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    • 2008

      Biology program Independent Research Poster Session

      December 8
      RKC lobby

      Biology program

      Fall 2008
      Independent Research
      Poster Session
      Students presenting:
      Alex Carlin
      Jyoti Dev
      Margo Finn
      Samuel Israel
      Allison James
      Anna Josephson-Day
      Sarah Mount
      Jessica Philpott
      Wyatt Shell
      Ilya Smirnoff
      Rachel Steinhorn
      Emma Taylor-Salmon
      William Wylie

      Fall 2008 Science, Mathematics & Computing Senior Project Poster Session

      December 8
      RKC lobby

      The Science, Mathematics & Computing Division presents...

      Fall 2008
      Senior Project Poster Session

      Students presenting:
      Priyanka Oberoi
      Adviser: Felicia Keesing

      "The Effect of Invasive Plant Species, Garlic Mustard Plant (Alliaria petiolata), on Entomopathogenic Fungi, Beauveria bassiana"

      Faqir Usman
      Adviser: Sam Hsiao

      "Using Graphs to Model the Spread and Containment of Fire"

      Math seminar-"Rigidity and Flexibility of Structures"

      December 4
      RKC 111

      A lecture by
      Maria Belk
      Mathematics program
      Why are some structures rigid, but others fall down?  We'll look at some simple structure and examine their rigidity.  We'll start by considering bar frameworks - place the vertices of a graph in 2 or 3 dimensions, and think of the edges of the graph as bars, forced to maintain their length.  After examining the rigidity of bar frameworks, we'll move to consider tensegrities.  In a tensigrity framework, some of the edges are called struts and are allowed to increase in length while others are called cables and are allowed to decrease in length.  These are tensegrities where the struts are suspended in the air by the cables, and yet the entire structure is rigid.

      Science on the Edge lecture - "Preventing Web-bot Spam: Intelligence is the Key"

      December 2
      Reem-Kayden Center Laszlo Z. Bito '60 Auditorium

      A lecture by
      Sven Anderson
      Computer Science program
      Telling the difference between human and automated programs such as Web-bots has become important in preventing Web-bot access to e-mail addresses, private information and limited electronic resources. CAPTCHAs, programs that can accurately judge whether a user is human or machine, are the primary line of defense against Web-bot access. For example, Google's Mail program uses CAPTHCAs to prevent Web-bots from creating bogus user accounts from which to launch spam messages. Every day humans solve about 60 million CAPTHCAs. The human "computation" expended has an unintended benefit: it can be recycled to help digitize old printed texts that are unrecognizable using optical character recognizers. This talk, intended for a general audience, will explore the vanishing difference between humans and computer programs on current text CAPTCHAs and outline efforts to keep one step ahead of the intelligent Web-bots. We will also consider other efforts to recycle human computation. 

      Biology search candidate lecture-"Mobile DNA: Reshaping and Rearranging the Yeast Genome"

      December 2
      Reem-Kayden Center Laszlo Z. Bito '60 Auditorium

      A lecture by
      Lisa Scheifele
      candidate for the position in Biology
      Mobile DNA presents a considerable challenge to genome stability due to its presence as dispersed repeats.  Could this instability enable adaption and thereby explain why genomes retain high levels of mobile DNA?  Indeed, we have found that following experimental evolution, strains with higher levels of repetitive DNA contain a broader variation in chromosome structure.  The abundance of repetitive DNA must therefore be fine-tuned so that benefit of chromosome rearrangements in promoting genome evolution outweights the potential for lethal damage.

      Computer Science candidate lecture - "Off the Desk and Into the Wild: Two Expeditions in Distributed Robot Systems Architecture"

      November 25
      RKC 111

      A lecture by
      Keith O'Hara
      candidate for the position in Computer Science

      Just as special purpose mainframe computers grew into general purpose personal computers, special purpose industrial robots are evolving into general purpose personal robots.  Drawing on ideas from computer systems architecture such as parallelism, redundancy, heterogeneity, locality, and scaling laws, we propose a "robot systems architecture" perspective on the design of robot computing systems.  From this perspective, two distributed robot systems built for tasks as varied as computing education and mobile robot navigation will be presented.

      Chemistry search candidate lecture - "Uncovering the World of Bacterial Small RNAs"

      November 24
      Reem-Kayden Center Laszlo Z. Bito '60 Auditorium

      A lecture by Jane Liu,  candidate for the open position in Chemistry.

