Posts Tagged ‘quote’

The Plague Year | The New Yorker

February 14, 2021

Nice discussion on the mistakes on aerosols + a vaccine development chronology

During the study’s initial stages, in February and March, the researchers were discomfited by the implications of their data. “The rapidity and degree of spread suggested it wasn’t a series of one-to-one-to-one transmissions,” Dr. Jacob Lemieux, a lead author, told me. Rather, it was “one-to-many transmission events.” That raised the question of airborne transmission. “At the time, the idea was heretical,” Lemieux said. “We were afraid to consider it, because it implied a whole different approach to infection control”—one in which masks played a central role, especially indoors. But the W.H.O. had repeatedly proclaimed that large respiratory droplets—as from a sneeze or a cough—drove the spread. This wasn’t based on data about the new virus, Lemieux said: “It was received wisdom based on how previous respiratory viruses had behaved. The global public-health
infrastructure has egg on its face. There’s a component of human nature that, until you get burned, you don’t know how hot the fire is.”

Until recently, one of the main imaging tools used by vaccinologists, the cryogenic electron microscope, wasn’t powerful enough to visualize viral proteins, which are incredibly tiny. “The whole field was referred to as blobology,” McLellan said. As a work-around, he developed expertise in X-ray crystallography. …McLellan showed me an “atomistic interpretation” of the F protein on the RSV virus—the visualization looked like a pile of Cheetos. It required a leap of imagination, but inside that murky world Graham and McLellan and their team manipulated the F protein, essentially by cloning it and inserting mutations that kept it strapped down. McLellan said, “There’s a lot of art to it.”

In 2013, Graham and McLellan published “Structure-Based Design of a Fusion Glycoprotein Vaccine for Respiratory Syncytial Virus,” in Science, demonstrating how they had stabilized the F protein in order to use it as an antigen—the part of a vaccine that sparks an immune response. Antibodies could now attack the F protein, vanquishing the virus. Graham and McLellan calculated that their vaccine could be given to a pregnant woman and provide enough antibodies to her baby to last for its first six months—the critical period. The paper opened a new front in the war against infectious disease. In a subsequent paper in Science, the team declared that it had established “clinical proof of concept for structure-based vaccine design,” portending “an era of precision vaccinology.”

Within a day after Graham and McLellan downloaded the sequence for sars-CoV-2, they had designed the modified proteins. The key accelerating factor was that they already knew how to alter the spike proteins of other coronaviruses. On January 13th, they turned their scheme over to Moderna, for manufacturing. Six weeks later, Moderna began shipping vials of vaccine for clinical trials. The development process was “an all-time record,” Graham told me. Typically, it takes years, if not decades, to go from formulating a vaccine to making a product ready to be tested: the process privileges safety and cost over speed.

After the vaccine was tested in animals, it became clear that Graham’s design choices had been sound. The first human trial began on March 16th. A week later, Moderna began scaling up production to a million doses per month.

Checkerboard Chocolates

January 29, 2021

A Look at Some of the World’s Most Modern and Beautiful Chocolates

When we saw the photo of these amazing chocolates, the first thing we asked was, “Would anyone want to eat them?” How can you mess up something that looks so cool? These perfectly shaped mathematical wonders were made by Japanese company Nendo for the big Maison & Objet design show in Paris (that’s French for “House and Object”). The candies were made by pouring chocolate into a “mold,” a hollow shape cut so that when the candies cool down, they pop out looking like these. Suddenly a flat chocolate bar doesn’t seem as exciting as a spiky crown or checkerboard chunk — but in any shape, it all tastes good.

When a Virus Is the Cure | The New Yorker

January 26, 2021

To make matters worse, fears of antibiotic resistance have, in recent decades, created a perverse incentive in medical research: new antibiotics, to remain effective, must be used sparingly, as so-called antibiotics of last resort. As a result, it is almost impossible to recoup the cost of developing them.

Great article!… But I don’t see how phages will solve the economic conundrum: the “perverse incentive [that]…new antibiotics, to remain effective, must be used sparingly…As a result, it is almost impossible to recoup the cost of developing them.”

‘Sanitizing’ functional genomics data may prevent privacy breaches | Spectrum | Autism Research News

January 16, 2021


The new data ‘sanitization’ technique obscures regions of a
participant’s genome in a dataset to secure her privacy, and may encourage more people to participate in genetic studies, says lead investigator Mark Gerstein, professor of biomedical informatics at Yale University.

“If someone hacks into your email, you can get a new email address; or if someone hacks your credit card, you can get a new credit card,” Gerstein says. “If someone hacks your genome, you can’t get a new one.”

