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Spring_2021_Bis2A_Singer_Lecture_23 - Biology


Spring_2021_Bis2A_Singer_Lecture_23

Fellowship Winner Announced

NA’AMAT USA is pleased to announce that Ms. Cara Rock-Singer of Ithaca, NY is the recipient of the Second NA’AMAT USA Research Fellowship in Honor of Elizabeth J. Raider. In addition, Dr. Tanya Zion-Waldoks of Beer-Sheva, Israel has been awarded an Honorable Mention.

The 2017-18 theme of the fellowship program is “Jewish Women’s Contributions to Israeli Society.” The fellowship carries an honorarium of $2500.

“The fellowship contest was highly competitive,” explained Dr. Mark A. Raider of the University of Cincinnati, who chairs the fellowship committee. The other committee members are Dr. Karla Goldman (University of Michigan), Dr. Daniel Greene (Northwestern University), Dr. Shirley Idelson (Independent Scholar), and Dr. Laura Levitt (Temple University).

“We believe Ms. Rock-Singer to be an especially promising young scholar and an especially deserving awardee,” Raider said. “We are confident her important work will reflect well on NA’AMAT USA and strengthen the research fellowship’s growing reputation – and, no less a consideration, that she will produce a distinctive and valuable scholarly monograph.”

Ms. Rock-Singer is a PhD candidate at Columbia University in the Department of Religion she is scheduled to defend her dissertation this winter. She is currently a Visiting Lecturer in Cornell University’s Department of Near Eastern Studies as well as its Department of Science and Technology Studies.

Ms. Rock-Singer’s research examines how Jewish women’s bodily knowledge and practice shape the relationships among religion, science, secularism, and spirituality. She has an extensive background in science and religion. She earned a BA in molecular biology at Princeton University, a Master’s in theology at Oxford University, and studied at the Conservative Yeshiva in Jerusalem. Her PhD dissertation, “Prophetesses of the Body: American Jewish Feminism and The Politics of Embodied Knowledge,” explores how Jewish women negotiate their positions as religious and secular citizens of Jewish communities in the United States and Israel.

With respect to the NA’AMAT USA Research Fellowship, Rock-Singer plans to expand on her work and produce an article about the impact of American-born scholar-activists on Israeli public discourse concerning women’s reproductive health and sexuality.

Zion-Waldoks received an Honorable Mention for her work on the role Orthodox Jewish women activists in Israel. She is currently an Israel Institute Postdoctoral Fellow at Ben-Gurion University’s Ben-Gurion Research Institute for the Study of Israel and Zionism and a Teaching Fellow in Bar Ilan University’s Gender Studies Program. She will receive her award at NA’AMAT Israel’s annual student awards ceremony in the spring.

Rock-Singer will give a public lecture about her research in early May 2018 in Chicago, IL. Details of the event, which is expected to coincide with the NA’AMAT USA national board meeting, are forthcoming.

The NA’AMAT USA Research Fellowship was inaugurated in 2015-16 and previously awarded to Dr. Pnina Lahav (Boston University) for her work on “The Political Leadership of Golda Meir: Pioneer Women and the Campaign for Jewish Statehood.”


Upcoming Talks: Spring 2021

January 13 , 2021 | 9:00 – 10:30am ET

Abstract: The talk concerns two fundamental themes of modern 3-dimensional topology and their unexpected connection with a theme coming from number theory. A deep insight of William Thurston in the mid-1970s is that the vast majority of complements of knots in the 3-sphere, or more generally of 3-manifolds, have a unique metric structure as hyperbolic manifolds of constant curvature -1, so that 3-dimensional topology is in some sense not really a branch of topology at all, but of differential geometry. In a different direction, the work of Vaughan Jones and Ed Witten in the late 1980s gave rise to the field of Quantum Topology, in which new types of invariants of knot complements and 3-manifolds are introduced that have their origins in ideas coming from quantum field theory. These two themes then became linked by Kashaev’s famous Volume Conjecture, now some 25 years old, which says that the Kashaev invariant _N of a hyperbolic knot K (this is a quantum invariant defined for each positive integer N and whose values are algebraic numbers) grows exponentially as N tends to infinity with an exponent proportional to the hyperbolic volume of the knot complement. About 10 years ago, I was led by numerical experiments to the discovery that Kashaev’s invariant could be upgraded to an invariant having rational numbers as its argument (with the original invariant being the value at 1/N) and that the Volume Conjecture then became part of a bigger story saying that the new invariant has some sort of strange transformation property under the action x -> (ax+b)/(cx+d) of the modular group SL(2,Z) on the argument. This turned out to be only the beginning of a fascinating and multi-faceted story relating quantum invariants, q-series, modularity, and many other topics. In the talk, which is intended for a general mathematical audience, I would like to recount some parts of this story, which is joint work with Stavros Garoufalidis (and of course involving contributions from many other authors). The “new types of modularity” in the title refer to a specific byproduct of these investigations, namely that there is a generalization of the classical notion of holomorphic modular form – which plays an absolutely central role in modern number theory – to a new class of holomorphic functions in the upper half-plane that no longer satisfy a transformation law under the action of the modular group, but a weaker extendability property instead. This new class, called “holomorphic quantum modular forms”, turns out to contain many other functions of a more number-theoretical nature as well as the original examples coming from quantum invariants.

