BIRS Workshop on Biological and Bio-Inspired 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 Bio-Inspired Information Theory.

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 Bio-Inspired 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:

BIRS: Biological and Bio-Inspired Information Theory

A 5 Day workshop on Biology and Information Theory hosted by the Banff International Research Station

  1. Wishing I was at the Gene Regulation and Information Theory meeting starting tomorrow  http://bit.ly/XnHRZs  #ITBio
  2. Mathematical and Statistical Models for Genetic Coding starts today.  http://www.am.hs-mannheim.de/genetic_code_2013.php?id=1  @andreweckford might borrow attendees for BIRS
  3. Mathematical Foundations for Information Theory in Diffusion-Based Molecular Communications  http://bit.ly/1aTVR2c  #ITBio
  4. Bill Bialek giving plenary talk “Information flow & order in real biological networks” at Feb 2014 workshop  http://mnd.ly/19LQH8f  #ITBio
  5. CECAM Workshop: “Entropy in Biomolecular Systems” starts May 14 in Vienna. http://t.co/F4Kn0ICIaT #ITBio http://t.co/Ty8dEIXQUT

    CECAM Workshop: “Entropy in Biomolecular Systems” starts May 14 in Vienna.  http://jhu.md/1faLR8t  #ITBio pic.twitter.com/Ty8dEIXQUT
  6. Last RT: wonder what the weather is going to be like at the end of October for my @BIRS_Math workshop
  7. @JoVanEvery I’m organizing a workshop in Banff in October … hopefully this isn’t a sign of weather to come!
  8. Banff takes its name from the town of Banff, Scotland, not to be confused with Bamff, also Scotland.
  9. Good morning from beautiful Banff. How can you not love the mountains? http://t.co/mxYBNz7yzl

