Posts Tagged ‘hasshadow’

Papers for Journal Club

June 7, 2018

Alternative evolutionary histories in the sequence space of an ancient protein Great viz of different potential but not necessarily realized evolutionary trajectories. Quite relevant for molecular #evolution & #pseudogenes

iPad Notebook export for Cooked: A Natural History of Transformation

May 26, 2018

Some quick quotes from
Cooked: A Natural History of Transformation
Pollan, Michael
Citation (MLA): Pollan, Michael. Cooked: A Natural History of Transformation. Penguin Publishing Group, 2013. Kindle file. }}
that I really liked

Each short quote below is preceded by the words “Highlight” & an indication of the location in the book.

Highlight(pink) – Page iv · Location 278
Along the way, a succession of “fermentos” tutored me in the techniques of artfully managing rot, the folly of the modern war against bacteria, the erotics of disgust, and the somewhat upside-down notion that, while we were fermenting alcohol, alcohol has been fermenting us.
Highlight(pink) – V. WILSON, NORTH CAROLINA > Page iv · Location 1234 According to a flavor chemist I consulted, putting smoke and fire to the proteins, sugars, and fats in meat creates anywhere between three thousand and four thousand entirely new chemical compounds, complex and often aromatic molecules forged from the simple building blocks of sugar and amino acids.
Highlight(pink) – V. WILSON, NORTH CAROLINA > Page iv · Location 1239 Maillard discovered that when amino acids are heated in the company of sugar, the reaction produces hundreds of new molecules that give cooked food its characteristic color and much of its smell. The Maillard reaction is responsible for the flavors in roasted coffee, the crust of bread, chocolate, beer, soy sauce, and fried meats— Highlight(pink) – V. WILSON, NORTH CAROLINA > Page iv · Location 1242 The second important reaction working on our pigs during the night was caramelization. The heating of odorless sucrose until it browns generates more than a hundred other compounds, with flavor notes reminiscent not just of caramel but also of nuts, fruits, alcohol, green leaves, sherry, and vinegar.
Highlight(pink) – V. WILSON, NORTH CAROLINA > Page iv · Location 1248 He points out that many of the aromatic compounds generated by the two browning reactions are similar or identical to compounds found in the plant world,
Highlight(pink) – VIII. CODA: AXPE, SPAIN > Page iv · Location 1671 As it happens, Ferran Adrià, perhaps the world’s most famous exponent of molecular gastronomy, a chef known for cooking with liquid nitrogen, xanthan gum,
Highlight(pink) – STEP ONE > Page iv · Location 1703
Hoping to make chopping onions more interesting, if not more pleasant, I looked into the onion’s strategy, and was surprised to learn that the plant does not mount its defense until the moment tooth or blade pierces cell wall. If you could shrink yourself down to the size of a mitochondria or nucleus and swim around inside an undamaged onion cell, you would find the environment surprisingly benign, the taste of the ambient fluid sweet, certainly no cause for tears.
Highlight(pink) – STEP ONE > Page iv · Location 1709
When a blade or tooth breaks open a vacuole, the enzyme escapes, locates one of the defensive molecules, and breaks it in two. The volatile new chemical compounds that result are what give raw onions their powerfully sulfurous and irritating smell. One of the most volatile of these compounds is, aptly, called “the lachrymator”–tear maker. It escapes from the damaged cell into the air and proceeds to attack the nerve endings in a mammal’s eyes and nasal passages, before breaking down into a noxious cocktail of sulfur dioxide, hydrogen sulfide, and sulfuric acid. “A very effective molecular bomb!” is how Harold McGee describes it.
