Information and Entropy in Biological Systems (Part 3)

I think you can watch live streaming video of our workshop on Information and Entropy in Biological Systems, which runs Wednesday April 8th to Friday April 10th. Later, videos will be made available in a permanent location.

To watch the workshop live, go here. Go down to where it says

Investigative Workshop: Information and Entropy in Biological Systems

Then click where it says live link. There’s nothing there now, but I’m hoping there will be when the show starts!

Below you can see the schedule of talks and a list of participants. The hours are in Eastern Daylight Time: add 4 hours to get Greenwich Mean Time. The talks start at 10 am EDT, which is 2 pm GMT.

Schedule

There will be 1½ hours of talks in the morning and 1½ hours in the afternoon for each of the 3 days, Wednesday April 8th to Friday April 10th. The rest of the time will be for discussions on different topics. We’ll break up into groups, based on what people want to discuss.

Each invited speaker will give a 30-minute talk summarizing the key ideas in some area, not their latest research so much as what everyone should know to start interesting conversations. After that, 15 minutes for questions and/or coffee.

Here’s the schedule. You can already see slides or other material for the talks with links!

Wednesday April 8

• 9:45-10:00 — the usual introductory fussing around.
• 10:00-10:30 — John Baez, Information and entropy in biological systems.
• 10:30-11:00 — questions, coffee.
• 11:00-11:30 — Chris Lee, Empirical information, potential information and disinformation.
• 11:30-11:45 — questions.

• 11:45-1:30 — lunch, conversations.

• 1:30-2:00 — John Harte, Maximum entropy as a foundation for theory building in ecology.
• 2:00-2:15 — questions, coffee.
• 2:15-2:45 — Annette Ostling, The neutral theory of biodiversity and other competitors to the principle of maximum entropy.
• 2:45-3:00 — questions, coffee.
• 3:00-5:30 — break up into groups for discussions.

• 5:30 — reception.

Thursday April 9

• 10:00-10:30 — David Wolpert, The Landauer limit and thermodynamics of biological organisms.
• 10:30-11:00 — questions, coffee.
• 11:00-11:30 — Susanne Still, Efficient computation and data modeling.
• 11:30-11:45 — questions.

• 11:45-1:30 — group photo, lunch, conversations.

• 1:30-2:00 — Matina Donaldson-Matasci, The fitness value of information in an uncertain environment.
• 2:00-2:15 — questions, coffee.
• 2:15-2:45 — Roderick Dewar, Maximum entropy and maximum entropy production in biological systems: survival of the likeliest?
• 2:45-3:00 — questions, coffee.
• 3:00-6:00 — break up into groups for discussions.

Friday April 10

• 10:00-10:30 — Marc Harper, Information transport and evolutionary dynamics.
• 10:30-11:00 — questions, coffee.
• 11:00-11:30 — Tobias Fritz, Characterizations of Shannon and Rényi entropy.
• 11:30-11:45 — questions.

• 11:45-1:30 — lunch, conversations.

• 1:30-2:00 — Christina Cobbold, Biodiversity measures and the role of species similarity.
• 2:00-2:15 — questions, coffee.
• 2:15-2:45 — Tom Leinster, Maximizing biological diversity.
• 2:45-3:00 — questions, coffee.
• 3:00-6:00 — break up into groups for discussions.

Participants

Here are the confirmed participants. This list may change a little bit:

• John Baez – mathematical physicist.

• Romain Brasselet – postdoc in cognitive neuroscience knowledgeable about information-theoretic methods and methods of estimating entropy from samples of probability distributions.

• Katharina Brinck – grad student at Centre for Complexity Science at Imperial College; did masters at John Harte’s lab, where she extended his Maximum Entropy Theory of Ecology (METE) to trophic food webs, to study how entropy maximization on the macro scale together with MEP on the scale of individuals drive the structural development of model ecosystems.

• Christina Cobbold – mathematical biologist, has studied the role of species similarity in measuring biodiversity.

• Troy Day – mathematical biologist, works with population dynamics, host-parasite dynamics, etc.; influential and could help move population dynamics to a more information-theoretic foundation.

• Roderick Dewar – physicist who studies the principle of maximal entropy production.

• Barrett Deris – MIT postdoc studying the studying the factors that influence evolvability of drug resistance in bacteria.

• Charlotte de Vries – a biology master’s student who studied particle physics to the master’s level at Oxford and the Perimeter Institute. Interested in information theory.

• Matina Donaldson-Matasci – a biologist who studies information, uncertainty and collective behavior.

• Chris Ellison – a postdoc who worked with James Crutchfield on “information-theoretic measures of structure and memory in stationary, stochastic systems – primarily, finite state hidden Markov models”. He coauthored “Intersection Information based on Common Randomness”, http://arxiv.org/abs/1310.1538. The idea: “The introduction of the partial information decomposition generated a flurry of proposals for defining an intersection information that quantifies how much of “the same information” two or more random variables specify about a target random variable. As of yet, none is wholly satisfactory.” Works on mutual information between organisms and environment (along with David Krakauer and Jessica Flack), and also entropy rates.

