ScienceWeek

SCIENCE-WEEK

A Weekly Email Digest of the News of Science

A journal devoted to the improvement of communication
between the scientific disciplines, and between scientists,
science educators, and science policy makers.

March 31, 2000 -- Vol. 4 Number 13

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I understand engineers. Physiology is just reverse
engineering. We get an organism dumped on the lab
table, and our job is to take it apart and find
out how it works.
-- Julian Tobias (1911-1964)

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Contents of This Issue:

1. History of Science:
The 18th Century Women Scientists of Bologna
--------------------------------------------
Although the 18th century was an era that produced a great and
influential flowering of human thought, in all the countries in
Europe except one, women were forbidden to study and lecture in
universities, and women had hardly any participation in the
sciences. The one exception was Italy.

2. Cell Biology:
Chemokines, Cell Migration, and the Immune Response
---------------------------------------------------
There is growing evidence that chemoattractive small proteins
(chemokines) play a central role in the immune response by
orchestrating the interactions between immune system cells.
(Includes related background material.)

3. Molecular Biology:
A Minimal Genome
----------------
The smallest known genome of an independently replicating cell
contains 480 protein-coding genes, and new evidence suggests only
265 to 350 of these genes are essential under laboratory growth
conditions.

4. Medical Biology:
Chlamydia Pneumoniae and Atherosclerosis
----------------------------------------
There is now strong evidence of an association of the bacterial
pathogen C. pneumoniae with atherosclerosis, and thus a possible 
association of the pathogen with stroke, coronary heart disease,
peripheral vascular disease, and aortic aneurysm. (Includes
related background material.)

5. Physical Chemistry
On First-Order Liquid-Liquid Transitions
----------------------------------------
Although first-order solid-solid structural phase transitions are
common in crystalline solids ("polymorphs"), first-order liquid-
liquid transitions (i.e., transitions between two distinct liquid
forms with different density and entropy) are exceedingly rare in
pure substances. Such a transition has now been observed in
liquid phosphorus at high pressure.

6. Applied Science
On Physics and the Information Revolution
-----------------------------------------
Current transistor technology has intrinsic limitations which
will soon prevent the continuation of significant increases in
computing power. Nanotechnology and quantum switches offer the
promise of a new "disruptive technology" that will push the
information revolution into its next phase. (Includes related
background material.)

In Focus: On Concepts in Mathematics

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1. HISTORY OF SCIENCE:
THE 18TH CENTURY WOMEN SCIENTISTS OF BOLOGNA
In the history of Europe, the 18th century is known as the Age of
Reason (the Enlightenment), a period when the educated upper
classes doted on rational thought and the beginnings of modern
science. This was an era that produced a great and influential
flowering of human thought, but in all the countries in Europe
except one, women were forbidden to study and lecture in
universities, and women had hardly any participation in the
sciences. The one exception was Italy.
... ... M. Cieslak-Golonka and B. Morten (2 installations, PL IT)
present an account of the 18th century women scientists of the
University of Bologna, the authors making the following points:
     1) The authors point out that in the 18th century, the
education of Italian women from the higher social classes was
exactly the same as that of men, the special attitude toward the
education of women apparently stemming from the influence of
ancient Rome. In the universities of Salerno, Bologna, Padua, and
elsewhere in Italy, women competed on an equal footing with men,
particularly in the fields of literature, natural sciences, and
medicine.
     2) The University of Bologna, founded in 1088, was a place
where the students elected both the faculty and the rector, and a
university distinguished by the unusual number of women
scientists it graduated and hired during the 18th century. At the
University of Bologna, intellectually gifted women from the upper
classes, and occasionally from the lower classes, had access to a
level of education not seen in most Western nations until the
20th century. Some of these women flourished as scholars and
scientists:
... ... a) Laura Bassi (1711-1778): Bassi was the pioneer among
the women professors of the University of Bologna. She became the
first woman to earn a doctor of philosophy degree, the
university's first female professor, and the first woman to
occupy a chair in physics. She focused on mechanics, hydraulics,
and anatomy, and she was particularly intrigued with the works of
Newton (1642-1727). She conducted physics tutorials and
experiments for her students throughout her academic career, and
for over 30 years, she offered an annual public lecture on
experimental physics. Her academic duties were combined with an
active family life: in 1738 she married a physician, and together
they had 12 children.
... ... b) Anna Morandi Manzolini (1716-1774): Morandi was
considered to be the finest practitioner of artistic anatomy of
her time. She is frequently cited as the first to make models of
internal organs, and her work showing details of the abdominal
cavity and the uterus gained her special notice. She produced a
model of the ear that could be taken apart to be used in the
instruction of medical students. At the present time, in the
Anatomical Museum at the University of Bologna, one can still see 
Morandi's wax models, including her self-portrait.
... ... c) Maria Gaetana Agnesi (1718-1799): Agnesi was a
brilliant linguist and a talented mathematician, the eldest of 21
children born to Pietro Agnesi, a professor of mathematics at the
University of Bologna. Her most famous work, in two volumes, was
_Analytical Institutions_, which for the first time provided a
synthesis of many different branches of mathematics. The first
volume focuses on algebra and its applications in geometry. One
chapter describes a curve that has become well-known as "Agnesi's
curl", or "versiera della Agnesi", which has become mistranslated
to "the witch of Agnesi". This curve, expressed by the equation
x^(2)y = a^(2)[a-y], was first described by Fermat (1601-1665).
The second volume of Agnesi's _Analytical Institutions_ contains
an analysis of differential and integral calculus. Agnesi was
admitted into the Academy of Sciences in Bologna, and in 1750 she
was offered an honorary chair at the University of Bologna in
Mathematics and Natural Philosophy.
... ... d) Maria Dalle Donne (1778-1842): Dalle Donne was born to
a peasant family in a small village on the outskirts of Bologna.
Her talents were recognized early, and she was encouraged to
study medicine. In 1799, she presented her dissertation and took
the examination that made her the first female doctorate in
medicine. She passed the examination with highest honors (maxima
cum laude). In 1800, Dalle Donne published three important
scientific papers. The first paper, on anatomy and physiology,
was a review and commentary on work previously done on female
reproduction and fertility, fetal malformations, and blood
circulation in the uterus. The second paper suggested for the
first time that diseases be classified on the basis of symptoms.
The third paper focused on midwifery and the care of newborns. In
1829, Dalle Donne became only the second woman, after Laura
Bassi, to become a member of the prestigious Ordine de
Benedettini Academici Pensionati, in which she was awarded the
title of "Academic". In 1832, Dalle Donne became Director of the
Department of Midwifery at the University of Bologna.
-----------
M. Cieslak-Golonka and B. Morten: The women scientists of
Bologna.
(American Scientist Jan/Feb 2000 88:68)
QY: Maria Cieslak-Golonka [golonka@ichn.ch.pwr.wroc.pl]
-------------------
Summary by SCIENCE-WEEK http://scienceweek.com 31Mar00

