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.


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]
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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

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A Mathematical Symphony

Robert B. Ash, mathematician
in A Primer of Abstract Mathematics (The Mathematical Association of America, 1998)

 

A Primer of Abstract Mathematics by Robert B. Ash
A Primer of Abstract Mathematics by Robert B. Ash

 

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Introduction to Lie Groups and Lie Algebras | UCLA Extension

Looking for some serious entertainment on Tuesday nights this fall? Professor Mike Miller has got you covered!

Exercise Your Brain

As many may know or have already heard, Dr. Mike Miller, a retired mathematician from RAND and long-time math professor at UCLA, is offering a course on Introduction to Lie Groups and Lie Algebras this fall through UCLA Extension.  Whether you’re a professional mathematician, engineer, physicist, physician, or even a hobbyist interested in mathematics you’ll be sure to get something interesting out of this course, not to mention the camaraderie of 20-30 other “regulars” with widely varying backgrounds (actors to surgeons and evolutionary theorists to engineers) who’ve been taking almost everything Mike has offered over the years (and yes, he’s THAT good — we’re sure you’ll be addicted too.)

“Beginners” Welcome!

Even if it’s been years since you last took Calculus or Linear Algebra, Mike (and the rest of the class) will help you get quickly back up to speed to delve into what is often otherwise a very deep subject.  If you’re interested in advanced physics, quantum mechanics, quantum information or string theory, this is one of the topics that is de rigueur for delving in deeply and being able to understand them better. The topic is also one near and dear to the hearts of those in robotics, graphics, 3-D modelling, gaming, and areas utilizing multi-dimensional rotations. And naturally, it’s simply a beautiful and elegant subject for those who have no need to apply it to anything, but who just want to meander their way through higher mathematics for the fun of it (this will comprise the largest majority of the class by the way.)

Whether you’ve been away from serious math for decades or use it every day or even if you’ve never gone past Calculus or Linear Algebra, this is bound to be the most entertaining thing you can do with your Tuesday nights in the fall.  If you’re not sure what you’re getting into (or are scared a bit by the course description), I highly encourage to come and join us for at least the first class before you pass up on the opportunity.  I’ll mention that the greater majority of new students to Mike’s classes join the ever-growing group of regulars who take almost everything he teaches subsequently. (For the reticent, I’ll mention that one of the first courses I took from Mike was Algebraic Topology which generally requires a few semesters of Abstract Algebra and a semester of Topology as prerequisites.  I’d taken neither of these prerequisites, but due to Mike’s excellent lecture style and desire to make everything comprehensible, I was able to do exceedingly well in the course.) I’m happy to chat with those who may be reticent. Also keep in mind that you can register to take the class for a grade, pass/fail, or even no grade at all to suit your needs/lifestyle.

My classes have the full spectrum of students from the most serious to the hobbyist to those who are in it for the entertainment and  ‘just enjoy watching it all go by.’

Mike Miller, Ph.D.

As a group, some of us have a collection of a few dozen texts in the area which we’re happy to loan out as well.  In addition to the one recommended text (Mike always gives such comprehensive notes that any text for his classes is purely supplemental at best), several of us have also found some good similar texts:

Given the breadth and diversity of the backgrounds of students in the class, I’m sure Mike will spend some reasonable time at the beginning [or later in the class, as necessary] doing a quick overview of some linear algebra and calculus related topics that will be needed later in the quarter(s).

Further information on the class and a link to register can be found below. If you know of others who might be interested in this, please feel free to forward it along – the more the merrier.

I hope to see you all soon.


Introduction to Lie Groups and Lie Algebras

MATH X 450.6  /  3.00 units /  Reg. # 249254W
Professor: Michael Miller, Ph.D.
Start Date: 9/30/2014
Location UCLA: 5137 Math Sciences Building
Tuesday, 7-10pm
September 30 – December 16, 2014
11 meetings total (no mtg 11/11)
Register here: https://www.uclaextension.edu/Pages/Course.aspx?reg=249254

Course Description

Lie group is a differentiable manifold that is also a group for which the product and inverse maps are differentiable. A Lie algebra is a vector space endowed with a binary operation that is bilinear, alternating, and satisfies the so-called Jacobi identity. This course, the first in a 2-quarter sequence, is an introductory survey of Lie groups, their associated Lie algebras, and their representations. This first quarter will focus on the special case of matrix Lie groups–including general linear, special linear, orthogonal, unitary, and symplectic. The second quarter will generalize the theory developed to the case of arbitrary Lie groups. Topics to be discussed include compactness and connectedness, homomorphisms and isomorphisms, exponential mappings, the Baker-Campbell-Hausdorff formula, covering groups, and the Weyl group. This is an advanced course, requiring a solid understanding of linear algebra and basic analysis.

