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.

January 28, 2000 -- Vol. 4 Number 4

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This vain presumption of understanding everything can
have no other basis than never understanding anything.
For anyone who had experienced just once the perfect
understanding of one single thing, and had truly tasted
how knowledge is accomplished, would recognize that
infinity of other truths of which he understands nothing.
-- Galileo Galilei (1564-1642)

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Contents of This Issue:

1. Medicine: Looking Backward 1000 years
2. Impact of Genetics on Bone Biology
3. Evolutionary Developmental Biology: Future Prospects
4. Biochemistry: Physical Basis for Protein Secondary Structure
5. Earth Science: Neotectonics
6. Cosmology: Expectations in the Next Century of Research
 
In Focus: History of Science: On the Development of Chemistry

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1. MEDICINE: LOOKING BACKWARD 1000 YEARS
To put it plainly, the primary goal of medicine is to save lives,
an objective that most people would agree is of considerable
importance. It is not surprising, therefore, that throughout its
history medicine has involved an intensive application of all the
sciences, particularly the application of fundamental physics,
chemistry, and biology. It is the application of basic science
which is the foundation of medicine, and for that reason the
future of medicine depends on the future of science, and is thus
only vaguely discernible. The past of medicine is another matter;
we know the history, we know most of the people who made that
history, and we know the effects through the centuries of what
they accomplished. The Editors of the _New England Journal of
Medicine_ present an extensive review of the history of medicine
in the last 1000 years, the authors making the following points:
     1) Except for some early work by the ancient Greeks, much of
it in error, there were few advances in clinical medicine until
the Renaissance. In the 1400 years between Galen (c. 129-200) and
Vesalius (1514-1564), medicine was stagnant, dominated by the
belief that illness reflected an imbalance in the four "humors"
of the body -- blood, phlegm, yellow, bile, and black bile. "Life
was nasty, brutish, and short, and medical care did not help.
There are many reasons little progress was made until the
Renaissance, but one of them was surely that the only fit pursuit
for scholars in those centuries was considered to be knowledge of
God, not of man. Only with the flowering of humanism that
characterized the Renaissance did that change, and it changed
very rapidly."
     2) The authors select the following developments in the past
1000 years as most important for medicine:
... ... a) The elucidation of human anatomy and physiology. 
... ... b) The discovery of biological cells and their
substructure.
... ... c) The elucidation of the chemistry of life.
... ... d) The application of statistics to medicine.
... ... e) The development of anaesthesia.
... ... f) The discovery of the relation of microbes to disease. 
... ... g) The elucidation of inheritance and genetics.
... ... h) Knowledge of the Immune System.
... ... i) The development of body imaging.
... ... j) The discovery of antimicrobial agents.
... ... k) The development of molecular pharmacotherapy.
     3) The authors suggest that emergence of a comprehensive
understanding of the structure and function of the organ systems
of the human body stands -- without question -- as one of the
most influential advances of the past 1000 years. Perhaps the
greatest anatomist of the Renaissance, if not of all time, was
Andreas Vesalius, whose anatomical treatise published in 1543 is
regarded as one of the most important works in medicine. The
extraordinary illustrations in the treatise (the drawings not by
Vesalius but by an unknown artist) set a new standard for the
understanding of human anatomy.
     4) The discovery of biological cells did not occur until the
invention of the microscope by the lens maker Antony van
Leeuwenhoek (1632-1723), and the microscope observations of
Leeuwenhoek and Robert Hooke (1635-1702) set the stage for the
era of cellular biology that flowered during the following
centuries. But the substructure of biological cells remained
unexplored until the 1930s, when the physicist Ernst Ruska (1906-
1988) made the first primitive electron microscope (a device with
magnification of 400 times). In the 1950s, George Palade
developed methods of fractionating subcellular components and was
able to isolate cell organelles such as *mitochondria, the
*endoplasmic reticulum, and the *Golgi apparatus.
     5) The fundamentals of biological chemistry as involved in
*fermentation have been of general importance to humans since
Neolithic times, so it is not surprising that fermentation played
a major part in the development of modern biochemical ideas. In
1659, Thomas Willis (1621-1675) noted that "every Disease acts
its tragedies by the strength of some Ferment", and this idea was
amplified over the next 250 years by Lavoisier (1743-1794),
Berzelius (1779-1848), Pasteur (1822-1895), and others, until the
biochemists of the early 20th century elucidated the
interconnected enzymatic reactions responsible for the stepwise
oxidation of foodstuffs that fuels the activity of biological
cells. Today, the notion of cascades of chemical reactions
initiated by enzymes whose catalytic activity is determined by
their complex structure and modulated by the products they
generate is at the very core of modern biochemistry, and the
application of this idea to clinical medicine has made
biochemistry as important as anatomy and physiology to medical
study and practice.
     6) Probabilistic ideas were first applied to mortality
statistics in 17th-century London at the time of the plague. John
Graunt (1620-1674) introduced the notion of inference from a
sample to an underlying population and described calculations of
life expectancy that launched the insurance industry in the 17th
and 18th centuries. The origin of modern epidemiology is often
traced to 1854, when John Snow demonstrated the transmission of
cholera from contaminated water by analyzing disease rates among
citizens served by the Broad Street Pump in London's Golden
Square. Snow stopped the further spread of the disease by
removing the pump handle from the polluted well.
     7) For most of recorded history, surgical procedures were
crude, quick, and agonizing. Surgery was a fearsome treatment of
last resort and rarely used. The development of anaesthesia by
William Morton (1819-1868) and others was the essential prelude
to modern surgery. Morton publicly demonstrated ether anaesthesia
on 16 October 1846, with surgeon John Collins Warren removing a
tumor from the lower jaw of a patient. The era of modern
anaesthesia began in 1942 with the introduction of the routine
use *muscle relaxants by Harold Griffith.
     8) For most of the past 1000 years, epidemic diseases such
as smallpox were thought to be caused by miasmas (toxic vapors
from decomposing organic matter), not by unseen transmissible
organisms. Although Louis Pasteur was not the first to see
microbes, he established bacteriology as a science and is
generally recognized as the most important bacteriologist of all
time. One of the consequences of the development of bacteriology
was the application of antiseptic principles to surgery by Joseph
Lister (1827-1912). In the pre-Listerian era, even a trivial
operation was often complicated by infection. With the adoption
of Lister's antiseptic principles, it became safe to perform
extensive surgical operations.
     9) For most of the past 1000 years, philosophical and
religious beliefs were used to explain the transmission of
genetic traits. The homunculus curled inside the head of a sperm
symbolizes a popular 19th century belief about inheritance. The
theory proposed by Charles Darwin in 1858 -- that evolution
depends on random variations that permit adaptation to changing
environments -- is a milestone in the history of genetics, and
laid the foundation for modern concepts of mutation and the
etiology of genetic diseases.