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2. CELL BIOLOGY:
CHEMOKINES, CELL MIGRATION, AND THE IMMUNE RESPONSE
     The ability of the vertebrate body to defend itself against
specific invading agents such as bacteria, toxins, viruses, and
foreign tissues is called "immunity", and the substances that are
recognized by the immune system and provoke immune responses are
called "antigens". This recognition-response system involves a
variety of immune system cell types, and a variety of
interactions between various cell types, and it is only during
the past several decades, through the work of hundreds of
laboratories, that many of the details from the molecular level
to the cellular level have become apparent. 
     In general, the cells that carry out immune responses are
classified as "lymphocytes" and "antigen-presenting cells". Of
the lymphocytes, there are in turn two types -- B cells and T
cells -- and these both develop from precursor cells (stem cells)
in bone marrow. B cells leave bone marrow as mature functional
immune cells, but T cells leave bone marrow as immature cells and
migrate from bone marrow into the thymus gland, where in a few
days they develop "immunocompetence". Before B cells leave bone
marrow or T cells leave the thymus, they acquire several
distinctive surface proteins which differentiate the subsequent
functions of these cells. Under the light microscope, B cells and
T cells look identical: the cells are distinguished by their
specific surface proteins. Concerning the "antigen-presenting
cells", these are large ameboid-like cells (macrophages) that
degrade antigens and present the resulting fragments to so-called
"helper T cells", which in turn activate specific B cells (see
below).
     The most remarkable feature of the immune system is its
ability to respond specifically to an enormous variety of
different antigens. A milestone in the understanding of this
process was the formulation of the "clonal selection theory" in
the 1950s by N.K. Jerne (1911-1994) and others, a theory now
amply supported by experimental evidence, and for which Jerne
received the Nobel Prize in Physiology and Medicine in 1984. The
key feature of the clonal selection theory is the idea that the
binding of antigen to a lymphocyte with complementary receptors
on its surface selectively activates that lymphocyte to
proliferate and differentiate. The antigen, therefore, selects
from a very large pool of lymphocytes the set capable of
recognizing the antigen or specific parts (epitopes) of the
antigen. Activation results in clones of lymphocytes, the members
of each clone being derived from the same ancestor and therefore
all having the same epitope specificity. Thus the immune system
can be viewed as a collection of a vast number of clones of B and
T lymphocytes, each descended from a single progenitor cell and
therefore committed to the synthesis of the same surface receptor
as the original cell. (One lymphocyte may have up to 10^(5)
receptor molecules on its surface, but all of the antigen-related
receptors on a given lymphocyte are identical in structure. What
is quite remarkable is that via a molecular mechanism, this
commitment to express a particular antigen receptor is acquired
by the lymphocyte during its development without any exposure to
antigen. In the human body, there are approximately 10^(12)
lymphocytes, and it is estimated these represent approximately
10^(8) to 10^(9) different receptor specificities. Moreover, most
antigens have many epitopes, and a given epitope can be
recognized by more than one kind of receptor, so the number of
lymphocytes in the population that can respond to a given epitope
is much larger than the number of cells possessing a specific
receptor: the response to even a single epitope is heterogeneous,
involving the participation of a number of different clones of
lymphocytes.)
     One of the key events in the response of the immune system
is the production of antibodies, which are protein molecules
(immunoglobulins) that bind to specific antigenic determinants.
The production of antibodies involves the interaction between
three cell types, antigen-presenting cells, B cells, and T cells,
and the activation of B cells and the differentiation of these B
cells into antibody-producing "plasma cells". This activation
requires the interaction of antigen-specific B cells with certain
complementary antigen-specific T cells ("helper T cells"), the
interaction at close quarters and involving the release of
specific activating substances called "lymphokines" (chemokines).
     In general, as few as 1 in 100,000 circulating B and T cells
are specific for the same single antigen, yet these cells must
come together if an antibody response is to occur. Bringing
antigen-presenting cells and relatively rare same-antigen-
specific B and T cells into physical contact is a principal
function of the so-called "secondary lymphoid [lymphatic]
organs": the lymph nodes, spleen, tonsils, and aggregated
lymphoid nodules of the small intestine (Peyer's patches). (The
primary lymphoid organs are bone marrow and the thymus gland).
... ... Jason G. Cyster (University of California San Francisco,
US) presents a review of research on chemokines in secondary
lymphoid organs, the author making the following points:
     1) The author points out that for much of the 20th century
it was known that the secondary lymphoid organs are the sites
where immune responses against antigens are initiated.
Specialized transport systems carry antigens from peripheral
sites of entry into each of the secondary lymphoid organs.
Antigens entering across the skin are carried by lymphatic
vessels into lymph nodes, those entering the gastrointestinal
tract are carried by specialized epithelial cells into tonsils
and Peyer's patches, and blood-borne antigens are filtered and
concentrated within the spleen.
     2) After being released from the primary lymphoid organs
(bone marrow and the thymus gland), new lymphocytes migrate
rapidly from the bloodstream into secondary lymphoid organs. By
being almost continually on the move, individual lymphocytes are
able in a matter of days to survey many of the secondary lymphoid
organs in the body for the presence of their specific antigen.
The survey process involves B cells and T cells migrating to
separate compartments within the secondary lymphoid organ (B cell
follicles and T cell areas), staying for several hours, and then
migrating back into circulation.
     3) When foreign antigen is detected, a new and more complex
series of movements begins, leading to a kind of "cellular dance"
that helps bring antigen-specific B and T cells together for an
immune response. Many of the cues needed for this cellular dance
are provided by the members of the chemokine family. Chemokines
are small chemoattractive proteins found in mammals, birds, and
fish. They are highly basic proteins that signal through
transmembrane receptors. Recently, chemokines have been
identified within lymphoid organs, the substances attracting
naive as well as activated lymphocytes. These "lymphoid
chemokines" appear to be critical for the various movements of
lymphocytes into the subcompartments of lymphoid organs, and it
is apparent that lymphoid organs contain an immensely complex
chemokine landscape, with any single cell likely to be exposed to
several chemokine gradients as it moves. A long-standing
fundamental problem in developmental biology has been
understanding over what distance tissue-morphology inducers
(morphogens) can act, and it will be a similarly important
challenge for immunologists to determine the distances over which
chemokines act, and to understand whether a chemokine can act
like a morphogen and induce different properties in a cell,
depending on the position of the cell in the chemokine gradient.
-----------
Jason G. Cyster: Chemokines and cell migration in secondary
lymphoid organs.
(Science 10 Dec 99 286:2098)
QY: Jason G. Cyster [cyster@itsa.ucsf.edu]
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 31Mar00
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
ON MODELS OF IMMUNE MEMORY
Higher vertebrates, including humans, have through evolution
developed an immune system that can selectively destroy or
inactivate foreign molecules and foreign cells (*antigens)
without harming the molecules or normal cells of the host. The
vertebrate immune system apparently retains a "memory" of each
antigen attack, allowing the immune system to respond more
efficiently the next time it encounters the same invader. One
group of immune system cells involved in this immune system
memory is a small fraction of the proliferating *B-lymphocyte
cell population, the fraction effectively set aside as a reserve
population of cells to be directed against a specific stimulating
antigen. Such cells, called "memory B cells", are
indistinguishable in appearance from other unstimulated
lymphocytes and like them do not secrete antibody. But if the
organism is exposed to the same antigen a second time, the
reserve population of antigen-specific memory cells quickly
proliferates and differentiates into antibody-secreting plasma
cells, thereby allowing what is called the "secondary response"
to a given antigen to occur more rapidly and produce more
antibody than the initial or "primary response". The
effectiveness of the secondary response is the apparent reason
why humans, for example, rarely contract such diseases as chicken
pox or mumps more than once. One of the central problems in
immunology is to provide a molecular explanation for immune
system memory (also called "immune memory). There has been much
debate concerning the relative contributions to immune memory of
processes such as the persistence of antigens, *cross-reactive
stimulation, *homeostasis, competition between different lineages
of lymphocytes, and the rate of cell turnover
... ... R. Antia et al (3 authors at 2 installations, US) present
several mathematical models designed to investigate the
