorly known. Recent
determinations of the constant differ by as much as 40 times
their individual estimates of uncertainty (a difference as much
as 0.5 percent), and this suggests the presence of significant
systematic errors. The difficulty in measuring the constant
arises in part from the extreme weakness of the gravitational
force and the consequent difficulty of generating a sufficiently
large signal for accurate measurement. Additional problems arise
from the difficulty of eliminating spurious forces due to such
things as electromagnetic fields and thermal gradients.
... ... J.P. Scwarz et al (4 authors at 3 installations, US) now
report an experiment that uses the gravity field of a one-half
metric ton source mass to perturb the trajectory of a free-
falling  mass, and *laser interferometry to track the falling
object. The authors state that since this experiment does not
suspend the test mass from a support system, it is therefore free
of many systematic errors associated with supports. The authors
report the measured value of the gravitational constant as 6.6873
+- 0.0094 x 10^(-11) m^(3) (kg)^(-1) sec^(-2), where m is meters,
(kg) is kilograms, and sec is seconds.
-----------
J.P. Schwarz et al: A free-fall determination of the Newtonian
constant of gravity.
(Science 18 Dec 98 282:2230)
QY: J.P. Schwarz, Univ. of Colorado Boulder 303-492-6694
-----------
Text Notes:
... ... *laser interferometry: In general, an optical
interferometer is an instrument in which light from a source is
split into two or more beams, and these beams are subsequently
reunited after traveling over different paths, with optical
interference fringes produced at the reunion. Such an instrument
can be used for precise measurements of various physical
entities, including precise measurements of very small distances.
A "laser interferometer" is an optical interferometer that uses
laser light as a source. Because of the monochromaticity and high
intrinsic brilliance of laser light, the laser interferometer can
operate with path differences in the intervening beams several
orders of magnitude higher than the path differences possible
with classical optical interferometers. The result is a
considerable improvement in measurement resolution.
-------------------
Summary & Notes by SCIENCE-WEEK [http://scienceweek.com] 12Mar99


4. ASSIGNMENT OF BIOCHEMICAL FUNCTIONS OF HYPOTHETICAL PROTEINS
In molecular biology, the term "reading frame" refers to a
specific permutation of nucleotide triplets in DNA as "framed" by
a preceding start triplet (start codon), and an "open reading
frame" is any DNA sequence of triplets that runs from an apparent
start codon to an apparent end codon, thus defining a possible
gene that encodes a potential functional protein (hypothetical
protein). After a possible gene in a genome is identified in the
form of an open reading frame, the question is what is the
function of the hypothetical protein apparently encoded by the
gene? At the present time, more than a dozen microbial genomes
have been completely sequenced, genomes from all three branches
of life, the *Archaea, the *Eukarya, and the *Bacteria, and the
majority of open reading frames identified in these genomes
encode proteins of unknown function. There are at present in
principle essentially two methods for predicting the function of
a protein of known composition: a) primary sequence genomics,
which compares amino acid sequences with functionally assigned
sequences in protein sequence databases, and b) structural
genomics, which involves determination of the 3-dimensional
structure of the protein by either x-ray crystallography or
nuclear magnetic resonance, and then comparison of the determined
3-dimensional structure with protein structure databases of
proteins of known function. Although these methods exist in
principle, the first method has not been successful for the
majority of open reading frames identified in known microbial
genomes, and the second method has been limited by the
difficulties of 3-dimensional structure determination.
... ... T.I. Zarembinski et al (7 authors at University of
California Berkeley, US) now report the crystal structure at 1.7
angstrom resolution of a protein of unknown function denoted as
MJ0577, the open reading frame of the protein present in the
genome of the *hyperthermophile Methanococcus jannaschii. The
protein was prepared by *polymerase-chain-reaction (PCR)
amplification of the DNA coding region of the protein, and this
region genetically engineered into the genome of the bacterium
Escherichia coli for final protein expression. The authors report
that the structure of the protein contains a bound *adenosine
triphosphate (ATP) molecule, suggesting the protein is an ATPase
(i.e., ATP-enzyme) or ATP-mediated molecular switch. The authors
further report the structure of the protein reveals different ATP
binding motifs that are apparently shared among many *homologous
hypothetical proteins in this family. The authors suggest their
results indicate that structure-based assignment of molecular
function (structural genomics) is a viable approach for the
large-scale biochemical assignment of proteins and for
discovering new binding motifs.