Recommended Textbook

Hall, Brian. Lie Groups, Lie Algebras, & Representations (Springer, 2004) ISBN: 9781441923134

 

Portrait of Sophus Lie (1842-1899)
Sophus Lie (1842-1899)

If I had a dollar for every time someone invited me to a Lie Algebra class, I’d be a…

 

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2014 Fields Medal and Nevanlinna Prize Winners Announced

Here's some of the best coverage I've seen about yesterday's awards.

The 2014 Fields Medal and Nevanlinna Prize winners were announced yesterday.

General announcement

Nature: “Iranian is first woman to nab highest prize in maths”
Also includes coverage of the Gauss Prize for research that has had an impact outside mathematics, which was awarded to Stanley Osher of the University of California at Los Angeles.)

Great personal profiles with short videos via Quanta Magazine

Artur AvilaA Brazilian Wunderkind Who Calms Chaos

Manjul BhargavaThe Musical, Magical Number Theorist

Martin HairerIn Noisy Equations, One Who Heard Music

Maryam MirzakhaniA Tenacious Explorer of Abstract Surfaces

Subhash KhotA Grand Vision for the Impossible

Technical explanation of their work

Terry Tao (previous Fields Medal Winner): Avila, Bhargava, Hairer, Mirzakhani

 

 

Syndicated copies to:

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:

Rap Genius, a Textual Annotation Browser for Education, Digital Humanities, Science, and Publishing

Since the beginning of January, I’ve come back to regularly browsing and using the website Rap GeniusI’m sure that some of the education uses including poetry and annotations of classics had existed the last time I had visited, but I was very interested in seeing some of the scientific journal article uses which I hadn’t seen before. Very quickly browsing around opened up a wealth of ideas for using the platform within the digital humanities as well as for a variety of educational uses.

Rap Genius logo

Overview of Rap Genius

Briefly, the Rap Genius website was originally set up as an innovative lyrics service to allow users to not only upload song lyrics, but to mark them up with annotations as to the meanings of words, phrases, and provide information about the pop-culture references within the lyrics themselves.  (It’s not too terribly different from Google’s now-defunct Sidewicki or the impressive Highbrow, textual annotation browser, but has some subtle differences as well as improvements.)

Users can use not only text, but photos, video, and even audio to supplement the listings. Built-in functionality includes the ability to link the works to popular social media audio services SoundCloud, and Spotify as well as YouTube. Alternately one might think of it as VH1’s “Pop-up Video”, but for text on the Internet. Ultimately the site expanded to include the topics of rock, poetry, and news.  The rock section is fairly straightforward following the format of the rap section while the poetry section includes not only works of poetry (from The Rime of the Ancient Mariner to the King James version of The Bible), but also plays (the works of William Shakespeare) and complete novels (like F. Scott Fitzgerald’s The Great Gatsby.) News includes articles as well as cultural touchstones like the 2013 White House Correspondents’ Dinner Speech and the recent State of the Union. Ultimately all of the channels within Rap Genius platform share the same types of functionality, but are applied to slightly different categories to help differentiate the content and make things easier to find.  Eventually there may be a specific “Education Genius” (or other) landing page(s) to split out the content in the future depending on user needs.

On even its first blush, I can see this type of website functionality being used in a variety of educational settings including Open Access Journals, classroom use, for close readings, for MOOCs, publishing in general, and even for maintaining simple-to-use websites for classes. The best part is that the ecosystem is very actively growing and expanding with a recent release of an iPhone app and an announcement of a major deal with Universal to license music lyrics.

General Education Use

To begin with, Rap Genius’ YouTube channel includes an excellent short video on how Poetry Genius might be used in a classroom setting for facilitating close-readings. In addition to the ability to make annotations, the site can be used to maintain a class specific website (no need to use other blogging platforms like WordPress or Blogger for things like this anymore) along with nice additions like maintaining a class roster built right in.  Once material begins to be posted, students and teachers alike are given a broad set of tools to add content, make annotations, ask questions, and provide answers in an almost real-time setting.

Screen capture from Poetry Genius featuring The Great Gatsby

MOOC Use Cases

Given the rapid growth of the MOOC-revolution (massively open online courseware) over the past several years, one of the remaining difficulties in administering such a class can hinge not only on being able to easily provide audio visual content to students, but allow them a means of easily interacting with it and each other in the learning process.  Poetry Genius (aka Education Genius) has a very interesting view into solving both of these problems, and, in fact, I can easily see the current version of the platform being used to replace competing platforms like Coursera, EdX, Udacity and others in a whole cloth fashion.

Currently most MOOC’s provide some type of simple topic-based threaded fora in which students post comments and questions as well as answers.  In many MOOCs this format becomes ungainly because of the size of the class (10,000+ students) and the quality of the content which is being placed into it. Many students simply eschew the fora because the time commitment per amount of knowledge/value gained is simply not worth their while. Within the Poetry Genius platform, students can comment directly on the material or ask questions, or even propose improvements, and the administrators (the professor or teaching assistants in this case) can accept, reject or send feedback request to students to amend their work and add it to the larger annotated work.  Fellow classmates can also vote up or down individual comments.

As I was noticing the interesting educational-related functionality of the Rap Genius platform, I ran across what is presumably the first MOOC attempting to integrate the platform into its pedagogical structure. Dr. Laura Nasrallah’s HarvardX course “Early Christianity: The Letters of Paul,” which started in January, asks students to also create Poetry Genius accounts to read and comment on the biblical texts which are a part of the course. The difficult portion of attempting to use Poetry Genius for this course is the thousands of “me-too” posters who are simply making what one might consider to be “throw-away” commentary rather than the intended “close reading” commentary for a more academic environment. (This type of posting is also seen in many of the fora-based online courses.) Not enough students are contributing substantial material, and when they are, it needs to be better and more quickly edited and curated into the main post to provide greater value to students as they’re reading along. Thus when 20,000 students jump into the fray, there’s too much initial chaos and the value that is being extracted out of it upon initial use is fairly limited – particularly if one is browsing through dozens of useless comments. It’s not until after-the-fact – once comments have been accepted/curated – that the real value will emerge. The course staff is going to have to spend more time doing this function in real time to provide greater value to the students in the class, particularly given the high number of people without intense scholarly training just jumping into the system and filling it with generally useless commentary. In internet parlance, the Poetry Genius site is experiencing the “Robert Scoble Effect” which changes the experience on it. (By way of explanation, Robert Scoble is a technology journalist/pundit/early-adopter with a massive follower base.  His power-user approach and his large following can drastically change his experience with web-based technology compared to the  common everyday user. It can also often bring down new services as was common in the early days of the social media movement.)

Typically with the average poem or rap song, the commentary grows slowly/organically and is edited along the way. In a MOOC setting with potentially hundreds of thousands of students, the commentary is like a massive fire-hose which makes it seemingly useless without immediate real-time editing. Poetry Genius may need a slightly different model for using their platform in larger MOOC-style courses versus the smaller classroom settings seen in high school or college (10-100 students). In the particular case for “The Letters of Paul,” if the course staff had gone into the platform first and seeded some of the readings with their own sample commentary to act as a model of what is expected, then the students would be a bit more accepting of what is expected. I understand Dr. Nasrallah and her teaching assistants are in the system and annotating as well, but it should also be more obvious which annotations are hers (or those of teaching assistants) to help better guide the “discussion” and act as a model. Certainly the materials generated on Poetry Genius will be much more useful for future students who take the course in future iterations. Naturally, Poetry Genius exists for the primary use of annotation, while I’m sure that the creators will be tweaking classroom-specific use as the platform grows and user needs/requirements change.

As a contrast to the HarvardX class, and for an additional example, one can also take a peek at Cathy Davidson’s Rap Genius presence for her Coursera class “The History and Future (Mostly) of Higher Education.”

Open Access Journal Use

In my mind, this type of platform can easily and usefully be used for publishing open access journal articles. In fact, one could use the platform to self-publish journal articles and leave them open to ongoing peer review. Sadly at present, there seems to be only a small handful of examples on the site, including a PLOS ONE article, which will give a reasonable example of some of the functionality which is possible.  Any author could annotate and footnote their own article as well as include a wealth of photos, graphs, and tables giving a much more multimedia view into their own work.  Following this any academic with an account could also annotate the text with questions, problems, suggestions and all of these can be voted up or down as well as be remedied within the text itself. Other articles can also have the ability to directly cross-reference specific sections of previously posted articles.

Individual labs or groups with “journal clubs” could certainly join in the larger public commentary and annotation on a particular article, but higher level administrative accounts within the system can also create a proverbial clean slate on an article and allow members to privately post up their thoughts and commentaries which are then closed to the group and not visible to the broader public. (This type of functionality can be useful for Mrs. Smith’s 10th grade class annotating The Great Gatsby so that they’re not too heavily influenced by the hundreds or possibly thousands of prior comments within a given text as they do their own personal close readings.) One may note that some of this type of functionality can already be seen in competitive services like Mendeley, but the Rap Genius platform seems to take the presentation and annotation functionalities to the next level. For those with an interest in these types of uses, I recommend Mendeley’s own group: Reinventing the Scientific Paper.

A Rap Genius representative indicated they were pursuing potential opportunities with JSTOR that might potentially expand on these types of opportunities.

Publishing

Like many social media related sites including platforms like WordPress, Tumblr, and Twitter, Rap Genius gives it’s users the ability to self-publish almost any type of content. I can see some excellent cross-promotional opportunities with large MOOC-type classes and the site. For example, professors/teachers who have written their own custom textbooks for MOOCs (eg. Keith Devlin’s Introduction to Mathematical Thinking course at Stanford via Coursera) could post up the entire text on the Poetry Genius site and use it not only to correct mistakes/typos and make improvements over time, but they can use it to discover things which aren’t clear to students who can make comments, ask questions, etc. There’s also the possibility that advanced students can actively help make portions clear themselves when there are 10,000+ students and just 1-2 professors along with 1-2 teaching assistants. Certainly either within or without the MOOC movement, this type of annotation set up may work well to allow authors to tentatively publish, edit, and modify their textbooks, novels, articles, journal articles, monographs, or even Ph.D. theses. I’m particularly reminded of Kathleen Fitzpatrick’s open writing/editing of her book Planned Obsolescence via Media Commons. Academics could certainly look at the Rap Genius platform as a simpler more user-friendly version of this type of process.

Other Uses

I’m personally interested in being able to annotate science and math related articles and have passed along some tips for the Rap Genius team to include functionality like mathjax to be able to utilize Tex/LaTeX related functionality for typesetting mathematics via the web in the future.

Naturally, there are a myriad of other functionalities that can be built into this type of platform – I’m personally waiting for a way to annotate episodes of “The Simpsons”, so I can explain all of the film references and in-jokes to friends who laugh at their jokes, but never seem to know why – but I can’t write all of them here myself.

Interested users can easily sign up for a general Rap Genius account and dig right into the interface.  Those interested in education-specific functionality can request to be granted an “Educator Account” within the Rap Genius system to play around with the additional functionality available to educators. Every page in the system has an “Education” link at the top for further information and details. There’s also an Educator’s Forum [requires free login] for discussions relating specifically to educational use of the site.

Are there particular (off-label) applications you think you might be able to use the Rap Genius platform for? Please add your comments and thoughts below.

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“We didn’t cover much, but we sure did learn.”

Steve Mitchell, algebraic topologist
on learning mathematics in Steve Mitchell short biography

 

Stephen Mitchell

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Information Theory is Something Like the Logarithm of Probability Theory

Dr. Daniel Polani, reader in Artificial Life, University of Hertfordshire
in “Research Questions”

 

Not only a great quote, but an interesting way to view the subjects.

