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.

April 30, 1999 -- Vol. 3 Number 18

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We may or may not be majestic as a species,
but if one considers an astronomer sitting alone
on a cold night at a telescope on a mountain top,
one must conclude we are certainly obsessed with
knowing what and where we are.
-- Anonymous

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Contents of This Issue:

1. On Fraud in Science
2. On Quintessence and the Evolution of the Cosmological Constant
3. Genesis and Evolution of the 1997-1998 El Nino
4. On the Differentiation of Germ Cells
5. A Molecular Phylogeny of Reptiles
6. Evidence for Lack of Protective Effect of Dietary Fiber

-- In Focus: On the Future of the Human Species

-----------------------------------------------------------

1. ON FRAUD IN SCIENCE
There are two prevalent myths concerning scientific fraud: The
first myth states that since most scientific experiments are
replicated by other laboratories, science is self-correcting
because the discovery of fraud involving the fabrication of data
is inevitable. The second myth is that scientific papers
involving fabrication of data are extremely rare, with only a few
fraudulent papers published in any one year. Concerning the first
myth, it is not true that all or even most published experiments
are sooner or later replicated. What is true is that research
results that are of apparent great significance will probably be
replicated, but not other research results. These days, in the
front lines of fast-moving fields in science, few laboratory
heads are inclined to waste precious manpower and funds simply
replicating the work of others: the most successful research
strategy is to assume the relevant published product of other
laboratories is honest and take the next step, or better yet the
step after that, in the push to solve a hot problem. Concerning
the second myth, the evidence that exists suggests the number of
scientific papers involving fabricated data published each year
may involve hundreds and perhaps thousands of publications. For
example, the Office of Research Integrity of the US National
Institutes of Health (NIH) found that between 1993 and 1997, 61
researchers receiving its grants were involved in the fabrication
of data. The total number of NIH grants during the same period
was approximately 150,000. These figures produce a fabrication
rate for published papers of 0.0004, assuming each research grant
produced on average the same number of papers. This fabrication
rate concerns the biomedical sciences in the US (the area with
which NIH is concerned), but there is no evidence of a lower rate
in other areas of science. In 1998, the top 5600 scientific
journals published approximately 1 million articles, and it is
estimated this is approximately one-tenth of the total world
output. Considering only the top 1 million publications and
applying the fabrication rate derived from the NIH evidence, we
find the expected number of publications each year in all
scientific fields involving fabricated data is approximately 400
papers for the top 5600 journals, and perhaps as much as 10 times
that if all scientific journals are considered. It is certainly
true that these estimates involve some assumptions; it is also
true that a small fabrication rate applied to a large number of
published articles will yield a significant number of fraudulent
publications. In general, the idea that only a few fraudulent
scientific papers are published each year is probably a complete
fallacy. ... ... Alison Abbott (_Nature_) presents an extensive
review of official handling of the problem of scientific
misconduct (especially the problem of scientific fraud), the
author making the following points: 1) Although the incidence of
proven scientific fraud remains low, several high-profile cases
have convinced the research community of the need for effective
action, in particular by enforcing codes of good laboratory
practice. 2) The extent of scientific misconduct of the
"fabrication-falsification-plagiarism" type is hotly debated in
both the US and Europe. Some scientists fear that publicized
cases are merely the tip of an iceberg. Others remain convinced
that the overall incidence remains low, and even those with
direct experience of misconduct cases are often optimistic. 3) In
one survey, published in _American Scientist_ in 1993, between 6
and 9 percent of respondents said they were personally aware of
results that had been plagiarized or fabricated within their
faculties. 4) Many journal editors believe that breaches of the
traditional ethics of scientific publication are increasing, but
few editors are confident of how they should react. 5) Last year,
two foundations in Germany set up a project to determine how many
of the 550 journal papers and 80-odd book chapters written by two
German cancer researchers, Friedhelm Herrmann and Marion Brach
(see SW background material below), and some of their former
colleagues, included apparently fabricated data. Investigating
committees have already identified 58 papers by Herrmann and
Brach that involve apparently fabricated data, but investigation
of the publications is only 20 percent finished. The
investigation will take months to complete, and the intention is
to publish the results in an international journal.
-----------
Alison Abbott: Science comes to terms with the lessons of fraud.
(Nature 4 Mar 99 398:13)
Alison Abbott [a.abbott@nature.com]
-------------------
Summary by SCIENCE-WEEK [http://scienceweek.com] 30Apr99
-------------------
Related Background:
RESEARCH FRAUD SCANDAL IN GERMANY: AN UPDATE
What has been called in Germany and elsewhere "Germany's biggest
ever scientific fraud" is apparently still without closure. The
essence of the case (details are provided in the attached
background material) is the involvement of 2 molecular
biologists, Marion Brach and Friedhelm Herrmann (who both worked
and lived together during their scientific collaboration at
Harvard, Freiburg, and Berlin), in an alleged systematic
fabrication of data in 37 publications over a 9 year period
ending in 1996. It is now nearly 2 years after the affair was
first revealed, but no case has yet been brought to court.
Prosecutors in Germany are evidently finding it more difficult
than expected to bring charges against the two scientists
involved, both of whom achieved full professorships on the basis
of the apparently fraudulent research reports. After being
dismissed as full professor at the University of Lubeck in 1997
(she assumed the post in 1996), Brach evidently left Germany and
she is now reported to be working in New York. Herrmann resigned
his professorship at the University of Ulm and now works in
private medical practice in Munich. Herrmann continues to deny
any involvement in misconduct, and says the failure to bring
charges against him is proof of his innocence. Meanwhile
Germany's main university research funding agency, Deutsche
Forschungsgemeinschaft, has set up a task force to determine the
"full extent of any scientific damage" caused by the alleged
fraudulent publications.
-----------
A. Abbott (*Nature*)
German scientists may escape fraud trial.
(Nature 8 Oct 98 395:532)
QY: Alison Abbot [a.abbott@nature.com]
-------------------
Summary by SCIENCE-WEEK [http://scienceweek.com] 6Nov98
-------------------
Related Background:
ABDERHALDEN'S FRAUD REVISITED
Last year was not a good year for German biological and medical
science, since 1997 was marked by a major fraud scandal involving
two full professors apparently involved in the fabrication of
data published in dozens of scientific papers during a 9-year
period. That story is not yet finished (see background material
below). Now from Germany comes the publication of a "commentary"
by two scientists, U. Deichmann and B. Muller-Hill, the
commentary revisiting what has come to be considered the
fraudulent career of German scientist Emil Abderhalden
(1877-1950). Abderhalden was a biochemist involved in designing
tests for various clinical disease entities, the tests involving
what he called "defense enzymes" (Abwehrfermente), enzymes which
he claimed to have identified, and which according to his
analyses were specific proteases produced when humans were
challenged by foreign proteins. During the years 1912 to 1950,
Abderhalden enjoyed the status of one of the most eminent
scientists in Germany, was professor of physiology and
physiological chemistry at Halle University, president of the
oldest German academy of science (the Leopoldina), editor of
several journals, and author of several books and more than 1000
research papers -- and all of this notwithstanding, the consensus
today is that nearly all of his research on the so-called
"defense enzymes" was completely fraudulent, with scores of
colleagues and underlings either explicitly or implicitly
colluding in the fraud over a period of decades. It is an ugly
story with political tangents (e.g., Joseph Mengele, the
notorious Auschwitz doctor, was one of Abderhalden's proteges).
In their commentary, Deichmann and Muller-Hill conclude: "The
elite of today [the biomedical elite in Germany] are loyal
students of the old elite, and they have learned and internalized
the old values. Has medical, clinical science in Germany today
really changed that much? We doubt it. The Brach-Herrmann-
Mertelsmann affair provides a brief glimpse into the abyss of
medical science in Germany. Will it be soon forgotten by the
German medical elite, or will there be real change in the spirit
of true science?" [Editor's note: Roland Mertelsmann, Professor
Herrmann's department head, was co-author of 25 suspected papers
produced by Herrmann, but has pleaded non-involvement in the
research.]
QY: Ute Deichmann, Institute of Genetics, Cologne University,
Weyertal 121, 50931, Koeln, DE.
(Nature 14 May 98 393:109) (Science-Week 5 Jun 98)
-------------------
Related Background:
GERMAN RESEARCHER ADMITS FRAUD AND CHARGES ACADEMIC COVER-UP
Producing another chapter in the scientific fraud case that has
caused an apparent sensation in Germany, Marion A. Brach, one of
the accused scientists, has published a letter in the journal
*Nature* in which she points out the following: 1) She has
confessed to falsifying scientific papers; 2) she has resigned
her position as a full professor at the University of Lubeck; 3)
she does not believe further victimization is appropriate; 4) she
has concluded that the various German investigating commissions
met only with the intention of limiting damage to the German
academic community rather than with the intention of discovering
the full extent of culpability; 5) the German government has
reneged on its legal agreement to provide her with severance pay
following her early confession and resignation; 6) official
bodies have found it expedient to imply that she was the major or
only culprit in the affair.
QY: Marion A. Brach, c/o Walter F. Kalthoff, Pacellistr. 14,
D-80333, Muenchen, DE.
(Nature 2 Apr 98) (Science-Week 17 Apr 98)
-------------------
Related Background:
MORE DEVELOPMENTS IN GERMAN SCIENTIFIC FRAUD CASE
The scientific fraud case that has been shocking the German
intellectual community these past months, and which is claimed to
be the worst case of scientific fraud in that country since 1945,
continues to be a public spectacle. The scandal involves two
German molecular biologists, Marion Brach (who has resigned as a
Professor at Lubeck University), and Friedhelm Herrmann (a
suspended Professor at Ulm University). Brach has admitted
falsifying published data while she worked under the supervision
of Herrmann at the Max Delbruck Center for Molecular Medicine a
few years ago. Herrmann claims he is only a clinician and had
nothing to do with the laboratory bench work. Herrmann is a
prominent hematologist and a leading genetic therapy researcher.
The two biologists had worked together for some time, and each
received professorships on the basis of that work. (Herrmann's
salary was apparently US$278,000 per year). Now it has been
announced that Herrmann is suing various academic investigators
in the case for DM10 million (US5.6 million) in compensation for
damage to his career. In addition, there is now a claim by a new
investigation team that the two accused researchers also
published falsified data earlier in their careers.
(Nature 11 Sep) (Science-Week 26 Sep 97)
-------------------
AN UPROAR OVER SCIENTIFIC FRAUD IN GERMANY
The German scientific community was rocked by scandal this
spring, and the resulting repercussions are apparently not yet
complete. The brouhaha involves two German molecular biologists,
Marion Brach (recently resigned as a Professor at Lubeck
University), and Friedhelm Herrmann (a suspended Professor at Ulm
University). Brach has admitted falsifying published data while
she worked under the supervision of Herrmann at the Max Delbruck
Center for Molecular Medicine a few years ago. Herrmann claims he
is only a clinician and had nothing to do with the laboratory
bench work. Herrmann is a prominent hematologist and a leading
genetic therapy researcher. The two biologists have worked
together for some time, and each received professorships on the
basis of that work. All of that work is now being investigated,
and the German government has established a commission of
international scientific experts to discuss research standards
and the procedures for scientific oversight in German and
internationally.
(Science 11 Jul 97) (Science-Week 18 Jul 97) 