To determine which information and how much of it should remain private to prevent a linkage attack, Gerstein and his colleagues performed linkage attacks on existing genetic datasets. In one sample attack, they compared two publicly available databases and RNA sequencing results to successfully identify 421 individuals.

In another linkage attack, Gerstein’s team sequenced the RNA of two volunteers and shuffled these data into a larger dataset. They then obtained DNA samples from the volunteers’ used coffee cups and sequenced their genomes. Again, they could link the two individuals to their genomes with a high degree of certainty.

Based on what they learned from the mock linkage attacks, Gerstein’s team developed a technique to mask some variants from a person’s genetic data while preserving where those variants are located in the genome. To do this, they replace the genetic variant of concern with one from a reference genome; which variants are removed depend on the genetic conditions or predispositions someone’s genetic data reveals.

Introducing too many of these privacy-masking variants can decrease the usefulness of the data. But Gerstein’s team struck a balance that enables researchers to obtain data on gene-expression values but also enables study participants to dictate how much of their genetic information they wish to keep hidden.


Top 20 Alexa commands you’ll wish you knew before

January 4, 2021


To use it, just say “Alexa, drop in on all devices” to reach every Alexa-enabled speaker or “Alexa, drop in on [device name]” to target just one. Then just wait for the confirmation tone before speaking. ….
For example, “Alexa, remember I have a doctor’s appointment at 9 a.m. on Wednesday morning” or “Alexa, remember I put the check in my bedside table.”

Monday night

December 21, 2020

For the past year, Jupiter and Saturn have been dancing ever closer in the night sky. On the evening of Dec. 21, the very nadir of winter, they will be so close — one-tenth of one angular degree — that if your eyes are as bad as mine, they will appear as one blurry, bright planet. With a little optical aid you should be able to discern them as separate orbs, almost kissing, although Jupiter will be 450 million miles in front of the ringed Saturn.

Go out and look southwest in the hour after sunset. According to astronomers, the two planets have not appeared this close to each other in the sky since 1623 — but the sun’s glare then would have rendered them invisible. To find a conjunction that humans could see, you must skip all the way back to 1226, or ahead to March 15, 2080. You might wonder who will be around to witness that event
“}} This Solstice, Solace for the Darkness
A rare conjunction of planets serves as a reminder that there is more to the universe than just ourselves.

How to watch tonight’s ‘great conjunction’ of Jupiter and Saturn

visible near the horizon

Dressing for the Surveillance Age | The New Yorker

December 13, 2020

Much of this @jmseabrook article about facial recognition will soon be applicable to genomic privacy & individuals’ attempts to protect themselves in this sphere as well…


Adversarial examples demonstrate that deep-learning-based C.V. systems are only as good as their training data, and, because the data sets don’t contain all possible images, we can’t really trust them. In spite of the gains in accuracy and performance since the switch to deep learning, we still don’t understand or control how C.V. systems make decisions. “You train a neural network on inputs that represent the world a certain way,” Goldstein said. “And maybe something comes along that’s different—a lighting condition the system didn’t expect, or clothing it didn’t expect. It’s important that these systems are robust and don’t fail catastrophically when they stumble on something they aren’t trained on.”

The early work on adversarial attacks was done in the digital realm, using two-dimensional computer-generated images in a simulation. Making a three-dimensional adversarial object that could work in the real world is a lot harder, because shadows and partial views defeat the attack by introducing nuisance variables into the input image. A Belgian team of researchers printed adversarial images on
two-dimensional boards, which made them invisible to yolo when they held the boards in front of them. Scientists at Northeastern University and at the M.I.T.-I.B.M. Watson A.I. Lab created an adversarial design that they printed on a T-shirt. Goldstein and his students came up with a whole line of clothes—hoodies, sweatshirts, T-shirts.


iPhone Notebook export for The Undoing Project: A Friendship That Changed Our Minds

December 7, 2020

The Undoing Project: A Friendship That Changed Our Minds
Lewis, Michael
Citation (APA): Lewis, M. (2016). The Undoing Project: A Friendship That Changed Our Minds

some quick quotes from the book that I liked are below:

