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ScienceWeek
SCIENCE-WEEK
A Weekly Email Digest of the News of Science
A journal devoted to the improvement of communication
between the scientific disciplines, and between scientists,
science educators, and science policy-makers.
September 28, 2001 -- Vol. 5 Number 39
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The father of the arrow is the thought:
How do I expand my reach?
-- Paul Klee (1879-1940)
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Section 1
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Contents of this Issue (Full reports in Section 2):
1. The Moons of Saturn
2. High Energy Physics: Energy and Dimensionality
3. Chaos-Assisted Tunneling
4. Biochemistry of Zinc
5. Polyunsaturated Lipids
6. Deterministic Delivery of Single Atoms
7. Chimpanzee Evolution
8. Two Elephant Species in Africa
9. Criticism of Nomenclature in Genetics
10. Misunderstandings of Cloning
11. Iron Metabolism
12. Hearing in the Fruit Fly
13. In Focus: The Square Root of N Rule
14. SW Archive: On Localization of Function in the Human Brain
15. Sources
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Section 2
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1. THE MOONS OF SATURN
B. Gladman et al (Cote d'Azur Observatory, FR) discuss new
observations of the moons of Saturn. The giant planets in the
Solar System each have two groups of satellites. The "regular
satellites" move along nearly circular orbits in the planet's
orbital plane, revolving about the planet in the same sense as
the spin of the planet. In contrast, the so-called "irregular
satellites" are generally smaller in size and are characterized
by large orbits with significant eccentricity, inclination, or
both. The differences in the characteristics of the two groups of
satellites suggest that the regular and irregular satellites
formed by different mechanisms: the regular satellites are
believed to have formed in an accretion disk around the planet,
like a miniature Solar System, whereas the irregular satellites
are generally thought to be captured planetesimals. The authors
report the discovery of 12 irregular satellites of Saturn, along
with the determinations of the orbits of these satellites. These
orbits, along with the orbits of irregular satellites of Jupiter
and Uranus, fall into groups on the basis of their orbital
inclinations. The authors interpret this result as indicating
that most of the irregular moons are collisional remnants of
larger satellites that were fragmented after capture, rather than
being captured independently.
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NAT 2001 412:163
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2. HIGH ENERGY PHYSICS: ENERGY AND DIMENSIONALITY
Joseph D. Lykken (Fermi National Accelerator Laboratory, US)
discusses new concepts of dimensionality in high energy physics.
Recent theoretical research by N. Arkani-Hamed et al (2001) and
C. Hill et al (in press) suggests a concrete mechanism for how
dimensions of space arise or disappear. The essential idea is
that at a microscopic level space is a lattice, an array of
discrete points. Elementary particles, such as electron, *quarks,
or photons, fundamentally inhabit only a single point. To move
from that point, there must be a force -- a hopping interaction
-- that destroys the particle at one point in space and creates a
copy of it a neighboring point. Since the idea of dimensionality
is dependent on existing constraints of motion, no force, no
motion, and no motion, no dimension. In the theoretical models
created by the two groups, the hopping interactions turn off at
high energies, thereby reducing the number of spatial dimensions
at high energies. Thus, in the high-energy environment of the
early Universe, there may have been no spatial dimensions at all,
and dimensionality may be a low-energy phenomenon that emerged as
the Universe cooled down. This is in contrast to standard *string
theory, the branch of high-energy physics that attempts a unified
description of all fundamental interactions. In string theory,
there are more spatial dimensions visible at higher energies, not
fewer. In a general way, the new space-lattice models should be
testable, since experiments now searching for extra dimensions at
high energies may reveal fewer dimensions rather than more
dimensions. Lykken concludes that this may be the beginning of
the era of "post-modern physics".
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NAT 2001 412:130
PRL 2001 86:4757
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Notes:
*For definitions of *quarks, *string theory, etc., see related
background material below.
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Related Background:
THEORETICAL PHYSICS: ON STRING THEORY
In particle physics, string theory is a theory of elementary
particles based on the idea that the fundamental entities are not
point-like particles but finite lines (strings), or closed loops
formed by strings, the strings one-dimensional curves with zero
thickness and lengths (or loop diameters) of the order of the
Planck length of 10^(-35) meters. ... ... B.R. Greene et al
present a short review of recent developments in string theory
and make the following points: 1) Particle physics has spent much
of this century grappling with one basic question in various
forms: What are the fundamental *degrees of freedom needed to
describe nature, and what are the laws that govern their
dynamics. 2) The current "standard model" of particle physics --
which is nearly 25 years old and which has much experimental
evidence in its favor -- involves 6 *quarks, 6 *leptons, 4
*forces, and the as yet unobserved *Higgs boson. But this model
contains internal indications that it too may be just another
step along the path of uncovering the truly fundamental degrees
of freedom. The standard model is valid to distances as small as
10^(-16) cm, and there is some evidence that the next level of
structure will be detected only at a distance scale of the order
of 10^(-32) cm, which is far beyond our abilities to measure in
the laboratory. 3) A related important issue concerns the
unification of general relativity and quantum mechanics. A
serious problem arises when general relativity is extrapolated to
small distance scales of the order of 10^(-32) cm where quantum
effects must be taken into account: the relevant theoretical
equations produce uncontrollable divergences, and the history of
particle physics suggests this is an indication of a new physics
occurring at these distance scales. 4) String theory offers hope
of addressing both of these issues. There is only one known way
to cure the divergence problem in the quantum-mechanical
expansion of general relativity, and that is to model the
particles in the theory not as points but as one-dimensional
loops of "string". Every consistent such string model necessarily
contains a special kind of particle -- the "*graviton" -- whose
long-distance interactions are described by general relativity.
So in a sense, string theory predicts gravity. 5) An exciting new
frontier was opened during the past few years with the discovery
of "string duality", which predicts equivalences among various
different physical systems. This discovery has its roots in the
properties of "supersymmetry", a novel type of symmetry that all
consistent string theories possess. Briefly, supersymmetry
relates properties of two basic types of particles -- bosons and
*fermions -- which cannot be related by ordinary symmetry. There
is a current belief that supersymmetry will play a role in the
structure of particle physics beyond the standard model. One of
the important achievements of string duality has been the
determination of the behavior of the 5 consistent string theories
when interactions become strong. All the consistent string
theories are apparently related to each other, and to an
elaboration known as "membrane theory" (M-theory). String duality
has produced hope that there may be only one possible string-
theoretic model of the universe, and that it may be possible to
eventually predict such features as particle masses and
interaction strengths directly from such a theory. The authors
conclude: "Development has been rapid on many fronts since string
duality was introduced. We may be seeing glimpses of the
underlying principle manifested in these new results. The
challenging task that lies ahead is to discover that principle
and thereby find what may well be the truly fundamental degrees
of freedom in our universe."
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PNAS 1998 95:11039
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Notes:
... ... *degrees of freedom: In general, this refers to the
independent variables that must be specified in order to define
the state of a system.
... ... *quarks: A quark is a hypothetical fundamental particle,
having charges whose magnitudes are one-third or two-thirds of
the electron charge, and from which the elementary particles may
in theory be constructed.
... ... *leptons: A class of elementary particles. Although they
are affected by electromagnetic and gravitational forces, apart
from that they are involved only with weak interactions, acted
upon by weak forces but not by strong forces, as opposed to
quarks, which are acted upon by strong forces but not by weak
forces. One further difference between leptons and quarks is that
leptons can be isolated as single particles, whereas quarks
apparently cannot. The leptons include the electron, the muon,
the tau, and their associated neutrinos. The mass of the tau is
approximately 3484 times the mass of the electron; the mass of
the muon is intermediate.
... ... *forces: The fundamental forces comprise the
gravitational force, the electromagnetic force, the nuclear
strong force, and the nuclear weak force.
... ... *Higgs boson: Higgs fields (named after Peter W. Higgs,
University of Edinburgh, UK) constitute a set of fundamental
theoretical fields that induce spontaneous symmetry breaking. In
general, spontaneous symmetry breaking occurs in systems whose
underlying symmetry state is unstable. A Higgs particle is
associated with a Higgs field in the same way that a photon is
associated with the electromagnetic field. Higgs bosons are
massive mesons whose existence is predicted by certain theories.
Mesons are apparently composed of quark and anti-quark pairs;
they are produced by various high-energy interactions and decay
into stable particles.
