biofilm

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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

The standard American diet of FODMAP carbohydrates allows opportunistic bacteria to thrive, infect the small intestine, and produce excess gas. Bacteria also produce protective biofilms (one of the most common examples of a biofilm is the “film” on your teeth that appears when you do not brush your teeth after a while) which make eradication with antibiotics very difficult. The biofilm protects the opportunistic bacteria from antibiotic treatment, bactericides, and probiotics. To eliminate the opportunistic bacteria you also have to disrupt the biofilm that protects the bacteria. Biofilm disruption can occur by either breaking down the biofilm itself using systemic enzymes or by chelating the iron out of the biofilm to dissolve it. To chelate the iron you can use either calcium disodium EDTA, lactoferrin, or NAC. The main symptoms of a SIBO infection are indigestion, a sharp increase or decrease in flatulence, constipation or diarrhea, reflux, and bloating.

Atrantil – follow supplement bottle recommendations. Anti-BioFilm Protocol: PREFERRED: Symbiotics lactoferrin - follow supplement bottle recommendations (can increase up to two grams daily if needed). OR CHOOSE ONE OF THE FOLLOWING FROM ANTI-BIOFILM AGENTS INSTEAD OF TAKING LACTOFERRIN Calcium Disodium EDTA: MRM Cardio Chelate – follow general supplement recommendations. Fulvic Acid: Food Grade fulvic acid – follow general supplement recommendations. Guaifenesin: Guai-aid – take one capsule every four to eight hours. Do not exceed four capsules daily. Guaifenesin is a systemic biofilm chelator; I do not recommend it as a first-line anti-biofilm agent in a protocol. NAC: Jarrow Formulas NAC Sustain – one tablet twice daily. NAC is a systemic biofilm chelator; I do not recommend it as a first-line anti-biofilm agent in a protocol.

Use with caution if you have hypoglycemia. Anti-BioFilm Protocol: PREFERRED: Symbiotics lactoferrin - follow supplement bottle recommendations (can increase up to two grams daily if needed). OR CHOOSE ONE OF THE FOLLOWING FROM ANTI-BIOFILM AGENTS INSTEAD OF TAKING LACTOFERRIN Calcium Disodium EDTA: MRM Cardio Chelate – follow general supplement recommendations. Fulvic Acid: Food Grade fulvic acid – follow general supplement recommendations. Guaifenesin: Guai-aid – take one capsule every four to eight hours. Do not exceed four capsules daily. Guaifenesin is a systemic biofilm chelator; I do not recommend it as a first-line anti-biofilm agent in a protocol. NAC: Jarrow Formulas NAC Sustain – one tablet twice daily. NAC is a systemic biofilm chelator; I do not recommend it as a first-line anti-biofilm agent in a protocol.


Genesis: The Deep Origin of Societies by Edward O. Wilson

biofilm, out of africa, phenotype, social intelligence

What the bacteria are able to read by chemical communication is the condition and density of the population to which they belong. With this information, the individual bacterium “decides” the rapidity of its movement, the rate of its reproduction, and, in the case of pathogenic species, even the virulence of its impact on the host in which it lives. In some incidents bacteria choose to form stable groups shielded by protective membranes and crusts, structures called biofilms. Bacteria have thus been found to be social to a degree almost unimaginable to scientists a generation ago. But of course the microbes are also mindless. Whether a persistent group of any kind of organism can evolve further than the microbial depends on the complexity of the individuals that compose it. Consider a pod of bottlenose dolphins feeding on a school of anchovies. The small fish that serve as prey enjoy the same advantages of group membership as do starlings.

Hölldobler, B., and E. O. Wilson. The Ants (Cambridge, MA: Belknap Press of Harvard University Press). Hunt, J. H. 2011. A conceptual model for the origin of worker behaviour and adaptation of eusociality. Journal of Evolutionary Biology 25: 1–19. Liu, J., R. Martinez-Corral, A. Prindle, D.-Y. D. Lee, J. Larkin, M. Gabalda-Sagarra, J. Garcia-Ojalvo, and G. M. Süel. 2017. Coupling between distant biofilms and emergence of nutrient time-sharing. Science 356(6338): 638–642. Michener, C. D. 1958. The evolution of social life in bees. Proceedings of the Tenth International Congress of Entomology 2: 441–447. Nalepa, C. A. 2015. Origin of termite eusociality: Trophallaxis integrates the social, nutritional, and microbial environment. Ecological Entomology 40(4): 323–335. Pruitt, J. N. 2012. Behavioural traits of colony founders affect the life history of their colonies.

