🔖 Statistical Mechanics, Spring 2016 (Caltech, Physics 12c with videos) by John Preskill

Statistical Mechanics, Spring 2016 (Physics 12c) by John Preskill (Caltech)
An introductory course in statistical mechanics.

Recommended textbook Thermal Physics by Charles Kittel and Herbert Kroemer

There’s also a corresponding video lecture series available on YouTube

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🎧 What a Cool New Podcast About Shipping Can Teach You About Coffee | Bite (Mother Jones)

What a Cool New Podcast About Shipping Can Teach You About Coffee by Kiera Butler and Maddie Oatman (Bite | Mother Jones)
That cuppa joe you just sipped? Its long journey to your cup was made possible by shipping containers—those rectangular metal boxes that carry everything from TVs to clothes to frozen shrimp. And there’s a whole host of characters whose lives revolve around this precious cargo: gruff captains, hearty cooks, perceptive coffee tasters, and competitive tugboat pilots. This is the world journalist Alexis Madrigal illuminates in his new podcast Containers. Alexis tells us how the fancy coffee revolution is shaking up the shipping industry, and reveals his favorite sailor snack. Bite celebrates its first birthday, and Kiera gets up-close-and-personal with a kitchen contraption that’s sweeping the nation: the InstantPot.

This is a cool new podcast I hadn’t come across before. This particular episode is a bit similar to my favorite podcast Eat This Podcast, though as a broader series it appears to focus more on culture and society rather than the more scientific areas that ETP tends to focus on, and which I prefer.

The bulk of this episode, which discusses shipping and containers (really more than food or coffee which is only a sub-topic here), reminds me of the book The Box: How the Shipping Container Made the World Smaller and the World Economy Bigger by Marc Levinson which I’d read in July/August 2014. (The book is now in its second addition with an additional chapter.) I suspect it was some of the motivating underlying material for Alexis Madrigal’s Containers podcast series.[1] The book had a lot more history and technical detail while I suspect Madrigal’s series has more of the human aspect and culture thrown in to highlight the effect of containerization. I’m subscribing to it and hope to catch it in the next few weeks. The discussion here is a quick overview of one of his episodes and it goes a long way towards humanizing the ever increasing linkages that makes the modern world possible. In particular it also attempts to put a somewhat more human face on the effects of increasing industrialization and internationalization of not only food production, but all types of manufacturing which are specifically impacting the U.S. (and other) economy and culture right now.

The InstantPot segment was interesting, particularly for cooking Indian food. I’m always intrigued by cooking methods which allow a modern home cook to better recreate the conditions of regional cuisines without the same investment in methods necessitated by the local cultures. Also following Alton Brown’s mantra, it sounds like it could be a useful multi-tasker.

h/t to Jeremy Cherfas and his excellent Huffduffer feed for uncovering this particular episode (and podcast series) for me.


A. Madrigal, “Containers,” Medium, 07-Mar-2017. [Online]. Available: https://medium.com/containers. [Accessed: 18-May-2017]
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👓 Can Darwinian Evolution Explain Lamarckism? | Quanta Magazine

Can Darwinian Evolution Explain Lamarckism? by Pradeep Mutalik (Quanta Magazine)
Answering three questions can help reveal how the “inheritance of acquired characteristic” fits into modern evolutionary theory.
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👓 The Quantum Thermodynamics Revolution | Quanta Magazine

The Quantum Thermodynamics Revolution by Natalie Wolchover (Quanta Magazine)
As physicists extend the 19th-century laws of thermodynamics to the quantum realm, they’re rewriting the relationships among energy, entropy and information.
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📖 Read pages 43-51 of Complexity and the Economy by W. Brian Arthur

📖 Read pages 43-51 of Complexity and the Economy by W. Brian Arthur

page 45

literally, as in Keynes’ (1936) phrase, taking into account “what average opinion expects the average opinion to be.”

page 46

…perfect rationality in the market cannot be well defined. Infinitely intelligent agents cannot form expectations in a determinate way.

