Complexity Digest 2001.28 July-9-2001

Archive:  www.comdig.org, European Mirror:  www.comdig.de

Asian Mirror:  http://www.phil.pku.edu.cn/resguide/comdig/ (Chinese GB-Code)

"I think the next century will be the century of complexity." Stephen Hawking

  1. UCSF Scientists Halt Tumor Growth By Manipulating Telomerase Enzyme, UCSF/Science Daily
  2. Silencing The Alarm: The First Few Days Of Hiv Infection, New Scientist Magazine
  3. Building The Bodies Of A New Machine, Boston Globe
  4. Innovation Networks - A Simulation Approach, JASSS
  5. Modelling And Simulating Innovation Behaviour Within Micro-Based Correlated Decision Processes, JASSS
  6. Competition As A Test Of Hypotheses: Simulation Of Knowledge-Generating Market Processes, JASSS
  7. Empirically Based Simulation: The Case Of Twin Peaks In National Income, JASSS
  8. Control Motifs For Intracellular Regulatory Networks, Annu. Rev. Biomed. Engr.
  9. Computer Modeling And Simulation Of Human Movement, Annu. Rev. Biomed. Engr.
  10. Lighting the Way To A Quantum Computer, Science
  11. Dynamical Tunnelling Of Ultracold Atoms, Nature
  12. Observation Of Quantum Shock Waves Created With Ultra-Compressed Slow Light Pulses, Science
  13. Ultrafast Manipulation Of Electron Spin Coherence, Science
  14. Carbon Nanotube Single-Electron Transistors At Room Temperature, Science
  15. By A Whisker, Harbor Seals Catch Their Prey, Science
    1. Hydrodynamic Trail-Following In Harbor Seals (Phoca vitulina), Science
  16. Galaxy Formation: Are We There Yet?, Science
    1. Star Formation, Supernovae Feedback And The Angular Momentum Problem, arXiv
  17. Short-Term Synaptic Plasticity As A Temporal Filter, Trends In Neurosciences
  18. Sensing Seizure Activity Earlier, Trends In Neurosciences
  19. From Intelligent Networks To Global Brains, Conference WebCast
  20. Links & Snippets
    1. Other Papers
    2. Announcements
      1. Complexity Digest Site Design Competition!

1. UCSF Scientists Halt Tumor Growth By Manipulating Telomerase Enzyme, UCSF/Science Daily

Excerpt: UCSF researchers report that they were able to slow the growth of human cancer cells - or cause them to commit suicide altogether -- by creating just a miniscule mutation in the telomerase enzyme.

The study, conducted in breast and prostate cells grown in culture and in tumors formed from human breast cancer cells grafted into mice, suggests that human cancer cells are much more sensitive to disruptions in the telomerase enzyme than had been thought. The finding hints, the researchers say, at a possible new strategy for thwarting human cancers.

In humans, telomerase is inactive in most adult cells, and only active at certain times in others, but it is highly active in cancer cells, and has been suggested as a potential therapeutic target. However, previous studies in human cancer cells have indicated that disrupting telomerase as a means of halting cancer cell replication or inducing cell suicide would require an almost complete loss of normal telomerase activity. And this would require either swamping the enzyme with an overwhelming amount of mutant telomerase or finding a sufficiently potent drug to completely inhibit the enzyme.

But in the current study, the researchers observed that inserting a tiny mutation in the gene coding for a small but critical portion of the telomerase enzyme prompted a dramatic response from cancer cells. The finding suggests a more efficient means of delivering therapy. Most of the human breast and prostate cancer cells grown in culture lost the ability to replicate or they committed suicide, while tumors formed from human breast cancer cells grafted into mice were smaller than those generated from cells that didn't have the mutation. Moreover the response occurred despite the fact that most of the normal telomerase was retained. The researchers induced the response with several different variations of the mutant gene.

2. Silencing The Alarm: The First Few Days Of Hiv Infection, New Scientist Magazine

Excerpt: A breakthrough molecular blow-by-blow account of the first few days of HIV infection has been recorded by a US team. The researchers monitored nearly 7,000 genes over 72 hours and say they have created the first sequential record of the steps leading to the death of critical immune system cells.

HIV attacks CD4+T (helper T) cells. Eventually this leads to the destruction of the immune system and the development of AIDS. (...) within 30 minutes of infection, the virus shuts down more than 500 genes in the infected

cells. (...)

