Showing posts with label itunes0mg. Show all posts
Showing posts with label itunes0mg. Show all posts

Saturday, August 02, 2025

Thoughts on Pearl's Book of Why: Lots of Good Intuition on Bayesian Networks, Sometimes with Strong Opinions

The Book of Why by Judea Pearl with great interest. The author is undoubtedly one of the most brilliant thinkers in recent years on causative reasoning and artificial intelligence. The book provides a detailed, somewhat technical, and historical account of causation. I particularly appreciated how it delved into key concepts such as Bayesian networks and confounders, topics that Pearl has explored extensively. 

I also enjoyed his discussion of smoking, the Bradford Hill criteria, and how we needed to move beyond mere correlation and association to make informed decisions. Pearl’s ability to place these discussions in a historical context, highlighting the contributions of figures like Fisher and Sewall Wright, was impressive. I particularly appreciated how Pearl explained the three key graphical elements in Bayesian networks, which he referred to as chains (A leads to B, which leads to C), colliders (A and C both point to B), and forks (B leads to both A and C). He explained how these motifs differ in terms of the independence of the three variables and the extent to which they remain independent when conditioned on B. He provided intuitive examples to help readers easily grasp these concepts and emphasized the fundamental problem of confounding in statistical design, as well as how randomized controlled trials address this issue.  

 However, at times, I found it challenging to distinguish between background information on established concepts and Pearl’s more polemical arguments advocating for what he calls the “causal revolution,” which may be less widely accepted in the statistical and AI communities. This occasionally led to some confusion, but overall, I enjoyed the book immensely and would highly recommend it to any reader.

Sunday, April 20, 2025

Thoughts on Zimmer's Airborne: Great book about an overlooked mode of disease transmission, now prominent because of the pandemic

Air-borne by Carl Zimmer is a well-researched and quite enjoyable book that combines the science of airborne disease transmission, the history of key researchers and their contributions, and the political debates over biodefense and the public health response to COVID-19. It provides a detailed account of airborne disease transmission research, from early pioneers to modern scientists who challenged long-standing misconceptions. The book also critiques how public health institutions, particularly the CDC and WHO, mishandled airborne transmission during the COVID-19 pandemic. Zimmer presents a strong argument that scientific knowledge on airborne transmission was ignored or resisted, leading to missteps in public health guidance. All of these elements come together to make for a compelling and insightful read.

The book begins with the original pioneers of germ theory, focusing on Louis Pasteur and Robert Koch in establishing that microorganisms cause disease. Zimmer walks the reader through some of their most famous experiments, which became a foundation for proving microbial causation of disease. Along the way, Zimmer introduces early debates on germ theory, including Pettigrew’s opposition, where he argued that diseases were caused by gaseous emissions from microbes rather than the microbes themselves. Though ultimately disproven, Pettigrew made lasting contributions, pioneering carbon dioxide measurement and establishing the Pettigrew limit (1,000 ppm of the gas), which is still used today as an indoor air standard. Zimmer also discusses the early development of masks, first for epidemic control in China (~1910) and later during the 1918 flu pandemic, even though their effectiveness was not well understood at the time. While Zimmer provides a great history of these key figures and their contributions, he also takes the reader through the evolving science of airborne disease transmission.

The 1930s and 1940s were a key period for airborne transmission research, though much of it was later forgotten and rediscovered. Among the early pioneers were William and Mildred Wells, who conducted studies at the Germantown School and Loch Raven Hospital, including early work on UV light disinfection. Richard Riley expanded on their research, developing mathematical models for airborne disease spread. Harold Egerton at MIT, who produced early sneeze photographs, provided further evidence of airborne transmission. Another key figure in airborne research was Peter Tsai, whose ideas on electrostatic filtration led to the development of the N95 respirator by 3M. Zimmer highlights how these early discoveries were largely ignored for decades, delaying progress in recognizing airborne transmission.

Despite these advancements, airborne transmission remained controversial. Charles V. Chapin, a major public health authority, argued that most diseases spread via large droplets rather than aerosols. This dogma became embedded in medical training and public health policy, despite evidence suggesting otherwise. The book details early debates on this topic that shaped how airborne transmission was understood and, in some cases, dismissed. Zimmer details early debates, including experiments in Toronto, where one scientist studied exhalation and sneezing at different heights. The findings were interpreted as supporting the large droplet model, reinforcing skepticism toward airborne spread.