Nest inheritance is the missing source of direct fitness in a primitively eusocial insect. Science 333(6044): 874–876. LeBlanc, S. A., and K. E. Register. 2003. Constant Battles: The Myth of the Peaceful, Noble Savage (New York: St. Martin’s Press). Liu, J., R. Martinez-Corral, A. Prindle, D.-Y. D. Lee, J. Larkin, M. Gabalda-Sagarra, J. Garcia-Ojalvo, and G. M. Süel. 2017. Coupling between distant biofilms and emergence of nutrient time-sharing. Science 356(6338): 638–642. Macfarlan, S. J., R. S. Walker, M. V. Flinn, and N. A. Cha­gnon. 2014. Lethal coalitionary aggression and long-term alliance formation among Yanomamö men. Proceedings of the National Academy of Sciences, USA 111(47): 16662–16669. Martinez, A. E., and J. P. Gomez. 2013. Are mixed-species bird flocks stable through two decades?


pages: 223 words: 62,564

Life in the Universe: A Beginner's Guide by Lewis Dartnell

anthropic principle, biofilm, carbon-based life, double helix, Kickstarter, Mars Rover, place-making, Pluto: dwarf planet, silicon-based life

Without life, the reactions producing these chemicals would run far too slowly ever to set up gradients like this: diffusion and water currents would mix them more quickly than they could form. The fact that the Black Sea is not an even mix of chemicals is an ironclad proof of biological processes. At different scales, all ecosystems show such tiers: across metres in lake water, centimetres in sediments and micrometres in biofilms (such as on the surface of stromatolites). This gives astrobiologists the ability to detect alien ecosystems without making any assumptions about the appearance, genetics or metabolic networks of the organisms within them. Life betrays its presence in a layered series of redox zones in the environment, a clear indication of the driving force of biologically-accelerated chemistry. Is there another way?

It is hotly debated whether they are cells at all, as similar forms can be produced by purely geological processes, such as the hydrothermal crystallisation of minerals. The third class of evidence involves the dome- or column-shaped layered rock formations stromatolites. Today, such structures are created by mats of photosynthetic and heterotrophic bacteria living in warm, shallow water. Mucus excreted by the cells traps drifting sediment and binds it into a covering layer. The bacteria recolonise the new top surface open to the sun, and so over time these biofilms build into large structures of layered sedimentary rock, as seen in Figure 8. Similar-looking structures have been found in 3.5 billion-year-old rock, in the Warrawoona area, and have been cited as evidence of bacterial action, including photosynthetic cyanobacteria, at this very early date. No fossils of cells are found in these ancient structures and the curved layers could simply have been produced by the deformation of abiotic sediments.

Index accretion disc acetylene acidity acidophiles aerobes aerobic respiration algae ALH84001 alien life alkaliphiles Alpha Centauri amino acids ammonia amono-peptides anaerobes anaerobic respiration Andromeda Galaxy Anomalocaris Antarctic Dry Valleys anthropic principle aquifers artificial life asteroids astrobiology definition astrometry atmosphere of Earth of Mars of Titan ATP ATP synthase autocatalysis autotrophs bacteria barophiles Betelgeuse Big Bang biofilms biosignature/biosign biosphere black smoker see hydrothermal vents blue shift bombardment Callisto (moon of Jupiter) Cambrian Explosion 55 Cancri A carbohydrate carbon isotopes carbonaceous chondrites carbonate-silicate cycle carbon dioxide carbon fixation carbonic acid cell membrane cells cryopreserved chemoautotrophs chemosynthesis chirality (handedness) chitin chlorophyll chloroplasts climate collagen comets complex life continental crust convergence co-rotation cycle cosmic radiation craters cryo-volcanism cryptoendoliths cyanide cyanobacteria cytoplasm Darwinian definition Darwin space telescope Darwin’s pond deep basalt aquifers Deimos (moon of Mars) denaturation Devon Island DNA Doppler effect Earth Earthshine EcoSphere ecosystem enantiomers Enceladus (moon of Saturn) endolithic environments endosymbiosis energy extraction inorganic environment enzymes Epsilon Eri Eridanus eukaryotes Europa (moon of Jupiter) evolution extinction extra-solar planets extremophiles eye fixation carbon methane nitrogen flight formaldehyde formamide fossil record free radicals Gaia galaxies Andromeda Galaxy metallicity Milky Way Galileo Galilei Galileo probe Ganymede (moon of Jupiter) glaciation, runaway glucose Goldilocks Principle Golgi body gravitational microlensing greenhouse effect grylloblattid insects habitable zone haemoglobin halophiles handedness see chirality Haughton Crater HD28185 HD209458b Herschel, William heterotrophs homeobox genes Hot Jupiters Hubble Space Telescope Huygens lander hydrogen hydrogen cyanide hydrosphere hydrothermal vents hyperthermophiles icebugs impact impact frustration inorganic energy interference patterns interferometry Io (moon of Jupiter) iron ferrous isotope jarosite Jupiter moons Kepler spacecraft Krebs cycle life artificial emergence of as energy disequilibrium as information transmission on Mars lithoheterotrophs lithosphere Lowell, Percival LUCA (last universal common ancestor) magnetic fields Mars atmosphere canals environmental collapse evolution of life on geography Hellas impact basin Meridiani Planum Olympus Mons survival of life Valles Marineris volcanoes water on M-class dwarves Mercury Meridiani Planum metabolism metallicity metamorphosis meteorites methane methane fixation methanogens Milky Way mitochondria Moon formation of mRNA multicellular organisms Murchison meteorite myxobacteria natural selection nebulae Neptune nitrogen nitrogen fixation nucleotides nucleus oceanic crust Opportunity Mars Rover organelles organics on Mars synthesis organisms multicellular organoheterotrophs Orion osmosis oxidation oxygen oxygenic processes ozone PAH see polycyclic aromatic hydrocarbons panspermia, permafrost Phobos (moon of Mars) photoautotrophs photosynthesis planetary orbits planet formation plate tectonics Pluto polarity polycyclic aromatic hydrocarbons polymers porphyrins potential difference prebiotic chemistry primordial soup progenote collective prokaryotes proteins protein synthesis protons Proxima Centauri psychrophiles pulsars radial velocity technique red dwarves see M-class dwarves redox redox couples redox potential red shift reduction respiration reverse transcriptase ribose ribosomes ribozymes Rio Tinto RNA RNA world rockcrawlers Rubisco enzyme salinity Saturn moons Schiaparelli, Giovanni sight silicon-based life Sirius SLiMEs Snowball Earth snow line Space Interferometry Mission spallation zone Spirit Mars rover stars birth of Sun-like stromatolites subduction zones subsurface lithotrophic microbial ecosystems see SLiMEs sugars Sun supernovae symbiosis tardigrades (water bears) Tau Bootis Tau Ceti temperature Terrestrial Planet Finder thermophiles threose/TNA tidal heating tidal locking Titan (moon of Saturn) transit method tree of life triple alpha process tRNA ultraviolet (UV) radiation uranium Uranus Urey-Miller reactions vegetation Venus Viking probes viruses volatiles volcanism Vostok, Lake water on Mars phase diagram