• Cameron Freer – MIT postdoc in Brain and Cognitive Sciences working on maximum entropy production principles, algorithmic entropy etc.

• Tobias Fritz – a physicist who has worked on “resource theories” and haracterizations of Shannon and Rényi entropy and on resource theories.

• Dashiell Fryer – works with Marc Harper on information geometry and evolutionary game theory.

• Michael Gilchrist – an evolutionary biologist studying how errors and costs of protein translation affect the codon usage observed within a genome. Works at NIMBioS.

• Manoj Gopalkrishnan – an expert on chemical reaction networks who understands entropy-like Lyapunov functions for these systems.

• Marc Harper – works on evolutionary game theory using ideas from information theory, information geometry, etc.

• John Harte – an ecologist who uses the maximum entropy method to predict the structure of ecosystems.

• Ellen Hines – studies habitat modeling and mapping for marine endangered species and ecosystems, sea level change scenarios, documenting of human use and values. Her lab has used MaxEnt methods.

• Elizabeth Hobson – behavior ecology postdoc developing methods to quantify social complexity in animals. Works at NIMBioS.

• John Jungk – works on graph theory and biology.

• Chris Lee – in bioinformatics and genomics; applies information theory to experiment design and evolutionary biology.

• Maria Leites – works on dynamics, bifurcations and applications of coupled systems of non-linear ordinary differential equations with applications to ecology, epidemiology, and transcriptional regulatory networks. Interested in information theory.

• Tom Leinster – a mathematician who applies category theory to study various concepts of ‘magnitude’, including biodiversity and entropy.

• Timothy Lezon – a systems biologist in the Drug Discovery Institute at Pitt, who has used entropy to characterize phenotypic heterogeneity in populations of cultured cells.

• Maria Ortiz Mancera – statistician working at CONABIO, the National Commission for Knowledge and Use of Biodiversity, in Mexico.

• Yajun Mei – statistician who uses Kullback-Leibler divergence and how to efficiently compute entropy for the two-state hidden Markov models.

• Robert Molzon – mathematical economist who has studied deterministic approximation of stochastic evolutionary dynamics.

• David Murrugarra – works on discrete models in mathematical biology; interested in learning about information theory.

• Annette Ostling – studies community ecology, focusing on the influence of interspecific competition on community structure, and what insights patterns of community structure might provide about the mechanisms by which competing species coexist.

• Connie Phong – grad student at Chicago’s Institute of Genomics and System biology, working on how “certain biochemical network motifs are more attuned than others at maintaining strong input to output relationships under fluctuating conditions.”

• Petr Plechak – works on information-theoretic tools for estimating and minimizing errors in coarse-graining stochastic systems. Wrote “Information-theoretic tools for parametrized coarse-graining of non-equilibrium extended systems”.

• Blake Polllard – physics grad student working with John Baez on various generalizations of Shannon and Renyi entropy, and how these entropies change with time in Markov processes and open Markov processes.

• Timothee Poisot – works on species interaction networks; developed a “new suite of tools for probabilistic interaction networks”.

• Richard Reeve – works on biodiversity studies and the spread of antibiotic resistance. Ran a program on entropy-based biodiversity measures at a mathematics institute in Barcelona.

• Rob Shaw – works on entropy and information in biotic and pre-biotic systems.

• Matteo Smerlak – postdoc working on nonequilibrium thermodynamics and its applications to biology, especially population biology and cell replication.

• Susanne Still – a computer scientist who studies the role of thermodynamics and information theory in prediction.

• Alexander Wissner-Gross – Institute Fellow at the Harvard University Institute for Applied Computational Science and Research Affiliate at the MIT Media Laboratory, interested in lots of things.

• David Wolpert – works at the Santa Fe Institute on i) information theory and game theory, ii) the second law of thermodynamics and dynamics of complexity, iii) multi-information source optimization, iv) the mathematical underpinnings of reality, v) evolution of organizations.

• Matthew Zefferman – works on evolutionary game theory, institutional economics and models of gene-culture co-evolution. No work on information, but a postdoc at NIMBioS.

3 Responses to Information and Entropy in Biological Systems (Part 3)

  1. John, can you or someone from NIMBioS provision me to log into the site at http://www.nimbios.org/wordpress-training/entropy/ as I watch/listen from afar? I wish I could have been there this week with everyone. Thanks for putting it together and good luck this week!

    For those on twitter, remember that the hashtag for the workhop is #entropyWS.

    • John Baez says:

      Hi! I don’t think you need to log into that website. That’s for conference participants to post their talks, and for me to post the schedule. You’ll be able to watch the workshop live as described above (if I understand correctly), you can also watch videos of the talks later, and you can leaves comments here.

  2. John Baez says:

    The slides weren’t originally available for all talks, but now they are.

    Videos for most talks should be available by Friday 17 April 2015, though Tom Leinster’s mike was off for the first part of his talk.

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