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The Diet Myth: The Real Science Behind What We Eat by Tim Spector
biofilm, British Empire, Colonization of Mars, cuban missile crisis, double helix, Drosophila, epigenetics, life extension, Mahatma Gandhi, meta analysis, meta-analysis, microbiome, phenotype, randomized controlled trial, Steve Jobs
Our normal microbes were just not used to the abundance of sugar, but one particular species, called Strep mutans, loved the new food and fed hungrily off the sugar around our teeth and gums and quickly multiplied. Unfortunately, unlike the other harmless microbes, they used the sugar to produce lactic acid which made little holes in our tooth enamel. The Strep mutans stuck to our teeth by attaching themselves to dental plaque. This substance so familiar to us is in fact a colony of six hundred species of harmless bacteria stuck together to form a sticky mucous commune (called a biofilm). Ingeniously they produce a glue-like substance from the sugar they metabolise, which allows them to keep feeding safely while they hang on. Ironically, people who use a daily mouthwash may be killing off their healthy microbes and allowing the harmful ones to take over, leading to even more gum and tooth disease.11 One small study suggested this habit also increases blood pressure and risk of heart disease.12 Even at the height of the cavity epidemic, around 15 to 20 per cent of children would be relatively untouched.
I knew from studies of antibiotic-treated patients and others who’d had colonoscopies that over 99 per cent are wiped out. Gritty survivors hang on in unusual places, and if, like me, you still have one, they can hide in the haven of the appendix – could this be its long-lost purpose, perhaps? They can also collect in the caecum, a corner of the colon that always contains some fluid, a smelly oasis in the desert. Microbes can lie low, too, in the tiny crevices of the intestinal wall, clinging on by forming biofilms with each other – although no one quite knows how they resist so well the tidal waves rushing through the bowel. The three-day prebiotic diet There are only a few reports following colonoscopy in humans, and the largest comprised fifteen patients. After a month, most recovered their previous microbial flora. However, three of them developed major changes for unknown reasons.14 Anecdotally, when I ask my Gastro colleagues they say that every now and again some patients with mild colitis or IBS do report a miraculous cure after the clear-out.
Olive oil intake and risk of cardiovascular disease and mortality in the PREDIMED Study. 11 Konstantinidou, V., FASEB J (Jul 2010); 24(7): 2546–57. In vivo nutrigenomic effects of virgin olive oil polyphenols within the frame of the Mediterranean diet: a randomized controlled trial. 12 Lanter, B.B., MBio (2014); 5(3): e01206–14. Bacteria present in carotid arterial plaques are found as biofilm deposits which may contribute to enhanced risk of plaque rupture. 13 Vallverdú-Queralt, A., Food Chem (15 Dec 2013); 141(4): 3365–72. Bioactive compounds present in the Mediterranean sofrito. 6 Trans Fats 1 https://www.youtube.com/watch?v=zrv78nG9R04 2 Lam, H.M., Lancet (8 Jun 2013); 381(9882): 2044–53. Food supply and food safety issues in China. 3 Mozaffarian, D., N Engl J Med (2006); 354: 1601–13.
Geek Wisdom by Stephen H. Segal
Ada Lovelace, Albert Einstein, Any sufficiently advanced technology is indistinguishable from magic, battle of ideas, biofilm, fear of failure, Henri Poincaré, Jacquard loom, Jacquard loom, Mark Zuckerberg, mutually assured destruction, Saturday Night Live, Vernor Vinge
And it’s alarming to see that the non-geek portions of the media have taken the same path; heck, the Jon Stewart/Stephen Colbert rally of 2010 was mostly an attempt to ask, “Can we please stop calling each other Hitler?” It would seem the answer is no. At least some geeks are fighting to take back the Hitler epithet in the name of good-spirited silliness. Thousands of YouTube videos have mashed up a scene in the Hitler bio-film Downfall with topics ranging from Xbox to Twilight. “I LOVE IT WHEN A PLAN COMES TOGETHER!” —JOHN “HANNIBAL” SMITH, THE A-TEAM HAN SOLO MAY HAVE SHOWN us the seat-of-your-pants thrill of improvising, but Hannibal Smith taught us there’s something to be said for taking the long view. And one thing you can’t accuse the jocular leader of the A-Team of is not taking the long view, with his daisy-chain schemas of elaborate disguises, car crashes, and lots of pyrotechnics making it all the sweeter when he deployed his trademark catchphrase as the payoff to a job well done.
