Complexity Digest 2001.31

30-Jul-2001

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Content

  1. Antibacterial Hits A Punch, Nature
    1. Antibacterial Agents Based On The Cyclic D,L- a-peptide Architecture, Nature
    2. Rings Of Destruction, Nature
  2. How Technology Spreads, NBER
  3. Proteomics Takes a Leap, Science
    1. Global Analysis of Protein Activities Using Proteome Chips, Science
  4. Cardiac Interbeat Interval Dynamics From Childhood to Senescence, Circulation
  5. Altered Complexity and Correlation Properties of R-R Interval Dynamics, Circulation
  6. A Model For Control Of Chagas Disease, Science
  7. Evolutionary Self-Organization Of Cell-Free Genetic Coding, Science
  8. The Complexity of Clickomania, arXiv
  9. Scientists Are Starting To Add Letters To Life's Alphabet, NYTimes
  10. Targeting Malaria - The Life Cycle Of A Malaria Parasite Is Complicated, BMN
  11. Symbiosis: Bugs Within Bugs Within Mealybugs, Nature
    1. Mealybug b-Proteobacterial Endosymbionts Contain g-Proteobacterial Symbionts, Nature
  12. Some Humpbacks Not Back: Whaling's Past Still Scars Recovered Humpback Populations, Nature S.U.
  13. Ancient Fishing Linked To Modern Crisis, CNN
    1. Historical Overfishing And The Recent Collapse Of Coastal Ecosystems, Science
  14. Segmentation Gets Pieced Together, Science Now
  15. Noisy Clockwork: Time Series Analysis Of Population Fluctuations In Animals, Science
  16. Complex Species Interactions And The Dynamics Of Ecological Systems: Long-Term Experiments, Science
  17. Clock Synchronization: A Quantum GPS, Nature
    1. Entangled Light Could Help Make Time Travel, Nature Science Update
    2. Quantum-Enhanced Positioning And Clock Synchronization, Nature
  18. The Coming Superintelligence: Who Will Be In Control?, KurzweilAI.Net Newsletter
  19. Nonlinear Dynamics And Chaos In Agricultural Systems, Book Announcement
  20. Links & Snippets
    1. Announcements

  1. Antibacterial Hits A Punch, Nature Next Article Bookmark and Share

    Excerpts: Naturally alluring as potential alternatives to conventional antibiotics, peptides - molecules to combat bacterial infections - are produced by a wealth of plants and animals. But unlike antibiotics, peptides are large and don't get transported to the site of infection, making them all but useless as drugs.

    (…) the building blocks of peptides, which stack up to form tubes in bacterial cell walls. These "self-assembling peptide nanotubes" cleared infections of the antibiotic-resistant bug Staphylococcus aureus in mice, even when injected far from the site of infection.


    1. Antibacterial Agents Based On The Cyclic D,L- a-peptide Architecture, Nature Next Article Bookmark and Share

      Excerpt: The rapid emergence of bacterial infections that are resistant to many drugs underscores the need for new therapeutic agents. Here we report that six- and eight-residue cyclic D,L- -peptides act preferentially on Gram-positive and/or Gram-negative bacterial membranes compared to mammalian cells, increase membrane permeability, collapse transmembrane ion potentials, and cause rapid cell death. The effectiveness of this class of materials as selective antibacterial agents is highlighted by the high efficacy observed against lethal methicillin-resistant Staphylococcus aureus infections in mice.

    2. Rings Of Destruction, Nature Next Article Bookmark and Share

      Excerpts: Many organisms use natural peptides to ward off microbes, but it's proved hard to make similar molecules for medical use. A ring-shaped peptide that might puncture microbial membranes could be the way forward.

      It is known only too well that many infectious bacteria are becoming resistant to antibiotics1. Multidrug-resistant strains of Staphylococcus aureus, Pseudomonas aeruginosa and Enterococcus faecium, among others, are now commonly encountered in hospitals and nursing homes. There is an increasing need for new drugs to fight these microorganisms.


  2. How Technology Spreads, NBER Next Article Bookmark and Share

    Excerpts: "Computer adoption strongly depends on having high levels of education of the labor force."

    The adoption of new technology is essential to long-term macroeconomic growth. In general, rich countries are on the technology frontier and rely on research and development to achieve further improvements in technical efficiency. Low-income countries, in contrast, have the option of adopting technologies already developed elsewhere. Yet not much is known about the process by which new technologies spread from one country to the others.