This type of behavior–coming up with appropriate hypothetical models to act upon, strengthening confidence in those that are validated, and discarding those that are not–is called inductive reasoning.

page 47

We see immediately that the market possesses a psychology. We define this as the collection of market hypotheses, or expectational models or mental beliefs, that are being acted upon at a given time.

page 48
the first(?) mention of a genetic model in the book

Complexity and the Economy by W. Brian Arthur

🔖 Proceedings of the Artificial Life Conference 2016

Proceedings of the Artificial Life Conference 2016 by Carlos Gershenson, Tom Froese, Jesus M. Siqueiros, Wendy Aguilar, Eduardo J. Izquierdo and Hiroki Sayama (The MIT Press)
The ALife conferences are the major meeting of the artificial life research community since 1987. For its 15th edition in 2016, it was held in Latin America for the first time, in the Mayan Riviera, Mexico, from July 4 -8. The special them of the conference: How can the synthetic study of living systems contribute to societies: scientifically, technically, and culturally? The goal of the conference theme is to better understand societies with the purpose of using this understanding for a more efficient management and development of social systems.

Free download available.

Proceedings of the Artificial Life Conference 2016

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🎧 Changing Global Diets: the website | Eat This Podcast

Changing Global Diets: the website by Jeremy Cherfas (Eat This Podcast)
A fascinating tool for exploring how, where and when diets evolve. Foodwise, what unites Cameroon, Nigeria and Grenada? How about Cape Verde, Colombia and Peru? As of today, you can visit a website to find out. The site is the brainchild of Colin Khoury and his colleagues, and is intended to make it easier to see the trends hidden within 50 years of annual food data from more than 150 countries. If that rings a bell, it may be because you heard the episode around three years ago, in which Khoury and I talked about the massive paper he and his colleagues had published on the global standard diet. Back then, the researchers found it easy enough to explain the overall global trends that emerged from the data, but more detailed questions – about particular crops, or countries, or food groups – were much more difficult to answer. The answer to that one? An interactive website.

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While this seems a short and simple episode with some engaging conversation, it’s the podcast equivalent of the floating duck–things appear smooth and calm on the surface, but the duck is paddling like the devil underneath the surface. The Changing Global Diet website is truly spectacular and portends to have me losing a day’s worth of work or more over the next few days.

Some of the data compilation here as well as some of the visualizations are reminiscent to me of some of César A. Hidalgo’s work at the MIT Media Lab on economic complexity and even language which I’ve briefly mentioned before or bookmarked.[1][2]

I’d be curious to see what some of the data overlays between and among some of these projects looked like and what connections they might show. I suspect that some of the food diversity questions may play into the economic complexities that countries exhibit as well.

If there were longer term data over the past 10,000+ years to make this a big history and food related thing, that would be phenomenal too, though I suspect that there just isn’t enough data to make a longer time line truly useful.


D. Hartmann, M. R. Guevara, C. Jara-Figueroa, M. Aristarán, and C. A. Hidalgo, “Linking Economic Complexity, Institutions, and Income Inequality,” World Development, vol. 93. Elsevier BV, pp. 75–93, May-2017 [Online]. Available: http://dx.doi.org/10.1016/j.worlddev.2016.12.020
S. Ronen, B. Gonçalves, K. Z. Hu, A. Vespignani, S. Pinker, and C. A. Hidalgo, “Links that speak: The global language network and its association with global fame,” Proceedings of the National Academy of Sciences, vol. 111, no. 52. Proceedings of the National Academy of Sciences, pp. E5616–E5622, 15-Dec-2014 [Online]. Available: http://dx.doi.org/10.1073/pnas.1410931111
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📺 Seed: The Untold Story | Independent Lens (PBS), S18 E13

Seed: The Untold Story by Taggart Siegel and Jon Betz (Independent Lens | PBS)
Worshiped and treasured since the dawn of humankind, few things on Earth are as miraculous and vital as seeds. SEED: The Untold Story follows passionate seed keepers intent on protecting our 12,000 year-old food legacy. In the last century, 94% of our seed varieties have disappeared. This once abundant seed diversity — painstakingly created by ancient farmers and gardeners over countless millennia — has been drastically winnowed down to a handful of mass-produced varieties. Under the spell of industrial "progress" and corporate profits, family farmsteads have given way to mechanized agribusinesses sowing genetically identical crops on a massive scale. But without seed diversity, crop diseases rise and empires fall. More than a cautionary tale of "man against nature," SEED reveals the work of farmers, scientists, lawyers, and indigenous seed keepers who are fighting a David versus Goliath battle to defend the future of our food. In a story both harrowing and heartening, we meet a wide variety of reluctant heroes working to rekindle a lost connection to our most treasured resource, from the pueblos of New Mexico to a seed bunker in Norway, from India to America’s heartland, from Peru to Hawaii. Among the dozens of people featured are Will Bonsall of the Scatterseed Project, Dr. Jane Goodall, environmental lawyer Claire Hope Cummings, ethnobotanist Gary Paul Nabhan, botanical explorer Joseph Simcox, Andrew Kimbrell of the Center for Food Safety, and physicist/activist Dr. Vandana Shiva. SEED explores the hidden fabric of our food and the people that painstakingly and meticulously curate its diversity, in an era of climate uncertainty and immense corporate power.

