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

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


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

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

NIMBioS Tutorial: Evolutionary Quantitative Genetics 2016

NIMBioS Tutorial: Evolutionary Quantitative Genetics 2016 by NIMBioS (nimbios.org)

This tutorial will review the basics of theory in the field of evolutionary quantitative genetics and its connections to evolution observed at various time scales. Quantitative genetics deals with the inheritance of measurements of traits that are affected by many genes. Quantitative genetic theory for natural populations was developed considerably in the period from 1970 to 1990 and up to the present, and it has been applied to a wide range of phenomena including the evolution of differences between the sexes, sexual preferences, life history traits, plasticity of traits, as well as the evolution of body size and other morphological measurements. Textbooks have not kept pace with these developments, and currently few universities offer courses in this subject aimed at evolutionary biologists. There is a need for evolutionary biologists to understand this field because of the ability to collect large amounts of data by computer, the development of statistical methods for changes of traits on evolutionary trees and for changes in a single species through time, and the realization that quantitative characters will not soon be fully explained by genomics. This tutorial aims to fill this need by reviewing basic aspects of theory and illustrating how that theory can be tested with data, both from single species and with multiple-species phylogenies. Participants will learn to use R, an open-source statistical programming language, to build and test evolutionary models. The intended participants for this tutorial are graduate students, postdocs, and junior faculty members in evolutionary biology.

    Syndicated to:

NIMBioS Tutorial: Evolutionary Quantitative Genetics 2016 was originally published on Chris Aldrich | Boffo Socko

Devourer of Encyclopedias: Stanislaw Lem’s “Summa Technologiae”

Devourer of Encyclopedias: Stanislaw Lem’s “Summa Technologiae”

Summa Technologiae

AT LAST WE have it in English. Summa Technologiae, originally published in Polish in 1964, is the cornerstone of Stanislaw Lem’s oeuvre, his consummate work of speculative nonfiction. Trained in medicine and biology, Lem synthesizes the current science of the day in ways far ahead of most science fiction of the time.

His subjects, among others, include:

  • Virtual reality
  • Artificial intelligence
  • Nanotechnology and biotechnology
  • Evolutionary biology and evolutionary psychology
  • Artificial life
  • Information theory
  • Entropy and thermodynamics
  • Complexity theory, probability, and chaos
  • Population and ecological catastrophe
  • The “singularity” and “transhumanism”

Source: Devourer of Encyclopedias: Stanislaw Lem’s “Summa Technologiae” – The Los Angeles Review of Books

I came across this book review quite serendipitously today via an Auerbach article in Slate, which I’ve bookmarked. I found a copy of the book and have added it to the top of my reading pile. As I’m currently reading an advance reader edition of Sean Carroll’s The Big Picture, I can only imagine how well the two may go together despite being written nearly 60 years apart.

Devourer of Encyclopedias: Stanislaw Lem’s “Summa Technologiae” was originally published on Chris Aldrich

The Information Universe Conference

The Information Universe Conference

Yesterday, via a notification from Lanyard, I came across a notice for the upcoming conference “The Information Universe” which hits several of the sweet spots for areas involving information theory, physics, the origin of life, complexity, computer science, and microbiology. It is scheduled to occur from October 7-9, 2015 at the Infoversum Theater in Groningen, The Netherlands.

I’ll let their site speak for itself below, but they already have an interesting line up of speakers including:

Keynote speakers

  • Erik Verlinde, Professor Theoretical Physics, University of Amsterdam, Netherlands
  • Alex Szalay, Alumni Centennial Professor of Astronomy, The Johns Hopkins University, USA
  • Gerard ‘t Hooft, Professor Theoretical Physics, University of Utrecht, Netherlands
  • Gregory Chaitin, Professor Mathematics and Computer Science, Federal University of Rio de Janeiro, Brasil
  • Charley Lineweaver, Professor Astronomy and Astrophysics, Australian National University, Australia
  • Lude Franke, Professor System Genetics, University Medical Center Groningen, Netherlands
Infoversum Theater, The Netherlands
Infoversum Theater, The Netherlands

Conference synopsis from their homepage:

The main ambition of this conference is to explore the question “What is the role of information in the physics of our Universe?”. This intellectual pursuit may have a key role in improving our understanding of the Universe at a time when we “build technology to acquire and manage Big Data”, “discover highly organized information systems in nature” and “attempt to solve outstanding issues on the role of information in physics”. The conference intends to address the “in vivo” (role of information in nature) and “in vitro” (theory and models) aspects of the Information Universe.

The discussions about the role of information will include the views and thoughts of several disciplines: astronomy, physics, computer science, mathematics, life sciences, quantum computing, and neuroscience. Different scientific communities hold various and sometimes distinct formulations of the role of information in the Universe indicating we still lack understanding of its intrinsic nature. During this conference we will try to identify the right questions, which may lead us towards an answer.

  • Is the universe one big information processing machine?
  • Is there a deeper layer in quantum mechanics?
  • Is the universe a hologram?
  • Is there a deeper physical description of the world based on information?
  • How close/far are we from solving the black hole information paradox?
  • What is the role of information in highly organized complex life systems?
  • The Big Data Universe and the Universe : are our numerical simulations and Big Data repositories (in vitro) different from real natural system (in vivo)?
  • Is this the road to understanding dark matter, dark energy?

The conference will be held in the new 260 seats planetarium theatre in Groningen, which provides an inspiring immersive 3D full dome display, e.g. numerical simulations of the formation of our Universe, and anything else our presenters wish to bring in. The digital planetarium setting will be used to visualize the theme with modern media.

The Information Universe Website

Additional details about the conference including the participants, program, venue, and registration can also be found at their website.

The Information Universe Conference was originally published on Chris Aldrich