pages: 218 words: 70,323

Critical: Science and Stories From the Brink of Human Life by Matt Morgan

agricultural Revolution, Atul Gawande, biofilm, Black Swan, Checklist Manifesto, cognitive dissonance, crew resource management, Daniel Kahneman / Amos Tversky, David Strachan, discovery of penicillin, en.wikipedia.org, hygiene hypothesis, job satisfaction, John Snow's cholera map, meta analysis, meta-analysis, personalized medicine, publication bias, randomized controlled trial, Silicon Valley, stem cell, Steve Jobs

American Journal of Respiratory and Critical Care Medicine 193, 43–51 (2016). ‘. . . a decompressive craniectomy does produce more survivors, but with an increased likelihood of severe, profound disability overall.’ Cooper, D. J. et al. Decompressive Craniectomy in Diffuse Traumatic Brain Injury. N Engl J Med 364, 1493–1502 (2011). ‘. . . gel-like material produced by bacteria (a biofilm) forms around the plastic of breathing tubes.’ Sands, K. M. et al. Respiratory pathogen colonization of dental plaque, the lower airways, and endotracheal tube biofilms during mechanical ventilation. J Crit Care 37, 30–37 (2017). 7: THE GUTS ‘Along with tobacco, alcohol is by far the most dangerous recreational drug that we encounter in intensive care.’ Secombe, P. J. & Stewart, P. C. The impact of alcohol-related admissions on resource use in critically ill patients from 2009 to 2015: an observational study.

His brain pressure reduced, no bleeding occurred and the surgeons were happy with their results. The second night shift of caring for Joe, we became concerned that he had developed a severe lung infection called ventilator-associated pneumonia. When patients are unconscious on breathing machines, the normal defence mechanisms that protect the lungs become impaired. The patient does not cough, their mucus is not swept out from the windpipe, and gel-like material produced by bacteria (a biofilm) forms around the plastic of breathing tubes. This creates a perfect environment for bacteria. It can be difficult to distinguish lung infection from other causes of low oxygen levels in critically ill patients. We scanned Joe’s chest, looking for characteristic shadows inside his blood vessels caused by blood clots, but there were none. Instead, we saw fluffy white areas where the lung’s black air spaces normally are found, representing excess fluid in the air sacs.


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

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.


Dinosaurs Rediscovered by Michael J. Benton

All science is either physics or stamp collecting, Bayesian statistics, biofilm, bioinformatics, David Attenborough, Ernest Rutherford, germ theory of disease, Isaac Newton, lateral thinking, North Sea oil, nuclear winter

Gender identification of the Mesozoic bird Confuciusornis sanctus. Nature Communications 4, 1381 Medullary bone identifies a female fossil bird. *Crichton, M. 1990. Jurassic Park. Alfred A. Knopf, New York The book that started it all. Doyle, A. C. 1912. The Lost World. Hodder & Stoughton, London Kaye, T. G., Gaugler, G., and Sawlowicz, Z. 2008. Dinosaurian soft tissues interpreted as bacterial biofilms. PLoS ONE 3, e2808 Rejection of reported blood vessels in dinosaur bone as bacterial biofilms. Kupferschmidt, K. 2014. Can cloning revive Spain’s extinct mountain goat? Science 344, 137–38 Lindahl, T. 1993. Instability and decay of the primary structure of DNA. Nature 362, 709–15 Evidence, from the start, that ancient DNA was unlikely to survive for millions of years. Muyzer, G., Sandberg, P., Knapen, M. H. J., Vermeer, C., Collins, M., and Westbroek, P. 1992.