     10) The authors state: "Readers will note that the
developments we discuss were the work largely of white men in
Europe and North America. For a variety of reasons, that is the
way it was. In the new millennium, it will be different. That is
one prediction we make with confidence. The other is that the
pace of change will continue to accelerate, as it did in the
second millennium. Beyond this, it would be foolhardy to
speculate about what the new millennium holds, just as it would
have been impossible for anyone in the year 1000 to dream of
everything that was to come."
-----------
Editors NEJM: Looking back on the millennium in medicine.
(New England J. Med. 6 Jan 00 342:42)
QY: Editors NEJM [editors@nejm.org]
-----------
Text Notes:
... ... *mitochondria: Organelles of the cell cytoplasm,
mitochondria are the principal energy source of the cell,
containing various enzymes involved in electron transport and
metabolic cycles.
... ... *endoplasmic reticulum: A complex system of flattened
sacs in eukaryotic cells, the site of many important syntheses,
apparently including the production of new surface membrane.
... ... *Golgi apparatus: The Golgi apparatus (Golgi complex) is
a collection of organelles (Golgi bodies) in eukaryotic cells
that essentially function as a collecting and packaging center
for substances that the cell manufactures for export.
... ... *fermentation: In general, the term "fermentation" refers
to controlled microbial action to produce useful products. In
biochemistry, there is often a more specific usage, with the term
"fermentation" referring to the breakdown of organic molecules,
typically sugars and fats, to yield simpler organic molecules.
The term is often loosely used as a synonym for anaerobic
metabolism, although in the case of yeast, the process need not
be anaerobic.
... ... *muscle relaxants: In general, "muscle relaxants" are
pharmacological agents that reduce the ability of muscle fibers
to contract. By using muscle relaxants, it is possible to use a
lighter level of anesthesia during surgery, a distinct advantage
in a variety of surgical procedures.
-------------------
Summary & Notes by SCIENCE-WEEK [http://scienceweek.com] 28Jan00
[For more information: http://scienceweek.com/search/search.htm]
-------------------
Related Background:
IN FOCUS: ON THE BEGINNING OF CELL THEORY IN BIOLOGY
"When organic nature, animals and plants, is regarded as a
Whole, in contradistinction to the inorganic kingdom, we do not
find that all organisms and all their separate organs are compact
masses, but that they are composed of innumerable small particles
of a definite form. These elementary particles, however, are
subject to the most extraordinary diversity of figure, especially
in animals; in plants they are, for the most part exclusively,
cells. This variety in the elementary parts seems to hold some
relation to their more diversified physiological function in
animals, so that it might be established as a principle that
every diversity in the physiological signification of an organ
requires a difference in its elementary particles; and, on the
contrary, the similarity of two elementary particles seems to
justify the conclusion that they are physiologically similar...
The greater the number of physiologically different elementary
parts, which, so far as can be known, originate in a similar
manner, and the greater the difference of these parts in form and
physiological signification, while they agree in the perceptible
phenomena of their mode of formation, the more safely we may
assume that all elementary parts have one and the same
fundamental principle of development... The elementary parts of
all tissues are formed of cells in an analogous, though very
diversified manner, so that it may be asserted, that there is one
universal principle of development for the elementary parts of
organisms, however different, and that this principle is the
formation of cells." [*Note #1]
-----------
Theodor Schwann: _Microscopical Researches into the Accordance in
the Structure and Growth of Animals and Plants_.
(Sydenham Society, London 1847, transl. Henry Smith, from the
original German published in 1839)
-----------
Text Notes:
... ... *Note #1: The "cell theory" is probably the most
important biological generalization of the first half of the 19th
century, a generalization that has grown in importance and which
serves as a unifying principle in the continued development of
modern biology. A number of biologists had been writing about the
cellular organization of animals and plants, but it was Theodor
Schwann (1810-1882) and Matthias Schleiden (1804-1881) who most
clearly stated and summarized the case for the cell theory,
Schwann for animals and Schleiden for plants. Although a major
weakness of the theory was its proposition that the formation of
cells involved the appearance of a nucleus first and the
remainder of the cell afterward, the general idea of cell theory,
that of individual physiological entities ("cells") as the
fundamental units of biological systems, was a correct and
profound conceptual contribution. Schwann also apparently coined
the term "metabolism" to represent the overall chemical changes
occurring in living systems. He also did important work on
digestion, fermentation, and histology. He identified yeast as
consisting of tiny plant-like organisms, and he was one of the
first to propose that fermentation of sugar and starch was the
result of a life process, a proposition that provoked so much
scientific criticism in Germany that Schwann left Germany and
moved to Belgium. He became professor of anatomy at Louvain in
1838 and at Liege in 1847. It is ironic that in the last 40 years
of his life he devoted most of his energies to mysticism and
religious meditation, doing nothing to match his earlier
intellectual and scientific accomplishments in the one decade of
the 1830s.
-------------------
Notes by SCIENCE-WEEK [http://scienceweek.com] 17Sep99
[For more information: http://scienceweek.com/search/search.htm]


2. IMPACT OF GENETICS ON BONE BIOLOGY
     In general, the term "connective tissue" refers to tissue
which protects and supports the body and its organs, binds organs
together, stores energy reserves as fat, and provides immunity.
Connective tissue is the most abundant and widely distributed
tissue in the mammalian body, with forms ranging from the fluid
of blood to the solid substance of bone (osseous tissue). Like
other connective tissue, bone contains an abundant matrix
surrounding widely separated cells, the matrix approximately 25
percent water, 25 percent protein, and 50 percent mineral salts.
There are 4 types of cells in mammalian bone tissue:
     1) Osteoprogenitor cells (stem cells): undifferentiated
cells capable of developing into other cell types.
     2) Osteoblasts: the cells that form bone, secreting collagen
and other organic components needed in bone construction.
     3) Osteocytes: mature bone cells derived from osteoblasts,
and which are the principal cells of bone tissue. Osteocytes
maintain the ongoing cellular activities of bone tissue, such as
the exchange of nutrients and wastes with the blood.
     4) Osteoclasts: cells on the surface of bone that function
in bone resorption (destruction of matrix), which is important in
the development, growth, maintenance and repair of bone.
... ... Gerard Karsenty (Baylor College of Medicine, US) presents
a review of the recent influences of the field of genetics on
bone biology, the author making the following points:
     1) The author states that the entire field of bone biology
is dominated by the impact of bone degenerative diseases such as
*osteoporosis. Similar to research in most other organogenesis
processes, human and mouse genetic studies have been major
driving forces in redefining bone biology. Genetic studies have
opened new areas of research, elucidated at the molecular level
various known phenomena, and sometimes challenged untested
textbook assumptions. In general, genetic studies have profoundly
transformed the field of bone biology.