2. ON QUINTESSENCE AND THE EVOLUTION OF THE COSMOLOGICAL CONSTANT
In cosmology, the "cosmological constant" is a mathematical term
introduced by Einstein into the equations of general relativity,
the purpose to obtain a solution of the equations corresponding
to a "static universe". The term describes a pressure (if
positive) or a tension (if negative) which can cause the Universe
to expand or contract even in the absence of any matter. In other
words, the cosmological constant represents an effective "vacuum
energy". When the expansion of the Universe was discovered,
Einstein apparently began to regard the introduction of this term
as a mistake, and he described the cosmological constant as the
"greatest mistake of my life". But the term has reappeared as the
proposed source of apparent accelerated cosmic expansion.
... ... P.J.E. Peebles (Princeton University, US) presents a
short review of current ideas concerning the cosmological
constant, the author making the following points: 1) Contrary to
expectations, the evidence is that the Universe is expanding at
approximately twice the velocity required to overcome the
gravitational pull of all the matter the Universe contains. The
implication of this is that in the past the greater density of
mass in the Universe gravitationally slowed the expansion, while
in the future the expansion rate will be close to constant or
perhaps increasing under the influence of a new type of matter
that some call "quintessence". 2) Quintessence began as
Einstein's cosmological constant, Lambda. It has negative
gravitational mass: its gravity pushes things apart. 3) Particle
physicists later adopted Einstein's Lambda as a good model for
the gravitational effect of the *active vacuum of quantum
physics, although the idea is at odds with the small value of
Lambda indicated by cosmology. 4) Theoretical cosmologists have
noted that as the Universe expands and cools, Lambda tends to
decrease. As the Universe cools, *symmetries among forces are
broken, particles acquire masses, and these processes tend to
release an analogue of *latent heat. The vacuum energy density
accordingly decreases, and with it the value of Lambda. Perhaps
an enormous Lambda drove an early rapid expansion that smoothed
the primeval chaos to make the near uniform Universe we see
today, with a decrease in Lambda over time to its current value.
This is the cosmological *inflation concept. 5) The author
suggests that the recent great advances in detectors, telescopes,
and observatories on the ground and in space have given us a
rough picture of what happened as our Universe evolved from a
dense, hot, and perhaps quite simple early state to its present
complexity. Observations in progress are filling in the details,
and that in turn is driving intense debate on how the behavior of
our Universe can be understood within fundamental physics.
----------
P.J.E. Peebles: Evolution of the cosmological constant.
(Nature 4 Mar 99 398:25)
QY: P.J.E. Peebles [pjep@pupgg.princeton.edu]
-----------
Text Notes:
... ... *active vacuum of quantum physics: This 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.
... ... *symmetries among forces are broken: If a theory or
process does not change when certain operations are performed on
it, the theory or process is said to possess a symmetry with
respect to those operations. For example, a circle remains
unchanged under rotation or reflection, and a circle therefore
has rotational and reflection symmetry. The term "symmetry
breaking" refers to the deviation from exact symmetry exhibited
by many physical systems, and in general, symmetry breaking
encompasses both "explicit" symmetry breaking and "spontaneous"
symmetry breaking. Explicit symmetry breaking is a phenomenon in
which a system is not quite, but almost, the same for two
configurations related by exact symmetry. Spontaneous symmetry
breaking refers to a situation in which the solution of a set of
physical equations fails to exhibit a symmetry possessed by the
equations themselves.
... ... *latent heat: In general, this is the quantity of heat
absorbed or released when a substance changes its physical phase
(e.g., solid to liquid) at constant temperature.
... ... *inflation concept: The inflationary model, first
proposed by Alan *Guth in 1980, proposes that quantum
fluctuations in the time period 10^(-35) to 10^(-32) seconds
after time zero were quickly amplified into large density
variations during the "inflationary" 10^(50) expansion of the
universe in that time frame.
-------------------
Summary & Notes by SCIENCE-WEEK [http://scienceweek.com] 30Apr99
-------------------
Related Background:
INFLATION IN A LOW-DENSITY UNIVERSE
There is an apparent consensus among cosmologists that recent
observational evidence is not consistent with the current
"*inflation theory" of the early evolution of the Universe, and
that to keep this theory relevant requires either the postulate
of an exotic form of energy or the addition of "a layer of
complexity" to inflation theory. ... ... M.A. Bucher and D.N.
Spergel (2 installations, UK US) present a review of the second
option, the authors making the following points: 1) Despite its
success, the standard *Big Bang theory cannot answer several
important questions: Why is the density and temperature of the
present Universe so uniform? Why did the early Universe have any
density variations at all? Why is the rate of cosmic expansion
just enough to counteract the collective gravity of all the
matter in the Universe? 2) The failure of the standard Big Bang
theory to answer these questions provoked, in the 1980s, the
formulation of the theory of inflation by Guth, Sato, Linde,
Albrecht, Steinhardt and others. 3) Inflation theory predicts a
flat (i.e., Euclidean) and uniform Universe, with an observed
value of the *Omega parameter either exactly 1 or so close to 1
that the deviation is not detectable. The implication of an Omega
value of 1 is that the cosmic gravitational energy exactly equals
the cosmic kinetic energy (i.e., the energy contained in the
motion of matter as space expands). The problem is that a wide
variety of recent astronomical observations involving galaxy
clusters and distant supernovae suggest that gravity is too weak
to combat cosmic expansion, that the density of matter must be
much less than predicted, and that the value of the Omega
parameter is equal to approximately 0.3. 3) The authors propose
there are 3 ways to interpret this result: a) Standard inflation
theory is completely wrong. Or b) Standard inflation theory is
correct: the Universe is flat, but an additional new form of
energy exists, and this is responsible for what appears to be an
accelerating expansion. Or c) Standard inflation theory is
partially correct, and its assumption of the inevitability of a
flat Universe needs to be revised. 4) The focus of the authors is
on the 3rd option. They review a revision of standard inflation
theory, the revision involving the introduction of a "*false-
vacuum decay" preceding the standard inflation, this false-vacuum
decay producing nonuniform "bubbles" of expansion [*Note #1]. The
new conception is called "open inflationary theory". 5) The
authors state that at the current levels of precision,
observations cannot distinguish between the predictions of the 2
theories of inflation. The authors suggest the "moment of truth"
will come with the planned deployment late next year of the
*Microwave Anisotropy Probe, and the launch in 2007 of its
European counterpart, *Planck. These satellites will perform
observations similar to those of the *Cosmic Microwave Background
Explorer (COBE) nearly a decade ago, but at a much higher
resolution. The authors suggest these new satellites will be able
to resolve which of the 3 theoretical options is correct: a) an
abandonment of any inflation theory; b) standard inflation theory
with a new form of energy; c) open inflation theory.
-----------
M.A. Bucher and D.N. Spergel: Inflation in a low-density
Universe.
(Scientific American January 1998)
QY: Martin A. Bucher, University of Cambridge, UK.
-----------
Editor's note: In addition to the background material below,
further material on this subject was presented last week in the
SW issue of 5 Feb 99. Also, there are a number of relevant SW
Focus Reports available at [http://scienceweek.com/swfr.htm].
-----------
Text Notes:
... ... *inflation theory: The inflationary model, first proposed
by Alan Guth in 1980, proposes that quantum fluctuations in the
time period 10^(-35) to 10^(-32) were quickly amplified into
large density variations during the "inflationary" 10^(50)
expansion of the universe in that time frame.
... ... *Big Bang theory: The Big Bang theory is the general
cosmological model that proposes that all matter and radiation in
the universe originated in an explosion at a finite time in the
past.
... ... *Omega parameter: Another approach to the Omega parameter
is to define it as the ratio of the density of matter (or energy)
in the Universe to the theoretical density required for flatness.
An Omega with a value of greater than 1 implies a closed
Universe; a value less than 1 implies an open Universe; a value
equal to 1 implies a flat Universe.
... ... *false-vacuum decay: A "false vacuum" is a peculiar state
of matter which has never been observed but whose properties are
unambiguously predicted by *quantum field theory. Essentially,
the idea of a false vacuum refers to a miniature energy minimum
above the true minimum, a saddle "trap". The most peculiar
property of the false vacuum is probably its pressure, which is
both large and negative. The term "false-vacuum decay" refers to
a breaking out of the trap, in this case via *quantum mechanical
tunneling through the miniature energy barrier, and then a fall
to the true zero-point (minimum vacuum energy). The application
of the idea of false vacuum to the inflation model was already
well underway in the late 1980s by Guth and others.
... ... *quantum field theory: Quantum field theory is the
mathematical fusion of quantum mechanics with special relativity
theory.
... ... *quantum mechanical tunneling: "Tunneling" is a quantum
mechanical phenomenon involving an effective penetration of an
energy barrier resulting from the width of the barrier being less
than the wavelength of the particle.
... ... *Note #1: It should be noted that this idea was already
described in the late 1980s by Alan Guth and others.
... ... *Microwave Anisotropy Probe: Information on this
satellite project can be found at URL [http://map.gsfc.nasa.gov].
... ... *Planck: Information on this satellite project can be
found at [http://astro.esctec.esa.nl/SA-general/Projects/Planck].
... ... *Cosmic Microwave Background Explorer (COBE): A NASA
orbiting satellite launched in 1989 and dedicated to the study of
