Through self-experimentation and posting his genome online, Carl Zimmer learns what heredity really means — and why DNA and lineage are not one and the same

Cathryn J. Prince in The Times of Israel:

Born to an Ashkenazi Jewish father and mother of Irish and German descent, science and heredity has long fascinated Carl Zimmer.

But when his wife became pregnant with their first child, heredity became a matter of urgency. He wondered what his child would inherit from him and how that inheritance would get passed down to future generations. Being a dedicated science journalist, Zimmer embarked on a quest to decipher the meaning of heredity.

To properly tell the story he knew he needed to delve into one person’s genome. And whose better than his own?

After he had it sequenced, he showed the results to several researchers and had them interpret the findings. He discovered he carries genes for two serious diseases and that he has many identical genes with a typical Nigerian and Chinese person. But perhaps most importantly, Zimmer learned heredity isn’t what we think it is.

More here.



A Sneaky Snapshot

Janet Malcolm at the NYRB:

G. Botsford: Untitled, 1971

In Diana and Nikon I reproduced four pictures from The Snapshot to illustrate the new aesthetic. Except that one of the pictures was not actually from the book, but from Gardner’s desk: the snapshot of the couple on the tennis court. The temptation was too great. The gates stood too wide open. When the book appeared, there on pages 70–71, illustrating the work of The Snapshot’s “sophisticated photographers,” was a spread of four pictures with the captions under them of Joel Meyerowitz, Untitled; Robert Frank, Untitled; Nancy Rexroth, Streaming Window, Washington D.C., 1972; and G. Botsford, Untitled, 1971.

The reader may be wondering how this act of mischief could have gone undetected. Didn’t anyone at David Godine, the book’s publisher, notice? Or was the estimable and amiable Godine in on the mischief? As an A.J. Liebling character once said, “memory grows furtive.” I no longer remember how it was done or whether Godine knew.

more here.

Stanley Cavell as Educator

Mark Greif at n+1:

Cavell, rather than being the type of all college professors, turned out to be unique. His tutelage at that time seemed the big experience of my life, and I can’t say that it wasn’t, even now. I was afraid of him, personally—afraid, I mean, of damaging the relation by something personal. I went in later years to his lectures on aesthetics, attended his screenings of operas and films, tried to focus on sessions on Wittgenstein, on language and epistemology.

I have often asked between then and now what I got myself in for, not that it was Cavell’s fault, not that I wouldn’t have gotten in for it anyway. Nietzsche, when young, advised the initiate, in “Schopenhauer as Educator,” which we read at Cavell’s direction, to cultivate an impersonal self-hatred in order to grow, hating that within yourself which is weak and inferior. It took me more years than it should have to learn that this advice wouldn’t work for me; hatred became personal. (This year, fourteen years later, I saw a note of Nietzsche’s set down when he was fourteen years older: “I wish men would begin by respecting themselves: everything else follows from that. To be sure, as soon as one does this one is finished for others: for this is what they forgive last: ‘What? A man who respects himself?’—”)

more here.

Doom and Gloom: The Role of the Media in Public Disengagement on Climate Change

Elizabeth Arnold at the Shorenstein Center of Harvard University:

In July of 2008, as a national broadcast correspondent, I reported on environmental conditions in Newtok, a remote community of roughly 400 Yup’ik people in Northwest Alaska. Newtok was losing forty to a hundred feet of coastline a year to erosion, and sinking because of “permafrost” that is no longer permanent, the direct result of a warming climate. Flooding threatened homes, the school, and the only supply of clean water. I chose to report on Newtok because the community was actively working on a relocation plan after voting to move to higher, more stable ground. My story compared the actions of Newtok with Kivalina, an Inupiaq community of the same size situated on a barrier island further north. Kivalina faced similar conditions and had filed suit that same year against ExxonMobil Corp. for damages caused by climate change.

In the decade since my report aired on National Public Radio, news outlets from all over the world visited Newtok, Kivalina, Shishmaref, Shaktoolik and a dozen other Alaska Native communities forced to consider relocation because of the effects of climate change. The national stories all fit the same narrative pattern. With images of houses tipping precariously off cliffs, and phrases such as “impending doom,” and “cultural extinction,” the reporting paints a picture of tragedy and hopelessness, framing community members as victims to sell the urgency of mitigation to the public. As a CNN correspondent unabashedly reported, “a trip here is like a trip into a disturbing future.”

The repetition of this narrow narrative in national and international media for more than ten years has not resulted in a groundswell of support for mitigation or adaptation. Nor has it resulted in public policy at the state or federal level. It may have even undermined the ability of these coastal communities to help themselves.

More here.