      Due to their central role in regulating bacterial pathogenesis, small non-coding RNAs (sRNAs) represent targets with therapeutic potential.  To investigate the entire repertoire of sRNAs in the human pathogen, Vibrio cholerae, we developed a method, sRNA-Seq, to directly clone and analyze whole populations of V. cholerae transcripts, 14 to 200 nucleotides, by high-throughput pyrosequencing.  From over 680,000 reads, 500 new intergenic sRNAs and 127 antisense sRNAs were identified.

      Math seminar - "Geometry of Infinite Graphs"

      November 20
      RKC 111

      A lecture by Jim Belk

      If you draw a grid on the plane and then zoom out, the empty squares between the gridlines become smaller and smaller until they are lost to sight.  The result is that the large-scale geometry of the plane is essentially the same as the large-scale geometry of an infinite grid.  In the same way, many non-Euclidean geometries can be understood on a large scale using infinite graphs.  In this talk, we will explore the geometry of several graphs that arise in this fashion, and we will discuss the sorts of questions that one might ask about the geometry of an infinite graph.

      Biology search candidate lecture - "Npl3: At the Interface of Transcription and mRNA processing"

      November 20
      Reem-Kayden Center Laszlo Z. Bito '60 Auditorium

      A lecture by Tracy Kress, candidate for the position in Biology.

      From the beginning of transcription, mRNAs are processed in a myriad of ways to specify the correct timing, localization, and quantity of protein synthesized. To ensure the efficiency and accuracy of gene expression, transcription and mRNA processing steps are tightly coordinated both spatially and temporally. Despite their critical importance, few factors that regulate this coordination are known. I identified Npl3 as one such factor, and my work aims to uncover the mechanism of Npl3, and other factors, in this coordination.

      Biology seminar - "The zebrafish as a model for heart disease"

      November 20
      Reem-Kayden Center Laszlo Z. Bito '60 Auditorium

      A lecture by Patrick Page-McCaw, Rensselaer Polytechnic Institute

      I will present two stories on how the zebrafish can be used as a model of heart disease.  In the first story, our lab has used genetic, pharmacological and surgical tools to dissect the affect of stress on cardiac output.  In the second story, we have discovered that Serum Amyloid A is required for cholesterol transport early in embryogenesis and that the failure to transport cholesterol results in defects in Hedgehog signaling.

      Chemistry search candidate lecture - "Electrostatics and Ribonuclease Biology"

      November 17
      Reem-Kayden Center Laszlo Z. Bito '60 Auditorium

      A lecture by Jeremy Johnson, candidate for the open position in Chemistry

      The mechanism of ribonuclease toxicity toward cancerous cells involves multiple steps, including cellular uptake and evasion of the ribonuclease inhibitor protein. Both of these steps of ribonuclease cytotoxicity are proposed to be controlled by the cationic nature of the ribonuclease and its interactions with the anionic cell membrane and anionic inhibitor. To understand the role that electrostatics play in ribonuclease biology, I investigated the effect that the positive charge of ribonuclease have on their cytotoxicity.

      Math seminar - REU information session

      November 13
      RKC 111

      Interested in summer research in mathematics?

      Come to an REU (Research Experience for Undergraduates) information session.
      Hosted by the Mathematics program

      Students Sylvia Naples and Tomasz Przytycki and faculty members John Cullinan and Lauren Rose will be speaking on the application process and their own experiences with past REU's.

      Biology search candidate lecture - "Small non-coding RNAs in the bacterium Shewanella oneidensis: Computational prediction and experimental validation"

      November 13
      Reem-Kayden Center Laszlo Z. Bito '60 Auditorium

      A lecture by Brett Pellock, candidate for the open position in Biology.

      Bacteria use small, non-coding RNAs (ncRNAs) to rapidly alter gene expression in response to changing conditions. Bacterial ncRNAs are small and difficult to identify experimentally. We are synthesizing computational and experimental methods to predict and validate the existence of ncRNAs in Shewanella oneidensis, a bacterium that can reduce a wide variety of substrates when grown anaerobically. Of particular interest is the ability of Shewanella to reduce soluble, toxic heavy metals to insoluble, much less toxic forms.

