microbiome

69 results back to index


pages: 298 words: 76,727

The Microbiome Solution by Robynne Chutkan M.D.

clean water, Community Supported Agriculture, David Strachan, discovery of penicillin, epigenetics, hygiene hypothesis, Mason jar, meta analysis, meta-analysis, microbiome

Americans today have only about two-thirds as many bacterial species as native tribesmen in the Amazon who haven’t been exposed to antibiotics. As we’ll learn in the second part of this book, restoring those lost microbes takes real commitment. While there is no perfect microbiome, some are clearly healthier than others, notwithstanding the incredible variation from one to the other. The Human Microbiome Project and other research efforts like it seek to establish what the “normal” human microbiome looks like today—an important endeavor, considering the rate at which our microbial landscape is changing. Companies like uBiome allow the citizen scientist to catalogue his or her own microscopic habitat, compare it to others, and reassess it as diet and habits change. The human microbiome may well be the next big frontier in medicine, providing answers to why we get sick and novel solutions for how to heal ourselves. In the next chapter we’ll learn more about what our gut bacteria actually do—besides make gas—and why they’re so essential to our health and well-being.

Since bacteria follow the food, instead of counting calories when we’re trying to slim down, a model that clearly falls short in accounting for weight gain or loss, we should be looking at how to shape our microbiome in a way that influences caloric extraction from food. Cutting down on processed grains and refined sugar can affect our microbiome in a positive way, but replacing those foods with too much animal protein and fat can be problematic, because they may crowd out the dietary fibers that are an important component of a microbiome associated with leanness. I see a plateau in weight loss in many of my patients who put themselves on restrictive low-carb diets or Paleo devotees who don’t eat enough vegetables, probably because they’re not cultivating the right microbes. I’ll go into more detail about the ideal mix of nutrients needed to optimize your microbiome and maintain a healthy weight in Chapter 9. Is Our Super-sanitized Lifestyle Making Us Fat?

I had been trained at world-class institutions and practiced gastroenterology at a leading teaching hospital, but, like most physicians, I had no idea that the antibiotics I thought were so helpful were actually creating illness by decimating her microbiome at a time when it was most vulnerable, making her more susceptible to infection and inflammation. I wish I had known then what I know now and what I continue to learn every day: that illness is often the result of a decreased, not increased, bacterial load, and that less is sometimes more when it comes to medical intervention. Rehab for Your Microbiome Every day in my gastroenterology practice I see patients with the telltale signs of a disordered microbiome: bloating, leaky gut, irritable bowel, gluten intolerance, Crohn’s disease, ulcerative colitis, eczema, thyroid disorders, weight problems, fatigue, and brain fog.


pages: 382 words: 115,172

The Diet Myth: The Real Science Behind What We Eat by Tim Spector

biofilm, British Empire, Colonization of Mars, cuban missile crisis, David Strachan, double helix, Drosophila, epigenetics, hygiene hypothesis, Kickstarter, life extension, longitudinal study, Mahatma Gandhi, meta analysis, meta-analysis, microbiome, phenotype, randomized controlled trial, Steve Jobs, twin studies

There was some variation, but within a year of entering the long-stay nursing home all the residents had very similar and unhealthy microbiomes. In elderly people there are many complex reasons why the body deteriorates. These include loss of muscle through lack of physical exercise, depression, social circumstances and loss of cognitive function. The loss of teeth, changes in saliva, and the increasing use of antibiotics and other drugs can also affect the microbiome. With age, we see increases in the number and dysfunction of the protective Treg cells, which as we know interact with our microbes and at this point in life can over-suppress the immune system. Even when all these other factors were accounted for, diet and nutrition remained the dominant factor in determining the microbiome and its relation to health in the elderly. The residents with the least diverse gut microbiomes were far more likely to be frail and suffer from illnesses – and whatever the cause, were more likely to die within a year.

While a great result for Mary, what this didn’t explain was why she hadn’t had problems earlier, or why her twin sister with the exact same genetic make-up was unaffected, despite following a similar diet. Once again, their microbiomes may have been to blame. Studies of other patients with lactose intolerance have shown the same variable response to milk, but when patients with consistent problems have been given a normally indigestible prebiotic substance called GOS (galacto-oligosaccharide) which can alter your microbiome, they saw dramatic benefits compared to subjects given the placebo treatment. After two months their microbiomes had changed quite dramatically.11 When questioned more deeply, Mary remembered she had suffered a bad stomach infection at the end of her trip to Delhi and had needed several long courses of broad spectrum antibiotics.

A microbe collaborator of mine, Paul O’Toole, who was working in Cork at the time, told me this story as typical of many in the area, in which a dramatic change in nutrition in an elderly person had preceded health problems. Paul’s research group is looking into the effects of the microbiome in the elderly, and particularly the effects of diet. In an important study they surveyed 178 Irish residents from local nursing homes aged 70 to 102, half of whom came temporarily for day care and the rest who lived there permanently.1 They found that within six months all the permanent residents on the same dull, institutional diet developed a similar microbiome. Unfortunately, it wasn’t a healthy mix and was lacking in diversity and many of the healthy microbes. It also indicated greater levels of inflammation. Those elderly part-time residents who sometimes cooked for themselves and ate non-institutional meals had healthier microbiomes than those with the communally prepared food. There was some variation, but within a year of entering the long-stay nursing home all the residents had very similar and unhealthy microbiomes.


pages: 372 words: 111,573

10% Human: How Your Body's Microbes Hold the Key to Health and Happiness by Alanna Collen

Asperger Syndrome, Barry Marshall: ulcers, Berlin Wall, biofilm, clean water, correlation does not imply causation, David Strachan, discovery of penicillin, Drosophila, Fall of the Berlin Wall, friendly fire, germ theory of disease, global pandemic, hygiene hypothesis, Ignaz Semmelweis: hand washing, illegal immigration, John Snow's cholera map, Kickstarter, Louis Pasteur, Maui Hawaii, meta analysis, meta-analysis, microbiome, phenotype, placebo effect, the scientific method

The DNA-sequencing technology invented during the Human Genome Project enabled another major genome-sequencing programme, but one that received far less media attention: the Human Microbiome Project. Rather than looking at the genome of our own species, the HMP was set up to use the genomes of the microbes that live on the human body – the microbiome – to identify which species are present. No longer would a reliance on Petri dishes and an over-abundance of oxygen hold back research into our cohabiters. With a budget of $170 million and a five-year programme of DNA sequencing, the HMP was to read thousands of times as much DNA as the HGP, from microbes living in eighteen different habitats on the human body. It was to be a far more comprehensive survey of the genes that make a person, both human and microbial. At the conclusion of the Human Microbiome Project’s first phase of research in 2012, not one world leader made a triumphant statement, and only a handful of newspapers featured the story.

In short, our environment: nurture. Now we have a third player, which sits uncomfortably between nature and nurture. Although the microbiome is strictly an environmental force at work on our eventual characteristics, it is genetic, and it is inherited. Not via eggs or sperm, not via human genes, but a good portion of the microbiome is passed from parents, especially mothers, to offspring. Many parents hope that they pass on the best of themselves to their children; films like Gattaca envisage a future where this wish is not left to chance. Most parents also hope to provide their children with the happiest and healthiest environment that they can manage. The microbiome, with its genetic influence but environmental control, gives parents the power to do both of these things. Despite all the hype, our human genome did not quite live up to our visions of becoming a blueprint for life, and a philosophy for living.

Nature Reviews Gastroenterology and Hepatology 9: 88–96. 16. Delzenne, N.M. et al. (2011). Targeting gut microbiota in obesity: effects of prebiotics and probiotics. Nature Reviews Endocrinology 7: 639–646. 17. Petrof, E.O. et al. (2013). Stool substitute transplant therapy for the eradication of Clostridium difficile infection: ‘RePOOPulating’ the gut. Microbiome 1: 3. 18. Yatsunenko, T. et al. (2012). Human gut microbiome viewed across age and geography. Nature 486: 222–228. Coda 1. Markle, J.G.M. et al. (2013). Sex differences in the gut microbiome drive hormone-dependent regulation of autoimmunity. Science 339: 1084–1088. 2. Franceschi, C. et al. (2006). Inflammaging and anti-inflammaging: a systemic perspective on aging and longevity emerged from studies in humans. Mechanisms of Ageing and Development 128: 92–105. 3. Haiser, H.J. et al. (2013).


Science Fictions: How Fraud, Bias, Negligence, and Hype Undermine the Search for Truth by Stuart Ritchie

Albert Einstein, anesthesia awareness, Bayesian statistics, Carmen Reinhart, Cass Sunstein, citation needed, Climatic Research Unit, cognitive dissonance, complexity theory, coronavirus, correlation does not imply causation, COVID-19, Covid-19, crowdsourcing, deindustrialization, Donald Trump, double helix, en.wikipedia.org, epigenetics, Estimating the Reproducibility of Psychological Science, Growth in a Time of Debt, Kenneth Rogoff, l'esprit de l'escalier, meta analysis, meta-analysis, microbiome, Milgram experiment, mouse model, New Journalism, p-value, phenotype, placebo effect, profit motive, publication bias, publish or perish, race to the bottom, randomized controlled trial, recommendation engine, rent-seeking, replication crisis, Richard Thaler, risk tolerance, Ronald Reagan, Scientific racism, selection bias, Silicon Valley, Silicon Valley startup, Stanford prison experiment, statistical model, stem cell, Steven Pinker, Thomas Bayes, twin studies, University of East Anglia

There have been recent calls from within the scientific community to cool down the gee-whiz hype surrounding the microbiome and its associated treatments, and to improve the quality of the research.88 In the meantime, the grossly exaggerated claims of these papers and press releases provide the semblance of scientific backing to a host of useless, harmful, or just plain daft microbiome-related remedies: a probiotic drink made using microbes found in the guts of elite athletes that can supposedly boost your performance; the craze for ‘colonic irrigation’, which involves flushing out your bowels with water and comes with ghastly-sounding risks like ‘rectal perforation’; and a direct-to-consumer microbiome testing company that allows you to discover ‘the nationality of your microbiome’.89 * * * Fads like microbiome mania wax and wane, but there’s one field of research that consistently generates more hype, inspires more media interest and suffers more from the deficiencies outlined in this book than any other.

The whole endeavour is pointless, in any case: two weeks after all the microbes are flushed out by a colonic irrigation, everything is back to the way it was pre-irrigation. See Naoyoshi Nagata et al., ‘Effects of Bowel Preparation on the Human Gut Microbiome and Metabolome’, Scientific Reports 9, no. 1 (Dec. 2019): p. 4042; https://doi.org/10.1038/s41598-019-40182-9. The nationality of your microbiome: https://atlasbiomed.com/uk/microbiome/results. See also Kavin Senapathy, ‘Keep Calm And Avoid Microbiome Mayhem’, Forbes, 7 March 2016; https://www.forbes.com/sites/kavinsenapathy/2016/03/07/keep-calm-and-avoid-microbiome-mayhem/ 90.  Milk: Josh Harkinson, ‘The Scary New Science That Shows Milk Is Bad For You’, Mother Jones, Dec. 2015; https://www.motherjones.com/environment/2015/11/dairy-industry-milk-federal-dietary-guidelines/; bacon: ‘Killer Full English: Bacon Ups Cancer Risk’, LBC News, 17 April 2019; https://www.lbc.co.uk/news/killer-full-english-bacon-ups-cancer-risk/; eggs: Physicians’ Committee for Responsible Medicine, ‘New Study Finds Eggs Will Break Your Heart’, 16 March 2016; https://www.pcrm.org/news/blog/new-study-finds-eggs-will-break-your-heart.

Not all studies of the microbiome are fundamentally statistically flawed like the mouse-autism paper, though many are just as shaky in terms of the over-the-top conclusions they draw. A 2019 study that followed a similar methodology to the autism paper argued that transferring the microbiomes of schizophrenia patients to mice can cause the rodents to display symptoms of psychosis. It concluded by saying that the results ‘may lead to new diagnostic and treatment strategies’ for schizophrenia, which seems more than a little premature.86 Nevertheless, it could still turn out that differences in the microbiome do play some role in the complex causes of autism or schizophrenia symptoms, or those of some of the other conditions listed above, in mice or in people.87 However, microbiome researchers need to accumulate solid research over time instead of thrusting into the media every small, possibly p-hacked study that finds an effect, claiming it’s a huge scientific breakthrough.


pages: 181 words: 52,147

The Driver in the Driverless Car: How Our Technology Choices Will Create the Future by Vivek Wadhwa, Alex Salkever

23andMe, 3D printing, Airbnb, artificial general intelligence, augmented reality, autonomous vehicles, barriers to entry, Bernie Sanders, bitcoin, blockchain, clean water, correlation does not imply causation, distributed ledger, Donald Trump, double helix, Elon Musk, en.wikipedia.org, epigenetics, Erik Brynjolfsson, Google bus, Hyperloop, income inequality, Internet of things, job automation, Kevin Kelly, Khan Academy, Kickstarter, Law of Accelerating Returns, license plate recognition, life extension, longitudinal study, Lyft, M-Pesa, Menlo Park, microbiome, mobile money, new economy, personalized medicine, phenotype, precision agriculture, RAND corporation, Ray Kurzweil, recommendation engine, Ronald Reagan, Second Machine Age, self-driving car, Silicon Valley, Skype, smart grid, stem cell, Stephen Hawking, Steve Wozniak, Stuxnet, supercomputer in your pocket, Tesla Model S, The Future of Employment, Thomas Davenport, Travis Kalanick, Turing test, Uber and Lyft, Uber for X, uber lyft, uranium enrichment, Watson beat the top human players on Jeopardy!, zero day

The next big medical frontier after genomics is also already on the horizon: the microbiome, the bacterial population that lives inside your gut. This is a field that I am most excited about because it takes us back to looking at the human organism as a whole. Scientists are coming to the conclusion that the microbiome may be the missing link between environment, genomics, and human health. They are discovering connections between what types of bacteria live inside your body, how your genes behave, and how healthy you feel. Microbiome: Bacterial Rainforest in Your Gut Many children are born with genetic predispositions to type-1 diabetes. Though some of those infants become diabetic in their earlier years, others do not. A key reason for this may lie in the microbiome. In February 2015, researchers from M.I.T. and from Harvard University released the results of the most comprehensive longitudinal study yet of how the diversity and types of gut flora affect onset of this type of diabetes.3 The scientists tracked what happened to the gut bacteria of a large number of subjects from birth to their third year in life, and found that children who became diabetic suffered a 25 percent reduction in their gut bacteria’s diversity.

But we may be able to work around that by creating ways to change the microbiome balance in our bellies using supplements or other delivery mechanisms. And here’s where a rapid pace in scientific advances pays off: a wide-ranging analysis of microbiomes to identify bacterial population patterns in the guts of millions of people could provide a blueprint for the gut contents of disease sufferers and healthy people. This census could inform treatment efforts and allow doctors to more effectively manipulate the microbiome. So a yogurt a day may keep the doctor away, and a tummy full of the right sorts of cheese may be better medicine for many metabolic syndromes than pharmaceuticals or other lifestyle changes. Genomic medicine, gene-targeted drug development, and microbiome manipulation all depend on the ability to read DNA.

In this light, the most promising and least controversial realm of breakthroughs discussed in this chapter is the ongoing analysis of the microbiome. Since this is more about restoring ancient healthy systems in our intestines that evolved naturally, rather than about permanently or radically altering life forms, the microbiome promises to be the least risky and perhaps the most important way to affect our health and quell the very lifestyle diseases that have proven so resistant to all manner of interventions. This will benefit everyone equally, will not lead to dependence on drugs and doctors, and will be affordable by all. It is where we must focus more energy—as we develop guidelines on how to safely use gene editing. Fortunately, the U.S. government agrees about the importance of doing so: the White House launched the National Microbiome Initiative in May 2016 to foster the integrated study of microbiomes across different ecosystems and committed more than $121 million for the research.16 PART FOUR Does the Technology Foster Autonomy or Dependency?


pages: 424 words: 114,905

Deep Medicine: How Artificial Intelligence Can Make Healthcare Human Again by Eric Topol

23andMe, Affordable Care Act / Obamacare, AI winter, Alan Turing: On Computable Numbers, with an Application to the Entscheidungsproblem, artificial general intelligence, augmented reality, autonomous vehicles, bioinformatics, blockchain, cloud computing, cognitive bias, Colonization of Mars, computer age, computer vision, conceptual framework, creative destruction, crowdsourcing, Daniel Kahneman / Amos Tversky, dark matter, David Brooks, digital twin, Elon Musk, en.wikipedia.org, epigenetics, Erik Brynjolfsson, fault tolerance, George Santayana, Google Glasses, ImageNet competition, Jeff Bezos, job automation, job satisfaction, Joi Ito, Mark Zuckerberg, medical residency, meta analysis, meta-analysis, microbiome, natural language processing, new economy, Nicholas Carr, nudge unit, pattern recognition, performance metric, personalized medicine, phenotype, placebo effect, randomized controlled trial, recommendation engine, Rubik’s Cube, Sam Altman, self-driving car, Silicon Valley, speech recognition, Stephen Hawking, text mining, the scientific method, Tim Cook: Apple, War on Poverty, Watson beat the top human players on Jeopardy!, working-age population

Some people had a low glycemic response to white bread and others had just the opposite. Again, the gut microbiome was the driver. In fact, in the case of these two bread types, it was not just the driver but the sole predictor.26 Our individual gut microbiomes—approximately 40 million communal cells of a thousand different species—play a far bigger role in response to food intake than we had anticipated. There have been many studies that tie the gut microbiome to issues related to diet, including obesity and diabetes, as well as immune disorders and a long list of other conditions, but without unequivocal proof of a cause-and-effect relationship. This might be because we shed about 10 percent of our gut microbiome in our stool each day—perhaps the populations are just too variable to have a reliable effect.

While initially in Israel it did the glucose monitoring and extensive self-tracking, its US launch involved only taking a gut microbiome sample and having the algorithm predict optimal dietary choices for $329. Subsequently, DayTwo adopted the same plan in Israel, so what I experienced is no longer an offering. DayTwo is not the only company in this space: Viome is a competitor, assessing the microbiome more comprehensively (not only bacteria but also viruses and fungi) for $399 and then using the data to recommend an individualized diet.37 Unlike the Weizmann Institute’s serial reports, however, Viome has not published any peer-reviewed research so far. FIGURE 11.7: My gut microbiome assessment, with my predominant Bacteroides stercoris coinhabitant. FIGURE 11.8: Individualized recommendations with grades for me based upon the DayTwo algorithm.

FIGURE 11.8: Individualized recommendations with grades for me based upon the DayTwo algorithm. The work from Elinav and Segal’s lab is not the only one that has reinforced the status of the microbiome as pivotal to each individual’s response to intake. Michael Snyder, who heads up the genetics department at Stanford University, led a multi-omic study (assessing microbiome, transcriptome, proteome, metabolome, and genome) in twenty-three overweight individuals to characterize what happens with weight gain and loss. With as little as a six-pound weight gain, there were dramatic changes in the gut microbiome species, more than 300 genes exhibited significant change in function, and a release of pro-inflammatory mediators showed up in the blood.38 And these substantial changes were fully reversed with weight loss. Let me be very clear: I don’t present my findings with DayTwo to recommend this company or idea.


pages: 346 words: 92,984

The Lucky Years: How to Thrive in the Brave New World of Health by David B. Agus

active transport: walking or cycling, Affordable Care Act / Obamacare, Albert Einstein, butterfly effect, clean water, cognitive dissonance, crowdsourcing, Danny Hillis, Drosophila, Edward Lorenz: Chaos theory, en.wikipedia.org, epigenetics, Kickstarter, longitudinal study, medical residency, meta analysis, meta-analysis, microbiome, microcredit, mouse model, Murray Gell-Mann, New Journalism, pattern recognition, personalized medicine, phenotype, placebo effect, publish or perish, randomized controlled trial, risk tolerance, statistical model, stem cell, Steve Jobs, Thomas Malthus, wikimedia commons

As I mentioned earlier, the microbiome is our term for the complex microbial world that thrives outside of our own cells, but still within us (micro for “small” or “microscopic,” and biome referring to a naturally occurring community of flora occupying a large habitat—in this case, the human body). Although the human genome is almost the same in every individual, give or take the genes that encode things like certain physical characteristics, risk factors for disease, and blood type, even identical twins can have hugely different gut profiles. The state of the microbiome is turning out to be so key to human health that it may actually be considered an organ in and of itself. And how we feel, both emotionally and physically, may hinge on the state of our microbiome. The NIH Human Microbiome Project started in 2008 as an extension of the Human Genome Project to catalog these microorganisms living in our body, and our appreciation for the influence of such organisms has grown rapidly with each passing year.9 Our growing knowledge about the microbiome comes from studying mice that have been altered so that they do not have any gut bacteria.

More than a century ago, he said that “oral administration of cultures of fermentative bacteria would implant the beneficial bacteria in the intestinal tract.” Yet only in the past decade has science validated and begun to understand Metchnikoff’s bold assertions. In 2015, more studies emerged showing the power of the microbiome, some of which showed how certain foods you eat can change the composition of the bacteria colonies in your gut to either lead your body down the path to metabolic syndrome and obesity, or keep you slender and humming to the right metabolic tune.11 We’ll be exploring more about these findings and the microbiome in chapter 4. In the future, leveraging your microbiome for the better will likely be part of your health equation. In 2008, the European Journal of Immunology paid tribute to Metchnikoff on the hundredth anniversary of his Nobel Prize in a beautifully written article chronicling his life and his contributions to society.12 He was the first scientist to understand natural immunity to infection, the significance of inflammation, the role of digestion in immunity, the importance of gut flora, the implications of “self” versus “nonself” within the context of immunity so the body knows the difference between its own cells and foreign invaders.

For this reason, it should come as no surprise that a significant disturbance in the human body can profoundly alter the makeup of otherwise stable microbial communities coexisting within it and that changes in the internal ecology known as the human microbiome can result in unexpected and drastic consequences for human health.15 Once again, we see the power of context. Bacteria were earth’s first inhabitants. In 2013, the oldest signs of life on earth—3.5 billion years old—were discovered in a remote region of northwest Australia, where evidence of a complex microbial ecosystem is locked in ancient rock formations. It was part of our evolution to forge a symbiotic relationship with bacteria. The science of understanding the microbiome is still in its infancy, but I expect it will explode in the coming decade. We’ll soon begin to understand how different microbiotic profiles, much like genetic profiles, are related to certain diseases or to optimal health. And we will begin to learn how we can leverage the microbiome to prevent and treat a variety of ailments, from neurodevelopmental challenges in early life to neurodegenerative problems and chronic illnesses in later life.


pages: 387 words: 99,158

Period Repair Manual, Second Edition: Natural Treatment for Better Hormones and Better Periods by Lara Briden, Jerilynn Prior

crowdsourcing, en.wikipedia.org, longitudinal study, meta analysis, meta-analysis, microbiome, mouse model, randomized controlled trial, selective serotonin reuptake inhibitor (SSRI), self-driving car, stem cell

If your doctor says you have a yeast infection or bacterial vaginosis, then it’s time to think about your vaginal microbiome. Earlier in this chapter, we discussed the gut microbiome which are the good bacteria living in your intestine. In reality, you have good bacteria living everywhere including your gut, lungs, skin, and, of course, your vagina. One of the many benefits of the vaginal microbiome is to protect you from the overgrowth of unwanted yeast and bacteria. If yeast or unwanted bacteria get the upper hand, then you have a yeast infection or bacterial vaginosis. Bacterial vaginosis may be best described as an “ecological disorder of the vaginal microbiome.” [86] bacterial vaginosis Vaginosis is an overgrowth of one or more species of normal vaginal bacteria. To maintain a healthy vaginal microbiome, you want to avoid as much as possible those things that disrupt good bacteria, including antibiotics, hormonal birth control, and the use of a vaginal douche or wash.

