Chris Aldrich | Chris Aldrich

🔖 The Epidemic Spreading Model and the Direction of Information Flow in Brain Networks

Bookmarked The Epidemic Spreading Model and the Direction of Information Flow in Brain Networks (NeuroImage, February 5, 2017)

The interplay between structural connections and emerging information flow in the human brain remains an open research problem. A recent study observed global patterns of directional information flow in empirical data using the measure of transfer entropy. For higher frequency bands, the overall direction of information flow was from posterior to anterior regions whereas an anterior-to-posterior pattern was observed in lower frequency bands. In this study, we applied a simple Susceptible-Infected-Susceptible (SIS) epidemic spreading model on the human connectome with the aim to reveal the topological properties of the structural network that give rise to these global patterns. We found that direct structural connections induced higher transfer entropy between two brain regions and that transfer entropy decreased with increasing distance between nodes (in terms of hops in the structural network). Applying the SIS model, we were able to confirm the empirically observed opposite information flow patterns and posterior hubs in the structural network seem to play a dominant role in the network dynamics. For small time scales, when these hubs acted as strong receivers of information, the global pattern of information flow was in the posterior-to-anterior direction and in the opposite direction when they were strong senders. Our analysis suggests that these global patterns of directional information flow are the result of an unequal spatial distribution of the structural degree between posterior and anterior regions and their directions seem to be linked to different time scales of the spreading process.

🎧 Potatoes are (almost) perfect | Eat This Podcast

Listened to Potatoes are (almost) perfect from Eat This Podcast, May 13, 2013

The USDA’s Food and Nutrition Service runs a program for Women, Infants and Children that subsidises specific foods for eligible women and their children. Back when it started, the WIC program excluded potatoes, on the grounds that “Americans already eat enough potatoes”. Potato growers – and their representatives – don’t like that. For one, they think it sends the wrong message about the nutritional value of potatoes. And so, in 2010, the Executive Director of the Washington State Potato Commission, Chris Voigt, launched a protest. He decided to eat nothing but potatoes for 60 days, gaining massive amounts of publicity but not – yet – a change in the WIC list of approved foods.[1] However, while the world marvelled at Voigt’s dedication to the people who pay his salary, one grower in neighbouring Oregon said “Hey, what’s so hard about that? Last winter, I ate pretty nearly all potatoes for about six months. It was a feast all winter!”

Carol Deppe – author of Breed Your Own Vegetable Varieties and The Resilient Gardener – ate almost nothing but potatoes because that’s what she had, and because she really understands the nutritional value of potatoes. She points out that potatoes contain more than 2% protein, which doesn’t sound like much when you compare it to the 9% in rice or the 12% and more in wheat. But those are dry-weight values. On that basis, potato comes in at better than 10% protein, and that protein is both more balanced and better absorbed that wheat protein. This isn’t exactly news. It’s been known since the late 19th century that if you’re getting all your calories from potatoes, then you’re probably getting all the protein you need too. But that knowledge seems to have been forgotten, and Deppe thinks she knows why:
When the USDA denies WIC-program women, infants, and children their potatoes, in spite of the potato’s known excellence as a food, in spite of how much we all like it, I think I detect a subtly Euro-centric as well as classist message: “The right way to eat is like upper-class Europeans, not like New Worlders or peasants.” The problem is bigger than failing to recognize that Americans are not all Europeans, that even most European-Americans now embrace food traditions from many lands and cultures, and that most of us are closer to being peasants than to being medieval European royalty. To reject the potato is to be several hundred years out of date. Rejecting the potato represents a failure to learn some of the most important climate-change lessons of the Little Ice Age. I think the USDA should revisit its potato policy.

So do lots of other people, including potato growers, and although potatoes are again up for consideration, it isn’t clear whether this time they will make it onto the hallowed WIC list. In the meantime, they remain an excellent and nutritious food.

Notes

The Effect of Food Restriction During War on Mortality in Copenhagen is Dr Mikkel Hindhede’s account, in the Journal of the American Medical Association, of the impact of the World War I blockade on deaths in Denmark. By encouraging Danes to switch to a more vegetarian diet, Hindhede effectively saved 6300 lives. Mortaility was actually lower during the blockade than before or after. By contrast Germany, also affected by the blockade, saw widespread famine.

There’s an online account of Chris Voigt’s 60-day 20-a-day potato marathon. It’s pretty broken.

I hope to have more from Carol Deppe in a future podcast.

Image from Colorado Potatoes.

Intro music by Dan-O at DanoSongs.com.

