Madison Chaos and Complex Systems Seminar

Fall 2008 Seminars

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

Short List


September 2, 2008

Complex nanostructures driven by screw-dislocation nanowire growth

Song Jin, UW Department of Chemistry

I will discuss some complex "Christmas Tree" like nanowire structures spontaneously formed through chemical reactions. These fascinating nanostructures demonstrate a ?new? nanowire formation mechanism that is completely different from the well-known metal catalyzed vapor-liquid-solid (VLS) mechanism. The screw component of an axial dislocation provides the self-perpetuating steps to enable 1-dimensional crystal growth, unlike previously understood mechanisms that require metal catalysts. This mechanism was found in hierarchical nanostructures of lead sulfide (PbS) nanowires resembling ?pine trees? that were synthesized via chemical vapor deposition. Structural characterization reveals a screw-like dislocation in the nanowire trunks with helically rotating epitaxial branch nanowires. The rotating trunks and branches are the consequence of the Eshelby twist of screw dislocations. We suggest that screw dislocation growth is overlooked and underappreciated in modern literature on one-dimensional nanomaterials. The proposed nanowire growth mechanism will be general to many materials and enable more complex nanostructures to be synthesized in the future to enable diverse applications.

September 9, 2008

Ecology and the evolution of reproductive isolation

Jenny Boughman, UW Department of Zoology

My research program addresses two venerable questions in evolutionary biology: How do new species arise? How does selection cause genetic change in nature? Both questions have a rich history in evolutionary biology going back to Darwin and the modern synthesis. Despite decades of research; however, we have only recently begun to reveal the mechanisms that generate new species in nature. Recent years have also seen phenomenal progress on understanding the genetic basis of traits. We are now able to ask questions that were simply impossible to address 20 years ago. Yet, progress on understanding how selection is acting in natural populations to cause evolutionary change at the genetic level has lagged behind. My work melds two rapidly advancing areas - mechanisms of speciation and genetics of adaptation - to investigate questions of fundamental importance to our understanding of biodiversity. I use an ideal system to study these questions - species pairs of stickleback fish (Gasterosteus spp.) found in the postglacial lakes of British Columbia. These are extremely young species and provide a window on the speciation process. Evolutionary replication allows direct experiments to test the evolutionary mechanisms involved.

September 16, 2008

What are your 'thinking genes' doing in a plant?

Edgar Spalding, UW Department of Botany

It’s hard to keep an open mind. If we don’t shut down some possibilities, create certain boundaries, we’d never get anywhere through thought. But it’s easy to go overboard and start throwing up blocks and dividers left and right to keep things simple and manageable. Excesses in this coping method inevitably run afoul of new facts and findings and then hindsight shows its waste. My presentation will be a story that exemplifies this folly of ours. The protagonist is a group of genes encoding protein molecules known as glutamate receptor channels. In our brains, they play fundamental signal-transmitting roles, chemically connecting one neuron to another. Their properties make learning and other higher cognitive functions possible. If ever there could be a molecule that sets sentient beings like us apart from the rest of the living world, the glutamate receptor channels might be it. So what on earth are genes encoding these ‘molecules for thinking’ doing in the DNA of plants? We have been researching this question with genetics, electrophysiology, and computerized image analysis. I will describe some of the progress we have made and what we may risk by letting conventional wisdom about plants and animals rule our thinking.

September 23, 2008
Native American science, technology, engineering, and mathematics before 1492
John Gustafson-Independent Scholar formerly of Fond du Lac Tribal & Community College, Cloquet, MN

A survey of Native Americans’ accomplishments in what we call the fields of science, technology, engineering, and mathematics (STEM) reveals an impressive list, a list of accomplishments that can serve as a new and attractive perspective to teach STEM to STEM-phobic students. In addition, the perspective provides new insights into other problems. For example,Europeans arriving in 1492 were small in number, yet they soon dominated the Americas.  Jared Diamond hypothesized that European technology had something to do with it. By looking at the pre-1492 Native American STEM-like accomplishments, we may be able to deduce more of why Europeans “went chaotic.”

September 30, 2008

Indicators of regime shifts in ecosystems
Steve Carpenter, UW Center for Limnology
Ecosystems occasionally undergo rapid massive changes – desertification, algae blooms of lakes, replacement of coral reefs by fleshy algae turf, trophic cascades, economic collapse of fisheries, and shrub invasion of rangelands are a few examples. Some regime shifts have big impacts on human life-support and are therefore important for environmental policy. Thus the detection and prediction of regime shifts has emerged as a research topic in basic and applied ecology. Theory shows that certain regular changes in time series should be measurable before an incipient regime shift – autoregression coefficients near one, variance spectra shifted to low frequencies, and rising variance, skewness and kurtosis, for example. However, not all regime shifts show these indicators, and some show opposite responses. While leading indicators show promise as tools for field science and ecosystem management, at present it is difficult to diagnose the characteristics of incipient regime shifts from the indicators alone. Field trials, and modeling to connect theory with the characteristics of particular ecosystems in the field, are needed to improve our understanding of these signals.

October 7, 2008

Molecular mechanisms of synaptic growth: insights from the Drosophila neuromuscular junction

Kate O'Connor-Giles, UW Department of Genetics

Neural function requires effective communication between neurons and their targets at synapses. Thus, the proper formation, growth and plasticity of synapses are critical to behavior. Despite this, the mechanisms that determine synapse size and complexity remain poorly understood. The Drosophila larval neuromuscular junction (NMJ) has become a powerful model system for dissecting the molecular mechanisms that regulate synaptic growth. Drosophila NMJs are dynamic structures that coordinate their size and strength with muscle growth and undergo changes in morphology and physiology in response to environmental stimuli and altered levels of activity. These processes depend on intercellular communication between neurons and their muscle targets. A retrograde (muscle to neuron) transforming growth factor (TGF-b/BMP) signal is required to promote synaptic growth, homeostasis and stability at NMJs. We have recently found that neuronal responsiveness to this signal is modulated by a presynaptic endocytic mechanism. This additional level of regulation underscores the high degree of molecular control over synaptic growth and highlights the importance to the organism of getting it right. I will present recent insights from studies at the Drosophila NMJ that have increased our understanding of how this complex task is achieved.

October 14, 2008

A perspective on evolution and psychiatry
Russ Gardner, UW Department of Psychiatry

This presentation summarizes key points in the troubled 20th century history of psychiatry and its guiding paradigms. These include, for example, a oddly restricted definition of the word “biology” – a definition that de facto includes cellular-molecular biology only. Psychiatric disorders presently appear out of the blue understood as molecular in origin with corrections to be achieved with medications in short impersonal sessions. The specialty does not exhibit parallels to other specialties such as pulmonology and orthopedics for which lung and bone anatomies represent physical organs substrate to their respective physiologies and rationalize their respective “pathophysiologies” that describe disease as deviation from how the body works normally.
Reasons stem from major opposing figures of the twentieth century: (1) Freud who did present pathophysiologies but not based on a real nervous system – his writings did not mention the brain after 1900 despite his prior researcher and neurologist credentials. (2) “Biological” psychiatrists typified and led by Eli Robins who reacted to the untested therapies that made claims based on authority and that eschewed data-gathering. But they threw out the pathophysiology baby with the bathwater and suggested any “future” pathophysiologies would primarily involve cellular-molecular foundations – without need of other levels of analysis, an assumption that presently seems as without foundation as Freud’s neglect of an actual brain.
Both traditions implied that the free-standing individual separable from other people suffices for their models. But although research shows psychotherapies of all kinds work effectively and that placebos account for much variance in drug treatment, these paradigmatic features persist in present day psychiatry, augmented in part by corporate financial factors. A psychiatric basic science with a focus on an evolved “social brain” with the physiological function of “relational neurobiology” would help provide order for psychiatry’s disorder. Social factors account for much larger human brain size compared, for example, to chimpanzee brains (3x larger by weight) despite close genomic identity. An approach that dissects pathophysiological mechanisms includes communicational states that transcend species combined with communicational features seemingly unique to humans.

October 21, 2008

Gender, power and peacemaking in Africa

Aili Mari Tripp, UW Departments of Political Science and Women¹s Studies

The presentation will look at why almost all post-conflict countries in Africa have double the rates of legislative representation of women compared with countries that have not undergone conflict. Moreover, these countries tend to have been more open to passing legislation and making constitutional changes relating to women's rights. In my talk, I explain why Rwanda has the highest rates of legislative representation of women in the world (49% of all seats are held by women) and why Liberia has the first elected woman president in Africa. The talk examines how and why the end of major civil conflicts, especially since the 1990s from South Africa to Namibia, Mozambique, Rwanda, Burundi, Liberia and Sierra Leone, opened up new opportunities for women activists. I discuss the broader international context of these changes, changing gender relations during civil war, and the role of women¹s movements. The talk is based on both comparative research across Africa as well as fieldwork in Uganda, Liberia and Angola.

October 28, 2008

Chaos and its application in secure communication

Kehui Sun, UW Department of Physics
Chaotic systems have several significant features favorable to secure communication, such as aperiodicity (useful for one-time pad cipher); sensitivity to initial conditions and parameters (useful for effective bit confusion and diffusion); and random behaviors (useful for producing output signals with satisfactory statistics). Thus, chaotic systems and their application in secure communication have received increasing attention. Up to now, four main secure communication schemes based on chaos synchronization have been investigated, such as chaos masking, chaos shifting key, chaos modulation, and chaos spread spectrum. In fact, chaos synchronization is one of the key technologies in the chaotic secure communication for its practical use. So I will focus on the chaos synchronization and chaos secure communication schemes in my talk.