This section is an overview of the main issues you should consider when it comes to digestive health. Gut Microbiome When you have friendly gut bacteria or a friendly gut microbiome, they do many good things for your hormonal health. For example, they regulate your HPA axis, activate thyroid hormone, reduce inflammation, and metabolize or detoxify estrogen. When you have unfriendly bacteria or an unfriendly microbiome, then you have a condition called dysbiosis, which means an unhealthy change to your normal bacterial ecology. Dysbiosis can disrupt your HPA axis, interfere with thyroid hormone, and impair estrogen metabolism. Dysbiosis is a common reason for many period problems. It can also affect your vaginal microbiome, which we’ll see later in the chapter. Fortunately, there are many things you can do to improve your gut health. How to maintain a healthy gut microbiome Avoid, as much as possible, drugs that damage gut bacteria.

If your symptoms do not improve, then please seek professional advice. Yeast Infections and Bacterial Vaginosis As we saw in Chapter 5, both yeast infections and bacterial vaginosis are caused by a disrupted vaginal microbiome. That means, ultimately, that they’re caused by a disrupted gut microbiome. The two populations of bacteria are connected. Think of it as your whole-body ecosystem. The best way to treat yeast infections and vaginosis is to do all the things described above to maintain a healthy gut microbiome plus these three additional recommendations for vaginal microbiome: Supplement with the probiotic strains Lactobacillus rhamnosus, GR-1 and Lactobacillus reuteri, RC-14 which have been clinically proven to improve yeast and bacterial vaginosis [421]. The probiotic combination works best when taken orally, but you can also insert it vaginally for additional benefit.


pages: 438 words: 103,983

Dirty Genes: A Breakthrough Program to Treat the Root Cause of Illness and Optimize Your Health by Ben Lynch Nd.

23andMe, clean water, double helix, epigenetics, Indoor air pollution, microbiome, post-work, selective serotonin reuptake inhibitor (SSRI)

* * * High-Histamine Foods and Drinks Here are some of the major histamine culprits: ■Aged cheeses ■Alcohol—all types, but especially champagne and red wine ■Bone broth ■Chocolate ■Citrus fruits and juices (except lemon, which is well tolerated by most) ■Cured meats: salami, some types of sausage, corned beef, pastrami, and the like ■Dried fruits ■Fermented foods, including yogurt, sour cream, kefir, raw sauerkraut, kimchi, pickles, and fermented vegetables ■Fish, especially smoked or canned; and certain types of fresh fish, especially when raw (as in sushi) ■Fruit juices ■Soured foods—for example, foods marinated in lemon or orange juice ■Tomatoes when raw; cooked are typically okay ■Spinach ■Vinegars (although some people do well with unfiltered, organic apple cider vinegar) * * * Your Marvelous Microbiome Just a few years ago, almost no one had heard of the microbiome, and yet it’s one of the most important parts of your anatomy. Well, it’s not exactly your anatomy. Your microbiome is composed of trillions of bacteria that live in your gut and elsewhere in your body, with cells outnumbering your human cells by a factor of 10 to 1, and genes outnumbering your human genes by a factor of 150 to 1. The microbiome evolved along with us, so there are many functions in our body that simply wouldn’t work without the assistance of this microbial community. For example, digestion. We don’t digest fiber; our gut bacteria do.

■Alzheimer’s disease ■Amyotrophic lateral sclerosis (ALS) ■Anxiety ■Autism ■Autoimmune conditions, including Graves’ disease, Hashimoto’s thyroiditis, multiple sclerosis, rheumatoid arthritis ■Cancer ■Chemical sensitivity ■Chronic infections such as hepatitis, mold reaction, Epstein-Barr, Helicobacter pylori, and Lyme disease ■Crohn’s disease ■Depression ■Diabetes, types 1 and 2 ■Eczema ■Fatigue ■Fibromyalgia ■Heart disease ■Hypertension ■Hearing loss ■Homocysteine surplus ■Infertility ■Keshan disease (a type of heart problem) ■Mental disorders, including major depressive disorder, bipolar disorder, schizophrenia, and obsessive-compulsive disorder ■Migraine ■Obesity ■Parkinson’s disease ■Pregnancy complications ■Psoriasis ■Seizure ■Stroke ■Ulcerative colitis ■Vision loss (progressive worsening) * * * GST and Your Microbiome There are many types of GST gene, each with its own unique job. They reside mainly in the intestines and liver—but your microbiome also has its own GST enzymes. In fact, your microbiome is a key player in your body’s effort to get rid of xenobiotics, protecting you against chemical and oxidative stress. Think of your microbiome as your GST’s main backup—and make sure to protect it! * * * What Makes GST/GPX Dirty? ■Exposure to a lot of industrial chemicals, heavy metals, bacterial toxins, and plastics. The more you lighten the chemical burden on your GST/GPX, the better chance you give this gene to function at its best.

I told him that we were going to strengthen his gut, improve his digestion, and replenish his microbiome, the community of gut bacteria that are crucial for digestion as well as many other functions. During the initial phase, while his digestive system was improving, he should avoid leftovers—which increase in histamine the longer they sit (due to bacteria-producing histamine, which occurs even with refrigeration; freezing prevents this from happening, however)—as well as other high-histamine foods, such as cured meats, soured foods, dried fruits, citrus fruits, aged cheese (including goat cheese), many types of nuts, smoked fish, and certain species of fresh fish. Hunter could enjoy some of those foods—which he was relieved to hear—but I told him that we were going to find his sweet spot. As his gut healed and his microbiome became more robust, he would probably be able to increase the amount and variety of histamine-containing foods.


Fix Your Gut: The Definitive Guide to Digestive Disorders by John Brisson

23andMe, big-box store, biofilm, butterfly effect, clean water, life extension, meta analysis, meta-analysis, microbiome, pattern recognition, publication bias, selective serotonin reuptake inhibitor (SSRI), Silicon Valley, Zimmermann PGP

L-lactate is produced in our body from lactic acid bacteria in our microbiome and is a natural byproduct produced during the Kreb’s cycle for metabolism. L-lactate is also up-regulated during exercise because of the increased need for mitochondrial energy and oxygen to support our muscles. L-lactate is oxidized back into glucose by our liver and is further used for energy production by our body. Finally, our brain can metabolize lactate for energy. D-lactate is not produced by our body and is only produced by the lactic acid bacteria in our microbiome. There is no issue with the D-lactate that is produced by the lactic acid bacteria within our gut. Little D-lactate is produced by these bacteria unless there is a significant overgrowth of these bacteria or severe carbohydrate malabsorption. Also, most microbiome produced D-lactate is eliminated through our stool or broken down by the enzyme D-lactate dehydrogenase.

It also appears that single colonization of one strain, like H. pylori cagA+, for example, might lead to it being normal flora, instead of multiple co-colonization or co-infections of multiple strains. H. pylori may be one instance where microbiome diversity of a specific strain might be a bad thing for your gastrointestinal health. The transient nature of the bacteria and being able to embed itself deeply within the mucosal barrier and avoid immune system detection is why it can be so hard to biopsy accurately. This causes issues for accurate studies and diagnosis of opportunistic bacteria to help further understand the nature of H. pylori and in being able to help people who are made ill by an overgrowth of this Gram-negative bacteria. There is so much we do not know about H. pylori or our microbiome as a whole. We will continue learning about this fascinating bacteria together in part three, which will be on the perils of opportunistic H. pylori.

If H. pylori do become a James Bond super-villain with his monocle, mustache, and a fluffy white cat, what can be done to knock it back into submission, so it becomes a tamer Dr. Evil? Supplementation Protocol to Reduce H. pylori Colonization Certain supplements are more localized to the upper gut, others affect the intestinal or systemic microbiome. Supplements that would reduce intestinal microbiota diversity and should not be used in a first round protocol unless necessary include: Allicin-C Berberine Lactoferrin Interphase plus NAC Oil of oregano Supplements that work systemically and may reduce systemic microbiome diversity and should not be used unless necessary include: NAC Oil of oregano Part 1: Antimicrobial Supplements Depending on the infection load of H. pylori, multiple agents may be needed to achieve remission. Supplements to Reduce Overgrowth In the Mouth: Colloidal silver (Mesosilver) – take one tablespoon and swish for a few minutes, spit out silver after swishing and wash your mouth out.


Entangled Life: How Fungi Make Our Worlds, Change Our Minds & Shape Our Futures by Merlin Sheldrake

biofilm, buy low sell high, carbon footprint, crowdsourcing, cuban missile crisis, dark matter, discovery of penicillin, experimental subject, Fellow of the Royal Society, Isaac Newton, Kickstarter, late capitalism, low earth orbit, Mason jar, meta analysis, meta-analysis, microbiome, moral panic, NP-complete, phenotype, randomized controlled trial, Ronald Reagan, the built environment, Thomas Bayes, Thomas Malthus, traveling salesman

“For creatures your size I offer / a free choice of habitat, / so settle yourselves in the zone / that suits you best, in the pools / of my pores or the tropical / forests of arm-pit and crotch, / in the deserts of my fore-arms, / or the cool woods of my scalp.” ubiquitous feature of life: For organ transplants and human cell cultures see Ball (2019). For an estimate of the size of our microbiome see Bordenstein and Theis. (2015). For viruses within viruses see Stough et al. (2019). For a general introduction to the microbiome see Yong (2016) and a special issue of Nature on the human microbiome (May 2019): www.nature.com/​collections/​fiabfcjbfj [accessed October 29, 2019]. dark matter, or dark life: In a sense, all biologists are now ecologists—but disciplinary ecologists have a head start and their methods are starting to seep into new fields: A number of biologists are starting to call for the application of ecological methods to historically non-ecological fields of biology.

“I dealt with these ‘contaminant’ organisms for a long time,” he recalled, “until I convinced myself that there was no such thing as lichens without ‘contamination,’ and we found that the ‘contaminants’ were remarkably consistent. The more we dug in, the more they seemed to be the rule not the exception.” Researchers have long hypothesized that lichens might involve additional symbiotic partners. After all, lichens don’t contain microbiomes. They are microbiomes, packed with fungi and bacteria besides the two established players. Nonetheless, until 2016, no new stable partnerships had been described. One of the “contaminants” Spribille discovered—a single-celled yeast—turned out to be more than a temporary resident. It is found in lichens across six continents and can make such a substantial contribution to lichens’ physiology as to give them the appearance of an entirely different species.

For fungal superbugs see Fisher et al. (2012, 2018), Casadevall et al. (2019), and Engelthaler et al. (2019); for fungal disease of amphibians see Yong (2019); for banana disease see Maxman (2019). Among animals, diseases caused by bacteria pose more of a threat than those caused by fungi. By contrast, among plants, diseases caused by fungi pose a greater threat than those caused by bacteria. It is a pattern that holds through sickness and through health: Animal microbiomes tend to be dominated by bacteria, while plant microbiomes tend to be dominated by fungi. This is not to say that animals don’t suffer from fungal diseases at all. Casadevall (2012) hypothesizes that the rise of mammals and decline of reptiles following the extinction event that wiped out the dinosaurs—the Cretaceous-Tertiary (K-T) extinction—was due to the ability of mammals to fight fungal diseases. Compared with reptiles, mammals have a number of handicaps: It is energetically costly to be warm-blooded, and even more so to produce milk and deliver intensive parental care.


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The Estrogen Fix: The Breakthrough Guide to Being Healthy, Energized, and Hormonally Balanced by Mache Seibel

longitudinal study, meta analysis, meta-analysis, microbiome, phenotype, randomized controlled trial, selective serotonin reuptake inhibitor (SSRI), women in the workforce, working poor, Yogi Berra

When I talk about the importance of diet and nutrition in this book, I encourage you to begin thinking about how your diet affects your gut microbiome. I believe one reason women who eat a healthy diet are better able to lose weight is because their food choices create a healthier gut microbiome. As we learn more about the association between a healthy diet and the human microbiome, we will have a better scientific understanding of how your gut microbiome affects estrogen metabolism. We already know that the gut microbiomes of men and women differ, and the most likely reason for that is estrogen44 and possibly testosterone. When a male’s gut microbiome is put under the microscope after castration, it is notably similar to the gut microbiome of a female. Also, in a study45 60 healthy postmenopausal women aged 55 to 69 who had not recently used either antibiotics or estrogen had their gut microbiomes tested. The ones with the most diverse gut microbiomes were able to metabolize and excrete more estrogen in their urine than those women with less diverse gut microbiomes.

The ones with the most diverse gut microbiomes were able to metabolize and excrete more estrogen in their urine than those women with less diverse gut microbiomes. The researchers believe this will put those women at less risk of breast cancer. Estrogen, particularly oral estrogen, is processed in the liver, and some of it enters the gut. There estrogen interacts with each woman’s gut microbiome, and some of these bacteria are able to metabolize estrogen. One enzyme produced by certain bacteria, beta-glucuronidase, is present in the guts of about 44 percent of women with healthy estrogen metabolism.46 Some people think these bacteria play a regulatory role in how much estrogen is in a woman’s bloodstream, and taking antibiotics throws off these bacteria’s regulation of estrogen. As this line of thinking and science becomes more established, it may be possible to impact any negative effects of estrogen by giving women probiotics with the “right” kind of bacteria.47 What it means to me now is to encourage you to do just what your mother said: Eat your fruits and vegetables and unprocessed foods.

When we combine the information from these studies with the fact that without estrogen women tend to have greater muscle loss, larger amounts of fat, thinner bones, and weight gain with aging, it’s clear that unless women eat healthfully, exercise, and possibly use estrogen, the end result is overweight women with sarcopenic obesity. You cannot sit this one out. The Estrogen Fix and Your Gut The human microbiome has been receiving a great deal of media attention lately. The microbiome refers to the 3 pounds of bacteria that live in your intestinal tract. They are responsible for everything from digesting food to manufacturing vitamins to brain function, and perhaps even playing a role in obesity, cancer, and other diseases.43 These 100 trillion good bacteria in our inner ecosystem contain two million unique bacterial genes compared to the mere 23,000 genes in all the cells of our bodies.


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The End of Illness by David B. Agus

Danny Hillis, discovery of penicillin, double helix, epigenetics, germ theory of disease, Google Earth, impulse control, information retrieval, longitudinal study, meta analysis, meta-analysis, microbiome, Murray Gell-Mann, pattern recognition, Pepto Bismol, personalized medicine, randomized controlled trial, risk tolerance, Steve Jobs, the scientific method

Bacteria obviously have their own DNA operating within us, and newly emerging technologies are finally helping us tune into these bacteria and their effects on us, for better or worse. One overarching feature that studies on the microbiome are revealing is the diversity of bacteria in the human body, akin to a rain forest. Different regions of the body are home to different combinations of species. From one person to another, we’re finding tremendous variety. I could have an entirely different colony of bacteria thriving in my mouth than you, which affects whether my diet helps me to maintain a healthy digestive system. In the future, perhaps I’ll know more about my unique enterotype to keep my digestive system running as smoothly as possible. Within the next ten years researchers will uncover mysteries of the microbiome and begin to find ways in which we can manipulate it to support health. The microbiome—not levels of vitamin D, for example—may explain why people who live at higher latitudes have a higher risk of developing cancer.

Until babies can eat solid foods, they get plenty of what they need from breast milk, formula, and, yes, even mushy baby foods probably created in a pulverizer. Mining and Minding the Microbiome Before we move on, I need to mention one more fact for your consideration. We are all different in how we metabolize our food, absorb its nutrients, and need or use the nutrients. This area of nutrition has to be personalized and will be in the future when new technologies become available that will allow each of us to tune in to our personal nutritional needs. Certainly genetics will play a role here, too, but the larger role will be played by the microbiome—the bacteria that fill your intestinal tract and that participate in your digestion, metabolism, and overall health. We each have bacteria in our GI tract. Within the body of a healthy adult, microbial cells are estimated to outnumber human cells by a factor of ten to one.

We had assumed this was due to diet—after all, so much can be blamed on the Western diet, and certainly immigrants probably start devouring our processed, packaged foods like the rest of us when they land in the United States—but it turns out that the microbiome plays a major role here. It controls how you metabolize your food, how fast and how much you absorb, and what enters your bloodstream, thereby affecting your hormone levels among other things. In turn, this influences the risk of developing certain cancers, such as prostate or breast. It’s common to categorize people by blood type, or in some cases by ethnicity. In the future, we’ll also begin to type people by “bug”—by the prevailing bacteria that inhabit their digestive tracts. In one of the more provocative studies to emerge, published in April 2011 in the journal Nature, a team of researchers led by Peer Bork of the European Molecular Biology Laboratory in Heidelberg, Germany, reported on three distinguishable “types” of people based on their microbiome. Each of the three types is composed of a different balance of species.


She Has Her Mother's Laugh by Carl Zimmer

23andMe, agricultural Revolution, clean water, clockwatching, cloud computing, dark matter, discovery of DNA, double helix, Drosophila, Elon Musk, epigenetics, Fellow of the Royal Society, Flynn Effect, friendly fire, Gary Taubes, germ theory of disease, Isaac Newton, longitudinal study, medical bankruptcy, meta analysis, meta-analysis, microbiome, moral panic, mouse model, New Journalism, out of africa, phenotype, Ralph Waldo Emerson, Scientific racism, statistical model, stem cell, twin studies

If the flashlight fish had no bacteria, it would have no flashlight. Other microbes carry out tasks that are harder to see but no less important. They synthesize vitamins, they nurture a well-tempered immune system, they form a living barrier against dangerous pathogens. The microbiome, as this collective is known, blurs any simple notion of what it means to be an individual organism. If we turned into true individuals, sterilized of our microbiome, we’d become sick and might well die. In each species, every new generation acquires a microbiome. In some regards, this cycle of renewal looks a lot like heredity. A new animal does not acquire its own genes out of the blue, synthesized from scratch. Its genes have been duplicated over and over again inside the cells of its ancestors, taking an extraordinary journey to get to each new animal.

Although microbiologists have been naming species of bacteria for well over a century, they’ve described only a tiny fraction of the Earth’s single-celled diversity. Marimonas was named for a deep-sea microbe, but the lineage likely includes many other species adapted to other environments, including human skin. Within the howling complexity of the human microbiome, however, you can still hear heredity’s signal. It begins when a mother seeds her children’s microbiome. When this seeding starts is still not clear. Although researchers have long held that embryos start off sterile, in a bacteria-free amniotic sac, a few studies have hinted that at least some maternal bacteria may slip into the fetal sanctuary. What is abundantly clear, however, is that once a baby starts moving down through the birth canal, it gets contaminated.

They can pick up bacteria from friends’ toys they stick in their mouths, from teachers who wipe the dirt off their cheeks, even from the air they breathe. Yet even the bacteria that move freely from stranger to stranger also become intertwined with our own heredity. To see this intertwining, you first have to think about our microbiomes as a heritable trait, just like our height, intelligence, and risk of getting a heart attack. And you have to study it as such. Julia Goodrich, a microbiologist at Cornell University, and her colleagues did just this, investigating the microbiomes of twins to see how their genetic similarities influenced the species they carried. The scientists collected stool samples from 1,126 pairs of twins and cataloged the microbial inhabitants. Out of thousands of species of bacteria, they identified twenty that were more strongly correlated in identical twins than in fraternal ones.


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The Patient Will See You Now: The Future of Medicine Is in Your Hands by Eric Topol

23andMe, 3D printing, Affordable Care Act / Obamacare, Anne Wojcicki, Atul Gawande, augmented reality, bioinformatics, call centre, Clayton Christensen, clean water, cloud computing, commoditize, computer vision, conceptual framework, connected car, correlation does not imply causation, creative destruction, crowdsourcing, dark matter, data acquisition, disintermediation, disruptive innovation, don't be evil, Edward Snowden, Elon Musk, en.wikipedia.org, Erik Brynjolfsson, Firefox, global village, Google Glasses, Google X / Alphabet X, Ignaz Semmelweis: hand washing, information asymmetry, interchangeable parts, Internet of things, Isaac Newton, job automation, Julian Assange, Kevin Kelly, license plate recognition, lifelogging, Lyft, Mark Zuckerberg, Marshall McLuhan, meta analysis, meta-analysis, microbiome, Nate Silver, natural language processing, Network effects, Nicholas Carr, obamacare, pattern recognition, personalized medicine, phenotype, placebo effect, RAND corporation, randomized controlled trial, Second Machine Age, self-driving car, Silicon Valley, Skype, smart cities, Smart Cities: Big Data, Civic Hackers, and the Quest for a New Utopia, Snapchat, social graph, speech recognition, stealth mode startup, Steve Jobs, the scientific method, The Signal and the Noise by Nate Silver, The Wealth of Nations by Adam Smith, Turing test, Uber for X, uber lyft, Watson beat the top human players on Jeopardy!, WikiLeaks, X Prize

Being able to tap into the whole range of an individual’s RNA transcripts, proteins, and metabolites at any given moment creates quite an extraordinary opportunity to understand one’s instantaneous biology, in an unbiased fashion. The Microbiome It’s hard for most of us to accept that we are nine parts microbe and only one part human, at least as far as a count of our cells goes. The era of sequencing has been especially instructive about the trillions of microbes (bacteria, viruses, fungi) that live within or on us. The diversity of DNA in us from microbes far outstrips our own DNA, with one hundred trillion instead of thirty-seven trillion cells, over eight million genes instead of only approximately nineteen thousand, and more than ten thousand species instead of one.18 The microbiome represents the interface between the individual and her environment. For example, one’s diet has a strong influence on one’s microbiome. And the medical importance of these microbes has escalated far beyond what most of us envisioned, with their influence in obesity, cancer, heart, allergic and autoimmune diseases, and many more conditions, in which the gut microbiome is particularly prominent.

The diagnosis also led Snyder to change his lifestyle and restore normal glucose homeostasis, and then go on to check this in some relatives who turned out to have unrecognized glucose intolerance, and for whom diet and exercise proved similarly helpful. More recently, Snyder’s Stanford forty-member research group has expanded the initial effort with sequencing Snyder’s epigenome, gut microbiome, and use of multiple biosensors. Getting this GIS-like information has generated a massive amount of data: 1 terabyte (TB, a trillion bits) for DNA sequence, 2 TB for the epigenomic data, 0.7 TB for the transcriptome, and 3 TB for the microbiome.5 For perspective, 1 TB would equate to one thousand copies of the Encyclopedia Britannica and 10 TB, which is approximately how much Snyder’s panoromic project amassed, would hold the entire Library of Congress. In the world each year about five zettabytes of data—or forty sextillion bits—are generated.20 If we divided this by the world’s seven billion people, this would put an average individual at nearly 1 TB of data generated per year.

Malnutrition is exceptionally important in the developing world both because it predisposes individuals to infection, and because the cause of many infections is highly influenced by the gut microbiome.35–39 More than twenty million children worldwide suffer from severe malnutrition, and fatality rates for hospitalized children with kwashiorkor—a protein-deficient form of malnutrition—is as high as 50 percent. A randomized trial in rural Malawi, representative of sub-Saharan Africa, tested two different antibiotics and matching placebo in 2,767 children, ages six months to five years (Figure 14.9). There was a significant reduction in fatalities with antibiotics, but it is clear the number of deaths is still exceedingly high on treatment.40,41 But in another study of 317 twin pairs from Malawi, with only one of the twins suffering from acute malnutrition, the gut microbiome showed that the imbalance in bacterial populations could be restored with fortified peanut butter.37 That represents a significant change from the typical Malawian diet, which is very high in starch.


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Messy: The Power of Disorder to Transform Our Lives by Tim Harford

affirmative action, Air France Flight 447, Airbnb, airport security, Albert Einstein, Amazon Mechanical Turk, Amazon Web Services, assortative mating, Atul Gawande, autonomous vehicles, banking crisis, Barry Marshall: ulcers, Basel III, Berlin Wall, British Empire, Broken windows theory, call centre, Cass Sunstein, Chris Urmson, cloud computing, collateralized debt obligation, crowdsourcing, deindustrialization, Donald Trump, Erdős number, experimental subject, Ferguson, Missouri, Filter Bubble, Frank Gehry, game design, global supply chain, Googley, Guggenheim Bilbao, high net worth, Inbox Zero, income inequality, industrial cluster, Internet of things, Jane Jacobs, Jeff Bezos, Loebner Prize, Louis Pasteur, Marc Andreessen, Mark Zuckerberg, Menlo Park, Merlin Mann, microbiome, out of africa, Paul Erdős, Richard Thaler, Rosa Parks, self-driving car, side project, Silicon Valley, Silicon Valley startup, Skype, Steve Jobs, Steven Levy, Stewart Brand, telemarketer, the built environment, The Death and Life of Great American Cities, Turing test, urban decay, William Langewiesche

But Professor Knight is now running a controlled study of much the same technique with babies born by cesarean section in Puerto Rico.9 Finally there is the simple fact that our microbiome is partially heritable, passed from mothers to daughters. It follows that if one generation thins out the messy diversity of their microbiome through antibiotics and antiseptics, the following generation will start from a less diverse foundation.10 It is worth acknowledging that these ideas have already become a fad—a great deal of nonsense is now being talked by quacks and purveyors of probiotic yogurt aiming to promote a “healthy microbiome.” There is no such thing, or rather there is a vast range of healthy microbiomes. People can have very different microbiota, yet still be perfectly healthy; the biological makeup of the same person can also change rapidly, day by day.

