IPAM Workshop on Regulatory and Epigenetic Stochasticity in Development and Disease, March 1-3

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.

Speaker List:
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))

IPAM Workshop on Regulatory and Epigenetic Stochasticity in Development and Disease, March 1-3 was originally published on Chris Aldrich | Boffo Socko

🔖 IPAM Workshop on Gauge Theory and Categorification, March 6-10

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.

🔖 IPAM Workshop on Gauge Theory and Categorification, March 6-10 was originally published on Chris Aldrich | Boffo Socko

Statistical Physics, Information Processing, and Biology Workshop at Santa Fe Institute

Statistical Physics, Information Processing, and Biology Workshop at Santa Fe Institute

I just found out about this from John Carlos Baez and wish I could go! How have I not managed to have heard about it?

Stastical Physics, Information Processing, and Biology

Workshop

November 16, 2016 – November 18, 2016
9:00 AM
Noyce Conference Room

Abstract.
This workshop will address a fundamental question in theoretical biology: Does the relationship between statistical physics and the need of biological systems to process information underpin some of their deepest features? It recognizes that a core feature of biological systems is that they acquire, store and process information (i.e., perform computation). However to manipulate information in this way they require a steady flux of free energy from their environments. These two, inter-related attributes of biological systems are often taken for granted; they are not part of standard analyses of either the homeostasis or the evolution of biological systems. In this workshop we aim to fill in this major gap in our understanding of biological systems, by gaining deeper insight in the relation between the need for biological systems to process information and the free energy they need to pay for that processing.

The goal of this workshop is to address these issues by focusing on a set three specific question:

  1. How has the fraction of free energy flux on earth that is used by biological computation changed with time?;
  2. What is the free energy cost of biological computation / function?;
  3. What is the free energy cost of the evolution of biological computation / function.

In all of these cases we are interested in the fundamental limits that the laws of physics impose on various aspects of living systems as expressed by these three questions.

Purpose: Research Collaboration
SFI Host: David Krakauer, Michael Lachmann, Manfred Laubichler, Peter Stadler, and David Wolpert

Statistical Physics, Information Processing, and Biology Workshop at Santa Fe Institute was originally published on Chris Aldrich

Twitter List for #DtMH2016 Participants | Dodging the Memory Hole 2016: Saving Online News

Twitter List for #DtMH2016 Participants | Dodging the Memory Hole 2016: Saving Online News

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.

Tweet: I'm attending #DtMH2016 @rji | Dodging the Memory Hole 2016: Saving Online News http://ctt.ec/5RKt2+ 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.

IFTTT Recipe: Create Twitter List of Attendees from search of people using conference hashtag connects twitter to twitter//ifttt.com/assets/embed_recipe.js

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.)

    Syndicated to:

Twitter List for #DtMH2016 Participants | Dodging the Memory Hole 2016: Saving Online News was originally published on Chris Aldrich | Boffo Socko

Workshop on Methods of Information Theory in Computational Neuroscience | CNS 2016

Workshop on Methods of Information Theory in Computational Neuroscience | CNS 2016

Workshop on Methods of Information Theory in Computational Neuroscience (CNS 2016) by Joseph T. Lizier(lizier.me)

Methods originally developed in Information Theory have found wide applicability in computational neuroscience. Beyond these original methods there is a need to develop novel tools and approaches that are driven by problems arising in neuroscience.

A number of researchers in computational/systems neuroscience and in information/communication theory are investigating problems of information representation and processing. While the goals are often the same, these researchers bring different perspectives and points of view to a common set of neuroscience problems. Often they participate in different fora and their interaction is limited.

The goal of the workshop is to bring some of these researchers together to discuss challenges posed by neuroscience and to exchange ideas and present their latest work.

The workshop is targeted towards computational and systems neuroscientists with interest in methods of information theory as well as information/communication theorists with interest in neuroscience.

    Syndicated to:

Workshop on Methods of Information Theory in Computational Neuroscience | CNS 2016 was originally published on Chris Aldrich | Boffo Socko