BioEssays 36, 482–90 A clear account of which biological molecules are likely to survive for millions of years, and which are not. Buckley, M., Warwood, S., van Dongen, B., Kitchener, A. C., and Manning, P. L. 2017. A fossil protein chimera: Difficulties in discriminating dinosaur peptide sequences from modern cross-contamination. Proceedings of the Royal Society B 284, 20170544 Rejection of reported blood vessels in dinosaur bone as bacterial biofilms. Burroughs, E. R. 1918. The Land that Time Forgot. A. C. McClurg, Chicago Cano, R. J., Poinar, H. N., Pieniazek, N. J., Acra, A., and Poinar, G. O., Jr. 1993. Amplification and sequencing of DNA from a 120–135-million-year-old weevil. Nature 363, 536–38 Cano, R. J., Poinar, H. N., Roubik, D. W., and Poinar, G. O., Jr. 1992. Enzymatic amplification and nucleotide sequencing of portions of the 18s rRNA gene of the bee Proplebeia dominicana (Apidae: Hymenoptera) isolated from 25–40-million-year-old Dominican amber.


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

Distinctive Human Cultures The picture we can draw for the human cultural mind and its cultures differs on numerous counts. The governing imperative is still the same—homeostasis—but there are more steps on the way to achieving results. First, capitalizing on the established existence of a corpus of simple social responses in existence since bacterial life began—competition, cooperation, simple emotivity, collective production of instruments of defense such as biofilms—the many species in the lineage that preceded us evolved and genetically transmitted a class of intermediate mechanisms capable of producing complex, pro-homeostatic emotive responses that are also, more often than not, social responses. The critical component of those mechanisms is lodged in the machinery of affect described in chapter 7. It is responsible for deploying drives and motivations and responding to varied stimuli and scenarios emotively.

Woodland Hastings, “Quorum Sensing on a Global Scale: Massive Numbers of Bioluminescent Bacteria Make Milky Seas,” Applied and Environmental Microbiology 72, no. 4 (2006): 2295–97; Stephen P. Diggle, Ashleigh S. Griffin, Genevieve S. Campbell, and Stuart A. West, “Cooperation and Conflict in Quorum-Sensing Bacterial Populations,” Nature 450, no. 7168 (2007): 411–14; Lucas R. Hoffman, David A. D’Argenio, Michael J. MacCoss, Zhaoying Zhang, Roger A. Jones, and Samuel I. Miller, “Aminoglycoside Antibiotics Induce Bacterial Biofilm Formation,” Nature 436, no. 7054 (2005): 1171–75; Ivan Erill, Susana Campoy, and Jordi Barbé, “Aeons of Distress: An Evolutionary Perspective on the Bacterial SOS Response,” FEMS Microbiology Reviews 31, no. 6 (2007): 637–56; Delphine Icard-Arcizet, Olivier Cardoso, Alain Richert, and Sylvie Hénon, “Cell Stiffening in Response to External Stress Is Correlated to Actin Recruitment,” Biophysical Journal 94, no. 7 (2008): 2906–13; Vanessa Sperandio, Alfredo G.

Fricchione, “Enkelytin and Opioid Peptide Association in Invertebrates and Vertebrates: Immune Activation and Pain,” Immunology Today 19, no. 6 (1998): 265–68; Michel Salzet and Aurélie Tasiemski, “Involvement of Pro-enkephalin-derived Peptides in Immunity,” Developmental and Comparative Immunology 25, no. 3 (2001): 177–85; Halina Machelska and Christoph Stein, “Leukocyte-Derived Opioid Peptides and Inhibition of Pain,” Journal of Neuroimmune Pharmacology 1, no. 1 (2006): 90–97; Simona Farina, Michele Tinazzi, Domenica Le Pera, and Massimiliano Valeriani, “Pain-Related Modulation of the Human Motor Cortex,” Neurological Research 25, no. 2 (2003): 130–42; Stephen B. McMahon, Federica La Russa, and David L. H. Bennett, “Crosstalk Between the Nociceptive and Immune Systems in Host Defense and Disease,” Nature Reviews Neuroscience 16, no. 7 (2015): 389–402. 3. Brunet and Arendt, “From Damage Response to Action Potentials”; Hoffman et al., “Aminoglycoside Antibiotics Induce Bacterial Biofilm Formation”; Naviaux, “Metabolic Features of the Cell Danger Response”; Icard-Arcizet et al., “Cell Stiffening in Response to External Stress Is Correlated to Actin Recruitment”; Kearns, “Field Guide to Bacterial Swarming Motility”; Erill, Campoy, and Barbé, “Aeons of Distress.” Transient receptor potential (TRP) ion channels serve as the sensors in single-celled organisms and are conserved throughout phylogeny.