    Good morning from beautiful Banff. How can you not love the mountains? pic.twitter.com/mxYBNz7yzl
  10. “Not an obvious connection between utility and information, just as there is no obvious connection between energy and entropy” @BIRS_Math
  11. Last RT: a lot of discussion of my signal transduction work with Peter Thomas.
  12. Live now: Nicolo Michelusi of @USCViterbi on Stochastic Model for Electron Transfer in Bacterial Cables  http://www.birs.ca/live  #ITBio
  13. Nicolo Michelusi (University of Southern California), A Stochastic Model for Electron Transfer in Bacterial Cables  http://www.birs.ca/events/2014/5-day-workshops/14w5170/videos/watch/201410271450-Michelusi.mp4 
  14. Listening to the always awesome @cnmirose talk about the ultimate limits of molecular communication.
  15. “Timing is fundamental … subsumes time-varying concentration channel” @cnmirose @BIRS_Math
  16. Standard opening quote of these talks: “I’m not a biologist, but …” @BIRS_Math
  17. Stefan Moser (ETH Zurich), Capacity Bounds of the Memoryless AIGN Channel – a Toy-Model for Molecular Communicat…  http://www.birs.ca/events/2014/5-day-workshops/14w5170/videos/watch/201410271610-Moser.mp4 
  18. Weisi Guo (University of Warwick), Communication Envelopes for Molecular Diffusion and Electromagnetic Wave Propag…  http://www.birs.ca/events/2014/5-day-workshops/14w5170/videos/watch/201410271643-Guo.mp4 
  19. .@ChrisAldrich @andreweckford @Storify @BIRS_Math Sounds like a fascinating workshop on bioinformation theory in Banff.
  20. Toby Berger, winner of the 2002 Shannon award, speaking right now. @BIRS_Math
  21. Naftali Tishby (Hebrew University of Jerusalem), Sensing and acting under information constraints – a principled a…  http://www.birs.ca/events/2014/5-day-workshops/14w5170/videos/watch/201410281032-Tishby.mp4 
  22. “…places such as BIRS and the Banff Centre exist to facilitate the exchange and pursuit of knowledge.” S. Sundaram  http://www.birs.ca/testimonials/#testimonial-1454 
  23. We’re going for a hike tomorrow. Many thanks to Lukas at the @ParksCanada info centre in Banff for helpful advice! @BIRS_Math
  24. Alexander Dimitrov (Washington State University), Invariant signal processing in auditory biological systems  http://www.birs.ca/events/2014/5-day-workshops/14w5170/videos/watch/201410281416-Dimitrov.mp4 
  25. Joel Zylberberg (University of Washington), Communicating with noisy signals: lessons learned from the mammalian v…  http://www.birs.ca/events/2014/5-day-workshops/14w5170/videos/watch/201410281450-Zylberberg.mp4 
  26. Robert Schober (Universitat Erlangen-Nurnberg), Intersymbol interference mitigation in diffusive molecular communi…  http://www.birs.ca/events/2014/5-day-workshops/14w5170/videos/watch/201410281549-Schober.mp4 
  27. Rudolf Rabenstein (Friedrich-Alexander-Universitat Erlangen-Nurnberg (FAU)), Modelling Molecular Communication Cha…  http://www.birs.ca/events/2014/5-day-workshops/14w5170/videos/watch/201410281627-Rabenstein.mp4 
  28. THis week @BIRS_Math ” Biological and Bio-Inspired Information Theory ” @thebanffcentre #biology #math @NSF
  29. “Your theory might match the data, but the data might be wrong” – Crick @BIRS_Math
  30. So information theory seems to be a big deal in ecology. @BIRS_Math
  31. Tom Schneider (National Institutes of Health), Three Principles of Biological States: Ecology and Cancer  http://www.birs.ca/events/2014/5-day-workshops/14w5170/videos/watch/201410290904-Schneider.mp4 
  32. “In biodiversity, the entropy of an ecosystem is the expected … information we gain about an organism by learning its species” @BIRS_Math
  33. Seriously, I’m blown away by this work in information theory in ecology. Huge body of work; I had no idea. @BIRS_Math
  34. I encourage @BIRS_Math attendees at Biological & Bio-Inspired Information Theory to contribute references here:  http://bit.ly/1jQwObk 
  35. Christoph Adami (Michigan State University), Some Information-Theoretic Musings Concerning the Origin and Evolutio…  http://www.birs.ca/events/2014/5-day-workshops/14w5170/videos/watch/201410291114-Adami.mp4 
  36. .@ChristophAdami talk Some Information-Theoretic Musings Concerning the Origin of Life @BIRS_Math this morning #ITBio http://t.co/VA8komuuSW

    .@ChristophAdami talk Some Information-Theoretic Musings Concerning the Origin of Life @BIRS_Math this morning #ITBio pic.twitter.com/VA8komuuSW
  37. ICYMI @ChristophAdami had great paper: Information-theoretic Considerations on Origin of Life on arXiv  http://bit.ly/1yIhK2Q  @BIRS_Math
  38. Baez has a post on Tishby's talk "Sensing &  Acting Under Information Constraints" http://t.co/t1nPVI1pxa @BIRS_Math http://t.co/dFuiVLFSGC

    Baez has a post on Tishby’s talk “Sensing & Acting Under Information Constraints”  http://bit.ly/1yIDonR  @BIRS_Math pic.twitter.com/dFuiVLFSGC
  39. INFORMATION THEORY is the new central ...