... ... *graviton: Several quantum field theories consistent with
both quantum mechanics and special relativity postulate that the
gravitational force between two quantum domain particles is
generated by the exchange of an intermediate particle called a
graviton.
... ... *fermions: Fermions (electrons, protons, neutrons) are
particles that obey the Pauli exclusion principle: i.e., no two
fermions of the same kind can occupy the same quantum state.
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SW 1998 16 Oct
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3. CHAOS-ASSISTED TUNNELING
In this context, the term "tunneling" refers to a quantum
mechanical phenomenon involving an effective penetration of an
energy barrier by a particle, the penetration resulting from the
width of the barrier being less than the wavelength of the
particle.
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.
... ... D.A. Steck et al (University of Texas Austin, US) discuss
chaos-assisted tunneling. Quantum-mechanical systems can display
very different behavior from their classical counterparts. In
particular, quantum effects suppress classical chaotic behavior
in which simple deterministic systems exhibit complicated and
seemingly random dynamics. Nevertheless, aspects of quantum
behavior can often be understood in terms of the presence or
absence of chaos in the classical limit. The authors focus on
quantum transport in a mixed system, where the classical dynamics
are complicated by the coexistence of chaotic and stable
behavior. The authors study quantum tunneling between two stable
regions ("islands of stability"; nonlinear resonances) in the
classical phase space. The classical transport between these
islands is forbidden by dynamical "barriers" in phase space. In
contrast, quantum tunneling can couple the two islands so that a
wave packet oscillates coherently between the two symmetry-
related stable regions. The authors report direct experimental
observation of quantum dynamical tunneling of atoms between
separated momentum regions in phase space. The authors study how
the tunneling oscillations are affected as a quantum symmetry is
broken and as the initial atomic state is changed. Evidence is
provided that the tunneling rate is greatly enhanced by the
presence of chaos in the classical dynamics. The authors suggest
this tunneling phenomenon represents a dramatic manifestation of
underlying classical chaos in a quantum system.
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SCI 2001 293:274
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Related Background:
QUANTUM PHYSICS: ON ATOMIC TUNNELING
In 1924, Louis de Broglie (1892-1987) suggested that all
particles have wave properties in addition to particle
properties, with the wave properties given by what is now called
the "de Broglie equation": l = h/(mv), where (l) is the
wavelength of the particle, (h) is Planck's constant, (m) is the
mass of the particle, and (v) is the velocity of the particle.
This relationship provided the basis for quantum mechanics as
formulated by Erwin Schroedinger (1897-1961) in 1925-1926. In
1927, the wave nature of electrons was detected experimentally.
Macroscopic objects have a computed wavelength much smaller than
that of electrons, so the wave properties of macroscopic objects
are never detected: macroscopic objects exhibit only particle
behavior.
In general, the term "quantum mechanical tunneling" refers
to a quantum mechanical phenomenon involving an effective
penetration of an energy barrier by a particle resulting from the
width of the barrier being less than the de Broglie wavelength of
the particle. Essentially, the idea is that the square of the
amplitude of the wavefunction of the particle determines the
probability distribution of the particle, and if the dimensions
of that probability distribution exceed the dimensions of the
barrier, there is a finite probability the particle will "tunnel"
through the energy barrier to the other side. In general, for
particles of known mass and velocity, if the height and thickness
of the energy barrier are known, this tunneling probability can
be calculated via quantum mechanics. The phenomenon of quantum
tunneling has many important applications, including explanations
of *alpha particle emission in radioactive decay, and in the
theory and engineering of the *Esaki diode (tunnel diode).
The new technology of scanning probe microscopy has created
a revolution in microscopy, with applications ranging from
condensed matter physics to biology. The first scanning probe
microscope, the scanning tunneling microscope, was invented by G.
Binnig and H. Rohrer in the 1980s (they received the Nobel Prize
in Physics in 1986), and the invention has been the catalyst of a
technological revolution. Scanning probe microscopes have no
lenses. Instead, a "probe" tip is brought very close to the
specimen surface, and the interaction of the tip with the region
of the specimen immediately below it is measured. The type of
interaction measured essentially defines the type of scanning
probe microscopy. When the interaction measured is the force
between atoms at the end of the tip and atoms in the specimen,
the technique is called "atomic force microscopy". When the
quantum mechanical tunneling current is measured, the technique
is called "scanning tunneling microscopy". These two techniques,
atomic force microscopy (AFM) and scanning tunneling microscopy
(STM) have been the parents of a variety of scanning probe
microscopy techniques investigating a number of physical
properties. In general, in scanning tunneling microscopy,
electrons quantum mechanically tunnel between the tip and the
surface of the sample. This tunneling process is sensitive to any
overlap between the electronic wave functions of the tip and
sample, and depends exponentially on their separation. The
scanning tunneling microscope makes use of this extreme
sensitivity to distance. In practice, the tip is scanned across
the surface, while a feedback circuit continuously adjusts the
height of the tip above the sample to maintain a constant
tunneling current. The recorded trajectory of the tip creates an
image that maps the electronic wave functions at the surface,
revealing the atomic landscape in fine detail.
In this context, the term "phonon" refers to a quantum of
vibrational energy, the quantum considered a discrete particle,
and used in mathematical models to calculate thermal and
vibrational properties of solids. This idea is essentially a
reversal of the application of the de Broglie equation to
particles: In general, any propagated wave (or field
perturbation) can be considered as a particle whose momentum (mv)
is given by the de Broglie equation as mv = h/l, where (mv) is
the momentum of the particle, h is Planck's constant, and (l) is
the wavelength of the propagated perturbation.
... ... Ali Yazdani (University of Illinois Urbana-Champaign, US)
presents a commentary on recent work (L.J. Lauhon and W. Ho:
Phys. Rev. Lett. 85:4566 2000) on tunneling of individual
hydrogen atoms on a metal surface. The author (Yazdani) makes the
following points:
1) The author points out that in condensed matter physics,
quantum tunneling of atoms is believed to play an important role
in phenomena such as the diffusion of impurities in solids and
the properties of *glasses at low temperatures. An atom can be
described as "resting" in an energy well, and it can tunnel to
another energy well if the mass of the atom is low enough and if
the energy barrier between the wells is sufficiently small.
Because the hydrogen atom is so low in mass, it is particularly
open to the possibility of quantum tunneling. On the surface of
metals, the constant movement of hydrogen has been reported down
to low temperatures, but whether this diffusion arises from
classical thermal motion or from quantum tunneling is unclear.
Some of the uncertainty can be attributed to the fact that
previous experiments measured the average behavior of a group of
atoms, and so could not resolve the role of surface defects in
the tunneling process. A localized probe, such as the tip of a
scanning tunneling microscope, sidesteps these complications.
2) Lauhon and Ho (2000) now report that they have tracked
and visualized the quantum tunneling of individual atoms for the
first time. By using a scanning tunneling microscope, they were
able to monitor the motion of individual hydrogen atoms on a
metal surface, and they found that the atoms remain mobile down
to temperatures as low as 9 degrees kelvin. Classically, thermal
diffusion or motion is expected to fade away as the temperature
is lowered. But the constant movement of hydrogen in these
experiments implies that there is a quantum effect that allows
the atoms to tunnel along the surface of the metal. Quantum
tunneling of atoms at low temperatures has been inferred from
experiments on relatively large groups of atoms, but never before
has quantum motion been observed so directly -- one atom at a
time.
3) By detailed analysis of the scanning-tunneling-microscope
-measured diffusion rate for hydrogen, Lauhon and Ho identify
different temperature regimes in which phonon- or electron-
*scattering predominates. Most intriguing is their observation
that at the lower temperatures in the experiment, the tunneling
rate increases as the surface is cooled. This classically
impossible behavior suggests that hydrogen tunneling improves
over longer periods of time as the surface gets colder. The
author (Yazdani) suggests that perhaps reducing the temperature
by a further factor of 10 or 100 will reveal a new regime in
which hydrogen atoms can eventually tunnel over greater
distances.
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NAT 2001 409:471
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Notes:
... ... *alpha particle emission in radioactive decay: In
radioactive decay alpha particle emission, a nucleus emits an
alpha particle (a helium nucleus). The alpha particle has
insufficient energy as a particle to overcome the force barrier
surrounding the nucleus, but as a wave the particle can tunnel
through the barrier, i.e., the particle has a finite probability
of being found outside the nucleus. The quantum explanation of
alpha particle emission in radioactive decay was provided
independently by George Gamow (1904-1968) and by Ronald W. Gurney
(?-?) and Edward Condon (1902-1974) in 1928.