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

The natural history of antibiotics is not, it turns out, the obvious one, in which unicellular life evolved defense mechanisms during billions of years of natural selection. Antibiotic molecules in nature aren’t always, or even usually, weapons. Bacterial populations react to the presence of low concentrations of antibiotic molecules in a variety of ways, and many of them are actually positive. Many antibiotics are what biologists call “hormetic”: beneficial in low doses, even promoting the creation of what are known as biofilms, matrices that hold bacterial cells together with a polymer “glue” and make them far more durable in the presence of both the animal immune system, and antibiotics themselves. This is especially true for the tetracyclines. Low doses of Aureomycin and Terramycin and all the other antibiotics related to them actually increase the virulence of large numbers of pathogens. Subtherapeutic doses of tetracycline help bacteria to form what is known as the type III secretion system, which is one of the key elements of any pathogen’s arsenal: a tiny hypodermic needle that Gram-negative bacteria—salmonella, chlamydia, even the organism responsible for bubonic plague—use to inject themselves into animals cells.

“the most versatile antibiotic”: (Podolsky, 2015) shipping samples of their gold maker to 142,000 doctors: (Silberman, 1960), quoted in (Podolsky, 2015) “We got soil samples”: (Rodengen, 1999) “because it came from the earth”: (Rodengen, 1999) “If you want to lose your shirt”: (Podolsky, 2015) Aureomycin accounted for 26 percent: (McEvilla, 1955) “outstanding achievements in the art of organic synthesis”: (Nobel Prize Foundation, 2014) complicated molecule known as Vitamin B12: (Woodward, 1973) “None of us thought he was really that great”: (Tishler, 1983) it was Woodward who demonstrated that the beta-lactam structure: (Abraham, “Ernst Boris Chain,” 1983) facts “both clear and misleading”: (Blout, 2001) “by thought alone, deduced the correct structure”: (Blout, 2001) the FDA approved it: (Daemmrich, 2004) on March 23, 1950: (Maeder, 1994) seventy third-year medical students: (Mahoney, 1958) By 1952, three hundred Pfizer reps: (Chandler, 2005) By the early 1950s, more money: (Podolsky, 2015) Lederle planned to launch Achromycin: (Maeder, 1994) stabilized thereafter for another decade: (Temin, 1980) Achromycin, its version of tetracycline: (Temin, 1980) “Doctors Get a Heap of Comfort”: (Grinnell, 1914) the journal was carrying more advertising pages: (Temin, 1980) virtually every issue of JAMA arrived: (Podolsky, 2015) The mechanism for this: (Gaskins, 2002) “dug residues out of the Lederle dump”: (Jukes, 1985) “Wonder Drug . . . had been found”: (Laurence, 1950) “The average weight”: (Jukes, 1985) what he called “Project Piglet” . . . as Terralac: (Rodengen, 1999) Only the 31 showed resistance: (North, 1945) May 1940, milk cows: (Bud, Penicillin, 2007) milked before the penicillin: (Bud, Penicillin, 2007) dosages were very small: (Graham, 2007) biofilms, matrices that hold: (Davies, 2009) EIGHT: “The Little Stranger” “the only House in the West” . . . and Wormseed: (Kahn, 1976) “profit on blood which has been donated”: (Madison, 1989) to three-quarters of the entire American market: (Chandler, 2005) were “unreasonably high”: (Madison, 1989) “novel compound having antibiotic properties”: (Bunch, 1952) “looks at present quite hopelessly complex”: (Todd, 1956) The drug was Chloromycetin: (McEvilla, 1955) “ether, sweet spirits of nitre”: (Hoeffle, 2000) Parke was its first president: (Mahoney, 1958) “difficult to believe that one is under the influence of any drug at all”: (Byck, 1974) “the different varieties of coca”: (Parke, Davis & Company, 1894) “involving four thousand miles”: (Parke, Davis & Company, 1894) Davis even hired Freud himself: (Maeder, 1994) Freud’s evaluation, for which he was paid an honorarium of 60 Dutch gulden—about $50—found that Merck’s cocaine was, compared to Parke-Davis’s, overpriced and difficult to find.