     2) One peculiar characteristic of bone resides in its
physiology. Bone is the only organ that contains a cell type, the
osteoclast, whose only apparent function is to constantly destroy
the organ hosting it. This destruction, or "resorption" of bone,
occurring throughout life and in healthy individuals, is
counterbalanced by new bone formation in a process called "bone
remodeling". It is through bone remodeling that bone mass is
maintained at a constant level between the end of puberty and
gonadal failure, and bone remodeling is the process affected
during osteoporosis, a disease characterized at the cellular
level by a relative increase of bone resorption over bone
formation. In recent years, we have begun to understand at the
molecular level how bone resorption is controlled, but it is
striking how little we know about the molecular mechanisms
governing bone formation.
     3) The aspect of bone biology that has made the most
progress in the last few years is the genetic control of
osteoclast differentiation and function. The osteoclast, the cell
type resorbing *mineralized bone matrix, is the last specific
cell type of the skeleton to appear during development, and the
systematic study of mouse mutants has led to the establishment of
a fairly detailed understanding of the *genetic cascade
controlling osteoclast differentiation and function. Some of this
progress has important implications not only for bone resorption,
but also for new hypotheses concerning the molecular control of
bone formation.
     4) Bones and teeth are the only tissues that mineralize
under physiological conditions; mineralization or calcification
in any other tissue is pathologic. Thus, a question could be
asked as follows: Is bone mineralization an active function
requiring active expression of one or multiple genes, or rather
is the absence of calcification in every other tissue an active
function genetically controlled? It has long been proposed that
certain proteins in the bone matrix could serve a crystal-
nucleation function at the beginning of the mineralization
process. However, many of the genes encoding these proteins have
been experimentally deleted in mice without any overt effects on
bone mineralization, which indicates that these proteins do not
alone control bone mineralization in vivo. Although the current
lack of success in identifying activators of bone mineralization
does not mean they do not exist, it is possible that bone
mineralization is a passive phenomenon involving the absence of
inhibitors of mineralization in the bone matrix, and there is
some evidence to support this idea.
     5) Bone is not made only of cells, it also contains an
extracellular matrix. This bone extracellular matrix contains
mostly *type I collagen, which accounts for 90 percent of the
protein content of the matrix, plus a variety of noncollagenous
proteins and *proteolytic enzymes. Mouse and human genetics have
shown that most of these proteins and proteolytic enzymes are
required for the integrity of bone tissue, although it is not yet
understood how this requirement is manifested at the molecular
level.
     6) The author concludes: "In terms of the approaches used,
the history of bone biology can be divided into two parts.
Initially, bone biology, like most fields, was dominated by cell
biology; however, in the past 10 years it has been ruled by mouse
genetics. Mouse and human genetics are here to stay and rightly
so. However, no single approach, whether it is cell biology,
genetics, or biochemistry, will have all answers for any field of
biology. Thus, the main challenge in the short term will be to
understand at the biochemical level how many of the new gene
products that have been identified fulfill their functions."
-----------
Gerard Karsenty: The genetic transformation of bone biology.
(Genes & Development 1 Dec 99 13:3037)
QY: Gerard Karsenty [karsenty@bcm.tmc.edu]
-----------
Text Notes:
... ... *osteoporosis: Osteoporosis is a generalized progressive
diminution of bone density (bone mass per unit volume) that
causes skeletal weakness. The ratio of mineral to organic
elements is unchanged. The major clinical manifestations of
osteoporosis are bone fractures resulting from a reduction below
the fracture threshold of the amount of bone available for
mechanical support.
... ... *mineralized bone matrix: The inorganic part of bone
consists largely of calcium phosphate organized into small
crystals of hydroxyapatite 0.8 to 1.5 nanometers thick, 2.4
nanometers wide, 20 to 40 nanometers long. Other anions present
are carbonate, fluoride, hydroxide, and citrate. Most of the
body's magnesium, approximately 25 percent of its sodium, and a
smaller proportion of its potassium is found in bone.
... ... *genetic cascade: The "cascade" of sequential gene
expressions occurring during development.
... ... *type I collagen: The term "collagen" refers to a group
of fibrous proteins of very high tensile strength that form the
main component of connective tissue in animals. Collagen of bones
and skin is metabolically stable, in contrast with collagen of
organs such as the liver. The collagens are products of a
superfamily of closely related genes found in multicellular
animals, the products classified into types I to XIII in the
order in which they were purified and characterized. All contain
a typical triple helical domain formed from 3 independent chains.
Type 1 collagen is the most abundant collagen, forming well-
organized fibrils.
... ... *proteolytic enzymes: In general, "proteolysis" is the
enzyme-catalyzed degradation of protein by hydrolysis of one or
more peptide bonds.
-------------------
Summary & Notes by SCIENCE-WEEK [http://scienceweek.com] 28Jan00
[For more information: http://scienceweek.com/search/search.htm]


3. EVOLUTIONARY DEVELOPMENTAL BIOLOGY: FUTURE PROSPECTS
The various fields of science are conceptual categorizations,
constructions of the human mind, and as such are continually in
flux in response to new data and new ways of looking at old data.
At the beginning of the 20th century, the fields of evolutionary
biology and embryology were in an intellectual partnership, each
field invigorated by data and ideas of the other field. Then, in
the 1920s, evolutionary biology embraced the new science of
genetics and began a conceptual drift away from embryology and
embryological concepts. Embryology, in turn, came to rename
itself "developmental biology", and remained relatively distant
from evolutionary biology in ideas and methods for half a
century. Only in the 1980s did a second conjunction of these two
important biological disciplines begin.
... ... Peter W.H. Holland (University of Reading, UK) presents
an analysis of the new interface called "evolutionary
developmental biology", the author making the following points:
     1) The past 15 years have seen a reconciliation between
evolutionary biology and developmental biology, with the new
discipline of evolutionary developmental biology emerging at the
interface. This new discipline is concerned with a) how
developmental processes have evolved; b) how developmental
processes can be modified by genetic change; and c) how such
modifications produced the past and present diversity of
morphologies and body plans.
     2) Three main factors have contributed to the recent
emergence and phenomenal growth of evolutionary developmental
biology, all three factors dependent on genetics -- the
discipline that split evolution and development apart 60 years
earlier. The three factors are as follows:
... ... a) The first and perhaps major factor was the discovery
that animals as different as *nematodes, flies, and mammals use
similar genes for similar developmental purposes, such as
controlling the development of spatial organization in the
embryo. The author suggests that "we can now state with
confidence that most animal phyla possess essentially the same
genes, and that some (but not all) of these genes change their
developmental roles infrequently in evolution."