TED Talks, 2011, http://www.ted.com/talks/jessica_green_are_we_filtering_the_wrong_microbes/transcript?language=en. 9. Alanna Collen, “‘Microbial Birthday Suit’ for C-Section Babies,” BBC Magazine, September 11, 2015, http://www.bbc.com/news/health-34064012. 10. Blaser, Missing Microbes. 11. Ed Yong, “There Is No ‘Healthy’ Microbiome,” The New York Times, November 1, 2014, http://www.nytimes.com/2014/11/02/opinion/sunday/there-is-no-healthy-microbiome.html, and Gabrielle Canon, “Sorry, Your Gut Bacteria Are Not the Answer to All Your Health Problems,” Mother Jones, October 27, 2014, http://www.motherjones.com/environment/2014/10/microbiome-health-gut-bacteria; Blaser, Missing Microbes, pp. 31–32. 12. Jane Jacobs, The Death and Life of Great American Cities (New York: Vintage, 1992), p. 50. 13. Ibid., p. 193. 14. Maryann P. Feldman and David B. Audretsch, “Innovation in Cities: Science-Based Diversity, Specialization and Localized Competition,” European Economic Review 43 (1999). 15.

Some, such as H. pylori, can be dangerous or beneficial depending on the situation.3 Martin Blaser has become one of the leading champions of the view that our bacterial guests are starting to become less diverse, and that this thinning of the microbiome is doing us harm. Researchers at the University of Toronto found that it was easier to stay slim in the 1980s: looking at data about diet and exercise for tens of thousands of people since the early 1970s, they found that people today seem to be heavier than their forebears, even when they ate the same and were equally as active. One of the favored explanations for this is that young people today have denuded gut bacteria; a separate large study of European microbial genes has shown that a less diverse microbiome is correlated with a tendency to be obese. Meanwhile a team at the University of California at San Francisco found that Lactobacillus sakei—another of the bacteria we have cluttering up our bodies—appears to prevent sinusitis, presumably by outcompeting the more harmful bacteria that might inflame our sinuses.


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Cooked: A Natural History of Transformation by Michael Pollan

biofilm, bioinformatics, Columbian Exchange, correlation does not imply causation, creative destruction, dematerialisation, Drosophila, energy security, Gary Taubes, Hernando de Soto, hygiene hypothesis, Kickstarter, Louis Pasteur, Mason jar, microbiome, peak oil, Ralph Waldo Emerson, Steven Pinker, women in the workforce

A landmark article seeking to apply the lens of ecology to the microbial communities inhabiting the human body. Song, Yeong-Ok. “The Functional Properties of Kimchi for the Health Benefits.” Food Industry and Nutrition 9, 3 (2004): 27–28. Turnbaugh, P.J., et al. “An Obesity-Associated Gut Microbiome with Increased Capacity for Energy Harvest.” Nature 444 (2006): 1027–31. ———, et al. “The Human Microbiome Project.” Nature 449 (2007): 804–10. ———, et al. “A Core Gut Microbiome in Obese and Lean Twins.” Nature 457 (2009): 480–84. Walter, Jens. “Ecological Role of Lactobacilli in the Gastrointestinal Tract: Implications for Fundamental and Biomedical Research.” Applied and Environmental Microbiology (August 2008): 4985–96. Zivkovic, Angela M., J. Bruce German, et al.

* Margulis theorized that both photosynthesis and cellular metabolism in animals began when bacteria took up residence in the evolutionary ancestors of plant and animal cells, contributing their metabolic expertise; eventually these invaders became the chloroplasts in plant cells and the mitochondria in the cells of animals. * Turnbaugh, Peter J., et al., “An Obesity-Associated Gut Microbiome with Increased Capacity for Energy Harvest,” Nature 444 (2006): 1027–31; Turnbaugh, P. J., et al., “A Core Gut Microbiome in Obese and Lean Twins,” Nature 457 (2009): 480–84; Turnbaugh, Peter J., et al., “The Human Microbiome Project,” Nature 449 (2007): 804–10. † This particular probiotic is found in some kinds of yogurt. (Bravo, J. A., et al., “Ingestion of Lactobacillus Strain Regulates Emotional Behavior and Central GABA Receptor Expression in a Mouse via the Vagus Nerve,” Proceedings of the National Academy of Sciences 108 No. 38 [2011]: 16050–55)

.* No doubt scientists will soon find other examples of our microbiota mediating our relationship to the rest of nature, speeding our ability to adapt. In effect, the microbiome vastly extends our genome, giving us access to a tremendous bag of tricks we did not need to evolve ourselves. So it made very good sense, evolutionarily speaking, for us to join forces with the microbes, which are simply more skilled than we are at all the ways of biochemically contending. During the two billion years of natural selection that bacteria have undergone before more complex multicellular creatures arrived on the scene, they managed to invent virtually every important metabolic trick known to evolution, from fermentation to photosynthesis. (According to Lynn Margulis, who until her death in 2011 was the microbiome’s most eloquent human advocate, the only important biochemical innovations to come along in the billion years since then are snake venom, plant hallucinogens, and—this is a big one—cerebral cortices.)


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The Cancer Chronicles: Unlocking Medicine's Deepest Mystery by George Johnson

Atul Gawande, Cepheid variable, Columbine, dark matter, discovery of DNA, double helix, Drosophila, epigenetics, Gary Taubes, Harvard Computers: women astronomers, Isaac Newton, Magellanic Cloud, meta analysis, meta-analysis, microbiome, mouse model, Murray Gell-Mann, phenotype, profit motive, stem cell

id=chronic-inflammation-cancer] More references are in my notes for chapter 10. 43. molecules called sirtuins: For a review see Finkel Toren, Chu-Xia Deng, and Raul Mostoslavsky, “Recent Progress in the Biology and Physiology of Sirtuins,” Nature 460, no. 7255 (July 30, 2009): 587–91. [http://www.ncbi.nlm.nih.gov/pubmed/19641587] 44. the genes residing in the microbes: Steven R. Gill et al., “Metagenomic Analysis of the Human Distal Gut Microbiome,” Science 312, no. 5778 (June 2, 2006): 1355–59. [http://www.sciencemag.org/content/312/5778/1355.short] 45. a Human Microbiome Project: Peter J. Turnbaugh et al., “The Human Microbiome Project,” Nature 449, no. 7164 (October 18, 2007): 804–10. [http://www.nature.com/nature/journal/v449/n7164/abs/nature06244.html] 46. “ ’omics”: Joshua Lederberg christened the microbiome, and in a short essay, “Ome Sweet ’Omics,” he commented on the naming phenomenon: The Scientist 15, no. 7 (April 2, 2001): 8. [http://lhncbc.nlm.nih.gov/lhc/docs/published/2001/pub2001047.pdf] 47. separate the ridiculome from the relevantome: I thought I had invented these words, but an Internet search turns them up in a PowerPoint presentation: Andrea Califano, Brian Athey, and Russ Altman, “Creating a DBP Community to Enhance the NCBC Biomedical Impact, A National Center for Biomedical Computing Work Group Report,” July 18, 2006, National Alliance for Medical Image Computing website.

The genes inside these single-celled creatures transmit signals from microbe to microbe, and they can also exchange signals with human cells. Although we think of the bacteria as passengers, they outnumber our own cells by about ten to one. Even more impressive, the total number of microbial genes each of us harbors—the microbiome—outnumbers our human genes by 100 to 1. There is even a Human Microbiome Project to sequence the genomes of these cellular free agents. Cancer is a disease of information, of mixed-up cellular signaling. Now there is another realm to explore. The genome, the epigenome, the microbiome—scientists also now speak of the proteome (the entire set of proteins that can be expressed in a cell) and the transcriptome (all of the RNA molecules of various sorts). There is the metabolome, lipidome, regulome, allelome … the degradome, enzymome, inflammasome, interactome, operome, pseudogenome.

…A curious law of nature … Contemplating the odds CHAPTER 2 Nancy’s Story Food pyramidology … Pascal’s wager … Folates, antioxidants, and Finnish smokers … Fruits, vegetables, and giant steaks … Carcinogenic estrogen … The real risks of cigarettes … Emanations from the earth … Cancer clusters … A worrisome lump … Nancy’s cancer CHAPTER 3 The Consolations of Anthropology In the boneyards of Kenya … Face-to-face with Kanam man…Palaeo-Oncology…Hippocrates and the crabs … The wild beast of cancer … Metastasis in a Scythian king … Skeletons and mummies … Visions of an ancient paradise … Counting up the dead CHAPTER 4 Invasion of the Body Snatchers “Large and beautifully pellucid cells”…Morbid juices … Seeds and soil … The mysteries of metastasis … A horrifying precision … The ebb and flow of lymph … The surgeon’s diagnosis … Weeds from outer space CHAPTER 5 Information Sickness Man-made mutations … Funny-looking chromosomes…“A new kind of cell”…Matter that comes alive … The Radium Girls … Coal tar and tumors … Viral invaders … Oncogenes and tumor suppressors … Cellular suicide … Intimations of immortality … A conspiracy of cells CHAPTER 6 “How Heart Cells Embrace Their Fate” Embryos and tumors … Snail, slug, and twist … Sonic hedgehog … the Pokémon gene … Cyclopean sheep … Holoprosencephaly … 1 + 1 = 3 … Prayers of an agnostic … An endless day at the hospital CHAPTER 7 Where Cancer Really Comes From The surprising aftermath of Love Canal … What “environment” really means…“The Causes of Cancer”…An environmental turncoat … The carcinogens in coffee … Mitogenesis and mutagenesis … Making sense of the cancer statistics … A maverick presidential report CHAPTER 8 “Adriamycin and Posole for Christmas Eve” Cancer cells and magnets … The penicillin of cancer … A rare kind of malignancy … Disheartening statistics…“The Median Isn’t the Message”…Flying farolitos … A visit to MD Anderson … Rothko’s brooding chapel CHAPTER 9 Deeper into the Cancer Cell A physics of cancer … Epigenetic software … The stem cell conundrum … An enormous meeting in Orlando … Espresso and angiogenesis … The news from Oz.…Communing with the microbiome … Beyond the double helix … Dancing at the Cancer Ball CHAPTER 10 The Metabolic Mess Chimney sweeps and nuns … A “mysterious sympathy”…The case of the missing carcinogens … The rise and fall of vegetables … A mammoth investigation … The insulin-obesity connection…“Wounds that do not heal”…A hundred pounds of sugar … Skewing the energy equation CHAPTER 11 Gambling with Radiation Flunking the radon test … A ubiquitous carcinogen … Down in the uranium mines … Tourism at Chernobyl … Hiroshima and Nagasaki … Exhuming Curie’s grave … A pocketful of radium … Robot oncologists … Relay for Life CHAPTER 12 The Immortal Demon A flight to Boston … Stand Up to Cancer … A tale of two cousins … The return of the hedgehog … Where weird drug names come from … Waiting for super trastuzumab … Orphaned cancers … Biological game theory … Contagious cancer CHAPTER 13 Beware the Echthroi On Microwave Mountain … Cell phones and brain waves … Is cancer here “on purpose”?


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COVID-19: Everything You Need to Know About the Corona Virus and the Race for the Vaccine by Michael Mosley

Boris Johnson, call centre, coronavirus, COVID-19, Covid-19, Donald Trump, microbiome, randomized controlled trial, Silicon Valley

The extraordinary thing about viruses is not only can they hijack our bodies to do their dirty work, but over time they have inserted themselves into our genome (the human blueprint that makes us who we are and that we hand down to our children). It’s estimated that around 8 percent of the human genome is made up of viral DNA, which means that our cells are hard at work producing proteins for our viral “guests,” for purposes that, for now, we can only guess at. Are There “Good” Viruses? Just as we’ve discovered in recent years how important certain “good” bacteria in our guts (the gut microbiome) are for our mental and physical health, so we are discovering that some of the viruses we are infected with are essential for our very existence. There are vital parts of our immune system, for example, which we use to fight off viruses, that originally came from other viruses.20 How Often Does a Dangerous New Virus, Like Covid-19, Emerge and Cause a Pandemic? Novel viruses are infecting humans all the time, but most don’t go anywhere.

But intermittent fasting has other health benefits, including potentially helping improve your immune system. More on that in a moment. 3. Eat a more Mediterranean-style diet The traditional diet of Mediterranean countries, rich in olive oil, nuts, oily fish, and legumes, is regularly voted by health professionals as the healthiest diet on the planet. Changing the way you eat will not only reduce your risk of metabolic disease but should help support your immune system. 4. Boost your microbiome One of the reasons why the Mediterranean diet is so super healthy is because it boosts levels of the “good” microbes in your gut. This, in turn, has been shown to play an important role in the body’s immune response to infectious pathogens. 5. Improve your sleep We know that getting good quality sleep is essential for the production and release of key components of your immune system and there is strong evidence that getting a good night’s sleep is a great way to keep infections at bay.

The reason I am such a fan of the Mediterranean diet is because it tastes great, but also because there is so much solid scientific evidence that adopting this lifestyle will cut your risk of heart disease, cancer, type 2 diabetes, depression, and dementia. On top of that, thanks to recent studies, we know it can improve your sleep (see below) and improve the workings of your immune system, even if you are a bit older.31 One reason why this diet is so beneficial is because as well as nourishing us, it has a very positive effect on your gut microbiome—the trillions of microbes that live in your gut and that are so important for your physical and mental well-being. The Med diet is particularly effective at boosting levels of “good” bacteria in your gut, like bifidobacterium and lactobacillus. These turn the fiber and other nutrients in the Med diet into chemicals called short-chain fatty acids (SCFs), which reduce inflammation in the gut and throughout the body.


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Infinity in the Palm of Your Hand: Fifty Wonders That Reveal an Extraordinary Universe by Marcus Chown

Albert Einstein, Anton Chekhov, Arthur Eddington, Carrington event, dark matter, Donald Trump, double helix, Edmond Halley, gravity well, horn antenna, Isaac Newton, Kickstarter, microbiome, Richard Feynman, Search for Extraterrestrial Intelligence, Solar eclipse in 1919, Stephen Hawking, Turing machine

Being indiscriminate in their action, such drugs kill not only disease-causing bacteria but bacteria that you need as well. Bacteria are much smaller than the cells in your body, however. So, despite existing in comparable numbers to those cells, they account for only about 1.5 kilograms of the mass of a seventy-kilogram person. The US government set up a five-year study, the Human Microbiome Project (microbiome refers to the microorganisms in a particular environment), or HMP, designed to identify all the foreign microorganisms in the human body and figure out what they do—a gargantuan task.2 Its results were published in 2012 and revealed that there are more than 10,000 species of alien cells in your body—forty times the number of cell types that belong to you. In fact, every square centimeter of your skin is home to about five million bacteria.

“The Secrets of the Human Cell” by Peter Gwynne, Sharon Begley, and Mary Hager (Newsweek, 20 August 1979, p. 48). 5. DNA, or deoxyribonucleic acid, is the giant biomolecule that stores, in encoded form, the structure of a cell’s proteins. 5. Living With the Alien 1. “Revised Estimates for the Number of Human and Bacteria Cells in the Body” by Ron Sender, Shai Fuchs, and Ron Milo (PLOS Biology, 19 August 2016: https://doi.org/10.1371/journal.pbio.1002533). 2. NIH Human Microbiome Project (https://hmpdacc.org). 3. “Gut Microbiome Alterations in Alzheimer’s Disease” by Nicholas Vogt et al. (Nature, 19 October 2017: https://www.nature.com/articles/s41598-017-13601-y). 6. The Dispensable Brain 1. “The juvenile sea squirt wanders through the sea searching for a suitable rock or hunk of coral to cling to and make its home for life. For this task, it has a rudimentary nervous system. When it finds its spot, and takes root, it doesn’t need its brain anymore, so it eats it.

In fact, the HMP found that the nasal passages of 29 percent of people contain Staphylococcus aureus—better known as the MRSA superbug. This might sound worrying. However, in healthy people such bacteria are kept in check and cause no harm. It is only in sick people, whose immune systems are weakened, that MRSA bacteria are dangerous. Since hospitals contain sick people, it is obvious why MRSA can be a problem there. There is mounting evidence that an imbalance of the human microbiome may be a factor in causing a wide range of diseases. These include inflammatory bowel conditions such as Crohn’s disease and ulcerative colitis. There is even a suggestion that such imbalances may play a role in diseases such as Alzheimer’s.3 Nobody is born with a full complement of foreign microorganisms. Instead, they are acquired after birth from a mother’s milk and from the environment.


pages: 225 words: 70,180

Humankind: Solidarity With Nonhuman People by Timothy Morton

a long time ago in a galaxy far, far away, David Brooks, Georg Cantor, gravity well, invisible hand, means of production, megacity, microbiome, phenotype, planetary scale, Richard Feynman, self-driving car, Silicon Valley, Slavoj Žižek, Turing test, wage slave, zero-sum game

(I’ll be defining ‘‘implosive holism’’ throughout.) In symbiosis, it’s unclear which is the top symbiont, and the relationship between the beings is jagged, incomplete. Am I simply a vehicle for the numerous bacteria that inhabit my microbiome? Or are they hosting me? Who is the host and who is the parasite? The term “host” stems from the Latin hostis, a word that can mean both “friend” and “enemy.”1 Fully one-third of human milk, for instance, is not digestible by the baby; instead it feeds bacteria that coat the intestines with immunity-bestowing film.2 When a child is born vaginally, it gains all kinds of immunities from bacteria in the mother’s microbiome. In the human genome there is a symbiont retrovirus called ERV-3 that codes for immunosuppressive properties of the placental barrier. You are reading this because a virus in your mother’s DNA prevented her body from spontaneously aborting you.3 The loose connectivity of the symbiotic real affects other orders of being, such as language.

, Marx’s upside-down Hegelianism contains a glitch that is both logically strange (there’s an obvious infinite regress) and politically oppressive. Can we debug the Decider model—can we de-anthropocentrize it? “Species” means an entity that is real but not constantly present beneath appearances, not constantly the same. “Human” means me plus my nonhuman prostheses and symbionts, such as my bacterial microbiome and my technological gadgets, an entity that cannot be determined in advance within a thin, rigid outline or rigidly demarcated from the symbiotic real. The human is what I call a “hyperobject”: a bundle of entities massively distributed in time and space that forms an entity in its own right, one that is impossible for humans to see or touch directly.46 Here’s Marx writing about his concept of species-being in the Economic and Philosophical Manuscripts: Species-life, both for man and for animals, consists physically in the fact that man, like animals, lives from inorganic nature; and because man is more universal than animals, so too is the area of inorganic nature from which he lives more universal.

It’s this soft delicate pattering on my arm. It’s this thing I wrote some sentences about. Humankind is ontologically smaller than the humans who make it up! There is so much more that humans do other than be parts of humankind. Humans modify their bodies to change their gender and add electronic and decorative prostheses. Humans form relationships with nonhumans. Humans contain nonhumans such as the bacterial microbiome in such a way that if the nonhumans left, the humans would die. This means that the correct left concept of the human is of a partial object in a set of partial objects, such that it comprises an implosive whole that is less than the sum of its parts. This partiality extends in every dimension, including time. An event is a temporal partial object. An event is part of some set of events that comprises a whole, but this whole is always less than the sum of its parts.


pages: 435 words: 95,864

Childhood Disrupted: How Your Biography Becomes Your Biology, and How You Can Heal by Donna Jackson Nakazawa

epigenetics, fear of failure, impulse control, longitudinal study, meta analysis, meta-analysis, microbiome, randomized controlled trial, selective serotonin reuptake inhibitor (SSRI)

I felt all that weight of having to care for my mother and be the only grown-up in my adolescent world.” Over the course of many sessions, the pain of the past has begun to lessen. Mary feels a sense of “letting go.” 11. Managing the Mind Through the Gut Cell for cell, we’re largely made up of bacteria. In fact, single-celled organisms, mostly bacteria, outnumber our own cells ten to one. Many of these live in our gut. This gut “microbiome” determines the state of our digestive health, and influences the state of our brain. When you are under stress, the bacterial communities in your intestine become less diverse, allowing greater numbers of harmful bacteria to take over. Disorders of the gut such as irritable bowel and inflammatory bowel diseases are exacerbated by stress. Recent science shows that a sophisticated neural network transmits messages from those trillions of digestive bacteria to the brain, exerting a powerful influence on our state of mind—creating a feedback loop between the brain and the gut that goes both ways.

And second, good gut microbiota such as those found in probiotics have a direct effect on neurotransmitter receptors in the brain, such as GABA. Mice given probiotics had lower levels of stress-induced hormones, less anxiety, and less depression-related behavior. And guess how the messages between the bacteria exposed to the gut and the brain were transmitted? Via the vagus nerve—which is a primary mediator of the inflammatory stress response. That’s why scientists have begun to refer to our gut as “the second brain.” The gut microbiome heavily influences neural development, brain chemistry, emotional behavior, pain perception, learning, and memory. Some organisms in the gut might prove useful in treatments of stress-related disorders such as anxiety and depression. According to gastroenterologist Emeran Mayer, MD, PhD, director of the Center for Neurobiology of Stress at the University of California, Los Angeles, given the gut’s multifaceted ability to communicate with the brain, “it’s almost unthinkable that the gut is not playing a critical role in mind states.”

According to gastroenterologist Emeran Mayer, MD, PhD, director of the Center for Neurobiology of Stress at the University of California, Los Angeles, given the gut’s multifaceted ability to communicate with the brain, “it’s almost unthinkable that the gut is not playing a critical role in mind states.” Improving our diet and reducing our intake of processed foods and sugar, and adding in greens, fruits, and fermented foods rich in probiotics can play a critical role in healing the gut. This, in turn, can help patients who’ve suffered from early trauma to heal both body and brain. Because microorganisms in our gut control our brain, we need to do whatever we can to make our microbiome healthy, and give the pathways in our brain all the serotonin and nutrients they need to send the correct messages along our brain’s synapses. Why would you eat in a way that makes stress receptors more reactive when you are busy doing everything else you can to heal? A number of the individuals we’ve followed in these pages have used nutrition to promote healing. Ellie has used diet to reduce her autoimmune psoriasis, depression, and anxiety.


pages: 380 words: 104,841

The Human Age: The World Shaped by Us by Diane Ackerman

23andMe, 3D printing, additive manufacturing, airport security, Albert Einstein, augmented reality, back-to-the-land, carbon footprint, clean water, dark matter, dematerialisation, double helix, Drosophila, epigenetics, Google Earth, Google Glasses, haute cuisine, Internet of things, Loebner Prize, Louis Pasteur, Masdar, mass immigration, megacity, microbiome, nuclear winter, personalized medicine, phenotype, Ray Kurzweil, refrigerator car, Search for Extraterrestrial Intelligence, SETI@home, skunkworks, Skype, stem cell, Stewart Brand, the High Line, theory of mind, urban planning, urban renewal, Whole Earth Catalog

Joshua Lederberg, the Nobel-laureate biologist who, in 2000, coined the term “microbiome,” defines it as “the menagerie of the body’s attendant microbes.” Amid the hoopla surrounding the Human Genome Project, he urged, “We must study the microbes that we carry within us and on our surfaces as part of a shared embodiment.” If the Human Genome Project was a landmark feat of discovery, the Human Microbiome Project is gene cartography’s finest hour. NIH director Francis Collins compares it to “fifteenth-century explorers describing the outline of a new continent,” a triumph that would “accelerate infectious disease research in a way previously impossible.” For five years, a consortium of eighty universities and scientific labs sampled, analyzed, and audited over ten thousand species that share our human ecosystem, thus mapping our “microbiome,” the normal microbial makeup of healthy adults.