., 117 Bartz, Quentin, 244 BASF, 57, 62, 63, 178 battlefield injuries, 86, 87, 163, 167, 178, 180 Bayer, 62–71, 102, 160n, 225, 296, 299n Bean, William, 257 Beaverbrook, Max Aitken, Lord, 95, 100 Béchamp, Antoine, 52–53 Beecham Limited, 121 Behring, Emil von, 35, 43–47, 57, 62, 63, 104, 215, 242, 296 belladonna, 158, 159, 242, 261 Bell Labs, 162 Benadryl, 242 benzene, 250 Berenblum, Isaac, 109 Bernal, J. D., 144 Bernard, Claude, 26–27, 85n Bernhauer, Konrad, 137 Bernoulli, Daniel, 14 Bertheim, Alfred, 53–54 Best, Charles, 239 beta-lactam ring, 3, 175, 220–21, 304 Bi-Con, 233 Bigelow, Jacob, 73–74 bile, 7 biofilms, 236 biological warfare, 202–3 Biot, Jean-Baptiste, 16 Bismarck, Otto von, 29, 44 bismuth, 159 Blair, John, 276, 277 blistering, 10 blood, 7 blood dyscrasias, 248–50, 254, 264 bloodletting, 5, 7, 9, 14, 183 Washington and, 5 Blundell, James, 67n Bohr, Niels, 99n bone marrow, 250 Boots Pure Drug Company, 173 Bosch, Carl, 62, 63, 178 Boston Globe, 166 Bovet, Daniel, 69–70 Bragg, Lawrence, 143–44 Bragg, William Henry, 143–44 Bristol Laboratories, 225–27, 227n, 240 Bristol-Myers, 244n Bristol-Myers Squibb, 270, 296, 297 Britain: army of, 82, 84–86, 119 pharmaceutical industry in, 121–22, 141 Brown, Francis C., 278 bubonic plague, 13, 35, 194, 197, 217, 224, 237 Buchner, Eduard, 26n Buchner, Hans, 43 Bugie, Elizabeth, 205 Bumstead, John, 1–2 burial alive, 6n Burkholder, Paul, 243–44 burn patients, 166 Burroughs, Silas M., 122 Burroughs Wellcome, 122, 293–94 Bush, Vannevar, 152, 153, 177 caffeine, 158 Calmette, Albert, 189 calomel (mercurous chloride), 5, 9, 164 Campbell, Walter G., 74 camphor, 164 Canby, Henry Seidel, 265 cancer: leukemia, 43 Wilms’ tumor, 192n carbolic acid (phenol), 34, 35, 46, 56n, 86, 87, 159 Carnegie Foundation, 256 Caro, Heinrich, 53 Carter, Charles, 233 Cassella Manufacturing, 57, 62, 160n Celler, Emanuel, 271 Centers for Disease Control and Prevention, 251n, 302 cephalosporin, 3, 235n Chadwick, James, 3 Chain, Ernst, 103–15, 106, 117–18, 120–21, 125–27, 129, 140–42, 144, 145, 148, 155–57, 165, 174, 175, 180–81, 198, 201, 221, 235, 293, 305 Chamberland, Charles, 26 Chatton, Edouard, 24 cheese, 134n, 138n chemical reactions, 51 chemical synthesis, 50, 66 Chemie Grünenthal, 282 chemistry, 49 combinatorial, 63n chemotherapy, 49 Chester County Mushroom Laboratories, 170 chicken pox, 11n childbed (puerperal) fever, 67–68, 72 chlamydia, 217, 237 chloramphenicol, 3 chloroform, 164 Chloromycetin (chloramphenicol), 240, 244–54, 256–60, 268, 276, 279, 280, 287 aplastic anemia and, 249–52, 254, 258–62, 279, 281 gray baby syndrome and, 259–62 sales of, 253, 259 typhus and, 245–47 chlorophyll, 220 chlortetracycline, 244 Aureomycin, 216–19, 223–27, 231–34, 236, 237, 254, 272, 274 see also tetracyclines cholera, 13–15, 26, 28, 35, 194 cholesterol, 220, 296 Churchill, Winston, 76, 119, 173, 293 CIBA, 127 CIBA-Geigy, 181 citric acid, 137–38, 164, 171 Civil War, 81, 163, 241 Clark, William Mansfield, 153 Cline, Joseph, 162 clinical trials, 207–8, 273, 274n, 288 children in, 260n informed consent in, 289 of penicillin, 129–30, 132, 139, 141, 148 sampling in, 208–9 of streptomycin, 207–13 of Terramycin, 219 three-tiered structure for, 289–90, 292 clostridia, 87n, 125, 194, 198 coal tar extracts, 34, 46, 49, 159 coca, cocaine, 69, 73, 159, 241–42, 261 Coca-Cola, 73 Cocoanut Grove, 166–67 Coghill, Robert, 136, 137, 138, 148, 153, 157, 164, 168, 169 cognitive biases, 209 Cohn, Ferdinand Julius, 23, 25 Colebrook, Leonard, 68, 86–87 colistin, 297–98 Collier’s, 248 Commercial Solvents Corporation, 169 Committee on Medical Research (CMR), 151–53, 167, 169–71, 180, 216 computers, 173–74 Conant, James Bryant, 199 cortisone, 199, 220 Coulthard, C.


pages: 1,631 words: 468,342

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, 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.)


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, Mark Zuckerberg, mutually assured destruction, nuclear paranoia, 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.


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 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.


pages: 476 words: 148,895

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

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.


pages: 268 words: 76,709

Tomatoland: How Modern Industrial Agriculture Destroyed Our Most Alluring Fruit by Barry Estabrook

Bernie Sanders, biofilm, collective bargaining, Columbian Exchange, McMansion, medical malpractice, old-boy network, urban sprawl, women in the workforce

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.


pages: 327 words: 97,720

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, longitudinal study, 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.


pages: 379 words: 109,612

Is the Internet Changing the Way You Think?: The Net's Impact on Our Minds and Future by John Brockman

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, 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, John Markoff, Kevin Kelly, lifelogging, lone genius, loss aversion, mandelbrot fractal, Marc Andreessen, Marshall McLuhan, Menlo Park, meta analysis, meta-analysis, New Journalism, Nicholas Carr, out of africa, Paul Samuelson, peer-to-peer, Ponzi scheme, pre–internet, 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?