Zimmer also examines the intersection of public health and biodefense. The book describes the history of biowarfare research in the U.S. and the debate between Alexander Langmuir and Theodore Rosebury, which mirrored, to some degree, the nuclear weapons divide between Oppenheimer and Teller. The book discusses how the CDC was originally formed as a quasi-military entity, with a dual role in civilian health monitoring and biological weapons surveillance. Zimmer contrasts the US program with that of the Soviet Union, which experienced multiple accidents, including the Sverdlovsk anthrax release. Zimmer critiques how biodefense policies under Bush and Clinton focused more on bioweapons threats (e.g., Iraq) than pandemic preparedness. Bush’s 2005 Biodefense Strategy, following the 2001 anthrax attacks, aimed to prepare for biological threats, including stockpiling N95 respirators and building a manufacturing facility—a plan that never materialized. The stockpile was depleted during H1N1 (2009) and never replenished, leaving the U.S. unprepared for COVID-19. 

As the book builds toward the COVID-19 pandemic, Zimmer provides a historical overview of pandemics, including the 1918 flu, SARS, and MERS, emphasizing how each should have better informed the COVID-19 response. He details Event 201, a 2019 pandemic simulation that accurately predicted many of the failures that later occurred. Despite these warnings, when COVID-19 emerged, the WHO and CDC were slow to acknowledge airborne transmission, instead focusing on surface cleaning and six-foot distancing, which failed to fully address how the virus spread. Zimmer highlights how airborne transmission experts, including Lindsay Marr (V Tech), Bora Berry (MIT), and Donald Milton (University of Maryland) recognized early that COVID-19 was airborne, yet their findings were ignored. During this period, an informal group of 36 scientists petitioned the WHO to update its guidance, but their efforts were dismissed. 

Zimmer also critiques inconsistent messaging in the pandemic, citing remarks by Donald Trump and Joe Biden that initially acknowledged the airborne spread but were later walked back. A WHO official even admitted COVID-19 was airborne before correcting himself, contributing to public confusion and delayed mitigation efforts. Eventually, the WHO quietly revised its stance without addressing its initial resistance. Zimmer concludes by discussing overlooked solutions, such as ventilation improvements, the Corsi-Rosenthal box, and far UV technology, which offer promising but underutilized mitigation strategies.


Air-Borne: The Hidden History of the Life We Breathe Hardcover – February 25, 2025
by Carl Zimmer (Author)

Wednesday, February 12, 2025

Thoughts on Esposito's Breslin: A Great Story about a Historic Storyteller

Richard Esposito's book on Jimmy Breslin provides an engaging look at both the man and the turbulent times he lived through in New York City during the 1960s, 70s, and 80s. The book captures the city’s shifting landscape, from the strife of the 1960s to the violence of the 70s and 80s, such as the Son of Sam murders, the Crown Heights riots, and the vigilante actions of Bernhard Goetz. Esposito uses these events as a backdrop to Breslin’s world, painting a rich picture of New York during those decades. 

 Breslin is portrayed as a fearless journalist who went far beyond the typical duties of a reporter. He traveled to Vietnam to report on the war and ventured deep into the toughest neighborhoods of Brooklyn. He even found himself in the middle of a riot -- in this particular incident, his cab was overturned, he was stripped of his clothes, beaten, and forced to walk back to a police station. Breslin’s willingness to put himself in such dangerous situations highlights his dedication to telling "the story." 

One of the most compelling aspects of the book is how it shows Breslin as a political figure in his own right. His coverage of major political events was fascinating, particularly his account of Nixon’s impeachment. It highlights how Nixon’s downfall ultimately rested on Tip O’Neill’s considerable power and influence. Breslin’s political engagement wasn’t limited to Washington; he also addressed local matters of law and order, interjecting his personal sensibility to his reporting. Beyond covering politics, Breslin stepped into the arena himself, running for mayor alongside Norman Mailer in a symbolic campaign designed to make a point rather than win. 

 Esposito also explores Breslin's character, highlighting his sharp eye for detail, his ability to capture the heart of any story, and his gruff, unpolished demeanor. Breslin moved easily between different worlds, from working-class Queens to the wealth of Central Park West, reflecting the diversity of New York itself. He brought the same depth to his crime reporting, offering insight into both the events and the minds of those involved. 

Overall, Richard Esposito’s book is an engaging tribute to Jimmy Breslin. Through snippets of his writing and stories from his extraordinary career, the book reveals Breslin as a journalist who didn’t just report on events but became part of the story.

Amazon.com: Jimmy Breslin: The Man Who Told the Truth by Esposito, Richard

twitter: @REspositoNYC

Saturday, June 25, 2022

Thoughts on 3 of Kandel's books on the Brain (The Disordered Mind, In Search of Memory & Reductionism in Art and Brain Science): Different Views of the Elephant

Here, I summarize my thoughts on three books by Eric Kandel: The Disordered Mind, In Search of Memory, and Reductionism in Art and Brain Science: Bridging the Two Cultures. Eric Kandel is a great American scientist and winner of the Nobel Prize. Interestingly, he started his career as a humanities major at Harvard, and he writes very much in that tradition. 