November 4, 2008

Conversations with the silent majority in soil microbial communities

Jo Handelsman, UW Department of Bacteriology

The soil is the richest environment on Earth.  It contains the highest diversity and density of life forms of any habitat, with more than one billion bacterial cells per gram.  The chemical diversity is also unparalleled, providing a pharmaceutical cornucopia that has been exploited by humans.  For example, most of the antibiotics used in modern medicine are derived from bacteria that reside in soil.  The complexity of soil microbial communities makes their analysis challenging and an accurate census thus far impossible.  My lab’s work is directed toward describing the biological and chemical diversity in soil using diverse techniques.  In this talk, I will cover molecular analyses as well as statistical analyses that use great books as a metaphor for soil communities.

November 11, 2008

Engaging the flow: a creative dialogue

Harry Webne-Behrman, UW Office of Human Resource Development
Creative conversations don’t mechanically follow ‘outline form,’ they emerge from the synergies and interactions of participants in hard-to-predict ways. Is there a way to facilitate such dialogues, rather than direct them, so 1 + 1 >2? Is there a way to capture the creative ideas that emerge? Building from theories on synchronicity in innovation and the process used by Nathan Myhrvold at Intellectual Ventures, the Chaos & Complexity Seminar will engage in a creative dialogue whose outcome is unknown and whose parameters will be co-created by the group in the weeks ahead. Join us for fascinating conversation and see what happens!

I propose that we communicate this question to the C & C Seminar mailing list, in preparation for the conversation:

“In what ways might we creatively harness the campus’s intellectual, social and physical resources so they may be best applied to the most significant emergent challenges facing society?”

Notes from the seminar available.

November 18, 2008

The new science of chaos

Clint Sprott, UW Department of Physics

The ability to make accurate quantitative predictions and to replicate experiments with the same result are hallmarks of the scientific revolution. In the last few decades it has come to be widely recognized that deterministic systems governed by simple equations can behave unpredictably. This phenomenon is called "chaos," and it has excited the imagination of the public as well as the interest of scientists in diverse fields. Examples of chaos will be shown using simple apparatus and computer simulations.

A version of this talk is available on video.

November 25, 2008

Clouds and aerosol: their role and impact in the atmospheric and global climate processes

Pao K. Wang, UW Department of Atmospheric and Oceanic Sciences

Atmospheric clouds have great impact on the global climate process mainly due to their ability to influence the radiative budget of the earth system. But because of their high variability, they also make climate predictions complicated and unreliable so far. In addition, cloud formation is closely related to the aerosol in the atmosphere. This further complicates the climate predictions because we don't yet fully understand how clouds and aerosol interact and meanwhile human activities keep injecting large amount of aerosol into the atmosphere.  In this talk I would like to discuss fundamental cloud and aerosol interactions and how they may impact the global climate process.

This talk is available on video.

December 2, 2008

What did the IPCC say about impacts and adaptation?

John Magnuson, UW Department of Zoology 

The Intergovernmental Panel on Climate Change (IPCC) has three working groups; WG 1 on the climate system, WG 2 on impacts and adaptation, and WG3 on mitigation strategies to reduce greenhouse gas emissions. Most of the information in the public realm about the IPCC is about climatic change, per se, and about mitigation. Yet, even under the most optimistic IPCC scenario for mitigation, the challenges for adaptation to climate changes are immense. I will review what IPCC 2007 concluded about impacts and adaptation regarding freshwaters and also fish and fisheries both inland and marine. Additionally, I will describe the Wisconsin Initiative on Climate Change Impacts (WICCI) and results to date.

December 9, 2008

A technique for modeling radar interferograms without phase unwrapping: Application to the M 5 Fawnskin, California earthquake of 4 December 1992

Kurt Feigl, UW Department of Geology and Geophysics

Interferometric analysis of synthetic aperture radar images (InSAR) measures the phase shifts between two images acquired at two distinct times. These ambiguous “wrapped” phase values range from  ½ to +½ cycles. The standard approach interprets the phase values in terms of the change in distance between the ground and the radar instrument by resolving the integer ambiguities in a process known as “unwrapping”. To avoid unwrapping, we have developed, validated, and applied a new method for modeling the wrapped phase data directly. The method defines a cost function in terms of wrapped phase to measure the misfit between the observed and modeled values of phase. By minimizing the cost function with a simulated annealing algorithm, the method estimates parameters in a nonlinear model. Since the wrapped phase residuals are compatible with a von Mises distribution, several parametric statistical tests can be used to evaluate the fit of the model to the data. The method, named General Inversion for Phase Technique (GIPhT), can handle noisy, wrapped phase data. Applying GIPhT to two interferograms in the area of Fawnskin, California, we estimate a set of model parameters describing a magnitude 5 aftershock of the 1992 Landers earthquake. The resulting simulation fits the data well. The phase final residuals have a circular mean deviation less than 0.15 cycles/datum. Sampling the final residuals, we find the circular standard deviation of a phase measurement to be approximately 0.2 cycle, corresponding to 6 mm in range.