the *cosmic microwave background radiation. The most important
results were the discoveries of irregularities in the cosmic
background radiation on the level of one part in 10^(5), and the
confirmation that the spectrum of the cosmic background radiation
is that of a black body with a temperature of 2.73 degrees
kelvin.
... ... *cosmic microwave background radiation: The cosmic
microwave background is black-body radiation (the emission
radiation of a perfect absorber of radiation) at a present
temperature of 2.73 degrees Kelvin, and has an almost equal
intensity in all directions in space. The deviations from
isotropic intensity, however, are of extreme importance in
theoretical cosmology. The cosmic background radiation is
predicted by the Big Bang theory and is considered one of the
most important pieces of evidence for it.
-------------------
Summary & Notes by SCIENCE-WEEK [http://scienceweek.com] 12Feb99
-------------------
Related Background:
ASTROPHYSICS: ON ACCELERATING COSMIC EXPANSION
The idea of cosmic expansion derives from the observation that
radiation from distant galaxies is *redshifted, and the consensus
is that the distance between clusters of galaxies is continuously
increasing, with all galaxies beyond the Local Group apparently
receding from us [*Note #1]. In other words, the Universe as a
whole is expanding, a phenomenon discovered by Edwin Hubble in
1929 but previously suggested by several theoretical cosmologists
(e.g., A. Friedmann [1922], G. Lemaitre [1927]). This expansion
is the observational basis of the *Big Bang theory. Essential to
the study of cosmic expansion is the accurate measurement of
intergalactic distances, and such measurement is dependent on the
use of "standard candles", astronomical objects whose intrinsic
brightness is known and whose distance can therefore be
calculated from apparent brightness. ... ... C.J. Hogan et al (3
authors at 3 installations, US CL) present a review of current
research on the temporal history of cosmic expansion, with
emphasis on recent work concerning the use of *type 1a supernovae
as standard candles. The authors make the following points: 1)
Until recently, the intrinsic brightness of all standard candles
used in observations has been found to be too variable, changing
with the evolution of the object or showing too much diversity
from one object to the other. However, during the past decade,
astrophysicists have been able to precisely determine the
intrinsic brightness of one kind of astronomical object, the type
1a supernova, and these objects have become the best calibrated
standard candles known to astronomers. Currently, observations of
type 1a supernovae are challenging decades of conventional ideas
concerning cosmic expansion. 2) Locating distant supernovae
involves taking images of the same part of the sky a few weeks
apart and searching for changes that might be exploding stars.
Because the digital light detectors can precisely count the
number of photons in each picture element, one makes a simple
subtraction of the first image from the second and looks for
significant differences from zero. With present equipment,
thousands of galaxies are checked in each image pair... After
supernovae candidates are located, the *Keck telescopes in
Hawaii, the largest optical instruments in the world, are pointed
at the objects, and critical observations establish whether or
not the objects discovered are in fact type 1a supernovae. The
observations are then used to gauge the intrinsic brightness of
the objects more exactly and to determine their redshifts... Two
teams have now studied a total of approximately 40 high redshift
supernovae, objects that erupted between 4 and 7 billion years
ago, when the universe was between one-half and two-thirds of its
present age. The results have been surprising: the supernovae are
fainter than expected. The difference is slight, the distant
supernovae on average only 25 percent dimmer than forecast, but
this result is enough to call long-standing cosmological theories
into question. The conclusion from the observations is that the
cosmic expansion is slowing less quickly than previously thought.
3) If the Universe is made of normal matter, gravity must
steadily slow the cosmic expansion. A reduced slowing, as
indicated by the supernovae measurements, implies that the
overall density of matter in the Universe is low... However, the
big surprise is that the observed supernovae are fainter than
predicted even for a nearly empty universe. Taken at face value,
the observations appear to require that expansion is actually
accelerating with time. This is consistent with the "vacuum
energy" embodied in Einstein's equations as the so-called
"*cosmological constant". Unlike ordinary forms of mass and
energy, the vacuum energy adds gravity that is repulsive and can
drive the Universe apart at ever increasing speeds. The authors
conclude: "Evidence for a strange form of energy imparting a
repulsive gravitational force is the most interesting result we
could have hoped for, yet it is so astonishing that we and others
remain suitably skeptical."
-----------
C.J. Hogan et al: Surveying space-time with supernovae.
(Scientific American January 1999)
QY: Craig J. Hogan, Univ. of Washington Seattle 206-543-8992.
-----------
Text Notes:
... ... *redshifted: Redshift (symbol: z) is a lengthening of the
wavelengths of electromagnetic radiation from a source caused
either by the movement of the source (Doppler effect) or by the
expansion of the universe (cosmological redshift). Redshift is
defined as the change in wavelength of a particular spectral line
divided by the unshifted wavelength of that line. Large redshifts
imply large radial velocities (which imply large distances,
according to current cosmological theory), but at redshifts
greater than about 0.2 there is a relativistic divergence from a
linear relation. A redshift of 4.0 corresponds to an object
receding with a radial velocity 92% that of the velocity of
light. The largest astrophysical redshifts so far observed are of
the order of z = 4.9.
... ... *Note #1: In the expansion model, it is the space between
widely separated objects that is expanding. Neighboring objects,
such as close pairs of galaxies, do not move apart because their
mutual gravitational attraction exceeds the effect of the
cosmological expansion. However, the distance between two widely
separated galaxies, or clusters of galaxies, will increase as the
Universe expands.
... ... *Big Bang theory: The Big Bang theory is the general
cosmological model that proposes that all matter and radiation in
the universe originated in an explosion at a finite time in the
past.
... ... *type 1a supernovae: Type 1a supernovae are believed to
be *white dwarf stars that have accreted enough matter from
another star to be pushed over a mass threshold and into a
thermonuclear explosion.
... ... *white dwarf star: White dwarf stars are extremely dense
and compact stars that have undergone gravitational collapse.
They are the final stage in the evolution of low-mass stars after
they have lost their outer layers. White dwarf stars are about
the size of Earth, but with a mass about that of the Sun.
... ... *Keck telescopes: The Keck telescopes are a pair of twin
telescopes at the W. M. Keck Observatory on Mauna Kea, HI US,
each with 10 meter mirrors, the pair constructed 1992-1996. The
installation is managed by the University of California (US) and
the California Institute of Technology (US).
... ... *cosmological constant: A mathematical term introduced by
Einstein into the equations of general relativity, the purpose to
obtain a solution of the equations corresponding to a "static
universe". The term describes a pressure (if positive) or a
tension (if negative) which can cause the Universe to expand or
contract even in the absence of any matter ("vacuum energy").
When the expansion of the Universe was discovered, Einstein
apparently began to regard the introduction of this term as a
mistake, and he described the cosmological constant as the
"greatest mistake of my life". But the term has reappeared as the
proposed source of apparent accelerated cosmic expansion.
-------------------
Summary & Notes by SCIENCE-WEEK [http://scienceweek.com] 22Jan99
-------------------
Related Background:
COSMOLOGY: THE END OF THE OLD MODEL UNIVERSE
Cosmologists are apparently expecting the near-future necessity
for profound conceptual alterations in their field. Peter Coles
(University of London, UK) presents a short review of the current
situation and makes the following points: 1) Observations only
recently made possible by improvements in astronomical
instrumentation have put theoretical models of the Universe under
intense pressure. The standard ideas of the 1980s about the shape
and history of the Universe have now been abandoned -- and
cosmologists are now taking seriously the possibility that the
Universe is pervaded by some sort of "vacuum energy" whose origin
is not at all understood. 2) The weakness of the Big Bang model
is that the numerical values of certain essential parameters in
the model (the Hubble constant, the density parameter, and, in
some versions, the cosmological constant) are not predicted by
theory, and thus the parameters must be inferred from
observations. 3) The Big Bang model does not deserve to be called
a "theory" unless and until it can explain how nonuniformities of
galaxies and clusters of galaxies came into being and evolved. 4)
The Cold Dark Matter model of structure formation, first proposed
in the 1980s, is in serious difficulty because the consequent
significant gravitational brake on expansion is not evident, and
in fact expansion may be accelerating. Current observations
coupled with current dynamical arguments all suggest a global
density of matter in the Universe less than the value required to
make the Universe recollapse. 5) The existence of a cosmological
constant (or vacuum energy) of the required size necessary to
make the basic cosmological models work is not at all explained
by current theories of the fundamental interactions of matter. 6)
There is every reason to be confident that the important issues
will soon be resolved, because a data explosion is about to
engulf cosmology, a new generation of galaxy surveys. The Sloan
Digital Sky Survey, for example, will encompass more than a
million galaxies. The cosmological community is bracing itself
for the arrival of these enormous new data sets and the new
insights they will surely bring. 7) It is possible that none of
the available models will fit all the new data. Coles concludes:
"For many of us, that is the most exciting possibility of all, as
we would have to move to stranger theories, perhaps not even
based on General Relativity."
QY: Peter Coles [p.coles@qmw.ac.uk]
(Nature 25 Jun 98 393:741) (Science-Week 17 Jul 98)