      Biology seminar - "A Visual Narrative about Fruit Flies"

      November 13
      Reem-Kayden Center Laszlo Z. Bito '60 Auditorium

      A lecture by Alexis Gambis, The Rockefeller University

      Alexis Gambis will speak about the importance of visual imagery and narrative in both science understanding and communication. He will give insight into his current thesis work explaining the mechanisms of cellular death, how to use the fruit fly as a genetic model to study human neurodegenerative diseases, and the fluorescent toolkit to visualize neurons in the fruit fly eye . Using the camera eye, Alexis has also been actively making films with scientific themes during his graduate career. Alexis will talk about his recent films and the importance of visual storytelling in science communication, show a few clips of his film "A Fruit Fly in New York", and share his recent experience pioneering the first science film festival in New York.

      Science on the Edge lecture-"New Insights into the Chemistry of Depression"

      November 12
      Reem-Kayden Center Laszlo Z. Bito '60 Auditorium

      A lecture by Richard A. Gordon, Professor of Psychology.

      After the discovery of antidepressant drugs in the 1950s and the burst of research on neurotransmitters that took place in the 1960s, a scientific hypothesis about depression became firmly established in the community of researchers and clinicians: depression was rooted in depleted brain amines, such as norepinephrine and serotonin, a deficit that the antidepressants corrected. The amine hypothesis (known popularly and in pharmaceutical advertising as “chemical imbalance”) guided research throughout the rest of the 20th century. However, by the late 1990s it had become clear that direct research on the metabolism of depressed patients had failed to support the hypothesis. In this lecture I will discuss some exciting recent research that uses sophisticated techniques of brain imaging and has lent new support to the possibility that depleted amines are importantly involved in the chemistry of depression. Further commentary will be offered on the limitations and promise of this work, as well as some of the current thinking on the underpinnings of depression in the brain.

      Chemistry search candidate lecture - "Understanding Nucleic Acid Structure and its Interactions with Small Molecules"

      November 12
      Reem-Kayden Center Laszlo Z. Bito '60 Auditorium

      A lecture by Swapan Jain, candidate for the open position in Chemistry.

      According to RNA World hypothesis, early life used RNA for information storage and chemical catalysis. Small molecules may have played an important role in this endeavor by assembling nucleic acids during prebiotic evolution. Our results with proflavine and coralyne (small organic ligands) show that reactions carried out by protein enzymes today could have been achieved by non-enzymatic means. Mechanistic studies using hydroxyl radical footprinting have also been instrumental in our understanding of RNA structure. Future work aims to understand the structural changes that occur in riboswitches (noncoding region of mRNA) upon ligand binding. I would also like to investigate whether RNA can be regulated simultaneously by multiple pathways.

      Information Session - New Biology course for the spring semester: Tropical Ecology

      November 11
      RKC 111

      New Biology course for spring semester:
      Tropical Ecology

      Professor Catherine O'Reilly

      Tropical ecosystems are among the most biodiverse, most threatened, and the least studied in the world. This course will examine both practical and theoretical aspects that are unique to tropical ecosystems, including the role of geology, biogeochemical cycling, evolutionary processes and species interactions. In addition, we will discuss issues related to conservation, such as habitat fragmentation and climate change. This course will include lectures, student presentations, and research projects. Students will design, conduct, synthesize, and present a field research project. This course will involve a field trip to La Selva Biological Station in Costa Rica over spring break.

      Prerequisites: Moderation, Bio 202 Ecology and Evolution, Permission of the instructor.

      Come to the information meeting to learn more about the field trip, acceptance into this course, and the additional costs.

      Discrete Mathematics Day at Bard College

      November 8
      Reem-Kayden Center Laszlo Z. Bito '60 Auditorium

      Speakers include:

      Cristina Ballantine, College of the Holy Cross
      "Expander Graphs: Algebraic and Combinatorial Constructions"

      Margaret Bayer, University of Kansas
      "Flag Vectors of Polytopes: An Overview"

      Debra Boutin, Hamilton College
      "The Determining Set: A (Smallest) Set that Identifies Every Vertex in a Graph"

      Robert McGrail, Bard College
      "Knots, Quandles, and the Constraint Satisfaction Problem"

      Ed Swartz, Cornell University
      "f-Vectors of Manifolds"

      Math seminar - "Reflexive Polytopes, Comples Tori, and Elliptic Curves"

      November 6
      RKC 111

      A lecture by Charles Doran, University of Alberta.

      We'll start by investigating the combinatorial properties of certain lattice polytopes in R^n, specifically reflexive polygons. By reinterpreting these as Newton polygons, we will relate these combintorial objects to algebraic equations naturally defined on complex tori. The vanishing loci of these equations are then elliptic curves, whose basic geometric and topological properties we will discuss. If time permits, we may also describe an application to string theory.

