Madison Chaos and Complex Systems Seminar

Spring 2008 Seminars

All seminars are Tuesday at 12:05 pm in 4274 Chamberlin except as noted.

Short List

Join us for lunch during the summer on the Union Terrace at noon each Tuesday, starting May 13th!

January 22, 2008

Sleep need and synaptic homeostasis

Chiara Cirelli, UW Department of Psychiatry

Any proposal about the function of sleep should be able to provide a convincing explanation of why the proposed function can only be fulfilled by sleep and not by quiet wakefulness. Otherwise, why would sleep—a potentially dangerous behavior characterized by loss of contact with the environment—be so universal, and why would sleep pressure be so overwhelming? I will discuss a novel hypothesis—the synaptic homeostasis hypothesis (SHY)—which claims that sleep plays a role in the regulation of synaptic weight in the brain. SHY states that during wakefulness many brain circuits undergo synaptic potentiation, resulting in a net increase in the strength of synaptic connections between neurons, and that the homeostatic increase in slow wave activity (SWA) during the subsequent sleep is a direct reflection of this synaptic potentiation. SHY also predicts that SWA mediates synaptic downscaling, which is tied to several beneficial effects of sleep, including performance enhancement. In summary, according to this hypothesis, sleep is the price we have to pay for plasticity, and its goal is the homeostatic regulation of the total synaptic weight impinging on neurons. I will discuss evidence supporting the hypothesis, its implications, as well as current limitations and unresolved issues.

January 29, 2008

Cluster optimization in protein docking

Julie Mitchell, UW Department of Mathematics

Recent progress in obtaining docked protein complexes will be discussed. The combination of exhaustive search, clustering and localized global optimization can reliably find energy minima to highly nonconvex biomolecular energy functions.  Using an energy function that adds desolvation and screened electrostatics to classical molecular mechanics potentials, the global minimum is found very near to the observed native state.  This is demonstrated across a large number of benchmark examples.

February 5, 2008

Seeing with the mind as well as the eye

Bob Greenler, UW-Milwaukee, Department of Physicsd

This presentation is an anecdotal treatment about ways of seeing the world, ways of looking beyond the visual scene to see what is behind it. It is not based on any scientific paradigm and I make no claim for either great insight or originality. It seems to me, however, to touch on a part of the creative process for a scientist.

One of the ways of seeing that I will discuss is that of looking for interesting questions suggested by the visual scene. Since the questions come out of the background peculiar to the viewer, my examples will necessarily be personal. But I hope to illustrate some ways of seeing the world around us that others can adapt to their own particular backgrounds, and, perhaps cultivate.

February 12, 2008

Electoral dynamics in the 2008 presidential primaries

Charles Franklin, UW Department of Political Science

The dynamics of electoral support are at least colloquially chaotic and certainly complex. Rather than follow standard autoregressive  processes, or continuous dynamics, electoral events are often punctuated by discontinuous shifts. Also, subsequent events are  strongly influenced by prior ones. We explore these dynamics with data from hundreds of polls taken during the 2008 nominating contests in both parties.

February 19, 2008

Acceleration of human evolution: interactions of genes with culture and geography

John Hawks, UW Department of Anthropology

Recent surveys of the human genome have shown that thousands of recent mutations have strong advantages and have increased greatly in frequency since their origins during the last 40,000 years. The rate of such changes appears to have increased by a factor of 100 times over the rate that characterized most of human evolution. Natural selection, as Darwin recognized, is fundamentally a demographic phenomenon: individuals with one allele have a higher intrinsic rate of growth than those having alternative alleles, resulting in the replacement of such alleles over time. When this process occurs across a population spread over geographic space, a wave of population growth and migration tends to disperse a selected allele outward from its source. This process is well understood when modeled for a single gene. However, the introduction of many (perhaps thousands) of simultaneously selected alleles may lead interactions between genes to outweigh the fitness consequences of individual genes.

February 26, 2008

Generalising the Reynolds number from turbulence to sand-piles (S.O.C.) to ecosystems

George Rowlands, University of Warwick

Some concepts such as scaling and universality common in the study of fluid turbulence are applied to self-organized criticality and simple predator-prey models more common in the biological field. The common thread is a generalisation of the Reynolds number.