3. GENESIS AND EVOLUTION OF THE 1997-1998 EL NINO
The term "El Nino" refers to a current of warm water that
periodically flows along the western coast of South America. The
name derives from Spanish and means "the Child", an association
with the Christmas season, the usual time for the formation of
the current. The "El Nino Southern Oscillation" (ENSO) is a shift
in the climate and ocean currents of the Pacific region that
occurs approximately once every 7 years. The equatorial
countercurrent of warm water from the west overrides the cold-
water Peru current from the south, and the consequent suppression
of the nutrient-rich *upswelling of cold water may result in die
off of *plankton and fish populations. The 1997-1998 El Nino was
by some measures the strongest on record, with major climatic
impacts around the world. A newly-completed atmosphere-ocean
system tracked this El Nino in detail, and the unprecedented
measurements are apparently challenging existing theories about
El Nino climate swings. In particular, present climate forecast
models apparently underpredicted the strength of this El Nino
before its onset. ... ... Michael J. McPhaden presents a review
of the new El Nino data, the author making the following points:
1) The ENSO observing system, consisting of satellite and in situ
measurements, was fully in place in time to capture the 1997-1998
El Nino. The new data provided not only the most comprehensive
description to date of a major El Nino event, but also led to
improved long-range seasonal weather forecasts around the globe.
2) In early 1997, a weakening and reversal of the *trade winds in
the western and central equatorial Pacific led to the rapid
development of unusually warm sea-surface temperatures east of
the international dateline. The western Pacific warm pool
(surface waters greater than approximately 29 degrees centigrade)
migrated eastward with the collapse of the tradewinds, and the
so-called equatorial "cold tongue" -- the strip of cool water
related to equatorial upswelling that normally occupies the
eastern and central Pacific between the coast of South America to
the international dateline -- failed to develop in *boreal summer
and fall 1997. The El Nino developed so rapidly that each month
from June to December 1997 a new monthly record high was set for
sea surface temperatures in the easter equatorial Pacific. 3) It
was not until the trade winds abruptly returned to near normal
strength in the eastern Pacific in mid-May 1998 that the cold
subsurface waters could be efficiently upswelled. Sea-surface
temperatures in the equatorial cold tongue then plummeted because
of the close proximity of the *thermocline to the surface. At one
location, sea-surface temperature dropped 8 degrees centigrade in
30 days, more than 10 times the normal cooling rate at that time
of year. The El Nino was brought to an end, and cold conditions
(called "La Nina") were established in its place. 4) The
predictability of the El Nino Southern Oscillation is ultimately
linked to large-scale wave dynamics that redistribute upper ocean
heat and mass on seasonal to interannual time scales. The skill
of the present ENSO forecasting schemes is limited by a number of
factors, such as model imperfections, errors in model initial
conditions, and tendencies toward *chaos in the climate system.
5) Further research is required to better understand the
multiscale interactions that potentially affect the ENSO cycle,
and to translate that understanding into improved climate
forecasting capabilities.
-----------
M.J. McPhaden: Genesis and evolution of the 1997-1998 El Nino.
(Science 12 Feb 99 283:950)
QY: Michael J. McPhaden [mcphaden@pmel.noaa.gov]
-----------
Text Notes:
... ... *upswelling: In this context, an "upswelling" is a
persistent and rising cold-water current in an oceanic
circulation system.
... ... *plankton: The term "plankton" is a general designation
for various drifting microscopic aquatic organisms in the upper
regions of the oceans.
... ... *trade winds: In general, easterly prevailing winds that
blow toward the equator from latitudes 30 degrees north and south
of the equator. The word "trade" arises from the fact that these
winds propelled the ships that explored the Americas and also
propelled cargo-bearing ships to the Americas from Africa and
Europe.
... ... *boreal: In general, relating to northern geographical
regions. Thus, the time-frame of a boreal summer is also the
time-frame of a Southern hemisphere winter.
... ... *thermocline: A water zone of rapidly decreasing
temperature and increasing density.
... ... *chaos: In this context, the term "chaos" refers to 
unpredictable behavior arising in a system that obeys
deterministic laws but exhibits unpredictability. The essential
idea is that in certain systems small perturbations may produce a
cascade of larger perturbations, so that eventually the behavior
of such systems cannot be predicted from prior states no matter
if the systems appear simple and obey deterministic laws.
-------------------
Summary & Notes by SCIENCE-WEEK [http://scienceweek.com] 30Apr99
-------------------
Related Background:
ATMOSPHERIC SCIENCE: EL NINO DYNAMICS
The term "El Nino" was originally used by Peruvian fishermen for
a warming of coastal waters that begins around Christmas (*El
Nino* is Spanish for "the Christ child"). The term is now used to
refer to the large-scale warming of the entire tropical Pacific
that takes place every 4 years on average and alternates with an
opposite cold phase (sometimes called La Nina).
... ... J.D. Neelin and M. Latif present a review of current
models of El Nino dynamics, the authors making the following
points: 1) The El Nino/Southern Oscillation phenomenon (called
ENSO) is the strongest source of natural variability in Earth's
climate system. Although ENSO originates in the tropical
latitudes of the Pacific Ocean, its climate impact is felt
globally. Variations in major rainfall systems that are
attributed to ENSO range from droughts in Indonesia and Australia
to storms and flooding in Ecuador and the US. 2) The crucial role
of the interaction between the ocean and the atmosphere in the
tropical Pacific was first postulated in 1969 by *Jacob Bjerknes,
and the development of quantitative models has progressed during
the past 3 decades. The essence of the current Bjerknes
hypothesis, as it is called, is that ENSO arises as a coupled
cycle in which anomalies in sea surface temperature in the
Pacific cause the trade winds to strengthen or slacken and, in
turn, drive the changes in ocean circulation that produce
anomalous sea surface temperatures. Ocean-atmosphere feedback can
amplify perturbations in either the equatorial sea surface
temperature or what is called the Walker Circulation -- the
thermodynamic circulation of air parallel to the equator. 3)
Although the oscillatory aspect of ENSO behavior is now
understood reasonably well, the irregularity of the observed
cycle is a subject of active research. There are currently 3
contending hypotheses for the source of ENSO irregularity: a)
*deterministic chaos within the *nonlinear dynamics of the slow
components of the coupled system; b) uncoupled atmospheric
weather noise; c) long-term variation in the climatic state
affecting ENSO. Since the irregularity of ENSO limits its
predictability, and since these 3 sources of irregularity affect
predictability differently, this particular issue has practical
as well as theoretical importance. The authors conclude: "We must
bear in mind... that only for particular circumstances can we
expect that forecasts will push past the limits to predictability
set by the internal variability of the atmosphere."
----------
J.D. Neelin and M. Latif: El Nino dynamics.
(Physics Today December 1998)
QY: J. David Neelin, Univ. of Calif. Los Angeles 310-825-4321.
-----------
Text Notes:
... ... *Jacob Bjerknes (1897-1975): Norwegian-American
meteorologist, not to be confused with his father Vilhelm
Bjerknes (1862-1951), the noted Norwegian atmosphere physicist.
... ... *deterministic chaos: See the note on chaotic
fluctuations in the following background report.
... ... *nonlinear dynamics: In general, this refers to any
dynamical system in which some or all of the behavior of the
system is not a linear function of the input to the system.
