Saturday, October 05, 2019

Thoughts on Pollan's Cooked: Explains the science & history of the most commonplace of things - really learned a lot about fermentation

I read Michael Pollan's masterwork Cooked with great interest. This book takes a simple thing – food and how we prepare it – and delves deep into the underlying science and history of this subject.

The book first discusses using fire and water for cooking. It covers topics such as the Maillard reaction, which gives food flavor, and the way a stewpot acts as a second stomach, in a sense, predigesting foods and opening up their nutritional value.

I found the final section of the book, on fermentation, the most interesting. Fermentation ("cold fire") uses microorganisms to digest foods partially and to create flavors. The book highlights several key fermented foods – in particular, bread, wine, and cheese – and discusses various aspects of the fermentation process.

First, considering bread, fermentation allows us to readily use grasses for food and reclaim much more solar energy. The book suggests that ~90 percent of the energy in food is lost at each step of the food pyramid; thus, being able to eat grass directly is a major triumph of the agricultural revolution. Of course, nowadays, we have taken this fantastic process even further and essentially industrialized grass in the form of white bread -- taking out much of the original nutrients, including fiber, and then putting different nutrients back in. Another exciting aspect of baking bread is what Pollan describes as an emergent phenomenon. Most other forms of cooking, for instance, heating by fire or warming in a pot, involve a simple extrapolation of the preparation conditions. Baking bread is different. It is a "system property," where one combines various ingredients and makes something completely different than the original constituents. Pollan also describes how gluten acts almost like an elastic to create cavities in bread that can fill with gas and facilitate rising.

The next fermented food Pollan discusses is wine. To make it clear how easy it is to achieve fermentation, he shares humorous stories from his childhood of fermenting grape juice and having the vessel burst. He also brings up a philosophical question of whether we have domesticated Saccharomyces cerevisiae or whether it has domesticated us: alcohol itself, which is the product of many fermentations, is toxic to most organisms, yet we have evolved enzymes and pathways in our liver to break it down. Pollan also talks about how one can understand the different flavors of wine in terms of the various microorganisms available. Humans, in a sense, have co-evolved with wine and can benefit from having a glass a day based on a variety of health indicators.

The final section on fermentation talks about cheese. Cheese represents the product of rotting or decay in its extreme. Pollan describes cheese fermentation as a multistep process where, initially, microorganisms aerobically colonize the center of a bit of milk, digesting it partially and raising its pH, but eventually, the increasing acidity fouls the microbes' nest. Then, there is effectively an ecological succession where other species of bacteria replace the initial microbes; this continues to raise the pH. What I found most interesting is that a secondary fermentation then occurs from the outside of the cheese, where yeasts – which are aerobic – send in their hyphae and partially neutralize the increasing pH. The competition between these different fermentations gives rise to new chemistries, flavors, and compounds.

Cheese is also unusual in that it represents the nexus for competition between two current groups of people: the fermentos, those who believe in the importance of microorganisms for health and for giving food its flavors, and the Pasteurians, those who want to purge all foods of microbes. Their differences are evident when choosing a vessel for making cheese: should it be made out of old rotten, moldy wood or modern stainless steel?

The overall discussion of fermented foods points to the legacy of the agricultural revolution and the great importance of microbes in day-to-day life.

Altogether, I highly recommend this book. I find myself revisiting many of the book's points when I enjoy various meals and purchase things at the grocery store.

Cooked: A Natural History of Transformation – April 23, 2013
by Michael Pollan


Monday, September 23, 2019

Thoughts on Dittrich’s Patient HM: Strong personalities bring the science of memory to life

I enjoyed reading Luke Dittrich's book entitled "Patient H.M.: A Story of Memory, Madness, and Family Secrets." This book combines a great story about the celebrated patient Henry Molaison with factual knowledge about the brain. The personalities involved in the story were intriguing, from a great surgeon and his grandson to recent scientists battling over control of tissue samples and data. I found reading about the personal struggles helpful to understand the scientific road taken. I also enjoyed the interspersed facts about brain anatomy and some of the peculiarities of the approaches and lives of neurosurgeons and neuroscientists, such as how we somewhat haphazardly get at the seat of memory and how we disentangle key concepts such as semantic memory.