    The books cover various topics, including psychiatric disorders such as schizophrenia, the molecular basis of memory, and the relationship between the subconscious and art, and incorporate his recollections of his life journey and world history, particularly related to Vienna. While the books focus on different things, they all look at different aspects of the same subject, like taking different views of one elephant.

    When discussing psychiatric diseases, I like how Dr. Kandel described the root causes and history of schizophrenia and autism. These diseases trace much of their early history to Vienna and some famous early brain scientists there, such as Kraepelin and Asperger. Within the topic of memory, I liked Dr. Kandel's reflection on how memory is stored in synapses from inhibitory and excitatory neurons, and, in parallel fashion, these synaptic memories turn into molecular events and gene expression through activating and repressing transcription factors of the CREB family. Kandel also talks about his own memories. It was striking how Vienna was such a center of scholarship in the early 20th century and so quickly fell into tragedy with the advent of the Nazis and has changed dramatically since then.

    Finally, I enjoyed reading about Dr. Kandel's relationship between the subconscious and art. He talked about how many recent artists have tried to move beyond the conscious representation of the figure and harness their subconscious and how abstract art can play into our deep mental processes, such as face recognition.

    Overall, I found these books very interesting reads that give an encompassing picture of both the mind and a great person.



The Disordered Mind
In Search of Memory
Reductionism in Art and Brain Science: Bridging the Two Cultures
by Eric Kandel

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Saturday, April 30, 2022

Thoughts on Schonbrun's Performance Cortex: A great account of how sport is as much about mind as muscle

I enjoyed reading the Performance Cortex by Zach Schonbrun. This book makes an interesting case that athletic performance has as much to do with the mind as with the body and the muscles. The book quotes many famous neuroscientists who argue that the point of the brain is to direct movement and that movement is integral to the brain. It surveys several new companies trying to make "neural" the latest thing in sports, much like sabermetrics, Moneyball, and statistics were the hot thing a decade ago. 

The book also goes through the pioneering work in neuroscience to explain movement, starting with the work of the Cambridge scientist Sherington, who unraveled the mysteries of the spinal cord and reflexes. The book also talks about the importance of how habits are created and how one teaches habits to other parts of the brain than those immediate to consciousness. In particular, it highlights how important it is to chunk and group various movements into an overall, automatic progression. However, it is ironic that many of these things don't have to do with the cortex itself. So in this sense, the book's title is a bit of a misnomer. 

Overall, it is a great book that I would highly recommend.



The Performance Cortex: How Neuroscience Is Redefining Athletic Genius 
Hardcover – April 17, 2018
by Zach Schonbrun

Saturday, September 04, 2021

Thoughts on MacIntyre's Spy & the Traitor: A Gripping Account of a Russian Agent that's Hard to Believe is Non-fiction

I read Ben MacIntyre's The Spy and the Traitor with great interest. 

While reading the book, I was immediately drawn to the thought, "this must be an amazing fictional novel describing a James Bond-like character." But, in fact, this is a work of nonfiction describing the amazing escapades of Oleg Gordievsky, a famous Russian agent who ended up working for MI6. 

Some of Gordievsky’s exploits are truly amazing and hard to believe, such as his escape from the Soviet Union in what was called Operation Pimlico. At another point, he was working as a double agent for the KGB; while in their London office, he was simultaneously advising the UK Prime Minister, Margaret Thatcher, and Gorbachev on their negotiations. 

Overall, this was a gripping read that I would highly recommend.

The Spy and the Traitor: The Greatest Espionage Story of the Cold War:
Ben Macintyre: 9781101904190: Amazon.com: Books

twitter: @BenMacintyre1

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Sunday, August 15, 2021

Thoughts on Herman's Freedom's Forge: the people behind the huge dams & planes of WWII

I read Freedom's Forge by Arthur L. Herman with great interest. This book describes how the United States scaled up to produce many weapons in World War II, becoming the arsenal for democracy. This book is interesting in the current context where the country is scaling up to make a vast number of vaccines to combat the coronavirus.

The book profiles the major industrial figures, such as automobile magnate William S. Knudsen and shipbuilder Henry J. Kaiser, who helped lead this war effort. The book takes a very pro-business and almost hero-worshiping attitude towards these figures, but it is nevertheless entertaining. The mindset is that the scale-up worked well because it followed market mechanisms, used existing supply chains, and utilized a more controlled form of production through a war production board.