Researchers are thinking of cobbling them into infant formula to help ward off asthma, allergies, and such autoimmune triggermen as diabetes, eczema, and multiple sclerosis. Babies pick up other useful bacteria in Mom’s dirt-and-crumb-garlanded home and landscape. At least, they should. Doctors are embracing the idea of personalized medicine based on a patient’s uniquely acquired flora and fauna, as revealed in his or her genome, epigenome, and microbiome. No more antibiotics prescribed by the jeroboam on the off chance they might prove useful. Instead, try unleashing enough beneficial bacteria to crowd out the pathogen. No more protecting children from the hefty stash of derring-do white-knight bacteria they need but we’ve learned to regard as icky. Patients whose gut flora have been wiped out by certain antibiotics are prey to Clostridium difficile, an opportunistic weasel of a bug that causes severe, debilitating diarrhea.

., 299 geothermal warmth, 95 Germany, 72, 78, 83, 101, 124, 132, 298 solar panels in, 106–7 Gershenfeld, Neil, 202–3 gestures, 26–27 giraffes, 276 global consciousness, 18 global warming, 11, 38–42, 154, 307–8 agriculture and, 56 in Bangladesh, 51–53 and development of seas, 64–65 evidence of, 108 extreme weather and, 36–43, 314 fishermen and, 56–57 gardens affected by, 38–39 habitats rearranged by, 133–40 human rights and, 48 glowworms, 144 glucocorticoids, 283 golden eagles, 132 Golden Lion Tamarin Conservation Program, 123 golden toads, 162 Golding, William, 162 Google, 192, 210 Google Glass, 260–61 gophers, 115 gorgonian, 38 grains, 71 Grand Canyon, 126 granite, 58–59 GraphExeter, 184–85, 317 grasshoppers, 173–74 Grassy Key, 131 great apes, 202 great auks, 151 Great Depression, 108 Greece, 124 Green Apple concept car, 103 Green Belt Corridor, 124 greenhouses, 90 Greenland, 42 green mussels, 131 Green over Grey, 83 growing season, 42 Guam, 139, 157 Guam rail, 139 Guatemala, 88 Gulag Archipelago (Solzhenitsyn), 218 Gurdon, John, 150, 160 Gut Erlasee Solar Park, 106–7 Guthrie, Barton, 261 habitat loss, 154 Haiyan, Typhoon, 46 Hamilton, Clive, 314 Hansen, James, 314 Hansmeyer, Michael, 236 Harvard University, 235 Hastings, Battle of, 190 heart, 150, 239, 248, 249, 250–51, 281 heat, 41 heaters, 87 heat recycling, 95–108 Helm, Barbara, 114 Henri, Pascal, 84 herbs, 89 Hernandez, Isaias, 264–65 herons, 193–94 Heuchera plants, 80–81 High Line, 77 Hitler, Adolf, 273 hockey, 40 Holocene, 9 Homer, 262 Honda, 236 Hong Sun Hye, 102 horse chestnut trees, 153 Horse Island, 58 horses, 137–38, 140, 145–46 hostas, 125 Hudson River, 54–55 hulls, 91 human genome, 13 Human Genome Project, 270, 274, 282, 285, 289, 300 Human Microbiome Project, 289 human rights, global warming and, 48 humans: as eusocial, 288 geographic expansion of, 10 geography changed by, 11 history of, 71 orangutan genes shared by, 3 population growth of, 10 technological changes to bodies of, 13 tools used by, 7, 9 humans, environmental effects of: climate change, see global warming and possibility of nuclear winter, 8–9 hummingbirds, 126 hunter-gatherers, 71 Huntington’s disease, 271 Hurricane Irene, 57 Hurricane Katrina, 46 hurricanes, 31, 41, 43, 55 Hurricane Sandy, see Sandy, Hurricane hybrid cars, 100 Hyde Park, 142 hydroelectronic power, 100, 107 hydroponic gardening, 83, 89, 90 Icarus, 224 icebergs, 195–96, 197 Iceland, 77 ice packs, 41–42 iCub, 218–19 iGlasses, 261 igloos, 86 iguanas, 131 Ike Dike, 50 Iliad (Homer), 262 India, 88, 107, 132, 175 Indian mongoose, 132 Indonesia, 132, 313 induced pluripotent stem cells (IPS), 150–51, 160–63 industrial farming, 60 Industrial Revolution, 34, 106, 185–86, 232, 235, 267 Inheritors, The (Golding), 162 insects, 166 insulin pumps, 253 intelligence of plants, 205–7 International Union for Conservation of Nature, 313 Internet, 199–200, 235 Inuit, 86 invasive species, 132, 154 Iran, 147 Iraq War, 258 Ireland, 132 Irene, Hurricane, 57 irises, 125 iron fertilization, 53 Island of Dr.


pages: 430 words: 107,765

The Quantum Magician by Derek Künsken

commoditize, epigenetics, industrial robot, iterative process, microbiome, orbital mechanics / astrodynamics, p-value, pattern recognition, Schrödinger's Cat, Turing test

He’s going to help penetrate the Puppet defenses.” Del Casal sipped his wine. “Correct a genetic flaw in a Puppet and create a false Numen. You have not come all this way without knowing that what you ask is impossible? The best that can be done with both is to make forgeries. The original designers created entirely novel sub-cellular organelles with unique molecular and genetic structures, as well as novel symbiotic microbiomes to alter biochemistry, immunity and neural responses. Even with authentic examples I cannot replicate either the Numen or the Puppets.” “I know,” Belisarius said. “This is an exercise in engineered mimicry. How close do you think your forgeries can get?” Del Casal’s eyes narrowed. He swirled his wine slowly, watching the wash cling to the inner surface of the glass. “As in all things,” Del Casal said, “the more money spent, the better the product, but I doubt you could afford even a distant approach.”

“No one alive today did,” Belisarius said, “but we play the hand we’ve been dealt.” Del Casal took one of the automata scuttling on Gates-15’s arm, regarded its sweat swabs, assay vents and thermal sensors, and set it back. “Gates-15 has all the chromosomal genes to experience the religious awe effect in the presence of a Numen,” Del Casal said. “From what I understand from him, his problem is in the microbiome around his synapses. In normal Puppets, an array of symbiotic bacteria located at the nerve endings modify the environment to strengthen and coordinate certain kinds of signal cascades. I do not know which bacteria are supposed to be there, and neither does Gates-15, so I have engineered tiny ecosystems of bacteria to colonize the synapses between his smell and taste receptors and his main and accessory olfactory systems.”

“Too bad we don’t have any canned Numen smell,” Belisarius said. “That is the genius of the early molecular biologists who engineered the Puppets and the Numen,” Del Casal said, with some admiration. “They designed their biochemical control system to be hack-proof. The Numen signal is a complex of dozens of smells produced by hundreds of nuclear genes that are modified after secretion by specific bacteria unique to the Numen microbiome. The successful reception of the signal is in the combinations and proportions of the scent molecules. It is ingenious. We will test the changes in Manfred against what I have built into William, but the live test will only come once he makes his way into the Forbidden City.” “I can’t believe I might be fixed,” Gates-15 said. His cheeks flushed pink to the edges of his beard. His hands clutched nervously between his knees, and his feet dangled between the chair legs.


Woolly: The True Story of the Quest to Revive History's Most Iconic Extinct Creature by Ben Mezrich

butterfly effect, Danny Hillis, double helix, Electric Kool-Aid Acid Test, Jeff Bezos, Kickstarter, life extension, Louis Pasteur, mass immigration, microbiome, personalized medicine, Peter Thiel, Silicon Valley, Silicon Valley ideology, stem cell, Stewart Brand

We can lock the cut pieces in their original places by using chemical “fixatives” and restraining polymers and then scan the clear three-dimensional cells using fluorescent confocal microscopy. Okay. But haven’t we lost the Mammoth microbiomes, and isn’t our ability to understand the biomes of viruses, bacteria, and fungi in our bodies too primitive? It should be noted that we have been engineering these invisible communities since the 1500s, with the dawn of smallpox vaccines in China. Today, the engineering of body ecosystems has become so advanced that companies have been founded around the process, such as Seres, SynLogics, AOBiome, Fitbiomics, and Holobiome. We study and use the microbiomes of modern elephants that eat and play in snow as well as other herbivores. Finally, isn’t the epigenome even more perplexing than the missing genomic DNA and the microbiome? Well, we can read important parts of the epigenome via the methylated cytosine bases that persist in ancient Mammoth DNA in a variety of body tissues.

As few as three thousand of these mega-base segments could cover the whole elephant genome, allowing nearly perfect conversion to a Mammoth genome. If all we want is a cold-resistant elephant, then we might want to make only a few dozen small changes, but as the technology gets cheaper we will probably try many versions, including some that are with obsessive-compulsive levels of molecular realism. If we get that good at genome engineering, what about the unsequenced part of genomes, plus the epi-genomes and microbiomes? Experts in ancient DNA reading have been dismissive of the prospects for sequencing a whole genome from ancient DNA. This is a fairly reasonable position today, since no mammalian genome has been completely sequenced even for living species (even for humans), and ancient DNA is shredded into millions of pieces per cell by radiation, which make it even more daunting. Beth Shapiro said in her 2015 book, How to Clone a Mammoth, “Because we cannot know the complete genome sequence of an extinct species, synthesizing a complete genome from scratch would not be an option.”


pages: 481 words: 125,946

What to Think About Machines That Think: Today's Leading Thinkers on the Age of Machine Intelligence by John Brockman

agricultural Revolution, AI winter, Alan Turing: On Computable Numbers, with an Application to the Entscheidungsproblem, algorithmic trading, artificial general intelligence, augmented reality, autonomous vehicles, basic income, bitcoin, blockchain, clean water, cognitive dissonance, Colonization of Mars, complexity theory, computer age, computer vision, constrained optimization, corporate personhood, cosmological principle, cryptocurrency, cuban missile crisis, Danny Hillis, dark matter, discrete time, Douglas Engelbart, Elon Musk, Emanuel Derman, endowment effect, epigenetics, Ernest Rutherford, experimental economics, Flash crash, friendly AI, functional fixedness, global pandemic, Google Glasses, hive mind, income inequality, information trail, Internet of things, invention of writing, iterative process, Jaron Lanier, job automation, Johannes Kepler, John Markoff, John von Neumann, Kevin Kelly, knowledge worker, loose coupling, microbiome, Moneyball by Michael Lewis explains big data, natural language processing, Network effects, Norbert Wiener, pattern recognition, Peter Singer: altruism, phenotype, planetary scale, Ray Kurzweil, recommendation engine, Republic of Letters, RFID, Richard Thaler, Rory Sutherland, Satyajit Das, Search for Extraterrestrial Intelligence, self-driving car, sharing economy, Silicon Valley, Skype, smart contracts, social intelligence, speech recognition, statistical model, stem cell, Stephen Hawking, Steve Jobs, Steven Pinker, Stewart Brand, strong AI, Stuxnet, superintelligent machines, supervolcano, the scientific method, The Wisdom of Crowds, theory of mind, Thorstein Veblen, too big to fail, Turing machine, Turing test, Von Neumann architecture, Watson beat the top human players on Jeopardy!, Y2K

What if, instead, an AI were more like a multicellular organism, a eukaryote evolution beyond our prokaryote selves? What’s more, what if we weren’t even the cells of such an organism, but its microbiome? And what if the intelligence of that eukaryote today was like the intelligence of Grypania spiralis, the oldest known multicellular eukaryote—not yet self-aware as a human is aware but still irrevocably on the evolutionary path leading to today’s humans. This notion is at best a metaphor, but I believe it’s a useful one. Perhaps humans are the microbiome living in the guts of an AI that’s only now being born! We know that without our microbiome we would cease to live. Perhaps the global AI has the same characteristics: not an independent entity but a symbiosis with the human consciousnesses living within it. Following this logic, we might conclude that there’s a primitive global brain, consisting not just of all connected devices but also of the connected humans using those devices.

SEJNOWSKI AI Will Make You Smarter SETH LLOYD Shallow Learning CARLO ROVELLI Natural Creatures of a Natural World FRANK WILCZEK Three Observations on Artificial Intelligence JOHN NAUGHTON When I Say “Bruno Latour,” I Don’t Mean “Banana Till” NICK BOSTROM It’s Still Early Days DONALD D. HOFFMAN Evolving AI ROGER SCHANK Machines That Think Are in the Movies JUAN ENRIQUEZ Head Transplants? ESTHER DYSON AI/AL TOM GRIFFITHS Brains and Other Thinking Machines MARK PAGEL They’ll Do More Good Than Harm ROBERT PROVINE Keeping Them on a Leash SUSAN BLACKMORE The Next Replicator TIM O’REILLY What If We’re the Microbiome of the Silicon AI? ANDY CLARK You Are What You Eat MOSHE HOFFMAN AI’s System of Rights and Government BRIAN KNUTSON The Robot with a Hidden Agenda WILLIAM POUNDSTONE Can Submarines Swim? GREGORY BENFORD Fear Not the AI LAWRENCE M. KRAUSS What, Me Worry? PETER NORVIG Design Machines to Deal with the World’s Complexity JONATHAN GOTTSCHALL The Rise of Storytelling Machines MICHAEL SHERMER Think Protopia, Not Utopia or Dystopia CHRIS DIBONA The Limits of Biological Intelligence JOSCHA BACH Every Society Gets the AI It Deserves QUENTIN HARDY The Beasts of AI Island CLIFFORD PICKOVER We Will Become One ERNST PÖPPEL An Extraterrestrial Observation on Human Hubris ROSS ANDERSON He Who Pays the AI Calls the Tune W.

Are we going to control these machines? Can we insist that they be motivated to look after us? No. Even if we can see what’s happening, we want what they give us far too much not to swap it for our independence. So what do I think about machines that think? I think that from being a tiny independent thinking machine, I am becoming a tiny part inside a far vaster thinking machine. WHAT IF WE’RE THE MICROBIOME OF THE SILICON AI? TIM O’REILLY Founder and CEO of O’Reilly Media, Inc. G. K. Chesterton once said, “The weakness of all Utopias is this, that they take the greatest difficulty of man and assume it to be overcome, and then give an elaborate account of the overcoming of the smaller ones.”5 I suspect we face a similar conundrum in our attempts to think about machines that think. We speculate elaborately about some issues while ignoring others that are fundamental.


A Natural History of Beer by Rob DeSalle

agricultural Revolution, British Empire, double helix, Drosophila, Louis Pasteur, microbiome, NP-complete, phenotype, placebo effect, wikimedia commons

The result is diarrhea, and disturbance of the microbiota of the gut. Scientists have known for a long time that our large intestines are filled with bacteria, and more recently have been able to determine the quantities of the different kinds of microbes that live in the long intestine, something that is apparently affected by drinking beer. In 2016 Gwen Falony and her colleagues examined the gut microbiomes of more than a thousand people using the DNA preserved in stool samples, much as DNA fingerprinting identifies the perpetrators in TV crime dramas. They showed that frequency of beer drinking had a big impact on the species of microbes living in the gut. Whether the difference makes beer drinkers more—or less—healthy overall is still unknown. Molecules that reach the bloodstream are carried to the other organs of the digestive system, where they are further broken down for nutrients and energy.

“Whole Genome Comparison Reveals High Levels of Inbreeding and Strain Redundancy across the Spectrum of Commercial Wine Strains of Saccharomyces cerevisiae.” G3: Genes, Genomes, Genetics 6, no. 4: 957–971. Cliften, P., P. Sudarsanam, A. Desikan, L. Fulton, B. Fulton, J. Majors, R. Waterston, B. A. Cohen, and M. Johnston. 2003. “Finding Functional Features in Saccharomyces Genomes by Phylogenetic Footprinting.” Science 301, no. 5629: 71–76. DeSalle, R., and S. L. Perkins. 2015. Welcome to the Microbiome: Getting to Know the Trillions of Bacteria and Other Microbes in, on, and around You. New Haven, CT: Yale University Press. Dunn, Rob. 2011. The Wild Life of Our Bodies. New York: Harper Collins. Gallone, B., J. Steensels, T. Prahl, L. Soriaga, V. Saels, B. Herrera-Malaver, A. Merlevede, et al. 2016. “Domestication and Divergence of Saccharomyces cerevisiae Beer Yeasts.” Cell 166, no. 6: 1397–1410.

Beverages 3, no. 3: 33. Spence, C., and Q. J. Wang. 2015. “Sensory Expectations Elicited by the Sounds of Opening the Packaging and Pouring a Beverage.” Flavour 4, no. 1: 35. Chapter 12. Beer Bellies More information on the beer belly can be found in Schütze et al (2009), Shelton and Knott (2014), and Bobak, Skodova, and Marmot (2003). Falony et al. (2016) is the source for our discussion of beer and microbiomes. For a great review of the impact of alcohol on the kidneys see Epstein (1997). Lu and Cederbaum (2008) describe the CYP2E1 gene interaction with alcohol, and the biology of ADH variants is discussed by Mulligan et al. (2003). GWAS and alcoholism is discussed in Bierut et al. (2010). Bierut, L. J., A. Agrawal, K. K. Bucholz, K. F. Doheny, et al. 2010. “A Genome-Wide Association Study of Alcohol Dependence.”


pages: 69 words: 18,998

Histamine Intolerance: A Comprehensive Guide for Healthcare Professionals by Janice Joneja

microbiome, risk tolerance

If you find that your symptoms resolve, or diminish in intensity, you will be able to control your reactions by dietary management. Supplementary diamine oxide, taken before eating, will further help by reducing the amount of histamine in the food. If your histamine excess is indeed due to a change in the microbial flora of your bowel (“your microbiome”) and no other cause, you may find that over time you will begin to tolerate more histamine-containing and releasing foods as your microbiome returns to its normal composition. Anxiety Question: “I turned 50 last September. Two years ago, one of my eyes got really itchy, and swelled hugely when I rubbed it. This has happened several times since then, but getting more severe each time; now both eyes swell up, plus I have a lot of anxiety and panic. My back and breasts also get itchy sometimes.


pages: 398 words: 105,032

Soonish: Ten Emerging Technologies That'll Improve And/or Ruin Everything by Kelly Weinersmith, Zach Weinersmith

2013 Report for America's Infrastructure - American Society of Civil Engineers - 19 March 2013, 23andMe, 3D printing, Airbnb, Alvin Roth, augmented reality, autonomous vehicles, connected car, double helix, Elon Musk, en.wikipedia.org, Google Glasses, hydraulic fracturing, industrial robot, information asymmetry, Kickstarter, low earth orbit, market design, megastructure, microbiome, moral hazard, multiplanetary species, orbital mechanics / astrodynamics, personalized medicine, placebo effect, Project Plowshare, QR code, Schrödinger's Cat, self-driving car, Skype, stem cell, Tunguska event

This further compounds the elephantishness problem, because a modern elephant may have crucially different womb conditions, due to genetics, diet, hormones, and so on. And, once born, the mammoth needs a modern elephant’s microbes. “So,” says Dr. Shapiro, “it’s born, it eats a little bit of elephant poo, because elephants do that to establish the community of microorganisms that live in the gut that can then be used to break down the food that elephants and mammoths eat. It will then have an elephant’s microbiome.” Welcome back to Earth, long-dead creature! Welcome back, sole representative of your kind! Now, eat some poop. Voila, you’ve got a mammoth, albeit it with some elephanty features. If the goal was to 100% recreate the lost mammoths, you probably fell short. But if the goal was to create an animal that played an important role in an ecosystem before it was lost, well then, maybe an elephantlike mammoth is pretty good.

So a geneticist studies particular genes while a genomicist studies all of the genes.* Like . . . all of them. This may make it sound like the genomicist is just smarter, but it’s kind of like the difference between a psychologist and a sociologist.* The -ome suffix is just a currently fashionable naming convention. The National Institutes of Health will get these individuals’ genomes, microbiomes, and other information, and will then follow them over time to track changes in their health. The data will be available to doctors, who can comb through them for associations among disease, genetics, and environmental factors. This is going to create a massive data set. Unfortunately, big piles of data don’t just leap up and tell you what’s going on. This is a problem that generally worries Pfizer’s Dr.

But suppose you happen to notice that there is a difference between explodey and nonexplodey patients—the explodey patients all have a particular set of microRNA markers. Now, you can take this drug that was formerly useless because it (seemingly) randomly killed users, and you can successfully cure cancer in a large portion of the population. Also, if you want to explode one sixth of the population, you can now do it in tablet form. Going further, by getting a genome, microbiome, metabolome, and a bunch of other -omes, you might be able to make very specific patient categories for clinical trials. This is a win on three fronts: (1) It means you can do statistically meaningful drug trials with smaller populations; (2) it means drugs don’t have to work for all or even most patients to be considered safe; and (3) it means old drugs that were shelved due to safety issues could be brought back to the market, to be used only on a particular patient category.


pages: 515 words: 117,501

Miracle Cure by William Rosen

Affordable Care Act / Obamacare, availability heuristic, biofilm, cognitive bias, cognitive dissonance, conceptual framework, Copley Medal, creative destruction, demographic transition, discovery of penicillin, Ernest Rutherford, experimental subject, Fellow of the Royal Society, Frederick Winslow Taylor, friendly fire, functional fixedness, germ theory of disease, global supply chain, Haber-Bosch Process, Ignaz Semmelweis: hand washing, Isaac Newton, James Watt: steam engine, Johannes Kepler, John Snow's cholera map, Joseph Schumpeter, Louis Pasteur, medical malpractice, meta analysis, meta-analysis, microbiome, New Journalism, obamacare, out of africa, pattern recognition, Pepto Bismol, randomized controlled trial, selection bias, stem cell, transcontinental railway, working poor

How much easier to deal with bacteria that produce a single enzyme that inactivates penicillin* than with a hospital full of patients infected with MRSA (for methicillin-resistant S. aureus), which doesn’t just laugh at penicillin, but cephalosporin, ampicillin, and every other beta-lactam antibiotic? Or XDR TB (extensively drug-resistant tuberculosis), a bacillus that is unaffected by either isoniazid or rifampin, the more recent agents called fluoroquinolones, and at least one of these second-line drugs: capreomycin, kanamycin, or amikacin. The human microbiome—the microorganisms in a particular environment—is largely composed of harmless or beneficial microbes, but it is also a perfect reservoir for spreading the genes for every imaginable form of antibiotic resistance. There are any number of reasons for the explosive growth in the number and virulence of antibiotic-resistant bacteria—as late as the 1990s, fewer than 15 percent of hospital-acquired infections were resistant to antibiotic treatment; acute-care hospitals today routinely report rates of 60 percent or more.

A compound that attacks the toxins produced as part of the bacterial infection is the anti-infective warfare equivalent of defusing the enemy’s artillery shells, rather than bombing the cannon themselves. Other researchers are developing ways to attack the source of antibiotic resistance: inhibiting the formation of the enzymes that penicillin-resistant bacteria use to disrupt the beta-lactam ring, for example. Michael Fischbach, at the University of California, San Francisco health campus, has discovered more than three thousand molecules within the human microbiome—the trillions of microorganisms that peacefully coexist inside our own bodies—that show antibiotic potential. Even better: Instead of relying on patience to await microbial innovation, Dr. Fischbach wrote a software program that could teach itself to recognize the patterns of successful antibiotic production in hundreds of existing microbial gene clusters. And then there’s GAIN. The tweaks it incorporates into the economics of antibiotic development—reducing the time, and therefore the costs, of bringing a drug to market; extending the patent life of drugs—are already bearing fruit.