-----------
T.I. Zarembinski et al: Structure-based assignment of the
biochemical function of a hypothetical protein: A test case of
structural genomics.
(Proc. Natl. Acad. Sci. US 22 Dec 98 95:15189)
QY: Sung-Hou Kim [shkim@lbl.gov]
-----------
Text Notes:
... ... *Archaea: The archaebacteria (also called the Archaea)
are considered to be ancient compared to other kingdoms, and
possibly the most ancient life forms and the ancestors of all
eukaryotes (see Eukarya note below). They typically exist in
extreme environments, and include the methane-producing bacteria
(methanogens), the "salt-loving" bacteria (halophilic bacteria),
and the sulfur-acid tolerant thermoacidophilic bacteria. There is
presently a controversy concerning whether the Archaea should be
classified as a kingdom separate from the Bacteria.
... ... *Eukarya: (eukaryote) Any organism whose cells possess a
nucleus bounded by a nuclear membrane and containing true
chromosomes.
... ... *Bacteria: Organisms in this superkingdom are unicellular
and without a cell nucleus (i.e., "prokaryotes").
... ... *hyperthermophile: In general, a "thermophile" is an
organism, especially a microorganism, that can tolerate high
temperatures and that grows optimally at temperatures above 45
degrees centigrade. Archaea hyperthermophiles have growth optima
as high as 105 degrees centigrade.
... ... *polymerase-chain-reaction (PCR): Polymerase chain
reaction (usually denoted as PCR) is a synthetic method allowing
bulk replication of minute quantities of a chosen segment of a
nucleic acid to take place accurately and efficiently in vitro.
... ... *adenosine triphosphate (ATP): ATP is the most important
chemical energy source in all living cells, intimately involved
in various cell functions and cell metabolism, and an entity in
numerous cyclic chemical pathways involved in the synthesis of
components.
... ... *homologous: In this context, the term "homologous"
refers to macromolecules having the same or similar residues at
corresponding positions.
-------------------
Summary & Notes by SCIENCE-WEEK [http://scienceweek.com] 12Mar99


5. ON MODELS OF MOLECULAR EVOLUTION AND PHYLOGENY
The term "phylogeny" refers to the evolutionary history of a
group of organisms, and the term "molecular phylogenetic
relationships" refers especially to relationships between the DNA
and proteins of one species and the DNA and proteins of other
species, such relationships evidently derived from evolutionary
relationships. Reconstructing evolutionary relationships is
called "phylogenetic reconstruction", and this is a fast-growing
field involving various statistical approaches and applications
of findings in a broad range of biological specialties.
Fundamental to the statistical approaches are mathematical models
used to describe the patterns of DNA base substitution and
protein amino acid replacement, and such models have potential as
a basis for comparative genome research. ... ... P. Lio and N.
Goldman present a review of current work on models of molecular
evolution and phylogeny, the authors making the following points:
1) A geneticist reconstructs molecular phylogenetic relationships
by proceeding hierarchically. The first step comprises DNA
sequence selection and alignment to determine site-by-site
homologies and to detect DNA (or amino acid) differences. 2) The
second step is to build a mathematical model describing the
evolution in time of the sequences. A model can be built
empirically, using properties calculated through comparisons of
observed sequences, or parametrically, using chemical or
biological properties of DNA and amino acids (e.g., the
*hydrophobicity values of each amino acid). Such models permit
estimation of the genetic distance between two *homologous
sequences, the distance measured by the expected number of
nucleotide substitutions per site that have occurred between the
genome of a species and the genome of its most recent common
ancestor. Such distances may be represented as branch lengths in
a phylogenetic tree: the extant sequences form the tips of the
tree, whereas the ancestral sequences form the internal nodes and
are generally not known. 3) The third step in molecular
phylogenetic reconstruction involves applying an appropriate
statistical method to find the tree topology and branch lengths
that best describe the phylogenetic relationships of the
sequences. The authors suggest that the modeling of processes of
sequence evolution is a thriving field of research with two
immediate and important benefits: a) an improved understanding of
the biological processes that shape evolution at the molecular
level, and b) an improved ability to infer from sequence data the
story of the evolution of life on Earth.