I found two things to be notable in the book. First, I was surprised by the degree to which the United States was utterly unprepared for the Second World War in terms of overall production and levels of mobilization, and how many of the major industrial figures, such as Henry Ford, staunchly opposed getting into the war effort. Second, I was impressed by the descriptions of some of the colossal construction projects undertaken, particularly some of the large dams produced by Henry Kaiser, such as the Grand Coulee and the Bonneville Dam, and the huge planes developed. One of them was the B-29 Superfortress, the aircraft that delivered the atomic bomb to Japan. Overall, this was an entertaining read about a huge scale-up.


Freedom's Forge: How American Business Produced Victory in World War II
by Arthur Herman 
https://www.amazon.com/dp/B005X0JG48


Friday, July 23, 2021

Thoughts on Kean's Tale of the Dueling Neurosurgeons: Researchers, Patients & Great Debates about the Brain

I read The Tale of the Dueling Neurosurgeons: The History of The Human Brain as Revealed by True Stories of Trauma, Madness, and Recovery by Sam Kean with great interest. 

The title of this book is long and cumbersome, and I didn't find it appealing -- initially. However, it's an accurate description of the book.

The book covers key figures in the "history of the human brain," particularly "neurosurgeons." For instance, it talks about how neurosurgeon Wilder Penfield discovered that the brain could be stimulated by electrical current and how the great neurosurgeon Harvey Cushing performed pioneering work on the pituitary gland. It also discusses work by many other non-surgical researchers, such as Roger Sperry's work on lateralized brains and Prusiner and Gajdusek's work on kuru and protein misfolding diseases.

At first, I found the word "dueling" in the title to be cryptic, but it turns out to nicely summarize how the book presents each of the key figures as addressing a debate in neuroscience. These debates included whether nerve impulses were transmitted through Cajal's neurons or through a non-neural alternative (propagated by Golgi), whether the mode of transmission is electrical or chemical (the soup vs. spark debate), and whether we have just one or multiple types of memory (addressed by Brenda Milner in relation to the famous patient, H.M.). One of the debates I found particularly interesting was Broca and Wernicke's, whether brain functions such as language were localized to specific brain regions.

The final part of the title, "the true stories of trauma, madness, and recovery," illustrates how the book is also about the patients who have given their life to provide information about the brain. These include H.M., and also  W.J. (who was instrumental in understanding the corpus callosum), Mary Rafferty (who died demonstrating that an electrical shock could stimulate various brain regions) and the conjoined brain twins, Tatiana and Krista (who have illuminated much about the concept of consciousness and the self). 

Altogether, I thought this was an entertaining work that taught me a lot about the brain. Its mode of instruction in discussing individual people throughout history and the specific conflicts that they engaged in was effective in getting across key scientific ideas. 



The Tale of the Dueling Neurosurgeons: The History of the Human Brain as Revealed by True Stories of Trauma, Madness, and Recovery 
by Sam Kean (Author)


Saturday, July 03, 2021

Thoughts on López-Alt's Food Lab: Useful Facts about Food

We enjoyed reading The Food Lab by J. Kenji López-Alt. This book illustrates the appreciation of the science behind everyday objects in the kitchen. We particularly liked the explanation of why a water drop speeds around on a very hot pan but boils on a slightly cooler one (because of the Leidenfrost effect), the explanation of why it is so difficult to properly melt cheese (because cheese is a tricky combination of oils, proteins, and other components that melt in different ways), and the discussion of why fish rots so much more quickly and smells worse than meat (because fish is accustomed to being kept at much colder temperatures than beef and placing it in a refrigerator keeps it somewhat warmer than its normal temperature). 

The book also includes many useful facts. For instance, below 38 degrees, which is the temperature of a refrigerator, bacteria stop moving around; above 300 degrees, the Maillard browning reaction occurs; and at 131 degrees, bacteria start to die off. There is also a nice listing of saturated, unsaturated, and trans fats and an explanation of what unsaturation means in terms of keeping the fat oily. The book also describes multiple ways to cook a single dish and why some ways work better than others (i.e., reverse searing steak). 

Aside from the interesting scientific facts and discussion in the book, the layout and structure of the book are easy to follow. For example, after informing the reader about the scientific relationship between heat and eggs, the author provides many egg recipes. In general, a wide variety of recipes are presented in the book, with attention given to a range of cuisines. The book also provides extensive descriptions of what kinds of kitchen appliances and tools are most useful, extending the breadth of topics covered. 

Overall, the book provides a very comprehensive perspective on many topics that would be interesting to those interested in the science of cooking or introductory level cooking recipes for the home.