., 153 Harvard-wide Program on Antibiotic Resistance (HWPAR), 303–4 Harvey, William, 9, 35 Hata, Sahachirō, 55, 58 Heatley, Norman, 2, 108–10, 112–13, 115, 117, 122–26, 128, 130, 132, 134, 135, 138n, 140, 141, 148, 151, 156, 157, 162, 164, 165, 195, 197, 198, 232, 280 bedpans used for growing penicillin, 123, 123, 136, 137 filtration machine of, 123–25, 124, 293 Helmont, Jan Baptist van, 208 Henle, Jacob, 22 heroic medicine, 7, 8, 10–11, 36 Heyden Chemical, 225–26 Hicks, Thomas, 261 Hill, Austin Bradford, 209–13, 288, 291 Hinshaw, Corwin, 196–201, 203, 206–7 Hippocrates, 8, 183, 187 Hippocratic Oath, 8n, 12, 36n, 262 histamines, 186 histology, 41 Hitler, Adolf, 179 HIV, 293–94 Hobby, Gladys, 165, 219 Hodgkin, Dorothy Crowfoot, 142–47, 143, 173–76, 221, 235n, 274, 293 Hodgkin, Thomas, 143 Hoechst AG, 45–47, 55, 57–58, 62, 160n, 296–97 Hoffmann-La Roche, 163, 230, 268 Hollaender, Alexander, 165 Holmes, Oliver Wendell, Sr., 36–37, 67n, 267 Homo sapiens, 183, 184 Hooke, Robert, 142 Hopkins, Frederick Gowland, 104–5 Hörlein, Heinrich, 63, 65, 68–69 hospitals: infections acquired in, 301–2 sanitary environment in, 33–35 Hughes, W. Howard, 150 human microbiome, 301, 304 humoral theory, 7–8, 14 Humphrey, Hubert, 285 Humphrey-Durham Amendment, 285–87 Hunt, Mary, 135–36 iatrogenesis, 7 I. G. Farben, 62–63, 68–69, 71, 95, 100, 131, 159, 163, 177–79, 230, 299n Ilotycin, 240 immune response, 48 immune system, 42, 61, 236 components of, 42–43 inflammatory response, 43, 48, 186, 278 immunity, 42–44 Imperial Chemical Industries (ICI), 121–22, 173, 176 Indinavir, 294 Industrial and Engineering Chemistry, 162 Industrial Revolution, 11, 16, 178, 290–91 inflammation, 43, 48 Institut de France, 18 Institut Pasteur, 15, 31, 37, 68, 69, 295 insulin, 176, 239 iodine, 65, 164 ions, 51 Jamestown, 81 Jefferson, Thomas, 154 Jenner, Edward, 13n, 26, 44 Jennings, Margaret, 125, 126 John Hopkins School of Medicine, 8 Johnson, Lyndon, 277 Johnson & Johnson, 297 Jones, Arthur, 130 Joseph, A.


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

A. Roger Ekirch, active measures, clockwatching, Dmitri Mendeleev, Donald Trump, Exxon Valdez, impulse control, lifelogging, longitudinal study, medical residency, meta analysis, meta-analysis, microbiome, mouse model, orbital mechanics / astrodynamics, placebo effect, RAND corporation, Ronald Reagan, the scientific method

South of the brain, we are also discovering that plentiful sleep makes your gut happier. Sleep’s role in redressing the balance of the body’s nervous system, especially its calming of the fight-or-flight sympathetic branch, improves the bacterial community known as your microbiome, which is located in your gut (also known as the enteric nervous system). As we learned about earlier, when you do not get enough sleep, and the body’s stress-related, fight-or-flight nervous system is revved up, this triggers an excess of circulating cortisol that cultivates “bad bacteria” to fester throughout your microbiome. As a result, insufficient sleep will prevent the meaningful absorption of all food nutrients and cause gastrointestinal problems.III Of course, the obesity epidemic that has engulfed large portions of the world is not caused by lack of sleep alone.

Ishii, “Effects of insufficient sleep on blood pressure monitored by a new multibiomedical recorder,” Hypertension 27, no. 6 (1996): 1318–24. II. While leptin and ghrelin may sound like the names of two hobbits, the former is derived from the Greek term leptos, meaning slender, while the latter comes from ghre, the Proto-Indo-European term for growth. III. I suspect we’ll discover a two-way relationship wherein sleep not only affects the microbiome, but the microbiome can communicate with and alter sleep through numerous different biological channels. IV. Beyond a simple lack of sleep, Dijk’s research team has further shown that inappropriately timed sleep, such as that imposed by jet lag or shift work, can have equally large effects on the expression of human genes as inadequate sleep. By pushing forward an individual’s sleep-wake cycle by a few hours each day for three days, Dijk disrupted a massive one-third of the transcribing activity of the genes in a group of young, healthy adults.

Downstairs in the body, sleep restocks the armory of our immune system, helping fight malignancy, preventing infection, and warding off all manner of sickness. Sleep reforms the body’s metabolic state by fine-tuning the balance of insulin and circulating glucose. Sleep further regulates our appetite, helping control body weight through healthy food selection rather than rash impulsivity. Plentiful sleep maintains a flourishing microbiome within your gut from which we know so much of our nutritional health begins. Adequate sleep is intimately tied to the fitness of our cardiovascular system, lowering blood pressure while keeping our hearts in fine condition. A balanced diet and exercise are of vital importance, yes. But we now see sleep as the preeminent force in this health trinity. The physical and mental impairments caused by one night of bad sleep dwarf those caused by an equivalent absence of food or exercise.


Drink?: The New Science of Alcohol and Your Health by David Nutt

Boris Johnson, carbon footprint, en.wikipedia.org, epigenetics, impulse control, Kickstarter, liquidationism / Banker’s doctrine / the Treasury view, microbiome, selective serotonin reuptake inhibitor (SSRI)

Over the years it had destroyed her liver, as alcohol can too. She’d become confused and delirious and the reason was that the toxic substances from her gut bacteria weren’t being cleared by the liver so they got into her brain and poisoned it. We showed this was the case when we treated her with antibiotics. They kill all the bacteria in the gut, all the microbiome, so the toxins disappear. For a few days, she woke up, was alert and conscious. But then her gut recolonised itself and she went back into a coma and died. Right now, the microbiome is a hot area of research. The suggestion is that your unique inner world of bugs is not only affected by what you drink (and eat), but is a key factor in whether you get ill and with which condition. Drinking alcohol (and/or having a bad diet) encourages the microbes in the gut to produce toxic substances that promote the inflammatory processes and gut permeability that allow diseases, including liver disease and cancer, to happen.

When your liver isn’t working, your protein levels go down and you get the fluid build-up in your abdomen that I described above. It’s this metabolic disturbance that eventually stops your heart. If you do have some liver function left, you can stay alive with cirrhosis for some years. But you are extremely vulnerable to catching a fatal infection; your body easily becomes overwhelmed as you don’t have the right level of proteins in your blood. The other thing the liver does is break down the toxins produced by the microbiome so that they don’t get to the brain. That’s why people at this stage get confused and delirious – a phenomenon called hepatic encephalopathy – because their brain is being poisoned by these substances. Doctors can give people antibiotics to kill the gut bugs, but this only gives temporary respite. At this point, life expectancy is very short – unless you have a transplant. George Best, a long-term alcoholic, was a classic case of cirrhosis.


pages: 406 words: 115,719

The Case Against Sugar by Gary Taubes

Albert Einstein, British Empire, cuban missile crisis, epigenetics, Everything should be made as simple as possible, Gary Taubes, Isaac Newton, meta analysis, meta-analysis, microbiome, phenotype, pre–internet, Ralph Nader, RAND corporation, randomized controlled trial, selection bias, the new new thing, the scientific method, Works Progress Administration

All of this is triggered by something in our diet and lifestyle, which is what we ultimately have to explain. Another issue that has recently added still another layer of complication to the science is the role played in obesity and diabetes by the bacteria in our guts, known as the gut microbiota or microbiome. New technologies will lead inevitably to new areas of research, new observations, and new discoveries. The ability to sequence the genomes of these bacterial species has opened up a new frontier of research, just as the ability to measure blood pressure, cholesterol, or insulin sensitivity did for earlier generations of researchers. The microbiome research, because it’s brand-new, is at a very preliminary stage. Still, as the new new thing (to borrow a phrase from the journalist Michael Lewis) in obesity and diabetes research, gut bacteria get an inordinate amount of attention, particularly from the media, though we may not know for decades what to make of the observations that ensue—what is signal and what is noise.

Still, as the new new thing (to borrow a phrase from the journalist Michael Lewis) in obesity and diabetes research, gut bacteria get an inordinate amount of attention, particularly from the media, though we may not know for decades what to make of the observations that ensue—what is signal and what is noise. Most of the work so far has been done in laboratory mice and rats, and the relevance to human life (or even to other laboratory animals) is unclear. The observations that come from human studies and the very few human experiments are still impossible to interpret reliably. Certain alterations in this gut microbiome associate with obesity, metabolic syndrome, and diabetes, but, as the researchers will acknowledge, “it remains to be determined whether these are the results of altered glucose metabolism and insulin resistance or contribute to their development.” Since the 1950s, if not earlier, researchers have known that the foods we eat and the form in which they come—indigestible fiber, refined grains and sugar, and all the rest—will influence which species of gut bacteria thrive and which don’t.

Hoogwerf, and F. C. Goetz. 1983. “Postprandial Glucose and Insulin Responses to Meals Containing Different Carbohydrates in Normal and Diabetic Subjects.” New England Journal of Medicine 309, no. 1 (July 7): 7–12. Barker, T. C., D. J. Oddy, and J. Yudkin. 1970. The Dietary Surveys of Dr Edward Smith 1862–3: A New Assessment. London: Staples Press. Barlow, G. M., A. Yu, and R. Mathur. 2015. “Role of the Gut Microbiome in Obesity and Diabetes Mellitus.” Nutrition in Clinical Practice 30, no. 6 (Dec.): 787–97. Barnard, E. F. 1928. “Too Much Sugar for the World to Eat.” New York Times, April 8: 112–14. Bart, P. 1962. “Advertising: Calorie Craze and Its Impact.” New York Times, Feb. 25: F12. Bashford, E. F. 1908a. Third Scientific Report on the Investigations of the Imperial Cancer Research Fund. London: Taylor and Francis. ———. 1908b.


pages: 836 words: 158,284

The 4-Hour Body: An Uncommon Guide to Rapid Fat-Loss, Incredible Sex, and Becoming Superhuman by Timothy Ferriss

23andMe, airport security, Albert Einstein, Black Swan, Buckminster Fuller, carbon footprint, cognitive dissonance, Columbine, correlation does not imply causation, Dean Kamen, game design, Gary Taubes, index card, Kevin Kelly, knowledge economy, life extension, lifelogging, Mahatma Gandhi, microbiome, p-value, Parkinson's law, Paul Buchheit, placebo effect, Productivity paradox, publish or perish, Ralph Waldo Emerson, Ray Kurzweil, Richard Feynman, selective serotonin reuptake inhibitor (SSRI), Silicon Valley, Silicon Valley startup, Skype, stem cell, Steve Jobs, survivorship bias, Thorstein Veblen, Vilfredo Pareto, wage slave, William of Occam

So far, two primary strains of bacteria have been found to influence fat absorption, almost regardless of diet: Bacteroidetes and Firmicutes. Lean people have more Bacteroidetes and fewer Firmicutes; obese people have more Firmicutes and fewer Bacteroidetes. As obese people lose weight, the ratio of bacteria in their gut swings confidently over to more Bacteroidetes. This finding has significant enough implications for national health that the National Institutes of Health (NIH) launched the multi-year Human Microbiome Project in late 2007. It is like a Human Genome Project for bacteria and intended to explore how some of the 40,000+ species of micro-friends (and fiends) are affecting our health and how we might modify them to help us more. This could take some time, but you don’t need to wait to act. There are a few things you can do now to cultivate healthy and fat-reducing gut flora: Get off the Splenda.

In a randomized, double-blind, placebo-controlled study of 39 patients with chronic fatigue syndrome, Lactobacillus casei strain Shirota was found to significantly decrease anxiety symptoms. Probiotics (bifidobacteria is one example) have also been shown as an effective alternative treatment for depression because of their power to inhibit inflammatory molecules called cytokines, decrease oxidative stress, and correct the overgrowth of unwanted bacteria that prevents optimal nutrient absorption in the intestines. Give your good bacteria an upgrade and get your microbiome in shape. Faster fat-loss and better mental health are just two of the benefits. TOOLS AND TRICKS Twelve Hours of Bingeing in Photos (www.fourhourbody.com/binge) See the binge from this chapter as I captured it in real time and posted the photos on Flickr. It will give you an appreciation for the quantity. Super Cissus Rx (www.fourhourbody.com/cq) This is the brand of CQ I used during the experimentation.

.], and sex, 19.1, 19.2, 20.1 GL (glycemic load), 8.1, 12.1 glucose monitor, 12.1, 12.2, 12.3, 12.4 GLUT-4 (glucose transporter type 4), 9.1, 9.2, 10.1, 10.2, 18.1 glutathione gluten glycemic index (GI), 8.1, 12.1 glycemic load (GL), 8.1, 12.1 GnRH (gonadotropin-releasing hormone) Goethe, Johann Wolfgang Goldacre, Ben, 43.1, 44.1 goLITE, 23.1, 23.2 GOMAD (gallon of milk a day) goose liver pâté Go Raw Carob Cashew Smoothie (recipe) gout Green Machine Pudding (recipe) green tea flavanols, 10.1, 10.2 g-spot, 19.1, 20.1 Guadango, Mike (Asshole) Guillette, Louis Gumbel, Bryant H Habit Forge Hackett, George Hahnemann, Samuel half military crawl Hall, Mike hamstring pull Harajuku Moment, 4.1, 4.2 Hartford Marathon Hartley, Nina, 19.1, 19.2 Hartmann, Gerard Hawthorne Effect HCB (Hungarian Core Blaster) hCG (human chorionic gonadotropin) headaches: and blood sugar dehydration heartburn heart rate monitor heat, and fat loss Heinlein, Robert helplessness, learned Hemwall, Gustav A. Herbert, Frank Hiei monk/athletes Hill, James hip extension Hippocrates HIT (high-intensity intermittent) exercise Hite, Shere Hoehn, Charlie holding your breath homeopathy Horton, Zar hot sauce Houdini, Harry HRM (heart rate monitor) human chorionic gonadotropin (hCG) Human Microbiome Project humidifier, 23.1, 23.2 hummus recipe Hungarian Core Blaster (HCB) Hutchins, Ken Hyde, Andrew hypertrophy hyperzine-A hypothalamus, 21.1, 33.1 I IAS (Insulin Autoimmune Syndrome) ice baths ice packs IF (intermittent fasting) IGF-1 (insulin-like growth factor 1) II (insulinemic index) imbalance, 27.1, 27.2 inaction, excuses for infertility injuries, reversing active-release technique AMIT biopuncture cocktail Egoscue method menu prolotherapy, 25.1, 25.2 shoe heel removal injury-proofing chop and lift cross-body one-arm single-leg deadlift fixing Functional Movement Screen (FMS), 27.1, 27.2 schedule sets and reps single-leg flexibility assessment testing Turkish get-up two-arm single-leg deadlift insomnia onset, 23.1, 23.2 insulinemic response insulin-like growth factor 1 (IGF-1) insulin release insulin sensitivity inulin in vitro fertilization iron excess Iron Penis Kung-Fu Irwin, Nic isoleucine IVF (in vitro fertilization) J James, William Japan, life expectancy in Japanese natto, 9.1, 46.1 Jarmey, Chris, The Concise Book of Muscles JayC (eating more) Jeff (variety) Jell-O, sugar-free Jeter, Derek Johnson, Ben, 29.1, 32.1 Johnson, Michael Jones, Arthur, 2.1, 2.2, 16.1, 16.2, 16.3, 16.4, 16.5 Jones, Brett Jones, Marion Jones, Reese Julee (bodyfat) jumping, 28.1, 33.1n Jurek, Scott, 30.1, 31.1, 31.2, 47.1, 47.2, 48.1 K Kaku, Michio Kamen, Dean Karlan, Dean Karnazes, Dean, 16.1, 31.1 Karwoski, Kirk, 33.1, 33.2, 33.3 Kauai Marathon Kay, Alan kefir Keith, Lierre Kelley, Johnny Kenya, marathoners of Kersschot, Jan ketogenic dieting kettlebells, 14.1, 14.2 for biceps certification, 30.1, 32.1 Fleur’s regimen Russian kettlebell swing Turkish get-up Zar Horton’s method Kimball, Charlie kimchi King, Martin Luther, Jr.


pages: 422 words: 113,525

Whole Earth Discipline: An Ecopragmatist Manifesto by Stewart Brand

agricultural Revolution, Asilomar, Asilomar Conference on Recombinant DNA, back-to-the-land, biofilm, borderless world, Buckminster Fuller, business process, Cass Sunstein, clean water, Community Supported Agriculture, conceptual framework, Danny Hillis, dark matter, decarbonisation, demographic dividend, demographic transition, Elon Musk, Exxon Valdez, failed state, Geoffrey West, Santa Fe Institute, glass ceiling, Google Earth, Hans Rosling, Hernando de Soto, informal economy, interchangeable parts, Intergovernmental Panel on Climate Change (IPCC), invention of agriculture, invention of the steam engine, Jane Jacobs, jimmy wales, Kevin Kelly, Kibera, land tenure, lateral thinking, low earth orbit, M-Pesa, Marshall McLuhan, megacity, microbiome, New Urbanism, orbital mechanics / astrodynamics, out of africa, Paul Graham, peak oil, Peter Calthorpe, Richard Florida, Ronald Reagan, Silicon Valley, smart grid, stem cell, Stewart Brand, The Fortune at the Bottom of the Pyramid, Thomas Malthus, University of East Anglia, uranium enrichment, urban renewal, wealth creators, Whole Earth Catalog, Whole Earth Review, William Langewiesche, working-age population, Y2K

Bacteria have been found living in profusion a mile below the bottom of the seafloor, possibly as old as the sediment around them—111 million years. Look closer to home. Ninety percent of you isn’t you—only a tenth of the cells in your body are human; the rest are microbes. We are a portable swamp. One program of the emerging worldwide Global Metagenomics Initiative is called the International Human Microbiome Consortium, which is busy shotgun-sequencing all of the microbial communities that share our bodily life. We humans have 18,000 distinct genes; our microbes have 3 million. We are one species; they are diverse—a thousand species in our digestive tract (a twenty-one-foot-long bioreactor running on 100 trillion microbes), another thousand in our mouth, five hundred on our skin, another five hundred in those of us with a vagina.

My wife, Ryan Phelan, had just sold a company, so we put some money into gathering the world’s leading taxonomists and systematists in San Francisco for a meeting to decide whether a push to identify all life was useful and feasible. Ed Wilson hosted a follow-on meeting at Harvard a few weeks later. The universal message from the scientists was to go for it. As the project took shape, I got to participate in species inventories in Costa Rica, in the Great Smoky Mountains National Park, and inside a wood rat. (Why inside a wood rat? As with the human microbiome project, we are learning the degree to which life lives on life. Carl Zimmer wrote in Parasite Rex [2000]: “There’s a parrot in Mexico with thirty different species of mites on its feathers alone. And the parasites themselves have parasites, and some of those parasites have parasites of their own. . . . According to one estimate, parasites may outnumber free-living species four to one. In other words, the study of life is, for the most part, parasitology.”)

Guanacaste Conservation Area, Costa Rica Guardian Guidetti, Geri Gwadz, Robert Haeckel, Ernst “Half Century of United States Federal Government Energy Incentives, A” (Bezdek and Wendling) Hallwachs, Winnie Hamming, Richard Hansen, James Hansson, Anders Harris, Michael Harrison, Jim Haseltine, William Hawaii Hawken, Paul Hawks, John heat waves Hebert, Paul Henderson, Donald herbicides Herman, Arthur Higgs, Eric High Country News Hillis, Danny Hiroshima, Japan HIV/AIDS Holdren, John Holistic Management (Savory) Homer-Dixon, Thomas Hopis horizontal gene transfer horses Howard, Albert Humanitarian Golden Rice Network hurricanes hybrid seeds hydroelectric power hydrogen ice-to-water albedo flip Idea of Decline in Western History, The (Herman) IEEE Spectrum iGEM Jamboree Iglesias-Rodríguez, Débora Illicit (Naím) “Implications of Rising Carbon Dioxide Content of the Atmosphere” (Conservation Foundation) Inconvenient Truth, An Independent India genetic engineering and Green Revolution and nuclear power and slums and Industry Association of Synthetic Biology informal economy infrastructure insect resistance insulin integral fast reactors integrated pest management intelligent design Intergovernmental Panel on Climate Change (IPCC) International Atomic Energy Agency (IAEA) International Consortium for Polynucleotide Synthesis International Council of Science (ICSU) International Human Microbiome Consortium International Maize and Wheat Improvement Center International Rice Research Institute International Soil Reference and Information Centre International Union for Conservation of Nature and Natural Resources (IUCN) Internet Internet Engineering Task Force Intertribal Bison Cooperative Intervention (Caruso) iron irrigation Islam, Muslims Italy jaguars Janzen, Daniel Japan atomic bombing of genetic engineering and nuclear power and Jefferson, Richard Jennings, Lois Judson, Horace Juniper, Tony Kahn, Herman Kahn, Lloyd Kaplan, Robert Kareiva, Peter Kaufman, Wallace Keeling, Charles Keith, David Kelly, Brian Kelly, Kevin Kenya Keynes, John Maynard Khosla, Vinod King, Franklin Hiram Kirk, Andrew Klaassen, Johann Kleiber’s law Knight, Tom Kohm, Kathy Korea, North Korea, South Kunstler, James Howard Kyoto Protocol (2001) L-1 Point (Inner Lagrange Point) Lackner, Klaus Lake Nyos, Cameroon, disaster in Lamarck, Jean-Baptiste Lament for an Ocean (Harris) landraces Langewiesche, William Lansing, Stephen Laquian, Aprodicio Last Forest, The (London and Kelly) Last Whole Earth Catalog Latham, John Latin America genetic engineering and see also specific countries Laws of Fear (Sunstein) LeBlanc, Steven LEED rating system Lehmann, Johannes Lerner, Jaime Lewis, John Liberation Biology (Bailey) Liferaft Earth Limits to Growth, The (Meadows et al.)


pages: 396 words: 112,832

Bread, Wine, Chocolate: The Slow Loss of Foods We Love by Simran Sethi

Chuck Templeton: OpenTable:, Food sovereignty, Intergovernmental Panel on Climate Change (IPCC), invisible hand, Louis Pasteur, microbiome, phenotype, placebo effect, Skype, The Wealth of Nations by Adam Smith, women in the workforce

Agriculture and Ecosystems (blog), CGIAR Research Program on Water, Land and Ecosystems, May 16, 2014, http://wle.cgiar.org/blogs/2014/05/16/will-pursuit-food-security-weaken-resilience-global-food-systems/. 9.Raj Patel, Stuffed and Starved: Markets, Power and the Hidden Battle for the World Food System (New York: Melville House, 2012). 10.Food and Agriculture Organization of the United Nations (FAO), International Fund for Agricultural Development (IFAD), and World Food Programme (WFP), The State of Food Security in the World 2015: Meeting the 2015 International Hunger Targets: Taking Stock of Uneven Progress (Rome: FAO, 2015), 1; and Marie Ng et al., “Global, Regional, and National Prevalence of Overweight and Obesity in Children and Adults During 1980–2013: A Systematic Analysis for the Global Burden of Disease Study 2013,” Lancet 384, no. 9945 (August 2014): 770, http://dx.doi.org/10.1016/S0140-6736(14)60460-8. 11.Veronique Greenwood, “You Are Your Bacteria: How the Gut Microbiome Influences Health,” Time, August 29, 2013, http://science.time.com/2013/08/29/you-are-your-bacteria-how-the-gut-microbiome-influences-health/. 12.Catherine A. Lozupone et al., “Diversity, Stability and Resilience of the Human Gut Microbiota,” Nature 489, no. 7415 (September 2012): 220–30, doi:10.1038/nature11550. 13.Food and Agriculture Organization of the United Nations (FAO), The State of the World’s Plant Genetic Resources for Food and Agriculture (Rome: FAO, 1997), 14, ftp://ftp.fao.org/docrep/fao/meeting/015/w7324e.pdf. 14.