Highlight(pink) – Page 144 · Location 1850
As Amos told it, the psychologists had brought people in and presented them with two book bags filled with poker chips. Each bag contained both red poker chips and white poker chips. In one of the bags, 75 percent of the chips were white and 25 percent were red; in the other bag, 75 percent of the chips were red and 25 percent were white. The subject picked one of the bags at random and, without glancing inside the bag, began to pull chips out of it, one at a time. After extracting each chip, he’d give the psychologists his best guess of the odds that the bag he was holding was filled with mostly red, or mostly white, chips.
Highlight(pink) – Page 146 · Location 1882
Amos presented research done in Ward Edwards’s lab that showed that when people draw a red chip from the bag, they do indeed judge the bag to be more likely to contain mostly red chips. If the first three chips they withdrew from a bag were red, for instance, they put the odds at 3: 1 that the bag contained a majority of red chips. The true, Bayesian odds were 27: 1. People shifted the odds in the right direction, in other words; they just didn’t shift them dramatically enough. Ward Edwards had coined a phrase to describe how human beings responded to new information. They were “conservative Bayesians.” Highlight(pink) – Page 155 · Location 2014
Danny was a pessimist. Amos was not merely an optimist; Amos willed himself to be optimistic, because he had decided pessimism was stupid. When you are a pessimist and the bad thing happens, you live it twice, Amos liked to say. Once when you worry about it, and the second time when it happens.
Highlight(pink) – Page 167 · Location 2176
As the graduate student performed eye exams, Hoffman turned up the hydraulic rollers and made the room roll back and forth. The psychologists soon discovered that people in a building that was moving were far quicker to sense that something was off about the place than anyone, including the designers of the World Trade Center, had ever imagined. This is a strange room,” said one. “I suppose it’s because I don’t have my glasses on. Is it rigged or something? It really feels funny.” The psychologist who ran the eye exams went home every night seasick.* When they learned of Hoffman’s findings, the World Trade Center’s engineer, its architect, and assorted officials from the New York Port Authority flew to Eugene to experience the sway room themselves. They were incredulous. Robertson later recalled his reaction for the New York Times: “A billion dollars right down the tube.” He returned to Manhattan and built his very own sway room, where he replicated Hoffman’s findings. In the end, to stiffen the buildings, he devised, and installed in each of them, eleven thousand two-and-a-half-foot-long metal shock absorbers.
Highlight(pink) – Page 184 · Location 2427
For instance, in families with six children, the birth order B G B B B B was about as likely as G B G B B G. But Israeli kids—like pretty much everyone else on the planet, it would emerge—naturally seemed to believe that G B G B B G was a more likely birth sequence. Why? “The sequence with five boys and one girl fails to reflect the proportion of boys and girls in the population,” they explained. It was less representative. What is more, if you asked the same Israeli kids to choose the more likely birth order in families with six children—B B B G G G or G B B G B G—they overwhelmingly opted for the latter. But the two birth orders are equally likely. So why did people almost universally believe that one was far more likely than the other? Because, said Danny and Amos, people thought of birth order as a random process, and the second sequence looks more “random” than the first.
Highlight(pink) – Page 186 · Location 2448
The average heights of adult males and females in the U.S. are, respectively, 5 ft. 10 in. and 5 ft. 4 in. Both distributions are approximately normal with a standard deviation of about 2.5 in.§ An investigator has selected one population by chance and has drawn from it a random sample. What do you think the odds are that he has selected the male population if 1. The sample consists of a single person whose height is 5 ft. 10 in.? 2. The sample consists of 6 persons whose average height is 5 ft. 8 in.? The odds most commonly assigned by their subjects were, in the first case, 8: 1 in favor and, in the second case, 2.5: 1 in favor. The correct odds were 16: 1 in favor in the first case, and 29: 1 in favor in the second case. The sample of six people gave you a lot more information than the sample of one person. And yet people believed, incorrectly, that if they picked a single person who was five foot ten, they were more likely to have picked from the population of men than had they picked six people with an average height of five foot eight.
Highlight(pink) – Page 187 · Location 2461
A certain town is served by two hospitals. In the larger hospital about 45 babies are born each day, and in the smaller hospital about 15 babies are born each day. As you know, about 50 percent of all babies are boys. The exact percentage of baby boys, however, varies from day to day. Sometimes it may be higher than 50 percent, sometimes lower. For a period of 1 year, each hospital recorded the days on which more than 60 percent of the babies born were boys. Which hospital do you think recorded more such days? Check one:—The larger hospital—The smaller hospital—About the same (that is, within 5 percent of each other) People got that one wrong, too. Their typical answer was “same.” The correct answer is “the smaller hospital.” The smaller the sample size, the more likely that it is unrepresentative of the wider population. “We surely do not mean to imply that man is incapable of appreciating the impact of sample size on sampling variance,” wrote Danny and Amos. “People can be taught the correct rule, perhaps even with little difficulty. The point remains that people do not follow the correct rule, when left to their own devices.”
Highlight(pink) – Page 189 · Location 2489
The frequency of appearance of letters in the English language was studied. A typical text was selected, and the relative frequency with which various letters of the alphabet appeared in the first and third positions of the words was recorded. Words of less than three letters were excluded from the count.
Highlight(pink) – Page 189 · Location 2492
You will be given several letters of the alphabet, and you will be asked to judge whether these letters appear more often in the first or in the third position, and to estimate the ratio of the frequency with which they appear in these positions. . . . Consider the letter K Highlight(pink) – Page 190 · Location 2506
The more easily people can call some scenario to mind—the more available it is to them—the more probable they find it to be. Any fact or incident that was especially vivid, or recent, or common—or anything that happened to preoccupy a person—was likely to be recalled with special ease, and so be disproportionately weighted in any judgment.