      Biology search candidate lecture - "Bacterial surface binding: Sweet attachments"

      November 6
      Reem-Kayden Center Laszlo Z. Bito '60 Auditorium

      A lecture by Brooke A. Jude, candidate for the open position in Biology.

      Investigation into Vibrio cholerae revealed that this organism colonizes both chitinous aquatic surfaces and the human small intestine via GbpA. Sequence analysis has revealed a GbpA homolog in all other Vibrio species that have been sequenced to date. We hypothesize that other aquatic Vibrio, such as Vibrio fluvialis, Vibrio vulnificus, or Vibrio parahemolyticus may also utilize GbpA to bind to environmental and intestinal surfaces. Current investigations include screening of aquatic isolates for attachment potential via GbpA.

      Mathematics Senior Project Prospectus Talks

      November 3
      RKC 111

      Tomasz Przytycki 4:30
      Dexin Zhou 4:50
      Scott McMillen 5:10
      Tina Zhang

      3-2 Combined Plan information session

      November 3
      Hegeman 107

      Interested in Studying Engineering? come hear about Bard's 3-2 combined plan with Columbia University. Derek Hernandez, former Bard student and current Columbia student, will speak about the program.

      Mathematics Summer Research Talks

      October 30
      RKC 111

      Sylvia Naples - 4:15 p.m.
      "An upper bound for the number of graceful labelings of a path with N edges"

      Nicholas Michaud - 4:35 p.m.
      "Delaunay Realizability of Certain Graphs"

      Mona Merling - 4:55 p.m.
      "Function Fields with Class Number Indivisible by a Prime 1"

      Computer science lecture - "Creating Realistic Graphical Agent Populations: An Integrated Artificial Intelligence (AI) Challenge"

      October 27
      Reem-Kayden Center Laszlo Z. Bito '60 Auditorium

      A lecture by Peter G. Selfridge, Ph.D.

      Virtual graphical environments (think Second Life or World Of Warcraft) have a number of real-world applications including training first responders, urban planning, and military training. Technology for creating both “geo-typical” terrain (e.g., a generic small city) and “geo-specific” terrain (e.g., downtown Kingston) has improved dramatically in recent years. What is missing is the ability to create realistic populations of regular people to populate the landscape: people commuting, going to lunch, taking their kids to daycare, et cetera.

      This talk will first review some motivating applications, the current state-of-the-art in terrain generation, and the general problem. Approaches to creating realistic agent populations will be reviewed, including crowd modeling, game technologies, and work in AI-style cognitive architectures. Two key challenges will then be described: the creation and maintenance of realistic behaviors, and the idea of scalable cognition or cognition on demand. Some research ideas to address these challenges will be briefly sketched.

      Peter Selfridge received his Ph.D. in Artificial Intelligence at the University of Rochester and spent 19 years at Bell Labs and then AT&T Bell Labs doing research into sensory robotics, artificial intelligence, knowledge representation, software visualization, interactive database exploration, 3D web technologies, and more. For the last 5 years he has supported the Defense Advanced Research Projects Agency (DARPA) in their mission of funding revolutionary R&D to help maintain the technological superiority of the United States. He also does independent research in Artificial Intelligence.

      Science on the Edge lecture-"The LHC: Testing the Standard Model and Beyond"

      October 21
      Reem-Kayden Center Laszlo Z. Bito '60 Auditorium

      A lecture by Matthew Deady, Physics program
      The Large Hadron Collider at the CERN laboratory in Switzerland has just been turned on for initial testing. The "Standard Model" of particles and fields has successfully matched theory and experiment for more than 30 years, and results from the LHC will put the model to its most stringent tests yet. The large energies available will also undoubtedly answer questions about extensions of and alternatives to the Standard Model, including supersymmetry, dark matter, dark energy, and string theory. In this lecture, these theories and what might be learned about them from the LHC will be explored. We will also discuss the spurious concerns that the LHC might cause a black hole that would swallow the universe.

      This talk will focus on the theories of particles, as a complement to the October 2007 talk which focused on the accelerator technology itself. An edited version of that talk appears in the latest issue of the Bardian.

