Chris Aldrich is reading “Department of Energy May Have Broken the Second Law of Thermodynamics”

Read Department of Energy May Have Broken the Second Law of Thermodynamics (Inverse)
“Quantum-based demons” sound like they'd be at home in 'Stranger Things.'

Physicists Hunt For The Big Bang’s Triangles | Quanta Magazine

Bookmarked Physicists Hunt for the Big Bang'€™s Triangles (Quanta Magazine )

“The notion that counting more shapes in the sky will reveal more details of the Big Bang is implied in a central principle of quantum physics known as “unitarity.” Unitarity dictates that the probabilities of all possible quantum states of the universe must add up to one, now and forever; thus, information, which is stored in quantum states, can never be lost — only scrambled. This means that all information about the birth of the cosmos remains encoded in its present state, and the more precisely cosmologists know the latter, the more they can learn about the former.”

Introduction to Information Theory | SFI’s Complexity Explorer

The Santa Fe Institute's free online course "Introduction to Information Theory" taught by Seth Lloyd via Complexity Explorer.

Many readers often ask me for resources for delving into the basics of information theory. I hadn’t posted it before, but the Santa Fe Institute recently had an online course Introduction to Information Theory through their Complexity Explorer, which has some other excellent offerings. It included videos, fora, and other resources and was taught by the esteemed physicist and professor Seth Lloyd. There are a number of currently active students still learning and posting there.

Introduction to Information Theory

About the Tutorial:

This tutorial introduces fundamental concepts in information theory. Information theory has made considerable impact in complex systems, and has in part co-evolved with complexity science. Research areas ranging from ecology and biology to aerospace and information technology have all seen benefits from the growth of information theory.

In this tutorial, students will follow the development of information theory from bits to modern application in computing and communication. Along the way Seth Lloyd introduces valuable topics in information theory such as mutual information, boolean logic, channel capacity, and the natural relationship between information and entropy.

Lloyd coherently covers a substantial amount of material while limiting discussion of the mathematics involved. When formulas or derivations are considered, Lloyd describes the mathematics such that less advanced math students will find the tutorial accessible. Prerequisites for this tutorial are an understanding of logarithms, and at least a year of high-school algebra.

About the Instructor(s):

Professor Seth Lloyd is a principal investigator in the Research Laboratory of Electronics (RLE) at the Massachusetts Institute of Technology (MIT). He received his A.B. from Harvard College in 1982, the Certificate of Advanced Study in Mathematics (Part III) and an M. Phil. in Philosophy of Science from Cambridge University in 1983 and 1984 under a Marshall Fellowship, and a Ph.D. in Physics in 1988 from Rockefeller University under the supervision of Professor Heinz Pagels.

From 1988 to 1991, Professor Lloyd was a postdoctoral fellow in the High Energy Physics Department at the California Institute of Technology, where he worked with Professor Murray Gell-Mann on applications of information to quantum-mechanical systems. From 1991 to 1994, he was a postdoctoral fellow at Los Alamos National Laboratory, where he worked at the Center for Nonlinear Systems on quantum computation. In 1994, he joined the faculty of the Department of Mechanical Engineering at MIT. Since 1988, Professor Lloyd has also been an adjunct faculty member at the Sante Fe Institute.

Professor Lloyd has performed seminal work in the fields of quantum computation and quantum communications, including proposing the first technologically feasible design for a quantum computer, demonstrating the viability of quantum analog computation, proving quantum analogs of Shannon’s noisy channel theorem, and designing novel methods for quantum error correction and noise reduction.

Professor Lloyd is a member of the American Physical Society and the Amercian Society of Mechanical Engineers.

Tutorial Team:

Yoav Kallus is an Omidyar Fellow at the Santa Fe Institute. His research at the boundary of statistical physics and geometry looks at how and when simple interactions lead to the formation of complex order in materials and when preferred local order leads to system-wide disorder. Yoav holds a B.Sc. in physics from Rice University and a Ph.D. in physics from Cornell University. Before joining the Santa Fe Institute, Yoav was a postdoctoral fellow at the Princeton Center for Theoretical Science in Princeton University.

