-
Abstract: The RNA folding map, understood as the relationship
between sequences and sec-ondary structures or shapes, exhibits
robust statistical properties summarized by three notions: (1) the
notion of a typical shape (that among all sequences of fixed length
certain shapes are realized much more frequently than others), (2)
the notion of shape space covering (that all typical shapes are
realized in a small neighborhood of any random sequence), and (3) the
notion of a neutral network (that sequences folding into the same
typical shape form networks that percolate through sequence
space).
The concept of a neutral network is particularly illuminating.
Neutral networks loosen the requirements on the mutation rate for
selection to remain effective. What needs to be preserved in a
population is not a particular sequence, but rather a shape. This
mandates a reformulation of the original (genotypic) error threshold
in terms of a phenotypic error threshold confirming the intuition
that more errors can be tolerated at higher degrees of
neutrality.
With regard to adaptation, neutrality has two seemingly
contradictory effects: It acts as a buffer against mutations ensuring
that a phenotype is preserved. Yet it is deeply enabling, because it
permits evolutionary change to occur by allowing the sequence context
to vary silently until a single point mutation can become
phenotypically consequential. Neutrality also in uences
predictability of adaptive trajectories in seemingly contradictory
ways. On the one hand it increases the uncertainty of their genotypic
trace. At the same time neutrality structures the access from one
shape to another, thereby inducing a topology among RNA shapes which
permits a distinction between continuous and discontinuous shape
transformations.
To the extent that adaptive trajectories must undergo such
transformations, their phenotypic trace becomes more predictable.
Chance
and Necessity in Evolution: Lessons from
RNA, P. Schuster and W.
Fontana, Physica D133, 427-452 (1999)
-
A
few weeks ago the plan was announced to create a global library of
interconnected, electronic documents (preprints) to which scientists
(and everyone else) can submit their papers. (See ComDig 99:beta 1).
While this is an important step towards a universal knowledge base it
lacks one element of scientific publication: peer review that is
supposed to reject submissions that do not satisfy minimal scientific
standards.
Today
we have the announcement of an equivalent global information network
but this time from a dominant group of the traditional keepers of
scientific knowledge, the peer reviewed journals. The agreement links
Academic Press, a Harcourt Science and Technology company, the AAAS,
the American Institute of Physics, the Association for Computing
Machinery, Blackwell Science, Elsevier Science, the Institute of
Electrical and Electronics Engineers, Inc. (IEEE), Kluwer Academic
Publishers, Nature, which is published by Macmillan, Oxford
University Press, Springer-Verlag, and John Wiley & Sons,
Inc..
They
created something like a URL (Uniform Resource Locater, the concept
that was largely responsible for the huge success of the world wide
web) for individual scientific (peer reviewed) publications. The DOI
(Digital Object Identifier) will make it possible to link references
electronically to a publication even if it resides on the server of a
different journal. Up to this point this system is very similar to
the Universal Preprint Service (UPS) and the NIH PubMed Central
described in ComDig 99:beta1 with the difference that the new network
is not accessible for free. In terms of complex adaptive systems
there is a clear and well defined fitness function in the latter
systems: Because of the reputation of the traditional journals an
accepted article translates directly into market value of the author.
In turn, the readers get "trusted" information about progress in
science.
For
the UPS project other forms of fitness functions will emerge, for
instance the reputation of the author or her home institution. At any
rate it will be interesting to observe in the coming years how these
two global knowledge networks will evolve and compete or
cooperate.
The
launch is expected for the first quarter of 2000.
Journals
Launch Private Reference
Network, Eliot Marshall,
Science, 286, Number 5444 Issue of 19 Nov 1999, p
1459
See also: Science
Journals to Link Up on
Internet, New York Times,
Reuters
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R. Dawkins (4) termed the unit of idea replication "ideosphere,"
suggesting that the soup in which memes (tunes, ideas) grow and
flourish--the analog to the primordial soup (out of which life first
emerged)--is the soup of human culture. Just as genes propagate in
the gene pool by leaping from body to body, so memes propagate by
leaping from brain to brain. The worldly consequences (for example,
market behavior) feed back to influence the competition among
templates rather than ideas.
Meme's
the Word, Jacob Goldenberg,
David Mazursky, Sorin Solomon, Science, 286,
Number 5444 ,19 Nov 1999, p 1477
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Researchers have shown that mice provided with a running wheel to
use in their spare time learn faster, have more new brain cells and
show more learning-associated changes in their brains than their
sedentary colleagues.
Mice love running wheels -- those with them ran, on average,
almost five kilometres a day. These mice, Van Praag's team found,
learned the water maze faster than those without wheels: this
suggests that exercise, or at least running, helped the mice to learn
more quickly.
LTP, a strengthening of the connections between brain cells, may
be what happens in the brain when we learn. Sure enough, the
marathon-running mice had more LTP in their hippocampal cells than
the couch potatoes.
So how could running help the brain to make new cells and learn a
maze more quickly?
Learning
on your feet, Rachel Smyly,
Nature Science update, Nov.18, 99
Se also Acrobatics
helps to re-grow neuronal connections
A spoonful of sugar helps the memory go down, Rachel Smyly, Nature 
Proteins are made from strings of smaller chemicals called 'amino
acids'. The RNA then tells the protein-making machinery in the cell
which amino acids to string together into the required protein.
Fiala and his colleagues used a technique called 'antisense'
technology to temporarily stop cells in the bees' brains from
'reading' the RNA necessary to make a protein called 'protein kinase
A', or PKA, which they thought might be needed for the insects to
learn. When a bee had been injected with antisense RNA, it still
learned to extend its proboscis in response to carnation oil, showing
that it expected sugar solution to follow. However, 24 hours after
the training, the treated bees had 'forgotten' their
conditioning.
A
spoonful of sugar helps the memory go
down, Rachel Smyly, Nature
Science update, Nov.18, 99
-
One of the successes of nonlinear dynamics and complex systems was
that it could demonstrate how biological rhythms could have their
origin in self-organized chemical oscillations. And already in the
early days of non-linear research Degn & Olsen and others could
find oscillations in simple biological systems that also could be
matched up with a non-linear dynamical systems theory. In a typical
experiment one would add a glucose pulse to a suspension of cells and
measure the resulting transient oscillations of one of the cell
chemicals, NADH.
Danø et al. could show, using a suspension of yeast cells,
that living cells can be kept in a well defined oscillating state
indefinitely. They starved cells and then put them into a container
through which a flow of glucose and cyanide is pumped. The results
show that the transitions between stationary and oscillatory behavior
are uniquely described mathematically by the Hopf bifurcation.
Transition (bifurcations) like Hopf bifurcations are indicative for
the presence of non-linearity in the equations.
Perturbation experiments show that the cells remain strongly
coupled very close to the transition. Therefore, the transition takes
place in each of the cells and is not a desynchronization phenomenon.
One chemical (acetaldehyde) was already known to synchronize the
oscillations of yeast cells. These results show that glucose is
another messenger substance.
Sustained
oscillations in living cells,
Sune Danø, Preben Graae Sørensen & Finn
Hynne, Nature 402, 320 - 322 (1999)
-
In the early days of chaos research the speculation came up that
fibrillation in the heart (very irregular contractions that prevent
the heart from pumping blood) could perhaps be a manifestation of
chaos. The underlying assumption was that something pathological like
a chaotic attractor surely must correspond to a pathological
condition for the heart. It turned out that fibrillation cannot be
described by a low-dimensional chaotic attractor but perhaps as
spatio-temporal chaos.
Later on, the heart rhythms themselves were analyzed with the
tools from non-linear dynamics. Instead of recording the full electro
cardiogram (ECG) it became soon clear that it is much more convenient
to measure the time differences between consecutive pulses. Because
of the nomenclature used to describe the ECG this became known as the
analysis of R-R intervals. It came to the surprise of many when
evidence accumulated that pathological conditions like fibrillation
are preceded by a reduction in the degree of chaos in the R-R
interval sequences. This can be measured with approximate fractal
dimensions or dynamical entropies. Thus the hypothesis was formulated
that "Chaos is good for your heart." This general claim could be
confirmed in a surprising number of situations.
One of the most recent such confirmations comes from Vikman et al.
They studied conditions that lead to atrial fibrillation AF, a
condition where the fibrillation is confined to the heart's ante
chamber or atrium. Traditional heart rate variability measures showed
no significant changes before the onset of AF. But with different
methods from non-linear dynamics they could observe a significant
reduction in the magnitude of chaos indicators like "ApEn" and "
short-term scaling exponent".
These results support the hope that one day portable, chaos-based
monitoring systems will warn patients of threatening fibrillation
attacks.
Altered
Complexity and Correlation Properties of R-R Interval
Dynamics Before the Spontaneous Onset of Paroxysmal
Atrial Fibrillation , Saila
Vikman, Timo H. Mäkikallio, Sinikka Yli-Mäyry,
Sirkku Pikkujämsä, Anna-Maija Koivisto, Pekka
Reinikainen, K. E. Juhani Airaksinen, Heikki V. Huikuri,
Circulation. 1999;100:2079-2084
-
In health food stores one can buy "anti-oxidants" as food
supplement to protect against some form of "internal corrosion".
'Oxidative stress', as this damaging process is called, may be an
important factor in ageing. Reporting in Nature Pier Giuseppe Pelicci
of the European Institute of Oncology, Milan, and colleagues describe
a strain of mouse genetically altered to manifest a defect in its
oxidative-stress-management system -- and a lifespan a third longer
than normal mice. Specifically, the mice studied by Pelicci's group
lack the gene for a protein called 'p66shc'. In normal mice exposed
to oxidative stress, p66shc changes. Whatever the reason, mice
without the p66shc gene live longer than those with it.
For example, keeping mice on a strict calorie-controlled diet can
extend lifespan by 50% or more, but the mice are smaller and less
fertile than normal mice. Although it is important that such
experiments use mice of known genetics, this particular strain may
have some unusual feature of oxidative-damage-response that interacts
with defective p66shc to produce longer-lasting mice.
In other studies of life-prolonging substances there always seemed
to be a trade-off between reduced aging processes and risk of cancer.
No negative side-effects have been reported so far for the mice with
the missing p66shc gene.
From
mice to Methuselah, Henry Gee,
Nature Science update, Nov.18, 99
See also: Migliaccio, E.,
Giorgio, M., Mele, S., Pelicci, G., Reboldi, P.,
Pandolfi, P.P., Lanfrancone, L. & Pelicci, P.G.
The
p66shc adaptor protein controls oxidative stress response
and life span in mammals
Nature 402, 309 (1999).
-
Stochastic resonance is a phenomenon that allows a system to take
advantage of a noisy environment to enhance the quality of signals.
Whereas it could be shown that some animals do indeed show that that
they can use stochastic resonance there is now clear evidence that at
least on species actively uses stochastic resonance to enhance its
chance to find food: The North American paddlefish (Polyodon
spathula, a promising candidate for the "World's Ugliest Fish"
competition but also producer of delicious caviar) graze on
microscopic animals or 'zooplankton' called 'Daphnia'. They have a
long antennae -- like a radio aerial -- in front of their mouths that
detects low-frequency oscillating electric fields. These sensitive
organs can pick up the tiny electric fields produced by other
organisms. With its antennae a hungry paddlefish can sense Daphnia
from a distance of four centimeters. Common sense would suggest that
the ability of these fish to detect dinner should decrease if, in
addition to the electrical signals that the prey produce, the water
is pervaded by a background electrical noise, akin to the hiss of
radio 'static'. The noise would, you'd expect, obscure the
signal.
So Russell's group set out to see whether paddlefish, whose
detectors sense electrical rather than mechanical signals, are better
able to locate plankton during feeding with or without background
noise. They let the fish feed in a flowing stream of water pervaded
by a random electric field and observed that the ability to find food
reaches an optimum for a specific magnitude of the random electrical
field.
