Month: October 2014
A banquet table for Dia de Los Muertos
Doritos covered cheese ball!
BIRS Workshop on Biological and BioInspired Information Theory  Storify Stream
Over the span of the coming week, I’ll be updating (and archiving) the stream of information coming out of the BIRS Workshop on Biological and BioInspired Information Theory.
Editor’s note: On 12/12/17 Storify announced they would be shutting down. As a result, I’m changing the embedded version of the original data served by Storify for an HTML copy which can be found below:
Edit
BIRS: Biological and BioInspired Information Theory
A 5 Day workshop on Biology and Information Theory hosted by the Banff International Research Station

I know where I’ll be in Oct 2014! Let’s hear it for Biology & Information Theory! https://www.birs.ca/events/2014/5dayworkshops/14w5170 … #ITBio #Banff @andreweckford

. @andreweckford You might be interested in this grouping of research papers: http://www.mendeley.com/groups/2545131/itbio/ … #ITBio #Banff

Wishing I was at the Gene Regulation and Information Theory meeting starting tomorrow http://bit.ly/XnHRZs #ITBio

#ITBio: @andreweckford has a new book on Molecular Communication available Oct 31. http://bit.ly/15uEUzF

Mathematical and Statistical Models for Genetic Coding starts today. http://www.am.hsmannheim.de/genetic_code_2013.php?id=1 … @andreweckford might borrow attendees for BIRS

John Baez has announced a workshop on Entropy & Information in Biological Systems http://johncarlosbaez.wordpress.com/2013/11/02/entropyandinformationinbiologicalsystems/ … #NIMBioS #ITBio @andreweckford

Mathematical Foundations for Information Theory in DiffusionBased Molecular Communications http://bit.ly/1aTVR2c #ITBio

Bill Bialek giving plenary talk “Information flow & order in real biological networks” at Feb 2014 workshop http://mnd.ly/19LQH8f #ITBio

Workshop on Information Theoretic Incentives for Artificial Life http://jhu.md/1lM8tAn #ITBio #ALife14 @alifeofficial @14thALIFE @cxdig

Researchers working in information theory & biology http://jhu.md/1gieQGR #ITBio @andreweckford @ChristophAdami @wbialek @johnhawks

Currently organizing my Banff workshop on bioinformation theory … https://www.birs.ca/events/2014/5dayworkshops/14w5170 …

Last RT: wonder what the weather is going to be like at the end of October for my @BIRS_Math workshop

@JoVanEvery I’m organizing a workshop in Banff in October … hopefully this isn’t a sign of weather to come!

Special issue of Entropy: “Information Theoretic Incentives for Cognitive Systems” http://boffosocko.com/2014/09/19/specialissueofentropyinformationtheoreticincentivesforcognitivesystems/ … #ITBio #CallForSubmissions

Next week @BIRS_Math: Biological and BioInspired Information Theory http://www.birs.ca/events/2014/5dayworkshops/14w5170 …  Live @ http://www.birs.ca/live #bioinformatics

Andrew Eckford (York University), The Landscape http://www.birs.ca/events/2014/5dayworkshops/14w5170/videos/watch/201410270858Eckford.mp4 …

“Not an obvious connection between utility and information, just as there is no obvious connection between energy and entropy” @BIRS_Math

Peter Thomas (Case Western Reserve University), Signal Transduction and Information Theory http://www.birs.ca/events/2014/5dayworkshops/14w5170/videos/watch/201410270940Thomas.mp4 …

Following @andreweckford @BIRS_Math 4 updates/video from Biological & BioInspired Information Theory https://storify.com/ChrisAldrich/biologicalandbioinspiredinformationtheory … @cxdig #ITBio

Live now: Nicolo Michelusi of @USCViterbi on Stochastic Model for Electron Transfer in Bacterial Cables http://www.birs.ca/live #ITBio

Nicolo Michelusi (University of Southern California), A Stochastic Model for Electron Transfer in Bacterial Cables http://www.birs.ca/events/2014/5dayworkshops/14w5170/videos/watch/201410271450Michelusi.mp4 …