How to use Complexity Explorer: How to use Complexity Explore
Prerequisites: At least one year of high-school algebra
Like this tutorial? 


Syllabus

  1. Introduction
  2. Forms of Information
  3. Information and Probability
  4. Fundamental Formula of Information
  5. Computation and Logic: Information Processing
  6. Mutual Information
  7. Communication Capacity
  8. Shannon’s Coding Theorem
  9. The Manifold Things Information Measures
  10. Homework

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

Read Devourer of Encyclopedias: Stanislaw Lem's "Summa Technologiae" (The Los Angeles Review of Books)
A review of Summa Technologiae by Stanislaw Lem by David Auerbach from the Los Angeles Review of Books.

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.

What is Information? by Christoph Adami

Bookmarked What is Information? [1601.06176] by Christoph AdamiChristoph Adami (arxiv.org)

Information is a precise concept that can be defined mathematically, but its relationship to what we call "knowledge" is not always made clear. Furthermore, the concepts "entropy" and "information", while deeply related, are distinct and must be used with care, something that is not always achieved in the literature. In this elementary introduction, the concepts of entropy and information are laid out one by one, explained intuitively, but defined rigorously. I argue that a proper understanding of information in terms of prediction is key to a number of disciplines beyond engineering, such as physics and biology.

Comments: 19 pages, 2 figures. To appear in Philosophical Transaction of the Royal Society A
Subjects: Adaptation and Self-Organizing Systems (nlin.AO); Information Theory (cs.IT); Biological Physics (physics.bio-ph); Quantitative Methods (q-bio.QM)
Cite as:arXiv:1601.06176 [nlin.AO] (or arXiv:1601.06176v1 [nlin.AO] for this version)

From: Christoph Adami
[v1] Fri, 22 Jan 2016 21:35:44 GMT (151kb,D) [.pdf]

A proper understanding of information in terms of prediction is key to a number of disciplines beyond engineering, such as physics and biology.

Forthcoming ITBio-related book from Sean Carroll: “The Big Picture: On the Origins of Life, Meaning, and the Universe Itself”

Physicist Sean Carroll has a forthcoming book entitled The Big Picture: On the Origins of Life, Meaning, and the Universe Itself (Dutton, May 10, 2016) that will be of interest to many of our readers.

In catching up on blogs/reading from the holidays, I’ve noticed that physicist Sean Carroll has a forthcoming book entitled The Big Picture: On the Origins of Life, Meaning, and the Universe Itself (Dutton, May 10, 2016) that will be of interest to many of our readers. One can already pre-order the book via Amazon.

Prior to the holidays Sean wrote a blogpost that contains a full overview table of contents, which will give everyone a stronger idea of its contents. For convenience I’ll excerpt it below.

I’ll post a review as soon as a copy arrives, but it looks like a strong new entry in the category of popular science books on information theory, biology and complexity as well as potentially the areas of evolution, the origin of life, and physics in general.

As a side bonus, for those reading this today (1/15/16), I’ll note that Carroll’s 12 part lecture series from The Great Courses The Higgs Boson and Beyond (The Learning Company, February 2015) is 80% off.

The Big Picture

 

THE BIG PICTURE: ON THE ORIGINS OF LIFE, MEANING, AND THE UNIVERSE ITSELF

0. Prologue

* Part One: Cosmos

  • 1. The Fundamental Nature of Reality
  • 2. Poetic Naturalism
  • 3. The World Moves By Itself
  • 4. What Determines What Will Happen Next?
  • 5. Reasons Why
  • 6. Our Universe
  • 7. Time’s Arrow
  • 8. Memories and Causes