January 27 , 2021 | 9:00 – 10:30pm ET

Abstract: Discrepancy theory tells us that it is possible to partition vectors into sets so that each set looks surprisingly similar to every other. By “surprisingly similar” we mean much more similar than a random partition. I will begin by surveying fundamental results in discrepancy theory, including Spencer’s famous existence proofs and Bansal’s recent algorithmic realizations of them.

Randomized Controlled Trials are used to test the effectiveness of interventions, like medical treatments. Randomization is used to ensure that the test and control groups are probably similar. When we know nothing about the experimental subjects, uniform random assignment is the best we can do.

When we know information about the experimental subjects, called covariates, we can combine the strengths of randomization with the promises of discrepancy theory. This should allow us to obtain more accurate estimates of the effectiveness of treatments, or to conduct trials with fewer experimental subjects.

I will introduce the Gram-Schmidt Walk algorithm of Bansal, Dadush, Garg, and Lovett, which produces random solutions to discrepancy problems. I will then explain how Chris Harshaw, Fredrik Sävje, Peng Zhang and I use this algorithm to improve the design of randomized controlled trials. Our Gram-Schmidt Walk Designs have increased accuracy when the experimental outcomes are correlated with linear functions of the covariates, and are comparable to uniform random assignments in the worst case.

February 23, 2021 | 9:00 – 10:30am ET

Abstract: Moduli spaces of various gauge theory equations and of various versions of (pseudo) holomorphic curve equations have played important role in geometry in these 40 years. Started with Floer’s work people start to obtain more sophisticated object such as groups, rings, or categories from (system of) moduli spaces. I would like to survey some of those works and the methods to study family of moduli spaces systematically.

Talk chair: Peter Kronheimer

March 23, 2021 | 5:00 – 6:30pm ET

Abstract: At least since the initial public proposal of public-key cryptography based on computational hardness conjectures (Diffie and Hellman, 1976), cryptographers have contemplated the possibility of a “one-way compiler” that translates computer programs into “incomprehensible” but equivalent forms. And yet, the search for such a “one-way compiler” remained elusive for decades.

In this talk, we look back at our community’s attempts to formalize the notion of such a compiler, culminating in our 2001 work with Barak, Goldreich, Impagliazzo, Rudich, Vadhan, and Yang, which proposed the notion of indistinguishability obfuscation (iO). Roughly speaking, iO requires that the compiled versions of any two equivalent programs (with the same size and running time) be indistinguishable to any efficient adversary. Leveraging the notion of punctured programming, introduced in our work with Waters in 2013, well over a hundred papers have explored the remarkable power of iO.

We’ll then discuss the intense effort that recently culminated in our 2020 work with Jain and Lin, finally showing how to construct iO in such a way that, for the first time, we can prove the security of our iO scheme based on well-studied computational hardness conjectures in cryptography.

Talk chair: Sergiy Verstyuk

March 30, 2021 | 9:00 – 10:30am ET

Abstract: About 30 years ago, string theorists made remarkable discoveries of hidden structures in algebraic geometry. First, the usual cup-product on the cohomology of a complex projective variety admits a canonical multi-parameter deformation to so-called quantum product, satisfying a nice system of differential equations (WDVV equations). The second discovery, even more striking, is Mirror Symmetry, a duality between families of Calabi-Yau varieties acting as a mirror reflection on the Hodge diamond.

Later it was realized that the quantum product belongs to the realm of symplectic geometry, and a half of mirror symmetry (called Homological Mirror Symmetry) is a duality between complex algebraic and symplectic varieties. The search of correct definitions and possible generalizations lead to great advances in many domains, giving mathematicians new glasses, through which they can see familiar objects in a completely new way.

I will review the history of major mathematical advances in the subject of HMS, and the swirl of ideas around it.

April 6, 2021 | 9:00 – 10:30am ET

Abstract: I will review two famous papers of Ray and Singer on analytic torsion written approximately half a century ago. Then I will sketch the influence of analytic torsion in a variety of areas of physics including anomalies, topological field theory, and string theory.