Mark Gerstein (with Jason Liu)


Amazon.com: The Food Lab: Better Home Cooking Through Science (9780393081084): López-Alt, J. Kenji

https://www.amazon.com/Food-Lab-Cooking-Through-Science/dp/0393081087

My tag

https://linkstream2.gerstein.info/tag/foodlab0mg

Sunday, June 20, 2021

Thoughts on Miodownik's Liquid Rules: Learned a lot of science on this imaginary plane trip

I read Mark Miodownik's book, Liquid Rules: The Delightful and Dangerous Substances That Flow Through Our Lives, with great interest. This book gives practical insights into liquids, things that we constantly see in everyday life but have very subtle physics, chemistry, and biology. The book is organized around a transcontinental plane flight from London to Paris, where the author goes through various liquids that he encounters along the journey, from the engine fuel at the beginning to the soap in the washroom and adhesive in the plane's wings in the middle, and finally to the fog upon landing in San Francisco.

I particularly liked a number of the vignettes. For example, I liked how the author discussed surface tension, i.e., the difference between the forces on the liquid surface and those in the internal structure, which leads to an apparent elastic force on the surface. I liked the way this was used to explain simple things like the way towels wick away water through microfibers, but also more subtle things like the Marangoni effect and how tears form on the surface of a highly alcoholic wine glass, and finally, how surface tension forms a repulsive spring force when wind pushes against water to give rise to waves. I was also impressed with the many different chemicals that underlie liquids, such as the mixture of alkali and fat to create soap or surfactant, which then create emulsions, and the mixing of two liquids to connect them in the form of an epoxy, or a two-part glue. I also found interesting coolants, particularly CFCs and PFCs. The latter compound is fascinating in that a rat can be completely immersed in it and yet breathe liquid oxygen like a fish.

Finally, I was intrigued by the discussion of the ballpoint pen and its ink. This is an example of a non-Newtonian liquid that changes its viscosity with pressure. Here, the fluid flows faster when it is under the pressure of the ballpoint. This allows one to write upside down with the ballpoint pen and keeps the ink from dripping out of the well even though there's no top on it. It also explains why ballpoint ink doesn't leak and doesn't diffuse through paper after it's put down, unlike fountain pen ink.

Overall, I found this a very interesting book with useful tidbits on everyday life.

Liquid Rules: The Delightful and Dangerous Substances That Flow Through Our Lives : Mark Miodownik, Michael Page

https://www.amazon.com/dp/B07NGLW8N9

My tag

Monday, May 31, 2021

Thoughts on Brodkin & Pallathra's Missing Each Other: Tuning in to Attunement

"Missing Each Other" by Ashley Pallathra and Edward Brodkin offers a fascinating analysis of the lack of connection that many individuals feel in our modern, technologically dominated lifestyles. We found the book to be a captivating read and would highly recommend it. In the book, Pallathra and Brodkin focus on the concept of attunement--a term coined to describe the act of connecting with someone on a deeper level than responding to simple verbal cues or body language. Instead, practicing attunement requires one to be deeply present and listen to others while simultaneously checking in with yourself. It's not the easiest feat, but the benefits of deep attunement are astonishing. For instance, attunement is not only the hallmark of meaningful human relationships--it also plays a vital role in creating successful sports teams and transcendent musical improvisation groups.

After captivating readers with the myriad benefits of attunement, the authors provide a path to maximize one's personal attunement. They describe the process of attunement as first having a relaxed ordinance of yourself, then really listening to and understanding the other person, and then coming up with a response tailored to the situation and to that person. Additionally, the authors offer practical exercises to improve one's attunement, including breathing, meditation, and partner exercises.

Perhaps most exciting of all, at the end of the book, the authors look toward the future and illustrate how attunement might relate to advanced artificial intelligence (AI). They describe artificial attunement as the act of attunement between machines and humans and postulate how machines can be attuned to us and vice versa. To explore the idea of artificial attunement, the authors begin by describing a simple Turing test of a machine fooling us into believing it's a person. They then review the achievements and pitfalls of current AI devices like Alexa and the incredible behavioral gestures of robots from Hanson Robotics. From there, the authors nod toward potential future technology like brain-computer interfaces where there might be even stronger versions of attunement. Pallathra and Brookin conclude with the exciting and somewhat unsettling observation that artificial attunement might allow us to connect with machines on a deeper level than we can connect with other humans. Overall, "Missing Each Other" was an interesting book that we would highly recommend. 