Yes, this increase in carbs, fats and proteins has helped feed hungry people, but on a global scale it’s also increased our chances of becoming what author Raj Patel calls “stuffed and starved.”9 The world overconsumes energy-dense foods but eats fewer foods rich in micronutrients (the small but essential amounts of vitamins and minerals we need for healthy metabolism, growth and physical development). While 795 million people go hungry, over 2 billion people are overweight or obese.10 And both groups suffer from micronutrient malnutrition. The global standard diet is changing the biodiversity of nearly every ecosystem, including the 100 trillion bacteria that live in our gut, part of what’s known as our microbiome.11 The foods and drinks we consume add to or, increasingly, detract from the diversity of our intestinal flora and have implications for how healthy or unhealthy we are over the long term.12 The factors that contribute to this change are complex and interconnected, but the main reason for this shift is that we’ve replaced the diversity of foods we used to eat with monodiets of megacrops, funneling our resources and energy into the cultivation of megafields of cereals, soy and palm oil.


pages: 501 words: 114,888

The Future Is Faster Than You Think: How Converging Technologies Are Transforming Business, Industries, and Our Lives by Peter H. Diamandis, Steven Kotler

Ada Lovelace, additive manufacturing, Airbnb, Albert Einstein, Amazon Mechanical Turk, augmented reality, autonomous vehicles, barriers to entry, bitcoin, blockchain, blood diamonds, Burning Man, call centre, cashless society, Charles Lindbergh, Clayton Christensen, clean water, cloud computing, Colonization of Mars, computer vision, creative destruction, crowdsourcing, cryptocurrency, Dean Kamen, delayed gratification, dematerialisation, digital twin, disruptive innovation, Edward Glaeser, Edward Lloyd's coffeehouse, Elon Musk, en.wikipedia.org, epigenetics, Erik Brynjolfsson, Ethereum, ethereum blockchain, experimental economics, food miles, game design, Geoffrey West, Santa Fe Institute, gig economy, Google X / Alphabet X, gravity well, hive mind, housing crisis, Hyperloop, indoor plumbing, industrial robot, informal economy, Intergovernmental Panel on Climate Change (IPCC), Internet of things, invention of the telegraph, Isaac Newton, Jaron Lanier, Jeff Bezos, job automation, Joseph Schumpeter, Kevin Kelly, Kickstarter, late fees, Law of Accelerating Returns, life extension, lifelogging, loss aversion, Lyft, M-Pesa, Mary Lou Jepsen, mass immigration, megacity, meta analysis, meta-analysis, microbiome, mobile money, multiplanetary species, Narrative Science, natural language processing, Network effects, new economy, New Urbanism, Oculus Rift, out of africa, packet switching, peer-to-peer lending, Peter H. Diamandis: Planetary Resources, Peter Thiel, QR code, RAND corporation, Ray Kurzweil, RFID, Richard Feynman, Richard Florida, ride hailing / ride sharing, risk tolerance, Satoshi Nakamoto, Second Machine Age, self-driving car, Silicon Valley, Skype, smart cities, smart contracts, smart grid, Snapchat, sovereign wealth fund, special economic zone, stealth mode startup, stem cell, Stephen Hawking, Steve Jobs, Steven Pinker, Stewart Brand, supercomputer in your pocket, supply-chain management, technoutopianism, Tesla Model S, Tim Cook: Apple, transaction costs, Uber and Lyft, uber lyft, unbanked and underbanked, underbanked, urban planning, Watson beat the top human players on Jeopardy!, We wanted flying cars, instead we got 140 characters, X Prize

What’s more critical here is it’s not just stem cells or gene therapy or CRISPR—it’s the combined power of all these techniques, their convergence, that holds the most potential. Perhaps the biggest consequence of this convergence will be individually customized medicine or what’s called “N-of-1 medicine.” In N-of-1 medicine, every treatment you receive has been specifically designed for you—your genome, transcriptome, proteome, microbiome, and all the rest. It’s a level of preventative care not seen before. You’ll know the foods, supplements, and exercise regimen that are perfect for you. You’ll understand which microbes inhabit your gut, and what diet keeps them healthy and fit. You’ll know which diseases you’re most likely to develop and be able to take steps to prevent them. It’s an era of incredibly personalized medical care, where the tools of life have become tools for the preservation of life, and many of the diseases that plagued earlier generations have begun to fade from memory.

“Hey Google, how’s my health this morning?” “One moment,” says your digital assistant. It takes thirty seconds for the full diagnostic to run, which is pretty good considering the system deploys dozens of sensors capturing gigabytes of data. Smart sensors in toothbrush and toilet, wearables in bedding and clothing, implantables inside your body—a mobile health suite with a 360-degree view of your system. “Your microbiome looks perfect,” Google tells you. “Also, blood glucose levels are good, vitamin levels fine, but an increased core temperature and IgE levels…” “Google—in plain English?” “You’ve got a virus.” “A what?” “I ran through your last forty-eight hours of meetings. It seems like you picked it up Monday, at Jonah’s birthday party. I’d like to run additional diagnostics, would you mind using the…” Well, take your pick.

Thanks to always-on, always watching sensors, your smartphone is about to become your doctor. Reading, Writing, and Editing the Code of Life For a decade, experts have been trumpeting personalized genomics as a healthcare revolution. When we understand your genome, the thinking goes, we’ll know how to optimize “you.” We’ll know the perfect foods, the perfect drugs, and the perfect exercise regimen, just for you. We’ll know the types of gut flora best suited for your microbiome, the supplements that best commingle with your physiology. You’ll learn the diseases to which you’re most susceptible, and, more importantly, how to prevent them. Or so the story goes.… In 2017, Jason Vassy, a professor of medicine at Boston’s Brigham and Women’s Hospital, decided to take a closer look at that story. A hundred patients were recruited. Half had their DNA screened; the other half answered questions about family medical history, which is the standard method for establishing genetic risk.


Survival of the Friendliest: Understanding Our Origins and Rediscovering Our Common Humanity by Brian Hare, Vanessa Woods

Cass Sunstein, cognitive bias, desegregation, Donald Trump, drone strike, income inequality, Jane Jacobs, Law of Accelerating Returns, meta analysis, meta-analysis, microbiome, Milgram experiment, Nelson Mandela, New Urbanism, nuclear winter, out of africa, phenotype, Ray Kurzweil, Richard Florida, Ronald Reagan, selective serotonin reuptake inhibitor (SSRI), self-driving car, smart cities, social intelligence, Stanford marshmallow experiment, stem cell, Steven Pinker, The Death and Life of Great American Cities, theory of mind, Tim Cook: Apple, trade route, white flight, zero-sum game

In people, it can be as simple as approaching someone and wanting to socially interact or as complicated as reading someone else’s mind in order to cooperatively accomplish a mutual goal.8 It is an ancient strategy. Millions of years ago, mitochondria were free-floating bacteria until they entered larger cells. Mitochondria and the larger cells joined forces and became the batteries that power cell function in animal bodies.17 Your microbiome, which, among other things, allows your body to digest food, make vitamins, and develop organs, is the result of similar, mutually beneficial partnerships between microbes and your body.18 Flowers appeared later than most plants, but their mutually beneficial relationship with pollinating insects made them so successful that they now dominate the landscape19 Ants, estimated to have the same mass as a fifth of all the other terrestrial animals on earth combined, can form superorganisms of up to 50 million individuals that function as a single social unit.20 Each year I*2 challenge my students to use evolutionary theory to solve the world’s problems.

Gray, “Mitochondrial Evolution,” Cold Spring Harbor Perspectives in Biology 4, a011403 (2012), published online September 1, 10:1101/cshperspect.a011403. 18. L. A. David, C. F. Maurice, R. N. Carmody, D. B. Gootenberg, J. E. Button, B. E. Wolfe, A. V. Ling, A. S. Devlin, Y. Varma, M. A. Fischbach, S. B. Biddinger, R. J. Dutton, P. J. Turnbaugh, “Diet Rapidly and Reproducibly Alters the Human Gut Microbiome,” Nature 505, 559–63 (2014), published online EpubJan 23, 10:1038/nature12820. 19. S. Hu, D. L. Dilcher, D. M. Jarzen, “Early Steps of Angiosperm-Pollinator Coevolution,” Proceedings of the National Academy of Sciences 105, 240–45 (2008). 20. B. Hölldobler, E. O. Wilson, The Superorganism: The Beauty, Elegance, and Strangeness of Insect Societies (New York: W. W. Norton, 2009). 21.


pages: 294 words: 87,429

In Pursuit of Memory: The Fight Against Alzheimer's by Joseph Jebelli

Albert Einstein, Alfred Russel Wallace, Berlin Wall, double helix, epigenetics, global pandemic, Isaac Newton, Kickstarter, lateral thinking, longitudinal study, Louis Pasteur, Mahatma Gandhi, megacity, meta analysis, meta-analysis, microbiome, mouse model, phenotype, placebo effect, Ronald Reagan, Rosa Parks, Skype, stem cell, Thomas Kuhn: the structure of scientific revolutions

It’s all due to a foggy connection between the brain and the gut. Collectively known as the microbiome, the bacteria that reside symbiotically inside us are vital to brain health. This was demonstrated most starkly in November 2014, when Swedish researchers at the Karolinska Institute in Stockholm showed that germ-free mice–gnotobiotic mice, housed and fed inside sterile containers–are born with leaky, defective blood–brain barriers.3 The blood–brain barrier is a wall of cells that decides what can and cannot enter the brain from the blood coursing through its capillaries. In Alzheimer’s, it’s one of the first things to break down, especially around the hippocampus, where memories are made. But the microbiome can be a dangerous bedfellow too. If excessive amounts of bacteria breach the blood–brain barrier, they will activate the brain’s immune cells–microglia, the cellular protagonists of the Alzheimer’s vaccination story in chapter seven–and cause a form of inflammation that weakens the blood–brain barrier even more, setting in motion a vicious cycle in which more bacteria are let in and more inflammation ensues.


pages: 286 words: 87,168

Less Is More: How Degrowth Will Save the World by Jason Hickel

air freight, Airbnb, basic income, Bernie Sanders, Big bang: deregulation of the City of London, Boris Johnson, Bretton Woods, British Empire, capital controls, cognitive dissonance, coronavirus, corporate governance, corporate personhood, COVID-19, David Graeber, decarbonisation, declining real wages, deindustrialization, dematerialisation, Elon Musk, energy transition, Fellow of the Royal Society, Fractional reserve banking, Francis Fukuyama: the end of history, full employment, gender pay gap, income inequality, Intergovernmental Panel on Climate Change (IPCC), invention of the steam engine, James Watt: steam engine, Jeff Bezos, John Maynard Keynes: Economic Possibilities for our Grandchildren, land reform, liberal capitalism, longitudinal study, Mahatma Gandhi, Mark Zuckerberg, McMansion, means of production, meta analysis, meta-analysis, microbiome, moral hazard, mortgage debt, Naomi Klein, new economy, offshore financial centre, oil shale / tar sands, out of africa, passive income, planetary scale, plutocrats, Plutocrats, quantitative easing, rent control, rent-seeking, Ronald Reagan, Scramble for Africa, secular stagnation, shareholder value, sharing economy, Simon Kuznets, structural adjustment programs, the scientific method, The Spirit Level, transatlantic slave trade, trickle-down economics, universal basic income

Biologists believe that this second set, the mitochondrial DNA, is derived from bacteria that were engulfed by our cells at some point in the evolutionary past. Today these little organelles play an absolutely essential role in human life: they convert food into energy that our bodies can use. This is mind-bending: that our most basic metabolic functions, and even the genetic codes that constitute the very core of who we are, depend on other beings. The implications of this are profound. A team of scientists associated with the Interdisciplinary Microbiome Project at Oxford University have suggested that discoveries related to bacteria may revolutionise not only our science but our ontology too: ‘Our ability to map previously invisible forms of microbial life in and around us is forcing us to rethink the biological constitution of the world, and the position of humans vis-a-vis other forms of life.’ * Just as bacteria are revolutionising how we think about our relationship with the world, biologists are also discovering some remarkable things about trees and forests that are upending how we think about plants.

See, for instance, ‘Cosmological deixis and Amerindian perspectivism,’ Journal of the Royal Anthropological Institute, 1998. 8 Hannah Rundle, ‘Indigenous knowledge can help solve the biodiversity crisis,’ Scientific American, 2019. 9 For more on Spinoza’s naturalism, see Hasana Sharp, Spinoza and the Politics of Renaturalization (University of Chicago Press, 2011). 10 David Abram, The Spell of the Sensuous: Perception and Language in a More-Than-Human World (Vintage, 2012). 11 This research is reported by Carl Zimmer, ‘Germs in your gut are talking to your brain. Scientists want to know what they’re saying,’ New York Times, 2019. 12 Jane Foster and Karen-Anne McVey Neufeld, ‘Gut–brain axis: how the microbiome influences anxiety and depression,’ Trends in Neurosciences 36(5), 2013, pp. 305–312 13 John Dupré and Stephan Guttinger, ‘Viruses as living processes,’ Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 59, 2016, p. 109–116. 14 Ron Sender, Shai Fuchs and Ron Milo, ‘Revised estimates for the number of human and bacteria cells in the body,’ PLoS Biology 14(8). 15 John Dupré, ‘Metaphysics of metamorphosis,’ Aeon, 2017. 16 Robert Macfarlane, ‘Secrets of the wood wide web,’ New Yorker, 2016. 17 Brandon Keim, ‘Never underestimate the intelligence of trees,’ Nautilus, 2019.


pages: 488 words: 148,340

Aurora by Kim Stanley Robinson

back-to-the-land, cognitive bias, cognitive dissonance, dark matter, epigenetics, gravity well, mandelbrot fractal, microbiome, orbital mechanics / astrodynamics, traveling salesman, Turing test

Some pathogens had to be tolerated, others had to be killed, if possible; but any attempt to kill bacteria meant that resistant surviving strains of that species would become more dominant and more resistant, in the usual way of things at the micro levels of life, or at all levels of life perhaps. Dangerous to try to kill things, Freya reminded them. She knew full well, with a sinking sense that she was remembering her earliest memories, that Devi had believed that trying to kill any invasive species usually created more problems than it solved. A destabilized microbiome often caused more harm than anything a balanced microbiome could inflict. Better, therefore, to try to balance things with the least amount of intrusion. Subtle touches, all designed to finesse things for balance. Balance was the crucial thing. Teeter-totters, gently teeter-tottering up and down. Devi had even been an advocate of everyone getting an inoculation of helmiths, meaning ringworms, to give them better resistance to such parasites later.

The outstanding questions often had to do with what they called the Universal Minimum Metabolic Rate, the slowest viable speed of a metabolism, which was nearly constant across all Terran creatures, from bacteria to blue whales. A downshift in any species’s metabolism almost certainly could not go below this universal minimum rate; on the other hand, that rate was very slow. So the theoretical possibility seemed to exist to put humans and their internal microbiomes into a very slow state, which would last for a long time without ill effects. It would involve a slowed heartbeat (bradycardia); peripheral vasoconstriction; greatly slowed respiration; very low core temperature, buffered by antifreeze drugs; biochemical retardations; biochemical infusion drips; antibacterials; occasional removal of accumulated wastes; and physical shifts and manipulations, small enough not to rouse the organism too much, but nevertheless very important.


Growth: From Microorganisms to Megacities by Vaclav Smil

2013 Report for America's Infrastructure - American Society of Civil Engineers - 19 March 2013, 3D printing, agricultural Revolution, air freight, American Society of Civil Engineers: Report Card, autonomous vehicles, Benoit Mandelbrot, Berlin Wall, Bernie Madoff, Bretton Woods, British Empire, business cycle, colonial rule, complexity theory, coronavirus, decarbonisation, deindustrialization, dematerialisation, demographic dividend, demographic transition, Deng Xiaoping, disruptive innovation, Dissolution of the Soviet Union, endogenous growth, energy transition, epigenetics, happiness index / gross national happiness, hydraulic fracturing, hydrogen economy, Hyperloop, illegal immigration, income inequality, income per capita, industrial robot, Intergovernmental Panel on Climate Change (IPCC), invention of movable type, Isaac Newton, James Watt: steam engine, knowledge economy, labor-force participation, Law of Accelerating Returns, longitudinal study, mandelbrot fractal, market bubble, mass immigration, McMansion, megacity, megastructure, meta analysis, meta-analysis, microbiome, moral hazard, Network effects, new economy, New Urbanism, old age dependency ratio, optical character recognition, out of africa, peak oil, Pearl River Delta, phenotype, Pierre-Simon Laplace, planetary scale, Ponzi scheme, Productivity paradox, profit motive, purchasing power parity, random walk, Ray Kurzweil, Report Card for America’s Infrastructure, Republic of Letters, rolodex, Silicon Valley, Simon Kuznets, South China Sea, technoutopianism, the market place, The Rise and Fall of American Growth, total factor productivity, trade liberalization, trade route, urban sprawl, Vilfredo Pareto, yield curve

The biosphere’s most numerous, oldest and simplest organisms are archaea and bacteria. These are prokaryotic organisms without a cell nucleus and without such specialized membrane-enclosed organelles as mitochondria. Most of them are microscopic but many species have much larger cells and some can form astonishingly large assemblages. Depending on the species involved and on the setting, the rapid growth of single-celled organisms may be highly desirable (a healthy human microbiome is as essential for our survival as any key body organ) or lethal. Risks arise from such diverse phenomena as the eruptions and diffusion of pathogens—be they infectious diseases affecting humans or animals, or viral, bacterial and fungal infestations of plants—or from runaway growth of marine algae. These algal blooms can kill other biota by releasing toxins, or when their eventual decay deprives shallow waters of their normal oxygen content and when anaerobic bacteria thriving in such waters release high concentrations of hydrogen sulfide (UNESCO 2016).

American milk consumption was stable during the first half of the 20th century and steadily declined afterwards, while Dutch consumption was increasing until the 1960s and, despite its subsequent decline, is still above the US level; Dutch males, smaller than Americans before WWII, surpassed their American peers after 1950. There may be other important explanatory variables. Perhaps most intriguingly, Beard and Blaser (2002) have suggested that the human microbial environment played a substantial role in determining the increase of average human height during the 20th century. Its change has included both exogenous and indigenous biota (now the much-researched human microbiome), and particularly microbial transmission of Helicobacter pylori in childhood. The recent slowdown of this secular increase (especially among better-off population groups) indicates that we have become increasingly specific pathogen-free. We do not have as much historical information on changing body weights as we do on growth in height. Skeletal studies of hominins and early humans yielded two general, and opposite, trends, while the modern, and virtually universal, body mass trend is obvious even without any studies.

In terms of macroscopic components, complex machines are easily as “species-rich” as complex ecosystems: the average Toyota car has 30,000 parts, Boeing 737 (the smallest plane of the 700 series) has about 400,000 parts (excluding wiring, bolts, and rivets), the new Boeing 787 has 2.3 million, and Boeing 747–8 has 6 million parts (Boeing 2013). Of course, the functioning of living systems (be they rain forests or human bodies) depends on assemblages of microbial species (microbiomes), and the numbers of bacteria, archaea, and microscopic fungi in a unit mass of forest will be vastly larger than the total of the smallest functional components in a unit mass of even the most complicated machine. And, obviously, there can be no true comparison between biomass, the mass of living (and, in wood, dead) cells that form the bodies of organisms, and the mass of metals, composite materials, plastics, and glass that form the bodies of complex machines.


pages: 416 words: 106,582

This Will Make You Smarter: 150 New Scientific Concepts to Improve Your Thinking by John Brockman

23andMe, Albert Einstein, Alfred Russel Wallace, banking crisis, Barry Marshall: ulcers, Benoit Mandelbrot, Berlin Wall, biofilm, Black Swan, butterfly effect, Cass Sunstein, cloud computing, congestion charging, correlation does not imply causation, Daniel Kahneman / Amos Tversky, dark matter, data acquisition, David Brooks, delayed gratification, Emanuel Derman, epigenetics, Exxon Valdez, Flash crash, Flynn Effect, hive mind, impulse control, information retrieval, Intergovernmental Panel on Climate Change (IPCC), Isaac Newton, Jaron Lanier, Johannes Kepler, John von Neumann, Kevin Kelly, lifelogging, mandelbrot fractal, market design, Mars Rover, Marshall McLuhan, microbiome, Murray Gell-Mann, Nicholas Carr, open economy, Pierre-Simon Laplace, place-making, placebo effect, pre–internet, QWERTY keyboard, random walk, randomized controlled trial, rent control, Richard Feynman, Richard Feynman: Challenger O-ring, Richard Thaler, Satyajit Das, Schrödinger's Cat, security theater, selection bias, Silicon Valley, Stanford marshmallow experiment, stem cell, Steve Jobs, Steven Pinker, Stewart Brand, the scientific method, Thorstein Veblen, Turing complete, Turing machine, twin studies, Vilfredo Pareto, Walter Mischel, Whole Earth Catalog, WikiLeaks, zero-sum game

In one-fifth of a teaspoon of seawater, there are a million bacteria (and 10 million viruses), Craig Venter says, adding, “If you don’t like bacteria, you’re on the wrong planet. This is the planet of the bacteria.” That means that most of the planet’s living metabolism is microbial. When James Lovelock was trying to figure out where the gases come from that make the Earth’s atmosphere such an artifact of life (the Gaia hypothesis), it was microbiologist Lynn Margulis who had the answer for him. Microbes run our atmosphere. They also run much of our body. The human microbiome in our gut, mouth, skin, and elsewhere, harbors three thousand kinds of bacteria with 3 million distinct genes. (Our own cells struggle by on only eighteen thousand genes or so.) New research is showing that our microbes-on-board drive our immune systems and important parts of our digestion. Microbial evolution, which has been going on for more than 3.6 billion years, is profoundly different from what we think of as standard Darwinian evolution, where genes have to pass down generations to work slowly through the selection filter.

