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iFOCUS Science Colloquium Lecture Series

iFOCUS Science Colloquium Series is a semester long lecture series that offers everyone in the Linfield community the opportunity to learn about science across the traditional science disciplines of biology, chemistry, math, physics, and computer science. *Made possible in part by generous gifts from the Hearst Foundations. Sponsored by Linfield Physics Department.

Spring Series 2015

Seeing is believing: Image and experience in the information age

All lectures are on Thursdays at 4:15 pm in Murdock 105, unless otherwise noted.
Refreshments will be available starting at  4 pm. Additional information on lectures and events will be added as they are scheduled. 

February 19, 2015 Ronald Hause, University of Washington Dept. of Genome Sciences:
Ron Hause in lab

"From genotype to phenotype: how to find, test, and predict the effects of mutations"
Abstract: 
Genome-wide association analyses have discovered many DNA variants that influence complex human diseases and phenotypes. Furthermore, the advent of next-generation sequencing has enabled the identification of large numbers of mutations across humans, many of unknown effects. Although we now excel at ascertaining variation, our ability to interpret variation remains limited. Along these lines, I would like to discuss three projects I’m involved in related to the identification of associations between mutations and cellular phenotypes, new approaches to experimentally test mutational effects, and novel algorithms being developed to predict the functional effects or deleteriousness of mutations. The first project centers on the development of a proteomic platform for quantifying protein levels across a human population and relating those proteins to genetic variation, variation in disease risk, and variation in response to chemotherapy between individuals. I would then like to discuss the development of deep mutational scanning and saturation genome editing with CRISPR/Cas9 to introduce thousands of programmed variants into cells to experimentally test their effects. Lastly, I will discuss CADD and Envision, two machine learning algorithms developed by our group to predict the effects of mutations in humans by leveraging large-scale mutational data, genomic annotations, and simulations. These projects demonstrate new potentials for acquiring precise measurements of intermediate functional phenotypes across human populations, experimentally examining the consequences of large numbers of genomic mutations, and interpreting variants of uncertain significance observed in clinical sequencing.

February 26, 2015  "Linfield Makers"-an exhibition and discussion of hands-on projects made by students, and of campus resources for such projects Hosted By: Dr. Jennifer Heath, Physics Department, Linfield College in Riley 201 

March 5, 2015  Anne Kruchten, Linfield Dept. of Biology on the iFOCUS program and Interdisciplinary First year Orientation Camp for Undergraduate Students (iFOCUS BC)

March 12, 2015  Daniel Borrero Reed College Dept. of Physics:
Dr.Borrero
"On the importance of visualization in nonlinear dynamics: From Huygens' clocks to hurricanes"
Abstract:
 Many systems in science and engineering are governed by nonlinear evolution equations. Starting with the familiar case of the simple pendulum, I will discuss some of the ways that nonlinear systems differ from linear ones and discuss how nonlinearity can lead to unexpected behavior. One famous example is the so-called "butterfly effect" where small differences in initial conditions can lead drastically different long term behavior. Another consequence of nonlinearity is that systems can have multiple solutions for a given set of parameters. The competition between solutions often leads to very complicated spatial and temporal dynamics. As it turns out many of the most time honored mathematical techniques used in the analysis of linear systems fail miserably in the analysis of the complex systems, forcing us to resort to more qualitative and graphical approaches. As an example of this, I will discuss recent advances in identifying a special class of solutions of the Navier-Stokes equations (the governing equations for fluid flows) and how these are being used being used to shed light on one of the oldest open problems in mechanics, the study of hydrodynamic turbulence. 

