Madison Chaos and Complex Systems Seminar

Fall 2007 Seminars

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

Short List


September 4, 2007

On the complexity of the human genome: new insights from the ENCODE project

Colin Dewey, UW Department of Biostatistics

It has been six years since the human genome was first sequenced, yet we are still in the early stages of determining the biological role of each of its roughly three billion nucleotides. The pilot phase of the Encyclopedia of DNA Elements (ENCODE) project, a large international effort to construct a catalog of all functional elements in the human genome, has recently concluded and revealed that genomic biology is more complex than previously thought. In this talk, I will report on the major findings of the ENCODE project thus far and present an up-to-date picture of how the genome functions. I will argue that people need to stop the liberal use of the phrase “junk DNA,” as the majority of the genome is at least transcribed into RNA. The fundamental tenets of comparative genomics will also be challenged with the project’s finding that the correlation between evolutionary constraint and function is not so strong. The human genome is looking more and more like an incredibly complex and random system, our understanding of which will require many more years of challenging research.

September 11, 2007

Making order in the market

Alfonso Morales, UW Department of Sociology, Urban and Regional Planning

In this talk, I will discuss how merchants at Maxwell Street Market created social order in the absence of workable legal expectations. Originally vending space, the heart of social order in this Market, was allocated by a Market Master. In 1973 the last Master died and was not replaced. Instead the City of Chicago imposed unworkable ordinances and temporarily the Market disintegrated into the stereotypical street market, a lawless, chaotic, and dangerous place. But, to the surprise of many the heterogeneous merchant population swiftly brought order by creating stable, flexible and durable mechanisms for allocating vending spaces. I will describe the remarkably stable and flexible methods of allocating vending space that evolved in the absence of the leviathan, City government.

September 18, 2007

Chaos, Schrodinger's Cat, and the Uncertainty principle engage because they are narratives, and that's how humans think

Tim Allen, UW Department of Botany

Chaos theory has a surprising following (e.g. in Jurassic Park). Not as big in popular culture, but still iconic, are the uncertainty principle, and Schrodinger's cat. All three fit easily into the narrative posture. Models must be internally consistent but narratives do not. What makes us humans so distinctive is the way we can jump from continuous to discrete and from reversible to irreversible in all combinations without losing coherence. We tell stories to map the impossible into a context that feels right. Representational models fix to a point and give the state. Experimental analogues map to 1st derivatives and are compressions. 2nd derivatives indicate the interaction with the context. Narratives tell only of what matters, and so are representations of compressions in a context. So it follows that attractors are the narratives of the observable. For a chaotic strange attractor, the story never ends, but we soon recognize what it is.

September 25, 2007

Global climate change: Current scientific views

John Young, UW Department of Atmospheric and Oceanic Sciences

Climate change science has been growing rapidly in sophistication and conclusiveness. This talk will focus on highlights of the current scientific evidence for human-induced climate change, the understanding of that change, and predicted scenarios of future change. The material is based primarily upon six years of international efforts summarized in the 2007 report of the IPCC (Intergovernmental Panel on Climate Change).

Future directions will increasingly include many new dimensions: applied and interdisciplinary studies addressing regional climate change, its local impacts on human activity, assessment of vulnerability, adaptation and mitigation strategies. A variety of University of Wisconsin researchers will collaborate in these efforts in the coming decades. Stay tuned. 

October 2, 2007

Language development in children and adolescents with Down syndrome

Robin Chapman, UW Department of Communicative Disorders

Research on language development in individuals with developmental disabilities can illuminate fundamental issues in our theories of language development. Is language acquisition modular or interactive? Are there critical periods for the acquisition of syntax? Our work shows that a specific pattern of language development can be found in children with Down syndrome, that individual variation is traceable to general learning and short-term memory mechanisms, and that language comprehension and production diverge in ways consistent with interactive, emergentist theories of language acquisition and continued language learning of complex syntax in adolescence. Factors improving fast mapping of new vocabulary and storytelling are also reviewed.

This talk is available as a PowerPoint presentation.

October 9, 2007

Low dose effects of pesticide mixtures on neurological, endocrine, immune function and developmental processes (not hormesis).

Warren Porter, UW Department of Zoology 

Endocrinologists in the 1960s knew that over narrow parts per billion and parts per trillion ranges of concentration hormones could have potent effects on the body. Outside that range there is typically no effect. Hormones communicate with the nervous system and the immune system in at least 50 different ways.  Thus, agents in the environment that impact any one of those three systems are likely to impact the other two.  I will describe data showing how current exposure levels may be impacting animal and human learning abilities, birth defects, endocrine and immune functions.  These impacts can come from environmental contaminants introduced into our waters and foodstuffs at environmentally relevant concentrations.

