What I’ve Been Reading Recently – My Bookshelf #9

What I've Been Reading Recently - My Bookshelf #9

Intro

I read 39 books in 2016 (as of April). I’m ahead of my last year’s count (this time, last year). I don’t do speed reading. I try to read slowly. I enjoy it. It’s not a hobby. It’s something I do everyday for a substantial amount of my time.

Most of the books I read this year are non-fiction. A few of them are audiobooks (fiction and self-development) and approximately 10-12 of them are programming books – which I had to go through even slower because they implied practicing with code.

What I’m currently mostly interested in is: genomics, bioinformatics, epigenetics and small-scale entrepreneurship. It’d be only reasonable to think that the books I read come from these fields.

Additionally, I read research studies, and, besides audiobooks, I listen to podcasts, interviews and watch lectures on these subjects. Coursera’s online courses also take a stretch of my time.

I said it previously and I’ll keep saying it: knowledge without action is meaningless. That’s why I strive to immediately apply the concepts I learn about. Case in point: I cannot become a good programmer simply by reading a programming book. My skill grows only when I engage in extensive practice.

In this post, I’m going to share a few of the titles that I read this year so far. All my previous book/reading related posts are: #1 #2 #3 #4 #5 #6 #7 and #8

Mantra from the past:

The more I read, the more I realize the little I know.
Reading is not a hobby; it is part of my daily routine. It wasn’t always like that.
I don’t do speed reading. I avoid being superficial.
I don’t want to skim through the books I read.
I take a significant amount of time to digest each of them slowly.
I read 7-10 books at a time. It’s not easy. But I enjoy it a lot.
Even though I do not practice speed reading, it seems that I can visualize and process words faster; so I read faster.
I think that through practice, I’ve been able to develop this skill.

The List #9

  1. Claude Piantadosi – The Biology of Human Survival – Life and Death in Extreme Environments

“The book presents environmental physiology using modern, integrated concepts of stress, tolerance, and adaptation. Barriers to life in extreme environments, such as dehydration, starvation, and radiation, are described in separate chapters.”

As pointed out by Piantadosi, the degree to which human physiology can be stretched to the extremes depends on:

– the physics of the environment
– the duration of the exposure to the stressor
– the limits of human physiology
– behavioral adaptation

I specifically enjoyed learning about adaptation to extreme cold as this is something that I experiment with, a lot. I also learned about the distinction between acclimation and acclimatization:

“For example, individuals generally adapt to life in the desert or at high altitude by acclimatizing to all the features of the new environment. Acclimation involves physiological adaptation to a single environmental factor, or stressor, such as a change in environmental temperature or a change in altitude.”

  1. Ben Goldacre – Bad Science – Quacks, Hacks, and Big Pharma Flacks

This is one from a list of books that I consider extremely helpful in developing critical thinking skills. For those who do not know, we are innately prone to bias. Our brains fall prey to a host of logical fallacies; and most people are not aware of this. While Goldacre’s book does not teach about these fallacies, he exposes how the masses (people lacking critical thinking skills) are at the mercy of pharma, food companies, nutritionists and many alternative medical practitioners and, most humorously, snake oil salesmen:

“We will see this time and again, on a grander scale, in the work of dubious healthcare practitioners, and specifically in the field of ‘nutritionism’, because scientific knowledge – and sensible dietary advice – is free and in the public domain. Anyone can use it, understand it, sell it, or simply give it away. Most people know what constitutes a healthy diet already. If you want to make money out of it, you have to make a space for yourself in the market: and to do this, you must overcomplicate it, attach your own dubious stamp.”

Oh, he does seem to briefly mention about our innate fallacies:

“As human beings, we have an innate ability to make something out of nothing. We see shapes in the clouds, and a man in the moon; gamblers are convinced that they have ‘runs of luck’; we take a perfectly cheerful heavy-metal record, play it backwards, and hear hidden messages about Satan. Our ability to spot patterns is what allows us to make sense of the world; but sometimes, in our eagerness, we are oversensitive, trigger-happy, and mistakenly spot patterns where none exist.”

  1. Nicholas Carr – The Glass Cage – How our Computer are Changing Us

I wasn’t too thrilled about this one and I hope that his other titles are more appealing to me (in terms of content). Carr goes through and describes numerous technological changes that have been taking place in the last couple of years and how they may leave a mark on our physiology and, most importantly, on our psyche. For example, architects who only use CAD (computer aided design) may lag in performance compared to those who use both paper and CAD:

“Sketches on paper serve to expand the capacity of working memory, allowing an architect to keep in mind many different design options and variations. At the same time, the physical act of drawing, by demanding strong visual focus and deliberate muscle movements, aids in the forming of long-term memories.”