Highlight(pink) – STEP ONE > Page iv · Location 1801
Let me propose a radically simplified version of that structure, something that might serve as a kind of template or Ur-recipe for dishes organized around the element of water: Dice some aromatic plants Sauté them in some fat Brown piece( s) of meat (or other featured ingredient) Put everything in a pot Add some water (or stock, wine, milk, etc.) Simmer, below the boil, for a long time
Highlight(pink) – STEP TWO > Page iv · Location 1947
that the low, slow heat was breaking down the long necklaces of protein in the vegetables into their amino acid building blocks, some of which
Highlight(pink) – STEP TWO > Page iv · Location 1948
(like glutamic acid) are known to give foods the meaty, savory taste called “umami”—from the Japanese word umai, meaning “delicious.” Umami is now generally accepted as the fifth taste, along with salty, sweet, bitter, and sour, and
Highlight(pink) – STEP TWO > Page iv · Location 1968
Onions happen to be one of the most potent of all antimicrobial food plants. Highlight(pink) – STEP TWO > Page iv · Location 1991
Prosperous and blessed with good grass for grazing cattle and sheep the year round, the English enjoyed access to high-quality meat that required little more than fire to taste good. Whereas the less well-to-do and well-provisioned French were thrown back on their wits in the kitchen, developing techniques that allowed them to make the most of meat scraps and root vegetables and whatever liquid might be handy.
Highlight(pink) – STEP THREE > Page iv · Location 2036
The problem is that meat won’t ever brown in a liquid that consists mostly of water. In order for the Maillard reaction to take place, meat needs to reach a higher temperature—
Highlight(pink) – STEP THREE > Page iv · Location 2038
250 ˚ F at least—than water can ever attain, since water can never exceed the boiling point—212 ˚ F. To caramelize the sugars in meat requires an even higher temperature, in excess of 330 ˚ F. Because oil can reach these temperatures that water can’t, the best way to brown meat is in a pan with a little fat.
Highlight(pink) – STEP FOUR > Page iv · Location 2087
Boiling water vastly expanded the horizons of edibility for our species, especially in the world of plants. All kinds of formerly inedible seeds, tubers, legumes, and nuts could now be rendered soft and safe—and therefore the exclusive nutritional property of Homo sapiens. In
Highlight(pink) – STEP FOUR > Page iv · Location 2093
The cook pot is a kind of second human stomach, an external organ of digestion that allows us to consume plants that would otherwise be inedible or require elaborate processing.
Highlight(pink) – STEP FIVE > Page iv · Location 2262
The idea of a fifth taste was controversial in the West until 2001, when American scientists identified a dedicated taste receptor for glutamate on the human tongue.
Highlight(pink) – STEP FIVE > Page iv · Location 2280
Curiously, umami receptors have been found in the stomach as well as on the tongue. Their purpose, presumably, is to prepare the body to digest meat, alerting
Highlight(pink) – STEP FIVE > Page iv · Location 2354
It stands to reason that everything in milk is there for an
evolutionary reason; since every chemical compound in it comes at a metabolic cost to the mother, natural selection would quickly dispense with any constituent of milk that didn’t do the infant some good. So what good does all that glutamate do?
Highlight(pink) – STEP SIX > Page iv · Location 2642
Highlight(pink) – I. A GREAT WHITE LOAF > Page iv · Location 2732 One way to think about bread—and there are so many: as food or Food, matter and Spirit, commonplace, communion, metaphor, and medium (of exchange, transformation, sociality, etc.)—is simply this: as an ingenious technology for improving the flavor, digestibility, and nutritional value of grass.