October 16, 2007

The temporal lobe push theory of artistic zeal and religious experience

Russell Gardner, Jr., UW Department of Psychiatry

Temporal lobe epilepsy has been diagnosed in many artists and religious figures. The interictal characteristics of more usual such patients often include such features as religiosity (with frequent experience of religious awe) and hypergraphia (incessant writing with pleasure in the act of doing so). Some artists exhibit variants, for example, Van Gogh. Triggering of manic episodes can occur with temporal lobe disturbances. The temporal lobe push theory hinges on the idea that people without seizures may nonetheless possess non-clinical variations of these attributes. This does not "reduce" artistic and religious experience to temporal lobe pathology but rather to suggest that normal variants of activity in the medial temporal lobe may provide an alphabet to complex human experience. As one non-epileptic artist suggested hearing these ideas, "Oh, I guess I have pushy temporal lobes!"

October 23, 2007

Research organizations, major discoveries, and the performance of the American system of science
Rogers Hollingsworth, UW Departments of History and Sociology
The lecture will present three interrelated themes: (1) It will discuss the characteristics of research organizations and their laboratories as well as the traits of individual scientists which are associated with the making of major scientific discoveries. (2) The lecture will emphasize that there are sharply decreasing returns to the investments in science and technology relative to the making of major discoveries. (3) The lecture will conclude with several suggestions for improving the conditions for the making of fundamental discoveries in American society.
The data set for the lecture involves many years of research about more than 750 research organizations in Britain, France, Germany, and the United States; and approximately 2100 laboratories. It is based on an analysis of 291 major discoveries; in-depth interviews with more than 560 scientists, administrators, and officers of major funding agencies on both sides of the Atlantic; and archival research. The research focuses on the characteristics of research organizations and laboratories where major discoveries occur and do not occur.

October 30, 2007

The challenges of stabilizing photosynthetic reactions

Tom Sharkey, UW Department of Botany

Photosynthesis is the source of essentially all metabolic energy used by living organisms. A number of factors make control of photosynthetic reactions particularly challenging. In human metabolism, the input of energy is highly controlled (consider the controls on the supply of glucose in the blood). Similarly, the environment of the metabolic reactions is strictly controlled (consider the narrow range of temperature over which human metabolic reactions occur). Photosynthesis happens in leaves, which are optimized for solar collection, leaving them with little capacity to buffer changes in inputs or in the environment in which the metabolism occurs. Intuitive examples include sunflecks, which can occur in the understory of a forest or on a partly cloudy day. The energy input (sunlight) varies rapidly by several orders of magnitude dozens or even hundreds of times per day. The environment can also change, with leaf temperature changing by over 10°C with a characteristic time constant of 20 seconds. Photosynthetic metabolic reactions are essentially unbuffered. Human muscles have enough of the energy molecule ATP to last just 20 seconds, but a photosynthesizing leaf has only enough for 100 milliseconds. Other metabolites turn over even faster. On top of this, photosynthesis control usually exists in one of two states corresponding roughly (but not precisely) to the concept of light versus dark reactions. As inputs and environment change, photosynthesis will flip between these two control states with almost no intermediate, shared control state. These challenges are met with a large number of control mechanisms. However, the metabolic control signals most often considered, changes in metabolite cascading through a pathway, seems to play at most a minor role. The major components of photosynthetic metabolism have mechanisms for rapid disengagement so that all components can safely go at the rate of the slowest component. The result is rapid adjustment of photosynthesis to changing conditions with just one, relatively rare, state being prone to oscillations.

November 6, 2007

Age and sex effects on human mutation rates: An old problem with a curious new wrinkle

Jim Crow, UW Department of Genetics

It has been known for decades that the human mutation rate is higher in males than females and increases with paternal age. This is readily explained by the greater number of cell divisions ancestral to a sperm than to an egg and the increased number of divisions if the male is old. This is true for base-substitution mutations, but not for small insertions and deletions (indels), which are essentially independent of age and sex. The relation between sex and age therefore differs for different mutations, depending on the size of the indel component.

Three loci (and probably more) produce mutations that are almost entirely paternal and with a sharp age increase. I'll discuss evidence for a quite different, and surprising explanation that may have a broader significance.

Finally I hope to say a bit about the greater accumulation of harmful mutations under the relaxed selection in societies with a high living standard. Is it something to worry about?

November 13, 2007

Game theory: Strategy, communication and belief

Moe Hirsch, UW Department of Mathematics

In an infinitely repeated game, each player seeks to maximize her long-term  average payoff, basing her strategy on on her beliefs, which evolve as the game is repeated, about opponents' payoffs, desires and strategies. Steve Smale devised a strategy for repeated Prisoner's Dilemma (or "Arms Race") which, if adopted by one player, will induce rational, non-greedy opponents to play strategies that achieve long-run mutual satisfaction. In many games a very different probabilistic strategy called "fictitious play" leads to ultimate convergence to a Nash equilibrium (undesirable in PD), even though players are acting on false beliefs (which in the long run become true). I will try to present these results with a minimum of technicalities.