Often when I try to improve a certain skill, I find that challenging myself just outside the boundaries of comfort leads to growing that certain skill, while overwhelming myself with stimuli related to the skill is counterproductive. Carr brings some light to this:

“Like dancing mice, we humans learn and perform best when we’re at the peak of the Yerkes-Dodson curve, where we’re challenged but not overwhelmed. At the top of the bell is where when enter the state of flow.”

  1. Emma Barrett – Extreme – Why some People Thrive at the Limits

More on extreme physiology. Compared to Piantadosi’s book which is more like a textbook, Barrett’s book is overloaded with experiences and stories, most of them from people living in the last 200 years. Her book is very gentle to the non-technical reader:

“Drawing on real-life cases, including those of explorers, mountaineers, deep-sea divers, and astronauts, we explore their personal characteristics and complex motivations, and analyse the psychological attributes that lead to success (or failure) for individuals and teams.”

What I enjoyed a lot is that she puts great humor in the narrative:

“More recent spacecraft have been equipped with toilets, but microgravity makes these remarkably difficult to use. The toilet on the Space Shuttle had an aperture of only 10 centimetres, and astronauts required training in how to use it. Mishaps were common: free-floating faeces were known as ‘escapees’.”

She talks about deliberate and dedicated practice if one wants to develop exceptional levels of performance in anything. And she seems to build on the concepts from Carr’s book:

“Practice involves repetition, such that successful actions are reinforced. Repetition only gets you to ‘good’, however. To become excellent, your practice sessions must involve effort. As you get better, they should become more challenging so that you continue improving.

People who are determined to excel in extreme environments therefore repeatedly expose themselves to increasingly challenging situations, learning lessons and building resilience as they go.”

And more on beneficial stressors:

“Intermittent fasting may therefore be one example of a broader principle— namely, that repeated exposure to moderate, short-lived, and controllable stressors can make us tougher and more resilient, both physically and psychologically.”

  1. Steven Novella – Your Deceptive Mind – A Scientific Guide to Critical Thinking

Just a few lines to the top of this post I was telling you about getting educated on the logical fallacies humans are innately prone to. Well, Novella’s book and course serve to that purpose. I dedicated an entire post to discussing about his book, so I’d recommend you go and read it here. And a quick tidbit:

“There are numerous ways in which human memory is flawed. Far from being a passive recording of events, memory is constructed, filtered through our beliefs, and subjected to contamination and morphing over time. Memories can even be fused or entirely fabricated. It’s naive to implicitly trust our memories, and it’s important to recognize that we need to be realistic and humble about the limitations and flaws of human memory.”

  1. Carey Nessa – The Epigenetics Revolution

Epigenetics is a topic that I’m currently interested in. In Carey Nessa’s words, epigenetics refers to:

“…the set of modifications to our genetic material that change the ways genes are switched on or off, but which don’t alter the genes themselves.”

It involves processes such as methylation and acetylation (and not only) which change the way genes are expressed and proteins are being made. Studying epigenetics provides one the acknowledgement and the knowledge of the fact that their genes are not their destiny and that one can change how their genes express themselves with different lifestyle and non-lifestyle related factors.

For example, you are someone who consumes a normal diet with decent proportions of highly processed low nutritious foods (fast-foods, foods with added sugars and oils, etc.). You are sedentary. You find out that you have a mutation in a gene related to Parkinson’s disease. You have 3x the risk of developing Parkinson’s compared to a person with a similar lifestyle but not carrying the gene mutation.

Armed with this information you can drastically reduce your risk of developing Parkinson by cleaning your diet and starting an exercising regimen. Of course, you don’t have to know you’re more susceptible to a certain disease to make these changes in your life. Everyone may benefit from such advice. But there are situations when some people benefit more than others.

From another side of the spectrum, there are those with extreme longevity and poor lifestyle choices. Some centenarians and supercentenarians posses a better functioning FOXO3 gene that allowed them to reach very old age despite their apparent chaotic, unorganized, and poor lifestyle (smoking, diet considered ‘bad’ by many norms, alcohol consumption, etc). The average mortal should not assume we are all like that. Well, at least not until CRISPR/Cas9 and other genome editing technologies would allow us to posses similar genetic makeup to the centenarians.