-----------
P. Lio and N. Goldman: Models of molecular evolution and
phylogeny.
(Genome Research December 1998 8:1233)
QY: Nick Goldman [N.Goldman@gen.cam.ac.uk]
-----------
Text Notes:
... ... *hydrophobicity: In general, the term "hydrophobic"
refers to a tendency not to dissolve in water, to have a low
affinity for water, etc. In chemistry, a "hydrophobic
interaction" is an association of nonpolar molecules or groups in
aqueous media, the interaction resulting from the tendency of
water molecules to exclude nonpolar species.
... ... *homologous sequences: In this context, the term
"homologous" refers to DNA or protein macromolecules having the
same or similar residues at corresponding positions.
-------------------
Summary & Notes by SCIENCE-WEEK [http://scienceweek.com] 12Mar99
-------------------
Related Background:
ZEBRAFISH AND VERTEBRATE GENOME EVOLUTION
To an engineer with open eyes, the assemblage of parts that
constitute a living organism is an engineering marvel. The
exterior anatomy of an insect, for example, involves a complex
arrangement of numerous parts with specific mechanical and
sensory functions, and this assemblage is replicated with great
precision in the production of each generation. In an ordinary
manufacturing plant, the various parts of a machine are usually
manufactured independently of each other and then the finished
parts assembled according to an external grand plan to produce
the final manufactured product. In a biological organism,
however, the "manufacturing" scheme is quite different: In the
first place, the "grand plan" is internal and not external: each
cell of the organism carries the "grand plan" -- the genome --
with specific parts of the plan activated in each cell type, and
the activation/inactivation of specific parts of the genome
differentially dynamic in various cell types during the
developmental process. Secondly, during development of the
embryo, body parts are developed in parallel, in tandem, in
sequence, with an intricate network of control loops, until
finally the complete developed product emerges in toto as a
functioning entity. How is this biological development and
assembly process orchestrated? One of the most spectacular
findings of this decade has been that flies and mice use the same
genes for specifying embryonic developmental regions along the
anterior-posterior axis of the body. In general, "homeotic" genes
are genes that control development, and "homeogenes" are the
subset of homeotic genes that contain "homeoboxes". A "homeobox"
is a part of a gene encoding a protein "homeodomain", a protein
domain that binds to DNA. (The protein functions as one of a
number of "*transcription factors".) The DNA-binding homeodomain
consists of approximately 60 amino acids, and these homeodomain
motifs are apparently involved in orchestrating the development
of a wide range of organisms. "Hox" genes are a subset of
homeogenes, the Hox genes encoding proteins (and protein
homeodomains) that determine positional cell differentiation and
development. Mutations in Hox genes result in the conversion of
one body part into another: for example, in the fruit fly
Drosophila, a specific Hox mutation results in a leg appearing
where an antenna usually appears. There are clusters of Hox genes
in the genome: e.g., 1 Hox cluster in *nematode worms, 2 Hox
clusters in the fruit fly Drosophila, 4 Hox clusters in
vertebrates. Since mammals have more clusters of Hox genes than
lower forms, it has been thought that Hox cluster duplication
facilitated the evolution of the vertebrate body plans.
... ... A. Amores et al (13 authors at 7 installations, US CA)
now report that *zebrafish (Danio verio) have 7 Hox clusters.
Thus, *teleosts, the most species-rich group of vertebrates,
appear to have more copies of these developmental regulatory
genes than do mammals, despite less complexity in the anterior-
posterior axis. The authors report that *phylogenetic analysis
and *genetic mapping suggest a *chromosome doubling event,
probably by whole genome duplication, after the *divergence of
*ray-finned and lobe-finned fishes, but before the teleost
*radiation. The authors state: "The conclusion that the genetic
complexity of Hox clusters in teleost fish has exceeded that of
mammals for more than 100 million years calls into question the
concept of a tight linkage of Hox cluster number and
morphological complexity along the body axis."
-----------
A. Amores et al: Zebrafish Hox clusters and vertebrate genome
evolution.