... ... *Esaki diode: A semiconductor electron-hole (p-n)
junction diode based on the tunnel effect. The device has a
current-voltage curve described by a cubic equation, with one
limited region of the curve showing a "negative resistance",
i.e., the current falling as the bias voltage is increased.
... ... *glasses: In this context, the term "glass" refers to an
amorphous solid whose atoms form a random network.
... ... *scattering: In this context, the term "scattering"
refers to the change in direction of a particle resulting from
collision with another particle.
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SW 2001 16 Feb
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Related Background:
THEORETICAL PHYSICS: CHAOS AND NONLINEAR DYNAMICS
In general, a nonlinear dynamical system is a system
described by time-dependent differential equations such that the
rates of change of one or more dependent variables of the system
depend in a nonlinear fashion on the variables themselves.
Certain nonlinear dynamical systems, some of which are of great
scientific interest, exhibit "chaotic dynamics". 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. Examples of chaotic
nonlinear dynamical systems are the weather and populations of
organisms, and instances of chaotic dynamics have now been
documented in most scientific disciplines.
Because the differential equations for many nonlinear
systems are often intractable (i.e., no explicit quantitative
solutions are possible), a focus of theoretical research on
nonlinear systems has been on analysis of the qualitative
behavior of such systems, in particular on analysis of the "phase
space" and "trajectories" in the phase spaces of such systems.
The idea is essentially as follows: If the state of a system
depends upon N variables, the instantaneous state of the system
can be viewed as a point (phase point) in an N-dimensional space
(phase space; system hyperspace), and as the state of the system
changes, its phase point can be viewed as describing a trajectory
in its phase space. Qualitative analysis of the possible families
of solutions of nonlinear differential equations can provide
information about such phase space trajectories, and there are
certain real systems for which qualitative analysis of the phase
space trajectories of the system has revealed significant
properties of the system otherwise difficult to delineate.
... ... J.P. Gollub and M.C. Cross (2 installations, US) present
a commentary on recent research on chaotic nonlinear dynamics,
the authors making the following points:
1) The techniques of nonlinear dynamics are well-developed,
but the impact of this field has been largely confined to
phenomena in which there are only a few important time-dependent
quantities. Unfortunately, this excludes a vast range of
important problems in which the behavior of one point in space
can be quite different (though statistically similar) to that at
another location. A particular example is convective behavior.
2) The traditional approach to studying nonlinear dynamical
behavior is to plot the dynamical variables of the system as a
multidimensional phase space graph indicating how the behavior
changes over time. For example, a simplified model of the Solar
System consisting of the Sun and 9 planets would require a phase
space with as many as 60 dimensions (3 position and 3 momentum
coordinates for each body). In the case of a convecting fluid, a
complete description of the flow pattern requires knowledge of
the velocity and temperature at a very large number of locations,
so the number of dimensions of the phase plot are enormous (from
thousands to millions, depending on the desired spatial
resolution). As a result, the methods of nonlinear dynamics are
cumbersome and progress has been slow, even though many
interesting examples of spatiotemporal chaos have been explored
both experimentally and numerically.
3) Recent research (D.A. Egolf et al: Nature 404:733 2000)
involving numerical studies of an accepted model of thermal
convection indicates that the origin of unpredictable motion in
chaotic thermal convective systems, at least in one particular
form of spatiotemporal chaos, lies in what occurs in small
regions of space and over short time-scales. These local changes
in the organization of the flow affect the surrounding regions in
such a way that the entire future evolution is affected. The
authors state: "This is something akin to Ed Lorenz's famous
remark [E.N. Lorenz: J. Atmos. Sci. 20:130 1963] that the
localized flapping of a butterfly's wings might change the
weather dramatically over the entire world a few weeks later."
Although such sensitivity to localized fluctuations has never
been confirmed as the source of the unpredictability of the
weather, it is apparently the origin of chaotic dynamics in
thermal convection.
4) The authors conclude: "The methods used by Egolf et al
should apply to many other forms of chaos in spatially extended
systems (physical, chemical, and biological) for which reliable
model equations are available, so that the key processes leading
to the complex dynamics can be identified. Applications to areas
as diverse as cardiology and atmospheric dynamics might be
expected eventually. Moreover, it is not unreasonable to imagine
that insight into the processes leading to unpredictability will
also lead to progress in modifying or controlling the dynamics of
these systems."
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NAT 2000 404:710
SW 2000 23 Jun
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4. BIOCHEMISTRY OF ZINC
S.C. Burdette et al (Massachusetts Institute of Technology, US)
discuss zinc ions in biological systems. Zinc is a vital
component in many cellular processes. Although traditionally the
study of the biochemistry of ionic zinc, Zn(sup2+), has focused
on its structural and catalytic functions in proteins, the
neurobiology of ionic zinc has been a subject of increasing
attention. Whereas most ionic zinc in biological systems is
tightly bound in proteins, a pool of free ionic zinc in cells has
been demonstrated, including sub-nanomolar concentrations in
undifferentiated mammalian cells, and higher concentrations
approaching 300 micromolar in the mossy fiber terminals of the
hippocampus. The zinc ion has the ability to modulate a variety
of ion channels, may play a role in neuronal death during
seizures, is pertinent to neurodegenerative disorders, and may be
vital to neurotransmission. The levels of ionic zinc in the brain
and other parts of the body are regulated by at least three
homologous ionic zinc-transport proteins and by metallothioneins
that are expressed mainly in the brain. Zinc transport proteins
and metallothioneins are probably responsible for distributing
the required amounts of ionic zinc to proteins and enzymes,
minimizing the amounts of free and potentially toxic levels of
ionic zinc present in cells. But in addition to protein
regulators, ionic zinc can be released from synaptic vesicles and
can enter cells via voltage-dependent calcium-ion channels,
indicating that free ionic zinc is available for neurological
functions. Limited methods for detecting ionic zinc in these
systems have hampered research. The authors report the synthesis
of two new fluorescent sensors for ionic zinc that utilize
fluorescein as a reporting group.
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JACS 2001 123:7831
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5. POLYUNSATURATED LIPIDS
L. Saiz and M.L. Klein (University of Pennsylvania, US) discuss
polyunsaturated lipids in biological systems. Fatty acids with
multiple double bonds (unsaturations) are abundant in cerebral
and retinal tissues, and in the olfactory bulb. These
unsaturations are known to affect a number of biophysical
properties of membranes composed of phospholipids with one or
both acyl chains containing cis double bonds. Examples of these
effects are the low main order-disorder phase transition
temperatures, the enhanced permeability to small organic solutes
and water, the enhanced elasticity or decrease in area
compressibility modulus, and so on. However, the importance of
polyunsaturated lipids seems not to be limited to a mere
structural role, since in some situations polyunsaturated lipids
are required for the proper function of membrane-embedded
proteins. This is the case, for example, with the G-protein-
coupled visual receptor molecule rhodopsin, which is found in the
rod cells of the retina. Polyunsaturated fatty acids, especially
the docosahexanaenoic fatty acid (DHA), are present in large
amounts in these rod membranes, and the DHA content apparently
influences the function of rhodopsin pigment. The authors report
an NMR and molecular dynamics simulation study of the effects of
polyunsaturation in acyl chains on the conformations of
phospholipids in a model membrane system.
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JACS 2001 123:7381
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6. DETERMINISTIC DELIVERY OF SINGLE ATOMS
S. Kuhr et al (University of Bonn, DE) discuss single-atom
manipulations. The manipulation of individual atomic particles is
a key factor in the quantum engineering of microscopic systems.
These techniques require full control of physical degrees of
freedom with long coherence times. In comparison to well-
established single-ion trapping methods, a similar level of
control of neutral atoms has yet to be achieved because of their
weaker interactions with external magnetic fields. Thermal
sources of neutral atoms, such as atomic beams, provide a flux of
uncorrelated atoms with random arrival times. However, there is
great interest in a source that would deliver a desired number of
cold atoms at a time set by the experimenter. The authors report
the realization of a deterministic source of single atoms. A
standing-wave dipole is loaded with one or any desired number of
cold cesium atoms from a magneto-optical trap. By controlling the
motion of the standing wave, the atom can be adiabatically
transported with sub-micrometer precision over macroscopic
distances on the order of a centimeter. The displaced atom is
observed directly in the dipole trap by fluorescence detection.
