🎧 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.

References

[1]
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
[2]
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.

References

[1]
J. Cherfas, “Why save seeds?,” Eat This Podcast, 07-Oct-2013. [Online]. Available: http://www.eatthispodcast.com/why-save-seeds/. [Accessed: 25-Apr-2017]
[2]
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

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Study debunks old concept of how anesthesia works | Phys.Org

Study debunks old concept of how anesthesia works by Alyssa Sunkin-Strube (phys.org)
Anesthesia induces unconsciousness by changing the function of proteins that reside on the surface of a thin membrane that forms a barrier around all cells, according to new research from Weill Cornell Medicine scientists. The findings challenge a century-old concept of how anesthetics work and may help guide the development of new agents associated with fewer side effects.

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🎧 Sugar and salt: Industrial is best | Eat This Podcast

Sugar and salt: Industrial is best by Jeremy Cherfas (Eat This Podcast)
Henry Hobhouse’s book Seeds of Change: Five Plants That Transformed Mankind (now six, with the addition of cacao) contains the remarkable fact that at the height of the slave trade a single teaspoon of sugar cost six minutes of a man’s life to produce. Reason enough to cheer the abolition of slavery, I suppose. But that doesn’t mean that everything is sweetness and light in the business of sugar. Or salt. A photo gallery in The Big Picture made that very clear, and inspired Rachel Laudan, a food historian, to write in praise of industrial salt and sugar.

Industrial food processing sketch

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We often don’t know how lucky we are to live in the modern highly linked world. The concept of industrialized foods like salt and sugar and their prior histories will certainly bring our situation into high relief. The history here and its broad effects could certainly be fit into the broader category of big history as well.

Authagraph by Hajime Narukawa [ 鳴川 肇 ] | TEDxSeeds 2011

The AuthaGraph Map by Hajime NARUKAWA [ 鳴川 肇 ] (TEDxSeeds 2011 | YouTube)
An endless world map: Viewing the world through "Authagraph"

"Mr. Narukawa is the inventor of Authagraph, a world map designed to fit the world into a rectangle while almost perfectly maintaining the continents' relative size. It is mathematically impossible to precisely project the earth's sphere onto a rectangle. As such, previous methods would succeed in either taking on a rectangular shape or being true to the size ratio and shape of each continent, but never in both. Authagraph is groundbreaking in that it takes on both of those qualities, making it applicable to various themes such as sea routes, geology, meteorology and world history in ways never thought possible.

Instead of abstracting the globe into a cylinder, then a plane, as the more common Mercator projection map does, the AuthaGraph turns the Earth into a tetrahedron, which then unfolds in any number of ways.  The map can then be tessellated similar to the way that we can traverse the planet–without ever coming to an end.

Rather than having just one focal point—the North Atlantic in Mercator’s case—nearly any place around the Earth can be at the center. The effect also means that the relative sizes of countries and their locations are much more representative than prior maps.

Those who remember the Gall-Peters Projection map featured on The West Wing will see that this is a step better.

For more details, see also Japanese Designers May Have Created the Most Accurate Map of Our World: See the AuthaGraph | Open Culture

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🔖 "Opposite-of"-information improves similarity calculations in phenotype ontologies

"Opposite-of"-information improves similarity calculations in phenotype ontologies by Sebastian Koehler, Peter N. Robinson, Christopher J. Mungall (bioRxiv)
One of the most important use cases of ontologies is the calculation of similarity scores between a query and items annotated with classes of an ontology. The hierarchical structure of an ontology does not necessarily reflect all relevant aspects of the domain it is modelling, and this can reduce the performance of ontology-based search algorithms. For instance, the classes of phenotype ontologies may be arranged according to anatomical criteria, but individual phenotypic features may affect anatomic entities in opposite ways. Thus, "opposite" classes may be located in close proximity in an ontology; for example enlarged liver and small liver are grouped under abnormal liver size. Using standard similarity measures, these would be scored as being similar, despite in fact being opposites. In this paper, we use information about opposite ontology classes to extend two large phenotype ontologies, the human and the mammalian phenotype ontology. We also show that this information can be used to improve rankings based on similarity measures that incorporate this information. In particular, cosine similarity based measures show large improvements. We hypothesize this is due to the natural embedding of opposite phenotypes in vector space. We support the idea that the expressivity of semantic web technologies should be explored more extensively in biomedical ontologies and that similarity measures should be extended to incorporate more than the pure graph structure defined by the subclass or part-of relationships of the underlying ontologies.
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@lpachter Your cup of tea over at UCLA next week? Regulatory & Epigenetic Stochasticity in Development & Disease http://www.ipam.ucla.edu/programs/workshops/regulatory-and-epigenetic-stochasticity-in-development-and-disease

@lpachter Your cup of tea over at UCLA next week? Regulatory & Epigenetic Stochasticity in Development & Disease http://www.ipam.ucla.edu/programs/workshops/regulatory-and-epigenetic-stochasticity-in-development-and-disease


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