Despite being an overall interesting book, I definitely felt Dittrich took it "to the edge" with some of his points about Suzanne Corkin's treatment of Henry Molaison's brain, his famous grandmother, and the operations he performed. I wonder whether these highly controversial points are backed up by robust factual research. Nonetheless, the book was thought-provoking and enjoyable to read.

Patient H.M.: A Story of Memory, Madness, and Family Secrets
by Luke Dittrich


Sunday, September 15, 2019

Thoughts on Carreyrou's Bad Blood: Riveting tale, contrasting the tech & biotech worlds

We thoroughly enjoyed reading John Carreyrou's book, Bad Blood, about the Theranos debacle. Overall, it is a gripping story about the fall of a poster-child company operating at the intersection of computer tech and biotech.

We were struck by a number of points in the book.

First of all, it was amazing that Elizabeth Holmes was able to recruit and fool such an eminent board of directors. Her ability to control the narrative and grow the company in spite of some early warning signs and skepticism was interesting. This was most evident in the family conflict amongst the Shultzes, and the huge personal and financial burden on Tyler Schultz in this conflict was amazing.

We also found the book's indictment of the “fake it until you make it” culture in Silicon Valley quite telling. What can work for software might not work so well in the regulated world of health devices -- where bugs or incorrect results can have life-altering consequences. This cautionary tale continues to demonstrate its relevance in light of recent accusations at the microbiome sequencing company uBiome. DNA sequencing technology and many of the companies seeking to commercialize its use as a tool or diagnostic similarly spans the tech and biotech worlds. The tale of Theranos illustrates what can go wrong when these two worlds collide and highlights the need for care and attention when merging tech and biotech in order to realize the promise of advances in digital health.

Finally, we were struck by how Theranos managed to keep its secrets for so long, perhaps through such tight legal regulation and surveillance. It's amazing that they could keep so many people from talking for so long.

All together a gripping, great read that we highly recommend.

Mark Gerstein (with Paul Muir)

Bad Blood: Secrets and Lies in a Silicon Valley Startup
by John Carreyrou

Wednesday, August 28, 2019

Thoughts on Soni & Goodman's A Mind at Play - A portrait of one of the few great American mathematicians, Has an interesting interplay of practical tinkering & abstract thought

I enjoyed reading “A Mind at Play: How Claude Shannon Invented the Information Age,” by Jimmy Soni and Rob Goodman. Shannon was one of the great American scientists and mathematicians and deserves tremendous praise for his ideas that underlie the Computer Age.

What I found most appealing about the book was the mixture of Shannon’s life in historical context with technical knowledge about information theory. The book interweaves Shannon’s early learning on electrical switches and wires at Bell labs with his later development of information theory. I found this conjunction between Shannon’s practical hands-on tinkering and the abstract mathematical work, for which he is famous, quite interesting and inspirational in terms of developing mathematical ideas.

The book also makes clear how much Shannon was impacted by his early training. Shannon benefited greatly from his initial experiences at MIT and his mentorship by the great scientific administrator Vannevar Bush. In a sense, Shannon embodied many of MIT’s characteristics when he returned to the institution. It is also interesting that while Shannon is famous for his work in communication theory, the substance of his PhD was actually related to genetics. Only now, many years later, do people realize the connection between genomics and information theory.

Overall, I found this book to be a great read that I would highly recommend to people interested in mathematical sciences and American scientists in general.

A Mind at Play: How Claude Shannon Invented the Information Age Hardcover – July 18, 2017
by Jimmy Soni (Author), Rob Goodman (Author)

Friday, August 23, 2019

Thoughts on Dehaene's Consciousness & the Brain: Nice overview of the higher functions of the brain, Describing measurement approaches & theories of consciousness

Consciousness and the Brain by Stanislas Dehaene is a great introduction for anyone interested in learning about key ideas in neuroscience. Consciousness is a fascinating natural phenomenon, although it is not yet completely understood. Dehaene provides a solid overview of the many disparate fields that probe this concept.