“Timing is fundamental … subsumes timevarying concentration channel” @cnmirose @BIRS_Math

Chris Rose (Rutgers University), Molecular Communication Channels: timing vs. payload http://www.birs.ca/events/2014/5dayworkshops/14w5170/videos/watch/201410271538Rose.mp4 …

Standard opening quote of these talks: “I’m not a biologist, but …” @BIRS_Math

Stefan Moser (ETH Zurich), Capacity Bounds of the Memoryless AIGN Channel – a ToyModel for Molecular Communicat… http://www.birs.ca/events/2014/5dayworkshops/14w5170/videos/watch/201410271610Moser.mp4 …

Biodiversity, Entropy and ThermodynamicsI’m giving a short 30minute talk at a workshop on Biological and BioInspired Information Theory at the Banff International Research Institute. I’ll say more about the workshop later, but here’s my talk: * Biodiversity, entropy and thermodynamics. Most of the people at this workshop study neurobiology and cell signalling, not evolutionary game theory or…

Weisi Guo (University of Warwick), Communication Envelopes for Molecular Diffusion and Electromagnetic Wave Propag… http://www.birs.ca/events/2014/5dayworkshops/14w5170/videos/watch/201410271643Guo.mp4 …


.@Storify stream coming out of @BIRS_Math: Biological & BioInspired Information Theory this week: http://boffosocko.com/2014/10/27/birsworkshoponbiologicalandbioinspiredinformationtheorystorifystream/ …


Terrific introduction of Canada/Banff by Andrew Eckford (York)The Landscape http://www.birs.ca/events/2014/5dayworkshops/14w5170/videos/watch/201410270858Eckford.mp4 …”

@andreweckford “The Landscape” to become a permanent resource for @BIRS_Math participants http://www.birs.ca/events/2014/5dayworkshops/14w5170/videos/watch/201410270858Eckford.mp4 …”

Biological and BioInspired Information Theory workshop videos! http://www.birs.ca/events/2014/5dayworkshops/14w5170/videos … @BIRS_Math

.@ChrisAldrich @andreweckford @Storify @BIRS_Math Sounds like a fascinating workshop on bioinformation theory in Banff.

Mathematical Modeling of Biological Processes (by Avner Friedman & ChiuYen Kao) http://www.amazon.com/MathematicalModelingBiologicalProcessesModelling/dp/3319083139/ref=as_sl_pc_ss_til?tag=compldiges20&linkCode=w01&linkId=3H5F3QNHI6IDWAFQ&creativeASIN=3319083139 …

Toby Berger, winner of the 2002 Shannon award, speaking right now. @BIRS_Math

Naftali Tishby (Hebrew University of Jerusalem), Sensing and acting under information constraints – a principled a… http://www.birs.ca/events/2014/5dayworkshops/14w5170/videos/watch/201410281032Tishby.mp4 …

“…places such as BIRS and the Banff Centre exist to facilitate the exchange and pursuit of knowledge.” S. Sundaram http://www.birs.ca/testimonials/#testimonial1454 …

We’re going for a hike tomorrow. Many thanks to Lukas at the @ParksCanada info centre in Banff for helpful advice! @BIRS_Math

Behnaam Aazhang (Rice University), RealTime Network Modulation for Intractable Epilepsy http://www.birs.ca/events/2014/5dayworkshops/14w5170/videos/watch/201410281337Aazhang.mp4 …

Alexander Dimitrov (Washington State University), Invariant signal processing in auditory biological systems http://www.birs.ca/events/2014/5dayworkshops/14w5170/videos/watch/201410281416Dimitrov.mp4 …

Joel Zylberberg (University of Washington), Communicating with noisy signals: lessons learned from the mammalian v… http://www.birs.ca/events/2014/5dayworkshops/14w5170/videos/watch/201410281450Zylberberg.mp4 …

Robert Schober (Universitat ErlangenNurnberg), Intersymbol interference mitigation in diffusive molecular communi… http://www.birs.ca/events/2014/5dayworkshops/14w5170/videos/watch/201410281549Schober.mp4 …