Highlight(pink) – I. A GREAT WHITE LOAF > Page iv · Location 2741 Yet second-or third-hand is a wasteful way to eat grass. Only about 10 percent of the energy consumed by an animal passes up the food chain to an eater of that animal.
Highlight(pink) – I. A GREAT WHITE LOAF > Page iv · Location 2743 In fact, for every step up a food chain (or “trophic pyramid”), 90 percent of the food energy is lost, which is why big predators are so much more rare than ruminants,
Highlight(pink) – I. A GREAT WHITE LOAF > Page iv · Location 2747 Learning how to eat lower on the food chain gave us access to more solar energy than ever before,
Highlight(pink) – I. A GREAT WHITE LOAF > Page iv · Location 2793 The work of these yeasts and bacteria is the reason that the airy loaf of bread coming out of the oven cannot be inferred from a wet mash of powdered grass seed in the way that, say, a pork roast or stew can be inferred from a pig. By comparison, the delicate spongelike structure that rises in a loaf of bread to trap the gaseous waste products of those microbes has the complexity of an emergent system: something that is much more than, and qualitatively different from, the sum of its simple parts.
Highlight(pink) – I. A GREAT WHITE LOAF > Page iv · Location 2921 Though commercial yeast is alive, its behavior is linear, mechanical, and predictable, a simple matter of inputs and outputs—which is no doubt why it so quickly caught on. S. cerevisiae can be counted on to perform the same way everywhere and give the same results, making it supremely well suited to industrial production.
Highlight(pink) – I. A GREAT WHITE LOAF > Page iv · Location 2924 S. cerevisiae is notable for not playing well with others, especially bacteria. Compared with wild yeasts, commercial yeast cannot survive very long in the acidic environment created by lactobacilli. Highlight(pink) – I. A GREAT WHITE LOAF > Page iv · Location 2943 Perhaps the USDA team’s most important contribution was to demonstrate that a sourdough culture functions as a kind of ecosystem, with the various species performing distinct roles that lend stability to the culture over time.
Highlight(pink) – I. A GREAT WHITE LOAF > Page iv · Location 2976 The chemical development is the formation of gluten (the word means “glue” in Latin), an interesting if somewhat problematic substance that is found primarily in wheat, and to a much lesser extent in rye, another species of grass. To be precise, gluten as such is not found in wheat itself, but, rather, its two precursors are, the proteins gliadin and glutenin, which when moistened in water combine to form the mesh of proteins known as gluten.
Highlight(pink) – I. A GREAT WHITE LOAF > Page iv · Location 2989 And, most important of all, the yeasts are busy transforming each molecule of glucose they consume into two molecules of alcohol and two of carbon dioxide.
Highlight(pink) – II. THINKING LIKE A SEED > Page iv · Location 3381 ever since the nutritional vacuousness of white flour became impossible to ignore, early in the twentieth century, governments have required that millers add back in a handful of the nutrients (B vitamins, mainly) that they have gone to such great lengths to take out.
Highlight(pink) – II. THINKING LIKE A SEED > Page iv · Location 3399 After figuring out an ingenious system for transforming an all but nutritionally worthless grass into a wholesome food, humanity pushed on intrepidly until it had figured out a way to make that food all but nutritionally worthless yet again!
Highlight(pink) – II. THINKING LIKE A SEED > Page iv · Location 3402 But there eventually came a moment when, propelled by the logic of human desire and technological progress, we began to overprocess certain foods in such a way as to actually render them detrimental to our health and well-being.