Nessa’s book discusses how obesity can be inherited through epigenetic changes in the germline (sperm and egg). Your poor diet and lifestyle may partially be responsible for the future of your offspring).

One clear example comes from the Dutch Hunger data. Of course, in this case, the poor pregnant women could not be responsible for the famine they’ve been through.

What I've Been Reading Recently - My Bookshelf #9 - Nessa

  1. Cal Newport – Deep Work – Rules for Focused Success in a Distracted World

“Decades of work from multiple different subfields within psychology all point toward the conclusion that regularly resting your brain improves the quality of your deep work. When you work, work hard. When you’re done, be done.”

Cleaning the space, eliminating distractions, being systematic in your approach are all highly demanded qualities for many high-achievers, especially in the world of overload of information that we live in today.

Honestly, this book helped me a lot in my approach to my research and my writing by making clear deliniations between work and play. Mental isolation, either in plain-sight or in a non-distracting environment is a matter of #1 priority when I do mental work.

So, when I work, I work. Clearly defining my strategy, I’m able to produce ridiculously greater mental output in shorter timeframes – compared to my previous less-organized approach.

And then, I’m left with boredom for the great majority of my schedule. Obviously, I organize/devote that time to different activities – as I do not embrace boredom.

Funny enough, Newport has a chapter with that title: “Embracing boredom”. From his book I also learned about Roosevelt’s over-productiveness and wide range of activities of interest:

“amazing array of interests’ in his collage years – boxing, wrestling, body building, dance lessons, poetry readings, obssession with naturalism.”

I’m going to let you discover for yourself how he was able to efficiently engage in all those activities.

  1. Steven Bratman – Health Food Junkies – Orthorexia Nervosa – The Health Food Eating Disorder

I’m fairly amused when I see people trying to control every molecule of foodstuff they put in their mouths and every ‘chemical‘ they are exposed to. Things like “grass fed non-GMO and all the natural blah blah blah” look ridiculous and very fragilizing, especially when you put them in the context of something called hormesis (how toxic chemicals can make you more resilient). Bratman coined ‘orthorexia’. I’ll let him explain it for you:

“…anorexics may know they are harming themselves, but orthorexics feel nothing but pride at taking care of their health in the best possible way. I know how this feels, because I’ve been there myself. I’ve been at various times a raw-foodist, a total vegetarian, and a macrobiotic follower, and although I learned a lot from those experiences, it finally dawned on me that there is a dark side to dietary virtue. Similarly, as a holistic physician, I used to prescribe pure diets to my patients and only gradually came to understand that I wasn’t necessarily doing them a favor. It’s not that I don’t support eating healthy food; it’s only that when healthy eating becomes an obsession, it’s no longer so healthy.”

This shouldn’t mean that vegetarianism, if appropriately approached, is bad. On the contrary, many vegetarians are healthier that people on normal diets and than those on diets from the other extreme (high-fat, low-carb, ketogenic, etc). I think, in great part, it’s a matter of nutrient richness.

Orthorexia often leads to:

“As we will see in later chapters, raw-foodism becomes fruitarianism (eating only fruit) and finally breatharianism (trying to live on air alone—I am not kidding).”

I’m hungry. Can I have some air please? Make it double.

“Is wheat actually an evil food? Is corn? Is soy? These three common food allergens are not toxic like alcohol, nor necessarily polluted with food preservatives and artificial colors. Soy is even popularly described in other healing systems as a miracle healing food. Yet they are at the top of the allergenic list. To be fair about it, if you are allergic to these innocent foods, the problem is in you, not in the food.”

“In other words, removing food allergens from the diet is a Band Aid treatment. It doesn’t get to the root of the problem, the root being “Why can’t my body handle these perfectly good foods?” This is ironic, because practitioners of holistic medicine love to accuse conventional medicine of treating the symptom and ignoring the cause of the illness.”

Well yeah. This is a good point if you look it that way. Why would some food be of blame for one’s inability to metabolize and derive energy from it efficiently?

  1. Sue Armstrong – p53 – The Gene that Cracked the Cancer Code

This book is not for the non-technical. The entire book is about p53, a gene highly studied in the context of cancer. It makes some bold affirmations here and there, but overall it gives a very clear picture for those interested in the topic.

“This means that from a molecular viewpoint there is one basic condition to get a cancer: p53 must be switched off. If p53 is on, and hence functioning properly, cancer will not develop.”