-------------------
Summary & Notes by SCIENCE-WEEK [http://scienceweek.com] 1Jan99
-------------------
Related Background:
ON CLIMATE FORCINGS IN THE INDUSTRIAL ERA
A "climate forcing" is an imposed perturbation of the Earth's
energy balance with space, for example, a change of the solar
radiation incident on the planet, or a change of carbon dioxide
in the Earth's atmosphere. The unit of measure of climate forcing
is Watts per square meter. Thus, the forcing due to the increase
of atmospheric carbon dioxide since pre-Industrial times is
approximately 1.5 Watts per square meter. Climate change is
combination of deterministic response to forcings and *chaotic
fluctuations -- the chaos a consequence of the nonlinear
equations governing the dynamics of the system. Quantitative
knowledge of all significant climate forcings is needed to
establish the contribution of deterministic factors in observed
climate change and to predict future climate. J.E. Hansen et al,
in a review of current considerations concerning climate forcings
in the Industrial era, make the following points: 1) The forcings
that drive long-term climate change are not known with an
accuracy sufficient to define future climate change. 2)
Anthropogenic greenhouse gases, which are well-measured, cause a
strong positive (warming) force. But other, poorly measured,
anthropogenic forcings, especially changes of atmospheric
aerosols, clouds, and land-use patterns, cause a negative forcing
that tends to offset greenhouse warming. 3) One consequence of
this partial balance is that the natural forcing due to solar
irradiance changes may play a larger role in long-term climate
change than inferred from comparison with greenhouse gases alone.
Current trends in greenhouse gas climate forcings are smaller
than in popular "business as usual" or 1 percent per year carbon
dioxide growth scenarios. The authors suggest that a summary
implication of their considerations is a paradigm change for
long-term climate projections: uncertainties in climate forcings
have supplanted global climate sensitivity as the predominant
issue. The authors further suggest that climate forcing scenarios
are essential for climate predictions, but if only one forcing
scenario is used in climate simulations, as has been a recent
tendency, the scenario itself is likely to be taken as a
prediction, as well as the calculated climate change. The authors
recommend that the use of multiple scenarios will aid objective
analysis of climate change as it unfolds in coming years.
-----------
J.E. Hansen et al (6 authors at National Aeronautics and Space
Administration, US)
Climate forcings in the Industrial era.
(Proc. Natl. Acad. Sci. US 27 Oct 98 95:12753)
QY: James E. Hansen 
-----------
Text Notes:
... ... *chaotic fluctuations: The term "chaotic", in this
context, is specific. In the study of physical systems, the
term "chaotic behavior" has a specific meaning: the behavior of a
system is said to be "chaotic" if its final state is so sensitive
to the system's precise initial conditions that the behavior of
the system is in effect unpredictable and cannot be distinguished
from a random process, even though the behavior of the system is
strictly determinate in a mathematical sense. In other words, a
deterministic system characterized by extremely sensitive
instabilities, despite the system being determinate, can exhibit
behavior that is unpredictable, and the system is then called
"chaotic". During the past several decades, the analysis of such
chaotic systems has intrigued both physicists and mathematicians.
-------------------
Summary & Notes by SCIENCE-WEEK [http://scienceweek.com] 4Dec98
-------------------
Related Background:
A SCIENTIFIC BASIS FOR CLIMATE FORECASTING
At the beginning of the 20th century it was believed that it
should be possible to predict weather by solving the mathematical
equations that describe the physical laws that govern the motion
of air. It took several decades to develop an appropriate set of
equations and numerical and computational techniques to solve
these equations, and by 1960, routine weather predictions using
global observations, complex mathematical equations, and fast
computers seemed immediately at hand. The promise, however, was
short lived, because in the early 1960s it was discovered that
the mathematical equations for weather forecasting represent a
forced *dissipative nonlinear dynamic system that exhibits
*chaotic behavior, which means that even an infinitesimally small
uncertainty in the initial conditions will grow exponentially to
make the forecast useless after a finite amount of time.
... ... J. Shukla now presents a study involving analyses of
weather observations coupled with model simulations. The author
reports that although the Earth's atmosphere is generally
considered to be an example of a chaotic system that is
sensitively dependent on initial conditions, certain regions of
the atmosphere are an exception, with wind patterns and rainfall
in certain regions of the tropics so strongly determined by the
temperature of the underlying sea surface that they do not show
sensitive dependence on the initial conditions of the atmosphere.
The author suggests it should therefore be possible to predict
the large-scale tropical circulation and rainfall for as long as
the ocean temperature can be predicted, and that if changes in
tropical Pacific sea-surface temperature are quite large, even
the extratropical circulation over some regions, especially over
the Pacific-North American sector, is predictable. In particular,
the author suggests that for all future major *El Nino events, it
should be possible to predict large-scale changes in the winter
season mean circulation over North America several months in
advance, provided we can predict tropical sea surface
temperatures.
-----------
J. Shukla (George Mason University, US)
Predictability in the midst of chaos: A scientific basis for
climate forecasting.
(Science 23 Oct 98 282:728)
QY: J. Shukla, George Mason University 703-993-2400
-----------
Text Notes:
... ... *dissipative: In general, a dissipative system
is a system that loses energy by conversion of energy into heat.
... ... *El Nino: El Nino is an aperiodic intermittent (2 to 10
years) flow of unusually warm surface water along the western
coast of South America, the flow capable of causing abnormally
high rainfall in usually dry areas and severe local ecosystem
dislocations -- what is termed an El Nino "event". El Ninos are
regional phenomena, but they have global consequences. The name
"El Nino" ("The Child") arose because the phenomenon usually
occurs around Christmas. In 1986, M.A. Cane and S.A. Zebiak
proposed a model for making forecasts of El Nino several seasons
ahead by applying Newton's equations of motion and the laws of
thermodynamics to the dynamics of the ocean and atmosphere of the
tropical Pacific.
-------------------
Summary & Notes by SCIENCE-WEEK [http://scienceweek.com] 20Nov98
-------------------
Related Background:
PREDICTING THE COURSE AND CONSEQUENCES OF EL NINO
El Nino is an aperiodic intermittent (2 to 10 years) flow of
unusually warm surface water along the western coast of South
America, the flow capable of causing abnormally high rainfall in
usually dry areas and severe local ecosystem dislocations -- what
is termed an El Nino "event". El Ninos are regional phenomena,
but they have global consequences. The name "El Nino" ("The
Child") arose because the phenomenon usually occurs around
Christmas. In 1986, M.A. Cane and S.A. Zebiak proposed a model
for making forecasts of El Nino several seasons ahead by applying
Newton's equations of motion and the laws of thermodynamics to
the dynamics of the ocean and atmosphere of the tropical Pacific.
Webster and Palmer (Univ. of Colorado, US; European Center for
Medium Range Weather Forecasts, UK), in a short review of the
past behavior and possible future behavior of El Nino, summarize
the use of the Cane-Zebiak model in making global weather
predictions, and suggest that the present El Nino may be
approaching a climax, with increased rainfall in the southwestern
US and on the Pacific coast of Peru and Ecuador, drought
continuing over Indonesia and New Guinea and increasing over
Australia. QY: Peter J. Webster 
(Nature 11 Dec 97) (Science-Week 2 Jan 98)