Highlight(pink) – II. THINKING LIKE A SEED > Page iv · Location 3437 To begin, the seed is dropped between a pair of corrugated drums rotating in opposite directions. During the “first break,” the bran and germ are sheared from the endosperm.
Highlight(pink) – FERMENT I. VEGETABLE > Page iv · Location 3887 Consider, just for a moment, the everyday proximity of death. No, not the swerve of the oncoming car or the bomb in the baby carriage. I’m thinking more of the bloom of yeast on the ripe fruit, patiently waiting for a breach in its skin so that it might invade and decompose its sweet flesh. Or the lactobacillus loitering on the cabbage leaf for the same purpose.
Highlight(pink) – FERMENT I. VEGETABLE > Page iv · Location 3934 The molds and bacteria now have a small but growing tribe of human defenders. These post-Pasteurians,* as they sometimes call themselves, form one of the more curious subcultures in America. It is sometimes called the fermentation underground, a word that seems fitting, given the fierceness of their devotion to microbes and their willingness to break the law to consume them.
Highlight(pink) – FERMENT I. VEGETABLE > Page iv · Location 3997 Katz likened a sauerkraut to a forest ecosystem, in which one type of bacteria succeeds another, each species transforming the environment in such a way as to prepare the ground for the next. In a vegetable ferment, each succeeding species is more acid tolerant than the last, until the environment arrives at a climax stage dominated by L. plantarum—
Highlight(pink) – FERMENT I. VEGETABLE > Page iv · Location 3999 the great acid-loving oak of the pickle ecosystem.
Highlight(pink) – FERMENT I. VEGETABLE > Page iv · Location 4087 Think of the kraut crock as a burbling auxiliary stomach, doing much of the work of digestion before your body has to.
Highlight(pink) – FERMENT I. VEGETABLE > Page iv · Location 4095 “Between fresh and rotten,” Katz has written, “there is a creative space in which some of the most compelling flavors arise.”
Highlight(pink) – FERMENT I. VEGETABLE > Page iv · Location 4205 The objective of all these bugs is to render the environment safe for themselves and inhospitable to competitors. In the case of the lactobacilli, this is accomplished by producing copious amounts of acid, rapidly lowering the pH of the environment. But the L. mesenteroides eventually go overboard, acidifying the environment to the point where they have, in effect, fouled their own nest. (Remind you of anyone?)
Highlight(pink) – FERMENT I. VEGETABLE > Page iv · Location 4291 a phenomenon now known among researchers as “the great plate anomaly.” Without realizing it, they were practicing what is sometimes called parking-lot science—named for the human tendency to search for lost keys under the streetlights not because that’s where we lost them but because that is where we can best see. The petri dish was a
Highlight(pink) – FERMENT I. VEGETABLE > Page iv · Location 4408 “The big problem with the Western diet,” Stephen O’Keefe, a
gastroenterologist at the University of Pittsburgh, told me, “is that it doesn’t feed the gut, only the upper GI [gastrointestinal tract]. Highlight(pink) – FERMENT II. ANIMAL > Page iv · Location 4480 In the intensifying struggle between the Pasteurians and
post-Pasteurians, raw-milk cheese has emerged as perhaps the single most fiercely contested terrain.