... ... b) The second crucial factor was the rise of molecular
phylogenetics -- the comparison of nucleic acid sequences from
different organisms and the construction of evolutionary trees
from these data.
... ... c) The third factor was the set of technological advances
in molecular biology (e.g., the *polymerase chain reaction)
invented or refined in the 1980s, and which facilitated the
*cloning and analysis of genes in any species, not just the
handful of model species traditionally studied.
     3) The author points out that the link between the genetic
make-up of an organism (its "genotype") and its form and function
(its "phenotype") lies at the heart of evolutionary developmental
biology. In the coming decades, a fundamental question to be
addressed is how alterations to the genotype as a result of
mutation are transformed through the intermediary of development
into changes in form. Another question in need of resolution
concerns the importance of gene duplication in the evolution of
development. Are there developmental processes that are possible
with two copies of a gene but not with one copy? At present, this
is a controversial idea, since it implies that gene number could
impose tight genetic constraints on evolution.
     4) Concerning the conjunction of developmental biology and
the study of fossils and the evolutionary relationships and
ecologies of organisms which formed these relationships (i.e.,
the field of paleontology), the authors points out that 15 years
ago few developmental biologists would have heard of the
*Ediacaran fauna, and few paleontologists would have admitted an
interest in *Drosophila genetics. Much has changed:
paleontologists and developmental biologists are now regularly
combining data to tackle key questions in evolutionary
developmental biology. Paleontology is vital to estimating when a
particular evolutionary change occurred, and paleontology can
also reveal whether such a change was correlated with other
evolutionary events or with environmental change. The "*Cambrian
explosion" of animal phyla is the classic example, but its
interpretation remains controversial. Paleontology clearly
records a rapid increase in the abundance and diversity of animal
fossils at the base of the Cambrian period, but there is
disagreement as to whether this increase reflects increases in
body size, the origin of shells and skeletons, or a true rapid
diversification of body plans. Even if the last explanation is
accepted, did this burst of evolution occur in the ancestors of
all multicellular animals, or only among the lineages exhibiting
bilateral symmetry (bilaterians)?
-----------
Peter W.H. Holland: The future of evolutionary developmental
biology.
(Nature 2 Dec 99 402supp:C41)
QY: Peter W.H. Holland [p.w.h.holland@reading.ac.uk]
-----------
Text Notes:
... ... *nematodes: An abundant and ubiquitous phylum of
unsegmented roundworms.
... ... *polymerase chain reaction: (PCR): A technique for
isolating and amplifying any specifically desired DNA sequence.
PCR is considered by many molecular biologists to be the most
important technical advance in molecular biology in the second
half of the 20th century. The inventor of the technique, Kary
Mullis, received the Nobel Prize in Chemistry in 1993 for his
discovery. 
... ... *cloning: The term "cloning" has several meanings which
depend on context. With reference to DNA (the present context),
cloning is any process by which a gene or fragment of DNA is
spliced into a *vector so that the DNA can be amplified many
times by transferring the recombinant (i.e., foreign) DNA
molecule into a host organism (usually a bacterium or yeast) that
can be grown in large quantities.
... ... *vector: In this context, a vector is any DNA that can
propagate itself rapidly in a host cell and maintain this
capability after insertion of foreign DNA into the vector. For
example, one can introduce a human DNA fragment (e.g., a gene)
into the DNA of a virus, have this virus infect its usual host
cells (e.g., bacteria or animal cells), and if the virus is
rapidly replicating, the fragment of human DNA will also be
rapidly replicated. The procedure, in other words, uses viral DNA
as a means (a vector) to introduce the foreign DNA (here a human
DNA fragment incorporated into the viral DNA) into a host cell to
use the host cell-virus system as a chemical factory to produce
relatively large quantities of the foreign DNA fragment.
... ... *Ediacaran fauna: The term "Ediacaran" refers to an
assemblage (until recently the oldest) of soft-bodied marine
animals, the assemblage first discovered in the Ediacara Hills in
Australia. Although the recent discoveries of Ediacaran metazoans
have extended the record of sponges and bilateral animals to 570
million years ago, the biological affinities of many Ediacaran
organisms remains controversial.
... ... *Drosophila: A fruit fly genus, the organism widely used
in 20th century genetics and developmental biology.
... ... *Cambrian explosion: The geological period known as the
Cambrian is the time frame from about 505 million years ago to
545 million years ago. Its most outstanding aspect is the rather
sudden appearance of numerous invertebrate fossils, so numerous
that some have termed it an explosion of evolutionary processes.
-------------------
Summary & Notes by SCIENCE-WEEK [http://scienceweek.com] 28Jan00
[For more information: http://scienceweek.com/search/search.htm]


4. BIOCHEMISTRY: PHYSICAL BASIS FOR PROTEIN SECONDARY STRUCTURE
     The term "protein" was first used by the chemist Gerardus
Mulder (1802-1880) to denote the basic building block of the heat
coagulable (albuminous) material found in living systems, but it
was not until the 1920s that proteins were generally recognized
as a special type of macromolecule (a polypeptide) and studied as
polymers. Currently, biochemists and protein chemists distinguish
four orders of polymeric structure in proteins:
     1) The term "primary" structure refers to the linear
structure of the polypeptide as determined solely by the number,
sequence, and type of amino acid residues.
     2) The "secondary structure" of a protein is determined by
interactions between the sequential units, particularly hydrogen
bonding between particular amino acids and nonpolar interactions
between hydrophobic regions, the interactions producing, in
general, three local or global secondary structure variants:
alpha helix, beta sheet, and tight turn. An "alpha helix" is a
spiral configuration of a polypeptide chain in which successive
turns of the helix are held together by hydrogen bonds between
the amide (peptide) links, the carbonyl group of any given
residue being hydrogen-bonded to the imino group of the 3rd
residue behind it in the chain. The term "beta sheet" (beta-
pleated sheet) refers to an array of two or more "beta strands",
with each beta strand consisting of two polypeptide chains in a
so-called "beta configuration", which in turn is a stable
configuration of a polypeptide chain in which the chain is almost
fully extended and hydrogen-bonded to an adjacent polypeptide
chain. The third secondary structure variant, "tight turn" (beta
bend; beta turn) refers to a bending of a short stretch of
polypeptide chain that allows the main direction of the chain to
change. The turn consists of 4 amino acid residues in which the
CO group of residue n is hydrogen-bonded to the NH group of
residue n + 3.
     3) The "tertiary structure" of a polypeptide is a 3-
dimensional configuration, a folding or coiling of the molecule
primarily determined by interactions of hydrophobic regions and
to a lesser extent by hydrogen bonding.