This was an interesting documentary on seed which people obviously take heavily for granted.

I think I preferred the shorter podcasts I recently listened to: Why Save Seeds and Seed Law on the fantastic Eat This Podcast [1][2] mostly because they were a bit more scientific and policy-minded. This documentary was interesting, told some great personal stories, but could be viewed as not the most balanced of presentations. It obviously went for a more uplifting and poignant stance surrounding the people and the communities as well as their stories.

It could easily have spent 20-30 minutes delving into more of the science and the policy portions of the story to better underpin the overall arc of the story and simply had a longer 90 minute running time instead of just an hour spent primarily focused on trying to pull simply at our heartstrings.

I agree that the decrease in diversity of our seed stores is an appalling travesty, but the topic deserves better coverage and a more nuanced viewpoint of the relevant science and policy could have done far more to get people interested in the subject. I certainly would have appreciated it.


J. Cherfas, “Why save seeds?,” Eat This Podcast, 07-Oct-2013. [Online]. Available: http://www.eatthispodcast.com/why-save-seeds/. [Accessed: 25-Apr-2017]
J. Cherfas, “Seed Law,” Eat This Podcast, 27-May-2013. [Online]. Available: http://www.eatthispodcast.com/seed-law/. [Accessed: 25-Apr-2017]
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🔖 Complex Networks & Their Applications V

Complex Networks & Their Applications V: Proceedings of the 5th International Workshop on Complex Networks and their Applications by Hocine Cherifi, Sabrina Gaito, Walter Quattrociocchi, Alessandra Sala (Springer)
This book highlights cutting-edge research in the field of network science, offering scientists, researchers and graduate students a unique opportunity to catch up on the latest advances in theory and a multitude of applications. It presents the peer-reviewed proceedings of the fifth International Workshop on Complex Networks & their Applications (COMPLEX NETWORKS 2016), which took place in Milan during the last week of November 2016. The carefully selected papers are divided into 11 sections reflecting the diversity and richness of research areas in the field. More specifically, the following topics are covered: Network models; Network measures; Community structure; Network dynamics; Diffusion, epidemics and spreading processes; Resilience and control; Network visualization; Social and political networks; Networks in finance and economics; Biological and ecological networks; and Network analysis. DOI: 10.1007/978-3-319-50901-3; Part of the Studies in Computational Intelligence book series (SCI, volume 693)

Book cover of Complex Networks and Their Applications V

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🔖 From Matter to Life: Information and Causality by Sara Imari Walker, Paul C. W. Davies, George F. R. Ellis

From Matter to Life: Information and Causality by by Sara Imari Walker, Paul C. W. Davies, George F. R. Ellis (Cambridge University Press)
Recent advances suggest that the concept of information might hold the key to unravelling the mystery of life's nature and origin. Fresh insights from a broad and authoritative range of articulate and respected experts focus on the transition from matter to life, and hence reconcile the deep conceptual schism between the way we describe physical and biological systems. A unique cross-disciplinary perspective, drawing on expertise from philosophy, biology, chemistry, physics, and cognitive and social sciences, provides a new way to look at the deepest questions of our existence. This book addresses the role of information in life, and how it can make a difference to what we know about the world. Students, researchers, and all those interested in what life is and how it began will gain insights into the nature of life and its origins that touch on nearly every domain of science. Hardcover: 514 pages; ISBN-10: 1107150531; ISBN-13: 978-1107150539;
From Matter to Life: Information and Causality
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📖 Read pages 30-43 of Complexity and the Economy by W. Brian Arthur

📖 Read pages 30-43 of Complexity and the Economy by W. Brian Arthur

Chapter 2 is a nice piece on the El Farol Problem which is a paradox which “represented a decision problem where expectations (forecasts) that many would attend [the El Farol bar] would lead to few attending, and expectations that few would attend would lead to many attending: expectations would lead to outcomes that would negate these expectations.”

Zhang and Challet generalized this problem into the Minority Game in game theoretic form.