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

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.


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

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.


pages: 571 words: 124,448

Building Habitats on the Moon: Engineering Approaches to Lunar Settlements by Haym Benaroya

3D printing, biofilm, Black Swan, Brownian motion, Buckminster Fuller, carbon-based life, centre right, clean water, Colonization of Mars, Computer Numeric Control, conceptual framework, data acquisition, Elon Musk, fault tolerance, gravity well, inventory management, Johannes Kepler, low earth orbit, orbital mechanics / astrodynamics, performance metric, RAND corporation, risk tolerance, Ronald Reagan, stochastic process, telepresence, telerobotics, the scientific method, urban planning, X Prize, zero-sum game

Whether through EVA operations, or on the lunar surface, exposure to hydrazine, found in spacecraft propulsion systems, can be fatal, “with reported effects involving the central nervous system, the blood, the liver, the kidneys, and the immune system.” The enclosed spaceflight and lunar habitat environment represent serious challenges, in particular to “controlling the growth of microflora [and] biofilms ... from the standpoint of the potential for contaminant generation, and the possibility of their deliberate controlled use in bioregenerative life support systems ... may pose additional complications such as 1) a source of chemical corrosion on containment vessel surfaces, which are usually extremely thin, and 2) a secondary source for the generation of toxic chemical species. ... There is the question of whether the chemical products of biotransformation are more toxic than the parent compounds.”


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

Frontiers in Microbiology 9: 2325. Lintott C. 2019. The Crowd and the Cosmos: Adventures in the Zooniverse. Oxford, UK: Oxford University Press. Lipnicki LI. 2015. The role of symbiosis in the transition of some eukaryotes from aquatic to terrestrial environments. Symbiosis 65: 39–53. Liu J, Martinez-Corral R, Prindle A, Lee D-YD, Larkin J, Gabalda-Sagarra M, Garcia-Ojalvo J, Süel GM. 2017. Coupling between distant biofilms and emergence of nutrient time-sharing. Science 356: 638–42. Lohberger A, Spangenberg JE, Ventura Y, Bindschedler S, Verrecchia EP, Bshary R, Junier P. 2019. Effect of organic carbon and nitrogen on the interactions of Morchella spp. and bacteria dispersing on their mycelium. Frontiers in Microbiology 10: 124. Löpez-Franco R, Bracker CE. 1996. Diversity and dynamics of the Spitzenkörper in growing hyphal tips of higher fungi.


pages: 736 words: 147,021

Safe Food: The Politics of Food Safety by Marion Nestle

Asilomar, biofilm, butterfly effect, clean water, double helix, Fellow of the Royal Society, illegal immigration, out of africa, Ralph Nader, Ronald Reagan, software patent, Upton Sinclair

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.


pages: 529 words: 150,263

The Pandemic Century: One Hundred Years of Panic, Hysteria, and Hubris by Mark Honigsbaum

Asian financial crisis, biofilm, Black Swan, clean water, coronavirus, Donald Trump, en.wikipedia.org, germ theory of disease, global pandemic, indoor plumbing, Louis Pasteur, Mark Zuckerberg, megacity, moral panic, Pearl River Delta, Ronald Reagan, Skype, the built environment, trade route, urban renewal, urban sprawl

Hotels, hospitals, and other large buildings are home to a number of devices that utilize water at ideal temperatures for the growth of Legionella bacteria. These include showerheads, hot tubs, whirlpool spas, water fountains, humidifiers, misting equipment, and architectural fountains. Cooling towers are of particular concern because the pools of warm water are open to the atmosphere—indeed, Legionella bacteria have been repeatedly isolated from the biofilms of slime and encrusted sludge on top of such towers, with some surveys indicating that as many as half of all cooling towers in the United States may be contaminated with the organisms. If such towers are not regularly serviced, this contaminated water can be aerosolized into microscopic droplets containing Legionella, enabling the organism to be drawn directly into a person’s lungs. One way this may occur is during the cooling process, when warm water from the condenser or chiller unit is sprayed across the fill at the top of a cooling tower, splintering the water into tiny droplets.


pages: 1,293 words: 357,735

The Coming Plague: Newly Emerging Diseases in a World Out of Balance by Laurie Garrett

Albert Einstein, Berlin Wall, biofilm, British Empire, Buckminster Fuller, clean water, correlation does not imply causation, discovery of penicillin, double helix, European colonialism, Fall of the Berlin Wall, germ theory of disease, global pandemic, global village, indoor plumbing, invention of air conditioning, John Snow's cholera map, land reform, Live Aid, Louis Pasteur, Marshall McLuhan, mass incarceration, megacity, Menlo Park, Mikhail Gorbachev, Nelson Mandela, New Urbanism, phenotype, price mechanism, Ralph Nader, Ronald Reagan, Rosa Parks, South China Sea, the scientific method, trade route, transfer pricing, upwardly mobile, urban renewal, urban sprawl, Zimmermann PGP