     4) The "quaternary structure" of proteins is characterized
by the interaction of 2 or more individual polypeptides, often
via disulfide bonds, the result a larger functional molecule.
     Although given the above rough categorization of protein
structures, there are many aspects that might be of interest,
there are two salient generalizations concerning proteins which
command attention: a) when, as the result of the expression of a
gene, a specific protein is synthesized in a living system, that
protein rapidly assumes a configuration specific for its type;
and b) whatever it is that a specific protein does in a living
system, that action is dependent primarily and directly on its
configuration rather than on its specific amino acid sequence.
These two generalizations form the basis for much of the research
on protein structure, with two resultant questions: a) What rules
govern the rapid folding into a particular configuration by a
protein? and b) How is the particular configuration of a protein
related to its biochemical actions in the living system? The
first question is currently viewed as a problem in the physical
chemistry of macromolecules, and research on the question has
been heavily theoretical, with models based on a wide range of
quantitative techniques.
     The problem of protein folding is essentially as follows:
Given an ordinary polypeptide, the number of possible
configurations is astronomical. If a particular protein always
assumes the same configuration in a living system (its "native
configuration"), and if that configuration represents some sort
of energy minimum for the polypeptide chain, how does the protein
find that energy minimum within milliseconds? Does the protein
pass through every possible configuration state until the energy-
minimum configuration is "discovered"? Or are there constraints
that reduce the number of possible configurations to a much
smaller number? As easy as it is to state this problem, the
problem is a puzzle that has confounded researchers for 40 years.
... ... R. Srinivasan and G. Rose (Johns Hopkins University, US)
present a physical theory for protein secondary structure, the
authors making the following points:
     1) The authors propose a physical theory for secondary
protein structure based on steric and local interactions, and
suggest their finding demonstrate that local, intrinsic,
sequence-dependent biases toward helix, strand, and turn
configurations are densely dispersed throughout the polypeptide
chain and are unlikely to be merely accidental. The authors
report tests of the theory by *Monte Carlo simulations.
     2) The authors suggest that in essence, secondary structure
bias is largely a consequence of the balance between two opposing
local forces that govern the position of equilibrium between the
two mainchain states of contraction or extension. The competing
forces are attractive local interactions vs. sidechain
conformational restriction.
     3) The authors point out that C.B. Anfinsen (1973) proposed
that proteins attain their native state by folding to a global
minimum of *Gibbs free energy, and that this hypothesis has
usually been interpreted to mean that the native conformation of
individual molecules also corresponds to a global minimum in
internal energy because a fully folded protein will have lost its
*conformational entropy, or almost so. Thus, conformational
entropy is thought to play an insignificant role in the
thermodynamics of protein folding. Specifically, the statistical-
mechanical- (Boltzmann-) weighted populations of any two states
are thought to depend predominantly on their energy difference.
In contrast, the work of the authors suggests the conclusion that
conformational entropy is the main factor that discriminates
between two energetically equivalent (degenerate) ground states,
and in so doing "preorganizes" the protein.
     3) The authors point out that the problem of secondary
structure is intimately related to the Levinthal paradox [C.
Levinthal (1969)], which argues that a folding protein does not
"explore" conformational hyperspace freely; otherwise, the
protein would encounter an insoluble search problem. For
Levinthal, this insight was not a paradox at all, but a
convincing demonstration that some intrinsic constraint limits
the effective size of the conformational space. In this view,
proteins solve the "multiple-minimum problem" not by an extensive
search that identifies the deepest minimum, but by a limited
search that avoids false minima. The existence of intrinsic bias
resolves this paradox by prejudicing the ensemble of available
folding trajectories toward the native minimum. Thus, a folding
protein need not discriminate among an astronomical number of
conformations, because intrinsic bias "steers" the molecule
toward a high degree of preorganization. [*Note #1]
     4) In summary, the authors suggest their analysis has
demonstrated that pronounced biases toward protein secondary
structure are present in natural protein sequences, that these
biases have a discernible physical basis, and that their
existence suggests reinterpretations of current folding models.
-----------
R. Srinivasan and G. Rose: A physical basis for protein secondary
structure.
(Proc. Natl. Acad. Sci. US 7 Dec 99 96:14258)
QY: George D. Rose [rose@grserv.med.jhmi.edu]
-----------
Text Notes:
... ... *Monte Carlo simulations: In general, a "Monte Carlo
method" is any method for obtaining a statistical estimate of a
desired quantity by random sampling. In the most successful
applications, the desired quantity is a statistical parameter,
and the sampling is made from an artificial population that may
be a model of the physical system itself. The method is of
considerable utility in handling certain intractable applied
mathematical problems.
... ... *Gibbs free energy: (Gibbs function; thermodynamic
potential) A thermodynamic function of a system. In the present
context, if a system is considered at constant pressure and
temperature, and the only work done is that caused by changes in
volume, it can be shown that the system is in equilibrium when
the Gibbs free energy has a minimum value.
... ... *conformational entropy: In general, the entropy of a
system is a measure of the unavailability of its internal energy
to do work in a cyclic process. From the standpoint of
statistical mechanics, entropy is in general a measure of the
disorder of a system. The term "conformational entropy" refers to
that part of the total entropy of a system due to specific
orientations of atoms.
... ... *Note #1: In this paragraph, terms such as "hyperspace"
and "trajectory" derive from statistical mechanics and the
following considerations: If the state of a system depends upon N
variables, the 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. There are certain systems for which qualitative analysis
of the phase space trajectories of the system reveals significant
properties of the system otherwise difficult to delineate.
-------------------
Summary & Notes by SCIENCE-WEEK [http://scienceweek.com] 28Jan00
[For more information: http://scienceweek.com/search/search.htm]
-------------------
Related Background:
ON EXPLANATIONS OF PROTEIN FOLDING
Since the 3-dimensional configuration of a protein is an
essential determinant of what the protein does in a biological
system, protein "folding", the process that leads to this
configuration, is a central focus in biophysical chemistry.
... ... William A. Eaton (National Institutes of Health, US)
presents a review of current research in this field, the author
making the following points:
     1) There are two aspects to the problem of protein folding.
The first is predicting the 3-dimensional structure of a protein
from its amino acid sequence; the second is to understand _how_
proteins fold. The problem of protein folding has recently
assumed additional importance as more and more human diseases
(e.g., Alzheimer's and Parkinson's diseases) are believed to be
caused by aggregation of misfolded proteins.
     2) The question of _how_ a protein folds can be phrased more
precisely as follows: What are the sequences of structural
changes that occur in a polypeptide as it finds its way from the
myriad of possible structures in the *denatured state to the
final unique *native structure? How many different folding routes
exist, and what are their relative probabilities?