4. ON THE DIFFERENTIATION OF GERM CELLS
In many species, a specialized portion of egg cytoplasm gives
rise to cells that are the precursors of the gametes (sperm cells
and egg cells). These precursor cells are called "germ cells",
and they are set aside for reproductive function. All the other
cells of the body are called "somatic cells". This separation of
germ cells from somatic cells is often one of the first
differentiations to occur during animal development. The germ
cells eventually migrate to the gonads (the reproductive organs),
where they differentiate into gametes. ... ... Anne McLaren
(Wellcome/Cancer Research Campaign Institute, UK) presents a
short review of current research concerning the differentiation
of embryonic cells into germ cells, the author making the
following points: 1) In the fruit fly Drosophila, the very first
cells to be formed in the embryo, the "*pole cells", are germ
cells whose descendants have no fate other than to give rise to
gametes. In the *nematode worm *Caenorhabditis elegans and in
zebrafish, germ cell determinants present in the egg are
asymmetrically segregated at each consecutive cell division until
a definitive germ cell lineage is achieved. But in mice, and by
extrapolation in all mammals, cells apparently have germ cell
status thrust upon them as a result of relatively late signaling
mechanisms. 2) The earliest that primordial germ cells have been
identified in the mouse is midway through *gastrulation,
approximately 7.25 days after fertilization. Recognized by their
high *alkaline phosphatase activity, germ cells are seen as a
cluster of cells located in the *extraembryonic region. 3) The
evidence indicates that germ cell status in the mouse embryo is
not achieved, as in lower forms, by segregation of egg cell
cytoplasmic determinants. Instead, in mammals, germ cell status
is apparently the result of differentiation in response to local
signals approximately 7 days after fertilization. The signals
have not yet been identified, but apparently more than one signal
is involved. 4) The author concludes: "In Drosophila, the unequal
distribution of determinants within the oocyte is induced by
signals emanating from the surrounding somatic tissues, which
make no material contribution to later development. In mammals,
the two extraembryonic lineages (*trophectoderm and primitive
*endoderm) make no material contribution to fetal development,
but they may turn out to be the source for many of the signals
that regulate that development. The distinction [between non-
mammals and mammals] could be regarded as essentially one of
timing."
-----------
Anne McLaren: Signaling for germ cells.
(Genes & Development 15 Feb 99 13:373)
QY: Anne McLaren [A.McLaren@welc.cam.ac.uk]
-----------
Text Notes:
... ... *pole cells: At an early stage in insect development, all
the *cleavage nuclei are contained within a common cytoplasm. No
cell membranes exist other than that of the egg itself. Those
nuclei migrating to the posterior pole of the egg soon become
enveloped by new cell membranes to form the "pole cells" of the
embryo. These cells give rise to the germ cells of the adult.
... ... *cleavage: In general, the early and rapid division stage
that divides the fertilized egg into smaller and smaller cells
(blastomeres) while retaining the same overall size of the
embryo.
... ... *nematode worm: An abundant and ubiquitous phylum of
unsegmented roundworms. 
... ... *Caenorhabditis elegans: This is a small (1 mm) nematode
worm. It is transparent, hermaphroditic, free-living, and found
in soil. It has a relatively small genome (approximately 3000
genes), and only a few types of cells in its body. It has a 16-hr
embryogenesis that can be achieved in a petri dish, and is thus
highly suitable for the study of developmental and behavioral
genetics.
... ... *gastrulation: In the embryos of higher animals, there
occurs the transformation of a single-layer "blastula" into a
3-layered "gastrula" consisting of ectoderm (outermost layer),
mesoderm (middle layer), and endoderm (innermost layer)
surrounding a cavity with one opening. The 3 layers are called
the "germ layer", and these layers, via further cell
differentiation and proliferation, determine the development of
all the major body systems and organs. The term "gastrulation"
refers to the process that transforms the single-layered blastula
into the 3-layered gastrula.
... ... *alkaline phosphatase: In general, any phosphatase enzyme
that works optimally at an alkaline pH. A phosphatase is any
enzyme that catalyzes the removal of a phosphate group from an
organic compound.
... ... *extraembryonic region: A region essentially outside the
embryo that occurs in many vertebrates, the apparent role of
which is nutrition and protection.
... ... *trophectoderm: (trophoblast) In the early vertebrate
embryo, the outer ectodermal cell layer of the *blastocyst.
... ... *blastocyst: A mammalian egg in the later stages of
cleavage, but before implantation in the uterus.
... ... *endoderm: The innermost germ cell layer (see above).
-------------------
Summary & Notes by SCIENCE-WEEK [http://scienceweek.com] 30Apr99