It is even possible that Potato Pride is a genuine North Korean folk song?

I remember hearing about the USDA potato controversy at the time, but never dug into the details. Jeremy Cherfas kindly lays out lots of interesting potato information in his interview here.

🎧 Neanderthal Diets | Eat This Podcast

Listened to Neanderthal Diets from Eat This Podcast, April 29, 2013

Neanderthals did not descale their teeth regularly, for which modern scientists can be very thankful. Embedded in the fossilized calculus, or tartar, on teeth from the Shanidar cave, in Iraqi Kurdistan, and elsewhere are some remarkable remains that are beginning to shed far more light on what Neanderthals ate. I don’t want to give too much away just yet. Let’s just say that if, like me, when you think of the Neanderthal diet you think of a bunch of cavemen and women sitting around chewing their way through a woolly mammoth, you’re in for a surprise.

My guide through the recent discoveries on Neanderthal diet is John Speth, Emeritus Professor of Anthropology at the University of Michigan.

Amanda Henry’s research clearly points to moist-cooked starch grains in the mouths of Neanderthals (but did they swallow?). Archaeologists, however, have found almost no evidence of Neanderthals using the hot-rocks boil-in-a-bag method of modern people who lack fire-proof containers. And surprisingly, they didn’t know what John Speth discovered while watching TV in a motel room: that it is perfectly possible to boil water in a flimsy container over a direct fire. In the interests of time I had to cut his fascinating description of an experiment to make maple syrup by boiling the sap in a birch-bark tray over an open fire, which concluded that it was “both efficient and worthwhile”. So, now that they know it can be done, how long before they discover it was done?

There is evidence that Neanderthals ate moist-cooked starch. There is evidence that one can moist-cook without fire-proof containers and hot rocks. All we need now is evidence that Neanderthals used similar techniques, and the palaeo-dieters can add a nice mess of potage to their daily fare.

Notes

Microfossils in calculus demonstrate consumption of plants and cooked foods in Neanderthal diets (Shanidar III, Iraq; Spy I and II, Belgium). (A scientific paper.)

National Geographic’s early report on Amanda Henry’s discovery of plant remains on Neanderthal teeth and a more recent report from the Smithsonian Museum of Natural History.

More on Neanderthal diets at John Hawks’ weblog.

Photograph of the Regourdou Neanderthal mandible used by permission of the photographer, Patrick Semal, and the Musée d’art et d’archéologie du Périgord.

Intro music by Dan-O at DanoSongs.com.

Final music played by Ljuben Dimkaroski on a replica of a Neanderthal bone flute found in a cave in western Slovenia.

While I’ve read lots of research surrounding this area, this is the kind of area which more mainstream food journalists, entertainers, and educators could and should be covering. Aside from a semi-regular appearance of Deb Duchon, a nutritional anthropologist, appearing on Alton Brown‘s Good Eats, this may be one of the few places I’ve seen such an interesting interview of this type.

📖 5.27% done with American Amnesia by Jacob S. Hacker and Paul Pierson

📖 Read loc 1-682 of 12932 (5.27%) of American Amnesia by Jacob S. Hacker and Paul Pierson

This portends to be very interesting in that they plan to show what has changed over much of the 1900’s to indicate the drastic evolution in American politics, life, and philosophy over the recent decades. In light of the political battles between the left and the right over the past several years, this could provide some much needed help and guidance.

Their basic thesis seems to be that a shift away from a mixed economy has slowed American growth and general prosperity. While they do seem to have a pointed (political) view, so far it’s incredibly well documented and footnoted for those who would like to make the counter-argument. They’ve definitely got some serious evidence to indicate how drastic the situation is, but I’m curious if they can directly tie their proposed cause to the effect. If nothing else, they’ve created a laundry list of problems in America which need to be addressed by some serious leadership soon.

In some sense I’m torn about what to think of a broader issue this touches upon and which I mentioned briefly while reading At Home in the Universe. Should we continue on the general path we’ve struck out upon (the mixed economy with government regulation/oversight), or should we continue evolving away? While we can’t see the complexity effects seven levels further in, they may be more valuable than what we’ve got now. For example Cesar Hidalgo looks at the evolution along a continuum of personbyte to larger groups: firms (firmbyte), governments, and mega-corporations in Why Information Grows, so I can easily see larger governments and corporations like Google drastically changing the world in which we live (operating at a level above what most humans can imagine presently), but the complexity of why and how they operate above (and potentially against) the good of the individual should certainly be called into question and considered as we move forward.