Home Comforts: The Art and Science of Keeping House by Cheryl Mendelson
biofilm, Broken windows theory, clean water, deskilling, Ignaz Semmelweis: hand washing, Indoor air pollution, indoor plumbing, Jacquard loom, Jacquard loom, Own Your Own Home, sensible shoes, spice trade, Telecommunications Act of 1996, telemarketer
Microbes can fairly quickly—in as little as twenty minutes—attach themselves to kitchen and other household surfaces; other microbes can then attach themselves to these, forming layers twenty to thirty microbes thick. Embedded in these layers of microorganisms may be bacteria, yeasts, molds, algae, and food particles. The biofilm sticks tenaciously to even the slickest, hardest, least-porous surfaces, including glass and stainless steel. Worse, microorganisms embedded in biofilms are more resistant to sanitizers, and the longer they remain, the harder it is to kill them. Scrubbing—muscle power—helps remove a biofilm. When and Where. Sanitizers and disinfectants are useful outside the kitchen in the following ordinary household circumstances: • Regularly, on the toilet, inside and out, and on surfaces and floors near the toilet • Occasionally, in the tub and shower stall to prevent mildew as well as bacterial growth • In whirlpool baths and hot tubs, in accordance with manufacturers’ instructions • Frequently, in sink drains and connecting pipes • Wherever a musty odor appears (an indication of mold) • Regularly, in diaper pails or when washing diapers • Regularly, on changing tables (but see “Special Cautions for Homes with Infants,” below) • In damp basements • When children or pets have accidents • When cleaning pets’ cages and litter boxes (But be sure what you use is safe for the pet.
You may read recommendations to use stronger recipes. The USDA, however, says this recipe is effective. Stronger solutions might leave residues or cause unpleasant bleach smells. In other places in this book, such as chapter 30, different recipes are recommended for other purposes. Bacteria have been found to create an invisible, strongly adhering, slimy layer or film of cells, called a biofilm, on even hard and smooth surfaces such as stainless steel. Some research indicates that a biofilm is not easily removed with chemical means alone—for example, detergent or sanitizer—because the film prevents penetration by the chemical. Mechanical force, such as a stream of hard-running water or scrubbing, was found to be important in getting the film off. (“Microbial Attachment Similar for Wooden, Plastic Cutting Boards,” Food Chemical News, September 30, 1996.)
Murphy, 656 old-style, nostalgia for, 682 pillows, choosing, 684-86 snoring and, 658 turning down of, 668 waterbeds, 684 see also bedding; comforters; mattresses; pillows bedsheets: absorbency and, 678 all-combed-cotton percale, 675, 677, 678, 680, best fibers for, 676 bottom, fitted and flat, 665 changing of, how often, 662 colorfastness and, 679 colors and prints of, 676-77, 679 comfort of, factors affecting, 677-79 cotton/polyester blend, 677-78, 679, 680 crib, 678, 679 decorative stitching on, 676, 678-79 designer, 680 dry-cleaning fluid fumes and, 679 durability of, 675-77 Egyptian cotton, 675 fading of, 676 flannel, 678 folding of, 356 hand of, 677-78 knit, 678 launderability of, 679-80 laundering of, 661 linen (flax), 678, 680 mitered or “hospital” corners for, 665 muslin, 675, 679 no-iron, 680 percale, 675, 679 pilling of, 680 pima cotton, 675 plain-weave, 675 polyester, 678 prewashed percale, 678 removing stains from, 676 rubberized cotton waterproof, 664 sateen, 675 satin-weave, 675, 677 shrinkage and, 673, 679 silk, 677, 678 size, calculating, 674 standard measurements, 673 thread counts of, 675, 677 top, 665 twill, 675 “universal” or deep corners on, 673 untreated all-cotton, 680 warmest and coolest fabrics for, 678 warmth and, 678 weave and weight of, 675 whites vs. colors and prints, 676-77 wrinkle-resistant all-cotton percale, 678 wrinkle-treated, 679 wrinkly, 680 see also bedding; beds; mattresses; pillows bedsores, 683 bedspreads, 664, 666, 674 Beecher, Catharine, 13 beetles, 160 carpet, 688 powderpost, 496 beetling, 225, 234 benzene, 403, 404, 405, 416 benzopyrene, 415 benzoyl peroxide, 372 Bettelheim, Bruno, 595-97 Better Business Bureau, 771, 794 