This talk is part of a subprogram of the Mathematical Science Literature Lecture series, a Memorial Conference for the founders of index theory: Atiyah, Bott, Hirzebruch and Singer.

April 8, 2021 | 9:00 – 10:30am ET

Abstract: We will go over the fundamentals of quantum error correction and fault tolerance and survey some of the recent developments in the field.

April 16, 2021 | 1:00 – 2:30pm ET

Abstract: In this talk, we offer an entirely “white box’’ interpretation of deep (convolution) networks from the perspective of data compression (and group invariance). In particular, we show how modern deep layered architectures, linear (convolution) operators and nonlinear activations, and even all parameters can be derived from the principle of maximizing rate reduction (with group invariance). All layers, operators, and parameters of the network are explicitly constructed via forward propagation, instead of learned via back propagation. All components of so-obtained network, called ReduNet, have precise optimization, geometric, and statistical interpretation. There are also several nice surprises from this principled approach: it reveals a fundamental tradeoff between invariance and sparsity for class separability it reveals a fundamental connection between deep networks and Fourier transform for group invariance – the computational advantage in the spectral domain (why spiking neurons?) this approach also clarifies the mathematical role of forward propagation (optimization) and backward propagation (variation). In particular, the so-obtained ReduNet is amenable to fine-tuning via both forward and backward (stochastic) propagation, both for optimizing the same objective. This is joint work with students Yaodong Yu, Ryan Chan, Haozhi Qi of Berkeley, Dr. Chong You now at Google Research, and Professor John Wright of Columbia University.

April 20, 2021 | 9:00 – 10:30am ET

Abstract: The story of the index theorem ties together the Gang of Four—Atiyah, Bott, Hirzebruch, and Singer—and lies at the intersection of analysis, geometry, and topology. In the first part of the talk I will recount high points in the early developments. Then I turn to subsequent variations and applications. Throughout I emphasize the role of the Dirac operator.

This talk is part of a subprogram of the Mathematical Science Literature Lecture series, a Memorial Conference for the founders of index theory: Atiyah, Bott, Hirzebruch and Singer.

April 27, 2021 | 9:00 – 10:30am ET

Abstract: In the early 1980s Michael Atiyah and Raoul Bott wrote two influential papers, ‘The Yang-Mills equations over Riemann surfaces’ and ‘The moment map and equivariant cohomology’, bringing together ideas ranging from algebraic and symplectic geometry through algebraic topology to mathematical physics and number theory. The aim of this talk is to explain their key insights and some of the new directions towards which these papers led.

This talk is part of a subprogram of the Mathematical Science Literature Lecture series, a Memorial Conference for the founders of index theory: Atiyah, Bott, Hirzebruch and Singer.

Talk chair: Peter Kronheimer

Rescheduled date: May 25|9:00 – 10:30am ET

Abstract: We will discuss the K-theory of complex vector bundles on topological spaces and of holomorphic vector bundles on complex manifolds. A central question is the relationship between K-theory and cohomology. This is done in topology by constructing characteristic classes, but other constructions appear in the holomorphic or algebraic context. We will discuss the Hirzebruch-Riemann-Roch formula, the Atiyah-Hirzebruch spectral sequence, the role of complex cobordism, and other tools developed later on, like the Bloch-Ogus spectral sequence.

This talk is part of a subprogram of the Mathematical Science Literature Lecture series, a Memorial Conference for the founders of index theory: Atiyah, Bott, Hirzebruch, and Singer.

June 15, 2021 | 11:00am – 12:30pm ET

Abstract: According to a well-known conjecture, initial data sets, for the Einstein vacuum equations, sufficiently close to a Kerr solution with parameters $a, m$, $|a|/m <1$, have maximal developments with complete future null infinity and with domain of outer communication (i.e complement of a future event horizon) which approaches (globally) a nearby Kerr solution.

I will describe the main ideas in my recent joint work with Jeremie Szeftel concerning the resolution of the conjecture for small angular momentum, i.e. $, $|a|/m $ sufficiently small. The work, ArXiv:2104.11857v1, also depends on forthcoming work on solutions of nonlinear wave equations in realistic perturbations of Kerr, with Szeftel and Elena Giorgi, which I will also describe.


News and Notable

(Please click on the "Publications" tab above to see complete publication lists for all CQB faculty)

Wilma Olson has been elected a 2018 Fellow of the American Physical Society.