contributions of the various processes to the longevity of immune
memory. The authors define immune memory as the maintenance of an
elevated population of antigen-specific cells, and they define
the longevity of immune memory as the rate of decline of the
population of antigen-specific memory cells. The models presented
by the authors incorporate a repertoire of immune cells, each
lineage with distinct antigenic specificities, the basic
equations describing the dynamics of individual lineages and the
total population of cells. The authors suggest their results
indicate that if homeostatic control regulates the total
population of memory cells, then immune memory will be long-lived
(half-life > 1 year). The authors also suggest that the longevity
of immune memory in this situation will be insensitive to the
relative rates of cross-reactive stimulation, the rate of
turnover of immune cells, and the functional form of the
mathematical term for the maintenance of homeostasis. Further,
the authors suggest their models predict that when the frequency
of antigenic stimulation from other infectious agents is very
high, the duration of immune memory is likely to be relatively
low: i.e., sufficiently frequent exposure to new pathogens will
result in a relatively high rate of decline of immune memory with
respect to a given pathogen.
-----------
R. Antia et al: Models of immune memory: On the role of cross-
reactive stimulation, competition, and homeostasis in maintaining
immune memory.
(Proc. Natl. Acad. Sci. US 8 Dec 98 95:14926)
QY: Rustom Antia [rantia@biology.emory.edu]
-----------
Editor's note: In addition to the background material below, see
the SW Focus Report "Immunology: Biological and Medical Aspects"
at URL [http://scienceweek.com/swfr037.htm]
-----------
Text Notes:
... ... *antigens: In general, an antigen is any entity that
provokes an immune response, and this includes, in certain
disease states, entities that are not "foreign" to the body.
... ... *B-lymphocyte cell: Lymphocytes (lymph cells, lympho-
leukocytes) are a type of leukocyte (white blood cell)
responsible for the immune response. In general, there are two
classes of lymphocytes: 1) the B-cells, when presented with a
foreign chemical entity (antigen), change into antibody producing
plasma cells; 2) the T-cells interact directly with foreign
invaders such as bacteria and viruses.
... ... *cross-reactive stimulation: In general, in this context,
a "cross-reaction" is an immunological phenomenon in which an
antigen reacts with an antibody that has been raised (produced)
against a different antigen. The term "cross-reactive
stimulation" refers to the production of cross-reacting antibody
(or immune cell), i.e., an antibody (or immune cell) able to
react with an antigen that did not specifically stimulate its
original production.
... ... *homeostasis: The term "homeostasis" refers to a
physiological equilibrium necessary in general for the viability
of an organism, and in particular for the operation of many
cellular functions. Homeostatic mechanisms in biological systems
usually involve an element of negative feedback signaling. In
vertebrates, for example, when blood temperature is too high,
temperature receptors provoke a sequence of events involving many
pathways that ultimately results in a lowering of body
temperature. Similar homeostatic mechanisms operate at cellular
levels.
-------------------
Summary & Notes by SCIENCE-WEEK [http://scienceweek.com] 12Feb99
-------------------
Related Background:
NEW EVIDENCE CONCERNING EVOLUTION OF THE IMMUNE SYSTEM
*Lymphocytes of the *vertebrate adaptive immune system rely on an
array of variable *immunoglobulin (antibody) and *T-cell *antigen
*receptors for specific recognition of antigens. In the genome,
the genes encoding the variable portions of these receptors are
typically split into variable components (V), joining components
(J), and in some cases, diversity gene components (D). One of
each type of each component or gene segment is joined together in
a site-specific *recombination reaction to form the *exon that
encodes the antigen-binding portion of the polypeptide that forms
the antibody or T-cell receptor. This reaction, known as V(D)J
recombination, occurs only in lymphocytes, and in some vertebrate
species is responsible for generating much of the diversity seen
in antigen receptors. It is known that the two proteins encoded
by the recombination-activating genes [RAG1] and [RAG2] are
essential to the V(D)J recombination reaction, the proteins
mediating sequence-specific DNA recognition of recombination
"signals" (specific short base-pair sequences involved in this
particular recombination process) and DNA cleavage next to these
signals. ... ... Agrawal et al report that in vitro the proteins
RAG1 and RAG2 together form a *transposase capable of excising a
piece of DNA containing recombination signals from a donor site
and inserting the excised piece into a target DNA molecule. The
products formed contain a structure similar to that created by
*retroviral integration and by all known *transposition
reactions. The authors point out that all jawed vertebrates
studied thus far possess adjacent [RAG1] and [RAG2] genes as well
as immunoglobulin and T-cell receptor genes, which usually must
be assembled by *somatic recombination before they can be
expressed. There is no evidence that any of these molecules, or
antigen-specific lymphocytes, are found in jawless vertebrates
(hagfish and lamprey) or invertebrates. This indicates that split
antigen-receptor genes and the enzymatic machinery necessary for
their assembly into functional units arose in the approximately
100 million years between the divergence of jawless and jawed
vertebrates and the divergence of cartilaginous and bony fishes.
The authors suggest their results are evidence in favor of the
theory that a pivotal event in the evolution of the antigen-
specific immune system was the insertion of a "RAG *transposon"
into the genome of a vertebrate ancestor.
-----------
A. Agrawal et al (Yale University, US): Transposition mediated by
RAG1 and RAG2 and its implications for the evolution of the
immune system. (Nature 20 Aug 98 394:744)
QY: David G. Schatz [david.schatz@yale.edu]
-----------
Text Notes:
... ... *Lymphocytes: These are a type of leukocyte responsible
for the immune response. There are two classes of lymphocytes: 1)
the B-cells, which when presented with an activating chemical
entity (antigen) change into antibody producing plasma cells;
and, 2) the T-cells, which interact directly with foreign
invaders such as bacteria and viruses. There are also forms of T-
cells that are involved with B-cell activation.
... ... *vertebrate adaptive immune system: The term "adaptive"
here refers to those parts of the immune system that are capable
of adaptation to chemical experience.
... ... *immunoglobulin (antibody): In general, antibodies are
immunoglobulin proteins.
... ... *T-cell: see *Lymphocyte note above.
... ... *antigen: Any chemical entity that activates an immune
response, especially an entity originating outside the body.
... ... *receptors: In this context, cell surface macromolecules
that bind antigens.
... ... *recombination: In general, integration of DNA fragments
into a particular site in a genome.
... ... *exon: In general, any DNA sequence encoding and giving
rise to a translated polypeptide sequence.
... ... *transposase: Any enzyme required for the transposition
of DNA segments (see below, *transposition reactions).
... ... *retroviral integration: Retroviruses are single-stranded
RNA viruses that have an enzyme called reverse transcriptase, and
with this enzyme the viral RNA is used as a template to produce
viral DNA from cellular material. This DNA is then incorporated
(integrated) into the host cell's genome, where it codes for the
synthesis of viral components.
... ... *transposition reactions: In general, any reactions that
insert or excise DNA fragments into or from a genome.
... ... *somatic recombination: Somatic cells are any cells other
than germ cells (gametes). Somatic recombination, where it
occurs, involves the transposition of DNA fragments from one DNA
molecule to another, or within the same DNA molecule. Somatic
recombination theory is one of the theories proposed to explain
the enormous variety of antibodies produced by the immune system.
... ... *transposon: A large transposable genetic element having
at least the genes necessary for its own transposition to the
same or another genome.
-------------------
Summary & Notes by SCIENCE-WEEK [http://scienceweek.com] 18Sep98
-------------------
Related Background:
ON CHEMOKINES AND LEUKOCYTE TRAFFIC
There is intense interest among immunologists and virologists in
chemokines, which are immune system signaling molecules. The
receptors for chemokines are proteins on the surfaces of cells,
and there is evidence that HIV uses these receptors to force
entry into immune system T-cells. Leukocytes are white blood
cells, immune system cells that migrate to tissues as part of the
immune response. ... ... M. Baggiolini (University of Bern, CH)
reviews the control of leukocyte traffic by chemokines. Over the
past 10 years, numerous chemokines have been identified as
attractants of different types of blood leukocytes to sites of
infection and inflammation. Chemokines are produced locally in
tissues and act upon leukocytes through selective receptors, and
the chemokines are now known to also function as regulatory
molecules in leukocyte maturation, in traffic and homing of
lymphocytes, and in the development of lymphoid tissues. A more
speculative issue is the possible role of chemokines in bringing
or keeping together cells that form a functional unit. A
potential role of chemokines in morphogenesis is possible.
QY: Marco Baggiolini, Theodor Kocher Inst., Univ. of Bern, PO Box
CH-3000, Bern 9, CH.
(Nature 9 Apr 98 392:565) (Science-Week 1 May 98)
For more information: http://scienceweek.com/swfr.htm

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3. MOLECULAR BIOLOGY:
A MINIMAL GENOME
     The field of molecular biology is currently engaged in the
most extensive project of reverse engineering ever conceived: the
elucidation of the molecular components and events that
constitute living systems. One central question is simply stated:
What is the minimal number of genes necessary to maintain the
viability of a living system?
     Apart from viruses, the smallest replicating biological
systems known are the mycoplasmas (mollicutes). There are over
150 species of this class of cell-wall-free bacteria, some of
which are human pathogens. Mycoplasmas apparently evolved from
other bacteria by reduction of genome size: the smallest genome
of the mycoplasmas is little more than twice the genome size of
certain large viruses. Mycoplasmas are the smallest organisms
that can be free-living in nature and self-replicating on
laboratory media (viruses replicate only in bacteria and other
cells). Mycoplasmas range from 125 to 250 nanometers in size.
They change shape readily (pleomorphism) because they lack a cell
wall, being bounded by a triple-layered lipoprotein membrane that
contains a sterol.
     The genome of Mycoplasma genitalium (an organism that causes
one form of the urinary tract infection urethritis), which has
been completely sequenced, consists of 580 kilobases comprising
517 genes (480 protein-coding genes; 37 genes for RNAs), and this
is the smallest gene complement for any independently replicating
cell so far identified.
... ... C.A. Hutchinson III et al (8 authors at 2 installations,
US) now report the use of molecular genetic methods (global
transposon mutagenesis) to identify nonessential genes in M.
genitalium under laboratory growth conditions. The authors report
their analysis suggests that 265 to 350 of the 480 protein-coding
genes of M. genitalium are essential under laboratory growth
conditions, including approximately 100 genes of unknown
function. The authors conclude: "The presence of so many genes of
unknown function among the essential genes of the simplest known
cell suggests that all the basic molecular mechanisms underlying
cellular life may not yet have been described. The essential gene
set is not the same as the minimal genome. It is clear that genes
that are individually dispensable may not be simultaneously
dispensable. The data presented here suggest some specific
experiments that could be carried out as a first step in the
engineering of a cell with a minimal genome in the laboratory
environment."
-----------
C.A. Hutchinson III et al: Global transposon mutagenesis and a
minimal Mycoplasma genome.
(Science 10 Dec 99 286:2165)
QY: J. Craig Venter, Celera Genomics, 45 West Gude Drive,
Rockville, MD 20850 US.
-------------------
Summary by SCIENCE-WEEK http://scienceweek.com 31Mar00
For more information: http://scienceweek.com/swfr.htm

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4. MEDICAL BIOLOGY:
CHLAMYDIA PNEUMONIAE AND ATHEROSCLEROSIS
     "Arteriosclerosis" is a generic term for several diseases in
which the arterial wall becomes thickened and loses elasticity,
and "atherosclerosis" is a form of arteriosclerosis characterized
by patchy thickening (atheroma) in the subintimal layer (i.e.,
immediately below the innermost layer [intima]) of medium and
large arteries, the thickening capable of reducing or obstructing
blood flow. In this context, the term "plaque" refers to any
patch or small differentiated area in or on arterial endothelium.
In general, the term "endothelium" refers to a layer of flat
cells lining blood vessels, lymphatic vessels, the heart, etc.
Atherosclerotic plaque consists of accumulated intracellular and
extracellular lipids, smooth muscle cells, connective tissue, and
*glycosaminoglycans. Atherosclerosis is a major cause of stroke,
coronary heart disease, peripheral vascular disease, and *aortic
aneurysm.
     The bacteria called "Chlamydiae" are obligate intracellular
parasites, replicating only inside host cells. There are 3
species, all of which are human pathogens: Chlamydia trachomatis,
Chlamydia pneumoniae, and Chlamydia psittaci. The extracellular
infectious particle is approximately 0.3 microns in diameter, the
particle ingested by the host cell and later reorganizing into a
larger entity 0.5 to 1 micron in diameter. Chlamydia are
intracellular parasites because they cannot synthesize adenosine
triphosphate (ATP): they need the metabolism of the host cell for
viability.
     Chlamydia pneumoniae was first isolated in the 1960s, but
not identified as a separate species until the 1980s. Humans are
the only known hosts. The pathogen causes respiratory infections,
usually mild, and there are no signs or symptoms that
differentiate C. pneumoniae infections from those caused by many
other agents. In young people, 5 to 20 percent of community-
acquired pneumonia is thought to be caused by C. pneumoniae.
... ... A. Shor and J.I. Phillips (National Center for
Occupational Health, ZA) present a commentary concerning the
relationship between Chlamydia pneumoniae infection and
atherosclerosis, the authors making the following points:
     1) The authors point out that while many risk factors for
atherosclerosis have been identified, the mechanism by which the
lesions are formed remains unknown. The most popular idea is that
the endothelium lining the lumen of the artery becomes damaged,
with this damage altering the properties of the endothelium and
leading to a cascade of events culminating in *fibrosis,
*necrosis, lipid accumulation, and eventually calcification.
Several candidates have been suggested as initiators of
endothelial injury, including microorganisms, and recent studies
have indicated an association between Chlamydia pneumoniae and
atherosclerosis.
     2) The association of C. pneumoniae with heart disease was
first demonstrated serologically in a Finnish population in 1988,
and this work was confirmed in the 1990s: individuals
demonstrating antibodies to C. pneumoniae have a 2-fold relative
risk for heart disease. The association of C. pneumoniae and
atherosclerotic lesions was first demonstrated in 1992 in a South
African population, and the association has now been established
in several countries, in a wide range of arteries, using a
variety of techniques. C. pneumoniae is detected in 59 percent of
atheromatous arteries and in only 3.1 percent of control arterial
tissue.
     3) The authors conclude: "The presence of C. pneumoniae in
many atherosclerotic lesions can no longer be disputed. The
organisms have been demonstrated to be viable and present in
early lesions. They have been identified in the *smooth muscle
cells of the intima and are associated with pathological changes.
Determining the exact nature of the association between C.
pneumoniae and atherosclerosis is extremely important. If C.
pneumoniae is found to be causal or to significantly contribute
to the lesion, some of the world's major diseases become amenable
to new regimens for treatment or prevention."
-----------
A. Shor and J.I. Phillips: Chlamydia pneumoniae and
atherosclerosis.
(J. Amer. Med. Assoc. 1 Dec 99 282:2071)
QY: Allan Shor [AShor@ncoh.pwv.gov.za]
-----------
Text Notes:
... ... *glycosaminoglycans: In general, any polysaccharide
containing a substantial proportion of aminomonosaccharide
residues.
... ... *aortic aneurysm: An "aneurysm" is a localized dilation
of an artery or a cardiac chamber, usually due to an acquired or
congenital weakness of the wall of the artery or chamber. The
aorta is the main trunk artery of the systemic arterial system.
... ... *fibrosis: In general, the formation of fibrous tissue as
a reparative or reactive process (e.g., scarring).
... ... *necrosis: In general, pathological death of cells or
tissue.
... ... *smooth muscle: Smooth muscle was originally
differentiated from striated muscle on the basis of microscopic
appearance, but there are important other differences both
functional and molecular. In general smooth muscle is
specialized for slow sustained contractions such as those
involved in the control of the diameters of blood vessels.
"Striated muscle" is skeletal or voluntary muscle in which
cross striations occur in the fibers as a result of regular
overlapping of thick and thin filaments. Although cardiac muscle
is not "voluntary" muscle, it is also striated in appearance.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 31Mar00
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
BIOLOGY OF ATHEROSCLEROSIS
"Arteriosclerosis" is a generic term for several diseases in
which the arterial wall becomes thickened and loses elasticity,
and "atherosclerosis" is a form of arteriosclerosis characterized
by patchy thickening (atheroma) in the subintimal layer (i.e.,
immediately below the innermost layer) of medium and large
arteries, the thickening capable of reducing or obstructing blood
flow. In this context, the term "plaque" refers to any patch or
small differentiated area in or on arterial endothelium. In
general, the term "endothelium" refers to a layer of flat cells
lining blood vessels, lymphatic vessels, the heart, etc.
Atherosclerotic plaque consists of accumulated intracellular and
extracellular lipids, smooth muscle cells, connective tissue, and
*glycosaminoglycans. Two main hypothesis have been proposed to
explain the pathogenesis of atherosclerosis: a) the lipid
hypothesis postulates that an elevation in plasma low-density-
lipoprotein (LDL) cholesterol levels results in penetration of
LDL into the arterial wall with a consequent series of cellular
events leading to the formation of plaque; b) the chronic
endothelial injury hypothesis postulates that endothelial injury
by various mechanisms produces loss of endothelium and a
consequent series of events (inflammatory response) involving
blood cellular entities, the events leading to the formation of
plaque. The current consensus is that these two hypotheses are
probably interrelated. ... ... Russell Ross (University of
Washington Seattle, US) presents a review of atherosclerosis with
a focus on atherosclerosis as an *inflammatory disease, the
author making the following points: 1) Atherosclerosis is an
inflammatory disease. Because high plasma concentrations of
cholesterol, in particular those of low-density lipoprotein (LDL)
cholesterol, are one of the principle risk factors for
atherosclerosis, the process of atherogenesis has been considered
by many to consist largely of the accumulation of lipids within
the artery wall. However, the disease is much more than that.
Despite changes in lifestyle and the use of new pharmacologic
approaches to lower plasma cholesterol concentrations,
cardiovascular disease continues to be the principal cause of
death in the US, Europe, and much of Asia. In fact, the lesions
of atherosclerosis represent a series of highly specific cellular
and molecular responses that can best be described, in aggregate,
as an inflammatory disease. 2) The lesions of atherosclerosis
occur principally in large and medium-sized elastic and muscular
arteries and can lead to *ischemia of the heart, brain, or
extremities, resulting in *infarction. They may be present
throughout a person's lifetime. In fact, the earliest type of
lesion, the so-called "*fatty streak", which is common in infants
and young children, is a pure inflammatory lesion, consisting
only of *monocyte-derived *macrophages and *T-lymphocytes. In
persons with *hypercholesterolemia, the influx of these cells is
preceded by the extracellular deposition of amorphous and
membranous lipids. The author suggests that by asking questions
about arterial inflammation, we may be able to gain insight into
the process of atherogenesis. 3) The author proposes the
following as possible causes of endothelial dysfunction (and a
concomitant inflammatory response) leading to atherosclerosis: a)
elevated and modified LDL; b) free radicals caused by cigarette
smoking, *hypertension, and *diabetes mellitus; c) generic
alterations; d) elevated plasma *homocysteine concentrations; e)
infectious microorganisms such as *herpesviruses or *Chlamydia
pneumoniae; e) combinations of these or other factors. The author
suggests that regardless of the cause of endothelial dysfunction,
atherosclerosis is a highly characteristic response of particular
arteries. 4) The author concludes: "Atherosclerosis is clearly an
inflammatory disease and does not result simply from the
accumulation of lipids."
-----------
Russell Ross: Atherosclerosis -- an inflammatory disease.
(New England J. Med. 14 Jan 99 340:115)
QY: Russell Ross [rross@u.washington.edu]
-----------
Text Notes:
... ... *glycosaminoglycans: In general, any polysaccharide
containing a substantial proportion of aminomonosaccharide
residues.
... ... *inflammatory disease: In general, inflammation is a
fundamental pathologic process consisting of a dynamic complex of
cellular and chemical reactions occurring in affected blood
vessels and adjacent tissues in response to an injury or abnormal
stimulation caused by physical, chemical, or biological agents.
... ... *ischemia: In general, a sudden loss of blood supply to a
tissue caused by blockage of a blood vessel.
... ... *infarction: (infarct) An area of necrosis caused by a
sudden insufficiency of blood supply.
... ... *fatty streak: Consists of lipid-laden *monocytes and
*macrophages (together, in a fatty streak, called "foam cells"),
plus *T-lymphocytes. Later, these cell types are joined by
various numbers of smooth muscle cells, the entire mass partially
obstructing the lumen of the artery.
... ... *monocyte: The monocytes are the largest of the
leukocytes (white blood cells). macrophages are amoeba-like
leukocytes that are able
to surround and digest foreign entities such as bacteria and
protozoa.
... ... *macrophages: Amoeba-like leukocytes that are able
to surround and digest foreign entities such as bacteria and
protozoa.
... ... *T-lymphocytes: (T-cells) Lymphocytes (lymph cells,
lympho-leukocytes) are a type of leukocyte (white blood cell)
involved in the immune response. There are two classes of such
lymphocytes: 1) the B-cells, which after a cascade of immune
system events involving a specific antigen change into
proliferating specific antibody producing plasma cells; 2) the
T-cells, one subclass of which (cytotoxic T-cells) interacts
directly with foreign invaders such as bacteria and viruses,
while the other subclass of T-cells (helper T-cells) is involved
in the proliferation of antibody-specific B-cells.  
... ... *hypercholesterolemia: The presence of an abnormally
large amount of cholesterol in the cells and plasma of
circulating blood.
... ... *hypertension: In general, high blood pressure.
... ... *diabetes mellitus: Diabetes mellitus is a metabolic
disease in which carbohydrate utilization is reduced and that of
lipid and protein enhanced. The disease is caused by an absolute
or relative deficiency of insulin, and there are many forms of
the disease recognized. The term "diabetes" can refer to either
diabetes mellitus or diabetes insipidus, both diseases
characterized by chronic excretion of large amounts of urine
(polyuria). But when the term "diabetes" is used alone, what is
usually meant is diabetes mellitus.
... ... *homocysteine: An intermediate in the biosynthesis of
cysteine, recently considered to be of significance in
cardiovascular disease.
... ... *herpesviruses: The herpesviruses are a class of viruses
producing the complex of herpes diseases. The outstanding
property of herpesviruses is their ability to establish lifelong
persistent infections in their hosts and to undergo periodic
reactivation. They are large viruses, 150 to 200 nanometers in
diameter, with a core of double-stranded DNA.
... ... *Chlamydia pneumoniae: A common species of pathogenic
gram-negative bacteria. Worldwide, 30 to 50 percent of people
have antibodies to this pathogen.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 16Apr99