March 4, 2008

How does your garden grow: the complex nature of plant growth below ground

Simon Gilroy, UW Department of Botany

Nutrient and water uptake by the root system is a critical component of plant productivity and plant root systems have evolved to be extremely effective at exploring and exploiting the soil. However, we still have a remarkably poor understanding of the dynamics of the development of the root systems and how, at a cellular and molecular level, control systems operate to precisely regulate the direction and extent of growth. Similarly, we are now only just beginning to appreciate how these features of growth are integrated into the role of the root system in nutrient and water uptake. Our research has revealed a highly dynamic and complex regulatory network involving rapid, fluctuating patterns of acidity, chemical oxidation and classic signaling molecules such as the calcium ion that are integrated to modulate root growth. I will discuss how these patterns play out with time courses of a few seconds, bringing the regulation of plant growth into the temporal realm we usually associate with animal responses.

March 11, 2008

Technological change and the global energy system

Greg Nemet, UW La Follette School of Public Affairs

Meaningfully addressing the large scale challenges associated with the way we use and consume energy -- including security of supply, air pollution, and climate change -- will require transformation of the global energy system.  Designing policies to encourage this change in societally beneficial directions is plagued by an array of uncertainties.  In particular, attempts to model optimal policy design reach vastly different normative conclusions depending on assumptions about the expected rate of technical change and the extent to which government actions can affect it.  Empirical work on parameterizing technical change is plagued by concerns about the inherent stochasticity of the process of innovation and the idiosyncrasies of individual technologies.  Still, the search for useful models of technological change continues. This talk presents recent efforts to model the process of technological change in low-carbon energy technologies.

March 25, 2008

Learning is a dangerous thing: connectivity, temporal recurrences, and epileptogenesis

David Hsu, UW Department of Neurology

The ability of the brain to absorb and incorporate within itself new ideas implies that it is a metastable system. It must continually change and yet not devolve into randomness. How does it do this, and what are the consequences? Brain activity can be represented in terms of a large collection of excitable bodies that possess both spontaneous activity and that can stimulate other bodies to become excited. I discuss a simple computer model of such a system and study (1) what is necessary for such a system to learn, and (2) what is necessary for it to maintain itself in a state capable of further learning. It turns out that the highest performing brain models that are able to maintain stable learning also show self-organized criticality. Unfortunately, the homeostatic constraints that maintain optimal brain performance also predispose the brain toward neurological disease. The relationship to epilepsy is presented, and an approach to its cure is proposed.

April 1, 2008

Metabolomics of human embryonic stem cells: elucidating biochemical pathways and biomarkers of neurodevelopmetal disorders.

Gabriela Gebrin Cezar, UW Department of Animal Science

There are few sentinel biomarkers for early diagnosis of neurodevelopmental disorders. The convergence of human embryonic stem cell (hESC) technology to metabolomics enables the discovery of small molecules which can unravel biochemical pathways associated with neurodevelopmental disorders while serving as translational biomarkers for disease diagnosis. Our laboratory seeks to identify biochemical pathways that are altered by known disruptors of human development (valproate, alcohol), using metabolomics of hESC and neural precursors derived from hESC. Prenatal exposure to the anti-epileptic valproate is associated with the onset of autism. This approach offers a unique advantage over other models since it employs cells derived directly from human embryos. Moreover, in addition to elucidating mechanisms of anti-epileptic and alcohol activity during early human development, the biomarkers discovered in hESC are applicable to preclinical safety evaluation of pharmaceutical compounds on human development. Unfortunately, current animal models can only predict human developmental toxicity with ~50% accuracy.

April 8, 2008

Dynamics on spatially symmetric networks

Sean Cornelius, UW Department of Physics

Self-organization and spontaneous symmetry breaking are features of many physical and social systems. This talk considers these phenomena as they arise in artificial neural networks. A simple nonlinear model of neural feedback is considered in which a large number of identical neurons are arranged in a one-dimensional lattice. Chaos is rare in these networks, and limit cycle dynamics are predominant. This contradicts our empirical understanding of "generic"  high-dimensional systems, where chaos is the rule, not the exception. The spectrum of Lyapunov exponents is used as the primary metric of chaoticity and attractor geometry. Issues of sparsity and distribution of the synaptic couplings in chaotic networks are discussed, as well as applications.