The trapping field can also be accelerated to eject a single atom
into free flight with well-defined velocities. The authors
suggest this system may be a versatile tool for future
experiments with full control of internal and external atomic
degrees of freedom.
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SCI 2001 293:278
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7. CHIMPANZEE EVOLUTION
The terms "hominoid", "hominid", and "hominin" are not
interchangeable, but their classification criteria are variously
in a state of flux. In general, the hominoids are a primate
superfamily; the hominid family is currently considered to
comprise both the great ape lineages and human lineages within
the hominoid superfamily; the "homininae" comprise both the human
lineages and the African ape lineages within the hominids, and
the "hominini" comprising only the human lineages. The current
scheme is as follows:
--------------------------------------------------
I. Suborder Hominoids
A. ...
B. Family Hominids
1. ...
2. Subfamily Homininae
a. Tribe Gorillini (African apes)
b. Tribe Hominini
(1) Genus Australopithecus
(2) Genus Homo
(3) Other genera (see below)
--------------------------------------------------
The term "hominins" almost always refers to the tribe
Hominini, and not to the subfamily Homininae.
It is important to note that in the older scheme (before
about 1980), the Hominoids comprised the gibbons (Hylobatidae),
the great apes (Pongidae), and the Hominidae, with the Hominidae
(hominids) consisting only of the two genera Homo and
Australopithecus. The new scheme is therefore considerably
different. For example, under the old scheme, the statement
"modern man is the only living hominid" is correct. Under the new
scheme, that statement is incorrect.
The human lineages (the hominins) are characterized by a
number of features, including bipedalism. In effect, hominins are
the group of fossils more closely related to modern humans than
to any other group. In terms of dating, the hominin group
apparently originated sometime between 5 and 8 million years ago.
Concerning the "apes", there are two categories of relevance
here: The term "great apes" refers to chimpanzees, gorillas, and
orangutans. The term "African apes" refers only to chimpanzees
and gorillas. The distinction is important, since on the basis of
molecular evidence, the African apes are close to humans, while
the orangutans are not that close, and the gibbons are even
further removed.
The classification and interpretation of hominin fossils has
never been free of controversy, partly because hominin fossils
are not that plentiful, and perhaps partly because there are a
number of rival discovery teams, and the significance of a new
hominin fossil discovery is enhanced if the discovery apparently
requires new classifications and/or new interpretations.
At present, 5 genera of hominins are recognized:
Ardipithecus, Australopithecus, Paranthropus, Kenyanthropus, and
Homo. A fossil recently discovered in the Lukeino Formation of
the Tugen Hills in Kenya, the fossil named Orrorin tugenensis,
has now been proposed by its discoverers as another genus of
hominin and a direct ancestor of the Homo group, but
classification and interpretation of this fossil, as indicated
below, is in dispute.
... ... Henry Gee (NAT) discusses the record of chimpanzee
evolution. Although hominid fossils are famously rare, the
chimpanzee lineage has no fossil record whatsoever. One
explanation has been that chimpanzees have always lived in
forested environments, and that forest creatures are rarely
preserved as fossils. The idea is that hominids only became
relatively abundant as fossils after they moved from forests to
more open habitats. However, this argument is turned on its head
by strong evidence that the apparent hominids Orrorin and
Ardipithecus lived in woodland. The fossils of animals such as
monkeys and small antelopes found alongside these hominids, as
well as paleobotanical and isotopic evidence, suggest that
Ardipithecus lived in a relatively well-forested and high-
altitude environment. Indeed, this creature may have been
confined to such a habitat: searches for early hominids in
geological settings indicative of the open-country habitats
associated with later hominids have been less rather than more
likely to produce results. So it may be that hominids were
woodland creatures until approximately 4.4 million years ago.
Given that chimpanzees today live in environments similar to
those inhabited by Ardipithecus and Orrorin, could it be that at
least one of these early hominids is actually more closely
related to chimpanzees than to humans? The accumulating data on
paleoenvironments should at least improve our understanding of
the lives and times of early hominids (and perhaps of early
chimpanzees), even though the evolutionary relationships remain
murky.
-----------
NAT 2001 412:131
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Related Background:
MOLECULAR BIOLOGY: ON THE NEED FOR A CHIMPANZEE GENOME
The human genome will soon be completely sequenced, a milestone
in the history of biology and medical science. Intensive research
effort is now focused on the next logical biomedically relevant
target -- the mouse. As a mammalian species of importance in
biomedical research, primarily due to economies of research on
this small easily bred animal, the mouse has no equal. And after
the mouse, what next? There have been calls to sequence the
genomes of the rat (Rattus rattus), the African clawed toad
(Xenopus laevis), and the zebra fish (Danio rerio), all
laboratory animals for which there is an enormous literature of
published laboratory experiments. These are certainly species of
great importance to biology. From a biomedical standpoint,
however, a strong argument can be made that the complete
sequencing of the genomes of none of these animals would be as
important as the complete sequencing of the genome of our closest
evolutionary relative, the chimpanzee (Pan troglodytes).
... ... Ajit Varki (University of California San Diego, US)
presents a commentary calling for the sequencing of the
chimpanzee genome, the author making the following points:
1) Chimpanzees and humans share nearly 99 percent of their
genomes. Knowing the complete chimpanzee genome will give us a
window into genes that contribute to "humanness". The emergence
of humans can be regarded as one of the major transitions in
evolution, and the complete explanation of this phenomenon ranks
as one of the greatest unsolved mysteries of science.
2) Extrapolating findings in physiology and pathology from
mice, rats, toads, or fish to humans can be difficult, because of
the physiological and genetic differences between humans and
these species. In contrast, the greater than 99 percent identity
of amino acid sequences of most chimpanzee and human proteins
predict a stronger likelihood of finding genetic explanations for
any disease differences. Studies of the chimpanzee genome could
be considered a logical extension of the current emphasis on
exploiting sequence differences between various human groups to
identify important disease susceptibility genes.
3) Some pathological states in humans seem to represent the
normal situation in chimpanzees, including closure of the skull
sutures around the time of birth (perinatal period)
(craniosynostosis), a high white blood cell count (general
leukocytosis), and hairiness (extensive hypertrichosis). Several
other diseases or physiological states of humans appear to be
rare or markedly attenuated in the chimpanzee. Some of these
diseases can be attributed to anatomic differences between the
species, including protracted, painful, and dangerous childbirth
(resulting from the larger head of the human fetus and the
altered pelvis of the bipedal human female), wisdom tooth
impaction (resulting from reduced jaw size in humans and the lack
of a post-molar gap), and various diseases attributed to gravity
effects on bipedal humans (vertebral osteoarthritis,
intervertebral disc protrusion, varicose veins, and hemorrhoids).
There are also a few anatomically unique diseases of great apes
that do not occur in humans, such as infection of the pharyngeal
air sacs (an organ that is absent in humans). The higher
frequency in humans of anatomical disorders of the central
nervous system (e.g., hydrocephalus) is also intriguing, but
could be explained on the basis of increased perinatal trauma.
4) But many other differences between humans and chimpanzees
cannot be explained on any obvious behavioral, dietary, anatomic,
cellular, or biochemical basis. The author suggests it is these
differences that justify the biomedical imperative of the
sequencing of the chimpanzee genome. The author summarizes these
significant differences as follows:
... ... a) The failure of HIV infection to progress to AIDS in
the chimpanzee. Despite many studies attempting to find the
answer, the mystery remains: the HIV retrovirus seems to live in
a symbiotic state within the chimpanzee immune system, whereas it
almost routinely destroys the helper T cells of humans.
... ... b) Alzheimer's disease is a common and devastating
disease causing dementia in elderly humans, the human brain
pathology characterized by the accumulation of amyloid plaques
together with neurofibrillary tangles. The pathological lesion,
including the neurofibrillary tangles, has never been observed in
the brains of elderly chimpanzees. In contrast, age-matched
samples from human brain specimens show a significant rate of
these classic lesions, often well before symptoms of dementia
have become evident. Neurofibrillary tangles can even exist in
human brains independent of plaques, beginning virtually at birth
and reaching a 50 percent prevalence by age 48. The fact that the
full-blown lesion of Alzheimer's disease has also not been
observed in other long-lived animals (e.g., elderly elephants),
increases the significance of this finding, and makes a
comparison between humans and the corresponding chimpanzee genes
of great potential benefit.