* Part Two: Understanding

  • 9. Learning About the World
  • 10. Updating Our Knowledge
  • 11. Is It Okay to Doubt Everything?
  • 12. Reality Emerges
  • 13. What Exists, and What Is Illusion?
  • 14. Planets of Belief
  • 15. Accepting Uncertainty
  • 16. What Can We Know About the Universe Without Looking at It?
  • 17. Who Am I?
  • 18. Abducting God

* Part Three: Essence

  • 19. How Much We Know
  • 20. The Quantum Realm
  • 21. Interpreting Quantum Mechanics
  • 22. The Core Theory
  • 23. The Stuff of Which We Are Made
  • 24. The Effective Theory of the Everyday World
  • 25. Why Does the Universe Exist?
  • 26. Body and Soul
  • 27. Death Is the End

* Part Four: Complexity

  • 28. The Universe in a Cup of Coffee
  • 29. Light and Life
  • 30. Funneling Energy
  • 31. Spontaneous Organization
  • 32. The Origin and Purpose of Life
  • 33. Evolution’s Bootstraps
  • 34. Searching Through the Landscape
  • 35. Emergent Purpose
  • 36. Are We the Point?

* Part Five: Thinking

  • 37. Crawling Into Consciousness
  • 38. The Babbling Brain
  • 39. What Thinks?
  • 40. The Hard Problem
  • 41. Zombies and Stories
  • 42. Are Photons Conscious?
  • 43. What Acts on What?
  • 44. Freedom to Choose

* Part Six: Caring

  • 45. Three Billion Heartbeats
  • 46. What Is and What Ought to Be
  • 47. Rules and Consequences
  • 48. Constructing Goodness
  • 49. Listening to the World
  • 50. Existential Therapy
  • Appendix: The Equation Underlying You and Me
  • Acknowledgments
  • Further Reading
  • References
  • Index

Source: Sean Carroll | The Big Picture: Table of Contents

Donald Forsdyke Indicates the Concept of Information in Biology Predates Claude Shannon

In the 1870s Ewald Hering in Prague and Samuel Butler in London laid the foundations. Butler's work was later taken up by Richard Semon in Munich, whose writings inspired the young Erwin Schrodinger in the early decades of the 20th century.

As it was published, I had read Kevin Hartnett’s article and interview with Christoph Adami The Information Theory of Life in Quanta Magazine. I recently revisited it and read through the commentary and stumbled upon an interesting quote relating to the history of information in biology:

Polymath Adami has ‘looked at so many fields of science’ and has correctly indicated the underlying importance of information theory, to which he has made important contributions. However, perhaps because the interview was concerned with the origin of life and was edited and condensed, many readers may get the impression that IT is only a few decades old. However, information ideas in biology can be traced back to at least 19th century sources. In the 1870s Ewald Hering in Prague and Samuel Butler in London laid the foundations. Butler’s work was later taken up by Richard Semon in Munich, whose writings inspired the young Erwin Schrodinger in the early decades of the 20th century. The emergence of his text – “What is Life” – from Dublin in the 1940s, inspired those who gave us DNA structure and the associated information concepts in “the classic period” of molecular biology. For more please see: Forsdyke, D. R. (2015) History of Psychiatry 26 (3), 270-287.

Donald Forsdyke, bioinformatician and theoretical biologist
in response to The Information Theory of Life in Quanta Magazine on

These two historical references predate Claude Shannon’s mathematical formalization of information in A Mathematical Theory of Communication (The Bell System Technical Journal, 1948) and even Erwin Schrödinger‘s lecture (1943) and subsequent book What is Life (1944).