Highlight(pink) – FERMENT II. ANIMAL > Page iv · Location 4509 Instead of technology, the post-Pasteurians want us to put our faith in the microbes themselves and in striking a healthier, more tolerant relationship with them. They cite studies demonstrating that children who grow up drinking raw milk are measurably healthier than other children, with markedly lower rates of allergy and asthma.* Some of these children live in environments teeming with deadly pathogens, including E. coli and listeria, yet they don’t get sick from them. Highlight(pink) – FERMENT II. ANIMAL > Page iv · Location 4634 What this suggests is that terroir—the French term for the taste of place—is influenced not just by the local climate or soil but also by differences in the local bacteria and fungi.
Highlight(pink) – FERMENT II. ANIMAL > Page iv · Location 4681 The acidification would continue in the cheese for several weeks before reversing course, as the fungi—also already present in the milk, as spores—took over, inaugurating a second fermentation in the rind.
Highlight(pink) – FERMENT II. ANIMAL > Page iv · Location 4747 And so it goes for the two months it takes a Saint-Nectaire to ripen, each species altering the rind environs in such a way as to pave the way for the next, in a predictable ecological succession that Sister Noëlla carefully documented in her dissertation.
Highlight(pink) – FERMENT II. ANIMAL > Page iv · Location 4800 Compared with some other mammals, we humans have long been alienated from our sense of smell. From the moment we began to walk upright, the eye took precedence over the nose.
Highlight(pink) – FERMENT III. ALCOHOL > Page iv · Location 4981 Most vertebrates possess the metabolic equipment needed to detoxify ethyl alcohol and burn it for fuel. A tenth of the enzymes in the human liver are dedicated to metabolizing ethyl alcohol.
Highlight(pink) – FERMENT III. ALCOHOL > Page iv · Location 4984 A beehive falls or drips honey into a hollow in a tree, rainwater collects in the hollow, and the diluted honey ferments: You’ve got mead. Or a gruel of mashed grass seeds—the wild ancestors of barley or wheat—begin to ferment: You’ve got beer.
Highlight(pink) – FERMENT III. ALCOHOL > Page iv · Location 5036 Because aerobic metabolism gives the yeast the maximum amount of energy from its food, oxygenating the liquid in question is a good way to kick-start a fermentation. So I started a new batch of mead, diluting the honey with four parts water and leaving it out on the kitchen counter for several days, uncovered.
Highlight(pink) – FERMENT III. ALCOHOL > Page iv · Location 5070 Alcohol is a rich source of calories as well as nutrients. People who drink in moderation (which a 5-percent mead pretty much guarantees) live longer and endure lower rates of many diseases than both people who don’t drink at all and people who drink to excess. The exact mechanisms for these effects have yet to be identified, but the scientific consensus today is that drinking alcohol (of any kind) in moderation protects against heart attack, stroke, type 2 diabetes, arthritis, dementia, and several types of cancer. The teetotaler is at greater risk for disease and early death than the drinker.
Highlight(pink) – FERMENT III. ALCOHOL > Page iv · Location 5175 (Only centuries of British devotion to beer making could produce such a superbly earthy vocabulary of Anglo-Saxon brewing terms: “trub,” “wort,” “pitch,” “malt,” “mash tun,” and, my favorite, “sparge.”) Highlight(pink) – FERMENT III. ALCOHOL > Page iv · Location 5253 But for our relationship to this yeast to qualify as coevolution, the changes must be reciprocal.
Highlight(pink) – FERMENT III. ALCOHOL > Page iv · Location 5254 While we were altering the genome of S. cerevisiae, it was altering ours: Our ancestors evolved the metabolic pathways to detoxify ethyl alcohol in order to make use of its prodigious energy (and,
conceivably, some of its other benefits). Even today, not all humans possess the required genes, and some ethnic groups, lacking the ability to produce the necessary enzymes in their liver, have more trouble metabolizing alcohol than others. For them, alcohol remains more toxin than intoxicant.