... ... c) Of all the different forms of malaria, that caused by
the pathogen Plasmodium falciparum is the most aggressive and
acutely life-threatening; it is a major cause of mortality
worldwide. Chimpanzees are apparently immune to infection by this
parasite, and instead get infected by its close relative
Plasmodium reichnowii, which evidently does not make the
chimpanzee very ill. The knowledge gleaned from comparative
studies of the relevant parasite genomes as well as the human and
chimpanzee genomes could be of great importance.
... ... d) The most common human cancers, epithelial neoplasms
such as carcinomas of the breast, ovary, lung, stomach, colon,
pancreas, and prostate, cause more than 20 percent of deaths in
modern human populations. In contrast, the cancer incidence rates
for non-human primates is only approximately 2 to 4 percent and
seems to be even lower in the great apes. It is of interest that
a cell-surface sugar modification that is lost in the human
lineage due to genomic mutation is reported to reappear in human
cancers.
... ... e) Several aspects of female reproductive biology appear
to be different between great apes and humans. For example,
menopause has not been observed in long-lived captive female
chimpanzees. Compared to chimpanzees, human females are unusual
in having a high frequency of breast diseases such as fibrocystic
disease and cancer. Also, the absence of external signs of
ovulation in human females may result in fertilization taking
place at suboptimal times with regard to the condition of the
ovum. Thus, the question arises whether fertilization of
deteriorating eggs may explain -- at least partly -- the
relatively high rate of gross chromosomal and other genetic
abnormalities in human fetuses.
... ... f) In addition to the above examples, anecdotal evidence
suggests that some other common human conditions are rare in
great apes in captivity: i) Despite a high frequency of atopic
rhinitis and polyps, bronchial asthma is rarely diagnosed in
chimpanzees. ii) Acne vulgaris, the common skin affliction of
human teenagers, also appears to be uncommon in the adolescent
chimpanzee. iii) Rheumatoid arthritis has not been detected in
chimpanzees.
-----------
GR 2000 10:1065
SW 2000 15 Sep
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Related Background:
NUMBERS AND COUNTING IN A CHIMPANZEE
In this context, let us define "animals" as all living multi-
cellular creatures other than humans that are not plants. In
recent decades it has become apparent that the cognitive skills
of many animals, especially non-human primates, are greater than
previously suspected. Part of the problem in research on
cognition in animals has been the intrinsic difficulty in
communicating with or testing animals, a difficulty that makes
the outcome of a cognitive experiment heavily dependent on the
ingenuity of the experimental approach. Another problem is that
when investigating the non-human primates, the animals whose
cognitive skills are closest to that of humans, one cannot do
experiments on large populations because such populations either
do not exist or are prohibitively expensive to maintain. The
result is that in the area of primate cognitive research reported
experiments are often "anecdotal", i.e., experiments involving
only a few or even a single animal subject. But anecdotal
evidence can often be of great significance and have startling
implications: a report, even in a single animal, of important
abstract abilities, numeric or conceptual, is worthy of
attention, if only because it may destroy old myths and point to
new directions in methodology. In 1985, T. Matsuzawa reported
experiments with a female chimpanzee that had learned to use
Arabic numerals to represent numbers of items. This animal (which
is still alive and whose name is "Ai") can count from 0 to 9
items, which she demonstrates by touching the appropriate number
on a touch-sensitive monitor. Ai can also order the numbers from
0 to 9 in sequence.
... ... N. Kawai and T. Matsuzawa (Primate Research Institute
Kyoto, JP) now report an investigation of Ai's memory span by
testing her skill in numerical tasks, the authors making the
following points:
1) The authors point out that humans can easily memorize
strings of codes such as phone numbers and postal codes if they
consist of up to 7 items, but above this number of items, humans
find memorization more difficult. This "magic number 7" effect,
as it is known in human information processing, represents an
apparent limit for the number of items that can be handled
simultaneously by the human brain.
2) The authors report that the chimpanzee Ai can remember
the correct sequence of any 5 numbers selected from the range 0
to 9.
3) The authors relate that in one testing session, after
choosing the first correct number in a sequence (all other
numbers still masked), "a fight broke out among a group of
chimpanzees outside the room, accompanied by loud screaming. Ai
abandoned her task and paid attention to the fight for about 20
seconds, after which she returned to the screen and completed the
trial without error."
4) The authors conclude: "Ai's performance shows that
chimpanzees can remember the sequence of at least 5 numbers, the
same as (or even more than) preschool children. Our study and
others demonstrate the rudimentary form of numerical competence
in non-human primates."
-----------
NAT 2000 403:39
SW 2000 21 Apr
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Related Background:
PRIMATOLOGISTS PROPOSE CHIMPANZEES DISPLAY CULTURAL VARIATION
An international team of primatologists led by A. Whiten, in a
comprehensive synthesis of chimpanzee research, has proposed that
chimpanzees display cultural variation. The findings are
apparently the most detailed evidence yet that nonhuman animals
can acquire through observation and imitation, and then convey
those learned skills to their neighbors and kin, elements of an
anthropological definition of culture. The research is
interpreted as buttressing the nurture half of the class nature-
nurture controversy over whether culture or genetics predominate
in determining behavior.
-----------
NYT 1999 17 Jun
SW Bulletin 1999 18 Jun
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Related Background:
IN FOCUS: ON CHIMPANZEES
"Evolutionary scientists are therapists for the human species.
People go to therapy to explore what molded them into who they
are today. That desire, writ large, is exactly what the study of
human origins is all about. A word of warning... Both lay
[people] and scientists misread evolution's signature easily and
often. Chimpanzees are not evolutionary challenged people, and
people did not evolve from gorillas. They and we share a common
ancestor in the nearly invisible past, a past that we try to
reconstruct in hopes of catching a sidelong glimpse of that
chimerical great grandparent. There are amazing similarities
between us today, but also profound differences. While they may
look like hirsute, sloped-foreheaded, primitive humans,
chimpanzees evolved for some 5 million years after their
ancestors diverged from our own. I offer a cautionary shout to
all those seeking to extrapolate from apes to humans and vice
versa: the great apes are highly evolved in their own right. They
inform us of the range of paths taken by our ancestors long ago.
This gives us an extraordinarily richer view of humanity than we
could have otherwise, but it can also deceive us if we are not
careful. At every turn, [we] should remember that humans,
chimpanzees, gorillas, bonobos, orangutans and all other higher
primates evolved for equally unique reasons. If we are going to
understand the meaning of the term "human nature", we must get to
the heart of what apes can and cannot tell us about our own
cognitive abilities and behavioral tendencies. No claim in
science is at once more banal and more profound than that of
human uniqueness. Explaining human uniqueness is what
anthropologists do for a living. At the same time, primatologists
are fond of asserting that apes are more like people than people
like to admit. Somewhere between these two claims is evidence of
the shared and separate ancestry of humans and their genetic
kin."
-----------
Craig Stanford: _Significant Others: The Ape-Human Continuum and
the Quest for Human Nature_
(Basic Books, New York 2001, p.xv)
[The author is Associate Professor of Anthropology at the
University of Southern California and Director of the Bwindi-
Impenetrable Great Ape Project, Uganda.]
http://www.amazon.com/exec/obidos/ASIN/0465081711/scienceweek
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SW 2001 6 Jul
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8. TWO ELEPHANT SPECIES IN AFRICA
A.L. Roca et al (National Cancer Institute, US) discuss genetic
evidence for two species of elephant in Africa. Conservation
strategies for African elephants have consistently been based on
the consensus that all African elephants belong to the single
species Loxodonta Africana. Yet relative to African savannah
elephants, the elephants in Africa's tropical forests are
smaller, with straighter and thinner tusks, rounded ears, and
distinct skull morphology. The authors report DNA analysis of
biopsy samples from 195 free-ranging African elephants in 21
populations, the analysis involving examination of DNA sequence
variation in 4 nuclear genes (1732 base pairs). Phylogenetic
distinctions between African forest elephant and savannah
elephant populations corresponded to 58 percent of the difference
in the same genes between African (Loxodonta) and Asian (Elephas)
elephants. The authors suggest that large genetic distance,
multiple genetically fixed nucleotide site differences,
morphological and habitat distinctions, and extremely limited
hybridization of gene flow between forest and savannah elephants
support the recognition and conservation management of two
African elephant species: Loxodonta africana and Loxodonta
cyclotis. The authors further suggest that given the rapid
depletion of both forest and savannah elephant numbers in the
past century, and the ongoing destruction of their habitats, the
implications for conservation and species-level management of
these distinct taxa are considerable.