     3) Until approximately a decade ago, the problem of
understanding how proteins fold was addressed by identifying and
characterizing one or two metastable structures believed to be
obligatory intermediates in a sequential process along a well-
defined protein-folding pathway. The prevailing view was that
structural characterization of such intermediates would give the
clue to the basic underlying mechanism, as in the study of
organic chemical reactions. However, unlike small-molecule
chemical reactions, in which covalent bonds are broken and new
bonds formed in a structurally well-defined transition state, the
many degrees of freedom of a polypeptide chain demand a different
approach. A polypeptide of 100 amino acids has a huge number of
conformations, even if only a tiny fraction of the more than
2^(100) (= 10^(30)) possible conformations are thermally
occupied. Understanding the complexities of protein folding at
the microscopic level, and developing models that make
quantitative predictions, therefore requires a statistical
approach, i.e., the theoretical and computational tools of modern
statistical mechanics.
     4) Nonexponential kinetics have played an important role in
understanding conformational changes in native proteins. They are
particularly interesting for protein folding because they could
arise from a process that is "downhill" in free energy, i.e, one
in which the overall free energy barrier separating the native
from the denatured state is very small or nonexistent. For large
barriers, only the structures of the initial and final states are
observable, because structures along the folding route are too
sparsely populated. If, however, the barrier becomes very small
or disappears altogether, all of the structures can in principle
be detected and characterized by spectroscopy.
     5) At the present time, there exists the exciting prospect
of performing single molecule experiments for direct exploration
of the energy landscape and folding routes. Finding proteins that
fold with a "downhill scenario" is an essential first step in
this quest. That some proteins will exhibit downhill folding,
moreover, is one of the novel theoretical predictions of an
energy landscape analysis of protein folding.
-----------
Editor's note: In addition to the background material below, see
the 8 Aug 99 issue of SW (#32), report #3)
-----------
William A. Eaton: Searching for "downhill scenarios" in protein
folding.
(Proc. Natl. Acad. Sci. US 25 May 99 96:5897)
QY: William A. Eaton [eaton@helix.nih.gov]
-----------
Text Notes:
... ... *denatured state: In biochemistry, the term
"denaturation" refers to the complete unfolding
and loss of catalytic activity of a protein.
... ... *native structure: The "native" structure or
configuration of a biological macromolecule is the functional
state or configuration ordinarily assumed by the molecule in the
biological system in which the molecule occurs.
-------------------
Summary & Notes by SCIENCE-WEEK [http://scienceweek.com] 3Sep99
-------------------
Related Background:
ON THE CHEMICAL PHYSICS OF PROTEIN FOLDING
... ... C.L. Brooks et al present a short review of protein
folding from the perspective of chemical physics, and with a
focus on the work of their own group, the authors make the
following points: 1) The question of the mechanism of protein
folding was once thought to be entirely analogous to the question
of mechanism in intermediary metabolism or classical organic
chemistry: the essential classical idea was that a protein
folding pathway involves a series of discrete intermediates. Such
discrete intermediates do occur in the late stages of protein
folding, but to answer the practical questions of structure
prediction and design, a new viewpoint on folding is required. 2)
The authors suggest this new viewpoint is that of chemical
physics rather than that of classical chemistry, and that the
chemical physics view requires a new set of theoretical ideas,
computational techniques, and major advances in experimental
methodology. 3) The authors suggest the theoretical framework for
the new chemical physics approach to protein folding should be
that of "*energy landscape theory", which asserts that "a full
understanding of the folding process requires a global overview
of the energy landscape." 4) The authors propose that the protein
folding energy landscape resembles a partially rough funnel
riddled with energy traps where the protein can transiently
reside. There is no unique pathway but a multiplicity of
convergent folding routes toward the native state... The authors
state that the essence of the funnel energy landscape idea is
competition between the tendency toward the folded state and
trapping because of "ruggedness" of the funnel. 5) Concerning
theoretical modeling, the authors point out that simulations with
detailed atomic models are extremely intensive numerically, so
that the number and size of systems that can be studied is
limited. Simulation models of intermediate complexity have
therefore been used. 6) Concerning experimental approaches to
exploring the energy landscape of protein folding, there are
various new methods involving the physical monitoring of folding
from an unfolded state, for example, monitoring in the
microsecond range following initiation of folding by a
nanosecond-scale step-change in ambient temperature. The authors
conclude: "Experiments are beginning to build up a *phase diagram
of folding kinetics that can be used to test and refine
theoretical models."
-----------
C.L. Brooks et al (4 authors at 3 installations, US)
Chemical physics of protein folding.
(Proc. Natl. Acad. Sci. US 15 Sep 98 95:11037)
QY: Charles L. Brooks, Scripps Research Institute 619-784-1000.
-----------
Text Notes:
... ... *energy landscape: The "energy landscape" here refers to
the contours of what is essentially a classical energy/entropy
diagram, with the native configuration state positioned at the
bottom of a deep potential well, in this case a funnel with sides
containing miniature energy wells or "traps".
... ... *phase diagram: In this context, a classical graphical
representation of the equilibrium relationships between phases of
a chemical system.
-------------------
Summary & Notes by SCIENCE-WEEK [http://scienceweek.com] 23Oct98
[For more information: http://scienceweek.com/search/search.htm]


5. EARTH SCIENCE: NEOTECTONICS
     Seismic studies indicate the interior of the Earth consists
of three parts: a metallic core, a dense rocky mantle, and a thin
low-density crust. The central part of the core is solid, but the
outer part of the core is evidently liquid. The mantle, the layer
of dense rock and metal oxides between the molten part of the
core and the surface, has plastic properties (i.e., it is a solid
capable of flow under pressure). The term "lithosphere" refers to
the outer layer of the Earth, comprising the crust and upper
mantle, and extending to a depth of 50 to 70 kilometers. The
traditional view of tectonics (changes in the structure of the
Earth's crust) is that the lithosphere consists of a strong
brittle layer overlying a weak ductile layer. "Plate tectonics"
is the current consensus theory that the Earth's lithosphere is
broken into fairly rigid plates, seven or eight major plates and
many smaller plates, and that convection within the underlying
less rigid "asthenosphere" causes the plates (and the associated
continents and crust) to move relative to each other. 
     What is called the "Global Positioning System" consists of a
total of 18 satellites in different orbits, with 4 of the
satellites visible at any time from any point on the surface of
the Earth. This system provides a locational accuracy of less
than 1 centimeter for receiving points on the surface, and the
system is used (in addition to certain military applications) to
measure the motions of small blocks of the Earth's crust. For
example, global positioning system surveys in 1989 and 1993
determined that southwestern Greece moved systematically to the
southwest relative to Italy at a mean annual rate of 2 to 4
centimeters per year. Thus, movements of the Earth's crust are
now being measured directly by satellite systems rather than
inferred from models and paleogeological data. 