For those interested in reading more on this historical tidbit, I’ve dug up a copy of the primary Forsdyke reference which first appeared on arXiv (prior to its ultimate publication in History of Psychiatry [.pdf]):

🔖 [1406.1391] ‘A Vehicle of Symbols and Nothing More.’ George Romanes, Theory of Mind, Information, and Samuel Butler by Donald R. Forsdyke  [1]
Submitted on 4 Jun 2014 (v1), last revised 13 Nov 2014 (this version, v2)

Abstract: Today’s ‘theory of mind’ (ToM) concept is rooted in the distinction of nineteenth century philosopher William Clifford between ‘objects’ that can be directly perceived, and ‘ejects,’ such as the mind of another person, which are inferred from one’s subjective knowledge of one’s own mind. A founder, with Charles Darwin, of the discipline of comparative psychology, George Romanes considered the minds of animals as ejects, an idea that could be generalized to ‘society as eject’ and, ultimately, ‘the world as an eject’ – mind in the universe. Yet, Romanes and Clifford only vaguely connected mind with the abstraction we call ‘information,’ which needs ‘a vehicle of symbols’ – a material transporting medium. However, Samuel Butler was able to address, in informational terms depleted of theological trappings, both organic evolution and mind in the universe. This view harmonizes with insights arising from modern DNA research, the relative immortality of ‘selfish’ genes, and some startling recent developments in brain research.

Comments: Accepted for publication in History of Psychiatry. 31 pages including 3 footnotes. Based on a lecture given at Santa Clara University, February 28th 2014, at a Bannan Institute Symposium on ‘Science and Seeking: Rethinking the God Question in the Lab, Cosmos, and Classroom.’

The original arXiv article also referenced two lectures which are appended below:

[Original Draft of this was written on December 14, 2015.]

References

[1]
D. Forsdyke R., “‘A vehicle of symbols and nothing more’. George Romanes, theory of mind, information, and Samuel Butler,” History of Psychiatry, vol. 26, no. 3, Aug. 2015 [Online]. Available: http://journals.sagepub.com/doi/abs/10.1177/0957154X14562755

The Information Universe Conference

"The Information Universe" Conference in The Netherlands in October hits several of the sweet spots for areas involving information theory, physics, the origin of life, complexity, computer science, and microbiology.

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.

Videos from the NIMBioS Workshop on Information and Entropy in Biological Systems

Videos from the NIMBioS workshop on Information and Entropy in Biological Systems from April 8-10, 2015 are slowly starting to appear on YouTube.

Videos from the April 8-10, 2015, NIMBioS workshop on Information and Entropy in Biological Systems are slowly starting to appear on YouTube.

John Baez, one of the organizers of the workshop, is also going through them and adding some interesting background and links on his Azimuth blog as well for those who are looking for additional details and depth

Additonal resources from the Workshop:

 

NIMBioS Workshop: Information Theory and Entropy in Biological Systems

Web resources for participants in the NIMBioS Worshop on Information Theory and Entropy in Biological Systems.

Over the next few days, I’ll be maintaining a Storify story covering information related to and coming out of the Information Theory and Entropy Workshop being sponsored by NIMBios at the Unviersity of Tennessee, Knoxville.

For those in attendance or participating by watching the live streaming video (or even watching the video after-the-fact), please feel free to use the official hashtag , and I’ll do my best to include your tweets, posts, and material into the story stream for future reference.

For journal articles and papers mentioned in/at the workshop, I encourage everyone to join the Mendeley.com group ITBio: Information Theory, Microbiology, Evolution, and Complexity and add them to the group’s list of papers. Think of it as a collaborative online journal club of sorts.

Those participating in the workshop are also encouraged to take a look at a growing collection of researchers and materials I maintain here. If you have materials or resources you’d like to contribute to the list, please send me an email or include them via the suggestions/submission form or include them in the comments section below.

Resources for Information Theory and Biology

RSS Icon  RSS Feed for BoffoSocko posts tagged with

 

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. #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. #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.


Information Theory is the New Central Discipline

Replied to 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]

Announcement: Special issue of Entropy: “Information Theoretic Incentives for Cognitive Systems”

Dr. Christoph Salge asked me to cross-post this notice from the Entropy site here.

Editor’s Note: Dr. Christoph Salge asked me to cross-post the following notice from the Entropy site here. I’m sure many of the readers of the blog will find the topic to be of interest.