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5. PHYSICAL CHEMISTRY
ON FIRST-ORDER LIQUID-LIQUID TRANSITIONS
     The usual change of state (solid to liquid, liquid to gas,
etc.) is called a "first-order transition". In such a transition,
at the transition temperature, at constant pressure, the free
energies of the two forms are equal, but there is a discontinuous
change in the slope of the free energy versus temperature curve
for the substance. This implies a break in the entropy versus
temperature curve, the value of the entropy differential at the
transition temperature being related to the observed *latent heat
for the transition. There is also a discontinuous change in
volume, since the densities of the two forms are not the same.
     There are also known transitions in which no latent heat or
density change can be detected, for example, the transformations
of certain metals from *ferromagnetic to paramagnetic solids at
their *Curie points, the transitions of some metals at low
temperature to a condition of superconductivity, and the
transition observed in helium from one liquid form to another. In
these cases, there is a change in slope, but no discontinuity in
the entropy vs. temperature curve, and such a change is called a
"second-order transition".
     The terminology "first-order, second-order" (also "third-
order", etc.), in this context, derives from a theoretical
analysis by Paul Ehrenfest (1880-1933) of various categories of
discontinuities in the differential behavior of thermodynamic
equations of state .
     In general, first-order solid-solid structural phase
transitions are common in crystalline solids ("polymorphs"), but
first-order liquid-liquid transitions (i.e., transitions between
two distinct liquid forms with different density and entropy) are
exceedingly rare in pure substances. However, recent theoretical
and experimental studies have provided evidence for such a
transition in several materials, including supercooled water and
liquid carbon.
... ... Y. Katayama et al (6 authors at 2 installations, JP) now
report an in situ x-ray diffraction observation of a liquid-
liquid transition in phosphorus, the transition involving an
abrupt, pressure-induced structural change between two distinct
liquid forms. In addition to a known form of liquid phosphorus (a
molecular liquid comprising tetrahedral P(sub4) molecules), the
authors report they have found a polymeric form at pressures
above 1 gigapascal. Changing the pressure results in a reversible
transformation from the low-pressure molecular form into the
high-pressure polymeric form. The authors report the
transformation is sharp and rapid, occurring within a few minutes
over a pressure range of less than 0.02 gigapascals. During the
transformation, the two forms of liquid coexist. The authors
suggest these features strongly indicate a first-order liquid-
liquid phase transition. The authors conclude: "The present study
is consistent with the general argument that the best candidates
to exhibit a liquid-liquid transition are liquids having open
molecular coordination environments, especially those with a
local tetrahedral molecular structure. However, the present study
also shows that [such transitions] are not restricted to liquids
having extended network structure at low pressures, or to
supercooled liquids. The [first-order transition in liquid carbon
(proposed by others)] is a transition between thermodynamically
stable phases, as in the case of phosphorus. It is worth pointing
out that *black phosphorus is remarkably similar to the graphite
form of carbon in its crystal structure, anisotropy, and melting
behavior."
-----------
Y. Katayama et al: A first-order liquid-liquid phase transition
in phosphorus.
(Nature 13 Jan 00)
QY: Y. Katayama [katayama@spring8.or.jp]
-----------
Text Notes:
... ... *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.
... ... *ferromagnetic to paramagnetic: In general, ferromagnetic
materials are substances showing magnetic properties similar to
those of iron, i.e., high magnetic susceptibility, permanent
magnetism, etc. Such materials include nickel, cobalt, and many
alloys. Ferromagnetic materials are capable of being magnetized
by weak magnetic fields and exhibit magnetic hysteresis. In these
materials, the variation of magnetization with temperature is
such that at a certain temperature (Curie point; Curie
temperature) there is a transition from ferromagnetism to
*paramagnetism. The characteristics of ferromagnetic substances
have been explained by the presence of domains, regions of
crystalline matter containing atoms whose magnetic moments are
aligned in the same direction.
... ... *paramagnetism: Paramagnetic substances such as liquid
oxygen have a capability to be magnetized which is slightly
greater than that of a vacuum and much less than that of iron.
When placed in a magnetic field, paramagnetic substances are
magnetized parallel to the lines of force of the field to an
extent proportional to the intensity of the field (but not at
extremely low temperatures or extremely high fields). When
removed from an applied magnetic field, the magnetization of
paramagnetic substances returns to zero.
... ... *Curie points: The various critical temperatures above
which various ferromagnetic materials become paramagnetic.
... ... *black phosphorus: The element phosphorus exists in 3
main forms (allotropes): The most reactive form is white
phosphorus. Heating white phosphorus for a long period at high
temperature produces red phosphorus, a polymeric material.
Heating white phosphorus under high pressure produces black
phosphorus, which has a graphite-like structure. White phosphorus
is spontaneously inflammable; black phosphorus is almost non-
inflammable.
-------------------
Summary & Notes by SCIENCE-WEEK http://scienceweek.com 31Mar00
For more information: http://scienceweek.com/swfr.htm

