Monday, May 11, 2020

Thoughts on Lents' Human Errors: Fascinating physiological & molecular anecdotes on our species' weaknesses, illuminating the non-obvious paths of evolution

I read Nathan Lents' book Human Errors with great interest. This book goes over a variety of physiological and molecular errors in humans that are somewhat paradoxical: they make us, in a sense, significantly more vulnerable than our immediate animal cousins. In particular, writing this review from the vantage point of mid-2020, I found it fascinating that this book was published in 2018 and cautions us on how vulnerable the human species is to global pandemic.

The book begins by describing examples of physiological oddities, such as our prevalence of knee injuries (i.e., ACL) and our upside-down sinus drainage patterns, which to some degree were caused by our recently upright posture. Next, the book delves into molecular defects, looking at the large amount of supposedly junk DNA and the many pseudogenes in our genome. Lents relates the pseudogenes to vitamin deficiencies such as the pseudogene for the GULO enzyme being associated with vitamin C deficiency. Lents then talks about autoimmune diseases, such as Graves disease and Myasthenia gravis, that we are much more prone to than our immediate animal relatives. The book culminates with a focus on the human brain and how it, too, sometimes suffers in comparison to cognitive set-ups elsewhere in the animal kingdom. For instance, our flicker-fusion threshold is considerably lower than that of dogs and birds, meaning that we are less able to resolve things moving quickly. In addition, we tend to be easily overwhelmed by large amounts of data, despite our belief that we can reason with "big data" well.

Overall, the book is a good read. I have some small quibbles on the discussion of junk DNA, which I think is a bit exaggerated. I believe that much of this DNA does have various uses, albeit somewhat indirect. Nevertheless, Lents' illustration of how evolution doesn't always lead to the optimal endpoint is compelling.


Human Errors: A Panorama of Our Glitches, from Pointless Bones to Broken Genes
by Nathan H. Lents (Author)
https://www.amazon.com/Human-Errors-Panorama-Glitches-Pointless-ebook/dp/B07432D5GB

Tags:
https://linkstream2.gerstein.info/tag/errors0mg

My quotes on goodreads:
https://www.goodreads.com/notes/36606264-human-errors/114528832-mark-b?ref=bsop

https://twitter.com/nathanlents

Tuesday, January 28, 2020

Thoughts on Strogatz's Infinite Powers: Great intuition on calculus, from a master teacher

I enjoyed Steven Strogatz's new work, Infinite Powers: How Calculus Reveals the Secrets of the Universe. The book gives an excellent overview of calculus, which permeates all branches of mathematics and so much of life. I should say at the outset that I had the great opportunity of being taught calculus in college by Dr. Strogatz. After reading this book, I feel even more fortunate for this experience because he's such a gifted communicator.

What I liked mainly about the book was the intuitive way Strogatz describes differentials and the development of calculus from Newton and Leibniz onwards. He introduces these concepts in several ways. My favorite was the way he demonstrated simply cubing the number 2 and contrasting it with cubing 2.01, where the latter can be expressed as the cube of a sum (2 + .01) and then expanded out with Pascal's triangle. From merely looking at the multiplication of these numbers, one can immediately get a sense of which terms can be neglected in this specific sum and in the whole process of differentiation.

Strogatz also clearly explains many classic equations in mathematics and physics, such as the heat and the wave equations. I particularly liked the way he described the development of the Fourier series and how this series converts differentiation of sine and cosine into a simple multiplication by minus one, making it easy to deal with. I also liked how he explained how one can easily express even very angular shapes such as a triangular waveform in terms of Fourier series.

I enjoyed many of the practical examples of how we can see calculus in everyday life, ranging from the oscillations of HIV in people, as tracked by Alan Perelson and David Ho, to the development of CT scans by Hounsfield and Cormack. Strogatz gives an especially hands-on understanding of the fundamental theorem of calculus by describing it in terms of a well-known paint roller analogy and how it can link together the disparate ideas of the slope of a function and the area under a curve.

Finally, I enjoyed the discussion of many of the personalities in mathematics, such as Descartes and Fermat. I hadn't appreciated the famous feud between these two until I read the book.

Overall, a great read. I'd highly recommend it, especially for anyone studying or using calculus.


https://www.amazon.com/Infinite-Powers-Calculus-Reveals-Universe/dp/1328879984
Infinite Powers: How Calculus Reveals the Secrets of the Universe
by Steven Strogatz

Tags:
https://linkstream2.gerstein.info/tag/infinite0mg

https://twitter.com/stevenstrogatz

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.



http://www.amazon.com/The-Emperor-All-Maladies-Biography/dp/1439170916
Amazon.com: The Emperor of All Maladies: A Biography of Cancer (8580001040431): Siddhartha Mukherjee: Books

https://linkstream2.gerstein.info/tag/emperor0mg

https://twitter.com/DrSidMukherjee



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 (http://blog.gerstein.info/2017/04/fun-things-about-liquids-illustrated-by.html).

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 (https://www.amazon.com/dp/B015TAH9S6) 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 (https://www.amazon.com/TEDCO-502-Hand-Boiler/dp/B008J4DOAM), 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" (https://www.amazon.com/dp/B07H7B1L41)
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
https://linkstream2.gerstein.info/tag/toys0mg

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)

https://www.amazon.com/dp/1451687249

https://linkstream2.gerstein.info/tag/greenline0mg

https://twitter.com/sullivanpaul



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)
https://www.amazon.com/Weather-Machine-Journey-Inside-Forecast-ebook/dp/B072HLRW96

https://twitter.com/ajblum

https://linkstream2.gerstein.info/tag/weather0mg

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
https://www.amazon.com/Weapons-Math-Destruction-Increases-Inequality-ebook/dp/B019B6VCLO

https://weaponsofmathdestructionbook.com

https://twitter.com/mathbabedotorg

https://linkstream2.gerstein.info/tag/wmd0mg