Rudolf Rabenstein (FriedrichAlexanderUniversitat ErlangenNurnberg (FAU)), Modelling Molecular Communication Cha… http://www.birs.ca/events/2014/5dayworkshops/14w5170/videos/watch/201410281627Rabenstein.mp4 …

THis week @BIRS_Math ” Biological and BioInspired Information Theory ” @thebanffcentre #biology #math @NSF

“Your theory might match the data, but the data might be wrong” – Crick @BIRS_Math

So information theory seems to be a big deal in ecology. @BIRS_Math

Tom Schneider (National Institutes of Health), Three Principles of Biological States: Ecology and Cancer http://www.birs.ca/events/2014/5dayworkshops/14w5170/videos/watch/201410290904Schneider.mp4 …

“In biodiversity, the entropy of an ecosystem is the expected … information we gain about an organism by learning its species” @BIRS_Math

Seriously, I’m blown away by this work in information theory in ecology. Huge body of work; I had no idea. @BIRS_Math

.@andreweckford @QuantaMagazine had a nice overview of some of John Harte’s work in September http://bit.ly/1DwIWCD @BIRS_Math

ChanByoung Chae (Yonsei University), Molecular MIMO: From Theory to Practice http://www.birs.ca/events/2014/5dayworkshops/14w5170/videos/watch/201410281705Chae.mp4 …

John Baez (University of California, Riverside), Biodiversity, entropy and thermodynamics http://www.birs.ca/events/2014/5dayworkshops/14w5170/videos/watch/201410291038Baez.mp4 …

I encourage @BIRS_Math attendees at Biological & BioInspired Information Theory to contribute references here: http://bit.ly/1jQwObk

Christoph Adami (Michigan State University), Some InformationTheoretic Musings Concerning the Origin and Evolutio… http://www.birs.ca/events/2014/5dayworkshops/14w5170/videos/watch/201410291114Adami.mp4 …

Twitter Lists for @BIRS_Math workshop #Biology #InformationTheory:
#ITBIO: http://bit.ly/1yIfzfJ
#complexitytheory http://bit.ly/1scfZbw 
ICYMI @ChristophAdami had great paper: Informationtheoretic Considerations on Origin of Life on arXiv http://bit.ly/1yIhK2Q @BIRS_Math

Sensing and Acting Under Information ConstraintsI’m having a great time at a workshop on Biological and BioInspired Information Theory in Banff, Canada. You can see videos of the talks online. There have been lots of good talks so far, but this one really blew my mind: * Naftali Tishby, Sensing and acting under information constraints—a principled approach to biology and…

I’m listening to a talk on the origin of life at a workshop on Biological and BioInspired Information Theory. … https://plus.google.com/117562920675666983007/posts/gqFL7XY3quF …

Ilya Nemenman @EmoryUniversity on Predictive information http://bit.ly/1titfOw
Follow his research: http://bit.ly/1tithFW @BIRS_Math 

Ilya Nemenman (Emory University), Predictive information http://www.birs.ca/events/2014/5dayworkshops/14w5170/videos/watch/201410300907Nemenman.mp4 …

Toby Berger (University of Virginia), Neruoscience Applications of GIG Distributions http://www.birs.ca/events/2014/5dayworkshops/14w5170/videos/watch/201410280914Berger.mp4 …

Daniel Polani (University of Hertfordshire), Informational Principles in PerceptionAction Loops http://www.birs.ca/events/2014/5dayworkshops/14w5170/videos/watch/201410301038Polani.mp4 …

Fascinating stuff! #Information Theory #Entropy #Thermodynamics #Chemistry #Physics & lastly #Life itself: https://medium.com/thephysicsarxivblog/informationtheoryandtheoriginoflife4cf6b93d156c …

Didn’t get enough information theory & biology this week @BIRS_Math? Apply for NIMBioS workshop in April 2015 http://bit.ly/1yIeiWe #ITBio