(Science 27 Nov 98 282:1711)
QY: John H. Postlethwait, Univ. of Oregon Eugene 541-346-1000.
-----------
Text Notes:
... ... *transcription factors: Transcription is the process by
which the genetic information in DNA is converted into RNA, and
transcription factors are a class of DNA-binding proteins that
regulate RNA transcription.
... ... *nematode worms: An abundant and ubiquitous phylum of
unsegmented roundworms.
... ... *zebrafish: A common tropical aquarium species.
... ... *teleosts: In general, this refers to any of the bony
fish, the most advanced in terms of evolution and the largest
group of fish. Besides the calcified internal skeleton, the most
obvious uniform characteristic of the teleost fish is their tail,
with upper and lower halves of about equal size, whereas in
cartilaginous fish the tail has two lobes of unequal size. Almost
all sport, commercial, and ornamental fish are teleosts.
... ... *phylogenetic analysis: In general, an analysis of
evolutionary history.
... ... *genetic mapping: (chromosome mapping; linkage mapping)
In general, elucidation of the linear arrangement of genes on a
*chromosome or of sites within a gene. 
... ... *chromosome: In cells with chromosomes, the
chromosomes are the physical structure into which DNA is
organized and on which genes are carried.
... ... *divergence: In this context, the acquisition of
dissimilar characteristics by related organisms in unlike
environments.
... ... *ray-finned and lobe-finned fishes: Actinopterygii and
Crossopterygii.
... ... *radiation: In this context, the term "radiation" refers
to the spread of a group of biological entities into new
environments with consequent diversification.
-------------------
Summary & Notes by SCIENCE-WEEK [http://scienceweek.com] 22Jan99
-------------------
Related Background:
A DROSOPHILA HOMOLOG OF RX VERTEBRATE HOMEOBOX GENE
Homeobox genes are a family of similar nucleotide sequences that
encode sequence-specific DNA binding proteins that are essential
for embryological development and cell differentiation. They were
first discovered in the fruit fly Drosophila, but they have
homologs in the genomes of many organisms, including humans and
plants. A homeodomain is a protein motif encoded by a homeobox
DNA sequence, and an {Rx} gene is a vertebrate homeobox gene that
has been linked to the embryological development of the
vertebrate eye. Xenopus is a vertebrate, a species of African
toad. ... ... Eggert et al (5 authors at 2 installations, DE CH)
report the isolation of an Rx gene from Drosophila (called DRx).
The homeodomains of the Drosophila and the Xenopus Rx genes are
identical, suggesting that the Drosophila DRx gene is a homolog
of the vertebrate Rx gene. The Drosophila gene is expressed
during early embryonic development, and later in the brain and
central nervous system, and the sequence conservation and
expression pattern suggest an important role of the gene during
brain development in Drosophila. But no expression of this gene
has been detected in embryological precursor tissue of the eye.
The authors suggest that vertebrate Rx genes might be involved in
brain patterning processes and specification of eye fields in
different phyla.
QY: Uwe Walldorf [walldorf@uni-hohenheim.de]
(Proc. Natl. Acad. Sci. US 3 Mar 98) (Science-Week 3 Apr 98)
-------------------
Related Background:
HOMEOBOX GENES AND ECHINODERM EVOLUTION
Echinoderms are members of a phylum of marine invertebrates, and
they include starfish, sea urchins, sea cucumbers, etc. Most
echinoderms exhibit radial symmetry, but the free-swimming larvae
are bilaterally symmetrical before they metamorphose into adults.
The evolution of the dramatic morphological changes evidenced in
echinoderms, which apparently evolved from bilaterally symmetr-
ical forms, is not yet clarified, and the problem is a challenge
to molecular evolutionary biologists. Homeobox is a family of
similar nucleotide sequences that encodes sequence-specific DNA-
binding proteins, and they are apparently essential for the
differentiation of various cell groups during embryonic develop-
ment. Homeobox sequences were first discovered in the fruit fly,
but they have homologues in many organisms, including humans.
Homeodomains are the protein motifs encoded by the homeobox DNA
sequences, these protein motifs apparently binding to DNA and
activating or repressing specific target genes. Christopher J.
