Sunday, December 29, 2019

Thoughts on Mukherjee's Emperor of All Maladies: Learned about the science of cancer & many of its personalities (finally know who Dana & Farber were!)

I had heard that The Emperor of All Maladies – written by award-winning oncologist Siddhartha Mukherjee – is a “must-read” about cancer. I was not disappointed. The book is fascinating, examining all aspects of the disease in the framework of a broad story arc. Mukherjee did an excellent job interspersing captivating language and vignettes – such as a quote from Susan Sontag about illness being the dark side of life – with science and history on an all-important disease.

The book provides a comprehensive history of cancer, beginning from its first identification by the Greeks (as “oncos” ) to the present. The detailed descriptions of the development of chemotherapy, radiation, and surgery treatments were engrossing. I was struck by the importance of blood cancers for the development of the first chemotherapeutic agents, as well as the importance of surgeons such as William Halsted in devising various ways to remove tumors.

I was interested to learn about the early work on epidemiology and prevention in relation to lung cancer. Richard Doll and Austin Bradford Hill pioneered a new approach to epidemiological statistics to link cigarette smoking and cancer. These researchers deserve high praise for making this critical link and changing the field of epidemiology.

Mukherjee also discusses other aspects of cancer, including the development of a massive apparatus for cancer funding with institutions such as the Dana-Farber Cancer Institute and the Jimmy Fund, and how these came together successfully to raise millions of dollars to fight the disease.

The only thing I felt the book was missing was a section describing how recent developments in cancer immunotherapy fit into the whole discussion. Nonetheless, I whole-heartedly recommend the book. The Emperor of All Maladies: A Biography of Cancer (8580001040431): Siddhartha Mukherjee: Books

Saturday, December 28, 2019

Reflections on repeating the liquid-stack demo - now with some additional twists & toys

I repeated the three liquid stack demonstration described in an earlier post (

Based on doing it again, here are some pointers:
(1) It is good to put the honey in first because it takes such a long time to get into the bottle.
(2) The best thing for each layer is putting the coins on the bottom, followed by pasta noodles at the honey water interface, blueberries at the oil-water interface, and, finally, cork at the very top.

There are several other toys that can be coupled with this demonstration.

(A) The Ooze tube ( can act as a timer to indicate resistance to flow very well in the honey oil situation.

(B) Moreover, one can use a hand boiler (, which has alcohol, to demonstrate other aspects of liquids such as boiling; this isn't evident in the three liquid stack.

(C) Finally, one could perform a circuit demonstration, using a "Sci-Fi Sensor Stick" (
This is a lot of fun and shows flow in another type of liquid -- in the sense of electrons flowing through a circuit, which is somewhat connected to the flow of liquids.

See also

Tuesday, December 24, 2019

Thoughts on Sullivan's Thin Green Line: Practical financial advice, via engaging anecdotes

I read Paul Sullivan's book, The Thin Green Line, with great interest. Sullivan is a well-known columnist on Money Matters for The Times, and he writes with great clarity about the abstract world of finance and money in terms of individual anecdotes and stories about people. Overall, I found his simple messages -- about you can't avoid taxes and instead of thinking about investing, best to worry about your spending -- quite heartening in the world of high finance and hedge funds. And I found that a lot of these messages seemingly apply across a whole wide range of economic situations. Overall, a good book with straightforward advice about dollars and cents.

The Thin Green Line: The Money Secrets of the Super Wealthy Hardcover – March 10, 2015
by Paul Sullivan (Author)

Sunday, December 22, 2019

Thoughts on Blum's Weather Machine: Great account of a recent but unappreciated scientific miracle, combining massive data gathering, international information sharing and physically-based modeling

I read Andrew Blum's book about the weather with great interest. Blum explains how the simple act of picking up our iPhones to check the weather and then planning for how to dress or pack for a trip is a modern miracle of technology and a calculation that is unappreciated.

Blum goes through many aspects of this miracle. First, he talks about the history of weather forecasting and the early pioneers who could only dream about collecting massive amounts of data and forecasting accurately into the future. Second, he goes into the modern weather data collection apparatus, with satellites circling above the earth, and how this was rapidly developed after World War II. He discusses the considerable infrastructure of weather modeling that infuses all of this data with physical calculations to make model predictions. Making accurate predictions has become a very competitive and specialized business that produces worldwide weather models.
Third, he describes how these models are then fused with the input of local forecasters to predict the weather that we access on our TV or via an app. Finally, he talks about the all-important idea of diplomacy and data sharing, and how worldwide data sharing is so crucial for this infrastructure. The original WWW, in fact, was the world weather watch as opposed to the worldwide web.