November 20, 2007

The dynamic and multi-scale diffuse interstellar medium in the Galaxy

Snezana Stanimirovic, UW Department of Astronomy

 The interstellar medium (ISM) is the matter which occupies the enormous volume between stars. It consists mainly of gas and dust particles. At a scientific symposium in 1977, astrophysicist George Herbig said: "Let me say at first, rather naively, how struck I am by the delicate symbiosis that exists between the stars and the interstellar medium, how each is nourished by the other, and how the Galaxy as we know is entirely a consequence of that balance and interplay". It is this fascinating interplay between stars and the ISM that also provides constant energy input, making the ISM highly structured and dynamic.

The interstellar gas in the ISM possesses an extremely wide range of physical properties, and is versatile in 'structures' over a wide range of spatial scales. By imaging the 21-cm emission line of neutral hydrogen with radio telescopes we can study the inventory and properties of the diffuse ISM. Recent studies are revealing an astonishing inhomogeneity of the ISM, with many levels of hierarchy, a picture very different from the traditional two-level hierarchical system consisting of clouds uniformly dispersed in the intercloud medium.

In this talk, I will summarize the basic properties of the ISM and attempt to explore what can be learnt if we treat the ISM as a complex system.

November 27, 2007

Protein biotechnology; The problem of refolding proteins

Richard Burgess, UW Department of Oncology

Modern molecular biology and genetic engineering has given us the ability with relatively ease to clone any gene from any organism and to design a recombinant bacterial strain that can be used to produce in unlimited quantities the protein corresponding to that gene. Such proteins (often enzymes) can be used in basic research, as ways of treating human disease, and in industrial processes. However, when one produces a large amount of a given protein in a bacterial host, it is very often found that the protein is insoluble and inactive. In theory, one can isolate this insoluble protein, solubilize it in a chemical denaturing agent that unfolds the protein, and then remove the denaturant, allowing the protein to refold into its native, active form. It is thought that the amino acid sequence of the protein determines the most stable refolding state. However, a major problem exists in finding the optimal conditions to allow the protein to refold efficiently. My lab has developed methods to carry out this refolding with a high degree of success. I will discuss why producing proteins is important, the nature of the refolding problem (the nearly infinite possible ways a protein can fold) and how we have at least partially solved the problem.

December 4, 2007

Learning conceptual representations from perceptual inputs

Tim Rogers, UW Department of Psychology

Over the first year of life, infants gain conceptual skills that allow them to construe semantically related items as similar, even when they have few if any directly-perceived attributes in common. Moreover, this skill first encompasses quite broad semantic categories, and only later extends to more subtle distinctions, when conceptual and perceptual similarity relations do not coincide. I will describe a simple computational mechanism that illustrates how such conceptual change is possible. In agreement with many others, I will suggest that early-developing conceptual representations are organized with respect to certain especially useful or salient properties, regardless of whether such properties can be directly observed. In contrast to other views, I will argue that in many cases this salience may itself be acquired, through a domain-general learning mechanism that is sensitive to the high-order coherent covariation of directly-observed stimulus properties across a breadth of experience. To support this argument I will describe simulations with a simple parallel-distributed-processing (PDP) model of semantic memory. When trained with backpropagation to complete queries about the properties of different objects, the model’s internal representations show a nonlinear, coarse-to-fine pattern of differentiation. As a consequence, different sets of properties come to be especially “salient” to the model at different points during development—so that objects sharing such properties are represented as similar even if they differ in many other respects. These dynamics provide a basis for understanding conceptual change generally, and more specifically, for understanding developmental change in the meanings of words.

December 11, 2007

The Internet threat landscape and what we can do about it

Paul Barford, UW Department of Computer Science

Attacks and intrusions in the Internet are a significant problem, causing damages estimated in the billions of dollars.  Furthermore, the emerging underground economy based on malicious activity is fueling increased sophistication and organization among malicious parties.  In this talk, I will describe the basic mechanisms for cyber attacks and how they are used in viruses, worms, pfishing, spyware and the latest and most serious threat -- distributed botnets.  I will also describe the basic mechanisms for cyber security aimed at reducing the attack surface of cyber infrastructure and providing comprehensive information about malicious activity.  Unfortunately, the lack of intrinsic security mechanisms and the inherent imbalance between the objectives of attackers and defenders places defenders at a significant disadvantage.  However, there is hope that new security technologies, including those developed at UW-Madison will significantly narrow this gap.