Lowe and Gregory A. Wray (State University of New York Stony
Brook, US) report the expression domains in echinoderms of 3
developmental regulatory genes ([distal-less], [engrailed],
[orthodenticle]), all of which encode transcription factors that
contain a homeodomain, and evidence that evolutionary reorganiz-
ation of body architecture in echinoderms involved extensive
changes in the deployment and roles of homeobox genes. The
authors suggest this demonstrates the evolutionary lability of
regularity genes that are widely viewed as conservative.
QY: G. Wray [gwray@life.bio.sunysb.edu]
(Nature 16 Oct 97) (Science-Week 14 Nov 97)
-------------------
Related Background:
EVOLUTION: RENEWED INTEREST IN THE LANCELET (AMPHIOXUS)
One of the important questions in evolutionary biology concerns
the details of the path of evolution of the vertebrates from the
invertebrates. The vertebrates constitute a subphylum of the
chordates, which are animals that possess a "notochord" as
embryos and/or as adults. The notochord is a stiff rod of
cartilage supporting the nerve cord and present only in the
embryos of vertebrates. During the 19th century, the biologist
*Ernst Haeckel promoted a now defunct theory of "recapitulation",
sloganized as "*ontogeny repeats *phylogeny", the essence of the
theory proposing that embryonic stages represent past stages in
the evolution of the organism. This theory had a powerful impact
on late 19th century research in embryology, and thus the
presence of a notochord in particular lower forms was taken as
suggestive of the role of these particular forms in the evolution
of vertebrates. Of all such lower forms, perhaps none received
such popular attention as the lancelet (also called amphioxus), a
1 to 2 inch long invertebrate fishlike marine animal, which as an
adult possesses a semi-rigid notochord running from one end to
the other. Apparently the interest of evolutionary biologists in
the lancelet has in recent years revived. ... ... M.D. Stokes and
N.D. Holland present an extensive review of the biology of the
lancelet and of its history as a research object, and the authors
make the following points: 1) Around the beginning of the 20th
century, the rate of publication of research papers in lancelet
biology declined sharply and did not pick up again until
approximately 1960, when advances in electron microscopy
stimulated a new surge of interest. A second surge of interest,
which is still in full swing, was triggered approximately 10
years ago when lancelets began to be studied by the methods of
molecular biology, with the techniques of comparative molecular
genetics now being used to address classical questions concerning
the evolutionary origin of the vertebrates. 2) Molecular
biological studies have now shown that the lancelet is the
closest living invertebrate relative of the vertebrates. A
phylogenetic tree based on the DNA sequence of the large
*ribosomal subunits in various animal subphyla supports the view
that the *cephalochordates (of which the lancelet is a member)
are the sister group of the vertebrates. 3) Other clues to early
vertebrate evolution have been provided by studies of
developmental genes, which are remarkable conserved throughout
the animal kingdom, and which are clustered on a single
chromosome in the lancelet and on 4 separate chromosomes in
vertebrates. The current consensus is that modern lancelets and
vertebrates apparently had a cephalochordate-like ancestor in
common. The authors conclude: "Molecular biology has now shown
that Haeckel was correct in placing a lancelet-like creature at
the base of the vertebrates... Thus lancelets seem to have come
full circle in the history of biology. After years of neglect,
they have now regained the prominence that they enjoyed in the
last decades of the 19th century when they were the centerpiece
of Haeckel's recapitulation theory."
-----------
M.D. Stokes and N.D. Holland (2 installations, US)
The lancelet.
(American Scientist Nov/Dec 1998 86:552)
QY: M. Dale Stokes, Univ. of Calif. San Diego 619-534-2230.
-----------
Text Notes:
... ... *Ernst Haeckel (1834-1919): Haeckel was apparently the
first German biologist to promote Darwinism and evolution, and he
was one of the centers of the intense and often vituperative 19th
century controversy between science and religion. Haeckel was
also apparently the first to use the term "ecology" to refer to
the study of living organisms in relation to one another and to
the inanimate environment. A major difficulty with Haeckel's
recapitulation theory is that it produces too many apparent
errors when used to delineate evolutionary connections.
... ... *ontogeny: The development of an individual from zygote
to maturity. The term "zygote" refers to the cell formed by the
union of male and female gametes (sperm and egg cells).
