|
ComDig 1999:beta4 |
|
26-Nov-1999 |
Complexity Digest 1999:beta4(http://www.personal.psu.edu/faculty/g/x/gxm21/ComDig/)
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)
2.Journals Launch Private Reference Network, Eliot Marshall, Science
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 1459See also: Science Journals to Link Up on Internet, New York Times, Reuters
3. Meme's the Word, Jacob Goldenberg et al., Science
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
4. Learning on your feet, Rachel Smyly, Nature
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, 99Se also Acrobatics helps to re-grow neuronal connections
5. 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
6.Sustained oscillations in living cells, Sune Danø et al., Nature
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)
7. Finnish group confirms: Chaos is good for your heart, Saila Vikman et al.,Circulation
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
8. From mice to Methuselah, Henry Gee, Nature
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, 99See 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).
9. Using din to find dinner, Philip Ball, Nature
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, 99See 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
10. How to get a head, Henry Gee, Nature
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, 99See 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)
11. Sudden Change of Large Scale Weather Pattern,Yukari N. Takayabu et al., Nature
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)
12. Growing Y-junction carbon nanotubes, Jing Li et al., Nature
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)
13. Taming Laser Light, Malcolm H. Dunn, and Majid Ebrahimzadeh, Science
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.
14. 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.
15. Software: Visualizing a Changing World, Andreas Madlung, Science
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
16. Complexity Book List by Ken Baskin, David K. Lee, NECSI mailing list
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 )
ComDig 1999:beta4 26-Nov-1999