Anirvan Sengupta and his collaborators showed that similarity-preserving networks of rectifying neurons, when presented with sensory inputs populating a low-dimensional manifold, learn localized receptive fields naturally. The paper, titled “Manifold-tiling Localized Receptive Fields are Optimal in Similarity-preserving Neural Networks”, will be presented at the Annual Conference on Neural Information Processing Systems (NIPS), to be held in Montreal in December 2018.

Alexandre Morozov gave a keynote talk at BELBI 2018 which took place June 18-22 in Belgrade, Serbia.

Morozov's group published a paper in Physical Review Letters which explains how sizes of large, complex networks can be reliably inferred by exploring only a small fraction of each network: link.

Khiabanian's lab recently published two papers on statistical modeling of noise in deep DNA sequencing data in the Journal of Statistical Physics (link) and BMC Bioinformatics (link). The application of these results to clinical data from cancer patients showed that age-related somatic mutation in infiltrated hematopoietic cells are often present within the solid tumor miroenvironment. This study was published in Blood (link) and was covered by GenomeWeb (link).

Jui Wan Loh, a PhD student in Khiabanian's lab, was awarded a pre-doctoral fellowship grant by the New Jersey Commission on Cancer Research to study clonal dynamics of leukemia under targeted gene-specific therapy.

In collaboration with researchers from the Vanderbilt Ingram Cancer Center and Cancer Institute of New Jersey, Gyan Bhanot's group has found that endogenous retroviruses transcripts are amplified by histone modification in a subset of kidney cancers, which causes an immune response blocked by the tumor, making the tumor susceptible to immune checkpoint therapy. This discovery was highlighted at the recent ASCO-SITC conference: link.

Under Gyan Bhanot's supervision, Anshuman Panda graduated from the Rutgers Department of Physics and Astronomy with a PhD thesis titled “Immune Checkpoint Therapy,” won an NJCCR Fellowship, and is now a post-doctoral associate at the Cancer Institute of New Jersey.

Eduardo Sontag and collaborators have published a manuscript in PLoS Computational Biology on the dynamical responses of biological networks in Mycobacterium tuberculosis (link in the news: "New theorem helps reveal tuberculosis' secret").


Coffee With the Dean

Wednesday, March 3, 2021 - 12:00 pm to 12:45 pm

Graduate students are invited to join Dr. Jennifer Waldron, Dean of the Graduate College, for Coffee With the Dean on Wednesday, March 3 from noon-12:45 p.m. on Zoom. This is a drop in event and an opportunity for casual conversation and to ask any questions about the Graduate College.

Location: https://uni.zoom.us/j/94354496415?pwd=TWRsbXNmeXRrdnMrdHZJTm1JRm96QT09 https://uni.zoom.us/j/94354496415?pwd=TWRsbXNmeXRrdnMrdHZJTm1JRm96QT09

Contact Information

Name: Susie Schwieger Email: [email protected] Phone: (319) 273-2748

Link to Event: Coffee With the Dean


David Lessinger: From Recovery to Resilience: Planning in Post-Katrina New Orleans

David Lessinger (M.R.P. '07) is the chief of staff to the deputy mayor/chief administrative officer and chief resilience officer for the City of New Orleans. Lessinger supports the chief administrative officer in managing the budget and operations of city government with a focus on critical projects and priorities. Within the resilience portfolio, he works to establish resilience as a business practice across city government and interfaces between the city's Office of Resilience and Sustainability and other city departments and agencies. Formerly, Lessinger served as the director of planning and strategy at the New Orleans Redevelopment Authority (NORA) where he worked to enhance NORA's neighborhood revitalization strategies and managed resilience planning and its connection to NORA's mission of delivering affordable housing, commercial development projects, and the creative reuse of vacant land. Previously, Lessinger was a deputy director in the City of New Orleans Code Enforcement and Hearings Bureau where he directed research and analysis.

Lessinger first became involved in recovery planning in New Orleans as a graduate student in Department of City and Regional Planning at AAP where he and a team of graduate and undergraduate students developed components of the Unified New Orleans Plan. After graduating from Cornell, Lessinger was a Rockefeller Foundation Redevelopment Fellow at Neighborhood Housing Services of New Orleans working on blight reduction and neighborhood revitalization.

Lessinger holds a bachelor's degree in biology and environmental studies from Oberlin College, a master's degree in regional planning from Cornell University, and a certificate in urban redevelopment from the University of Pennsylvania.

Abstract:

As New Orleans began its long road to recovery from the devastating effects of Hurricane Katrina and the federal levee failures, each step in the process was an opportunity to not only rebuild what had been but to reimagine what could and should be. Twelve years later, New Orleans is pivoting from looking back to looking ahead, planning for the risks and opportunities of the future, and seeking to become a model for adapting to climate change.