The epidemiology team in Philadelphia meanwhile noticed that most of the Legionnaires’ Disease sufferers had spent time schmoozing in the five cocktail suites run by the candidates for leadership of the veterans’ group. Further analysis revealed that the bacteria thrived in the Bellevue-Stratford Hotel’s cooling tower. From that water supply, the hotel derived its air conditioning. The Legionella organisms were hidden in biofilm “scums” along the edges of the cooling tower, and were actively pumped into the hotel’s hospitality suites during the hot month of July. It wasn’t long before similar cases of Legionnaires’ Disease surfaced all over the world. First, the CDC spotted isolated cases in eleven different states.57 By September 1977, the federal agency was busily tracking three hospital outbreaks in Ohio,58 one in Vermont,59 and one in Tennessee.60 The combined fatalities in the Ohio, Vermont, and Tennessee outbreaks and sporadic isolated cases in 1977 reached thirty-two by December, about 25 percent of all reported Legionnaires’ cases.61 In the fall of 1977 a small epidemic of Legionnaires’ broke out in a hospital in Nottingham, England, leaving three patients dead.62 In the summer of 1977 Legionnaires’ struck a brand-new hospital located in one of the wealthiest parts of Los Angeles.

In the case of Legionella, a new human disease had emerged in 1976, brought from ancient obscurity by the modern invention of air conditioning. At the CDC’s International Legionnaires’ Disease meeting in 1978, several particularly ominous facets of the bug were scrutinized. CDC scientists revealed that the organism could be found in tap water, shower nozzles, and other allegedly clean water sources. One tap water study showed Legionella could survive over a year inside pipe biofilms, emerging in wholly infectious form once the faucet was turned on full force. It thrived in temperatures from ice cold to steamy hot. Even distilled water samples occasionally contained small numbers of Legionella organisms. A team of scientists from the Denver Veterans Administration Medical Center was particularly prescient, predicting the bacteria might survive chlorine purification efforts.


Betrayal of Trust: The Collapse of Global Public Health by Laurie Garrett

accounting loophole / creative accounting, airport security, Albert Einstein, anti-communist, Ayatollah Khomeini, Berlin Wall, biofilm, clean water, collective bargaining, desegregation, discovery of DNA, discovery of penicillin, Drosophila, employer provided health coverage, Fall of the Berlin Wall, germ theory of disease, global pandemic, illegal immigration, indoor plumbing, Induced demand, John Snow's cholera map, Jones Act, Louis Pasteur, Mahatma Gandhi, mass incarceration, Maui Hawaii, means of production, Menlo Park, Mikhail Gorbachev, mouse model, Nelson Mandela, new economy, nuclear winter, phenotype, profit motive, Project Plowshare, RAND corporation, randomized controlled trial, Right to Buy, Ronald Reagan, sexual politics, Silicon Valley, stem cell, the scientific method, urban decay, urban renewal, War on Poverty, working poor, Works Progress Administration, yellow journalism

And it was spread by a means that hadn’t previously been a source of disease. Such novelty is rarely subject to swift analysis. In January 1977 the CDC announced that the culprit was a bacterium they dubbed Legionella, and it was spread through air-conditioning systems. Legionella, it turned out, was a scum bacterium that grew in the biofilms that formed at the interfaces of air and nonsalty water. Air conditioners, showers, misters, humidifiers, and similar devices that sprayed moist air were rife with biofilms, and if the device was not cleaned regularly and filtered, those scum layers would grow and become Legionella breeding grounds. Once the organism was discovered, the CDC and the state public health agencies set to work testing human samples saved from past, mysterious pneumonia outbreaks. It turned out that 235 people in the United States had suffered Legionnaires’ disease at two different locations in 1976.


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Behave: The Biology of Humans at Our Best and Worst by Robert M. Sapolsky

autonomous vehicles, Bernie Madoff, biofilm, blood diamonds, British Empire, Broken windows theory, Brownian motion, car-free, clean water, cognitive dissonance, corporate personhood, corporate social responsibility, Daniel Kahneman / Amos Tversky, delayed gratification, desegregation, different worldview, double helix, Drosophila, Edward Snowden, en.wikipedia.org, epigenetics, Flynn Effect, framing effect, fudge factor, George Santayana, global pandemic, hiring and firing, illegal immigration, impulse control, income inequality, John von Neumann, Loma Prieta earthquake, long peace, longitudinal study, loss aversion, Mahatma Gandhi, meta analysis, meta-analysis, Mohammed Bouazizi, Monkeys Reject Unequal Pay, mouse model, mutually assured destruction, Nelson Mandela, Network effects, out of africa, Peter Singer: altruism, phenotype, placebo effect, publication bias, RAND corporation, risk tolerance, Rosa Parks, selective serotonin reuptake inhibitor (SSRI), self-driving car, Silicon Valley, social intelligence, Stanford marshmallow experiment, Stanford prison experiment, stem cell, Steven Pinker, strikebreaker, theory of mind, transatlantic slave trade, traveling salesman, trickle-down economics, twin studies, ultimatum game, Walter Mischel, wikimedia commons, zero-sum game

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