Amin Emad (University of Illinois at UrbanaChampaign), Applications of Discrete Mathematics in Bioinformatics http://www.birs.ca/events/2014/5dayworkshops/14w5170/videos/watch/201410301329Emad.mp4 …

Paul Bogdan (University of Southern California), Multiscale Analysis Reveals Complex Behavior in Bacteria Populati… http://www.birs.ca/events/2014/5dayworkshops/14w5170/videos/watch/201410301401Bogdan.mp4 …

Robert Shaw (ProtoLife Inc.), Information and Causality in a ReactionDiffusion System http://www.birs.ca/events/2014/5dayworkshops/14w5170/videos/watch/201410301434Shaw.mp4 …

Lubomir Kostal (Institute of Physiology, Academy of Sciences of the Czech Republic), Efficient information transmi… http://www.birs.ca/events/2014/5dayworkshops/14w5170/videos/watch/201410301534Kostal.mp4 …

Nima Soltani (Stanford University), Applications of Directed Information to Neuroscience http://www.birs.ca/events/2014/5dayworkshops/14w5170/videos/watch/201410301647Soltani.mp4 …

@lrvarshney I shoulda invited you to this BIRS workshop …

@conservativelez I’m a big fan of your dad’s research & was reminded of much of it via a workshop on Biological Information Theory

@conservativelez Though he may not have been able to attend, he can catch most of the talks online if he’d like https://www.birs.ca/events/2014/5dayworkshops/14w5170 …

Depressed that @BIRS_Math Workshop on Biological & BioInspired Information Theory is over? Relive it here: http://bit.ly/1rF3G4B #ITBio

Kudos @andreweckford, Toby Berger, Peter Thomas, @NGhoussoub, @BIRS_Math & friends on a fantastic workshop! http://bit.ly/1ckttZq

This @BIRS_Math Workshop was biggest thing in #informationtheory & #biology since the Gatlinburg Symposium in 1956. http://bit.ly/1rF4RRr

1/ Everyone I talked to said it was the best workshop they’d ever been to, and they’d like to do a followup workshop @BIRS_Math

2/ There is an amazing diversity of work under the umbrella of “information theory”. @BIRS_Math

3/ Much of this work is outside the IT mainstream, and an issue is that people use different terms for related concepts. @BIRS_Math

4/ Some community building is in order. I think this workshop was a good first step. @BIRS_Math

5/ Many many thanks to @BIRS_Math and huge kudos to @NGhoussoub for excellent service to the Canadian scientific community. BIRS is a gem.

6/ Also many thanks to the participants for their excellent talks, and to @ChrisAldrich for maintaining a Storify.

@andreweckford Perhaps we could consider tying in our friends from @sfiscience? @MelMitchell1 https://www.birs.ca/events/2014/5dayworkshops/14w5170 … @BIRS_Math #complexity

Entropy and Information in Biological Systems (Part 1)John Harte is an ecologist who uses maximum entropy methods to predict the distribution, abundance and energy usage of species. Marc Harper uses information theory in bioinformatics and evolutionary game theory. Harper, Harte and I are organizing a workshop on entropy and information in biological systems, and I’m really excited about it!

Entropy and Information in Biological Systems (Part 2)John Harte, Marc Harper and I are running a workshop! Now you can apply here to attend: * Information and entropy in biological systems, National Institute for Mathematical and Biological Synthesis, Knoxville Tennesee, WednesdayFriday, 810 April 2015. Click the link, read the stuff and scroll down to “CLICK HERE” to apply.

BioInspired Information TheoryThere will be a 5day workshop on Biological and BioInspired Information Theory at BIRS from Sunday the 26th to Friday the 31st of October, 2014. It’s being organized by * Toby Berger (University of Virginia) * Andrew Eckford (York University) * Peter Thomas (Case Western Reserve University) BIRS is the Banff International Research Station,…

Andrew Eckford: The BlogHow does it feel to (co)write a book and hold the finished product in your hands? About like this: Many, many thanks to my excellent coauthors, Tadashi Nakano and Tokuko Haraguchi, for their hard work; thanks to Cambridge for accepting this project and managing it well; and thanks to Satoshi Hiyama for writing a nice blurb.

Andrew Eckford: The BlogYou may have seen our PLOS ONE paper about tabletop molecular communication, which received loads of media coverage. One of the goals of this paper was to show that anyone can do experiments in molecular communication, without any wet labs or expensive apparatus.

Meeting: Gene Regulation and Information Theoryhttp://www.uniulm.de/~sschober/fachgruppe/Meeting2013/Meeting2013.shtml
See Leopold. See Molly. Hear Molly’s Soliloquy.
Inquire in the Margine
Reply to What is the Bibliotheca Fictiva?
Any intention of acquiring the new text Bibliotheca Fictiva by Freedman as well? http://www.quaritch.com/wpcontent/uploads/sites/23/2014/09/BibliothecaFictiva.pdf
I’m not seeing it available on Amazon yet…
Information Theory is the New Central Discipline
[My comments posted to the original Facebook post follow below.]
I’m coming to this post a bit late as I’m playing a bit of catch up, but agree with it wholeheartedly.
In particular, applications to molecular biology and medicine are really beginning to come to a heavy boil in just the past five years. This particular year is the progenitor of what appears to be the biggest renaissance for the application of information theory to the area of biology since Hubert Yockey, Henry Quastler, and Robert L. Platzman’s “Symposium on Information Theory in Biology at Gatlinburg, Tennessee” in 1956.
Upcoming/recent conferences/workshops on information theory in biology include:
 BIRS Workshop: Biological and BioInspired Information Theory
 Entropy and Information in Biological Systems at NIMBios
 CECAM Workshop: Entropy in Biomolecular Systems
 ALife breakout session on Information Theoretic Incentives for Artificial Life (which will also spawn off a special issue of the journal Entropy):
At the beginning of September, Christoph Adami posted an awesome and very sound paper on arXiv entitled “Informationtheoretic considerations concerning the origin of life” which truly portends to turn the science of the origin of life on its head.
I’ll note in passing, for those interested, that Claude Shannon’s infamous master’s thesis at MIT (in which he applied Boolean Algebra to electric circuits allowing the digital revolution to occur) and his subsequent “The Theory of Mathematical Communication” were so revolutionary, nearly everyone forgets his MIT Ph.D. Thesis “An Algebra for Theoretical Genetics” which presaged the areas of cybernetics and the current applications of information theory to microbiology and are probably as seminal as Sir R.A Fisher’s applications of statistics to science in general and biology in particular.
For those commenting on the post who were interested in a layman’s introduction to information theory, I recommend John Robinson Pierce’s An Introduction to Information Theory: Symbols, Signals and Noise (Dover has a very inexpensive edition.) After this, one should take a look at Claude Shannon’s original paper. (The MIT Press printing includes some excellent overview by Warren Weaver along with the paper itself.) The mathematics in the paper really aren’t too technical, and most of it should be comprehensible by most advanced high school students.
For those that don’t understand the concept of entropy, I HIGHLY recommend Arieh BenNaim’s book Entropy Demystified The Second Law Reduced to Plain Common Sense with Seven Simulated Games. He really does tear the concept down into its most basic form in a way I haven’t seen others come remotely close to and which even my mother can comprehend (with no mathematics at all). (I recommend this presentation to even those with Ph.D.’s in physics because it is so truly fundamental.)
For the more advanced mathematicians, physicists, and engineers Arieh BenNaim does a truly spectacular job of extending ET Jaynes’ work on information theory and statistical mechanics and comes up with a more coherent mathematical theory to conjoin the entropy of physics/statistical mechanics with that of Shannon’s information theory in A Farewell to Entropy: Statistical Thermodynamics Based on Information.
For the advanced readers/researchers interested in more at the intersection of information theory and biology, I’ll also mention that I maintain a list of references, books, and journal articles in a Mendeley group entitled “ITBio: Information Theory, Microbiology, Evolution, and Complexity.”
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