5. A MOLECULAR PHYLOGENY OF REPTILES
There is a quiet but nonetheless important upheaval occurring in
evolutionary biology, the essentials of which are as follows: the
evolutionary relationships delineated with great effort during
the past 150 years by studies of morphology and fossils are now
frequently challenged by data based on molecular analysis. The
study of the evolution of reptiles is an example. The classical
phylogeny of living reptiles pairs *crocodilians with birds,
*tuataras with *squamates, and places turtles at the base of the
phylogenetic tree, but this is apparently not consistent with
data from molecular analysis of genomic material.
... ... S.B. Hedges and L.L. Poling (Pennsylvania State
University, US) report a study of both *nuclear genes and
mitochondrial DNA, the results apparently establishing a
phylogenetic joining of crocodilians with turtles and placing
squamates at the base of the tree. The authors suggest that
morphological and paleontological (i.e., fossil) evidence for
this molecular phylogeny is unclear. They suggest that molecular
time estimates support a *Triassic origin for the major groups of
living reptiles, and that their results highlight a significant
discordance between morphological and molecular estimates of
phylogeny for a major group of organisms. The authors conclude:
"The consistent pattern of a turtle-crocodilian relationship
across independent nuclear genes stands in contrast to the
traditional phylogeny of *amniote vertebrates. Determining how
the many groups of extinct reptiles of the late *Paleozoic and
early *Mesozoic fit into this molecular phylogeny will be a
challenge to paleontologists."
-----------
S.B. Hedges and L.L. Poling: A molecular phylogeny of reptiles
(Science 12 Feb 99 283:998)
QY: S. Blair Hedges [sbh1@psu.edu]
-----------
Text Notes:
... ... *crocodilians: Crocodilia is the sole surviving order of
*archosaurs, and currently consists of alligators and crocodiles.
Crocodilia apparently first appeared in the *Triassic period, and
are believed to have been bipedal.
... ... *archosaurs: Literally means "ruling" reptiles, a group
that includes carnivorous dinosaurs, bird-like dinosaurs,
crocodiles, alligators, and from which birds apparently evolved.
... ... *tuataras: (rhynchocephalia) Order of lepidosaurian
reptiles now represented solely by the tuatara (Spenodon) of New
Zealand. Apparently first appeared in the *Mesozoic. In general,
lizard-like animals with many primitive features.
... ... *squamates: (Squamata) Order of the Reptilia, containing
lizards, snakes, amphisbaenids, and the tuatara. (Amphisbaenids
are a family of tropical snake-like lizards.)
... ... *nuclear genes and mitochondrial DNA: In eukaryotes
(cells with internal membrane-bound organelles such as a
nucleus), two separate regimes of genetic material exist: in the
cell nucleus and in mitochondria. Mitochondria are organelles of
the cell cytoplasm, and they are the principal energy source of
the cell, containing various enzymes involved in electron
transport and metabolic cycles. The mitochondria may have
originated as separate organisms that became resident in
eukaryotic cells. Mitochondrial DNA, which has found important
uses in evolutionary studies, is independent of nuclear DNA. It
consists of a circular molecule, 16,569 base pairs long in
humans, with a known nucleotide sequence. Mitochondrial DNA is
inherited primarily through the maternal lineage, and accumulates
mutations at a rate an order of magnitude greater than nuclear
DNA, which facilitates comparisons between groups. In general,
modern DNA sequencing techniques have made possible the tracing
of mitochondrial DNA differences among individuals to reveal
evolutionary relationships. 
... ... *Triassic: The approximate time-frame 225 to 195 million
years ago. A temporal subdivision of the *Mesozoic.
... ... *amniote vertebrates: In general, reptiles, birds, or
mammals distinguished by the presence of extra-embryonic
membranes in development.
... ... *Palaeozoic: (paleozoic) The earliest fossil-bearing
geologic period, the approximate time-frame 600 to 225 million
years ago.
... ... *Mesozoic: The approximate time-frame 225 to 70 million
years ago.
-------------------
Summary & Notes by SCIENCE-WEEK [http://scienceweek.com] 30Apr99
-------------------
Related Background:
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