    INFORMATION THEORY is the new central …
  40. I’m listening to a talk on the origin of life at a workshop on Biological and Bio-Inspired Information Theory. …  https://plus.google.com/117562920675666983007/posts/gqFL7XY3quF 
  41. Now accepting applications for the #Research Collaboration Workshop for Women in #MathBio at NIMBioS  http://ow.ly/DzeZ7 
  42. We removed a faulty microphone from our lecture room this morning. We’re now fixing the audio buzz in this week’s videos, and reposting.
  43. Didn’t get enough information theory & biology this week @BIRS_Math? Apply for NIMBioS workshop in April 2015  http://bit.ly/1yIeiWe  #ITBio
  44. Amin Emad (University of Illinois at Urbana-Champaign), Applications of Discrete Mathematics in Bioinformatics  http://www.birs.ca/events/2014/5-day-workshops/14w5170/videos/watch/201410301329-Emad.mp4 
  45. Paul Bogdan (University of Southern California), Multiscale Analysis Reveals Complex Behavior in Bacteria Populati…  http://www.birs.ca/events/2014/5-day-workshops/14w5170/videos/watch/201410301401-Bogdan.mp4 
  46. Lubomir Kostal (Institute of Physiology, Academy of Sciences of the Czech Republic), Efficient information transmi…  http://www.birs.ca/events/2014/5-day-workshops/14w5170/videos/watch/201410301534-Kostal.mp4 
  47. Banff ☀️❄️🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲❤️
  48. @conservativelez I’m a big fan of your dad’s research & was reminded of much of it via a workshop on Biological Information Theory
  49. @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/2014/5-day-workshops/14w5170 
  50. Depressed that @BIRS_Math Workshop on Biological & Bio-Inspired Information Theory is over? Relive it here:  http://bit.ly/1rF3G4B  #ITBio
  51. A few thoughts about that workshop while I wait for my flight back to Toronto.
  52. 1/ Everyone I talked to said it was the best workshop they’d ever been to, and they’d like to do a follow-up workshop @BIRS_Math
  53. 2/ There is an amazing diversity of work under the umbrella of “information theory”. @BIRS_Math
  54. 3/ Much of this work is outside the IT mainstream, and an issue is that people use different terms for related concepts. @BIRS_Math
  55. 4/ Some community building is in order. I think this workshop was a good first step. @BIRS_Math
  56. 5/ Many many thanks to @BIRS_Math and huge kudos to @NGhoussoub for excellent service to the Canadian scientific community. BIRS is a gem.
  57. 6/ Also many thanks to the participants for their excellent talks, and to @ChrisAldrich for maintaining a Storify.


Inquire in the Margine

"If the Page satisfie not, inquire in the Margine" - John Selden
John Selden (1584-1654), English jurist and a scholar
in Illustrations (1612), a commentary on Poly-Olbion, a poem by Michael Drayton
in the margin next to ‘A table to the chiefest passages, in the Illustrations, which, worthiest of observation, are not directed unto by the course of the volume.’

 

Photo courtesy of Sjoerd Levelt
Photo courtesy of Sjoerd Levelt

 

Information Theory is the New Central Discipline

Information Theory is the new central discipline. by Nassim Nicholas Taleb (facebook.com)

INFORMATION THEORY is the new central discipline. This graph was from 20y ago in the seminal book Cover and Thomas, as the field was starting to be defined. Now Information Theory has been expanded to swallow even more fields.

Born in, of all disciplines, Electrical Engineering, the field has progressively infiltrating probability theory, computer science, statistical physics, data science, gambling theory, ruin problems, complexity, even how one deals with knowledge, epistemology. It defines noise/signal, order/disorder, etc. It studies cellular automata. You can use it in theology (FREE WILL & algorithmic complexity). As I said, it is the MOTHER discipline.

I am certain much of Medicine will naturally grow to be a subset of it, both operationally, and in studying how the human body works: the latter is an information machine. Same with linguistics. Same with political “science”, same with… everything.

I am saying this because I figured out what the long 5th volume of the INCERTO will be. Cannot say now with any precision but it has to do with a variant of entropy as the core natural generator of Antifragility.

[Revised to explain that it is not *replacing* other disciplines, just infiltrating them as the point was initially misunderstood…]

Nassim Nicholas Taleb via Facebook

[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:

At the beginning of September, Christoph Adami posted an awesome and very sound paper on arXiv entitled “Information-theoretic 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 Ben-Naim’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 Ben-Naim 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.”

Venn Diagram of how information theory relates to other fields.
Figure 1.1 [page 2] from
Thomas M. Cover and Joy Thomas’s textbook Elements of Information Theory, Second Edition
(John Wiley & Sons, Inc., 2006) [First Edition, 1991]
Syndicated copies to: