This article provides answers to the two questions posed in the title. It is argued that, contrary to many statements made in the literature, neither entropy, nor the Second Law may be used for the entire universe. The origin of this misuse of entropy and the second law may be traced back to Clausius himself. More resent (erroneous) justification is also discussed.
The Santa Fe Institute, in New Mexico, is a place for studying complex systems. I’ve never been there! Next week I’ll go there to give a colloquium on network theory, and also to participate in this workshop.
I just found out about this from John Carlos Baez and wish I could go! How have I not managed to have heard about it?
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November 16, 2016 – November 18, 2016
Noyce Conference Room
This workshop will address a fundamental question in theoretical biology: Does the relationship between statistical physics and the need of biological systems to process information underpin some of their deepest features? It recognizes that a core feature of biological systems is that they acquire, store and process information (i.e., perform computation). However to manipulate information in this way they require a steady flux of free energy from their environments. These two, inter-related attributes of biological systems are often taken for granted; they are not part of standard analyses of either the homeostasis or the evolution of biological systems. In this workshop we aim to fill in this major gap in our understanding of biological systems, by gaining deeper insight in the relation between the need for biological systems to process information and the free energy they need to pay for that processing.
The goal of this workshop is to address these issues by focusing on a set three specific question:
- How has the fraction of free energy flux on earth that is used by biological computation changed with time?;
- What is the free energy cost of biological computation / function?;
- What is the free energy cost of the evolution of biological computation / function.
In all of these cases we are interested in the fundamental limits that the laws of physics impose on various aspects of living systems as expressed by these three questions.
Purpose: Research Collaboration
SFI Host: David Krakauer, Michael Lachmann, Manfred Laubichler, Peter Stadler, and David Wolpert
I ran across a link to this textbook by way of a standing Google alert, and was excited to check it out. I was immediately disappointed to think that I would have to wait another month and change for the physical textbook to be released, but made my pre-order directly. Then with a bit of digging around, I realized that individual chapters are available immediately to quench my thirst until the physical text is printed next month.
If you’re not already doing so, you should follow Barabási on Twitter.
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— Laszlo Barabasi (@barabasi) August 3, 2016
Went on vacation or fell asleep at the internet wheel this week? Here’s some of the interesting stuff you missed.
Science & Math
- Context Specific and Differential Gene Co-expression Networks via Bayesian Biclustering | PLOS Computational Biology
- The Competing Incentives of Academic Research in Mathematics
- [1607.08473] Quantum circuits and low-degree polynomials over F_2
- This Physics Pioneer Walked Away from it All | Nautilus
- Monumental proof to torment mathematicians for years to come: Conference on Shinichi Mochizuki’s work inspires cautious optimism. | Nature
- What Your Brain Looks Like When It Solves a Math Problem | New York Times
- Habits of Highly Mathematical People
- Why You Should Care About High-Dimensional Sphere Packing | Roots of Unity
- Initial steps toward reproducible research
- Bridging the Curation Gap between Research and Libraries – A Case Study
- Quantum steampunk: Quantum information applied to thermodynamics
- How Vector Space Mathematics Reveals the Hidden Sexism in Language
- How Sound Can Make Food Taste Better | Nautilus
- Top 10 algorithms of 20th century numerical analysis, from a talk by Alex Townsend
- UK vs. US: Who’s got the right way to teach math(s)? | Math with Bad Drawin
- Physics & Caffeine: Stop Motion Film Uses a Cup of Coffee to Explain Key Co
- The Water Kingdom: A Secret History of China by Philip Ball (review)
- The master of them all: Book review for”Leonhard Euler: Mathematical Genius in the Enlightenment” | The Economist
- Biologists Search for New Model Organisms: The bulk of biological research is centered on a handful of species. Are we missing a huge chunk of life’s secrets?