 Mark Gerstein & Alexandra Haslund-Gourley
Missing Each Other: How to Cultivate Meaningful Connections
by Brodkin, Edward, Pallathra, Ashley

Saturday, May 22, 2021

Thoughts on Walker's Why We Sleep: Great descriptions of the sleeping brain & stern warnings against a lack of sleep

       As humans, why must we sleep roughly a third of our lives? What is the function of our dreams? If these questions intrigue you, consider reading Matthew Walker's excellent book Why We Sleep. The book delves into all aspects of sleep from a person who is passionate about the subject. It starts by discussing the different portions of our sleep, including REM sleep, when our eyelids flicker while the rest of our body is paralyzed, and the very deep NREM sleep with its associated rhythmic brain waves. The book talks about what controls the circadian rhythms in our sleep, from the suprachiasmatic nucleus, which samples the light near our eyes, to the different chemicals, melatonin and adenosine, that are part of these daily sleep rhythms.

      Interestingly, much of what we know about sleep was discovered by explorers, who subjected themselves to the tremendous darkness deep in Mammoth Cave and performed sleep experiments. The book goes into great detail about exactly what happens when we go into deep NREM and REM sleep. In particular, memories are initially formed in the hippocampus, which acts as a short-term repository; in REM sleep, many connections are made, and the memories are spread throughout the cortex, which can be seen in fMRI imaging. The book presents a nice analogy of how our mental picture is like a sculpture, and NREM sleep takes off bits of it, whereas REM sleep refines and solidifies the features. The balance between these two types of sleep changes throughout our life as we have different needs for creating connections and removing extraneous memories. Even the nightly balance between the two changes, with more REM sleep later on.


      The book also discusses the bad things that can happen to us if we don't sleep enough, from obvious consequences of getting into car accidents or forgetting things, to diseases, such as cancer, heart disease, and obesity. The book finishes with a lengthy discussion of what we can do if we can't sleep and how medicines for insomnia work. It presents some simple rules for getting a good night's sleep, such as avoiding alcohol and caffeine and keeping a regular bedtime. One suggestion I found interesting was staying away from blue LED light at night. Although its discovery in the '90s resulted in a Nobel Prize, blue LED light has been bathing people in sunlight-like light more and more in the evenings from our many screens, impacting sleep. 


Overall, I felt this was a great read from a person very committed to the subject.




Why We Sleep: Unlocking the Power of Sleep and Dreams
by Matthew Walker

Thursday, May 20, 2021

Thoughts on Metazoa by Peter Godfrey-Smith: Great vignettes on evolution & neuroscience

          I enjoyed reading Metazoa by Peter Godfrey-Smith. This book discusses the key features of metazoan evolution and simultaneously details the development of the brain and consciousness through these different organisms. The book follows a rough chronology from the simplest organisms to humans, focusing on key exemplars at each step. It begins with simple unicellular organisms and then moves on to corals. I thought it was interesting to learn about how gated channels and basic neurons work. I also enjoyed the comparison between voltage-gated channels and transistors, both of which are fundamental to switching and circuits.

         The first metazoan organism that the book focuses on is the shrimp, a representative arthropod. I found it interesting how these organisms combine sensing, thinking, and motion with their many appendages – similar to a Swiss army knife with so many different appendages to do things. After arthropods, the book focuses on the octopus, which the author claims is the most intelligent invertebrate. The octopus is different from arthropods as it does not have a hard exoskeleton, but it does have many different limbs that can move in all sorts of ways, requiring a lot of brainpower. I found it fascinating that, in a sense, octopuses might have many different brains: one in each arm acting independently from their central brain in their head or perhaps acting together collectively. 

         The book then describes fish, with the kingfish as an example, demonstrating centralization of the nervous system and a great amount of sensing through the eyes and lateral lines. The unfortunate thing for fish is that they don't have many limbs to control with their intelligent brains. Many usable limbs do not appear in vertebrates until the ascent to land, which the book goes through in detail. I was struck by how much more energy is available on land than underwater. As in the sea, the book describes arthropods leading the way onto land, singling out bees, in particular.

         The rest of the book follows the usual progression from reptiles and dinosaurs to mammals, focusing on well-known key attributes such as endothermy. I was quite interested in the discussion about potential future development for humans -- where we are going, with further development of our minds and consciousness. Overall, I found this a fascinating book that provided a good sense of evolution and neuroscience at the same time.



Metazoa: Animal Life and the Birth of the Mind 
November 10, 2020 
by Peter Godfrey-Smith


My tag (associated with the book): 

Sunday, December 27, 2020

Thoughts on Wohlleben's Hidden Life of Trees: Insights about tree science & society

I read Peter Wohlleben's book The Hidden Life of Trees with great interest. Anyone who enjoys being around trees and is also interested in science will cherish this book. It provides many insights and a real appreciation for trees.