... ... *phylogeny: The evolutionary history of a species or
group of species in terms of their derivation and relationships.
A "phylogenetic tree" is a schematic diagram that represents that
evolution.
... ... *ribosomal subunits: A ribosome (not to be confused with
riboZYME) is a small particle, a complex of various ribonucleic
acid component subunits and proteins that functions as the site
of protein synthesis in cells.
... ... *cephalochordates: (Acrania) A subphylum of marine
chordates characterized by the presence of a notochord, dorsal
nerve cord, and gill slits in both embryo and adult. They lack a
brain and vertebral column.
-------------------
Summary & Notes by SCIENCE-WEEK [http://scienceweek.com] 4Dec98
-------------------
Related Background:
A MOLECULAR TIMESCALE FOR VERTEBRATE EVOLUTION
A timescale is necessary for estimating rates of molecular and
morphological change in organisms, and for interpreting patterns
of macroevolution and biogeography. Timescales have usually been
obtained from the fossil record, where the earliest represent-
atives of two lineages establish a minimum time of divergence of
these lineages. An alternative method involves the clock-like
accumulation of sequence differences in certain genes. Estimates
from single genes may have large statistical errors, but studies
of multiple genes provide a more reliable estimate of divergence
time. ... ... Kumar and Hedges (Pennsylvania State University,
US) report an analysis of 658 nuclear genes to provide divergence
time estimates for mammalian orders and major lineages of
vertebrates. The molecular times agree with most early
(Paleozoic) and late (Cenozoic) fossil-based times, but indicate
major gaps in the Mesozoic fossil record. The authors propose
that at least 5 lineages of placental mammals arose more than 100
million years ago, and most of the modern orders seem to have
diversified before the Cretaceous/Tertiary extinction of the
dinosaurs. The authors suggest their molecular timescale for
vertebrate evolution will be useful in calibrating local
molecular clocks and in estimating intra-ordinal divergence times
more reliably, especially in groups with poor fossil records.
QY: S. Blair Hedges [sbh1@psu.edu]
(Nature 30 Apr 98 392:917) (Science-Week 22 May 98)
-------------------
Related Background:
A MODEL FOR THE EVOLUTION OF THE GENETIC CODE
Eukaryotic cells are cells with discrete organelles such as
nuclei, mitochondria, etc. As organelles, the mitochondria, which
are of prime importance in the oxygen metabolism of eukaryotes,
are a special class, since it is generally believed they probably
originated as primitive cells that established themselves in
symbiotic arrangements in the interiors of larger cells. The
mitochondria, in fact, carry their own DNA and thus their own
genetics. In mathematics, a Lie algebra (named after M.S. Lie
1842-1899) is a system of vector fields on a topological space in
which independent quantities are reduced to groupings whose
relationships are then subject to algebraic operations. In the
context of this report, the term "representation theory" refers
to the study of algebraic groups by the use of their represent-
ations, with the representation of a group given by a virtual
"mapping" of the group onto a group of another type. Pyrimidine
and purine are precursors of DNA nucleotide bases. A codon is the
elemental genetic coding unit, a triplet of 3 consecutive
nucleotides that define a specific amino acid. Some amino acids
are determined by more than one codon, leading to a degeneracy
(redundancy) in the genetic code. ... ... Bashford et al (3
authors at University of Tasmania, AU) present a model for the
structure and evolution of the eukaryotic and vertebrate
mitochondrial genetic codes based on the representation theory of
a Lie superalgebra, with a key role played by pyrimidine and
purine exchange symmetries in codon quartets. The authors suggest
that the group theoretical technique is able to give a succinct
account of many of the currently understood aspects of the
evolution of the genetic code and the observed degeneracy
structure of the codon:amino-acid correspondences, and that their
particular model is susceptible to quantitative verification.
QY: P.D. Jarvis [jarvis@oberon.phys.utas.edu.au]
(Proc. Natl. Acad. Sci. US 3 Feb 98)
(Science-Week 20 Feb 98)


6. 20TH CENTURY TRENDS IN US INFECTIOUS DISEASE MORTALITY
During the past 100 years, North America and Europe have
experienced a substantial decline in mortality and an increase in
life expectancy. What is called the "theory of epidemiologic
transition"  attributes these trends to the transition from "an
age of pestilence and famine", in which the mortality pattern was
dominated by high rates of infectious disease deaths, especially
in the young, to the current "age of degenerative and man-made
diseases" in which mortality from chronic diseases predominates.