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6. APPLIED SCIENCE
ON PHYSICS AND THE INFORMATION REVOLUTION
Since the dawn of the modern computer era, physicists and
computer technologists have been involved in a symbiosis --
physicists active in research in the fundamental science
underlying computer technology, and computer technologists
designing the high-speed machines that physicists use to solve
quantitative problems previously off-limits to physicists when
such machines were not available. Of course, this symbiosis is a
particular instance of the general interaction between science
and technology, but the interaction between physicists and
computer technologists is perhaps more direct and clear than any
other, and it continues to be mutually vital. Many people, both
physicists and computer technologists, believe that because of
intrinsic limitations in current computer technology, a new phase
in the "information revolution" will soon be required if advances
in computing power are to occur, and that this new phase will
depend on new contributions of fundamental physics, particularly
quantum physics.
... ... J. Birnbaum and R.S. Williams (Hewlett-Packard, US)
review the current state of computer technology and what must be
done to sustain the momentum of the past few decades. The authors
make the following points:
     1) The first stored-program electronic computer was ENIAC
(Electronic Numerical Integrator and Computer), built in 1946.
This was a vacuum-tube machine that could 5000 numbers in one
second. ENIAC could calculate the trajectory of an artillery
shell in only 30 seconds, compared to 40 hours required by a
human with a mechanical calculator. The machine contained 17,468
vacuum tubes, weighed 60,000 pounds, occupied 16,200 cubic feet,
and consumed 174 kilowatts (233 horsepower). The authors point
out that the amount of energy expended by ENIAC to compute a
single shell trajectory was comparable to that of the explosive
discharge required to actually fire the shell. In 1954, nine
years later, ENIAC was still the fastest computer on Earth, when
it was turned off because the US Army could no longer justify the
expense of running and maintaining it. In 1949, a panel of
experts confidently predicted that the future of computer
technology would involve a machine such as ENIAC with only 1500
vacuum tubes, weighing only 3000 pounds, requiring only 10
kilowatts of power, and about the size of an automobile. So much
for the experts: at the present time, a palmtop computer is
thousands of times more powerful than ENIAC.
     2) The authors point out that the reason for the now-
laughable error of the experts in 1949 was that their prediction
was based on the wrong foundation: reasonable extrapolation of
the in-place vacuum-tube technology. Although the transistor,
which represented a "disruptive technology" (i.e., a technology
that could replace vacuum tubes in computers), had already been
invented, the transistor was completely ignored. The authors
point out that even though transistors as discrete devices had
significant advantages over vacuum tubes and progress on
transistors was steady during the 1950s, the directors of many
large electronic companies believed that the vacuum tube held an
unassailable competitive position. These companies were
eventually eclipsed by companies that invested heavily in
transistor research and development and were thus poised to
exploit new advances. The authors state: "There are eerie
parallels with the situation today."
     3) "Moore's Law", first formulated by Gordon Moore of Intel
Corporation, states that the number of transistors that can be
built on a chip increases exponentially with time. During the
past 28 years, computer technology has exhibited a factor-of-four
increase every 3.4 years in the number of bits that can be stored
on a memory chip. But there is also "Moore's Second Law": the
cost of building fabrication facilities to manufacture chips has
also been increasing exponentially. Thus the cost of
manufacturing chips is increasing significantly faster than the
market is expanding. In 1995, to build a single fabrication
facility required approximately US$1 billion, or approximately 1
percent of the entire annual chip market. By the year 2010, a
fabrication facility could cost US$30 billion to US$50 billion,
or approximately 10 percent of the total annual market at that
time.
     4) The authors point out that by 2010 the individual
transistors in computer circuits will be turned on or off by the
addition or removal of only 8 electrons on the gate of a
transistor, compared to approximately 1000 electrons today. The
statistics of small numbers will become a significant factor, and
the ability to distinguish between zero and one in a digital
circuit will be severely compromised. By 2020, the continuation
of geometric scaling would mean that less than one electron would
be available to switch the transistor. The authors state: "That
would require getting around a fundamental physical limitation,
and not just an engineering obstacle. Yet, many researchers and
corporate executives seem to have a blind optimism that somehow
that will happen... If there is to be any hope of sustaining the
economic benefits to the national economy that come from
containing Moore's Law, then we have no choice but to develop
quantum switches and the means to interconnect them."
     5) Concerning nanostructured devices, the authors suggest
that perhaps the search for a way to make such devices should
concentrate on wires and switches, because those are the
components that will allow high-defect-tolerant systems to be
built. The most desirable types of wires would be those that
could conduct information without having to conduct electric
current (e.g., information conducted in the form of the phase of
a charge density wave). The switches should be a form of
nonvolatile memory that requires the expenditure of power only to
open or close a circuit, but not to maintain the state of the
switch.
     6) The authors conclude: "Today, we have the silicon field-
effect transistor, but we speculate that a quantum-state switch
could be better. Many laboratories are now engaged in basic
research on fabricating materials into arbitrary shapes and
sizes. They are searching for the device concept that will lead
to a disruptive new technology. Breakthroughs will significant
advances in the understanding of fundamental issues and will
undoubtedly act as the foundation for new mathematical and
scientific disciplines. Those companies that convert the
breakthroughs into a new manufacturable technology will be the
survivors of the quantum age of information processing."
-----------
J. Birnbaum and R.S. Williams: Physics and the information
revolution.
(Physics Today January 2000)
QY: Joel Birnbaum, Chief Scientist, Hewlett-Packard, Palo Alto,
CA US.
-------------------
Summary by SCIENCE-WEEK http://scienceweek.com 31Mar00
For more information: http://scienceweek.com/swfr.htm
-------------------
Related Background:
ON THE FUTURE OF QUANTUM COMPUTING
     The superposition principle in quantum mechanics derives
from the superposition principle in pure mathematics, which
states that for a linear homogenous differential equation, if
y(sub1)(x) and y(sub2)(x) are solutions, then so is y(sub1)(x) +
y(sub2)(x). In other words, for such a differential equation, the
sum of solutions is itself a solution. A corollary is that any
physical system which can be described by a linear homogeneous
differential equation (or a set of such equations) will obey the 
superposition principle.
     This principle produces various applications and
formulations in the physics of oscillating systems. In quantum
mechanics, where the time-independent Schroedinger equation is a
linear homogenous differential equation and systems are described
by oscillating probability amplitudes, the principle of
superposition results in the postulate that any state function of
a given quantum mechanical system corresponding to a given
observable (e.g., energy) can be expressed as a linear expansion
of the eigenstates of the system for the same observable, with
the term "eigenstate" referring to any one of the wave function
solutions (probability amplitude function solutions) to the
Schroedinger equation for the given boundary conditions.
     Another way to state the quantum mechanical principle of
superposition is as follows: If a physical state of a system can
be realized in a number of different but unknown distinct ways,
then the actual state of the system is a superposition for each
distinct way, and there is a distinct probability amplitude for
each way in which the physical state can be realized.
     This is essentially a restatement of Feynman's rule: The
probability amplitude of an event that can occur in two or more
indistinguishable ways is the sum of the probability amplitude
for each considered separately.
     And Feynman's rule, in turn, is an analog of Bayes' rule in
classical probability theory: The probability of an event which
can occur in two indistinguishable ways is the sum of the
probabilities for each way considered separately.
     The quantum mechanical principle of superposition is of
major importance in considerations of quantum computing,
particularly in connection with "decoherence". In this context,
the term "decoherence" refers to the observed destruction of the
superposition of pure quantum states, the destruction due to
interactions with uncontrolled or unknown physical effects (e.g.,
interactions with the environment of the system). It is currently
believed that quantum computers, which manipulate quantum states
rather than classical "bits", may someday be able to perform
tasks that would be inconceivable with conventional digital
technology.
... ... John Preskill (California Institute of Technology, US)
presents a review of current problems in the development of
quantum computers, the author making the following points:
     1) Formidable obstacles must be overcome before large-scale
quantum computers can become a reality. A major difficulty is
that quantum computers are highly susceptible to making errors.
The considerable theoretical power of a quantum computer derives
from its ability to process *coherent quantum states (i.e.,
quantum states obeying the principle of superposition), but the
coherence of such quantum states is very easily damaged by
uncontrolled interactions with the environment (decoherence). 
     2) The indivisible unit of classical information is the
"bit", which takes one of two possible values, 0 or 1. Any amount
of classical information can be expressed as a sequence of bits.
A classical computer executes a series of simple operations
("gates"), each of which acts upon a single bit or pair of bits.
By executing many gates in succession, the computer can evaluate
any *Boolean function of a set of input bits.
     3) Quantum information can also be reduced to elementary
units, called quantum bits or "qubits". A qubit is a two-level
quantum system (e.g., the spin of an electron). A quantum
computer executes a series of elementary quantum gates, each of
which is a *unitary transformation that acts on a single qubit or
pair of qubits. By executing many such gates in succession, the
quantum computer can apply a complicated unitary transformation
to a particular initial state of a set of qubits. Finally, the
qubits can be measured, the measurement outcome the final result
of a quantum computation.
     4) It was Richard Feynman (1982) who suggested that using a
quantum computer might enormously speed up finding solutions to
certain difficult computational problems. David Deutsch (1985),
developing the idea further, observed that a quantum computer can
invoke the equivalent of a massive parallelism by operating on a
coherent superposition of a vast number of classical states. In
fact, a single computation acting on just 300 qubits can achieve
the same effect as 2^(300) simultaneous computations acting on
classical bits, more than the number of atoms in the visible
Universe. It is not possible to build a conventional computer
with that many processors.
     5) There is, however, a problem of principle that is
potentially very serious for the future of quantum computers --
namely, decoherence. Unavoidable interactions with the
environment will cause the quantum information stored in a
quantum computer to decay, thus inducing errors in the
computation. Decoherence occurs very rapidly in complex quantum
systems, which is the reason we never observe macroscopic
superpositions. If quantum computers are ever to be capable of
solving difficult problems, a method must be found to control
decoherence and other potential sources of error.
     6) At present, quantum information technology remains in the
pioneering stage. It is currently possible to do experiments
involving a few qubits and a few quantum gates. For a quantum
computer to compete with a state-of-the-art classical computer,
we will need machines with hundreds or thousands of qubits
capable of performing millions or billions of operations. The
technology clearly has far to go before quantum computers can
assume their rightful place as the world's fastest machines. But
recent advances in the theory of quantum error correction suggest
there are no insurmountable obstacles, and quantum computers of
the 21st century may indeed unleash the vast computational power
woven into the fundamental laws of physics.
-----------
John Preskill: Battling decoherence: The fault-tolerant quantum
computer.
(Physics Today June 1999)
QY: John Preskill, Dept. of Theoretical Physics, California
Institute of Technology 818-395-6811.
-----------
Text Notes:
... ... *coherent quantum states: In order for a system to be
used to process and transfer information, the system must be
"coherent" in its parts. In quantum physics, coherence is a
matter of locking of phase differences between wave functions.
The wave functions of two or more particles are said to be
coherent if the phase difference between their wave functions
remains constant. So if new quantum electrodynamic information
processing devices are to be developed, methods must be found to
keep the quantum states of the parts of the system coherent long
enough for information to be processed and transferred from one
place to another. 
... ... *Boolean function: In general, a "Boolean function" is
any function assembled by the application of the operations AND,
OR, NOT to a set of variables and elements whose common domain is
a "Boolean algebra". The term "Boolean algebra" refers to a form
of symbolic logic devised by George Boole (1815-1864), such an
algebra providing a mathematical procedure for manipulating
logical relationships in symbolic form. In the realm of
computers, Boolean algebra is an important tool enabling the bits
0 and 1 to be related to logical functions of the computer.
... ... *unitary transformation: In this context, the term
"unitary transformation" refers to a linear operator whose
adjoint is equal to its inverse. The "adjoint" A* of an operator
A is an operator such that for all f and g in the domain of A:
(Af,g) = (f,A*g). If A* = A, then A is said to be self-adjoint.
-------------------
Summary & Notes by SCIENCE-WEEK [http://scienceweek.com] 24Sep99
-------------------
Related Background:
ON QUANTUM COMPUTING WITH MOLECULES
In general, in quantum mechanics, the "superposition principle"
holds that any two quantum mechanical states can be combined in
infinitely many ways to form states that have characteristics
intermediate between those of the two that are combined.
Entanglement is unique to quantum mechanics, and involves a
relationship (a "superposition of states") between the possible
quantum states of two entities such that when the possible states
of one entity collapse to a single state as a result of suddenly
imposed boundary conditions, a similar and related collapse
occurs in the possible states of the entangled entity no matter
where or how far away the entangled entity is located. The idea
of quantum computing received a significant impetus in 1994 when
Peter W. Shor of ATT (US) proposed that quantum entanglement and
superposition could in principle be used to accomplish many
numerical tasks, in particular the factoring of large numbers,
much faster than the best classical calculator. Since the
security of many important encryption systems depends on the
difficulty of factoring large numbers, quantum computing suddenly
became of great practical importance, and Shor's algorithm
provoked computer scientists to learn about quantum mechanics,
and physicists to begin serious considerations of the
requirements of a quantum computer science. ... ... Gershenfeld
and Chuang (2 installations, US), review the theoretical bases
and current status of quantum computing, in particular their own
work applying nuclear magnetic resonance techniques. The authors
point out the following: 1) In classical computation, the state
of a bit (the fundamental unit of information) is specified by
one number, 0 or 1. An n-bit binary word in a typical computer is
thus described by string of n zeroes and ones. In contrast, in a
quantum computer, the qubit (the fundamental unit of information)
might be represented by an atom in one of two different states, 0
or 1, but unlike classical bits, qubits can exist simultaneously
as 0 or 1, with the probability for each state given by a
numerical coefficient. 2) A quantum computer promises to be
immensely powerful because it can be in multiple states at once
(superposition), and because it can act on all its possible
states simultaneously. Thus, a quantum computer could naturally
perform myriad operations in parallel, using only a single
processing unit. This is the essence of the idea of quantum
computing, although one must understand the expression here is
quite general. 3) The authors have investigated the construction
of a quantum computer based on the nuclear magnetic resonance
behavior of a simple molecular liquid [chloroform, CHCl(sub3)],
with the 2 possible quantum mechanical "spin" states of atoms as
the basic qubit states. Since chloroform is a simple molecule,
the fundamental limitation in this particular system is the small
number of qubits. The authors and other researchers are actively
working to increase the size of the basic molecule in
experimental quantum computing systems, and thus increase the
number of available qubits. 4) The authors conclude: "All along,
ordinary molecules have known how to do a remarkable kind of
computation. People were just not asking them the right
questions."
QY: Neil Gershenfeld, Massachusetts Institute of Technology 617-
253-1000.
(Scientific American June 1998) (Science-Week 12 Jun 98)
[Editor's note: Experimental details of the method and algorithm
used in the above mentioned NMR quantum computing technique were
recently presented by Chuang et al (5 authors 4 installations,
US) in Nature 14 May 1998 393:143] 
-------------------
Related Background:
A SILICON-BASED NUCLEAR SPIN QUANTUM COMPUTER
B.E. Kane (University of New South Wales, AU) presents an
analysis of quantum computing and a new scheme for implementing a
quantum mechanical computer. The author proposes: 1) Although the
concept of information underlying all modern computer technology
is essentially classical, "physicists know that nature obeys the
laws of quantum mechanics." The idea of a quantum computer has
been developed theoretically over several decades in order to
understand the capabilities and limitations of machines in which
information is treated quantum mechanically. 3) Logical
operations carried out on the qubits and their measurement to
determine the result of the computation must obey
quantum-mechanical laws. 4) Quantum computation can in principal
only occur in systems that are almost completely isolated from
their environment and which consequently must dissipate no energy
during the process of computation, conditions that are extra-
ordinarily difficult to fulfill in practice. The author presents
a scheme for implementing a quantum computer on an array of
nuclear spins located on donors in silicon. Logical operations
and measurements can in principle be performed independently and
in parallel on each spin in the array. Specific electronic
devices are described for the manipulation and measurement of
nuclear spins, and the author suggests that the development of a
silicon-based quantum computer can benefit from already existing
highly developed silicon technology.
QY: B.E. Kane [kane@newt.phys.unsw.edu.au]
(Nature 14 May 98 393:133) (Science-Week 12 Jun 98)