Page 31:

There are two reasons for perfect or deductive rationality to break down under complication. The obvious one is that beyond a certain level of of complexity human logical capacity ceases to cope–human rationality is bounded. The other is that in interactive situations of complication, agents cannot rely upon the other agents they are dealing with to behave under perfect rationality, and so they are forced to guess their behavior. This lands them in a world of subjective beliefs and subjective beliefs about subjective beliefs. Objective, well-defined, shared assumptions then cease to apply. In turn, rational, deductive reasoning (deriving a conclusion by perfect logical processes from well-defined premises) itself cannot apply. The problem becomes ill-defined.

This passage, though in an economics text, seems to be a perfect statement about part of the problem of governing in the United States at the moment. I have a thesis that Donald Trump is a system 1 thinker and is generally incapable of system 2 level thought, thus he has no ability to discern the overall complexity of the situations in which he finds himself (or in which the United States finds itself). As a result, he’s unable to effectively lead. From a complexity and game theoretic standpoint, he feels he’s able to perfectly play and win any game. His problem is that he feels like he’s playing tic-tac-toe, while many see at least a game as complex as checkers. In reality, he’s playing a game far more complex than either chess or go.

The overall problem laid out in this chapter is an interesting one vis-a-vis the issues many restaurant startups face, particularly in large cities. How can they best maximize their attendance not only presently, but in the long term while staying afloat in very crowded market places.

Page 38:

The level at which humans can apply perfect rationality is surprisingly modest. Yet it has not been clear how to deal with imperfect or bounded rationality.

Chapter 3 takes a similar problem as Chapter 2 and ups the complexity of the problem somewhat substantially. While I understand that at the time these problems may have seemed cutting edge and incomprehensible to most, I find myself wondering how they didn’t see it all from the beginning.

Complexity and the Economy by W. Brian Arthur
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🔖 An Introduction to Transfer Entropy: Information Flow in Complex Systems

An Introduction to Transfer Entropy: Information Flow in Complex Systems by Terry Bossomaier, Lionel Barnett, Michael Harré, Joseph T. Lizier (Springer; 1st ed. 2016 edition)
This book considers a relatively new metric in complex systems, transfer entropy, derived from a series of measurements, usually a time series. After a qualitative introduction and a chapter that explains the key ideas from statistics required to understand the text, the authors then present information theory and transfer entropy in depth. A key feature of the approach is the authors' work to show the relationship between information flow and complexity. The later chapters demonstrate information transfer in canonical systems, and applications, for example in neuroscience and in finance. The book will be of value to advanced undergraduate and graduate students and researchers in the areas of computer science, neuroscience, physics, and engineering. ISBN: 978-3-319-43221-2 (Print), 978-3-319-43222-9 (Online)

Want to read; h/t to Joseph Lizier.
Continue reading “🔖 An Introduction to Transfer Entropy: Information Flow in Complex Systems”

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Repost of John Carlos Baez’ Biology as Information Dynamics

Biology as Information Dynamics by John Carlos Baez (Google+)
I'm giving a talk at the Stanford Complexity Group this Thursday afternoon, April 20th. If you're around - like in Silicon Valley - please drop by! It will be in Clark S361 at 4 pm. Here's the idea. Everyone likes to say that biology is all about information. There's something true about this - just think about DNA. But what does this insight actually do for us? To figure it out, we need to do some work. Biology is also about things that can make copies of themselves. So it makes sense to figure out how information theory is connected to the 'replicator equation' — a simple model of population dynamics for self-replicating entities. To see the connection, we need to use relative information: the information of one probability distribution relative to another, also known as the Kullback–Leibler divergence. Then everything pops into sharp focus. It turns out that free energy — energy in forms that can actually be used, not just waste heat — is a special case of relative information Since the decrease of free energy is what drives chemical reactions, biochemistry is founded on relative information. But there's a lot more to it than this! Using relative information we can also see evolution as a learning process, fix the problems with Fisher's fundamental theorem of natural selection, and more. So this what I'll talk about! You can see slides of an old version here: http://math.ucr.edu/home/baez/bio_asu/ but my Stanford talk will be videotaped and it'll eventually be here: https://www.youtube.com/user/StanfordComplexity You can already see lots of cool talks at this location! #biology

Wondering if there’s a way I can manufacture a reason to head to Northern California this week…

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A new fossil could push back the start of life on Earth | The Economist

A new fossil could push back the start of life on Earth (The Atlantic)
The putative fossils formed just a few hundred million years after Earth itself

Continue reading “A new fossil could push back the start of life on Earth | The Economist”

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