 

Logo for the journal Entropy

 

Dear Colleagues,

In recent years, ideas such as “life is information processing” or “information holds the key to understanding life” have become more common. However, how can information, or more formally Information Theory, increase our understanding of life, or life-like systems?

Information Theory not only has a profound mathematical basis, but also typically provides an intuitive understanding of processes, such as learning, behavior and evolution terms of information processing.

In this special issue, we are interested in both:

  1. the information-theoretic formalization and quantification of different aspects of life, such as driving forces of learning and behavior generation, information flows between neurons, swarm members and social agents, and information theoretic aspects of evolution and adaptation, and
  2. the simulation and creation of life-like systems with previously identified principles and incentives.

Topics with relation to artificial and natural systems:

  • information theoretic intrinsic motivations
  • information theoretic quantification of behavior
  • information theoretic guidance of artificial evolution
  • information theoretic guidance of self-organization
  • information theoretic driving forces behind learning
  • information theoretic driving forces behind behavior
  • information theory in swarms
  • information theory in social behavior
  • information theory in evolution
  • information theory in the brain
  • information theory in system-environment distinction
  • information theory in the perception action loop
  • information theoretic definitions of life

Submission

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are refereed through a peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Entropy is an international peer-reviewed Open Access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1200 CHF (Swiss Francs).

Deadline for manuscript submissions: 28 February 2015

Special Issue Editors

Guest Editor
Dr. Christoph Salge
Adaptive Systems Research Group,University of Hertfordshire, College Lane, AL10 9AB Hatfield, UK
Website: http://homepages.stca.herts.ac.uk/~cs08abi
E-Mail: c.salge@herts.ac.uk
Phone: +44 1707 28 4490
Interests: Intrinsic Motivation (Empowerment); Self-Organization; Guided Self-Organization; Information-Theoretic Incentives for Social Interaction; Information-Theoretic Incentives for Swarms; Information Theory and Computer Game AI

Guest Editor
Dr. Georg Martius
Cognition and Neurosciences, Max Planck Institute for Mathematics in the Sciences Inselstrasse 22, 04103 Leipzig, Germany
Website: http://www.mis.mpg.de/jjost/members/georg-martius.html
E-Mail: martius@mis.mpg.de
Phone: +49 341 9959 545
Interests: Autonomous Robots; Self-Organization; Guided Self-Organization; Information Theory; Dynamical Systems; Machine Learning; Neuroscience of Learning; Optimal Control

Guest Editor
Dr. Keyan Ghazi-Zahedi
Information Theory of Cognitive Systems, Max Planck Institute for Mathematics in the Sciences Inselstrasse 22, 04103 Leipzig, Germany
Website: http://personal-homepages.mis.mpg.de/zahedi
E-Mail: zahedi@mis.mpg.de
Phone: +49 341 9959 535
Interests: Embodied Artificial Intelligence; Information Theory of the Sensorimotor Loop; Dynamical Systems; Cybernetics; Self-organisation; Synaptic plasticity; Evolutionary Robotics

Guest Editor
Dr. Daniel Polani
Department of Computer Science, University of Hertfordshire, Hatfield AL10 9AB, UK
Website: http://homepages.feis.herts.ac.uk/~comqdp1/
E-Mail: d.polani@herts.ac.uk
Interests: artificial intelligence; artificial life; information theory for intelligent information processing; sensor Evolution; collective and multiagent systems

Workshop Announcement: Entropy and Information in Biological Systems

I rarely, if ever, reblog anything here, but this particular post from John Baez’s blog Azimuth is so on-topic, that attempting to embellish it seems silly.

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, Wednesday-Friday, 8-10 April 2015.

Click the link, read the stuff and scroll down to “CLICK HERE” to apply. The deadline is 12 November 2014.

Financial support for travel, meals, and lodging is available for workshop attendees who need it. We will choose among the applicants and invite 10-15 of them.