 

3. Building The Bodies Of A New Machine, Boston Globe

Excerpts: Inside a circular box just larger than a watch face, she has built what she hopes will be tomorrow's poison detector: a teeming colony of liver cells on a tiny wafer of silicon.(…)

The liver chip, which combines advances in miniaturized manufacturing with breakthroughs in cell biology, is part of an engineering revolution: the mingling of cells and electronics to create machines with living components.(…)

The groundbreaking insight behind the liver chip was a way to grow what its creator calls 3-D liver cells.

4. Innovation Networks - A Simulation Approach, JASSS

Abstract: A multi-agent simulation embodying a theory of innovation networks has been built and used to suggest a number of policy-relevant conclusions. The simulation animates a model of innovation (the successful exploitation of new ideas) and this model is briefly described. Agents in the model representing firms, policy actors, research labs, etc. each have a knowledge base that they use to generate 'artefacts' that they hope will be innovations. The success of the artefacts is judged by an oracle that evaluates each artefact using a criterion that is not available to the agents. Agents are able to follow strategies to improve their artefacts either on their own (through incremental improvement or by radical changes), or by seeking partners to contribute additional knowledge. It is shown though experiments with the model's parameters that it is possible to reproduce qualitatively the characteristics of innovation networks in two sectors: personal and mobile communications and biotechnology.

 

5. Modelling And Simulating Innovation Behaviour Within Micro-Based Correlated Decision Processes, JASSS

Abstract: The economic evolution and production has been subject to major shocks and structural changes during the last decades. Beside the standard production factors such as the capital and labour force new production factors for taking into account technological progress and knowledge production and knowledge transfer have to be considered.

Modelling of the evolution of technologies as well as structural changes in the management of firms however, require a better understanding of knowledge production and the knowledge transfer process within and between industries, the role and efficiency of transfer institutions such as universities, technology-transfer centres and consulting companies. The paper aims to provide a decision-based framework for this kind of complex interwoven processes.

 

6. Competition As A Test Of Hypotheses: Simulation Of Knowledge-Generating Market Processes, JASSS

Abstract: Hayek's well-known evolutionary concept of "competition as a discovery procedure" can be characterized as a parallel process of experimentation, in which rivalrous firms generate and test hypotheses about the best way to fulfill the consumers' preferences. Through this permanent process of variation and selection of hypotheses (innovation / imitation) a process of knowledge accumulation can take place. The central aim of our paper is to model the basic Hayekian learning mechanism, which consists of experimentation and mutual learning, and to ask for determinants of the rapidity of knowledge accumulation. In our multilevel simulation model, on the micro level, firms create new hypotheses through mutation. On the macro level, on the market, these hypotheses meet and the best firm is determined. All firms then imitate the best firm. In our model, 100 of these periods which consist of an innovation and an imitation phase are simulated. We presume that decentrality is crucial for the working of the knowledge-generating process, because a larger number of independently innovating firms leads to more experimentation. We investigate into the impact of firm concentration, the impact of the decentralization of firms, as well as the impact of impediments in imitation like lock-ins on the growth rate of knowledge accumulation. Our simulation results show that the number of firms is positively correlated with the rapidity of knowledge accumulation suggesting a new argument for a critical assessment of mergers in competition policy.

 

7. Empirically Based Simulation: The Case Of Twin Peaks In National Income, JASSS

Abstract: Only recently a new stylised fact of economic growth has been introduced, the bimodal shape of the distribution of per capita income or the twin-peaked nature of that distribution. Drawing on the Summers/Hestons Penn World Table 5.6 (1991) we determine kernel density distributions which are able to detect the aforementioned twin peaked structure and show that the world income distribution starting with an unimodal structure in 1960 evolves subsequently to a bimodal or twin-peak structure. This empirical results can be explained theoretically by a synergetic model based on the master equation approach as in Pyka/Kruger/Cantner (1999). This paper attempts to extend this discussion by taking the reverse procedure, that is to find empirical evidence for the working mechanism of the theoretical model. We determine empirically the transition rates used in the synergetic approach by applying alternatively NLS to chosen functional forms and genetic programming in order to determine the functional forms and the parameters simultaneously. Using the so determined transition rates in the synergetic model leads in both cases to the emergence of the bimodal distribution, which, however, is only in the latter case a persistent phenomenon.