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Lecture Series Review: “Augustine: Philosopher and Saint” by Phillip Cary

Augustine: Philosopher and Saint (Great Courses, #611)Augustine: Philosopher and Saint byProfessor Phillip Cary, Ph.D., Eastern University (The Learning Company, 1997)

My rating: 4 of 5 stars

This series of 12 audio lectures is an excellent little overview of Augustine, his life, times, and philosophy. Most of the series focuses on his writings and philosophy as well as their evolution over time, often with discussion of the historical context in which they were created as well as some useful comparing/contrasting to extant philosophies of the day (and particularly Platonism.)

Early in the series there were some interesting and important re-definitions of some contemporary words. Cary pushes them back to an earlier time with slightly different meanings compared to their modern ones which certainly helps to frame the overarching philosophy presented. Without a close study of this vocabulary, many modern readers will become lost or certainly misdirected when reading modern translations. As examples, words like perverse, righteousness, and justice (or more specifically their Latin counterparts) have subtly different meanings in the late Roman empire than they do today, even in modern day religious settings.

My favorite part, however, has to have been the examples discussing mathematics as an extended metaphor for God and divinity to help to clarify some of Augustine’s thought. These were not only very useful, but very entertaining to me.

As an aside for those interested in mnemotechnic tradition, I’ll also mention that I’ve (re)discovered (see the reference to the Tell paper below) an excellent reference to the modern day “memory palace” (referenced most recently in the book Moonwalking with Einstein: The Art and Science of Remembering Everything) squirreled away in Book X of Confessions where Augustine discusses memory as:

“fields and spacious palaces” “…where are the treasures of innumerable images, brought into it from things of all sorts perceived by the senses. There is stored up, whatsoever besides we think, either by enlarging or diminishing, or any other way varying those things which the sense hath come to; and whatever else hath been committed and laid up, which forgetfulness hath not yet swallowed up and buried.”

Those interested in memes and the history of “memoria ex locis” (of which I don’t even find a reference explicitly written in the original Rhetorica ad Herrenium) would appreciate an additional reference I subsequently found in the opening (and somewhat poetic) paragraph of a paper written by David Tell on JSTOR. The earliest specific reference to a “memory palace” I’m aware of is Matteo Ricci’s in the 16th century, but certainly other references to the construct may have come earlier. Given that Ricci was a Jesuit priest, it’s nearly certain that he would have been familiar with Augustine’s writings at the time, and it’s possible that his modification of Augustine’s mention brought the concept into its current use. Many will know memory as one of the major underpinnings of rhetoric (of which Augustine was a diligent student) as part of the original trivium.

Some may shy away from Augustine because of the religious overtones which go along with his work, but though there were occasional “preachy sounding” sections in the material, they were present only to clarify the philosophy.

I’d certainly recommend this series of lectures to anyone not closely familiar with Augustine’s work as it has had a profound and continuing affect on Western philosophy, thought, and politics.

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Renaissance for Information Theory in Biology

This 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. (I might argue it’s possibly even bigger than Claude Shannon’s Ph.D. thesis.)  It certainly portends to create a movement that will rapidly build upon and far surpass Norbert Weiner’s concept of Cybernetics and Ludwig von Bertalanffy’s concept of General Systems Theory.

This week John Baez has announced an upcoming three day workshop on “Entropy and Information in Biological Systems” to be hosted by the National Institute for Mathematical and Biological Synthesis in Knoxville, TN, tentatively scheduled for October 22-24, 2014.

Apparently unbeknownst to Baez, earlier this year Andrew Eckford, Toby Berger, and Peter Thomas announced a six day workshop on “Biological and Bio-Inspired Information Theory” to be hosted by the Banff International Research Station for Mathematical Innovation and Discovery scheduled for October 26-31, 2014 – just two days later!

What a bonanza!!

The BIRS workshop will be a bit more general in its approach while the NIMBioS workshop has a slightly tighter view specifically on maximum entropy as applied to biology.

Even more telling (and perhaps most promising) about the two workshops is the very heavy mathematical bent both intend to make their focus.  I have a theory that the bounds of science are held below the high water level of mathematics (aka are “bounded by” in mathematics-speak), so there is nothing more exciting than to see groups attempting to push the mathematics and its application further. It was both the lack of mathematical rigor and the general youth of biology (and specifically genetics and microbiology) in the 1950’s which heavily hampered the early growth of cybernetics as a movement. Fortunately this is no longer the case on either count. Now we just need more researchers who are more readily conversant in the two realms simultaneously.