IPAM Workshop on Regulatory and Epigenetic Stochasticity in Development and Disease (Institute for Pure and Applied Mathematics, UCLA | March 1-3, 2017)
Epigenetics refers to information transmitted during cell division other than the DNA sequence per se, and it is the language that distinguishes stem cells from somatic cells, one organ from another, and even identical twins from each other. In contrast to the DNA sequence, the epigenome is relatively susceptible to modification by the environment as well as stochastic perturbations over time, adding to phenotypic diversity in the population. Despite its strong ties to the environment, epigenetics has never been well reconciled to evolutionary thinking, and in fact there is now strong evidence against the transmission of so-called “epi-alleles,” i.e. epigenetic modifications that pass through the germline.
However, genetic variants that regulate stochastic fluctuation of gene expression and phenotypes in the offspring appear to be transmitted as an epigenetic or even Lamarckian trait. Furthermore, even the normal process of cellular differentiation from a single cell to a complex organism is not understood well from a mathematical point of view. There is increasingly strong evidence that stem cells are highly heterogeneous and in fact stochasticity is necessary for pluripotency. This process appears to be tightly regulated through the epigenome in development. Moreover, in these biological contexts, “stochasticity” is hardly synonymous with “noise”, which often refers to variation which obscures a “true signal” (e.g., measurement error) or which is structural, as in physics (e.g., quantum noise). In contrast, “stochastic regulation” refers to purposeful, programmed variation; the fluctuations are random but there is no true signal to mask.
This workshop will serve as a forum for scientists and engineers with an interest in computational biology to explore the role of stochasticity in regulation, development and evolution, and its epigenetic basis. Just as thinking about stochasticity was transformative in physics and in some areas of biology, it promises to fundamentally transform modern genetics and help to explain phase transitions such as differentiation and cancer.
This workshop will include a poster session; a request for poster titles will be sent to registered participants in advance of the workshop.
Adam Arkin (Lawrence Berkeley Laboratory)
Gábor Balázsi (SUNY Stony Brook)
Domitilla Del Vecchio (Massachusetts Institute of Technology)
Michael Elowitz (California Institute of Technology)
Andrew Feinberg (Johns Hopkins University)
Don Geman (Johns Hopkins University)
Anita Göndör (Karolinska Institutet)
John Goutsias (Johns Hopkins University)
Garrett Jenkinson (Johns Hopkins University)
Andre Levchenko (Yale University)
Olgica Milenkovic (University of Illinois)
Johan Paulsson (Harvard University)
Leor Weinberger (University of California, San Francisco (UCSF))
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IPAM Workshop on Gauge Theory and Categorification (Institute of Pure and Applied Mathematics at UCLA - March 6-10, 2017)
The equations of gauge theory lie at the heart of our understanding of particle physics. The Standard Model, which describes the electromagnetic, weak, and strong forces, is based on the Yang-Mills equations. Starting with the work of Donaldson in the 1980s, gauge theory has also been successfully applied in other areas of pure mathematics, such as low dimensional topology, symplectic geometry, and algebraic geometry.
More recently, Witten proposed a gauge-theoretic interpretation of Khovanov homology, a knot invariant whose origins lie in representation theory. Khovanov homology is a “categorification” of the celebrated Jones polynomial, in the sense that its Euler characteristic recovers this polynomial. At the moment, Khovanov homology is only defined for knots in the three-sphere, but Witten’s proposal holds the promise of generalizations to other three-manifolds, and perhaps of producing new invariants of four-manifolds.
This workshop will bring together researchers from several different fields (theoretical physics, mathematical gauge theory, topology, analysis / PDE, representation theory, symplectic geometry, and algebraic geometry), and thus help facilitate connections between these areas. The common focus will be to understand Khovanov homology and related invariants through the lens of gauge theory.
This workshop will include a poster session; a request for posters will be sent to registered participants in advance of the workshop.
Edward Witten will be giving two public lectures as part of the Green Family Lecture series:
March 6, 2017
From Gauge Theory to Khovanov Homology Via Floer Theory
The goal of the lecture is to describe a gauge theory approach to Khovanov homology of knots, in particular, to motivate the relevant gauge theory equations in a way that does not require too much physics background. I will give a gauge theory perspective on the construction of singly-graded Khovanov homology by Abouzaid and Smith.
March 8, 2017
An Introduction to the SYK Model
The Sachdev-Ye model was originally a model of quantum spin liquids that was introduced in the mid-1990′s. In recent years, it has been reinterpreted by Kitaev as a model of quantum chaos and black holes. This lecture will be primarily a gentle introduction to the SYK model, though I will also describe a few more recent results.
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Clean boards before complex analysis.
Los Angeles, California, United States of America
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Images from a conference at UCLA concerned with saving born digital news
Presentation: Technology and community: Why we need partners, collaborators, and friends Kate Zwaard, Library of Congress
Special guest speaker: Saving the first draft of history: The unlikely rescue of the AP’s Vietnam War files Peter Arnett, winner of the Pulitzer Prize for journalism
What Have We Heard?