    In "Cross-Country Technology Diffusion: The Case of Computers" , co-authors Francesco Caselli and Wilbur John Coleman II use cross-country panel data on computer imports from 1970-90 to analyze the determinants of technology diffusion.


  3. Proteomics Takes a Leap, Science Next Article Bookmark and Share

    Excerpts: In this era of high-speed biology, studying proteins can be maddeningly slow: Their complex chemistry and delicate 3D shapes make them hard to analyze. (…) researchers report creating a protein chip that can analyze 5800 yeast proteins all at once. Such chips could aid research--and clinical diagnostics--by quickly revealing the partners with which thousands of proteins interact.

    The new protein chip is a close cousin to DNA chips, postage-stamp-sized surfaces dotted with nucleic acid sequences that can track the activity of thousands of genes in a tissue at once.


    1. Global Analysis of Protein Activities Using Proteome Chips, Science Next Article Bookmark and Share

      Abstract: To facilitate studies of the yeast proteome, we have cloned 5800 open reading frames and overexpressed and purified their corresponding proteins. The proteins were printed onto slides at high spatial density to form a yeast proteome microarray and screened for their ability to interact with proteins and phospholipids. We identified many new calmodulin and phospholipid-interacting proteins; a common potential binding motif was identified for many of the calmodulin-binding proteins. Thus, microarrays of an entire eukaryotic proteome can be prepared and screened for diverse biochemical activities. They could also be used to screen protein-drug interactions and to detect posttranslational modifications.
      • Global Analysis of Protein Activities Using Proteome Chips, Heng Zhu, Metin Bilgin, Rhonda Bangham, David Hall, Antonio Casamayor, Paul Bertone, Ning Lan, Ronald Jansen, Scott Bidlingmaier, Thomas Houfek, Tom Mitchell, Perry Miller, Ralph A. Dean, Mark Gerstein, Michael Snyder, Science, Published online July 26 2001; 10.1126/science.1062191

  4. Cardiac Interbeat Interval Dynamics From Childhood to Senescence, Circulation Next Article Bookmark and Share

    Excerpt: New methods of R-R interval variability based on fractal scaling and nonlinear dynamics ("chaos theory") may give new insights into heart rate dynamics. The aims of this study were to (1) systematically characterize and quantify the effects of aging from early childhood to advanced age on 24-hour heart rate dynamics in healthy subjects; (2) compare age-related changes in conventional time- and frequency-domain measures with changes in newly derived measures based on fractal scaling and complexity (chaos) theory; and (3) further test the hypothesis that there is loss of complexity and altered fractal scaling of heart rate dynamics with advanced age.

  5. Altered Complexity and Correlation Properties of R-R Interval Dynamics, Circulation Next Article Bookmark and Share

    Excerpts: Trigger mechanisms for the onset of paroxysmal atrial fibrillation (AF) in patients without structural heart disease are not well established. New analysis methods of heart rate (HR) variability based on nonlinear system theory may reveal features and abnormalities in R-R interval behavior that are not detectable by traditional analysis methods. The purpose of this study was to reveal possible alterations in the dynamics of R-R intervals before the spontaneous onset of paroxysmal AF.(…)

    A decrease in the complexity of R-R intervals and altered fractal properties in short-term R-R interval dynamics precede the spontaneous onset of AF in patients with no structural heart disease.


  6. A Model For Control Of Chagas Disease, Science Next Article Bookmark and Share

    Summary: Chagas disease is a widespread, chronic, and ultimately fatal disease of the rural poor in Latin America that is (…) transmitted by blood-sucking triatomine bugs. It has long been suggested that improving the quality of housing could control this disease. Cohen and Gurtler (p. 694) have now mathematically modeled the complex set of variables that contribute to disease transmission within a household. They offer simple recommendations for exclusion of pets and structural improvement of sleeping areas that would virtually eliminate Chagas disease in human beings.

  7. Evolutionary Self-Organization Of Cell-Free Genetic Coding, Science Next Article Bookmark and Share

    Abstract: Genetic encoding provides a generic construction scheme for biomolecular functions. This paper addresses the key problem of coevolution and exploitation of the multiple components necessary to implement a replicable genetic encoding scheme. Extending earlier results on multicomponent replication, the necessity of spatial structure for the evolutionary stabilization of the genetic coding system is established. An individual-based stochastic model of interacting molecules in three-dimensional space is presented that allows the evolution of genetic coding to be analyzed explicitly. A massively parallel configurable computer (NGEN) is used to implement the model, on the time scale of millions of generations, directly in electronic hardware. The spatial correlations between components of the genetic coding system are analyzed and found to be essential for evolutionary stability.

  8. The Complexity of Clickomania, arXiv Next Article Bookmark and Share

    Abstract: We study a popular puzzle game known variously as Clickomania and Same Game. Basically, a rectangular grid of blocks is initially colored with some number of colors, and the player repeatedly removes a chosen connected monochromatic group of at least two square blocks, and any blocks above it fall down. We show that one-column puzzles can be solved, i.e., the maximum possible number of blocks can be removed, in linear time for two colors, and in polynomial time for an arbitrary number of colors. On the other hand, deciding whether a puzzle is solvable (all blocks can be removed) is NP-complete for two columns and five colors, or five columns and three colors.

  9. Scientists Are Starting To Add Letters To Life's Alphabet, NYTimes Next Article Bookmark and Share

    Excerpt: Scientists are taking the first steps toward creating alternative life forms - organisms that use a genetic code different from the one used by all other creatures on earth.

    Such organisms, bacteria to start with, would have novel chemical units in their DNA and synthetic building blocks in their proteins. Scientists hope that such organisms can be used to study biochemical processes in new ways and to produce new medical or electronic materials that cannot now be made by living things.

    Editor's Note: Early PCs used 8-bit words, today's fast multi-media computer achieve their performance to not only because of faster processors but also because the word length has been increased to 32 bits, some computers even 128 bits.

    Traditional life on this planet worked with the equivalent of 6-bit words (codons). What will be possible with a revision of the life-code that triple the number of admissible words by going from 4 to 6 DNA bases?


  10. Targeting Malaria - The Life Cycle Of A Malaria Parasite Is Complicated, BMN Next Article Bookmark and Share

    Excerpt: The Life Cycle Of A Malaria Parasite Is Complicated; it's often hidden from the human immune system. Nevertheless, researchers feel that a vaccine could be available in the next years.(...)

    Malaria strikes an estimated 500 million people a year, mostly in Africa and mostly women and young children. It kills nearly 3.5 million of its victims. Three stages characterize the symptoms of the disease: a "chill" stage, in which patients experience shaking chills, lasting from a few minutes to several hours; a "hot" stage, in which the patient's temperature rises to as high as 104° F; and a "sweating" stage, in which the fever subsides, but the patient experiences debilitating fatigue. If left untreated, this cycle returns every two or three days.

    The life cycles of the strains of plasmodia that cause malaria are complicated and render the plasmodia invisible to the human immune system for a large part of the cycle. This complicates the development of a vaccine and is one of the reasons that it cannot be approached in the same way as developing, say, a polio vaccine.


  11. Symbiosis: Bugs Within Bugs Within Mealybugs, Nature Next Article Bookmark and Share

    Summary: Symbiotic associations have spawned evolutionary innovations since events that led to the first multicellular organisms. In this issue van Dohlen et al. describe novel interaction within an insect, the first recorded case of modern bacteria living inside other bacteria. The 'host' bacterium is in turn an endosymbiont of a plant sap feeding mealybug. The association between the two species of bacteria within the mealybug may be compensatory, allowing lateral gene transfer and therefore a possible slowing down of genetic degradation as genes and gene products are more freely exchanged between species.


    1. Mealybug b-Proteobacterial Endosymbionts Contain g-Proteobacterial Symbionts, Nature Next Article Bookmark and Share

      Excerpts: Some insects have cultivated intimate relationships with mutualistic bacteria since their early evolutionary history. Most ancient 'primary' endosymbionts live within the cytoplasm of large, polyploid host cells of a specialized organ (bacteriome)1. Within their large, ovoid bacteriomes, mealybugs (Pseudococcidae) package the intracellular endosymbionts into 'mucus-filled' spheres, which surround the host cell nucleus and occupy most of the cytoplasm2. The genesis of symbiotic spheres has not been determined(…) This is the first report, to our knowledge, of an intracellular symbiosis involving two species of bacteria.


  12. Some Humpbacks Not Back: Whaling's Past Still Scars Recovered Humpback Populations, Nature S.U. Next Article Bookmark and Share

    Excerpt: Genetic profiles reveal that certain humpbacks stick together, almost like tribes, preferring discrete feeding grounds. Humpback calves follow their mothers from breeding grounds back to feeding grounds. (…).

    North Atlantic humpbacks are known to feed in specific areas: the gulf of Maine, Newfoundland and Labrador, Western Greenland, Iceland and Norway. It was thought these whales mixed freely in one large breeding area in the Caribbean but the new genetic data suggest that there could be at least one other winter breeding ground.


  13. Ancient Fishing Linked To Modern Crisis, CNN Next Article Bookmark and Share

    Excerpt: -- Ecological upheavals in coastal waters began thousands of years ago as primitive peoples massacred the denizens of the sea, leaving marine environments susceptible to the escalating pressures of contemporary times,(…).

    Examining ancient garbage mounds, sediment deposits and archeological records from four continents, scientists found that excessive hunting of sea mammals, turtles and fish upset delicate webs of life on a scale never before realized.

    The disruptions unleashed population explosions of opportunist species and lethal epidemics against less fortunate ones


    1. Historical Overfishing And The Recent Collapse Of Coastal Ecosystems, Science Next Article Bookmark and Share

      Excerpt: Ecological extinction caused by overfishing precedes all other pervasive human disturbance to coastal ecosystems (…). Paleoecological, archaeological, and historical data show that time lags of decades to centuries occurred between the onset of overfishing and consequent changes in ecological communities (…). Retrospective data not only help to clarify underlying causes and rates of ecological change, but they also demonstrate achievable goals for restoration and management of coastal ecosystems that could not even be contemplated based on the limited perspective of recent observations alone.
      • Historical Overfishing And The Recent Collapse Of Coastal Ecosystems, Jeremy B. C. Jackson, Michael X. Kirby, Wolfgang H. Berger, Karen A. Bjorndal, Louis W. Botsford, Bruce J. Bourque, Roger H. Bradbury, Richard Cooke, Jon Erlandson, James A. Estes, Terence P. Hughes, Susan Kidwell, Carina B. Lange, Hunter S. Lenihan, John M. Pandolfi, Charles, H. Peterson, Robert S. Steneck, Mia J. Tegner, Robert R. Warner, Science 2001 July 27; 293(5530): p. 629-637

  14. Segmentation Gets Pieced Together, Science Now Next Article Bookmark and Share

    Excerpts: Nature likes segmentation, the process of making repetitive embryonic units that serve as the building blocks of all insect bodies and those of many higher animals as well. (…)

    [Pourquié] showed that in vertebrates many of the genes involved in forming somites, the units that develop into the vertebrae and muscles of the torso, repeatedly cycle on and off. He suggested that a "segmentation clock" controls the timing of somite formation.


  15. Noisy Clockwork: Time Series Analysis Of Population Fluctuations In Animals, Science Next Article Bookmark and Share

    Excerpts: Both biotic interactions and abiotic random forcing are crucial influences on population dynamics. This frequently leads to roughly equal importance of deterministic and stochastic forces. The resulting tension between noise and determinism makes ecological dynamics unique (…). A range of dynamical components has been considered--density dependence, environmental and demographic stochasticity, and climatic forcing--as well as their often complex interactions. We discuss recent advances in understanding ecological dynamics and testing theory using long-term data and review how dynamical forces interact to generate some central field and laboratory time series.


  16. Complex Species Interactions And The Dynamics Of Ecological Systems: Long-Term Experiments, Science Next Article Bookmark and Share

    Excerpts: Research programs in U.S. desert shrubland and pinyon-juniper woodland have shown that (i) complex dynamics of species populations reflect interactions with other organisms and fluctuating climate; (ii) genotype x environment interactions affect responses of species to environmental change; (iii) herbivore-resistance traits of dominant plant species and impacts of "keystone" animal species cascade through the system to affect many organisms and ecosystem processes; and (iv) some environmental perturbations can cause wholesale reorganization of ecosystems because they exceed the ecological tolerances of dominant or keystone species(…).


  17. Clock Synchronization: A Quantum GPS, Nature Next Article Bookmark and Share

    Summary: Quantum mechanics may have the potential to produce a large increase in the accuracy of processes that rely on sending pulses of light from place to place and measuring their time of arrival. The accuracy of these procedures is limited by the available power and bandwidth, which can be overcome by the use of quantum entanglement and squeezing. Clock synchronization, geopositioning systems and radar ranging are amongst the applications that could benefit from the quantum approach.

    Editor's Note: MIT's "Meister Quantum Mechanic" Seth Lloyd, strikes again: After talking about laptop computer made out of black holes (who would ever want to put a black hole on one's lap?) he and his team now offer a whole collection of "q-appliances" (after "e" and "d", it seems we are ready for the "q-generation") such as a quantum-GPS (or QPS) for those of us who really need to know precisely where they are. "Minor" technical details still need to be worked out, for instance to make this idea really work one would need (a lot) more than two photons to tangle. His estimated speed-up for two entangled photon is only about 40%, that is if these two photons can be reliably detected over practical distances.

    One can envision Q-Meister Seth brooding over his next invention: "Hmmm, I wonder what entangled microwave photons would do to my frozen pizza…"


    1. Entangled Light Could Help Make Time Travel, Nature Science Update Next Article Bookmark and Share

      Excerpts: The use of photons whose frequencies are entangled means that photons in a laser pulse no longer arrive at a detector independently, Lloyd's team propose. If the frequency of one pulse depends on that of one of the others, travel times get bunched together, reducing uncertainty in timing.(…)

      At present, though, making more than two entangled photons is difficult.

      Eventually, the researchers hope, a host of high-precision quantum measurement technologies could arise, such as 'quantum radar' and 'quantum positioning systems' (QPS).


    2. Quantum-Enhanced Positioning And Clock Synchronization, Nature Next Article Bookmark and Share

      Excerpt: A wide variety of positioning and ranging procedures are based on repeatedly sending electromagnetic pulses through space and measuring their time of arrival. The accuracy of such procedures is classically limited by the available power and bandwidth. Quantum entanglement and squeezing have been exploited in the context of interferometry, frequency measurements, lithography and algorithms. Here we report that quantum entanglement and squeezing can also be employed to overcome the classical limits in procedures such as positioning systems, clock synchronization and ranging.

  18. The Coming Superintelligence: Who Will Be In Control?, KurzweilAI.Net Newsletter Next Article Bookmark and Share

    Excerpt: At some point in the next several decades, as machines become smarter than people, they'll take over the world. Or not. What if humans get augmented with smart biochips, wearables, and other enhancements, accessing massive knowledge bases ubiquitously and becoming supersmart cyborgs who stay in control by keeping machines specialized? Or what if people and machines converge into a mass-mind superintelligence?

    Panelists at the recent EXTRO-5 conference in San Jose thrashed out these and other mind-stretching scenarios in a session on "Convergent or Divergent Super-Intelligence?".

    Editor's Note: The anticipation of the emergence of human-computer networked and self-organized structures with new capabilities is formulated in several groups, coming from different perspectives but converging to similar structures. See for instance the recent workshop on the emergent Global Brain (ComDig WebCast.)


  19. Nonlinear Dynamics And Chaos In Agricultural Systems, Book Announcement Next Article Bookmark and Share

    Description: This book provides an introduction to the analysis of chaos and chaos theory as it relates to agricultural science. With clear explanations of chaos theory and principles, the first part of the book offers some basic facts, the fundamental terminology, and the concepts of deterministic chaos. The second part of this volume contains rich applications of the theory as applied to real agricultural systems. Applications include a wide area such as alternate bearing in tree crops, weed control and tillage, nonlinear vibrations in agricultural tractors, and piglet pricing analysis.

    Readers will find useful tools for calculating the order, rules and theory behind complex phenomena observed in arable land.

    Author's note: Agriculture is very complex and agricultural study must be interdisciplinary. Because of luck of common methodology over the fields, we have not had effective cooperation among research fields relating agriculture to deal with agricultural complexity. In my point of view, chaos theory, nonlinear dynamics and nonlinear time series analysis can be a candidate of common methodology for agricultural science.

    This book provides an introduction to the analysis of chaos and chaos theory as it relates to agricultural science. With clear explanations of chaos theory and principles, the first part of the book offers some basic facts, the fundamental terminology, and the concepts of deterministic chaos. The second part of this volume contains rich applications of the theory as applied to real agricultural systems. Applications include a wide area such as alternate bearing in tree crops, weed control and tillage, nonlinear vibrations in agricultural tractors, and piglet pricing analysis.


  20. Links & Snippets Next Article Bookmark and Share

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