There is no better time than the midpoint of prep when baking 6 dozen oatmeal cookies

Instagram filter used: Clarendon

Part of the alphabet in Palmer Park

Instagram filter used: Normal

Photo taken at: City of Glendale, CA

Annie (Sony, 2014)

Watched Annie from Sony Pictures, 2014

Directed by Will Gluck. With Quvenzhané Wallis, Cameron Diaz, Jamie Foxx, Rose Byrne. A foster kid, who lives with her mean foster mom, sees her life change when business tycoon and New York mayoral candidate Will Stacks makes a thinly-veiled campaign move and takes her in.

Finishing out the Adewale Akinnuoye-Agbaje 2014 mini-movie retrospective after watching Pompeii yesterday. What polar opposite characters in many senses. He didn’t seem as big or imposing here while he was positively brutal in the other.

The opening with the alternate red headed Annie would have played better if it was a tad more respectful to its own source material.

This incarnation of Annie was alright, but not as solid as the 1982 version. The update to a modern setting was relatively good, but New York didn’t feel much like New York. A part of the magic was missing and I’d suggest that it was the music that killed it for me. None of the singing felt live and all of it was auto-tuned even for actors for whom it probably wasn’t necessary. On top of this none of the classic songs from the book were understandable from a lyrics point of view, and this is sad since that’s where half of the story is hiding.

The other piece that was missing was the general chemistry between Annie and her benefactor. The ebullient joy of the 1982 Annie with the curmudgeon played by Albert Finney just overwhelmed the poorly developed relationship in this version.

This might have been better timed from a zeitgeist perspective if it had been released in Fall 2016 with more veiled references to Trump, though no one would have bought the rich-guy-with-a-heart ending.

🔖 Want to read: From Bacteria to Bach and Back: The Evolution of Minds by Daniel C. Dennett

Bookmarked From Bacteria to Bach and Back: The Evolution of Minds by

Daniel C. Dennett (W. W. Norton & Company; 1 edition, 496 pages (February 7, 2017))

One of America’s foremost philosophers offers a major new account of the origins of the conscious mind.

How did we come to have minds?

For centuries, this question has intrigued psychologists, physicists, poets, and philosophers, who have wondered how the human mind developed its unrivaled ability to create, imagine, and explain. Disciples of Darwin have long aspired to explain how consciousness, language, and culture could have appeared through natural selection, blazing promising trails that tend, however, to end in confusion and controversy. Even though our understanding of the inner workings of proteins, neurons, and DNA is deeper than ever before, the matter of how our minds came to be has largely remained a mystery.

That is now changing, says Daniel C. Dennett. In From Bacteria to Bach and Back, his most comprehensive exploration of evolutionary thinking yet, he builds on ideas from computer science and biology to show how a comprehending mind could in fact have arisen from a mindless process of natural selection. Part philosophical whodunit, part bold scientific conjecture, this landmark work enlarges themes that have sustained Dennett’s legendary career at the forefront of philosophical thought.

In his inimitable style―laced with wit and arresting thought experiments―Dennett explains that a crucial shift occurred when humans developed the ability to share memes, or ways of doing things not based in genetic instinct. Language, itself composed of memes, turbocharged this interplay. Competition among memes―a form of natural selection―produced thinking tools so well-designed that they gave us the power to design our own memes. The result, a mind that not only perceives and controls but can create and comprehend, was thus largely shaped by the process of cultural evolution.

An agenda-setting book for a new generation of philosophers, scientists, and thinkers, From Bacteria to Bach and Back will delight and entertain anyone eager to make sense of how the mind works and how it came about.

4 color, 18 black-and-white illustrations

IPAM Workshop on Regulatory and Epigenetic Stochasticity in Development and Disease, March 1-3

Bookmarked IPAM Workshop on Regulatory and Epigenetic Stochasticity in Development and Disease (Institute for Pure and Applied Mathematics, UCLA | March 1-3, 2017)

Epigenetics refers to information transmitted during cell division other than the DNA sequence per se, and it is the language that distinguishes stem cells from somatic cells, one organ from another, and even identical twins from each other. In contrast to the DNA sequence, the epigenome is relatively susceptible to modification by the environment as well as stochastic perturbations over time, adding to phenotypic diversity in the population. Despite its strong ties to the environment, epigenetics has never been well reconciled to evolutionary thinking, and in fact there is now strong evidence against the transmission of so-called “epi-alleles,” i.e. epigenetic modifications that pass through the germline.