The idea
Information theory and entropy methods are becoming powerful tools in biology, from the level of individual cells, to whole ecosystems, to experimental design, model-building, and the measurement of biodiversity. The aim of this investigative workshop is to synthesize different ways of applying these concepts to help systematize and unify work in biological systems. Early attempts at “grand syntheses” often misfired, but applications of information theory and entropy to specific highly focused topics in biology have been increasingly successful. In ecology, entropy maximization methods have proven successful in predicting the distribution and abundance of species. Entropy is also widely used as a measure of biodiversity. Work on the role of information in game theory has shed new light on evolution. As a population evolves, it can be seen as gaining information about its environment. The principle of maximum entropy production has emerged as a fascinating yet controversial approach to predicting the behavior of biological systems, from individual organisms to whole ecosystems. This investigative workshop will bring together top researchers from these diverse fields to share insights and methods and address some long-standing conceptual problems.

So, here are the goals of our workshop:

  •  To study the validity of the principle of Maximum Entropy Production (MEP), which states that biological systems – and indeed all open, non-equilibrium systems – act to produce entropy at the maximum rate.
  • To familiarize all the participants with applications to ecology of the MaxEnt method: choosing the probabilistic hypothesis with the highest entropy subject to the constraints of our data. We will compare MaxEnt with competing approaches and examine whether MaxEnt provides a sufficient justification for the principle of MEP.
  • To clarify relations between known characterizations of entropy, the use of entropy as a measure of biodiversity, and the use of MaxEnt methods in ecology.
  • To develop the concept of evolutionary games as “learning” processes in which information is gained over time.
  • To study the interplay between information theory and the thermodynamics of individual cells and organelles.

For more details, go here.

If you’ve got colleagues who might be interested in this, please let them know. You can download a PDF suitable for printing and putting on a bulletin board by clicking on this:

CECAM Workshop: “Entropy in Biomolecular Systems”

On Friday, I had an excellent and stimulating conversation with Arieh Ben-Naim about his recent writing and work, and he mentioned in passing that he had been invited to a conference relating to entropy and biology in Vienna.  A quick websearch found it quickly, and not having heard about it myself yet, I thought I’d pass it along to others who are regular readers and interested in the area.

The workshop on “Entropy in Biomolecular Systems” is being hosted by the Centre Européen de Calcul Atomique et Moléculaire (CECAM)

Logo for the Centre Européen de Calcul Atomique et Moléculaire (CECAM)

Location: DACAM, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9, A-1030, Vienna, Austria
Dates: May 14, 2014 to May 17, 2014

The workshop is being organized by:

  • Richard Henchman (University of Manchester, United Kingdom)
  • Bojan Zagrovic (University of Vienna, Austria)
  • Michel Cuendet (Swiss Institute of Bioinformatics, Lausanne, Switzerland and Weill Cornell Medical College, New York, USA)
  • Chris Oostenbrink (University of Natural Resources and Life Sciences, Austria)

It’s being supported by CECAM, the European Research Council, and the Royal Society of Chemistry’s Statistical Mechanics and Thermodynamics Group.

I’ll note that the registration deadline is on April 21 with a payment deadline of April 30, so check in quickly if you haven’t already.

The summary from the workshop website states:

This workshop brings together the world’s experts to address the challenges of determining the entropy of biomolecular systems, either by experiment or computer simulation. Entropy is one the main driving forces for any biological process such as binding, folding, partitioning and reacting. Our deficient understandng of entropy, however, means that such important processes remain controversial and only partially understood. Contributions of water, ions, cofactors, and biomolecular flexibility are actively examined but yet to be resolved. The state-of-the-art of each entropy method will be presented and explained, highlighting its capabilities and deficiencies. This will be followed by intensive discussion on the main areas that need improving, leading suitable actions and collaborations to address the main biological and industrial questions.

Further details on the workshop can be found on the CECAM website.

 

As always, details on other upcoming workshops and conferences relating to information theory and biology can be found on our ITBio Conferences/Workshops page.