April 15, 2008

Chaotic dynamics on large networks

Clint Sprott, UW Department of Physics

Many systems in nature are governed by a large number of agents that interact nonlinearly through complex feedback loops. When the networks are sufficiently large and interconnected, they typically exhibit self-organization and chaos. This talk describes the results of computer simulations of such large networks and shows the conditions under which chaos can be expected for an unweighted network of ordinary differential equations with sigmoidal nonlinearities and unit coupling. The largest Lyapunov exponent is used as the signature and measure of chaos, and the study includes the effects of damping, asymmetries in the distribution of coupling strengths, network symmetry, and sparseness of connections. Minimum conditions and optimal network architectures are determined for the existence of chaos. The results have implications to the design of social and other networks in the real world in which weak chaos is desired or as a way of understanding why certain networks might exist on “the edge of chaos.”

This talk is available in PowerPoint format at

April 22, 2008

A Complex Systems Engineering approach to software development in large organizations

Jacob Jesson, Shared Context Inc.

The codification of business and governmental processes in software systems means that an organization’s ability to adapt to its environment is highly dependent on its ability to effectively adapt its software systems.  As software systems grow in size and become  more interconnected, effective adaptation becomes increasingly difficult. Fast cycle iterative development methodologies such as Agile and architectures such as Service Oriented Architecture (SOA) are the most visible attempts to address the issue.  A small but growing alternative is Complex Systems Engineering (CxSE), also termed Enlightened Evolutionary Engineering (e3).  CxSE as a formal discipline is in its infancy but variations are already proving their worth in organizations such as Google.

I will describe the problematic aspects of systems development in large organizations.  I will then discuss CxSE as a discipline and potential option.  I will give special attention to the not-so-simple issue of how an organization can migrate from a control focused approach to a more exploratory CxSE approach.

April 29, 2008

Furan-based components from biomass-derived carbohydrates for the production of fuels and chemical intermediates
Yuriy Román-Leshkov, UW Department of Chemical and Biological Engineering

A major scientific interest in developing new technologies for the conversion of renewable resources into sustainable energy and chemical materials exists due to environmental, political, and economic concerns associated with our dependence on petroleum. In this respect, biomass plays an important role, as it is currently the only renewable source of carbon with the potential to supply a significant fraction of the energy and chemical intermediates (e.g. alcohols, aldehydes, ketones, carboxylic acids, esters) needed for the world economy. Specifically, furan derivatives such as 5-hydroxymethylfurfural (HMF) and furfural, obtained by the acid-catalyzed dehydration of carbohydrates, have been described as key substances that bridge carbohydrate chemistry and petroleum-based industrial chemistry because of the wide range of chemical intermediates and end-products that can be produced from these compounds. We present a novel catalytic strategy for the production of HMF in high yields (>80%) from concentrated fructose solutions (30-50 wt%) in a biphasic reactor containing aqueous and organic phases modified with chemical promoters. In addition, we also present a catalytic strategy for the conversion of HMF into 2,5-dimethylfuran for use as a next-generation biofuel. These breakthroughs provide new avenues for the development of cost-effective routes for the synthesis of disubstituted furan derivatives from renewable resources for the production fuels and chemicals.

May 6, 2008

Addressing complex challenges by engaging groups

Darin Harris and Harry Webne-Behrman, UW Office of Quality Improvement

We often hear about the power of group collaboration to answer the challenges of our age. However, addressing problems that cross disciplines, scales, cultures, and individual modes of learning can be very difficult to manage in practice. This presentation will outline a comprehensive approach that can maximize the capacity of groups to tackle tough issues. Four perspectives (called quadrants) and a number of competencies (skills) will be described. Participants will also learn how groups naturally develop through stages and how to encourage engagement that can lead to successful collaboration. Focus will be placed on creating conditions for synergies among group members and recognizing dynamical interactions to build effective solutions.