Sponsored by Russell Van Nest Black Lecture Fund.

Also of Interest


Colleges

Focus on courses and programs offered by specific colleges. Search for, and browse, specific courses and programs at the college you are interested in.

The courses listed on this VCCS website are updated on a term by term basis and reflect only those courses approved for offering during the most current term. All VCCS colleges must use, as a minimum, the standard course prefix, course number, credit value(s), and descriptions contained in this listing.

When scheduling courses, colleges may use the local rule to assign pre- or co-requisites that are not listed in the Master Course File.

Questions, additional information, and corrections regarding the Master Course File should be addressed here.


For students with computational backgrounds, I have listed some videos below that provide introductions into molecular and cell biology.

    (7:21 min): an overview of cell structure from Nucleus Medical Media
  • The DNA learning center has created several interesting videos.
      (I played this video in class) (several videos)
    • iBiology, an NSF- and NIGMS-funded intitiative to convey the excitement of modern biology and the process by which scientific discoveries are made has created several videos.
      • A flipped course on Cell Biology (19:06 min) (three parts)

      Special offers and product promotions

      About the Author

      Peter H. Raven, Ph.D., is director of the Missouri Botanical Garden and Engelmann professor of botany at Washington University at St. Louis. He oversees the garden's internationally recognized research program in tropical botany--one of the world's most active in the study and conservation of imperiled tropical habitats. Raven's botanical research and work in the area of tropical conservation have earned him numerous honors and awards, including a MacArthur Fellowship. He has written 17 textbooks and more than 400 articles, and he is a member of th National Academy of Science and the National Research Council.

      George B. Johnson, Ph.D., is a professor of biology at Washington University in St. Louis and a professor of genetics at the university's School of Medicine. He is a prolific author of life science texts and curriculum products in a variety of media. New to his list of works are the Explorations of Human Biology CD-ROM and the textbook Human Biology, both offered by Wm. C. Brown Publishers. Johnson is acknowledged as an authority on population genetics and evolution variability, and he has published more than 50 research papers dealing with these and related topics. Visitors to the St. Louis Zoo can appreciate Johnson's work in the Living World, the educational center of which he is the founding director.

      Kenneth A. Mason received his undergraduate degree in Molecular Biology from the University of Washington, worked at UC Berkeley, then pursued his PhD in Genetics at UC Davis. He has taught Gentics, Microbial Genetics, Microbiology, Advanced Molecular Genetics, Introductory Biology, and a Genetics Laboratory that he designed.

      Jonathan Losos is a Monique and Philip Lehner Professor for the Study of Latin America in the Department of Organismic and Evolutionary Biology and Curator of Herpetology at the Museum of Comparative Zoology at Harvard University. Losos's research has focused on studying patterns of adaptive ratiation and evolutionary diversification in lizards. The recipient of several awards including hte prestigious Theodosius Dobzhansky and David Starr Jordan Prizes for outstanding young evolutionary biologists, Losos has published more than 100 scientific articles.

      Susan Singer is the Laurence McKinley Gould Professor of the Natural Sciences in teh dpartment of biology at Carleton College in Northfield, Minnesota, where she has taught introductory biology, plant biology, genetics, plant development, and developmental genetics for 20 years. Her research interests are focused on the development and evolution of flowering plants. Singer has authored numberous scientific publications on plant development, contributed chapters to developmental biology texts, and is actively involved with teh education efforts of several professional societies. She received the American Society of Plant Biology's Excellence in Teaching Award, serves on teh National Academies Board on Science Education, and chaired the NRC study committee that produced America's Lab Report.


      2020-2021 Colloquium, Wednesdays

      The 2020-2021 Colloquium will take place every Wednesday from 9:00 to 10:00am ET virtually, using zoom. All CMSA postdocs/members are required to attend the weekly CMSA Members’ Seminars, as well as the weekly CMSA Colloquium series. Please email the seminar organizers to obtain a link. This year’s colloquium will be organized by Wei Gu and Sergiy Verstyuk. The schedule below will be updated as speakers are confirmed.

      Information on previous colloquia can be found here.

      Spring 2021:

      Date SpeakerTitle/Abstract
      1/27/2021Evelyn Tang (Max Planck Institute for Dynamics and Self-Organization)

      Abstract: How should a random quantity be summarized by a single number? We study mappings from random variables to real numbers, focussing on those with the following two properties: (1) monotonicity with respect to first-order stochastic dominance, and (2) additivity for sums of independent random variables. This problem turns out to be connected to the following question: Under what conditions on the random variables X and Y does there exist an independent Z so that X + Z first-order stochastically dominates Y + Z?