According to one recent study, infectious diseases now account
for only 4.2 percent of all disability-adjusted life years lost
in countries like the US that have established market economies,
whereas chronic and neoplastic (i.e., cancer) diseases account
for 81 percent of life years lost. Until recently, it was assumed
that the epidemiological transition had brought about a permanent
reduction in infectious disease mortality in the US. But in the
1980s, it became evident that this was not the case.
... ... G.L. Armstrong et al (Centers for Disease Control and
Prevention, US) report a study of the trends in infectious
disease mortality in the US during the 20th century. Deaths due
to infectious diseases from 1900 to 1996 in the US were tallied
by using mortality tables. Trends in age-specific infectious
disease mortality were examined by using age-specific death rates
for 9 common infectious causes of death [*Note #1]. The authors
report that infectious disease mortality declined during the
first 8 decades of the 20th century from 797 deaths per 100,000
in 1900 to 36 deaths per 100,000 in 1980. From 1981 to 1995, the
mortality rate increased to a peak of 63 deaths per 100,000 in
1995 and declined to 59 deaths per 100,000 in 1996. Pneumonia and
influenza were responsible for the largest number of infectious
disease deaths throughout the century. Tuberculosis caused almost
as many deaths as pneumonia and influenza early in the century,
but tuberculosis mortality dropped off sharply after 1945.
Infectious disease mortality increased in the 1980s and early
1990s in persons aged 25 years and older and was mainly due to
the emergence of the acquired immunodeficiency syndrome (AIDS) in
25 t0 64 year-olds, and to a lesser degree to increases in
pneumonia and influenza deaths among persons aged 65 years and
older. The authors conclude: "Although most of the 20th century
has been marked by declining infectious disease mortality,
substantial year-to-year variation as well as recent increases
emphasize the dynamic nature of infectious diseases and the need
for preparedness to address them."
-----------
G.L. Armstrong et al: Trends in infectious disease mortality in
the United States during the 20th century.
(J. Amer. Med. Assoc. 6 Jan 99 281:61)
QY: Gregory L. Armstrong [gca3@cdc.gov]
-----------
Text Notes:
... ... *Note #1: The 9 disease categories tabulated were as
follows:
... 1. Pneumonia and influenza diseases
... 2. Tuberculosis
... 3. Diphtheria
... 4. Pertussis ("whooping cough")
... 5. Measles
... 6. Typhoid fever
... 7. Dysentery diseases
... 8. Syphilis and its sequelae
... 9. AIDS
-------------------
Summary & Notes by SCIENCE-WEEK [http://scienceweek.com] 12Mar99
-------------------
Related Background:
ON THE RELATION BETWEEN HUMAN DISEASE AND OFFICE BUILDINGS
The following disease entities have been associated with
employment in office buildings: Legionnaire's disease, Pontiac
fever, influenza, common cold, tuberculosis, hypersensitivity
pneumonitis, humidifier fever, dermatitis, rhinitis, asthma,
contact urticaria, laryngeal edema, and upper and lower respir-
atory tract irritation. Menzies and Bourbeau (McGill University,
CA), in a review of evidence regarding office-building related
illnesses, point out that workers in the indoor environments of
office-buildings now make up more than half the entire work force
of industrialized countries, and although there is little direct
evidence to implicate specific causative agents, there is suffic-
ient indirect evidence of building-related illness to warrant
preventive measures such as maintenance of an outdoor air supply
of at least 10 liters per second per person, and selection of
building materials that will not release pollutants or be used as
proliferation substrates by microbes or dust mites.
QY: Dick Menzies, Respiratory Epidemiology Unit, McGill
University, 1110 Pine Avenue W., Montreal, QC H3A 1A3 CA.