 

8. Control Motifs For Intracellular Regulatory Networks, Annu. Rev. Biomed. Engr

Abstract: A number of technological innovations are yielding unprecedented data on the networks of biochemical, genetic, and biophysical reactions that underlie cellular behavior and failure. These networks are composed of hundreds to thousands of chemical species and structures, interacting via nonlinear and possibly stochastic physical processes. A central goal of modern biology is to optimally use the data on these networks to understand how their design leads to the observed cellular behaviors and failures. Ultimately, this knowledge should enable cellular engineers to redesign cellular processes to meet industrial needs (such as optimal natural product synthesis), aid in choosing the most effective targets for pharmaceuticals, and tailor treatment for individual genotypes. The size and complexity of these networks and the inevitable lack of complete data, however, makes reaching these goals extremely difficult. If it proves possible to modularize these networks into functional subnetworks, then these smaller networks may be amenable to direct analysis and might serve as regulatory motifs. These motifs, recurring elements of control, may help to deduce the structure and function of partially known networks and form the basis for fulfilling the goals described above. A number of approaches to identifying and analyzing control motifs in intracellular networks are reviewed.

 

9. Computer Modeling And Simulation Of Human Movement, Annu. Rev. Biomed. Engr.

Excerpt: Recent interest in using modeling and simulation to study movement is driven by the belief that this approach can provide insight into how the nervous system and muscles interact to produce coordinated motion of the body parts. With the computational resources available today, large-scale models of the body can be used to produce realistic simulations of movement that are an order of magnitude more complex than those produced just 10 years ago. This chapter reviews how the structure of the neuromusculoskeletal system is commonly represented in a multijoint model of movement, how modeling may be combined with optimization theory to simulate the dynamics of a motor task, and how model output can be analyzed to describe and explain muscle function. Some results obtained from simulations of jumping, pedaling, and walking are also reviewed to illustrate the approach.

 

10. Lighting the Way To A Quantum Computer, Science

Excerpt: Using a trio of vanishingly brief laser pulses, the team managed to tweak bits of quantum data in as little as 100 quadrillionths of a second, or femtoseconds. At that rate, they could theoretically carry out 1 million such manipulations before the quantum information falls apart. The group hasn't demonstrated any computation power yet. Nevertheless, the ability to manipulate quantum information so quickly "is a very important milestone," says Stuart Wolf, a quantum-computer expert at the Pentagon's Defense Advanced Research Projects Agency in Arlington, Virginia,

 

11. Dynamical Tunnelling Of Ultracold Atoms, Nature

Excerpts. The divergence of quantum and classical descriptions of particle motion is clearly apparent in quantum tunnelling between two regions of classically stable motion, say, through an energy barrier. In the 1980s, a 'dynamical' tunnelling, was predicted, involving no potential energy barrier; however, a constant of the motion (other than energy) still forbids classically the quantum-allowed motion. Such systems may be chaotic, consisting of regions in phase space of stable, regular motion embedded in a sea of chaos. Here we observe dynamical tunnelling of ultracold atoms from a Bose-Einstein condensate in an amplitude-modulated optical standing wave. Atoms coherently tunnel back and forth between their initial state of oscillatory motion and the state oscillating 180¢X out of phase with the initial state.
  • Dynamical Tunnelling of Ultracold Atoms, W. K. Hensinger, H. Haffner, A. Browaeys, N. R. Heckenberg, K. Helmerson, C. Mckenzie, G. J. Milburn, W. D. Phillips, S. L. Rolston, H. Rubinsztein-Dunlop, B. Upcroft,Nature 412, 52-55 (5 July 2001)

 

12. Observation Of Quantum Shock Waves Created With Ultra-Compressed Slow Light Pulses, Science

Abstract. We have used an extension of our slow light technique to provide a method for inducing small density defects in a Bose-Einstein condensate. These sub-resolution, micrometer-sized defects evolve into large-amplitude sound waves. We present an experimental observation and theoretical investigation of the resulting breakdown of superfluidity, and we observe directly the decay ofthe narrow density defects into solitons, the onset of the "snake" instability, and the subsequent nucleation of vortices.

 

13. Ultrafast Manipulation Of Electron Spin Coherence, Science

Excerpts: Here we present time-resolved Faraday rotation experiments that extend a technique first applied in atomic sodium (8) to semiconductor nanostructures by using ultrafast laser pulses to produce coherent rotations of electron spins (9). In our experiments, a pump pulse optically excites spin-polarized electrons that precess about a static magnetic field. A second below-band gap "tipping" pulse produces an additional effective magnetic field that can reach 20 T through the optical Stark effect (10). (¡K) This field is used to coherently rotate electron spins (¡K).

 

14. Carbon Nanotube Single-Electron Transistors At Room Temperature, Science

Abstract: Room-temperature single-electron transistors are realized within individual metallic single-wall carbon nanotube molecules. The devices feature a short (down to ~20 nanometers) nanotube section that is created by inducing local barriers into the tube with an atomic force microscope. Coulomb charging is observed at room temperature, with an addition energy of 120 millielectron volts, which substantially exceeds the thermal energy. At low temperatures, we resolve the quantum energy levels corresponding to the small island. We observe unconventional power-law dependencies in the measured transport properties for which we suggest a resonant tunneling Luttinger-liquid mechanism.

 

15. By A Whisker, Harbor Seals Catch Their Prey, Science

Abstract:  When mammals colonized the ocean some 50 million years ago, some species of dolphins and whales evolved echolocation, which allows them to "see" with their ears. How other marine mammals manage to hunt without echolocation has long been a mystery, though, as the sharp vision their ancestors had evolved on land was of little use in the ocean's murky darkness. On page 102, researchers report that part of the answer has been hiding in plain view: They use their whiskers.

 

Abstract: Marine mammals often forage in dark or turbid waters. Whereas dolphins use echolocation under such conditions, pinnipeds apparently lack this sensory ability. For seals hunting in the dark, one source of sensory information may consist of fish-generated water movements, which seals can detect with their highly sensitive whiskers. Water movements in the wake of fishes persist for several minutes. Here we show that blindfolded seals can use their whiskers to detect and accurately follow hydrodynamic trails generated by a miniature submarine. This shows that hydrodynamic information can be used for long-distance prey location.

 

16. Galaxy Formation: Are We There Yet?, arXiv/Science

Excerpts: The formation of the large-scale structure of the universe as revealed by observations of luminous ancient galaxies depends on the nature of dark matter. After the Big Bang, it is thought that dark matter started to clump together into halos and that the halos eventually merged to form galaxies. Dark matter can be cold or hot, and these two types lead to different scenarios for galaxy evolution. Although there is a growing preference for cold dark matter because it is consistent with recent observations of the background radiation in the universe (produced before galaxies formed), cold dark matter confounds galaxy formation by removing angular momentum from a protogalaxy during the halo-merging process. Thacker and Couch have developed a smoothed particle hydrodynamic simulation of galaxy formation that keeps the rotating gaseous disk of the protogalaxy from losing too much of its angular momentum. They tracked the evolution of tens of thousands of interacting dark matter, gas, and star particles during condensation (gravitational collapse). A gaseous high-density disk formed first, and then star formation began; later, stellar explosions (supernovae) heated the gas, which rose into the halo, but then returned to the disk, adding energy back to the system. It is this supernova energy feedback that allowed the disk to maintain its angular momentum long enough to form a simulated galaxy with properties similar to those of observed galaxies. Thus, the Big Bang and present-day galaxies can be connected through cold dark matter, and astrophysicists may be getting closer to a unified model of the evolution of the universe. -- LR Astrophys. J., in press (astro-ph/0106060).

 

17. Short-Term Synaptic Plasticity As A Temporal Filter, Trends in Neurosciences

Abstract: Synaptic efficacy can increase (synaptic facilitation) or decrease (synaptic depression) markedly within milliseconds after the onset of specific temporal patterns of activity. Recent evidence suggests that short-term synaptic depression contributes to low-pass temporal filtering, and can account for a well-known paradox – many low-pass neurons respond vigorously to transients and the onsets of high temporal-frequency stimuli. The use of depression for low-pass filtering, however, is itself a paradox; depression induced by ongoing high-temporal frequency stimuli could preclude desired responses to low-temporal frequency information. This problem can be circumvented, however, by activation of short-term synaptic facilitation that maintains responses to low-temporal frequency information. Such short-term plasticity might also contribute to spatio–temporal processing.

 

18. Sensing Seizure Activity Earlier, Trends In Neurosciences

Excerpt: Epilepsy patients often have an indescribable sense of when a seizure is on its way, and now doctors at the University of Pennsylvania have uncovered a way to predict its onset earlier and more quantitatively. By monitoring temporal lobe activity in non-medicated patients awaiting surgery and utilizing quantitative computer analysis of EEG recordings to extract features not obvious to the human eye, scientists have found that the energy of the EEG signal accumulates slowly but consistently up until the seizure onset. Furthermore, abrupt increases in accumulated energy occurs in the last hour before seizure onset, and determination of an impending seizure can be made with almost 90% accuracy, almost 20 minutes before seizure onset. These findings, published in the April issue of Neuron, open up the therapeutic window to include treatments that will short-circuit preconvulsant changes and prevent maturation into full clinical seizures