beverages, 70-87 alcoholic, 82-87 bidets, 531-32 biofilm, 174, 427 bird’s eye fabric, 199 birth certificates, 828, 836 blankets: acrylic, 680-81 cotton, 680 electric, 681, 725 folding of, 356 functional qualities of, 680-81 laundering of, 358-59, 661, 667-68 in making the bed, 665 nylon, 680 polyester, 680-81 sizes of, 674-75 weaves of, 197 wool, 681 “blanket tents,” for elderly, 670 bleach, 316-19 on acetate fabrics, 256 on acrylic fabrics, 260 on colored fabrics, 299 instructions on care labels, 281, 283-84, 286-87 on polyester fabrics, 259 on rayon fabrics, 255 on white laundry, 297-98 on wool fabrics, 247 see also bleach, chlorine; bleach, oxygen; hydrogen peroxide bleach, chlorine, 228, 258, 277, 282, 306, 307, 312-13, 318-19, 360, 373, 376-77, 421, 509, 649 bleach, chlorine (cont.)
Asperger Syndrome, Barry Marshall: ulcers, Berlin Wall, biofilm, clean water, correlation does not imply causation, discovery of penicillin, Drosophila, Fall of the Berlin Wall, friendly fire, germ theory of disease, Ignaz Semmelweis: hand washing, illegal immigration, John Snow's cholera map, Louis Pasteur, Maui Hawaii, meta analysis, meta-analysis, microbiome, phenotype, placebo effect, the scientific method
The appendix, which averages about 8 cm in length and a centimetre across, forms a tube, protected from the flow of mostly digested food passing its entrance. But rather than being a withered strand of flesh, it is packed full of specialised immune cells and molecules. They are not inert, but rather an integral part of the immune system, protecting, cultivating and communicating with a collective of microbes. Inside, these microbes form a ‘biofilm’ – a layer of individuals that support one another and exclude bacteria that might cause harm. The appendix, far from being functionless, appears to be a safe-house that the human body has provided for its microbial inhabitants. Like a nest egg stashed away for a rainy day, this microbial stockpile comes in handy at times of strife. After an episode of food poisoning or a gastrointestinal infection, the gut can be repopulated with its normal inhabitants, which have been lurking in the appendix.
I include just a handful of references for the most important and interesting of the studies I have written about in 10% Human, as well as some more general suggestions of general reading about this burgeoning field. Introduction 1. International Human Genome Sequencing Consortium (2004). Finishing the euchromatic sequence of the human genome. Nature 431: 931–945. 2. Nyholm, S.V. and McFall-Ngai, M.J. (2004). The winnowing: Establishing the squid–Vibrio symbiosis. Nature Reviews Microbiology 2: 632–642. 3. Bollinger, R.R. et al. (2007). Biofilms in the large bowel suggest an apparent function of the human vermiform appendix. Journal of Theoretical Biology 249: 826–831. 4. Short, A.R. (1947). The causation of appendicitis. British Journal of Surgery 53: 221–223. 5. Barker, D.J.P. (1985). Acute appendicitis and dietary fibre: an alternative hypothesis. British Medical Journal 290: 1125–1127. 6. Barker, D.J.P. et al. (1988). Acute appendicitis and bathrooms in three samples of British children.
Cooked: A Natural History of Transformation by Michael Pollan
biofilm, bioinformatics, Columbian Exchange, correlation does not imply causation, dematerialisation, Drosophila, energy security, Gary Taubes, Hernando de Soto, Louis Pasteur, Mason jar, microbiome, peak oil, Ralph Waldo Emerson, Steven Pinker, women in the workforce
And they were willing, with a shrug and a rueful smile, to throw out a bad batch every now and then. The phrase “live-culture foods” is of course a euphemism: for fermented foods teeming with living bacteria and fungi. “Live-culture” sounds a lot more appetizing than, say, “bacteria” for breakfast, in the same way that calling a cheese “washed rind” goes down more easily than “coated with a biofilm of bacteria and mold,” which is what a washed-rind cheese is. Enjoying my “live-culture” pickles and kimchi, I gave some thought to the billions of microbes I was ingesting along with the vegetables, wondering what in the world they might be doing down there. But somewhere deep in the coils of my intestines one community of microbes was presumably encountering another. I hoped for the best.