Highlight(pink) – Page 190 · Location 2517
They read lists of people’s names to Oregon students, for instance. Thirty-nine names, read at a rate of two seconds per name. The names were all easily identifiable as male or female. A few were the names of famous people—Elisabeth Taylor, Richard Nixon. A few were names of slightly less famous people—Lana Turner, William Fulbright. One list consisted of nineteen male names and twenty female names, the other of twenty female names and nineteen male names. The list that had more female names on it had more names of famous men, and the list that had more male names on it contained the names of more famous women. The unsuspecting Oregon students, having listened to a list, were then asked to judge if it contained the names of more men or more women. They almost always got it backward: If the list had more male names on it, but the women’s names were famous, they thought the list contained more female names, and vice versa. “Each of the problems had an objectively correct answer,” Amos and Danny wrote, after they were done with their strange mini-experiments.
Highlight(pink) – Page 192 · Location 2540
Another possible heuristic they called “anchoring and adjustment.” They first dramatized its effects by giving a bunch of high school students five seconds to guess the answer to a math question. The first group was asked to estimate this product: 8 × 7 × 6 × 5 × 4 × 3 × 2 × 1 The second group to estimate this product: 1 × 2 × 3 × 4 × 5 × 6 × 7 × 8 Five seconds wasn’t long enough to actually do the math: The kids had to guess. The two groups’ answers should have been at least roughly the same, but they weren’t, even roughly. The first group’s median answer was 2,250. The second group’s median answer was 512. (The right answer is 40,320.) The reason the kids in the first group guessed a higher number for the first sequence was that they had used 8 as a starting point, while the kids in the second group had used 1. 9. BIRTH OF THE WARRIOR PSYCHOLOGIST
Highlight(pink) – Page 254 · Location 3428
A rational person making a decision between risky propositions, for instance, shouldn’t violate the von Neumann and Morgenstern
transitivity axiom: If he preferred A to B and B to C, then he should prefer A to C. Anyone who preferred A to B and B to C but then turned around and preferred C to A violated expected utility theory. Among the remaining rules, maybe the most critical—given what would come—was what von Neumann and Morgenstern called the “independence axiom.” This rule said that a choice between two gambles shouldn’t be changed by the introduction of some irrelevant alternative. For example: You walk into a deli to get a sandwich and the man behind the counter says he has only roast beef and turkey. You choose turkey. As he makes your sandwich he looks up and says, “Oh, yeah, I forgot I have ham.” And you say, “Oh, then I’ll take the roast beef.”
Highlight(pink) – Page 258 · Location 3492
Most everyone, including American economists, looked at this choice and said, “I’ll take number 4.” They preferred the slightly lower chance of winning a lot more money. There was nothing wrong with this; on the face of it, both choices felt perfectly sensible. The trouble, as Amos’s textbook explained, was that “this seemingly innocent pair of preferences is incompatible with utility theory.” What was now called the Allais paradox had become the most famous contradiction of expected utility theory. Allais’s problem caused even the most cold-blooded American economist to violate the rules of rationality.* Highlight(pink) – Page 261 · Location 3524
When they made decisions, people did not seek to maximize utility. They sought to minimize regret.
Highlight(pink) – Page 263 · Location 3544
They asked their subjects to rate their unhappiness on a scale from 1 to 20. Then they went to two other groups of subjects and gave them the same scenario, but with one change: the winning number. One group of subjects was told that the winning number was 207358; the second group was told that the winning number was 618379. The first group professed greater unhappiness than the second. Weirdly—but as Danny and Amos had suspected—the further the winning number was from the number on a person’s lottery ticket, the less regret they felt. “In defiance of logic, there is a definite sense that one comes closer to winning the lottery when one’s ticket number is similar to the number that won,” Danny wrote in a memo to Amos, summarizing their data. Highlight(pink) – Page 265 · Location 3576
By testing how people choose between various sure gains and gains that were merely probable, they traced the contours of regret. Which of the following two gifts do you prefer? Gift A: A lottery ticket that offers a 50 percent chance of winning $ 1,000 Gift B: A certain $ 400 or Which of the following gifts do you prefer? Gift A: A lottery ticket that offers a 50 percent chance of winning $ 1 million Gift B: A certain $ 400,000 They collected great heaps of data: choices people had actually made. “Always keep one hand firmly on data,” Amos liked to say. Data was what set psychology apart from philosophy, and physics from metaphysics. In the data, they saw that people’s subjective feelings about money had a lot in common with their perceptual experiences. People in total darkness were extremely sensitive to the first glimmer of light, just as people in total silence were alive to the faintest sound, and people in tall buildings were quick to detect even the slightest swaying. As you turned up the lights or the sound or the movement, people became less sensitive to incremental change. So, too, with money. People felt greater pleasure going from 0 to $ 1 million than they felt going from $ 1 million to $ 2 million.
Highlight(pink) – Page 269 · Location 3651
When choosing between sure things and gambles, people’s desire to avoid loss exceeded their desire to secure gain.
Highlight(pink) – Page 275 · Location 3731
Problem A. In addition to whatever you own, you have been given $ 1,000. You are now required to choose between the following options: Option 1. A 50 percent chance to win $ 1000 Option 2. A gift of $ 500 Most everyone picked option 2, the sure thing. Problem B. In addition to whatever you own, you have been given $ 2,000. You are now required to choose between the following options: Option 3. A 50 percent chance to lose $ 1,000 Option 4. A sure loss of $ 500 Most everyone picked option 3, the gamble.
Highlight(pink) – Page 276 · Location 3744
Danny and Amos were trying to show that people faced with a risky choice failed to put it in context. They evaluated it in isolation. In exploring what they now called the isolation effect, Amos and Danny had stumbled upon another idea—and its real-world implications were difficult to ignore. This one they called “framing.” Simply by changing the description of a situation, and making a gain seem like a loss, you could cause people to completely flip their attitude toward risk, and turn them from risk avoiding to risk seeking.