Armstrong talks about the discovery of the gene, the pioneers of the field, its regulatory mechanisms, its connection with oncogenes and different metabolic pathways, and most exciting to me, p53 in the context of genomics. If you don’t have particular interest in cancer genomics/metabolomics, I’d say better leave this one on the shelf.

  1. Carol Dweck – Mindset – The New Psychology of Success

As I mentioned in the beginning, some of the books that I digest are in audio format. This was one of them. Nowadays, I get audiobooks on the topics that help me develop myself personally, while I avidly read/devour the books that are of my main interest.

Dweck’s book is, honestly, one of the best descriptors of mindsets. Yes, this is an abstract view. To be more precise, she talks about the fixed vs. flexible mindset.

Simply put: a fixed mindset, characteristic of most people, describes a caged mind that guides itself by stereotypes, preconceived notions, protected ideologies, beliefs, etc. It lacks the substance/drive to change. Conversely, a flexible mindset is prone to growth as it balances assumptions, does not take anything for granted, it is opened to the new, and most importantly it is ready to change when context is appropriate.

In a big part, Dweck’s description of a growth mindset should be included in the repertoire of becoming a better (more critical) thinker.

She presents her arguments on the fixed and the growth mindset with real life stories and with studies and experiments from the psychology field. Given the interest I paid to listening to the book, I will definitely re-listen to it in the future (as I do with many audiobooks). In her own words:

“In a fixed mindset, people believe their basic qualities, like their intelligence or talent, are simply fixed traits…

In a growth mindset, people believe that their most basic abilities can be developed through dedication and hard work—brains and talent are just the starting point. This view creates a love of learning and a resilience that is essential for great accomplishment. Virtually all great people have had these qualities.”

  1. Programming Books

One of my current interests is in developing a skill that connects biology to technology. Bioinformatics serves exactly to that purpose. I am studying and actively experimenting with Python (programming language) applied to genomic data. Simply put – analyzing/interpreting DNA sequences with Python.

What’s great about this is that these 2 topics are not isolated.

To get a good grasp of them you have to verse yourself in genomics, biotechnology, genomic sequencing technologies, protocols and practices, and other programming languages just to name a few. Additionally, you learn how to use tools like BLAST, Clustal, genome browsers, dbGap, ClinVar, GATK, and many other from the NCBI toolkit and from other research communities.

One cannot imagine the overwhelming quantity of information that needs to be digested to make this possible. For me it makes great sense then to read books like Deep Work, Thinking Fast and Slow, and Predictably Irrational that may help me better organize my mind and the quality and capacity of my thinking.

A few of the dozen programming books that I went through in the past 3 months are:

Dr. Martin Jones Python for Biologists and Advanced Python for Biologists
Dr. Chuck’s Python for Informatics which is free
Allegra Via Managing your Biological Data with Python
Al Sweigart Automate the Boring Stuff with Python

To serve my purpose I also took/take several courses related to the fields of genomics and programming.

If you’re interested in programming, Python is probably one of the most used, highly-versatile, most documented, and most developed/updated that’s out there. Its open-sourceness makes it rich in modules and tools that you can use in any field you can think of: statistics, medical, technological, astrophysics, physics, biology, machine learning, etc. For every topic of choice, there are at least a few modules to work with (on top of its core modules).

For example, for bioinformatics you have biopython – a collection of tools, modules, and libraries specifically designed to help work with/interpret DNA sequences and genomics data. The open community developing biopython (you are welcome to participate) has created an extended 340-pages long cookbook, that is updated every few months.

I don’t have to convince you of anything. Do your own research and see what programming languages (if any) may be more feasible and easy to learn at this moment in time.

Conclusion

Many of these books may not be relevant to you because they reflect my current interests (which may be different than yours). As I previously said:

Disregard them? You could. Challenge yourself to learn something new? That’s also a possibility. Make your choice.

A good take away message is that the person I am right now is the result of the experiences I’ve been through and, most importantly, the books that have passed through my hands. It could have been better. It could have been worse. I am fairly satisfied. Most importantly, I’m very driven to keep expanding my knowledge and skills through learning and deep practice.

If you have book recommendations, I’d be more than happy to see you posting them below.

Images: by Ginny and Nessa

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4 Responses to What I’ve Been Reading Recently – My Bookshelf #9

  1. henrich says:

    Try “Nutrient Power” from William J.Walsh

  2. Peter Ohlson says:

    The Diet Myth by Tim Spector, concentrates on how gut microbe research is affecting his view of what the best diet for him would be. I think he would be worried that a strict ketogenic diet might reduce the diversity of beneficial gut microbes.

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