... ... B. Clement et al (3 authors at 3 installations, US)
present a review of current research involving the use of the
Global Positioning System in the study of plate tectonics, the
authors making the following points:
     1) The theory of plate tectonics that revolutionized the
Earth sciences during the 1960s was based primarily on indirect
evidence of past movements of the Earth's crust [*Note #1].
Motions of the sea floor crust were inferred from the
magnetization of the crust, the magnetization having recorded
*polarity reversals of known age of the Earth's magnetic field.
The symmetric magnetic patterns suggested that new crust is
created at the *mid-ocean ridges and then spreads away from the
ridges. This sea floor-spreading hypothesis was successful in
explaining many longstanding problems in the Earth sciences and
became the basis of a new paradigm of crust mobility. 
     2) Recent advances in global positioning system technology
have made it possible to detect millimeter scale changes in the
Earth's surface. Using these systems, it has been possible to
detect relative motion between the large plates of the outermost
rigid layer of Earth. These motions previously had only been
inferred from indirect evidence of the motions of the plates. A
remarkable result from these studies is evidence that the plate
motions are nearly continuous and not an episodic process, even
on human time scales. Analyses of these motions indicate that
much of the motion between plates occurs without producing
earthquakes. In addition to monitoring interplate motions, global
positioning system arrays are making it possible to study present
deformation occurring within mountain belts.
     3) In summary, the global positioning system measurements
have revealed that crust deformation over distances greater than
200 kilometers is controlled by the bulk effects of crustal
thickness, crustal density, and upper mantle density, rather than
by local vertical variations in rheology or density.
-----------
B. Clement et al: Neotectonics: Watching the Earth move.
(Proc. Natl. Acad. Sci. US 7 Dec 99 96:14205)
QY: Bradford Clement, Dept of Geology, Florida International
University, US.
-----------
Text Notes:
... ... *Note #1: An important factor in the evolution of modern
plate tectonic theory was the development of oceanography in the
years following World War II, when technology designed for
warfare was turned to peaceful purposes. Extensive measurement of
the depth of the ocean floor (bathymetry) was accomplished by
echo-sounding, and within a few years several striking features
became evident: deep trenches, oceanic ridges (see notes below),
and long horizontal faults forming fracture zones.
... ... *polarity reversals: Geomagnetic polarity reversal is an
inversion of the *geomagnetic dipole. It is a global event,
experienced simultaneously all over the Earth, and such
reversals, apart from their intrinsic interest, provide a
convenient means of stratigraphic correlations and stratigraphic
dating. The term "stratigraphy" refers to the study of layered
sedimentary or metamorphic rocks, especially their relative ages
and the correlations between different areas. (In general,
"sedimentary rock" is any rock formed by the consolidation of
sediment, and "metamorphic rock" is any rock resulting from
partial or complete recrystallization under temperature and
pressure conditions elevated with respect to the Earth's
surface.)
... ... *geomagnetic dipole: In general, the best mathematical
fit to the observed geomagnetic field using a single dipole
approximation.
... ... *mid-ocean ridges: This is a long linear elevated
volcanic structure often lying along the middle of the ocean
floor, tending to occupy central positions as a consequence of
the oceans forming by symmetrical spreading of two lithosphere
plates from the ridge site. In extent, an oceanic ridge is
usually 1000 to 4000 kilometers wide and rising 2 to 3 kilometers
above the flanking basins.
-------------------
Summary & Notes by SCIENCE-WEEK [http://scienceweek.com] 28Jan00
[For more information: http://scienceweek.com/search/search.htm]


6. COSMOLOGY: EXPECTATIONS IN THE NEXT CENTURY OF RESEARCH
Cosmology is one of the grand sciences, a domain of research
whose results have enormous intellectual consequences, at least
for people who care about what they are and where they are.
Martin Rees (Cambridge University, UK) presents an essay on the
near-future research expectations of cosmologists, the author
making the following points:
     1) Astronomers still do not know what the Universe is made
of. Observable radiation-emitting objects -- such as stars,
*quasars, and galaxies -- apparently constitute only a small
fraction of the matter in the Universe. The vast bulk of matter
is dark and unaccounted for, and most cosmologists believe this
dark matter is composed of weakly interacting particles left over
from the *Big Bang. But dark matter could be something more
exotic. "Whatever the case, it is clear that galaxies, stars and
planets are a mere afterthought in a Cosmos dominated by quite
different stuff." The author suggests that intensive searches for
dark matter, mainly via sensitive underground experiments
designed to detect elusive subatomic particles, will continue in
the coming decade, and that within the next decade both the
amount and nature of dark matter will be clarified.
     2) The author suggests that research in the near-future is
also likely to focus on the evolution of the large-scale
structure of the Universe. The current view is that ever since
the Big Bang, gravity has been amplifying inhomogeneities,
building up structures and enhancing temperature contrasts -- "a
prerequisite for the emergence of the complexity that lies around
us now and of which we're a part." The author suggests that
astronomers are now learning more about the 10 billion year
process of Cosmic evolution by creating virtual universes on
computers, and that in the coming years researchers will be able
to simulate the history of the Universe with ever improving
realism and then compare the results with astronomical
observations.
     3) The author suggests that the great mystery for
cosmologists is the series of events that occurred less than 1
millisecond after the Big Bang, when the Universe was
extraordinarily small, hot, and dense. "The laws of physics with
which we are familiar offer little firm guidance for explaining
what happened during this critical period." To solve this
problem, it will necessary to improve and refine current
observations in order to understand the characteristics of the
Universe when it was only one second old: its expansion rate, the
size of its density fluctuations, and its proportions of ordinary
atoms, dark matter, and radiation.
     4) The author suggests the following Cosmic timeline for the
evolution of the Universe from the Big Bang to the present:
... ... a) 10^(-43) seconds after the Big Bang: the *Quantum
Gravity Era.
... ... b) 10^(-36) seconds after the Big Bang: Probable *Era of
Inflation.
... ... c) 10^(-5) seconds after the Big Bang: Formation of
protons and neutrons from *quarks.
... ... d) 3 minutes after the Big Bang: Synthesis of atomic
nuclei.
... ... e) 300,000 years after the Big Bang: First atoms form.
... ... f) 1 billion years after the Big Bang: Appearance of
first stars, galaxies, and quasars.
... ... g) 10 to 15 billion years after the Big Bang: Appearance
of modern galaxies.
     5) The author concludes: "How did a hot amorphous fireball
evolve, over 10 to 15 billion years, into our complex Cosmos of
galaxies, stars, and planets? How did atoms assemble -- here on
Earth and perhaps on other worlds -- into living beings intricate
enough to ponder their own origins? These questions are a
challenge for the new millennium. Answering them may well be an
unending quest."