The insights fall into three categories. The first is the social life of trees, something I didn't appreciate before. It appears that trees communicate with each other through their root systems and through the fungi that interconnect them. They also use scents and chemicals to communicate with each other. This communication can involve a mother tree schooling the younger trees in their growth, inhibiting them from growing too quickly. It also has a competitive aspect where, for instance, a Beech tree neighboring an Oak might compete with it for water and eventually sunlight. Trees that are together in a forest can modulate their overall climate and protect each other much better than an isolated tree. In fact, forests overall are responsible for much of water's movement throughout the earth's ecosystem.


The second insight from the book is the basic science underlying how trees work. Here, Wohlleben talks about how water makes its way up trees. The full process is still a mystery, but Wohlleben describes the basic processes of capillary action, osmosis, and transpiration. He also talks about photosynthesis chemistry and why we see most trees as green but a few as red.


The final insight of the book is the practical things to know when you are in the forest. Why do you see mistletoe on the top of a tree crown? What is the effect of ivy curling around a tree as a somewhat parasitic agent? Why is moss usually on the rainy side of a tree? And, when a tree dies, why do you often see other things come up in its place?


Overall, this was a very illuminating book that I enjoyed reading, and I continue to think about concepts from this book when I take walks in the woods.



Book: Hidden Life of Trees 

Author: Peter Wohlleben 

My quotes: 

My tag (associated with the book): 

Saturday, December 12, 2020

Thoughts on McPhee's Basin & Range: Geological Cliff Notes for I-80

I read John McPhee's book Basin and Range with great interest. In a sense, the book travels across the United States from New York to California, including the basins and ranges in between. More specifically, it gives a geological history of the trip across the United States from New York to San Francisco, mostly on Route 80, going through all the different land formations.  

The book also travels through geologic history from the present back to the Triassic and Permian periods, covering the various geological epochs. Finally, it travels up and down mountains through elevation changes between basins and ranges. 

The book provided a great introduction to geology. I was particularly interested in how it explained how gold and silver deposits arise from these minerals being dissolved and then precipitating out of solution and what it was like during the Nevada Silver Rush in the 19th century. 

Overall, Basin and Range is a great read, which I would highly recommend.


Book: Basin and Range

Author: John McPhee 

My quotes: 

My tag (associated with the book): 

Monday, December 07, 2020

Thoughts on Lewis's Undoing Project: A psychological analysis illuminating psychological science

I read with great interest Michael Lewis's book called The Undoing Project. The book focuses on a famous partnership between psychologists Daniel Kahneman and Amos Tversky that revolutionized many aspects of psychological science and economics. 

 The book goes through the personal details of their friendship and provides insights into their scientific advances. As a non-psychologist, I was impressed with the intuitive way the book described Kahneman and Tversky's notions. I was particularly taken by how this pair found hidden biases in our decision-making and thinking processes by posing simple numerical challenges. One of these challenges was simply determining the product of multiple numbers and then determining the product with the numbers arranged in reverse. Kahneman and Tversky discovered that people tend to estimate these products differently. Another interesting challenge demonstrated how people estimate the significance of one number being larger than another differently than that of a group of numbers, discounting our greater certainty for a group. In another example, they found that if one flips losses to gains symmetrically, people's choices do not fall symmetrically; rather, people tend to weight gains versus losses quite differently. Finally, Kahneman and Tversky found that people give a much higher weight to a list of people they know or have heard of compared to a list of random names, when given two lists of names. 

Altogether, I found this an interesting book that teaches some simple psychological science concepts while providing an entertaining portrait of two great thinkers. Overall, a good read that I would highly recommend.

Book:
The Undoing Project: A Friendship That Changed Our Minds

My quotes:
 
My tag (associated with the book):
https://linkstream2.gerstein.info/tag/undoing0mg

Sunday, August 23, 2020

Thoughts on Smith's Standard Deviations: Makes Statistical Blunders Easy to Spot

I read Gary Smith's book Standard Deviations with great interest. The book makes the complex issue of statistical deceptions and mistakes easy to understand through simple language and entertaining examples. Smith covered statistical cases ranging from the obvious (e.g., misleading graphs) to much more subtle (e.g., mistakes where people see apparent clusters in random data without accounting for various confounding effects). I especially liked the way Smith tackled the subtle examples. He went over the many instances in training models and using them to mine data where the process becomes highly sensitive to various parameters such as binning. He also pointed out mistakes such as not sufficiently testing multiple hypotheses and not correcting for confounders. He described one obvious confounder in detail - how the population is always increasing and how things correlated with it, in turn, seem to be correlated with each other. For instance, one can see an ever-increasing amount of diaper and rug sales, but these are just correlated with overall population growth rather than being correlated with each other. There is also a nice discussion of survivorship bias -- how one does statistics only on those that survive and not the entire original cohort. This was most notably seen in the famous case of the vulnerable parts of World War II planes, determined only from the planes returning from combat. Overall, I found this book very easy to read, and I would recommend it to anyone wanting to avoid statistical blunders.