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SCI 2001 293:1473
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9. CRITICISM OF NOMENCLATURE IN GENETICS
Helen Pearson (NAT) discusses current confusions in the
nomenclature of genes. In molecular genetics, genes with multiple
aliases are apparently the rule rather than the exception,
whereas genes that have no functional relationship with each
other can often bear the same names. As biologists strive to make
sense of the growing wealth of genomic information, the messy
nomenclature of genes is becoming a hindrance to research.
Attempts to impose standardization are meeting stiff resistance,
and approaches that would assign genes unique identification
numbers appear unlikely to succeed unless enforced by journals.
The extent of the nomenclature problem is illustrated by a recent
study [E. Hovig et al (2001)] that noted that of 22,008
identified distinct human genes, 10,352 had more than one name,
one gene had 15 aliases, 4257 abbreviated names were used to
refer to more than one gene, 5 functionally unconnected genes
carry the same name. Accustomed to working in relative isolation,
researchers studying different species have grown attached to
their respective gene-naming traditions. Drosophila geneticists,
for example, delight in using colorful names -- such as
"hedgehog", which produces a signaling protein involved in a
range of developmental processes, and "lost in space", a gene
that guides the growth of neurons -- and these researchers have
no intention of letting other geneticists spoil their fun.
-----------
NAT 2001 411:631
-----------
Editor's note: It should be noted that astronomers and chemists
are also confronted with hundreds of thousands of entities to be
studied, yet both these disciplines have managed to develop
stringent nomenclature rules to avoid research confusions. It
might be argued, in fact, that a chaotic nomenclature is a clear
characteristic of an immature science. Molecular geneticists may
be having their fun assigning arbitrary colorful names to various
genes, but it is doubtful that they are respected for it.
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Related Background:
HISTORY OF SCIENCE: ON LANGUAGE REFORM IN CHEMISTRY
An argument can be made that nomenclature in science is as
important as data, since nomenclature represents the prevailing
conceptual organization of observations. Certainly, researchers
in most sciences are constrained to adhere to the nomenclature
rules of their field. Molecular biology is currently in a phase
of general nomenclature chaos with respect to the naming of
genes, but hopefully that phase will soon pass. Meanwhile,
nomenclatures in other areas of biology are more organized, and
18th century plant taxonomy, in fact, served as a model for the
nomenclature revolution in chemistry that occurred in conjunction
with the "new chemistry" proposed by Antoine Lavoisier (1743-
1794).
Lavoisier is often cited as the instigator of chemical
nomenclature reform at the end of the 18th century, but four
chemists were the prime movers of this reform: Lavoisier, Louis
Guyton de Morveau (1737-1816), Claude Berthollet (1748-1822),
Antoine Fourcroy (1755-1809). Of the four, Guyton de Morveau,
probably deserves more credit than the others, his efforts
culminating in the publication of his _Method of Chemical
Nomenclature_ in 1787 [*Note #1]. All the above chemists,
however, collaborated in the nomenclature revision program, which
quickly became accepted after the publication of Lavoisier's
influential textbook _Elementary Treatise on Chemistry_ in 1789
[*Note #2]. Perhaps the most important general nomenclature
revision was the adoption of a binomial scheme for naming
compounds (influenced by the scheme then current in botany), but
of specific importance was the renaming of "*dephlogisticated
air" ("empyreal air; vital air) as "oxygen", and the renaming of
"inflammable air" as "hydrogen", both new names based on
prevailing knowledge of chemistry rather than on ambiguous
attributes.
... ... Bernadette Bensaude-Vincent (University of Paris, FR)
presents a commentary on language reform in chemistry, the author
making the following points:
1) Guyton de Morveau initiated the French 18th century
chemical nomenclature reform project and established a set of
basic principles: a) nomenclature should reveal "the nature of
things"; b) simple substances should have simple names evoking
their most characteristic property; c) compound names should
express the composition of chemical compounds; d) Greek
etymologies should be used in preference to Latin.
2) Guyton de Morveau began his attempt to reform chemical
nomenclature in 1782 and submitted his project to the Paris
Academy of Sciences in January 1787. At the Academy, Guyton
encountered a fierce debate concerning the existence of
"phlogiston", the principle that was believed to explain
combustion and reduction. Although most chemists at that time
believed in phlogiston, Lavoisier's explanation of combustion was
quite different. Guyton allied himself with Lavoisier, and with
the help of Lavoisier, Berthollet, and Fourcroy, Guyton published
a revised project in the spring of 1787, the revision making no
mention of "phlogiston", but instead containing new words such as
"oxygen", from Greek words meaning "acidifying principle", the
new term stemming from Lavoisier's idea that all acids contained
oxygen.
3) The author points out that the language reform of 1787-
1789 was an integral part of the formation of the autonomous
discipline of chemistry, contributed to the subordination of
pharmacy to chemistry, and contributed to the redefinition of the
chemical arts as applied chemistry. The new language forged by
academic chemists separated many users of chemical substances
from their own traditions. The new language ignored the
physiological senses of chemists, banished all reference to
geographical origins or the discovery of the substances, and
imposed an analytical quantitative logic on chemical
nomenclature. Although the use of this logic proved to be a
valuable method over time, the principles of the system were
never strictly applied. Oxygen, for example, should have been
renamed when Humphrey Davy (1778-1829) established that many
acids do not contain oxygen. Colors and odors were restored after
the discovery of chlorine and iodine, named from the Greek for
"yellowish-green" and "violet", respectively. Bromine was named
from the Greek word for "stink". Morphine was named after
Morpheus, the god of dreams. Benzene was named after Styrax
benzoin, a tree native to Sumatra and Java. Scandium, germanium,
and polonium were named after political entities, and in the 20th
century various new elements were named after historical
scientific figures. In general, the systematization imposed by
the four 18th century reformer chemists in the name of
rationality remained an ideal often contradicted by practice. At
present, nomenclature rules in chemistry are under the control of
a permanent commission, the International Union of Pure and
Applied Chemistry (IUPAC).
-----------
NAT 2001 410:415
-----------
Notes:
... ... *Note #1: Louis Bernard Guyton de Morveau (1737-1816) was
an interesting personage. His first profession was that of an
attorney. In 1776, while still an attorney, he published the
_Elements of Theoretical and Practical Chemistry_, a major
attempt to quantify chemical affinities. In 1782, he gave up the
law and devoted himself full-time to chemistry. In 1795, he
founded the Ecole Polytechnique and taught there until 1805.
Guyton was one of the first to conclude that iron and steel
differ solely in their carbon content. He made improvements in
the manufacture of gunpowder. He was the first to use chlorine
and hydrochloric acid gas as disinfectants. He was one of the
first balloonists, making two flights in 1784 and helping in the
organization of the world's first air force, the Compagnie
d'Aerostiers, whose reconnaissance balloonists assisted the
French army in several battles during the Napoleonic wars.
... ... *Note #2: Concerning nomenclature in chemistry, the
following passage appears in Lavoisier's _A General Introduction
to Chemistry_ (1789):
"It is impossible to dissociate language from science or
science from language, because every natural science always
involves three things: the sequence of phenomena on which the
science is based; the abstract concepts which call these
phenomena to mind; and the words in which the concepts are
expressed. To call forth a concept, a word is needed; to portray
a phenomenon, a concept is needed. All three mirror one and same
reality. Words are thus required to preserve and transmit ideas,
so that it is clear that the advancement of a science and the
improvement of its technical vocabulary go hand in hand. No
matter how certain we are of the phenomena, no matter how
adequately our concepts reflect them, we cannot help perpetuating
wrong ideas unless we have a precise terminology in which to
express ourselves."
Lavoisier, considered the father of modern chemistry, was no
doubt the most eminent scientist to ever suffer death by the
guillotine. In 1780, as a member of the French Academy of
Sciences, Lavoisier was active in rejecting the application to
the Academy of a certain physician Jean-Paul Marat (1743-1793).
Marat apparently did not forget. During the French Revolution
(1787-1799), Marat became a powerful revolutionary leader, and
Marat was instrumental in bringing Lavoisier to trial for his
investments in a much-hated company that collected taxes for the
French government. Lavoisier was guillotined May 8, 1794 and
buried in an unmarked grave. (Marat did not live to see this:
Marat himself was assassinated in July 1793.)