- One-sentence proof of Fermat’s theorem on sums of two squares | Fermat’s Library
- This protein designer aims to revolutionize medicines and materials
- Our last common ancestor inhaled hydrogen from underwater volcanoes
- Meet Luca, The Ancestor of All Living Things | New York Times
- *Disconnected, fragmented, or united? a trans-disciplinary review of network
- What’s Behind A Science vs. Philosophy Fight? | Big Think
- What is a “Neutral Network” Anyway? An Exploration and Rediscovery of the Aims of Net Neutrality in Theory and Practice
- The Brachistochrone Curve: The Problem of Quickest Descent | Fermat’s Library
- In what sense is Quantum Mechanics a theory of information? | Quora
- Major transitions in information technology | Philosophical Transactions of
- Human brain mapped in unprecedented detail: Nearly 100 previously unidentified brain areas revealed by examination of the cerebral cortex. | Nature
- Cell biologists should specialize, not hybridize: Dry cell biologists, who bridge computer science and cell biology, should have a pivotal role in driving effective team science, says Assaf Zaritsky | Nature
- Internet 3.0: How we take back control from the giants | New Scientist
- How a Guy From a Montana Trailer Park Overturned 150 Years of Biology | The Atlantic
- People can sense single photons | Nature News & Comment
- Defining synergy thermodynamically using quantitative measurements of entropy and free energy
- A Prime Case of Chaos | AMS.org
- Murray Gell-Mann (video interviews) – YouTube
- Mathematics & Chalk: A teary goodbye to Hagomoro | Jeremy Kun
- Want to Change Academic Publishing? Just Say No | Chronicle
- Textbooks Show Aging Signs: Curated Guides Are Next – 10+ Disruptive Factors Transforming the World of Education and Learning — Consequences, Opportunities, Tools
- Simon & Schuster, Penguin, Random House Don’t Want to Talk About Their Ebook Sales
- Amazon Sales Rank: Taming the Algorithm | Self-Publishing Author Advice
- What Authors Should Know About Advance Review Copies
- Ingram Launches Ingram Academic Services
- How a Publishing House Designs a Book Cover
- How Indie Bookstores Help Drive Book Discoverability
- How to Grow Your Email List
- 3 Ways Indie Publishers Sell Books | Digital Book World
- 10 Self-Publishing Trends to Watch
- Ingram Launches Academic Services for University Presses and Academic Publishers
- Indigo Goes Where Amazon, B&N, Goodreads, and a Dozen Publishers and Startus Have Dared to Tread
- How To Make An Ebook Feel More Like A Real Book
- Looking for open digital collections – Wynken de Worde
Indieweb, Internet, Identity, Blogging, Social Media
- What is Open Source?
- My Text Editor is Absolutely Sublime | Devon Zuegel
- My zsh aliases | Devon Zuegel
- XOXO Festival
- Web Design in 4 minutes
- Custom Elements
- Design Principles
- Infographic: The Optimal Length for Every Social Media Update
- Notes For New (and Potential) Twitter Followers | Whatever
- How Blogs Work Today – Whatever
- My reply to: How Blogs Work Today | Whatever
- Unicode Character ‘ZERO WIDTH SPACE’ (U 200B)
- A Book Apart, Practical SVG
- Gillmor Gang Trumpathon
- The best news aggregation service – The Sweet Setup
- Social Startup Sprinklr Is Now Valued At $1.8 Billion After $105 Million Raise | Forbes
- Epeus’ epigone: Digital publics, Conversations and Twitter
- The New Meaning of Success
- 7 Lessons from the Future of Content: Part One — Tools Are Cheap, Time Is Expensive
- 7 Lessons from the Future of Content: Part Two — Let’s Play Risk
- Aron Pilhofer Joining Temple University School of Media and Communication
- Secrets and agents: George Akerlof’s 1970 paper, “The Market for Lemons”, is a foundation stone of information economics. The first in our series on seminal economic ideas | The Economist
- John Oliver has the takedown of Donald Trump’s Republican convention
- Reference: New Interactive Map Of 100,000 Photos and Videos Reveal “Lost London in the Victorian Era”
- “better modifiers than “insane(ly)” (Grammar and Usage)
- A lesson in the errors of statistical thinking: Nate Silver on Trump
- Trump & Putin. Yes, It’s Really a Thing
- Charlie Parker Plays with Dizzy Gillespie in Only Footage Capturing the “Bird” in True Live Performance
- Let Me Remind You Fuckers Who I Am (Shit HRC Can’t Say/satire)
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.
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)
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:
- 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
Conference synopsis from their homepage:Syndicated copies to:
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 #entropyWS, 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.