 

19. From Intelligent Networks to Global Brains, Conference WebCast

Back in 1994 the Internet growth-rates were extrapolated to match the total world population by the year 2001. Today we can see that even that wild speculation was not too far off in historical time-scales. When we published our first paper with the topic of a "Global Brain" in that year, it was not taken very seriously. Today it becomes more evident that there are a number of parallels between biological brains and emerging structures on the Internet. These can be seen as mere "metaphors" or as expressions of universal classes of behavior of complex systems that reach a certain degree of connectivity that new forms of self-organized behavior can emerge. One of those bifurcation parameters appears to be the characteristic time-scales of the system. In our conference presentation we propose to view conferences as "binding events" similar to the cognitive binding events that are associated with synchronous gamma activity of neuronal cell assemblies in human brains.

It seems natural that conferences in the third millennium will have virtual component with global, (quasi) real-time Internet participation. This concept was illustrated with the help of a demonstration experiment where all presentations were up-loaded and viewed by at least one remote participant who in return gave a short presentation on his views with the help of a digital video clip in combination with electronic presentation slides. We want to stress that this webcasting experiment (sponsored by Complexity Digest) could be performed with minimal technical staff and interference with the on-site conference activity. We expect that similar web-cast procedures will become standard especially in small, technical meetings in the future.

 

20. Links & Snippets

20.1 Other Papers
  1. Multiphoton-evoked color change of DsRed as an optical highlighter for cellular and subcellular labeling, Nature Biotech, Jonathan S. Marchant, Grace E. Stutzmann, Malcolm A. Leissring, Frank M. LaFerla. Ian Parker, Nature Biotech 19, n7, 645-649 (July 2001)
  2. In vitro selection of nucleoprotein enzymes, Nature Biotech, Michael P. Robertson & Andrew D. Ellington, Nature Biotech 19, n7, 650-655 (July 2001 )
  3. Sequence-Specific Detection Of Individual DNA Strands Using Engineered Nanopores, Stefan Howorka, Stephen Cheley, Hagan Bayley, Nature Biotech 19, N7, 636 - 639 (July 2001)
  4. Biosphere 2 Redux: Columbia's Western Campus Takes On Global Warming, Steve Bunk, The Scientist 15[14]:1, 01/07/09
  5. The Quest for Perfect Timing, Karen Young Kreeger, The Scientist 15[14]:16, 01/07/09
  6. Quantum-Dot-Tagged Microbeads For Multiplexed Optical Coding Of Biomolecules, Mingyong Han, Xiaohu Gao, Jack Z. Su, Shuming Nie, Nature Biotech 19, n7, 631 -635 (July 2001 )
  7. Red Light In The Night Sky As Mars Passes 'Close' To Earth, David Perlman, The San Francisco Chronicle, 6/12/01
  8. Antibiotics Shown To Fight Off Lyme Disease, Daniel Q. Haney, The Associated Press, 6/12/01
  9. Change Of Expression: For Proteomics Predictions, Mrna Transcripts Won't Do, Steve Bunk, The Scientist 15[14]:17, 01/07/09
  10. History-Friendly Models: An Overview Of The Case Of The Computer Industry, Franco Malerba, Richard Nelson, Luigi Orsenigo and Sidney Winter, JASSS, 4 (3).
  11. Simulating the Evolution of Localised Industrial Clusters - An Identification of the Basic Mechanisms, Thomas Brenner, JASSS, 4 (3).
  12. Regional Climate Impacts of the Northern Hemisphere Annular Mode, David W. J. Thompson and John M. Wallace, Science 2001 293:85

     

20.2 Announcements:

20.2.1 Complexity Digest Site Design Competition!
We have had essentially the same site layout since November 1999. And it seems to work. But in the interest of embracing change and evolution, we want to consider modifications or a compete redesign. The people who have the most to gain from a redesign are the ComDig readers. And, given the experience of the community we served, you also have the most to offer.

To that end, we propose to run a design competition during the summer accepting entries of suggested layouts, structural ideas and anything that you think we should develop. The successful entry will have a monetary reward, offer to be hired to complete the details and the satisfaction of seeing the work implemented.

Anyone, anywhere, any age is welcome. Submissions can be sent to: editor@comdig.org

  

20.2.2 Other Announcements:

Complexity Digest is an independent publication available to organizations that may wish to repost ComDig to their own mailing lists. ComDig is published by Dean LeBaron and edited by Gottfried J. Mayer. For individual free e-mail subscriptions send requests to: subscriptions@comdig.org.