=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

IN FOCUS: ON CONCEPTS IN MATHEMATICS
"The principal emphasis [in mathematics] is on the invention of
concepts. Mathematics would soon run out of interesting theorems
if these had to be formulated in terms of concepts which already
appear in the axioms. Furthermore, whereas it is unquestionably
true that the concepts of elementary mathematics and particularly
elementary geometry were formulated to describe entities which
are directly suggested by the actual world, the same does not
seem to be true of the more advanced concepts, in particular the
concepts which play such an important role in physics. Thus, the
rules for operations with pairs of numbers are obviously designed
to give the same results as the operations with fractions which
we first learned without reference to 'pairs of numbers'. The
rules for the operations with sequences, that is with irrational
numbers, still belong to the category of rules which were
determined so as to reproduce rules for the operations with
quantities which were already known to us. Most more advanced
mathematical concepts, such as complex numbers, algebras, linear
operators, Borel sets -- and this list could be continued almost
indefinitely -- were so devised that they are apt subjects on
which the mathematician can demonstrate his ingenuity and sense
of formal beauty. In fact, the definition of these concepts, with
a realization that interesting and ingenious considerations could
be applied to them, is the first demonstration of the
ingeniousness of the mathematician who defines them. The depth of
thought which goes into the formation of the mathematical
concepts is later justified by the skill with which these
concepts are used. The great mathematician fully, almost
ruthlessly, exploits the domain of permissible reasoning and
skirts the impermissible. That his recklessness does not lead him
into a mass of contradictions is a miracle in itself..."
-----------
Eugene P. Wigner:
_Communications in Pure and Applied Mathematics_
(John Wiley & Sons, New York 1960)
[Editor's note: Eugene Paul Wigner (1902-1995) was both a
physicist and a mathematician. He received the Nobel Prize in
Physics in 1963, and he taught mathematics at Princeton
University 1930-1971)]

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