Recent advances in the life and physical sciences have made possible new and even unexpected expansions of this concept. The map of the human genome and of the diploid genomes of individuals; the map of our geographic spread; the map of the Neanderthal genome—these are new tools to address the age-old issues of human unity and diversity. Reading the life code of DNA does not stop there; it places humans in the vast and colorful mosaic of earthly life. “Otherness” is seen in a new light. Our microbiomes—the trillions of microbes on and in each of us, and essential to our physiology, become part of our selves. Astronomy and space science are intensifying the search for life on other planets—from Mars and the outer reaches of the solar system to Earth-like planets and super-Earths orbiting other stars. The chances of success may hinge on our understanding of the possible diversity of the chemical basis of life itself: “otherness” not among DNA-encoded species but among life-forms using different molecules to encode traits.


pages: 271 words: 52,814

Blockchain: Blueprint for a New Economy by Melanie Swan

23andMe, Airbnb, altcoin, Amazon Web Services, asset allocation, banking crisis, basic income, bioinformatics, bitcoin, blockchain, capital controls, cellular automata, central bank independence, clean water, cloud computing, collaborative editing, Conway's Game of Life, crowdsourcing, cryptocurrency, disintermediation, Edward Snowden, en.wikipedia.org, Ethereum, ethereum blockchain, fault tolerance, fiat currency, financial innovation, Firefox, friendly AI, Hernando de Soto, intangible asset, Internet Archive, Internet of things, Khan Academy, Kickstarter, lifelogging, litecoin, Lyft, M-Pesa, microbiome, Network effects, new economy, peer-to-peer, peer-to-peer lending, peer-to-peer model, personalized medicine, post scarcity, prediction markets, QR code, ride hailing / ride sharing, Satoshi Nakamoto, Search for Extraterrestrial Intelligence, SETI@home, sharing economy, Skype, smart cities, smart contracts, smart grid, software as a service, technological singularity, Turing complete, uber lyft, unbanked and underbanked, underbanked, web application, WikiLeaks

Blockchain technology, in the form of a universal model for record keeping and data storage and access (a secure, decentralized, pseudonymous file structure for data stored and accessed in the cloud) could be the technology that is needed to move into the next phase of industrialized genomic sequencing. This applies to genomic sequencing generally as an endeavor, irrespective of the personal data rights access issue. Sequencing all humans is just one dimension of sequencing demand; there is also the sequencing of all plants, animals, crops, viruses, bacteria, disease-strain pathogens, microbiomes, cancer genomes, proteomes, and so on, to name a few use cases. There is a scale production and efficiency argument for blockchain-based transnational genomic services. To move to large-scale sequencing as a “universal human society,” the scope and scale of sequencing and corresponding information processing workloads suggests not just transnationality, but more important, heavy integration with the cloud (genomic data is too big for current forms of local storage and manipulation), and the blockchain delivers both transnationality and the cloud.


pages: 561 words: 157,589

WTF?: What's the Future and Why It's Up to Us by Tim O'Reilly

4chan, Affordable Care Act / Obamacare, Airbnb, Alvin Roth, Amazon Mechanical Turk, Amazon Web Services, artificial general intelligence, augmented reality, autonomous vehicles, barriers to entry, basic income, Bernie Madoff, Bernie Sanders, Bill Joy: nanobots, bitcoin, blockchain, Bretton Woods, Brewster Kahle, British Empire, business process, call centre, Capital in the Twenty-First Century by Thomas Piketty, Captain Sullenberger Hudson, Chuck Templeton: OpenTable:, Clayton Christensen, clean water, cloud computing, cognitive dissonance, collateralized debt obligation, commoditize, computer vision, corporate governance, corporate raider, creative destruction, crowdsourcing, Danny Hillis, data acquisition, deskilling, DevOps, Donald Davies, Donald Trump, Elon Musk, en.wikipedia.org, Erik Brynjolfsson, Filter Bubble, Firefox, Flash crash, full employment, future of work, George Akerlof, gig economy, glass ceiling, Google Glasses, Gordon Gekko, gravity well, greed is good, Guido van Rossum, High speed trading, hiring and firing, Home mortgage interest deduction, Hyperloop, income inequality, index fund, informal economy, information asymmetry, Internet Archive, Internet of things, invention of movable type, invisible hand, iterative process, Jaron Lanier, Jeff Bezos, jitney, job automation, job satisfaction, John Maynard Keynes: Economic Possibilities for our Grandchildren, John Maynard Keynes: technological unemployment, Kevin Kelly, Khan Academy, Kickstarter, knowledge worker, Kodak vs Instagram, Lao Tzu, Larry Wall, Lean Startup, Leonard Kleinrock, Lyft, Marc Andreessen, Mark Zuckerberg, market fundamentalism, Marshall McLuhan, McMansion, microbiome, microservices, minimum viable product, mortgage tax deduction, move fast and break things, move fast and break things, Network effects, new economy, Nicholas Carr, obamacare, Oculus Rift, packet switching, PageRank, pattern recognition, Paul Buchheit, peer-to-peer, peer-to-peer model, Ponzi scheme, race to the bottom, Ralph Nader, randomized controlled trial, RFC: Request For Comment, Richard Feynman, Richard Stallman, ride hailing / ride sharing, Robert Gordon, Robert Metcalfe, Ronald Coase, Sam Altman, school choice, Second Machine Age, secular stagnation, self-driving car, SETI@home, shareholder value, Silicon Valley, Silicon Valley startup, skunkworks, Skype, smart contracts, Snapchat, Social Responsibility of Business Is to Increase Its Profits, social web, software as a service, software patent, spectrum auction, speech recognition, Stephen Hawking, Steve Ballmer, Steve Jobs, Steven Levy, Stewart Brand, strong AI, TaskRabbit, telepresence, the built environment, The Future of Employment, the map is not the territory, The Nature of the Firm, The Rise and Fall of American Growth, The Wealth of Nations by Adam Smith, Thomas Davenport, transaction costs, transcontinental railway, transportation-network company, Travis Kalanick, trickle-down economics, Uber and Lyft, Uber for X, uber lyft, ubercab, universal basic income, US Airways Flight 1549, VA Linux, Watson beat the top human players on Jeopardy!, We are the 99%, web application, Whole Earth Catalog, winner-take-all economy, women in the workforce, Y Combinator, yellow journalism, zero-sum game, Zipcar

Even if we never achieve artificial general intelligence or artificial superintelligence, though, I believe that there is a third form of AI, which I call hybrid artificial intelligence, in which much of the near-term risk resides. When we imagine an artificial intelligence, we assume it will have an individual self, an individual consciousness, just like us. What if, instead, an AI was more like a multicellular organism, an evolution beyond our single-celled selves? What’s more, what if we were not even the cells of such an organism, but its microbiome, the vast ecology of microorganisms that inhabits our bodies? This notion is at best a metaphor, but I believe it is a useful one. As the Internet speeds up the connection between human minds, as our collective knowledge, memory, and sensations are shared and stored in digital form, we are weaving a new kind of technology-mediated superorganism, a global brain consisting of all connected humans.

Digital services like Google, Facebook, and Twitter that connect hundreds of millions or even billions of people in near-real time are already primitive hybrid AIs. The fact that the intelligence of these systems is interdependent with the intelligence of the community of humans that makes it up is an echo of the way that we ourselves function. Each of us is a vast nation of trillions of differentiated cells, only some of which share our own DNA, while far more are immigrants, the vast microbiome of microorganisms that colonize our guts, our skin, our circulatory systems. There are far more microorganisms in our bodies than there are human cells, not invaders but a functioning part of the whole. Without the microorganisms we host, we could not digest our food or turn it into useful energy. The bacteria in our guts have even been shown to change how we think and how we feel. A multicellular organism is the sum of the communications, the ecosystem, the platform or marketplace if you will, of all its participants.


pages: 240 words: 65,363

Think Like a Freak by Steven D. Levitt, Stephen J. Dubner

Albert Einstein, Anton Chekhov, autonomous vehicles, Barry Marshall: ulcers, call centre, Cass Sunstein, colonial rule, Edward Glaeser, Everything should be made as simple as possible, food miles, Gary Taubes, income inequality, Internet Archive, Isaac Newton, medical residency, Metcalfe’s law, microbiome, prediction markets, randomized controlled trial, Richard Thaler, Scramble for Africa, self-driving car, Silicon Valley, Tony Hsieh, transatlantic slave trade, éminence grise

Brandt, “Fecal Microbiota Transplantation: Past, Present and Future,” Current Opinion in Gastroenterology 29, no. 1 (January 2013); “Jonathan Eisen: Meet Your Microbes,” TEDMED Talk, Washington, D.C., April 2012; Borody and Khoruts, “Fecal Microbiota Transplantation and Emerging Applications,” Nature Reviews Gastroenterology & Hepatology 9, no. 2 (2011); Khoruts et al., “Changes in the Composition of the Human Fecal Microbiome After Bacteriotherapy for Recurrent Clostridium Difficile–Associated Diarrhea,” Journal of Clinical Gastroenterology 44, no. 5 (May/June 2010); Borody et al., “Bacteriotherapy Using Fecal Flora: Toying with Human Motions,” Journal of Clinical Gastroenterology 38, no. 6 (July 2004). / 85 Looks like chocolate milk: That is according to Josbert Keller, a gastroenterologist at the HagaZiekenhuis hospital in the Hague, an author of “Duodenal Infusion of Donor Feces for Recurrent Clostridium difficile,” New England Journal of Medicine 368 (2013):407–415; see also Denise Grady, “When Pills Fail, This, er, Option Provides a Cure,” New York Times, January 16, 2013. / 85 Colitis “previously an incurable disease”: See Borody and Jordana Campbell, “Fecal Microbiota Transplantation: Techniques, Applications, and Issues,” Gastroenterology Clinics of North America 41 (2012); and Borody, Eloise F.


pages: 1,007 words: 181,911

The 4-Hour Chef: The Simple Path to Cooking Like a Pro, Learning Anything, and Living the Good Life by Timothy Ferriss

Airbnb, Atul Gawande, Buckminster Fuller, Burning Man, correlation does not imply causation, crowdsourcing, deliberate practice, en.wikipedia.org, Golden Gate Park, happiness index / gross national happiness, haute cuisine, Hugh Fearnley-Whittingstall, Isaac Newton, Johann Wolfgang von Goethe, Kevin Kelly, Kickstarter, Loma Prieta earthquake, loss aversion, Louis Pasteur, Mahatma Gandhi, Marc Andreessen, Mark Zuckerberg, Mason jar, microbiome, Parkinson's law, Paul Buchheit, Paul Graham, Pepto Bismol, Ponzi scheme, Ralph Waldo Emerson, Silicon Valley, Skype, spaced repetition, Stephen Hawking, Steve Jobs, the High Line, Y Combinator

Unlike most store-bought sauerkraut, which is pasteurized and devoid of bacteria (unless the label says “raw” or “naturally fermented” and is found in the refrigerated section), our homemade version will be loaded with, for lack of a better term, “good” bacteria.11 There are an estimated 10 times more bacterial cells in your body than human cells: 100 trillion of them to 10 trillion of you. These 100 trillion stowaways have been nicknamed the “microbiome.” The two primary strains of bacteria so far identified that influence fat absorption are Bacteroidetes and Firmicutes. Lean people have more Bacteroidetes and fewer Firmicutes; obese people have more Firmicutes and fewer Bacteroidetes. As obese people lose weight, the ratio of bacteria in their guts shifts to favor Bacteroidetes. Given that a strong cycle of antibiotics can leave your microbiome off-kilter for up to four years, I view sauerkraut as a smart investment in immune function and fat-burning capabilities. Forthwith fermentation 101—how you create food by taking the path of least resistance.


Blueprint: The Evolutionary Origins of a Good Society by Nicholas A. Christakis

agricultural Revolution, Alfred Russel Wallace, Amazon Mechanical Turk, assortative mating, Cass Sunstein, crowdsourcing, David Attenborough, different worldview, disruptive innovation, double helix, epigenetics, experimental economics, experimental subject, invention of agriculture, invention of gunpowder, invention of writing, iterative process, job satisfaction, Joi Ito, joint-stock company, land tenure, Laplace demon, longitudinal study, Mahatma Gandhi, Marc Andreessen, means of production, mental accounting, meta analysis, meta-analysis, microbiome, out of africa, phenotype, Pierre-Simon Laplace, placebo effect, race to the bottom, Ralph Waldo Emerson, replication crisis, Rubik’s Cube, Silicon Valley, social intelligence, social web, stem cell, Steven Pinker, the scientific method, theory of mind, twin studies, ultimatum game, zero-sum game

Nowadays, he spends most of his time in the Human Nature Lab, where his team explores a broad set of ideas, including understanding the evolutionary, genetic, and physiological bases of friendship; encouraging villages in the developing world to adopt new public health practices (working in locations in Honduras, India, and Uganda); mapping social networks in settings around the world; arranging people into online groups so that they behave better (such as being more cooperative and more truthful); developing artificial intelligence that helps humans address challenges in collective action; exploring the effect of social interactions on the human microbiome; and more. When he is not in the lab, he teaches at Yale University. Also by Nicholas A. Christakis Connected: The Surprising Power of Our Social Networks and How They Shape Our Lives Death Foretold: Prophecy and Prognosis in Medical Care Resounding Praise for Blueprint “The diversity of our cultures and personal identities masks the fact that we are one. In this brilliant, beautiful, and sweeping book, Christakis shows how eight universal human tendencies have bound us together and given us dominion over our planet, our lives, and our common fate.

., “Three-Dimensional Visualization and a Deep-Learning Model Reveal Complex Fungal Parasite Networks in Behaviorally Manipulated Ants,” PNAS: Proceedings of the National Academy of Sciences 114 (2017): 12590–12595. 28. D. P. Hughes, T. Wappler, and C. C. Labandeira, “Ancient Death-Grip Leaf Scars Reveal Ant-Fungal Parasitism,” Biology Letters 7 (2011): 67–70. 29. T. R. Sampson and S. K. Mazmanian, “Control of Brain Development, Function, and Behavior by the Microbiome,” Cell Host and Microbe 17 (2015): 565–576. 30. A. D. Blackwell et al., “Helminth Infection, Fecundity, and Age of First Pregnancy in Women,” Science 350 (2015): 970–972. 31. A. Y. Panchin, A. I. Tuzhikov, and Y. V. Panchin, “Midichlorians—the Biomeme Hypothesis: Is There a Microbial Component to Religious Rituals?,” Biology Direct 9 (2014): 14. See also S. K. Johnson et al., “Risky Business: Linking Toxoplasma gondii Infection and Entrepreneurship Behaviours Across Individuals and Countries,” Proceedings of the Royal Society B 285 (2018): 20180822. 32.


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Whiplash: How to Survive Our Faster Future by Joi Ito, Jeff Howe

3D printing, Albert Michelson, Amazon Web Services, artificial general intelligence, basic income, Bernie Sanders, bitcoin, Black Swan, blockchain, Burning Man, buy low sell high, Claude Shannon: information theory, cloud computing, Computer Numeric Control, conceptual framework, crowdsourcing, cryptocurrency, data acquisition, disruptive innovation, Donald Trump, double helix, Edward Snowden, Elon Musk, Ferguson, Missouri, fiat currency, financial innovation, Flash crash, frictionless, game design, Gerolamo Cardano, informal economy, interchangeable parts, Internet Archive, Internet of things, Isaac Newton, Jeff Bezos, John Harrison: Longitude, Joi Ito, Khan Academy, Kickstarter, Mark Zuckerberg, microbiome, Nate Silver, Network effects, neurotypical, Oculus Rift, pattern recognition, peer-to-peer, pirate software, pre–internet, prisoner's dilemma, Productivity paradox, race to the bottom, RAND corporation, random walk, Ray Kurzweil, Ronald Coase, Ross Ulbricht, Satoshi Nakamoto, self-driving car, SETI@home, side project, Silicon Valley, Silicon Valley startup, Simon Singh, Singularitarianism, Skype, slashdot, smart contracts, Steve Ballmer, Steve Jobs, Steven Levy, Stewart Brand, Stuxnet, supply-chain management, technological singularity, technoutopianism, The Nature of the Firm, the scientific method, The Signal and the Noise by Nate Silver, There's no reason for any individual to have a computer in his home - Ken Olsen, Thomas Kuhn: the structure of scientific revolutions, universal basic income, unpaid internship, uranium enrichment, urban planning, WikiLeaks

Casey, “Linked-In, Sun Microsystems Founders Lead Big Bet on Bitcoin Innovation,” Moneybeat blog, Wall Street Journal, November 17, 2014, http://blogs.wsj.com/moneybeat/2014/11/17/linked-in-sun-microsystems-founders-lead-big-bet-on-bitcoin-innovation/. 46 “Enabling Blockchain Innovations with Pegged Sidechains,” r/Bitcoin, Reddit, http://www.reddit.com/r/Bitcoin/comments/2k070h/enabling_blockchain_innovations_with_pegged/clhak9c. 47 Timothy Leary, “The Cyber-Punk: The Individual as Reality Pilot,” Mississippi Review 16, no. 2/3 (1988). 48 T.F. Peterson, Nightwork (Cambridge, MA.: The MIT Press, 2011), https://mitpress.mit.edu/books/nightwork. 49 While the science on the human microbiome, which includes gut bacteria, is still evolving, there’s intriguing evidence that our bacteria have a strong influence not only on our health, but also on our behavior. See, for example, Charles Schmidt, “Mental Health: Thinking from the Gut,” Nature 518, no. 7540 (February 26, 2015): S12–15, doi:10.1038/518S13a.; Peter Andrey Smith, “Can the Bacteria in Your Gut Explain Your Mood?,” The New York Times, June 23, 2015, http://www.nytimes.com/2015/06/28/magazine/can-the-bacteria-in-your-gut-explain-your-mood.html.; and David Kohn, “When Gut Bacteria Changes Brain Function,” The Atlantic, June 24, 2015, http://www.theatlantic.com/health/archive/2015/06/gut-bacteria-on-the-brain/395918/.


The End of Pain: How Nutrition and Diet Can Fight Chronic Inflammatory Disease by Jacqueline Lagace

longitudinal study, meta analysis, meta-analysis, microbiome, phenotype, placebo effect, randomized controlled trial, stem cell

Hyper-permeability of intestinal mucosa Studies have shown that a person’s tendency to develop type 1 diabetes or another autoimmune disease is usually linked to an abnormally permeable intestinal barrier,31 which is due to the alteration of tight junctions located between the intestinal mucosa’s epithelial cells.32 The increased permeability of the intestinal mucosa leaves the intestinal immune system more exposed to foreign antigens,33 which in turn encourages the development of type 1 diabetes. 5 8 > t h e e n d o f pa i n Intestinal immunity The third element that plays a key role in the development of type 1 diabetes is intestinal immunity. We know that 80 percent of immune cells reside within the intestinal wall. A well-balanced microbiome (intestinal flora) favors the development and the activation of a normal immune system. For example, the immune systems of children who are born by natural means and breastfed are better able to protect them from autoimmune diseases and allergies. Biopsies on children with type 1 diabetes show an abnormal activation in the system of cytokines in the lamina propria, the site where immune cells reside below the intestinal epithelium.34 In individuals suffering from type 1 diabetes, there have been more reports of an aberrant response to food, which is shown in an increased immune response towards wheat and cow’s milk, which can favor inflammation of the intestines.35 This type of reaction is based on the same general principles described above for the abnormal immune response to α-gliadin in celiac disease.


pages: 345 words: 84,847

The Runaway Species: How Human Creativity Remakes the World by David Eagleman, Anthony Brandt

active measures, Ada Lovelace, agricultural Revolution, Albert Einstein, Andrew Wiles, Burning Man, cloud computing, computer age, creative destruction, crowdsourcing, Dava Sobel, delayed gratification, Donald Trump, Douglas Hofstadter, en.wikipedia.org, Frank Gehry, Google Glasses, haute couture, informal economy, interchangeable parts, Isaac Newton, James Dyson, John Harrison: Longitude, John Markoff, lone genius, longitudinal study, Menlo Park, microbiome, Netflix Prize, new economy, New Journalism, pets.com, QWERTY keyboard, Ray Kurzweil, reversible computing, Richard Feynman, risk tolerance, self-driving car, Simon Singh, stem cell, Stephen Hawking, Steve Jobs, Stewart Brand, the scientific method, Watson beat the top human players on Jeopardy!, wikimedia commons, X Prize

Thanks to neural plasticity, the brain learns to interpret the sonic world from the patterns felt on the skin. But the Vest doesn’t stop there: it can also be used to feed data about the state of a plane to pilots, the state of the International Space Station to astronauts, the state of an artificial leg to amputees, the invisible states of a person’s health (such as blood pressure and the health of one’s microbiome), or the machinations of a factory. It can hook directly to the internet to feed Twitter or stock-market data to the user in real time. It can be used to sense robots at a distance, including, one day, on the moon. The Vest can also feed in new data streams such as infrared or ultraviolet. Which of these uses will find matches in the market? Who knows. But David and Scott’s company is busy exploring a wide field of options.


pages: 306 words: 82,765

Skin in the Game: Hidden Asymmetries in Daily Life by Nassim Nicholas Taleb

availability heuristic, Benoit Mandelbrot, Bernie Madoff, Black Swan, Brownian motion, Capital in the Twenty-First Century by Thomas Piketty, Cass Sunstein, cellular automata, Claude Shannon: information theory, cognitive dissonance, complexity theory, David Graeber, disintermediation, Donald Trump, Edward Thorp, equity premium, financial independence, information asymmetry, invisible hand, knowledge economy, loss aversion, mandelbrot fractal, mental accounting, microbiome, moral hazard, Murray Gell-Mann, offshore financial centre, p-value, Paul Samuelson, Ponzi scheme, price mechanism, principal–agent problem, Ralph Nader, random walk, rent-seeking, Richard Feynman, Richard Thaler, Ronald Coase, Ronald Reagan, Rory Sutherland, Silicon Valley, Steven Pinker, stochastic process, survivorship bias, The Nature of the Firm, transaction costs, urban planning, Yogi Berra

Second, there was no proper risk study, and the statistical methods in the papers in support of the argument were flawed. Third, we invoked the principle of simplicity, which was called antiscience. Why don’t we give these people rice and vitamins separately? After all, we don’t have genetically modified coffee that has milk with it. Fourth, we were able to show that GMOs brought a bevy of hidden risk to the environment, because of the higher use of pesticide, which kills the microbiome (that is, the bacteria and other life in the soil). I realized soon after that, owing to the minority rule, there was no point continuing. As I said in Book 3, GMOs lost simply because a minority of intelligent and intransigent people stood against them. THE COMPENSATION Simply, the minute one is judged by others rather than by reality, things become warped as follows. Firms that haven’t gone bankrupt yet have something called personnel departments.


pages: 289 words: 87,292

The Strange Order of Things: The Biological Roots of Culture by Antonio Damasio

Albert Einstein, biofilm, business process, Daniel Kahneman / Amos Tversky, double helix, Gordon Gekko, invention of the wheel, invention of writing, invisible hand, job automation, mental accounting, meta analysis, meta-analysis, microbiome, Norbert Wiener, pattern recognition, Peter Singer: altruism, planetary scale, profit motive, Ray Kurzweil, Richard Feynman, self-driving car, Silicon Valley, Steven Pinker, Thomas Malthus

Wall, “Cross-Excitation in Dorsal Root Ganglia of Nerve-Injured and Intact Rats,” Journal of Neurophysiology 64, no. 6 (1990): 1733–46; Eva Sykova, “Glia and Volume Transmission During Physiological and Pathological States,” Journal of Neural Transmission 112, no. 1 (2005): 137–47. 25. Emeran Mayer, The Mind-Gut Connection: How the Hidden Conversation Within Our Bodies Impacts Our Mood, Our Choices, and Our Overall Health (New York: HarperCollins, 2016). 26. Jane A. Foster and Karen-Anne McVey Neufeld, “Gut-Brain Axis: How the Microbiome Influences Anxiety and Depression,” Trends in Neurosciences 36, no. 5 (2013): 305–12; Mark Lyte and John F. Cryan, eds., Microbial Endocrinology: The Microbiota-Gut-Brain Axis in Health and Disease (New York: Springer, 2014); Mayer, Mind-Gut Connection. 27. Doe-Young Kim and Michael Camilleri, “Serotonin: A Mediator of the Brain-Gut Connection,” American Journal of Gastroenterology 95, no. 10 (2000): 2698. 28.


The Buddha and the Badass: The Secret Spiritual Art of Succeeding at Work by Vishen Lakhiani

Buckminster Fuller, Burning Man, call centre, Colonization of Mars, crowdsourcing, deliberate practice, Elon Musk, fundamental attribution error, future of work, Google Glasses, Google X / Alphabet X, iterative process, Jeff Bezos, meta analysis, meta-analysis, microbiome, performance metric, Peter Thiel, profit motive, Ralph Waldo Emerson, Silicon Valley, Silicon Valley startup, skunkworks, Skype, Steve Jobs, Steven Levy, web application, white picket fence

When I was part of the Innovation Board for the XPRIZE Foundation, I got to know many of America’s foremost visionaries and billionaires—from Peter Diamandis to Anousheh Ansari to Naveen Jain. Here is what they drilled into me: The BIGGER the vision, the EASIER it gets. Let me explain how Naveen Jain trained me on this. Naveen has founded multiple billion-dollar companies. And when we met first met, he had just created Viome, the gut microbiome testing company that is revolutionizing medicine. While scaling Viome to a $500 million valuation in two years he was also selected to receive $2.7 BILLION from NASA to send robots to the moon via Moon Express, another one of his companies. His prior company Infospace was first to realize the power of mobile phones and achieved market cap of over $35 billion. This is not a guy with small dreams.