Easy to clean and disinfect, stainless steel is the Pasteurian’s material of choice. Once scrubbed, its perfectly smooth, machine-tooled surface gleams, offering an objective correlative of good hygiene. Wood on the other hand bears all the imperfections of a natural material, with grooves and nicks and pocks where bacteria can easily hide. And indeed the inside of Sister Noëlla’s cheese-making barrel wears a permanent cloak of white—a biofilm of milk solids and bacteria. You could not completely sterilize it if you tried, and part of the recipe for Saint-Nectaire involves not trying: Lydie told Noëlla that between batches the barrel should only be lightly rinsed with water. So it happened that in 1985, after raw-milk cheese was implicated in the deaths of twenty-nine people in California, the state health inspector demanded that Sister Noëlla get rid of her wooden barrel and replace it with stainless steel.
Between 1998 and 2006, produce grown in Florida sickened over fourteen hundred consumers. Salmonella is of particular concern. Birds, reptiles, and infected fieldworkers are all vectors for salmonella, which can stay alive in the fields and irrigation water for months. The bacteria can get inside the fruits, where it is safe from external attempts to wash it away, through roots, flowers, cuts in stems, and breaks in the fruits’ skin. Salmonella can also encase itself in a biofilm, a natural protective sheath it creates for itself on the exterior of tomatoes, rendering washing ineffective and allowing the bacteria to survive packing, storing, and shipping. Once they had completed the circuit through the chlorination trough, Procacci’s tomatoes boarded an escalator, which took them out of the bath water and up toward an opening into the warehouse. Inside, the clatter of machinery was so loud that the verbal component of Procacci’s tour was reduced to gesticulations, mime, and the occasional shouted phrase.
Whole Earth Discipline: An Ecopragmatist Manifesto by Stewart Brand
agricultural Revolution, 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, invention of agriculture, invention of the steam engine, Jane Jacobs, jimmy wales, Kevin Kelly, Kibera, land tenure, M-Pesa, Marshall McLuhan, megacity, microbiome, New Urbanism, out of africa, Paul Graham, peak oil, 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, Whole Earth Catalog, Whole Earth Review, working-age population, Y2K
It’s a transgenic world. • Thanks to horizontal gene transfer, microbes have developed astounding skills. Tiny as they are, microbes can learn. (E. coli anticipate and prepare for the sequence of environments they face in our intestines during digestion.) Microbes do complex quorum sensing, both within species and between species—they are in that sense multicellular. (In order to coordinate group benefits such as biofilm structure and toxin release, they signal each other through chemical autoinducers.) They make rain on purpose. (Some bacteria have a surface protein that binds water molecules into raindrops and snow; when they get stuck in the air, this characteristic gets them back down to the ground. The total of such behavior is Gaian, a global feedback between life and the atmosphere.) They can survive for hundreds of millions of years inside rock and ice.
A Declaration of the Independence of Cyberspace, Albert Einstein, AltaVista, Amazon Mechanical Turk, Asperger Syndrome, availability heuristic, Benoit Mandelbrot, biofilm, Black Swan, British Empire, conceptual framework, corporate governance, Danny Hillis, Douglas Engelbart, Emanuel Derman, epigenetics, Flynn Effect, Frank Gehry, Google Earth, hive mind, Howard Rheingold, index card, information retrieval, Internet Archive, invention of writing, Jane Jacobs, Jaron Lanier, Kevin Kelly, lone genius, loss aversion, mandelbrot fractal, Marshall McLuhan, Menlo Park, meta analysis, meta-analysis, New Journalism, Nicholas Carr, out of africa, Ponzi scheme, pre–internet, Richard Feynman, Richard Feynman, Rodney Brooks, Ronald Reagan, Schrödinger's Cat, Search for Extraterrestrial Intelligence, SETI@home, Silicon Valley, Skype, slashdot, smart grid, social graph, social software, social web, Stephen Hawking, Steve Wozniak, Steven Pinker, Stewart Brand, Ted Nelson, telepresence, the medium is the message, the scientific method, The Wealth of Nations by Adam Smith, theory of mind, trade route, upwardly mobile, Vernor Vinge, Whole Earth Catalog, X Prize
So much quicker than random trial-and-error evolution, and it works . . . right now! And your children’s always-on community of friends, texting lols and other quick messages that really say “I’m here, I’m your friend, let’s have a party,” is no different than the quorum sensing of microbes, counting their numbers so that they can do something collectively, such as invade a host or grow a fruiting body from a biofilm. I’m starting to think like the Internet, starting to think like biology. My thinking is better, faster, cheaper, and more evolvable because of the Internet. And so is yours. You just don’t know it yet. The Internet Makes Me Think in the Present Tense Douglas Rushkoff Media analyst; documentary writer; author, Life, Inc.: How the World Became a Corporation and How to Take It Back How does the Internet change the way I think?