Paper for Journal Club Tomorrow

May 22, 2018

Susceptibility of brain atrophy to TRIB3 in #Alzheimer’s disease, evidence from functional prioritization in imaging genetics Nice connection of developing phenotypes from #imaging, combined w. simple polygenic scores from genotypes

Data-Driven Wellness & Personal Coaching – Arivale

May 20, 2018

Seo Young-Deok – Opera Gallery

May 5, 2018
bike chains!

iPad Notebook export for Significant Figures: The Lives and Work of Great Mathematicians

April 28, 2018

Some quick quotes from
Significant Figures: The Lives and Work of Great Mathematicians Stewart, Ian
Citation (MLA): Stewart, Ian. Significant Figures: The Lives and Work of Great Mathematicians. Basic Books, 2017. Kindle file.
that I really liked

Each short quote below is preceded by the words “Highlight” & indication of the location in the book.

9 The Heat Operator • Joseph Fourier
Highlight(orange) – Page 91 · Location 1439
The precise form of the equation led Fourier to a simple solution, in a special case. If the initial temperature distribution is a sine curve, with a maximum temperature in the middle which tails away towards the ends, then as time passes the temperature has the same profile, but this decays exponentially towards zero.
10 Invisible Scaffolding • Carl Friedrich Gauss
Highlight(orange) – Page 98 · Location 1536
When Gauss was eight, his schoolteacher Büttner set the class an arithmetic problem. It’s often stated that this was to add the numbers from 1 to 100, but that’s probably a simplification.
14 The Laws of Thought • George Boole
Highlight(orange) – Page 146 · Location 2255
The quadratic is then the square (px + qy) 2 of a linear form. A coordinate change is a geometric distortion, and it carries the original lines to the corresponding ones for the new variables. If the two lines coincide for the original variables, they therefore coincide for the new ones. So the discriminants must be related in such a manner that if one vanishes, so does the other. Invariance is the formal expression of this relationship.
21 The Formula Man • Srinivasa Ramanujan
Highlight(orange) – Page 223 · Location 3480
For the first three years of his life, he scarcely said a word, and his mother feared he was dumb. Aged five, he didn’t like his teacher and didn’t want to go to school. He preferred to think about things for himself, asking annoying questions such as ‘How far apart are clouds?’ Ramanujan’s mathematical talents surfaced early, and by the age of 11 he had outstripped two college students who lodged at his home.
23 The Machine Stops • Alan Turing
Highlight(orange) – Page 251 · Location 3929
After the war Turing moved to London, and worked on the design of one of the first computers, ACE (Automatic Computing Engine) at the National Physical Laboratory. Early in 1946 he gave a presentation on the design of a stored-program computer –far more detailed than the American mathematician John von Neumann’s slightly earlier design for EDVAC (Electronic Discrete Variable Automatic Computer). The ACE project was slowed down by official secrecy about Bletchley Park, so Turing went back to Cambridge for a year,
Highlight(orange) – Page 252 · Location 3940
He worked on phyllotaxis, the remarkable tendency of plant structures to involve Fibonacci numbers 2, 3, 5, 8, 13, and so on, each being the sum of the previous two.
24 Father of Fractals • Benoit Mandelbrot
Highlight(orange) – Page 261 · Location 4084
In general, if the rank-n item has frequency proportional to nc, for some constant c, we speak of a cth power law.
Highlight(orange) – Page 261 · Location 4085
Classical statistics pays little attention to power-law distributions, focusing instead on the normal distribution (or bell curve), for a variety of reasons, some good. But nature often seems to use power-law distributions instead.
Highlight(orange) – Page 265 · Location 4147
Julia, and another mathematician Pierre Fatou, had analysed the strange behaviour of complex functions under iteration. That is, start with some number, apply the function to that to get a second number, then apply the function to that to get a third number, and so on, indefinitely. They focused on the simplest nontrivial case: quadratic functions of the form f( z) = z2 + c for a complex constant c.

Gallium – Wikipedia

April 28, 2018

Gallium is a chemical element with symbol Ga and atomic number 31. It is in group 13 of the periodic table, and thus has similarities to the other metals of the group, aluminium, indium, and thallium. Gallium does not occur as a free element in nature, but as gallium(III) compounds in trace amounts in zinc ores and in bauxite.[5] Elemental gallium is a soft, silvery blue metal at standard temperature and pressure, a brittle solid at low temperatures, and a liquid at temperatures greater than 29.76 °C (85.57 °F) (above room temperature, but below the normal human body temperature).
The melting point of gallium is used as a temperature reference point. Gallium alloys are used in thermometers as a non-toxic and
environmentally friendly alternative to mercury, and can withstand higher temperatures than mercury. The alloy galinstan (68.5% gallium, 21.5% indium, and 10% tin) has an even lower melting point of −19 °C (−2 °F), well below the freezing point of water.

Maison Kayser

March 5, 2018 Blues & yogurt + table service
ssid=MKBakery129,passwd is phone
7a opening

Bulldog Mobile (LiveSafe) App | It’s Your Yale

March 4, 2018

China’s Selfie Obsession

February 12, 2018

“People would suspiciously ask what kind of camera it was before walking away with expressions ranging from offense to pity. “I can’t allow you to take a picture of me with that camera—it’ll be too ugly,” a woman from Chongqing told me. I assured her that I was not a wang hong and would not be posting it, and we reached a compromise: she would take a selfie of us on her Meitu phone, edit her face, and then send the photo to me.”