Altogether, this was a great read that I would highly recommend to those interested in recent synergistic technological progress.

The Weather Machine: A Journey Inside the Forecast Kindle Edition
by Andrew Blum (Author)

Sunday, November 17, 2019

Thoughts on O'Neil's Weapons of Math Destruction: What happens when learning for machines makes judgements on people

We read Cathy O’Neil’s book, Weapons of Math Destruction, with great interest. O’Neil discusses many of the biases and unfair situations that arise in the modern data science world based on mathematical models or algorithms. An avid mathematician and former academic who moved to industry to “carry mathematics from abstract theory into practice,” O’Neil realized that her favorite science field was part of a cycle of co-production with society: design of numerous mathematical models reflected and exacerbated social problems.

In a sense, it is obvious that an algorithm trained with biased data will be biased. While an algorithm can be efficient in the sense of optimizing and minimizing the number of false positives and false negatives, each of the “mistakes” might still lead to unjust and unfair outcomes if applied to an individual person or a group. The book makes this point with many clear case studies. Whether they are for loan approval, college ranking, law enforcement, or business optimization, models aimed at improving efficiency or boosting profits backfired. Such models created feedback loops that widened gaps within society because their limited designs proved to be oblivious to broader professional and social contexts.

A few recurring themes stand out from the book. The two most important of which, we think, are the emphases on balanced objectives and heightened awareness needed before building a “Big Data” model. O’Neil strongly makes the case for broadening a model’s objective, understanding its strengths and limitations, and being fully aware of how human biases can diffuse to collected (and uncollected) data. We particularly like the discussion of the widespread worry about the fall in standardized test performance in the United States, and how this turned out to be totally erroneous. In reality, SAT scores in each subgroup were actually increasing, but more disadvantaged kids were taking the test – a mistake due to the famous statistical error known as Simpson's paradox.

The book also touches on the proprietary nature of many commercial algorithms. In this regard, the book praises the well-known FICO score, which is viewed as a model of transparency compared to more closed types of rating systems. We also like the way the book goes through a lot of the jargon of modern commercial data sciences, such as proxies (which are often features that stand-in for a different feature that can’t be as easily measured or is not appropriate to measure) and micro-targeting. Pointing out the limitations of proxies is especially resonant today in light of several studies that followed the book’s publication in 2016, the most recent of which appeared in Science last month on the inherent bias in a widely used algorithm that inaccurately used health costs as a proxy to health needs.

The book is human-centered, no doubt. O’Neil calls for measures in favor of the protection and collective betterment of everyone’s lives. She acknowledges the potential utility of “Big Data,” thoroughly demonstrates that good intentions are not enough, and chooses to raise alarming issues at the heart of this rapidly unfolding field. Altogether, we found this book to be a fun read that we would recommend to anyone interested in large-scale data science that involves actual people as opposed to inanimate objects.

M Gerstein & H Mohsen

Weapons of Math Destruction: How Big Data Increases Inequality and Threatens Democracy
by Cathy O’Neil

Sunday, October 27, 2019

Thoughts on Tara's Secret Life of Fat: Scientific facts, practical tips & interesting personalities, related to the cells around your waist

I read Sylvia Tara’s The Secret Life of Fat with great interest. Similar in spirit to Justin and Erica Sonnenburg’s The Good Gut, this book combines hardcore science with practical pointers for daily life. Scientifically, Tara discusses the different types of fat – such as brown, visceral, subcutaneous – and how fat can essentially act as a regulating and self-regulated organ by interacting with the endocrine system. Practically, Tara notes how it is good to fast as long as possible each day to increase fat burning and how it is important to monitor one’s daily fat intake. The Secret Life of Fat also includes interesting profiles of leading scientists, such as those involved in the discovery of leptin, and patients’ who suffer from a variety of ailments associated with obesity and dysregulated fat regulation. Overall, I found this book a good read and a complement to the Good Gut.

The Secret Life of Fat: The Science Behind the Body's Least Understood Organ and What It Means for You
by Sylvia Tara


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