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, Isaac Newton, Jaron Lanier, John von Neumann, Kevin Kelly, mandelbrot fractal, market design, Mars Rover, Marshall McLuhan, microbiome, Murray Gell-Mann, Nicholas Carr, open economy, place-making, placebo effect, pre–internet, QWERTY keyboard, random walk, randomized controlled trial, rent control, Richard Feynman, Richard Feynman, Richard Feynman: Challenger O-ring, Richard Thaler, Schrödinger's Cat, security theater, Silicon Valley, stem cell, Steve Jobs, Steven Pinker, Stewart Brand, the scientific method, Thorstein Veblen, Turing complete, Turing machine, Walter Mischel, Whole Earth Catalog
Social Darwinism turned out to be a bankrupt idea. The term “cultural evolution” never meant much, because the fluidity of memes and influences in society bears no relation to the turgid conservatism of standard Darwinian evolution. But “social microbialism” might mean something as we continue to explore the fluidity of traits and the vast ingenuity of mechanisms among microbes—quorum sensing, biofilms, metabolic bucket brigades, “lifestyle genes,” and the like. Confronting a difficult problem, we might fruitfully ask, “What would a microbe do?” The Double-Blind Control Experiment Richard Dawkins Evolutionary zoologist, University of Oxford; author, The Greatest Show on Earth: The Evidence for Evolution Not all concepts wielded by professional scientists would improve everybody’s cognitive toolkit.
Loneliness: Human Nature and the Need for Social Connection by John T. Cacioppo
Alfred Russel Wallace, biofilm, butterfly effect, Celebration, Florida, corporate governance, delayed gratification, experimental subject, impulse control, income inequality, Jane Jacobs, mental accounting, meta analysis, meta-analysis, placebo effect, post-industrial society, Rodney Brooks, Ted Kaczynski, The Death and Life of Great American Cities, theory of mind, urban planning, urban renewal, Walter Mischel
But individual organisms also coordinate with one another, as do aggregations of organisms, and on and on up the ladder to greater and greater levels of complexity, from beehives to book clubs. The molecular biologists Ned Wingreen and Simon Levin argue that the term “single-celled,” even when applied to the amoeba, the classic creature studied by kids with microscopes, may be a misnomer. Even the lowly bacteria that cover our teeth form biofilms that are actually large interspecies collectives that provide benefit to us while taking care of their own. Similarly, four different species of bacteria live on the roots of tomato plants, working in coordinated fashion as they fix nitrogen, promote growth hormones, and fight off competitors. Again, there is no social contract—there is not even a coordinating intelligence—and yet these organisms have found a way to benefit from social connection and cooperation.
Safe Food: The Politics of Food Safety by Marion Nestle
The packing plant used state-of-the-art washing procedures under a HACCP plan. Investigations revealed only minor procedural flaws. Although this was the twentieth E. coli O157:H7 outbreak from leafy greens in recent years, nobody seemed to have come to grips with how firmly these bacteria adhere to leaf surfaces. They can be incorporated into lettuce or spinach leaves just under the surface and form tightly adhering biofilms.20 Although the spinach was marketed as conventional, industrial growers immediately blamed the outbreak on manure-based fertilizers used in organic production. In October 2006, I wrote an opinion piece for the San Jose Mercury News listing the obvious lessons taught by the outbreak—prevention is essential, voluntary never works, industrial agriculture has its down side—among them, “don’t blame organics this time.”21 A vegetable grower in California soon set me straight.