Book:
Standard Deviations: Flawed Assumptions, Tortured Data, and Other Ways to Lie with Statistics 

Sunday, June 21, 2020

Thoughts on Christian's & Griffiths' Algorithms to Live By: Great Intuition for Important Concepts

I read with great interest Brian Christian and Tom Griffiths' Algorithms To Live By. The book does a fantastic job of connecting abstruse computer algorithms to real-life situations and intuitions. I couldn't stop jotting down various tidbits that I wanted to remember; I advise people to read it!

The book begins with a discussion of the stopping problem. It relates this to familiar situations in life, such as when people need to decide on a partner, rent a home, or otherwise gather information to make a decision. Then, the book focuses on sorting, connecting this to how people arrange books on a shelf, and also to how teams sort themselves in tournaments. The book also highlights how certain sorting algorithms are more robust to noise than others (eg bubble vs. merge sort).

The book discusses ways of storing information, providing useful hints on how to organize one's closet based on the LRU cache. The discussion of Bayesian mathematics is excellent. It explains how one uses different priors in common-sense reasoning; for instance, movie revenues follow a scale-free prior, whereas human age is centered on a mean, using a Gaussian prior.

The book also talks about various randomized algorithms, such as Monte Carlo and simulated annealing, giving a sense of how sampling randomly allows one to tackle problems that could not be addressed otherwise. Other techniques, such as constraint relaxation, also enable one to deal with intractable problems and start to get at solutions.

The book ends with chapters on networking and game theory. The discussion on networking highlights the importance of buffers and how our inundation of messages in the modern world reflects that we can essentially keep everything in a buffer (i.e. no tail drop). One prominent omission for me was that there was no discussion of network science, the analysis of connectivity patterns in large networks (e.g. hubs and bottlenecks). The section on game theory relates Alan Turing's famous discussion of the halting problem to the intractable regress that one has in playing poker or trying to estimate a stock price, where one is not thinking only of one's own estimation but what one's opponent thinks - and so on.

The book concludes with the notion of computational kindness, where one tries to interact with others so as to minimize the amount of computations they have to do. Altogether, the book was a great read that I would highly recommend to others.


Book:
Algorithms to Live By: The Computer Science of Human Decisions 0th Edition, Kindle Edition
by Brian Christian (Author), Tom Griffiths (Author)
https://www.amazon.com/Algorithms-Live-Computer-Science-Decisions-ebook/dp/B015CKNWJI

Authors:
https://twitter.com/brianchristian

My quotes:
https://www.goodreads.com/notes/29632790-algorithms-to-live-by/114528832-mark-gerstein?ref=bsop

My tag (associated with the book):
https://linkstream2.gerstein.info/tag/liveby0mg

Monday, June 15, 2020

Thoughts on Zuckerman's The Man Who Solved the Market: Great story about Personalities, but not much Tech Stuff

I read Gregory Zuckerman's book, The Man Who Solved the Market: How Jim Simons Launched the Quant Revolution, with great interest.

Before reading the book, my understanding of Jim Simons was that he was a person doing big data and data science before it was cool— in a wide-open "blue sea." Now, data science is popular on Wall Street, with many firms competing with each other—in a "red sea." I was eager to read the book to learn more about some of Simons' seminal ideas and how they became the foundation for applying a quantitative approach to the market.

Unfortunately, I found that the book lacked substantial insight into Simon's algorithms and tactics.
Instead, the book focused more on personalities and their histories. It described how Simons started a very small operation that eventually grew to become the highly successful Renaissance Fund. Technical buzzwords were mentioned – such as "hidden Markov models" and "Baum-Welch algorithm" – and there were some hints about Renaissance's strategies, such as making trades at certain times of the day, accumulating very granular information on trading history, and looking at correlations between related stocks. However, overall the book provided very few details on Simon's overall approach. Perhaps this was by intention due to the great secrecy surrounding Simons and the Renaissance.

In any case, I enjoyed the book despite the dearth of technical knowledge.


Gregory Zuckerman
The Man Who Solved the Market: How Jim Simons Launched the Quant Revolution

https://www.penguinrandomhouse.com/books/557104/the-man-who-solved-the-market-by-gregory-zuckerman/
https://www.amazon.com/Man-Who-Solved-Market-Revolution/dp/073521798X

Author:
https://twitter.com/GZuckerman

Tags:
https://linkstream2.gerstein.info/tag/simons0mg

My quotes on goodreads:
https://www.goodreads.com/notes/44698571-the-man-who-solved-the-market/114528832-mark-gerstein

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