Tidal phenomenon: high and low tides | Ponant Magazine

November 26, 2020,between%20high%20and%20low%20tide.
The tidal coefficient is the size of the tide in relation to its mean. It usually varies between 20 and 120. The higher the tidal
coefficient, the larger the tidal range – i.e. the difference in water height between high and low tide. This means that the sea level rises and falls back a long way. The mean value is 70. We talk of strong tides – called spring tides – from coefficient 95. Conversely, weak tides are called neap tides.

Opinion | The Pandemic, from the Coronavirus’s Perspective – The New York Times

November 21, 2020

Joshua Lederberg, a Nobel Prize laureate in 1958, at age 33, wrote: “The future of humanity and microbes likely will unfold as episodes of a suspense thriller that could be titled ‘Our Wits Versus Their Genes.’ ”

Wits are fundamentally a product of genes, and in the end, genes beat wits. QT:{{”
Chimpanzees were a species in decline, alas, because of habitat loss and killing by humans; humans were a species in ascendance. The SIVcpz virus reversed its own evolutionary prospects by getting into us and adapting well to the new host. It jumped from a sinking lifeboat onto a luxury cruise ship.

SARS-CoV-2 has done likewise, though its success has occurred much more quickly. It has now infected more than 30 million people, just under half as many as the number of people infected by H.I.V., and in 10 months rather than 10 decades. It’s not the most successful human-infecting virus on the planet — that distinction lies elsewhere, possibly with the Epstein-Barr virus, a very transmissible species of herpesvirus, which may reside within at least 90 percent of all humans, causing syndromes in some and lying latent in most. But SARS-CoV-2 is off to a roaring start.

Now, for purposes of illustration, imagine a different scenario, involving a different virus. In the mountain forests of Rwanda lives a small, insectivorous bat known as Hill’s horseshoe bat (Rhinolophus hilli). This bat is real, but it has been glimpsed only rarely and is classified as critically endangered. Posit a coronavirus, for which this bat serves as reservoir host. Call the virus RhRW19 (a coded abbreviation of the sort biologists use), because it was detected within the species Rhinolophus hilli (Rh), in Rwanda (RW), in 2019 (19).