- References and Journal Articles
- Related Academic, Research Institutes, Societies, Groups, and Organizations
- Conferences, Workshops, and Symposia
- Bionet.Info-Theory (Google Group/Usenet Group)
- #ITBio on Twitter
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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.
[My comments posted to the original Facebook post follow below.]
I’m coming to this post a bit late as I’m playing a bit of catch up, but agree with it wholeheartedly.
In particular, applications to molecular biology and medicine are really beginning to come to a heavy boil in just the past five years. This particular year is the progenitor of what appears to be the biggest renaissance for the application of information theory to the area of biology since Hubert Yockey, Henry Quastler, and Robert L. Platzman’s “Symposium on Information Theory in Biology at Gatlinburg, Tennessee” in 1956.
Upcoming/recent conferences/workshops on information theory in biology include:
- BIRS Workshop: Biological and Bio-Inspired Information Theory
- Entropy and Information in Biological Systems at NIMBios
- CECAM Workshop: Entropy in Biomolecular Systems
- ALife breakout session on Information Theoretic Incentives for Artificial Life (which will also spawn off a special issue of the journal Entropy):
At the beginning of September, Christoph Adami posted an awesome and very sound paper on arXiv entitled “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.”Syndicated copies to:
In the publishing industry there is a general rule-of-thumb that every mathematical equation included in a book will cut the audience of science books written for a popular audience in half – presumably in a geometric progression. This typically means that including even a handful of equations will give you an effective readership of zero – something no author and certainly no editor or publisher wants.
I suspect that there is a corollary to this that every picture included in the text will help to increase your readership, though possibly not by as proportionally a large amount.
In any case, while reading Melanie Mitchell’s text Complexity: A Guided Tour [Cambridge University Press, 2009] this weekend, I noticed that, in what appears to be a concerted effort to include an equation without technically writing it into the text and to simultaneously increase readership by including a picture, she cleverly used a picture of Boltzmann’s tombstone in Vienna! Most fans of thermodynamics will immediately recognize Boltzmann’s equation for entropy, , which appears engraved on the tombstone over his bust.
I hope that future mathematicians, scientists, and engineers will keep this in mind and have their tombstones engraved with key formulae to assist future authors in doing the same – hopefully this will help to increase the amount of mathematics that is deemed “acceptable” by the general public.
This is a fantastic book which, for the majority of people, I’d give a five star review. For my own purposes, however, I was expecting far more on the theoretical side of information theory and statistical mechanics as applied to microbiology that it didn’t live up to, so I’m giving it three stars from a purely personal perspective.
I do wish that someone had placed it in my hands and forced me to read it when I was a freshman in college entering the study of biomedical and electrical engineering. It is far more an impressive book at this level and for those in the general public who are interested in the general history of science and philosophy of the topics. The general reader may be somewhat scared by a small amount of mathematics in chapter 4, but there is really no loss of continuity by skimming through most of it. For those looking for a bit more rigor, Avery provides some additional details in appendix A, but for the specialist, the presentation is heavily lacking.
The book opens with a facile but acceptable overview of the history of the development for the theory of evolution whereas most other texts would simply begin with Darwin’s work and completely skip the important philosophical and scientific contributions of Aristotle, Averroes, Condorcet, Linnaeus, Erasmus Darwin, Lamarck, or the debates between Cuvier and St. Hilaire.
For me, the meat of the book was chapters 3-5 and appendix A which collectively covered molecular biology, evolution, statistical mechanics, and a bit of information theory, albeit from a very big picture point of view. Unfortunately the rigor of the presentation and the underlying mathematics were skimmed over all too quickly to accomplish what I had hoped to gain from the text. On the other hand, the individual sections of “suggestions for further reading” throughout the book seem well researched and offer an acceptable launching pad for delving into topics in places where they may be covered more thoroughly.
The final several chapters become a bit more of an overview of philosophy surrounding cultural evolution and information technology which are much better covered and discussed in James Gleick’s recent book The Information.
Overall, Avery has a well laid out outline of the broad array of subjects and covers it all fairly well in an easy to read and engaging style.
- Started book on 07/11/11
- Finished book on 08/14//11
Finally, after 140 years, Robert Strain and Philip Gressman at the University of Pennsylvania have found a mathematical proof of Boltzmann’s equation, which predicts the motion of gas molecules.