      Mathematics Senior Project Prospectus Talks

      October 20
      RKC 111

      Mona Merling 4:30
      Nicholas Michaud 4:50
      Serena Randolph 5:10
      Ezra Winston 5:30

      Math seminar - "The Mathematics of Fairness"

      October 16
      RKC 111

      Lecture by Allison Pacelli, Williams College.

      How do you divide a candy bar fairly between two people? The most popular solution is known by many and can even be found in the bible: one person divides the bar in half, the other gets to choose which piece she wants. But what happens if three people are dividing the candy? Worse yet, what do you do if you're dividing a collection of indivisible goods? Things like TV's and pianos are not much use cut in half! The idea of fairness itself is considerably more complicated when more than two people are involved, but mathematics can be surprisingly useful in these situations.

      Biology Seminar - "Invasion Ecology and Metacommunity Dynamics"

      October 16
      Reem-Kayden Center Laszlo Z. Bito '60 Auditorium

      A lecture by Martha F. Hoopes, Mount Holyoke College

      Early metacommunity theory emphasized four distinct models to explain the spatial structure, dynamics, and species composition of communities: species sorting, patch dynamics, mass effects, and the neutral model. Several tests of metacommunity theory have focused on these models and on determining their relative importance in explaining spatial community structure. Applying metacommunity theory to invasion ecology redirects the focus to examine how theory on spatial community dynamics can inform our understanding of spatial interactions when all species are not considered equal. This talk examines how a focal species approach affects the interpretation of processes critical to metacommunity dynamics. I offer some preliminary thoughts on conceptual differences between the four conceptual metacommunity models and explore these with three invasion case studies.

      Bard Summer Research Institute Student Poster Session

      October 2
      RKC lobby

      Join the SM&C division faculty and students in presenting their summer research

      Math & Computer Science seminar-"Losing L'Hopital for Limits through Lazy Logic"

      October 2
      RKC 111

      A lecture by Robert McGrail, Computer Science program.

      L'Hopital's Rule is a useful tool for computing limits with indeterminate forms. In fact, it is too useful. The speaker demonstrates how some of these limits can be computed without this rule. This talk is a shamless ruse designed to introduce the 0-1 law of finite mondel theory as well as expose the unwitting members of the audience to some very beautiful mathematics.

      Math & Computer Science lecture-"Calculus, Supersized"

      September 25
      RKC 111

      A lecture by Gregory Landweber, Mathematics program.
      In calculus, we teach you how to take derivatives, and then once you're good at that, we tell you about second derivatives. But how do we go in the other direction and try to take HALF a derivative? It turns out that to take a half derivative, your functions need to come in pairs, analogously to how a complex number can be thought of as a pair of numbers, one real and another imaginary. Supersymmetry is the study of such pairings. This talk will discuss different ways that supersymmetry arises, both through explicit constructions, and through the notion of superspace.
      **Some exposure to multivariable calculus and linear algebra will be assumed**

      Biology seminar-"Phenotypic plasticity as an adaptive host response to parasitic infection"

      September 25
      Reem-Kayden Center Laszlo Z. Bito '60 Auditorium

      A lecture by Dr. Lisa Schwanz, Cary Institute of Ecosystem Studies.

      Parasites negatively impact their host’s fitness, potentially damaging host tissues and impairing host physiological or behavioral performance. In response to parasitic infection, hosts may alter their physiology, behavior or life history in ways that minimize the costs of infection. In this talk, I examine the optimal life history response of hosts when infected with parasites that have varying impacts. In addition, I explore the impacts of schistosome infection in deer mice by examining host physiology, survival and reproductive investment. In accordance with predictions, deer mice infected with this parasite increase their investment in offspring.

      Science on the Edge lecture-"Finding the genes that make us human"

      September 24
      Reem-Kayden Center Laszlo Z. Bito '60 Auditorium

      A lecture by Michael Tibbetts, Biology program.
      What are the genetic bases of the qualities that we think of as uniquely human? Is there a set of “humaness” genes? Large-scale genome sequencing projects in multiple species are generating the kind of data that allow us, for the first time, to seriously ask such big questions. An article published in the September 5 issue of Science Magazine (Human-specific gain of function in a developmental enhancer, by Prabhakar, S. et al.) describes a gene whose human-specific activity may be necessary to form an opposable thumb. The nature of the differences between the human and chimpanzee versions of the gene they identify supports a popular model for how small modifications in genomes can lead to significant changes in physical characteristics. The methodologies employed by these researchers may lead to the discovery of genes important for other human-specific characteristics.