... ... *dephlogisticated air: In this context, the term
"phlogiston" refers to a 17th and 18th century chemical theory
involving a hypothetical principle of fire. The idea was that
every combustible substance is in part composed of phlogiston,
with the phenomenon of burning caused by the liberation of
phlogiston and the "dephlogistonated" substance remaining as ash
or residue. The phlogiston theory was experimentally discredited
by Lavoisier beginning in 1770, who showed that the newly
discovered element oxygen was always involved in combustion.
-----------
SW 2001 18 May
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Related Background:
ON LINGUISTIC CHAOS IN MOLECULAR BIOLOGY
Nomenclature anarchy in molecular biology is apparently once
again the focus of attention, although no remedies are evident.
In a recent article, Paul Smaglik writes, "Gene and protein names
often are based on the flamboyant, the descriptive, and the
intentionally obscure. For many researchers, naming their
discovery may be a rare opportunity to imbue their science with
creativity." But Lawrence Puente (University of Alberta, CA)
points out that creativity plus competition can equal confusion.
Julia A. White (University College London, UK), a member of the
Nomenclature Committee of the Human Genome Organization, says
that although the committee strives to sort out linguistic chaos,
the committee remains behind as a result of the speed and scope
of the Human Genome Project. With hundreds of thousands of genes
and proteins still to be named, molecular biology is in dire need
of nomenclature regulation.
-----------
TS 1998 30 Mar
SW 1998 17 Apr 98
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Related Background:
MORE DISCUSSION OF ACRONYM ANARCHY IN MOLECULAR BIOLOGY
There are approximately 100,000 genes in the human genome, and
approximately 100,000 expressed proteins, the total certainly
enough to require a dictionary of names. Add to this total the
total of acronyms used to identify cell-lines, cell receptors,
metabolic pathways, carbohydrates, etc., and the dictionary would
require a second volume. In the early days of biochemistry and
molecular biology, when few genes and their expressed proteins
had been identified, everyone could more or less remember the
names of the macromolecular entities being studied by the people
in the laboratory down the hall. These days that is unlikely, and
made more unlikely by the tendency of many molecular biologists
to choose ad hoc names that are often more cute than technically
pertinent, and to obfuscate their research papers with acronyms
by the dozen in a single paper. We know of at least one instance
where an acronym for a cell-line in a paper from a group at the
US National Institutes of Health was not defined anywhere in the
paper, where telephone calls to molecular biologists produced no
one who knew what cell-line was involved, and where a query to
the authors of the paper did not produce a response for nearly
three weeks. As one scientist recently put it: "If you make your
paper difficult to read, at least no one can call you stupid." A
recent exchange of letters in the journal Nature revisits this
recurrent problem of nomenclature in molecular biology. It seems
there are indeed existing committees concerned with regulating
the nomenclature of molecular biology, but it also seems no one
pays any attention to them. Puente et al (Univ. of Alberta, CA)
refer to the present situation as "acronym anarchy". We agree. We
would add that if the in-house editors of the leading general
journals such as Science and Nature would refuse to publish these
unduly obfuscated papers, they would be doing a service to the
scientific community.
-----------
NAT 1997 27 Nov
SW 1997 19 Dec
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Related Background:
A CRITICISM OF NOMENCLATURE IN MOLECULAR BIOLOGY
Nomenclature is a serious problem in all the sciences, since as
new discoveries are made, new entities identified, new concepts
formulated, new names for these things must be found so that
scientists can communicate with each other with some degree of
precision. Most sciences have nomenclature committees that meet
regularly to standardize current terminology and make decisions
about new terminology. Molecular biology, one of the most active
scientific disciplines these days, has no such constraints, and
apparently there is growing concern that the arbitrary and some-
times whimsical naming of new entities ("miranda", "prospero",
"numb", "inscrutable") in molecular biology, with the same entity
often sporting a number of names, has reached the stage of
promoting confusion and the inability of scientists to deal
efficiently with the literature. In a recent editorial
criticizing nomenclature practices in molecular biology, the
journal Nature says, "Regrettably, molecular biologists have
followed the particle physicists' whimsy with obscurantist
enthusiasm." In particle physics, of course, we already have
"quark", "strangeness", "charm", "color", "top", "bottom", etc.,
which the editorial calls a "descent into whimsy" started by
Murray Gell-Mann in the 1960s, who evidently took the term
"quark" from a phrase in James Joyce's FINNEGAN'S WAKE. What is
interesting is that the same journal which is criticizing
whimsical scientific nomenclature is apparently quite fond of
headlines involving whimsical wordplay, puns, and metaphors when
describing scientific research results. If a consequence of this
attention to nomenclature will be a more rational use of language
in science, many people will no doubt be appreciative of it.
-----------
NAT 4 Sep 97
SW 1997 19 Sep
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SCIENCE-WEEK 28 Sep 2001 http://scienceweek.com
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Related Background:
PHYSICISTS ORGANIZE AGAINST IMPENETRABLE JARGON IN PHYSICS
A group of working physicists and journal editors, under the
leadership of Mitio Inokuti (Argonne National Laboratory, US) and
Ugo Fano (University of Chicago, US) has come into existence with
the objective of reforming the publication standards for papers
in physics. The problem is that physicists no longer understand
each other, their communication warped by "unexplained acronyms,
cryptic symbols, endless sentences, and monstrous graphs".
Analyzing the psychology of why this exists, Phillip Schewe
(American Institute of Physics, US) says, "You lose all your
readers, but at least you can't be accused of being an idiot.
Instead, the readers are made to feel like they're idiots." The
problem, of course, is just as severe in chemistry and biology.
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SCI 15 Aug 97
SW 1997 29 Aug
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SCIENCE-WEEK 28 Sep 2001 http://scienceweek.com
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10. MISUNDERSTANDINGS OF CLONING
Lee M. Silver (Princeton University, US) discusses current
confusions concerning cloning. Herbert J. Webber coined the word
"clone" in 1903 to describe a colony of organisms derived
asexually from a single progenitor, and the term was quickly
adopted by biologists. A clone of animal siblings can form
naturally, on occasion, as a result of asexual reproduction from
a single progenitor embryo. However, in contrast to plants, whole
animals cannot be grown directly from cells that have begun to
differentiate into a specialized form. The popular understanding
of cloning has its roots in Alvin Toffler's 1970 book _Future
Shock_, in which Toffler took a clear scientific concept and
muddled it into the fantastical prediction that "man will be able
to make biological carbon copies of himself". Unfortunately, this
fictitious version of cloning was presented in a highly-
influential non-fiction book, and in one fell swoop, clones
morphed from the simple progeny of asexual reproduction into
sophisticated products of biological engineering created by
scientists bent on controlling nature. Through the popular media,
this version of a clone was rapidly integrated into every major
language. The concept of a clone was extended to inanimate
objects such as computers ("PC clone"), as well as becoming a
figure of speech to describe people. No technology, however,
exists for making copies of people: real cloning technology can
lead only to the birth of a unique and unpredictable child who
has the same DNA sequence as someone else, but nothing more. The
scientific community has lost control over the term: cloning has
a popular connotation that is impossible to dislodge, and we must
accept that democratic debate on cloning is bereft of any
meaning. Science and scientists would be better served by
choosing other words to explain advances in developmental
biotechnology to the public.
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NAT 2001 412:21
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SCIENCE-WEEK 28 Sep 2001 http://scienceweek.com
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11. IRON METABOLISM
G. Nicolas et al (Cochin Institute of Molecular Genetics, FR)
discuss iron metabolism. Iron is an essential element required
for growth and survival of almost every organism. In mammals, the
iron balance is primarily regulated at the level of duodenal
absorption of dietary iron. Following absorption, ferric iron is
loaded into apotransferrin in the circulation and transported to
the tissues, including erythroid precursors, where it is taken up
by transferrin receptor-mediated endocytosis. Reticuloendothelial
macrophages play a major role in the recycling of iron via the
degradation of hemoglobin of senescent erythrocytes, whereas
hepatocytes contain most of the iron stores of the organism in
the form of ferritin polymers. During the past 5 years, a body of
information concerning the proteins involved in iron absorption
and in the regulation of iron homeostasis has resulted from the
study of inherited defects (both in humans and in mice) that lead
to distinct iron disorders. In the case of iron deficiency, the
pathophysiological consequences of identified gene defects are
well understood, because they usually result in loss of function
of proteins directly involved in the pathway of iron absorption.