However, genetic variants that regulate stochastic fluctuation of gene expression and phenotypes in the offspring appear to be transmitted as an epigenetic or even Lamarckian trait. Furthermore, even the normal process of cellular differentiation from a single cell to a complex organism is not understood well from a mathematical point of view. There is increasingly strong evidence that stem cells are highly heterogeneous and in fact stochasticity is necessary for pluripotency. This process appears to be tightly regulated through the epigenome in development. Moreover, in these biological contexts, “stochasticity” is hardly synonymous with “noise”, which often refers to variation which obscures a “true signal” (e.g., measurement error) or which is structural, as in physics (e.g., quantum noise). In contrast, “stochastic regulation” refers to purposeful, programmed variation; the fluctuations are random but there is no true signal to mask.

This workshop will serve as a forum for scientists and engineers with an interest in computational biology to explore the role of stochasticity in regulation, development and evolution, and its epigenetic basis. Just as thinking about stochasticity was transformative in physics and in some areas of biology, it promises to fundamentally transform modern genetics and help to explain phase transitions such as differentiation and cancer.

This workshop will include a poster session; a request for poster titles will be sent to registered participants in advance of the workshop.

Speaker List:
Adam Arkin (Lawrence Berkeley Laboratory)
Gábor Balázsi (SUNY Stony Brook)
Domitilla Del Vecchio (Massachusetts Institute of Technology)
Michael Elowitz (California Institute of Technology)
Andrew Feinberg (Johns Hopkins University)
Don Geman (Johns Hopkins University)
Anita Göndör (Karolinska Institutet)
John Goutsias (Johns Hopkins University)
Garrett Jenkinson (Johns Hopkins University)
Andre Levchenko (Yale University)
Olgica Milenkovic (University of Illinois)
Johan Paulsson (Harvard University)
Leor Weinberger (University of California, San Francisco (UCSF))

🔖 IPAM Workshop on Gauge Theory and Categorification, March 6-10

Bookmarked IPAM Workshop on Gauge Theory and Categorification (Institute of Pure and Applied Mathematics at UCLA - March 6-10, 2017)

The equations of gauge theory lie at the heart of our understanding of particle physics. The Standard Model, which describes the electromagnetic, weak, and strong forces, is based on the Yang-Mills equations. Starting with the work of Donaldson in the 1980s, gauge theory has also been successfully applied in other areas of pure mathematics, such as low dimensional topology, symplectic geometry, and algebraic geometry.

More recently, Witten proposed a gauge-theoretic interpretation of Khovanov homology, a knot invariant whose origins lie in representation theory. Khovanov homology is a “categorification” of the celebrated Jones polynomial, in the sense that its Euler characteristic recovers this polynomial. At the moment, Khovanov homology is only defined for knots in the three-sphere, but Witten’s proposal holds the promise of generalizations to other three-manifolds, and perhaps of producing new invariants of four-manifolds.

This workshop will bring together researchers from several different fields (theoretical physics, mathematical gauge theory, topology, analysis / PDE, representation theory, symplectic geometry, and algebraic geometry), and thus help facilitate connections between these areas. The common focus will be to understand Khovanov homology and related invariants through the lens of gauge theory.

This workshop will include a poster session; a request for posters will be sent to registered participants in advance of the workshop.

Edward Witten will be giving two public lectures as part of the Green Family Lecture series:

March 6, 2017
From Gauge Theory to Khovanov Homology Via Floer Theory
The goal of the lecture is to describe a gauge theory approach to Khovanov homology of knots, in particular, to motivate the relevant gauge theory equations in a way that does not require too much physics background. I will give a gauge theory perspective on the construction of singly-graded Khovanov homology by Abouzaid and Smith.

March 8, 2017
An Introduction to the SYK Model
The Sachdev-Ye model was originally a model of quantum spin liquids that was introduced in the mid-1990′s. In recent years, it has been reinterpreted by Kitaev as a model of quantum chaos and black holes. This lecture will be primarily a gentle introduction to the SYK model, though I will also describe a few more recent results.

5 pages to add to your academic website | Veronika Cheplygina

Read 5 pages to add to your academic website by Veronika Cheplygina (Veronika Cheplygina)

Previously I wrote about getting your setting up your own academic website in WordPress and installing some helpful plugins. But once you have all that, what content do you actually add to your new website? Of course, you are probably going to have pages for your CV (possibly split into different pages for research, teaching etc) and your publications. In this post I cover a few other pages I like to see on people’s professional websites. I admit I do not have all of these yet myself – but I’ve provided a few nice examples of those who do.