April 9, 2015  Arvind Satyanarayan, Stanford University Dept. of Computer Science:
Arvind
"Lowering the Threshold of Visualization Design"
Abstract:
Consuming data visualizations has become mainstream, with people and organizations embracing visualizations to record, analyze, and communicate data. However, designing effective visualizations remains difficult, as it requires a cross-cutting set of expertise. For example, designers need storytelling expertise to select visual forms that convey both the semantics and connotations of the data, design expertise to ensure visual and interactive elements are perceptually sound, and technical expertise to implement and publish the resultant visualization. In this talk, I will present two projects that begin to lower the threshold of custom visualization design by reducing necessary technical expertise. The first project, Lyra, is a new visualization design environment (VDE) that enables direct-manipulation authoring of visualizations. Data is imported and transformed visually, and drag-and-drop operations bind data values to the properties of graphical primitives. As a result, designers can create highly customized visualizations without any programming. Since its alpha release last March, approximately 2,000 users have used Lyra each month and reported it as being an effective prototyping and teaching tool. The second project, Reactive Vega, formulates a grammar of interaction design. Rather than constructing imperative event-handling callbacks, Reactive Vega introduces a set of primitives that can be composed declaratively in order to have input events trigger visual changes. As a result designers need only focus on specifying their interaction technique and leave the library to manage the complexity of propagating events and changes.

April 16, 2015  Maria Davis, University of Minnesota Dept. of Earth Sciences:
"When volcanoes erupt: Understanding why some explode and others fizzle"
Volcanic eruptions vary in intensity due to a variety of physical and chemical variables. One of the most significant variables that determines if an eruption will be explosive or effusive is the amount of pressure build-up inside the volcano conduit at the time of the eruption. The source of this pressure is primarily due to exsolved gases (bubbles) in the magma. Under certain conditions, bubbles are able to grow and form extensive networks within the conduit. These bubble-networks are believed to be the primary method for gasses to escape from the magma during an eruption, reducing the pressure within the conduit. Therefore, if the gasses are able to escape from the volcano conduit, an eruption will be effusive, analogous to typical Hawaiian eruptions. However, if the gas is not able to escape, pressure will build-up and the volcano will explode in a high-intensity eruption, such as with Mt. St. Helens in 1980. We can better understand why some volcanoes explode and others fizzle by understanding how bubbles behave in the volcano conduit during an eruption.

April 2, 2015 Rick Passey, Senior SEM/Small DualBeam Applications Engineer, FEI Company
"The Alphabet Soup of Electron and Ion Beam Imaging and Analysis"
Abstract:
From engineers of all disciplines to biologists, geologists, chemists, physicists, and beyond, electron and ion beam microscopy is applied to solve complex questions in industry and research. This talk covers the basics of how electron and ion microscopy works and  how it is applied in hundreds of labs across the world

April 23, 2015  Rob Williams, MD: on Experiences with Doctors Without Borders  

April 30, 2015 Ben McMorran, University of Oregon Dept of Physics:

"Imaging magnets at the nanoscale with sculpted electrons"
Abstract: Exactly what are magnets? How can a nail be turned into a magnet by applying another magnet? It turns our the answer to these questions plays a newsbreak role in today's technologies - computers, the internet - as well as tomorrow's. Here I will discuss how these questions can be answered by looking at magnets at nanometer lengthscales. I will discuss how various magnetic microscopes work. I will also discuss the role that electron angular momentum plays in magnetic material, and will explain our efforts to manipulate this angular momentum using "sculpted" electrons.

Tuesday May 5, 2015 Panel Discussion- 'How do scientists "know"..?' (panelists TBA) 

May 14, 2015 Niles Lehman, Portland State University
Dr.Lehman
"A convivial origins of life on the Earth: A cooperative network of RNA replicators
Abstract:Dr. Lehman will discuss the origins of life on the Earth some four billion years ago. His research has used RNA as a model system to study how chemicals first became self-replicating in the process of evolving life-like characteristics. In particular, this talk will focus on a set of catalytic RNAs (ribozymes) that has the ability to assemble itself from fragments. Recent experiments in the Lehman lab at Portland State have shown that cooperation among RNA fragments leads to networks of self-assembling molecules, and this has implications for how life may have arisen from an abiotic environment.