Using
din to find dinner, Philip
Ball, Nature Science update, Nov.18, 99
See also: Use
of behavioural stochastic resonance by paddle fish for
feeding, David F. Russell, Lon
A. Wilkens & Frank Moss, Nature 402, 291 - 294
(1999), P. Jung, G. Mayer-Kress, Spatio-Temporal
Stochastic Resonance in Excitable
Media, Physical Review
Letters, 74(11), 2130-2133, 13 March 1995
-
One of Hercules' more dangerous tasks was to subdue the ferocious
Hydra. Whenever the great hero decapitated the beast, more heads
instantly appeared in its place. Centuries later, zoologists
discovered a real-life animal with the same attribute and named it
after the story -- Hydra. Like a sea anemone, the hydra is basically
a cylinder. The hydra is one of the simplest animals that has a
distinct body axis -- that is, a distinct front end and back end.
But, just like Hercules' adversary, if you decapitate a real-life
hydra, it grows another head in its place. In the frog Xenopus,
transplanting the organizer, or grafting an organizer from one animal
to another, can produce animals with multiple heads and bodies --
just like the mythical hydra.
Broun and colleagues show that Cngsc in the hydra is an
evolutionary equivalent of goosecoid in frogs, and that it performs
similar functions. As amazing proof of this evolutionary kinship,
when Cngsc is injected into frog embryos, it produces additional body
axes, just as goosecoid would.
How
to get a head, Henry Gee,
Nature Science update, Nov.17, 99
See also Broun, M., Sokol, S. &
Bode, H. R.. Cngsc,
a homologue of goosecoid, participates in the patterning
of the head, and is expressed in the organizer region of
Hydra. Development 126,
5245-5254 (1999)
-
A characteristic feature of non-linear, complex systems is their
ability to exhibit "bifurcations", sudden qualitative changes in
behavior. In complex systems bifurcations occur when self-organized
structures or order parameters interact with each other. In the Earth
atmosphere self-organized, coherent structures (e.g. hurricanes)
typically have their own names. One of the better known patterns with
global impact is the El Niño phenomenon that occurs every few
years around Christmas time (hence the name) and originates in the
pacific ocean.
There is another coherent structure, the Madden-Julian
oscillation--a global atmospheric wave in the tropics that propagates
eastwards with a period of about 30-60 days-- that had been suspected
to be involved in triggering El Niño events before. For the
extreme 1997-98 El Niño event the ending was especially
sudden. Takayabu et al. studied the atmospheric conditions prior to
this transition in great detail by analyzing data like precipitation,
sea surface temperatures and wind speeds. They found that a
precipitation system associated with an exceptionally strong
Madden-Julian oscillation was travelling around the Equator in at
about the time of the termination. The propagation of this
atmospheric system was associated with an abrupt intensification of
the easterly trade winds over the eastern equatorial Pacific Ocean.
They conclude that combined with other factors in the central and
eastern Pacific Ocean at that time, these strong winds provided the
triggering mechanism for the observed accelerated ending of the
1997-98 El Niño event.
Abrupt
termination of the 1997-98 El Niño in response to
a Madden-Julian
oscillation,Yukari N.
Takayabu, Toshio Iguchi, Misako Kachi, Akira Shibata
& Hiroshi Kanzawa, Nature 402, 279 - 282
(1999)
-
It is a privilege of the young generation to take for granted what
often borders to technological miracles. One gets used to expecting
the next computer chip to appear regularly with significantly
increased performance in speed or memory. It is clear that we are
approaching fast the limits of micro-technology and we need a quantum
leap to build the type of computers that allow qualitatively new
applications, similar to the transition from mainframes to personal
computers.
In basic research the scientific foundations for next generation
of electronic devices have been studied for a number of years:
quantum computation and nano technology. A transition from micro to
nano would correspond to the reduction of size by a factor of one
thousand: A palmtop device a thousand times smaller could have the
size of a hair.
If engineers are to build those tiny gadgets it would be helpful
for them to have a basic construction set from which to build more
complicated structures. The discovery of a specially symmetric carbon
molecule, the "Bucky-ball" was the basis for exactly that type of
building element. Soon it became possible to modify them to build
"nano tubes" that were only a few atom sizes thick. Jing Li and
coworkers achieved another technological breakthrough when they
learned how to build Y-junction carbon nanotubes. Now it is possible
to start thinking about building more complex nano-structures as they
are needed for electronic devices.
Growing
Y-junction carbon nanotubes,
Jing Li, Chris Papadopoulos, Jimmy Xu, Nature 402, 253 -
254 (1999)
-
By exploiting nonlinear optical effects, a technology of
unprecedented flexibility for the production of tunable coherent
light has been developed. Referred to as optical parametric
generation, it provides sources with spectral coverage extending all
the way from the ultraviolet to the mid-infrared, and with temporal
coverage extending over all time domains from the femtosecond pulse
to the continuous wave. Such sources generate coherent light of
outstanding optical quality and are now finding wide-ranging
applications.
Parametric
Generation of Tunable Light from Continuous-Wave to
Femtosecond Pulses, Malcolm H.
Dunn, and Majid Ebrahimzadeh, Science 286:
1513-1517.
Nonlinear Optics for High-Speed Digital Information Processing, D. Cotter et al., Science
Recent advances in developing nonlinear optical techniques for
processing serial digital information at high speed are reviewed. The
field has been transformed by the advent of semiconductor nonlinear
devices capable of operation at 100 gigabits per second and higher,
well beyond the current speed limits of commercial electronics. These
devices are expected to become important in future high-capacity
communications networks by allowing digital regeneration and other
processing functions to be performed on data signals "on the fly" in
the optical domain.
Nonlinear
Optics for High-Speed Digital Information
Processing, D. Cotter, R. J.
Manning, K. J. Blow, A. D. Ellis, A. E. Kelly, D. Nesset,
I. D. Phillips, A. J. Poustie, and D. C. Rogers, Science
286: 1523-1528.
-
WorldWatcher is a new (and free) software package that brings
hard-to-grasp concepts of atmospheric science to life and helps
students visualize and understand large sets of climate-related
data.
The software contains a large library of Earth and atmospheric
science data. Students may also enter their own data, although,
according to the manual, the file import for raw data is somewhat
complex and requires "advanced computer skills." Atmospheric data
allow students to observe the greenhouse effect; incoming, absorbed,
and reflected energy; and surface temperatures over recent time. The
data conversion function does allow the user to convert data into
metric values, but it requires that the operator have a basic
knowledge of the appropriate conversion equations.
New projects and data sets are available for download from the
WorldWatcher Web page on a regular basis. WorldWatcher's strength
lies in providing an easy way to superimpose data or analytical
results on world maps.
WorldWatcher, SSciVEE: Supportive Scientific Visualization
Environments for Education, Northwestern University Evanston, IL,
http://www.worldwatcher.nwu.edu/
Software: Visualizing
a Changing World, Andreas Madlung, Science,
286, Number 5444 Issue of 19 Nov 1999, p 1497
-
Arthur Battram , Navigating
Complexity: The Essential Guide to Complexity Theory in Business and
Management
Michael Lissack, Johan Roos, Thomas, Jr. Petzinger, "The
Next Common Sense" (Nicholas Brealey, 1999), an attempt to define
how the business common sense dominated by a complexity approach
differs from the traditional common sense.
Ralph D. Stacey, "Complexity
and Creativity in Organizations" (Berrett-Kohler, 1996), defining
the conditions at the edge of chaos, in which creativity can best
occur.
Thomas Petzinger Jr, Thomas, Jr. Petzinger, "The
New Pioneers : The Men and Women Who Are Transforming the Workplace
and Marketplace" (Simon & Schuster, 1999), full of stories of
business people now using the principles suggested by complexity
theory in their daily work.
Jeffrey Goldstein, The
Unshackled Organization. Fairly basic but a good read.
Kelly and Allison, The
Complexity Advantage. A Business Week publication aimed at
business readers.
Fritjof Capra, The
Web of Life. Here you benefit from a knowledge of biology and
physics, but it is a great book.
Dorner, The
Logic of Failure. This book brilliantly describes how many bad
decisions are made and emphasizes that we like to think in linear,
isolated, instanteous terms. Most decisions are networked,
non-linear, and have time delays. A large variety of real world and
simulated examples. Has not gotten the attention it deserves. One
example is Chernobyl.
Ken Baskin "Corporate
DNA" (Butterworth-Heinemann, 1998), exploring what happens when
people think of their businesses as living things operating in market
ecologies.
( The above reading list was contributed from David Lee and Ken
Baskin in posts to the complex-science@necsi.org Forum )