A Crack in Creation: Gene Editing and the Unthinkable Power to Control Evolution by Jennifer A. Doudna, Samuel H. Sternberg

3D printing, Asilomar, Asilomar Conference on Recombinant DNA, carbon footprint, Chuck Templeton: OpenTable:, double helix, Drosophila, Mark Zuckerberg, microbiome, mouse model, phenotype, Ralph Waldo Emerson, Richard Feynman, Silicon Valley, Skype, stem cell, Steven Pinker

These risks were reflected in a recent report authored by the National Academies of Sciences, Engineering, and Medicine, which endorsed ongoing research and limited field trials but stopped short of recommending that gene drives be released into the environment. There’s also no way to guarantee that this incredibly powerful tool won’t wind up in the hands of people who have no compunction about using gene drives to cause harm—and who may, indeed, be attracted to them for exactly that purpose. The ETC Group, a biotech watchdog organization, worries that gene drives—what they call “gene bombs”—could be militarized and weaponized to target the human microbiome or major food sources. But as frightening as gene drives could be, we might find it impossible to justify keeping them locked away in the lab. As Austin Burt wrote, “Clearly, the technology described here is not to be used lightly. Given the suffering caused by some species, neither is it obviously one to be ignored.” Gene drives could help us address global problems in agriculture, conservation, and human health in a far more targeted way than previous approaches have allowed.


Grain Brain: The Surprising Truth About Wheat, Carbs, and Sugar--Your Brain's Silent Killers by David Perlmutter, Kristin Loberg

epigenetics, Gary Taubes, Kickstarter, longitudinal study, meta analysis, meta-analysis, microbiome, mouse model, phenotype, publication bias, Ralph Waldo Emerson, selective serotonin reuptake inhibitor (SSRI), stem cell

., “Ingestion of Lactobacillus Strain Regulates Emotional Behavior and Central GABA Receptor Expression in a Mouse Via the Vagus Nerve,” Proceedings of the National Academy of Sciences 108, no. 138 (September 20, 2011): 16050–55. 10. A. C. Bested, et al., “Intestinal Microbiota, Probiotics and Mental Health: From Metchnikoff to Modern Advances: Part I—Autointoxication Revisited,” Gut Pathogens 5, no. 1 (March 18, 2013): 5. See also Parts II and III of the same report. 11. J. F. Cryan and S. M. O’Mahony, “The Microbiome-Gut-Brain Axis: From Bowel to Behavior,” Neurogastroenterology and Motility 23, no. 3 (March 2011): 187–92. 12. Michael Gershon, MD, The Second Brain: The Scientific Basis of Gut Instinct and a Groundbreaking New Understanding of Nervous Disorders of the Stomach and Intestines (New York: Harper, 1998). 13. For more about the brain-gut connection, check out the work of Dr. Emeran Mayer, MD, director of the University of California Los Angeles’s Center for Neurobiology of Stress.


pages: 368 words: 96,825

Bold: How to Go Big, Create Wealth and Impact the World by Peter H. Diamandis, Steven Kotler

3D printing, additive manufacturing, Airbnb, Amazon Mechanical Turk, Amazon Web Services, augmented reality, autonomous vehicles, Charles Lindbergh, cloud computing, creative destruction, crowdsourcing, Daniel Kahneman / Amos Tversky, dematerialisation, deskilling, disruptive innovation, Elon Musk, en.wikipedia.org, Exxon Valdez, fear of failure, Firefox, Galaxy Zoo, Google Glasses, Google Hangouts, gravity well, ImageNet competition, industrial robot, Internet of things, Jeff Bezos, John Harrison: Longitude, John Markoff, Jono Bacon, Just-in-time delivery, Kickstarter, Kodak vs Instagram, Law of Accelerating Returns, Lean Startup, life extension, loss aversion, Louis Pasteur, low earth orbit, Mahatma Gandhi, Marc Andreessen, Mark Zuckerberg, Mars Rover, meta analysis, meta-analysis, microbiome, minimum viable product, move fast and break things, Narrative Science, Netflix Prize, Network effects, Oculus Rift, optical character recognition, packet switching, PageRank, pattern recognition, performance metric, Peter H. Diamandis: Planetary Resources, Peter Thiel, pre–internet, Ray Kurzweil, recommendation engine, Richard Feynman, ride hailing / ride sharing, risk tolerance, rolodex, self-driving car, sentiment analysis, shareholder value, Silicon Valley, Silicon Valley startup, skunkworks, Skype, smart grid, stem cell, Stephen Hawking, Steve Jobs, Steven Levy, Stewart Brand, superconnector, technoutopianism, telepresence, telepresence robot, Turing test, urban renewal, web application, X Prize, Y Combinator, zero-sum game

Right now your toothpaste is mostly chalk and flavoring, but with synthetic biology, it can be specifically designed to fight your breed of bad breath microbes. “That’s not all,” continues Hessel. “It can have tooth-polishing nanoparticles designed to continue cleaning long after you’ve stopped brushing. It can be designed to detect infection or cancer or diabetes, turning different colors in the presence of each, or to release custom-designed probiotics that balance your microbiome. It can do all of these things. And that’s just the first thing you do in the morning.” To many, synthetic biology still sounds like science fiction, but what is transforming it into science fact is the same force driving all the other exponential technologies—Moore’s law. Because DNA is nothing more than a four-letter code, when genetics went digital, it was transformed into an information science and thus hopped on the exponential expressway.


pages: 334 words: 100,201

Origin Story: A Big History of Everything by David Christian

Albert Einstein, Arthur Eddington, butterfly effect, Capital in the Twenty-First Century by Thomas Piketty, Cepheid variable, colonial rule, Colonization of Mars, Columbian Exchange, complexity theory, cosmic microwave background, cosmological constant, creative destruction, cuban missile crisis, dark matter, demographic transition, double helix, Edward Lorenz: Chaos theory, Ernest Rutherford, European colonialism, Francisco Pizarro, Haber-Bosch Process, Harvard Computers: women astronomers, Isaac Newton, James Watt: steam engine, John Maynard Keynes: Economic Possibilities for our Grandchildren, Joseph Schumpeter, Kickstarter, Marshall McLuhan, microbiome, nuclear winter, planetary scale, rising living standards, Search for Extraterrestrial Intelligence, Stephen Hawking, Steven Pinker, The Wealth of Nations by Adam Smith, Thomas Kuhn: the structure of scientific revolutions, trade route, Yogi Berra

Prokaryotes trade genes as we humans trade stocks and shares, which is why the idea of a distinct species is harder to define in the prokaryotic world than in our world. Today, prokaryotes still dominate the biosphere. On and within your body, there are probably more prokaryotic cells than cells with your own DNA. But we ignore them (until they give us a stomachache or cold) because they are so much smaller than our own cells. This vast shadow world that we share with prokaryotes is known as the microbiome. Until recently, it was tempting to think that the history of single-celled organisms was boring, so we could happily skip the first three billion years of the biosphere’s history. Today we are learning that we can’t make sense of the biosphere’s recent history without understanding the much longer era of little life. As they evolved, prokaryotes developed many new tricks that let them exploit different environments, and we still use several of the biochemical techniques they pioneered.


pages: 321 words: 97,661

How to Read a Paper: The Basics of Evidence-Based Medicine by Trisha Greenhalgh

call centre, complexity theory, conceptual framework, correlation coefficient, correlation does not imply causation, deskilling, knowledge worker, longitudinal study, meta analysis, meta-analysis, microbiome, New Journalism, p-value, personalized medicine, placebo effect, publication bias, randomized controlled trial, selection bias, the scientific method

But the withdrawal rate from the trial was high, partly because when participants found a medication that worked, they just wanted to keep taking it rather than swap to the alternative! But despite its conceptual elegance and a distant promise of linking to the ‘personalised medicine’ paradigm in which every patient will have their tests and treatment options individualised to their particular genome, physiome, microbiome, and so on, the n of 1 trial has not caught on widely in either research or clinical practice. A review article by Lillie and colleagues [27] suggests why. Such trials are labour intensive to carry out, requiring a high degree of individual personalisation and large amounts of data for every participant. ‘Washout’ periods raise practical and ethical problems (does one have to endure one's arthritis with no pain relief for several weeks to serve the scientific endeavour?).


pages: 945 words: 292,893

Seveneves by Neal Stephenson

clean water, Colonization of Mars, Danny Hillis, digital map, double helix, epigenetics, fault tolerance, Fellow of the Royal Society, Filipino sailors, gravity well, Isaac Newton, Jeff Bezos, kremlinology, Kuiper Belt, low earth orbit, microbiome, orbital mechanics / astrodynamics, phenotype, Potemkin village, pre–internet, random walk, remote working, selection bias, side project, Silicon Valley, Skype, statistical model, Stewart Brand, supervolcano, the scientific method, Tunguska event, zero day, éminence grise

“Do we even need to bother watching how this goes?” Bard asked. And then he looked to Ty to give the answer. It had not been a rhetorical question. He was awaiting orders. Beled Tomov looked at him too. “How is she?” Ty asked. “Pulse, respiration okay?” “I think it is the usual,” Beled said with a nod. Meaning that abrupt hormone shifts in Kath’s system were giving her something akin to morning sickness. Her microbiome—the ecosystem of bacteria that lived in her gut and on her skin—had been thrown into disarray, and she was being colonized by any old germs, including ones from the Diggers that had never been exposed to a Moiran body. “Can you put her on your back or something?” Beled nodded and dropped to one knee. He had been carrying a pack on his back. He emptied its contents on the ground and began slashing leg holes in its bottom corners so that Kath could just be inserted into it, like an infant into a carrier.

“She saw Doc and Memmie die, and suffered a blunt- force trauma to her arm, and was forced to draw her kat, and to use it. As soon as it happened she went into what I’m guessing is a classic POTESH.” This was military jargon for post-traumatic epigenetic shift. “That is confirmed,” said Hope, who seemed to have finished an initial scan of Kath’s vital signs. “Higher metabolism and hyperacute senses are observable. Her microbiome is a mess; I’m tuning it up with probiotic supplements that’ll be a better fit with her new phenotype. Suggested by the nausea are big hormone shifts. Possibly predictive of some future . . .” “Testosterone poisoning?” Ty suggested, finishing Hope’s thought. Hope responded with a diffident nod of the head. Ty turned his attention back to Arjun. “So three billion people just learned that the Diggers exist.


pages: 453 words: 130,632

Nine Pints: A Journey Through the Money, Medicine, and Mysteries of Blood by Rose George

Affordable Care Act / Obamacare, air freight, airport security, British Empire, call centre, corporate social responsibility, Edward Snowden, global pandemic, Ignaz Semmelweis: hand washing, index card, Jeff Bezos, meta analysis, meta-analysis, microbiome, Nelson Mandela, obamacare, period drama, Peter Thiel, Rana Plaza, RAND corporation, Silicon Valley, Skype, stem cell

Estrogen taken vaginally can produce blood serum levels ten times higher than with an oral dose.31 The vaginal walls are also loaded with tiny blood vessels, and the vagina is almost anaerobic. All this adds up to a perfect set of conditions for bacteria to thrive and this is desirable: of the thirty-nine trillion bacteria we’re now thought to carry (or perhaps they carry us), most are harmless.32 Even Staphylococcus aureus lives in the vaginas of 8–14 percent of women without causing harm.33 Our vaginal microbiome is useful and protective. But when certain conditions prevail, toxic strains of staph can flourish, particularly the toxic strain TSST-1, which in 1978 was first linked to what the pediatrician James Todd named “toxic shock syndrome” (TSS) after encountering a disturbingly virulent chain of infection in seven young children.34 I remember TSS, along with the punishing drought of 1976 and Duran Duran, as having a starring role during my teen years, because I knew it meant I should be scared of tampons.


pages: 473 words: 154,182

Moby-Duck: The True Story of 28,800 Bath Toys Lost at Sea and of the Beachcombers, Oceanographers, Environmentalists, and Fools, Including the Author, Who Went in Search of Them by Donovan Hohn

carbon footprint, clean water, collective bargaining, dark matter, Deng Xiaoping, Exxon Valdez, Filipino sailors, Google Earth, illegal immigration, indoor plumbing, intermodal, Isaac Newton, means of production, microbiome, Panamax, Pearl River Delta, post-Panamax, profit motive, Skype, standardized shipping container, statistical model, Thorstein Veblen, traveling salesman

When he boarded the Louis in Resolute, he’d brought with him, in addition to Erin Freeland-Ballantyne, a number of supernumeraries whom he referred to as VIPs—luminaries of oceanography, all dressed, like him, in matching fleece cardigan vests onto which was embroidered the logo of this expedition—the C30 project, Carmack had called it, for Canada’s Three Oceans. His idea for the second leg of our voyage was to turn the Louis into a kind of icebreaking, traveling oceanographic lyceum. During the lectures the VIPs delivered, I learned many interesting facts—for instance, that in the “microbiome” of the human body, only a portion of our cells, genetically speaking, are human in origin. The rest are bacterial. (While learning this, I found myself looking down, examining my midriff, into which, in the main mess, I’d recently deposited some potatoes, carrots, and buttery cod. The cloth between the buttons of my quick-dry adventure shirt was puckering over the waistband of my quick-dry adventure pants in an unflattering way, and I tried to smooth the puckers flat.)


pages: 471 words: 147,210

Children of Ruin by Adrian Tchaikovsky

experimental subject, gravity well, Kickstarter, longitudinal study, microbiome, pattern recognition, post scarcity, remote working, side project, telepresence, theory of mind

He sends the drone over the plateau’s edge, looking down on a vast expanse of red desert, disfigured by technicolour lakes like violent acne where some life or inorganic process stains the water angry rainbow colours. He sees stretches of mottling where some lifeform turns its darkness to drink the waning sunlight, and other regions of brown and rust-orange and even green, actual green, that tell of other life – little microbiomes around a meagre resource that lets some alien thing claw life out of the interior of the hot, dusty planet’s single continent. He sees another city. It is ten times larger than the mere hamlet near their crash site; another grid, or perhaps an expansion, a larger map that contains within it a copy of the smaller. The same city: ruined, false. Fabian sends the drone further, watching its battery indicator tumble but unable not to satisfy his curiosity and feed his fear.


pages: 855 words: 178,507

The Information: A History, a Theory, a Flood by James Gleick

Ada Lovelace, Alan Turing: On Computable Numbers, with an Application to the Entscheidungsproblem, Albert Einstein, AltaVista, bank run, bioinformatics, Brownian motion, butterfly effect, citation needed, Claude Shannon: information theory, clockwork universe, computer age, conceptual framework, crowdsourcing, death of newspapers, discovery of DNA, Donald Knuth, double helix, Douglas Hofstadter, en.wikipedia.org, Eratosthenes, Fellow of the Royal Society, Gödel, Escher, Bach, Henri Poincaré, Honoré de Balzac, index card, informal economy, information retrieval, invention of the printing press, invention of writing, Isaac Newton, Jacquard loom, Jaron Lanier, jimmy wales, Johannes Kepler, John von Neumann, Joseph-Marie Jacquard, lifelogging, Louis Daguerre, Marshall McLuhan, Menlo Park, microbiome, Milgram experiment, Network effects, New Journalism, Norbert Wiener, Norman Macrae, On the Economy of Machinery and Manufactures, PageRank, pattern recognition, phenotype, Pierre-Simon Laplace, pre–internet, Ralph Waldo Emerson, RAND corporation, reversible computing, Richard Feynman, Rubik’s Cube, Simon Singh, Socratic dialogue, Stephen Hawking, Steven Pinker, stochastic process, talking drums, the High Line, The Wisdom of Crowds, transcontinental railway, Turing machine, Turing test, women in the workforce

Of course, it acts and moves and procreates as a unit, and furthermore, in the case of at least one species, it feels itself, with impressive certainty, to be a unit. The gene-centered perspective has helped biologists appreciate that the genes composing the human genome are only a fraction of the genes carried around in any one person, because humans (like other species) host an entire ecosystem of microbes—bacteria, especially, from our skin to our digestive systems. Our “microbiomes” help us digest food and fight disease, all the while evolving fast and flexibly in service of their own interests. All these genes engage in a grand process of mutual co-evolution—competing with one another, and with their alternative alleles, in nature’s vast gene pool, but no longer competing on their own. Their success or failure comes through interaction. “Selection favors those genes which succeed in the presence of other genes,” says Dawkins, “which in turn succeed in the presence of them.”♦ The effect of any one gene depends on these interactions with the ensemble and depends, too, on effects of the environment and on raw chance.


pages: 600 words: 174,620

The Body Keeps the Score: Brain, Mind, and Body in the Healing of Trauma by Bessel van Der Kolk M. D.

anesthesia awareness, British Empire, conceptual framework, deskilling, different worldview, en.wikipedia.org, epigenetics, false memory syndrome, feminist movement, impulse control, longitudinal study, Louis Pasteur, meta analysis, meta-analysis, microbiome, Nelson Mandela, phenotype, placebo effect, profit motive, randomized controlled trial, selective serotonin reuptake inhibitor (SSRI), social intelligence, theory of mind, Yogi Berra

In 2010 Thomas Insel, director of the National Institute of Mental Health, published an article in Scientific American entitled “Faulty Circuits,” in which he called for a return to understanding mind and brain in terms of the rhythms and patterns of electrical communication: “Brain regions that function together to carry out normal (and abnormal) mental operations can be thought of as analogous to electrical circuits—the latest research shows that the malfunctioning of entire circuits may underlie many mental disorders.”34 Three years later Insel announced that NIMH was “re-orienting its research away from DSM categories”35 and focusing instead on “disorders of the human connectome.”36 As explained by Francis Collins, director of the National Institutes of Health (of which NIMH is a part), “The connectome refers to the exquisitely interconnected network of neurons (nerve cells) in your brain. Like the genome, the microbiome, and other exciting ‘ome’ fields, the effort to map the connectome and decipher the electrical signals that zap through it to generate your thoughts, feelings, and behaviors has become possible through development of powerful new tools and technologies.”37 The connectome is now being mapped in detail under the auspices of NIMH. As we await the results of this research, I’d like to give the last word to Lisa, the survivor who introduced me to the enormous potential of neurofeedback.


pages: 651 words: 180,162

Antifragile: Things That Gain From Disorder by Nassim Nicholas Taleb

Air France Flight 447, Andrei Shleifer, banking crisis, Benoit Mandelbrot, Berlin Wall, Black Swan, business cycle, Chuck Templeton: OpenTable:, commoditize, creative destruction, credit crunch, Daniel Kahneman / Amos Tversky, David Ricardo: comparative advantage, discrete time, double entry bookkeeping, Emanuel Derman, epigenetics, financial independence, Flash crash, Gary Taubes, George Santayana, Gini coefficient, Henri Poincaré, high net worth, hygiene hypothesis, Ignaz Semmelweis: hand washing, informal economy, invention of the wheel, invisible hand, Isaac Newton, James Hargreaves, Jane Jacobs, joint-stock company, joint-stock limited liability company, Joseph Schumpeter, Kenneth Arrow, knowledge economy, Lao Tzu, Long Term Capital Management, loss aversion, Louis Pasteur, mandelbrot fractal, Marc Andreessen, meta analysis, meta-analysis, microbiome, money market fund, moral hazard, mouse model, Myron Scholes, Norbert Wiener, pattern recognition, Paul Samuelson, placebo effect, Ponzi scheme, principal–agent problem, purchasing power parity, quantitative trading / quantitative finance, Ralph Nader, random walk, Ray Kurzweil, rent control, Republic of Letters, Ronald Reagan, Rory Sutherland, selection bias, Silicon Valley, six sigma, spinning jenny, statistical model, Steve Jobs, Steven Pinker, Stewart Brand, stochastic process, stochastic volatility, Thales and the olive presses, Thales of Miletus, The Great Moderation, the new new thing, The Wealth of Nations by Adam Smith, Thomas Bayes, Thomas Malthus, too big to fail, transaction costs, urban planning, Vilfredo Pareto, Yogi Berra, Zipf's Law

Psychology Press. Gray, John, 2002, Straw Dogs: Thoughts on Humans and Other Animals. London: Granta Books. Gray, John, 2011, The Immortalization Commission: Science and the Strange Quest to Cheat Death. Allen Lane. Greenwood, R., and R. Suddaby, 2006, “The Case of Disappearing Firms: Death or Deliverance?” Journal of Organizational Behavior 27(1): 101–108. Grice, E. A., and J. A. Segre, 2011, “The Skin Microbiome.” Nature Reviews Microbiology 9(4): 244–253. Griffith, S. C., I.P.F. Owens, and K. A. Thuman, 2002, “Extrapair Paternity in Birds: A Review of Interspecific Variation and Adaptive Function.” Molecular Ecology 11: 2195–212. Grob, Gerald N., 2002, The Deadly Truth: A History of Disease in America. Cambridge, Mass.: Harvard University Press. Guadalupe-Grau, A., T. Fuentes, B. Guerra, and J. Calbet, 2009, “Exercise and Bone Mass in Adults.”


Never Bet Against Occam: Mast Cell Activation Disease and the Modern Epidemics of Chronic Illness and Medical Complexity by Lawrence B. Afrin M. D., Kendra Neilsen Myles, Kristi Posival

Affordable Care Act / Obamacare, Albert Einstein, epigenetics, invisible hand, Isaac Newton, megacity, microbiome, mouse model, obamacare, pattern recognition, personalized medicine, phenotype, pre–internet, selective serotonin reuptake inhibitor (SSRI), stem cell

Typically caused by chronic oral infection, I’ve seen this as a symptom in some MCAS patients that “magically goes away” once the underlying problem (i.e., the MCAS) gets diagnosed and once effective (though, as usual, individualized) mast-cell-directed treatment is found. Get the underlying problem under control and then the immune system will start working better and get rid of chronic bacteria and fungi that shouldn’t be in our microbiome. Hashimoto's thyroiditis “Hash´-ih-moh´-tohz thy-roid-īt-is.” Hashimoto’s is an autoimmune disease in which the immune system attacks and largely destroys the thyroid gland (usually first by erroneously manufacturing an antibody against one part of the thyroid gland or another, and then the rest of the immune system follows the antibody’s lead and further attacks the gland), causing hypothyroidism.


pages: 693 words: 204,042

New York 2140 by Kim Stanley Robinson

availability heuristic, back-to-the-land, Black-Scholes formula, Burning Man, central bank independence, creative destruction, credit crunch, crowdsourcing, decarbonisation, East Village, full employment, happiness index / gross national happiness, hive mind, income inequality, invisible hand, Jane Jacobs, liquidity trap, Mason jar, mass immigration, megastructure, microbiome, music of the spheres, New Urbanism, offshore financial centre, plutocrats, Plutocrats, Ponzi scheme, precariat, quantitative easing, rent-seeking, the built environment, too big to fail

The hurricane had ripped off all the leaves, so the terraces and rooftops looked bare, and many a canal was still clogged with debris. But they were able to get through most of them, and city crews were out in force working on the cleanup. There was a dank vegetable jungly smell in the air, and many people on the water were wearing white face masks. Mr. Hexter snorted at this. “Little do they know they’re depriving themselves of needed nutrients and helpful microbiome teammates.” They found that the most common arboreal survivors of the wind’s onslaught had been potted trees, which had presumably been knocked on their sides and remained prone through the storm, and now only had to be lifted upright to restore some green to the scene. They looked battered but unbowed; they were like the city itself, Mr. Hexter declared. Up in the intertidal things were truly squalid.


pages: 993 words: 318,161

Fall; Or, Dodge in Hell by Neal Stephenson

Ada Lovelace, augmented reality, autonomous vehicles, back-to-the-land, bitcoin, blockchain, cloud computing, coherent worldview, computer vision, crossover SUV, cryptocurrency, defense in depth, demographic transition, distributed ledger, drone strike, easy for humans, difficult for computers, game design, index fund, Jaron Lanier, life extension, microbiome, Network effects, off grid, offshore financial centre, pattern recognition, planetary scale, ride hailing / ride sharing, sensible shoes, short selling, Silicon Valley, telepresence, telepresence robot, telerobotics, The Hackers Conference, Turing test, Works Progress Administration

Between the scientists from the Waterhouse/Forthrast camp and those who worked for El, there was vociferous agreement that the word “brain” needed to be banned from learned discourse, or put in scare quotes. They had to move beyond the practice of chopping off the heads of the deceased and throwing away the rest. Henceforward every client would be scanned in toto, heads to toes, and efforts would be made to collect data about their microbiome and any other non-neurological phenomena that would be overlooked by an ion-beam scanning system that only cared about neurons. “I beg your pardon,” C-plus said. “You have clients. Some of them are no longer among the living. You have been subjecting their remains to the most advanced protocols available.” “As have you.” “Of course.” “People die,” El said. “Some of them want what Richard Forthrast wanted.”