What does Peter Arnett, the most daring journalist of the past century, do to unwind? He reads comic books of course.
Slide from Technology and community: Why we need partners, collaborators, and friends Kate Zwaard, Library of Congress
Keynote speaker: Digital salvage operations — what’s worth saving? Hjalmar Gislason, vice president of data, Qlik and Deaf Teddy
Candid audience shot during DtMH2016
Presentation: Summarizing archival collections using storytelling techniques Michael Nelson, Ph.D., Old Dominion University
Conduits for Action
Greetings from Ginny Steel, university librarian, UCLA
Panel: Why save online news? Chris Freeland, Washington University; Matt Weber, Ph.D., Rutgers, The State University of New Jersey; Laura Wrubel, The George Washington University; moderator Ana Krahmer, Ph.D., University of North Texas
Lanyard and ID badge from DtMH2016
Architectural detail in Powell Library at UCLA
“Hi there Tiiiigggggrrr!” Edward McCain, digital curator of journalism, Donald W. Reynolds Journalism Institute (RJI) and University of Missouri Libraries warmly greets the participants of DtMH2016
Details for the conference can be found at Dodging the Memory Hole 2016.
The Journalism Digital News Archive has posted a nice bunch of photos as well.
My previous posts and notes about the conference:
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Some thoughts on creating conference lists, live tweeting and archiving events.
Live Tweeting and Twitter Lists
While attending the upcoming conference Dodging the Memory Hole 2016: Saving Online News later this week, I’ll make an attempt to live Tweet as much as possible. (If you’re following me on Twitter on Thursday and Friday and find me too noisy, try using QuietTime.xyz to mute me on Twitter temporarily.) I’ll be using Kevin Marks‘ excellent Noter Live web app to both send out the tweets as well as to store and archive them here on this site thereafter (kind of like my own version of Storify.)
In getting ramped up to live Tweet it, it helps significantly to have a pre-existing list of attendees (and remote participants) talking about #DtMH2016 on Twitter, so I started creating a Twitter list by hand. I realized that it would be nice to have a little bot to catch others as the week progresses. Ever lazy, I turned to IFTTT.com to see if something already existed, and sure enough there’s a Twitter search with a trigger that will allow one to add people who mention a particular hashtag to a Twitter list automatically.
Here’s the resultant list, which should grow as the event unfolds throughout the week:
🔖 People on Twitter talking about #DtMH2016
Feel free to follow or subscribe to the list as necessary. Hopefully this will make attending the conference more fruitful for those there live as well as remote.
Not on the list? Just tweet a (non-private) message with the conference hashtag: #DTMH2016 and you should be added to the list shortly.
Lazy like me? Click the bird to tweet: “I’m attending #DtMH2016 @rji | Dodging the Memory Hole 2016: Saving Online News http://ctt.ec/5RKt2+”
IFTTT Recipe for Creating Twitter Lists of Conference Attendees
For those interested in creating their own Twitter lists for future conferences (and honestly the hosts of all conferences should do this as they set up their conference hashtag and announce the conference), below is a link to the ifttt.com recipe I created for this, but which can be modified for use by others.
Naturally, it would also be nice if, as people registered for conferences, they were asked for their Twitter handles and websites so that the information could be used to create such online lists to help create longer lasting relationships both during the event and afterwards as well. (Naturally providing these details should be optional so that people who wish to maintain their privacy could do so.)
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Holy cow! I discovered on Friday that Terence Tao, a Fields Medal winner, will be teaching a graduate level Real Analysis class this fall at UCLA.
Surprisingly, to me, it ony has 4 students currently enrolled!! Having won a Fields Medal in August 2006, this is a true shock, for who wouldn’t want to learn analysis from such a distinguished professor? Are there so few graduate students at UCLA who need a course in advanced analysis? I would imagine that there would be graduate students in engineering and even physics who might take such a course, but perhaps I’m wrong?
Most of his ratings on RateMyProfessors are actually fairly glowing; the one generally negative review was given for a topology class and generally seems to be an outlier.
On his own website in a section about the class and related announcements we seem to find the answer to the mystery about enrollment. There he says:
I intend this to be a serious course, focused on teaching the material in the course description. As such, students who are taking or auditing the course out of idle curiosity or mathematical “sightseeing”, rather than to learn the basics of measure theory and integration theory, may be disappointed. I would therefore prefer that frivolous enrollments in the class be kept to a minimum.
This is generally sound advice, but would even the most serious mathematical tourists really bother to make an attempt at such an advanced course? Why bother if you’re not going to do the work?!
Fans of the Mathematical Genealogy Project will be interested to notice that Dr. Tao is requiring his Ph.D. advisor’s text Real Analysis: Measure Theory, Integration, and Hilbert Spaces. He’s also recommending Folland‘s often used text as well, though if he really wanted to scare off the lookie-loos he could just say he’ll be using Rudin‘s text.