6. EVIDENCE FOR LACK OF PROTECTIVE EFFECT OF DIETARY FIBER
Denis P. Burkitt, who died in 1993, was a British physician in
Uganda. In the 1970s, the rarity of colorectal cancer in Africa
suggested to Burkitt that the high-fiber diet of Africans was
protective against colorectal cancer. Since then, dietary fiber
has been postulated to prevent colorectal cancer by diluting or
adsorbing fecal carcinogens, reducing colonic transit time,
altering *bile acid metabolism, reducing colonic pH, or
increasing the production of short-chain fatty acids. Despite the
intuitive appeal of Burkitt's hypothesis, epidemiologic studies
of a possible link between dietary fiber and colorectal cancer
have been inconclusive. ... ... C.S. Fuchs et al (8 authors at 2
installations, US) now present the results of a long-term study
of the subject. The authors report they conducted a study of
88,757 women who were 34 to 59 years old, and who had no history
of cancer, inflammatory bowel disease, or *familial polyposis.
The women in the study (all registered nurses) completed a first
dietary questionnaire in 1980, and then follow-up questionnaires
every 2 years after that. During the 16-year follow-up period
(1980-1996), 787 cases of colorectal cancer were documented. In
addition, 1012 patients with *adenomas of the distal colon and
rectum ware found among 27,530 participants who underwent
*endoscopy during the follow-up period. The authors report that
after adjustment for age, established risk factors, and total
energy intake, they found no association between the intake of
dietary fiber and the risk of colorectal cancer. The authors
suggest their data do not support the existence of an important
protective effect of dietary fiber against colorectal cancer or
adenoma. The authors conclude: "There are cogent reasons for
increasing fiber intake, particularly the inverse association
with coronary heart disease observed in many studies. However, we
found no evidence to support the hypothesis that total dietary
fiber intake is protective against colorectal cancer or adenoma."
-----------
C.S. Fuchs et al: Dietary fiber and the risk of colorectal cancer
and adenoma in women.
(New England J. Med. 21 Jan 99 340:169)
QY: Charles S. Fuchs, Dana-Farber Cancer Institute, 44 Binney
St., Boston MA 02115 US.
-----------
Text Notes:
... ... *bile acid metabolism: Bile is a yellowish brown or green
fluid secreted by the liver and discharged into the beginning of
the small intestine (duodenum) where it assists in the
emulsification of fats, increases peristalsis, and retards
putrefaction. (The term "peristalsis" refers to the regulated
waves of alternating contraction and relaxation of the intestine
that move its contents onward.)
... ... *familial polyposis: (multiple intestinal polyposis) A
genetic disorder often a precursor to colon cancer and
characterized by multiple intestinal polyps.
... ... *adenomas: An adenoma is an ordinarily benign neoplasm in
which tumor cells form glands or glandular-like structures.
... ... *endoscopy: In this context, examination of the interior
of the distal colon and rectum with an endoscope. (The instrument
used for deep colon examination is an extended endoscope and is
usually called a "colonoscope". In this context, the term
"distal" means away from the center of the body.)
-------------------
Summary & Notes by SCIENCE-WEEK [http://scienceweek.com] 23Apr99
-------------------
Related Background:
A POSSIBLE NOVEL MECHANISM OF GENE MUTATION IN CANCER
Tumor suppressor genes are genes whose absence or corruption
allows a malignancy to manifest itself by permitting abnormal
proliferation or differentiation at particular stages of cell
growth. They are recessively acting genes, which means both
alleles (i.e., both variants on homologous chromosomes) must be
inactivated to cause loss of growth control. A number of tumor
suppressor genes have been identified, some cloned and others
still uncloned, and corruption or absence of these genes has been
shown to be involved with various cancers, including breast
cancer and colon cancer. The colon cancer tumor suppressor gene,
a cloned gene, is called the adenomatous polyposis coli (APC)
gene. It contains 8538 base pairs apparently coding for a 2843
amino acid polypeptide found in cytoplasm. If the APC gene is
severely mutated, serious colon cancer usually occurs before age
40, which is the end result of an inherited disease called
familial adenomatous polyposis. Now Bert Vogelstein and Kenneth
Kinzler (Johns Hopkins University, US) report that even an
extremely minor corruption of the APC gene, one that involves
only a change from thymine to adenine at a single location, can
result in colon cancer, but without the particular precancerous
condition associated with the absence or severe corruption of
APC. It is apparently not a dysfunction in the APC gene
expression which produces these other colon cancers, but a
misreading of the code on one or both sides of the gene,
producing defects in the adjacent genes on replication, that
evidently results in the other cancerous colon neoplasms. So the
idea is that single DNA base mutations, which themselves are too
trivial to effect the gene in which they occur, may produce
severe frame-shifting errors (a type of code-reading error) in
the replication of neighboring genes, and thus provoke
pathological processes. Some researchers are saying this may a
landmark study of a novel mechanism of cancer production.
QY: B. Vogelstein, Johns Hopkins Univ. (410) 516-8171
(Nature Genetics September 1997) (Science-Week 12 Sep 97)


=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
 
IN FOCUS: ON THE FUTURE OF THE HUMAN SPECIES
"The only certainty about the future of our species is that it is
limited. Of all the species that have ever existed, 99.999
percent are extinct. The average lifetime of a carnivore genus is
only 10 million years, and the average lifetime of a species is
much shorter. Indeed, life on Earth is nearly half-over: Fossil
evidence shows that life began about 3 billion years ago, and the
Sun is due to become a red giant about 4 billion years from now,
consuming life (and eventually the whole Earth) in its fire. It
is remarkably difficult to make any reliable predictions about
our future between now and the uncertain date of our extinction,
because human evolution depends so much on the state of cultural
organization. It is very likely that we will continue to be a
single species, because the forces of genetic cohesion,
especially migration and uniform selection, seem to be
increasing. It is hard to imagine a universal catastrophe of such
a nature that the species would be broken up into isolated small
groups for the tens of thousands of years that would be required
for the formation of separate species. We would need not only to
be returned to the Stone Age but to be deprived of all the
knowledge about the physical world that has been accumulated
since then. Total extinction seems more likely."

-- Richard Lewontin: _Human Diversity_
   (W.H. Freeman, New York 1982, p.169)

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