On a psychological level, Dehaene talks about specific phenomena, such as subliminal priming and the Wheatstone stereoscope related to binocular perception, and how they give clues into the conscious mind. He also underscores the importance of subliminal thinking for much of what we do. In terms of brain physiology, Dehaene describes the different areas of the brain and the importance of the prefrontal cortex and the large pyramidal neurons it has in maintaining conscious thought.

On a more basic chemical and physical level, Dehaene describes many of the techniques that scientists use to learn about the brain, such as EEG and fMRI. He touches upon some of the key underlying phenomena such as the P300 wave, thought to be a signal of consciousness. Dehaene also describes a number of grand, but speculative, theories of consciousness. For example, he discusses the workspace theory of the mind, as well as an “applause” concept that posits that conscious ideas are amplified and step above all the other things on one's mind.

Overall, I found this an excellent read for someone wanting to learn about the mind, and I would recommend it heartily.

Consciousness and the Brain: Deciphering How the Brain Codes Our Thoughts
Stanislas Dehaene: 9780670025435: Books

Tuesday, August 13, 2019

Thoughts on Winchester's Perfectionists: a History of Precision Engineering, Exacting accounts of Bramah locks, Winchester guns, Ford cars, Intel chips & the Hubble-telescope mirror

I read Simon Winchester's The Perfectionists with great interest. This book gives an overall history of precision engineering throughout the ages. It starts with the development of the Antikythera clock mechanism by the Greeks, which is inexact by today's standards but was still quite an accomplishment at the time. Then, the book goes through a succession of devices that become more and more precise – locks, rigging on ships, the famous H1 chronometer by Harrison, and so forth – many of which were made to advance military and commercial endeavors. The book culminates in today's contemporary world of atomic clocks, microchips, and GPS. Moreover, it touches upon the world of developing precise standards for various units such as the kilogram and meter. One of the most evocative stories was one drawn from the author's own childhood in which his father showed him precision of gauge blocks and how they tend to adhere simply because of their ultra-precise flatness. Finally, an interesting point was the fact that so many current precision devices and units – particularly with the redefinition of the metric system – rely on the measurement of time.

Overall, I would rate this a fascinating read, especially for anyone interested in gadgets and devices of precision.

The Perfectionists: How Precision Engineers Created the Modern World
May 8, 2018
by Simon Winchester (Author)

(Also, for CT natives, there's a bit of good stuff about the history of the CT River Valley.)

Sunday, May 20, 2018

Thoughts on Thaler & Sunstein's Nudge: General points about human decision making, with practical implications for one's day-to-day life

I read Cass Sunstein and Richard Thaler's Nudge with great interest. This work provides an overview of choice architecture from a policy planning perspective but also offers practical thoughts and tips that are related to how people might make their decisions in day-to-day life. It introduces the notion of essentially two brains. The one of the prefrontal cortex and the rational decision making and also the human brain that is rooted a little bit lower down. These make decisions differently, and all too often we think about decision making only regarding a mythical species called the homo economicus that is making decisions entirely irrationally. The authors go over some places where choice architects can help structure decisions either through creating defaults, placing options intelligently to help us make faster decisions with our less econ-like brain. They give some examples from simple design in food placement in cafeterias to default choices for organ donation that produce a relatively significant difference, without apparently affecting issues related to fairness. They discuss the notion of libertarian paternalism where people are free to choose but the State steps in, in a paternalistic way, to help them with these choices. People have the hardest time making decisions that they do not often confront, which often have significant consequences such as those they have to make when facing a disease, when choosing a job and so forth. Whereas they are good with everyday choices that they get rapid feedback on, deciding what to eat, products in a store and so forth.

The authors go through some simple situations where people tend to make misguided choices, forgetting the total costs in economic ventures such as buying a car in relation to the cost to rent or use one. They also talk a bit about practical ideas for changing things such as having taxes precomputed for us or having lights to remind us to change our air conditioner filters. I thought a lot of this was useful for simply arranging one’s everyday life, putting reminders out to help them make quick decisions and remembering that people, while they do have a rational brain, are also human.

Overall, a good book that I recommend heartily.

Nudge: Improving Decisions About Health, Wealth, and Happiness Paperback – February 24, 2009
by Richard H. Thaler (Author), Cass R. Sunstein (Author)