-----------
Martin Rees: Exploring our Universe and others.
(Scientific American December 1999)
QY: Martin Rees, Cambridge University, UK.
-----------
Text Notes:
... ... *quasars: (quasi-stellar objects). Extremely luminous
sources radiating energy over the entire spectrum from x-rays to
radio waves, and which are apparently the oldest and most distant
objects in the universe. They are believed to involve massive
black holes.
... ... *Big Bang: The Big Bang theory is the general
cosmological model that proposes that all matter and radiation in
the universe originated in an explosion at a finite time in the
past.
... ... *Quantum Gravity Era: Quantum field theory is the
mathematical fusion of quantum mechanics with special relativity
theory, and the term "quantum gravity" refers to the fusion of
quantum mechanics with general relativity theory. The essential
basis for these fusions is the so-called "equivalence principle",
which identifies the mass involved in the gravitational force
equation with the inertial mass in the equation that relates any
force to the product of inertial mass and acceleration. The
"quantum gravity era" is the time-frame during which both quantum
effects and gravity determined the behavior of particles.
... ... *Era of Inflation: The inflationary model, first
proposed by Alan Guth in 1980, proposes that quantum
fluctuations in the time period 10^(-35) to 10^(-32) seconds
after time zero were quickly amplified into large density
variations during the "inflationary" 10^(50) expansion of the
universe in that time frame.
... ... *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.
-------------------
Summary & Notes by SCIENCE-WEEK [http://scienceweek.com] 28Jan00
[For more information: http://scienceweek.com/search/search.htm]
-------------------
Related Background:
IN FOCUS: ON COSMIC HISTORY
"The history of our Universe divides into three parts. 1) The
first millisecond, a brief but eventful era spanning 40 powers of
10 in time, starting at the Planck era [10^(-43) seconds]. This
is the intellectual habitat of mathematical physicists and
quantum cosmologists. The relevant physics is still speculative
-- indeed, one motive for studying cosmology is that the early
Universe may offer the only real clues to the laws of nature at
extreme energies. 2) The second stage runs from a millisecond to
about 1 million years. It's an era where cautious empiricists
feel more at home. The densities are far below nuclear density,
but everything is still expanding quite smoothly. There is good
quantitative evidence -- the cosmic helium and deuterium
abundances, the background radiation, and so on -- and the
relevant physics is well tested in the lab. Part two of cosmic
history, though it lies in the remote past, is the easiest to
understand. 3) But the tractability lasts only so long as the
Universe remains amorphous and structureless. When the first
gravitationally bound structures condense out -- when the first
stars, galaxies, and quasars have formed and lit up -- the era
studied by traditional astronomers begins. We then witness
complex manifestations of well-known basic laws. Part three of
cosmic history is difficult for the same reason as all
environmental sciences -- from meteorology to ecology -- are
difficult: they involve ultracomplex manifestations of simple
laws."
-----------
Martin Rees: _Before the Beginning_
(Helix Books, Reading 1997, p.160)
[Sir Martin Rees is Astronomer Royal of the UK and former
Director of the Cambridge University Institute of Astronomy.]
-------------------
SCIENCE-WEEK [http://scienceweek.com] 16Jul99


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

IN FOCUS: HISTORY OF SCIENCE: ON THE DEVELOPMENT OF CHEMISTRY
"When we study the history of science, it is useful to direct our
attention to the intellectual obstruction which, at a given
moment, is checking the progress of thought -- the hurdle which
it was then particularly necessary for the mind to surmount...
[In chemistry,] it would seem that the difficulty in [the 17th
and 18th centuries] lay in certain primary things which are
homely and familiar -- things which would not trouble a schoolboy
in the 20th century, so that it is not easy for us to see why our
predecessors should seem to have been so obtuse. It was necessary
in the first place that they should be able to identify the
chemical elements, but the simplest examples were perhaps the
most difficult of all. For thousands of years, air, water, and
fire had been wrapped up in a myth somewhat similar to the myth
of the special ethereal substance out of which the heavenly
bodies and celestial spheres were thought to have been made. Of
all the things in the world, air and water seemed most certain to
be irreducible elements... Even fire seemed to be another element
-- hidden in many substances, but released during combustion, and
visibly making its escape in the form of flame. [Francis] Bacon
and some of his successors in the 17th century had conjectured
that heat might be a form of motion in microscopic particles of
matter. Mixed up with such conjectures, however, we find the view
that it was itself a material substance; and this latter view was
to prevail in the 18th century. Men who had made great advances
in metallurgy, and had accumulated much knowledge of elaborate
and complicated chemical interactions, were as yet unable to
straighten out their ideas on these apparently simple topics. It
would appear to us today that chemistry could not be established
on a proper footing until a satisfactory starting-point could be
discovered for the understanding of air and water; and for this
to be achieved it would seem to been necessary to have a more
adequate idea both about the existence of 'gases' and about the
process of combustion. The whole development depended on the
recognition and the weighing of gases; but at the opening of the
18th century there was no realization of the distinctions between
gases, no instrument for collecting a gas, and no sufficient
consciousness of the fact that the measurements of weight might
play the decisive part amongst the data of chemistry."
-----------
Herbert Butterfield: _The Origins of Modern Science 1300-1800_
(G. Bell & Sons 1957)
-------------------
SCIENCE-WEEK [http://scienceweek.com] 28Jan00
-------------------
Related Background:
IN FOCUS: ON THE FOUNDATION OF MODERN CHEMISTRY
"It is interesting that it was not until the early years of the
17th century that the word 'gas' was used. This word was invented
by a Belgian physician, J.B. van Helmont (1577-1644), to fill the
need caused by the new idea that different kinds of 'airs'
existed. Van Helmont discovered that a gas (the gas that we now
call carbon dioxide) is formed when limestone is treated with
acid, and that this gas differs from air in that when respired it
does not support life and that it is heavier than air. He also
found that the same gas is produced by fermentation, and that it
is present in the Grotto del Cane, a cave in Italy in which dogs
were observed to become unconscious (carbon dioxide escaping from
fissures in the floor displaces the air in the lower part of the
cave). During the 17th and 18th centuries, other gases were
discovered, including hydrogen, oxygen, and nitrogen, and many of
their properties were investigated. It was not until nearly the
end of the 18th century, however, that these three gases were
recognized as elements. When Lavoisier recognized that oxygen is
an element, and that combustion is the process of combining with
oxygen, the foundation of modern chemistry was laid."
-----------
Linus Pauling: _General Chemistry_
(W.H. Freeman, San Francisco 1970, p.306)
-------------------
SCIENCE-WEEK [http://scienceweek.com] 18Jun99


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