(New England J. Med. 20 Nov 1997) (Science-Week 28 Nov 97)


=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
 
IN FOCUS: ON THE STUDY OF COLLECTIVE PHENOMENA IN PHYSICS

"A number of common themes and elements unify the subfields of
collective phenomena. Among them are the concepts of long-range
order, changes of symmetry in phase transitions, collective
modes, low-lying excitations above the ground-state, Bose-
Einstein condensation, pairing, broken symmetry, order
parameters, and macroscopic quantum phenomena. Although certain
of these unities were recognized well before the Second World
War, even though often phrased in different language, recognition
alone did not weld the subfields together. And although
individuals did occasionally cross over among subfields in their
work (e.g., Landau on helium, superconductivity, and phase
transitions; Fritz London on superconductivity and helium), the
communities of researchers working on different problems of
collective phenomena did not generally see themselves as working
under a common umbrella. Only very gradually, in the 1950s and
1960s, did these subcommunities and subfields coalesce around the
unifying strands... Until the 1960s, phase transitions remained
somewhat apart from the streams that converged into many-body
physics. However, as superconductivity and superfluidity became
better understood, the attention of many-body physicists began to
turn to applications of their proven methods to problems of
critical phenomena... With the development of renormalization
group techniques starting in the mid-1960s, this area [critical
phenomena] too came under the umbrella, and the study of
collective phenomena had come together as a single area of the
physics of condensed matter."

-- L. Hoddeson et al: _Out of the Crystal Maze: Chapters from the 
   History of Solid-State Physics_
   (Oxford University Press, Oxford 1992, p.584,586)


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A COMPLETE LIST OF SW FOCUS REPORTS

SCIENCE-WEEK Focus Reports are in-depth explicating texts and
summary groups concerning a single topic. The summary groups are
extracted from back issues of SW.

Here are the titles of all the current free Focus Reports
available at the SCIENCE-WEEK website [http://scienceweek.com].
A significant number of new reports have been added since the
last update:

SUMMARY GROUPS:
Alzheimer's Disease
Anthropology and Human Evolution
Astrophysics: Extrasolar Planets
Astrophysics: Gamma Ray Bursts
Astrophysics: Origin of the Solar System
Astrophysics: Quasars
Biology of Aging
Biology of Breast Cancer
Biology of Cancer: Angiogenesis Inhibition
Biology of Cancer: Tumor Suppressor Genes
Biology of Malaria
Biology of Parkinson's Disease
Bio-Taxonomy: The Woese-Mayr Controversy
Biotechnology
Cell Biology: Embryonic Stem Cells
Cell Biology: The Cell Cytoskeleton
Chaos Theory
Cloning and Genetic Engineering: Policy Aspects
Cosmology: Dark Matter
Cosmology: Models and Extrapolations
Earth Science
Earth Science: Origin of Water on Earth
Evolution
Evolution: Meteorite Impact and Mass Extinction
Evolution: The Dinosaur-Bird Linkage
Herpes Simplex Virus
HIV and AIDS
Immunology: Biological and Medical Aspects
Medical Biology: Prions
Medical Biology: Xenotransplantation
Microbial Drug Resistance
Molecular Biology: Apoptosis
Molecular Biology: Estrogen and Estrogen Receptors
Molecular Biology: Leptin and Obesity
Molecular Biology: Peptide Nucleic Acids
Molecular Biology: Protein Folding
Molecular Biology: RNA Folding
Neurobiology
Neurobiology: Human Brain Plasticity and Memory
Neurobiology: Ion Channels
Neurobiology: Melatonin and Circadian Rhythms
Neurobiology: Neurotransmitter Release
Nicotine and the Tobacco Industry
Origin of Life
Particle Physics: An Exchange on Relevance
Particle Physics: Gluons and Glueballs
Polymers
Quantum Dots and Quantum Computing
Quantum Mechanics
Science and Commerce in Conflict
Science and the Media
Science Education
Science Policy: Genetic Testing
Scientific Information Distribution
Solar System: Water on Jovian Moons
Theoretical Physics: String Theory

EXPLICATING TEXTS:
Atomic and Molecular Spectroscopy
Biological Cell Membranes (1)
Biological Cell Membranes (2)
The Birth of Galaxies and Stars
The Death of Stars
The Neuron
Viruses
Weak Bonds in Chemistry and Biology


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