In contrast, several abnormalities associated with genetic iron
overload have led to identification of various proteins whose
functional role in the control of iron homeostasis remains only
poorly clarified. The authors report evidence that the liver
protein hepcidin acts as one of the signaling molecules
regulating both intestinal iron absorption and iron storage in
macrophages.
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PNAS 2001 98:8780
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SCIENCE-WEEK 28 Sep 2001 http://scienceweek.com
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12. HEARING IN THE FRUIT FLY
M.C. Gopfert and D. Robert (University of Zurich, CH) discuss
audition in the fruit fly Drosophila. The authors report an
investigation of the delicate biomechanism of the fly's minute
antennal hearing organs and demonstrate that the organs look and
work like a lock and key. Rotating in response to sound, the
distal segment of the antenna mechanically activates the auditory
receptors, the basic mechanism of Drosophila audition. In D.
melanogaster, the antennae mediate the detection of conspecific
"love songs". Anatomically, each antenna is an asymmetric
structure consisting of 3 segments and a feather-like structure
called the "arista". Laser vibrometric analysis of sound-induced
vibrations reveals that the arista and the club-shaped 3rd
segment together constitute a mechanical entity -- the sound
receiver. Unlike other animals, Drosophila makes use of sound-
induced rotation to channel acoustic energy to its auditory
receptor neurons -- it has "rotational ears". The 3rd segment of
the Drosophila antenna is also the primary organ of olfaction and
carries hundreds of olfactory sensilla. As hearing relies on
mechanical rotation and olfaction relies on chemical interaction,
the two sensory modalities can coexist without compromising their
respective functions. The fruit fly thus rotates its nose in
order to hear.
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NAT 2001 411:908
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SCIENCE-WEEK 28 Sep 2001 http://scienceweek.com
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13. IN FOCUS: THE SQUARE ROOT OF N RULE
"If I tell you that a certain gas under certain conditions of
pressure and temperature has a certain density, and if I express
this by saying that within a certain volume (of a size relevant
for some experiment) there are under these conditions just (n)
molecules of the gas, then you might be sure that if you could
test my statement in a particular moment of time, you would find
it inaccurate, the departure being of the order of n^(1/2). Hence
if the number n = 100, you would find a departure of about 10,
thus relative error = 10 percent. But if n = 1 million, you would
be likely to find a departure of about 1000, thus relative error
= 0.1 percent. Now, roughly speaking, this statistical law is
quite general. The laws of physics and physical chemistry are
inaccurate within a probable relative error of n^(-1/2), where
(n) is the number of molecules that cooperate to bring about that
law -- to produce its validity within such regions of space or
time (or both) that matter, for some consideration or for some
particular experiment. You see from this again that an organism
must have a comparatively gross structure in order to enjoy the
benefit of fairly accurate laws, both for its internal life and
for its interplay with the external world. For otherwise the
number of cooperating particles would be too small, the 'law' too
inaccurate. The particularly exigent demand is the square root.
For though a million is a reasonably large number, an accuracy of
just 1 in 1000 is not overwhelmingly good, if a thing claims the
dignity of being a 'Law of Nature'."
-----------
Erwin Schroedinger: _What is Life?_
(Doubleday, New York 1956, p.15)
http://www.amazon.com/exec/obidos/ASIN/0521427088/scienceweek
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SCIENCE-WEEK 28 Sep 2001 http://scienceweek.com
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14. SW ARCHIVE:
ON LOCALIZATION OF FUNCTION IN THE HUMAN BRAIN
For more than 200 years, neurobiologists have been concerned
with the general problem of what is called "localization of
function" in the human brain. That there is considerable
localization of function is indisputable: there are brain regions
involved with specific primary inputs such as vision, audition,
taste, etc., brain regions for specific primary outputs to
various muscle systems, and brain regions for speech and the
understanding of language. The still unclear aspects concern
anatomical localization of other so-called "higher faculties",
e.g., learning, memory, perceptual analysis, motivations, various
other cognitive abilities, etc.
Classical studies of localization of function in the human
brain essentially began with Franz Joseph Gall (1758-1828), who
postulated that the shape of the human brain, especially its
convolutions, was related to "mental capacity", and that
different parts of the brain were involved with different parts
of the human body. This latter proposal concerning the relation
between different parts of the brain and different parts of the
body was essentially a correct view. But Gall also believed he
could correlate the shape of the human brain with various
emotional and temperamental qualities, and that the shape of the
brain, particularly its convolutions, could be deduced from the
irregularities existing in the topology of the overlying skull.
Thus began the 19th century pseudoscience of "phrenology", a
quackery that postulated that various human character traits
could be identified by literally feeling bumps on the head. The
public adored the idea, and so-called "phrenologists" continued
to bamboozle the public long after Gall was dead. What started as
a useful view that correlated brain anatomy with function, ended
in a popular pseudoscience that still had the public confused and
misled 100 years later.
The next most important figure in this field was Pierre Paul
Broca (1824-1880), a neurosurgeon who in 1861 discovered the
motor area of the brain responsible for speech, and who studied a
series of patients with traumatic injuries in this area. As a
result of Broca's work, the idea that at least certain brain
functions are localized was put on a firm scientific footing, and
a long history of research by clinical neurologists attempting to
correlate traumatic brain injury to loss of specific brain
function began. Beginning in the 1950s, evidence from localized
electrophysiological studies was added to the data resulting from
studies of traumatic brain injury, and in the 1990s an entirely
new set of data from functional magnetic resonance imaging of
the human brain in action became available to researchers
studying localization of brain function. This field is now
intensely active and of signal importance in neurology and
cognitive science. But the human brain is profoundly complex, and
there are still more questions than answers about how things get
done in this 1400-gram mass of tissue that makes us what we are.
The term "cortex" (cerebral cortex), in this context, refers
to the thin surface layering of nerve cells of the brain, the
region only several millimeters thick but covering all of the
brain surface. This is the part of the central nervous system
most intimately involved with the so-called "higher faculties",
although the cortex generally operates in concert with other
parts of the brain. The structure is primitive in lower mammals,
and is found progressively more pronounced and with greater
surface area in primates and man. Many contemporary
neurobiologists who study the brain emphasize precise "mapping"
of the cerebral cortex into "areas" associated with specific
functions.
... ... Jonathan C. Horton (University of California San
Francisco, US) presents an essay on localization of function in
the human brain, the author making the following points:
1) Given the limitations of histology, researchers often
designate areas in brain cortex by topography. For example, any
region that contains its own representation of the visual world
qualifies for "area" status. Unfortunately, topographic order in
other than primary visual areas ("higher" visual areas) is often
too crude to provide a reliable definition of boundaries. Another
limitation is that topography may not be meaningful outside
sensory and motor cortices. The author asks: "What constitutes
topography in regions concerned with language, motivation, or
personality?"
2) The author points out that relentless experimental
efforts and a battery of technical advances have provided us with
better maps of the brain. But much of the cortex stubbornly
refuses to be mapped, and the author suggests it is worth
questioning the assumption that the cerebral cortex consists of a
finite number of areas with sharp borders. An alternative is that
only certain regions -- mostly motor and sensory cortex -- are
organized in this way. Other regions might be diffuse fields
separated by gradual transitions in function, properties, and
connections. As Broca said in 1861: "Although I believe in the
principle of localization, I have asked and still ask myself
within what limits this principle can be applied." The author
(Horton) concludes: "For brain cartographers, the last frontier
is in their heads."
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NAT 2000 406:565
SW 2000 1 Sep
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15. SOURCES:
AS: Amer. Scientist; CEN: Chem. & Eng. News; GD: Genes & Dev.;
GR: Genome Res.; JACS: J. Amer. Chem. Soc.; JAMA: J. Amer. Med.
Assoc.; JCE: J. Chem. Educ.; MMWR: CDC Morbidity and Mortality
Weekly Report; NAT: Nature; NATM: Nature Medicine; NEJM: New
Engl. J. Med.; NS: New Scientist; NYT: New York Times; NYR: New
York Review; PNAS: Proc. Natl. Acad. Sci.; PRL: Phys. Rev. Lett.;
PT: Physics Today; SA: Scientific American; SCI: Science; SW:
ScienceWeek; TS: The Scientist.
In the text, the affiliation following the author's name is the
affiliation of the lead author. The indication (na) signifies no
known research affiliation.
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