Donald Hall on Eagle Pond

Donald Hall at The American Scholar:

Old houses are full of holes. Creatures sneak into the living room. A summer ago, a garter snake entered and slithered across my living room. I stepped on its head and threw it outside. The same year, I discovered a visitor who became my favorite for persistence. A chipmunk took up residence and remained on the first floor for two or three months. Every day I would hear chirping, at first sounding like an electronic signal. Then the chipmunk came into sight, pausing with its paws tucked or folded before it, I suppose sustained by my cat’s kibble and water. As for my cat, she stared at it intently, fascinated. My housekeeper, Carole, bought a tiny Havahart trap and baited it with whatever we imagined was a chipmunk treat. Every morning the bait was gone, but so was the chipmunk. One morning the creature skittered from the kitchen into the toolshed, where the door showed a wide space at its bottom, and never appeared again. I felt abandoned. When autumn descended into winter, I walked into the cluttered dining room, never used in old age, and smelled something rotten in a box of unsorted snapshots. Under a layer of pictures I found the small body of our chipmunk. It had not escaped after all. With a paper towel I picked it up, rigid and almost weightless, and threw it from the door as far as I could. Next morning when I opened the door to pick up the newspaper, half of his small mummified corpse lay beside the door.

more here.

The Unpunished Vice: A Life of Reading by Edmund White

Rachel Cooke in The Guardian:

Books are so intimate, somehow, and perhaps this is one reason why so many of the current glut of reading memoirs leave me cold. Even as they strain for this sense of disclosure – don’t you feel like this, too? they ask – their tone is proprietorial, hellbent on exceptionality (I love the Brontës even more than you). You would, I think, accept this from a lover, but not from a writer you’ve never met – unless, I will now add, that writer happens to be Edmund White, the tone of whose new book, The Unpunished Vice: A Life of Reading, quite often resembles the gentle whisper of a sweetheart. Ownership, you see, is not at all his style. In fact, he doesn’t claim always to understand the books that he loves most. “I’ve read it 10 times, though I’m none the wiser for it,” he writes of Anna Karenina, the novel he believes to be the greatest in all of literature.

White’s book is a collection of essays, each connecting the seemingly thousands of books he has read – I find it impossible to imagine anyone better read than White, though with typical modesty he insists he knows lots of people who are – to his long writing life (the author of A Boy’s Own Story is now 78). This is done in loose fashion; like any passionate reader, he hops “from one lily pad to another”. Colette cosies up to Jean Cocteau, and Penelope Fitzgerald to Henry Green, and you must therefore concentrate quite hard, particularly in the matter of writers with whose work you are not familiar (in my case, these included two of his favourites, Jean Giono and Pierre Loti). But it’s wonderful, too: wisdom and a certain kind of tenderness are to be found on every page.

More here.

How Long Can We Live? The Limit Hasn’t Been Reached

Carl Zimmer in The New York Times:

Since 1900, average life expectancy around the globe has more than doubled, thanks to better public health, sanitation and food supplies. But a new study of long-lived Italians indicates that we have yet to reach the upper bound of human longevity. “If there’s a fixed biological limit, we are not close to it,” said Elisabetta Barbi, a demographer at the University of Rome. Dr. Barbi and her colleagues published their research Thursday in the journal Science. The current record for the longest human life span was set 21 years ago, when Jeanne Calment, a Frenchwoman, died at the age of 122. No one has grown older since — as far as scientists know. In 2016, a team of scientists at Albert Einstein College of Medicine in the Bronx made the bold claim that Ms. Calment was even more of an outlier than she seemed. They argued that humans have reached a fixed life span limit, which they estimated to be about 115 years.  A number of critics lambasted that research. “The data set was very poor, and the statistics were profoundly flawed,” said Siegfried Hekimi, a biologist at McGill University. Anyone who studies the limits of longevity faces two major statistical challenges. There aren’t very many people who live to advanced ages, and people that old often lose track of how long they’ve actually lived. “At these ages, the problem is to make sure the age is real,” said Dr. Barbi.

…But that’s not what Dr. Barbi and her colleagues found. Among extremely old Italians, they discovered, the death rate stops rising — the curve abruptly flattens into a plateau. The researchers also found that people who were born in later years have a slightly lower mortality rate when they reach 105.

More here.

Tuesday Poem

Barbarians

They do not come with furred caps
Smelling of maresmilk, scimitared,
Dour, as tellable as kites.

They live quietly next door,
Speak almost the same language,
Wear almost the same clothes.

Inside the walls. But
Do not think they lack
Precisely the same intentions.
.

John Fowles, 1973
from Poems, John Fowles
Ecco Press, 1973

Monday, July 2, 2018

Tyrants Aren’t Smarter Than Democrats, Just More Evil

by Thomas R. Wells

Tyrants like Vladamir Putin and Kim Jong Un seem to win a lot of their geopolitical contests against democratic governments. How do they do it?

A common explanation is that these tyrants are better at playing the game. They are strategic geniuses leading governments with decades of experience in foreign affairs and characterised by single-mindedness and a long-term horizon. Of course they are going to make better geopolitical moves than democratic governments riven by political factionalism and only able to think as far ahead as the next election.

This explanation is wrong. Tyrants don’t succeed because they are especially skilled at the game of geopolitics, but because they are baddies. Tyrants make bold moves because they are willing to subject their country (and the whole world) to more risk. They can do that because they care less than democrats, and hence worry less, about bringing harms to their people. Like a hedge fund manager, they can afford to take big risks because they are not playing with their own money. When tyrants win it is because of luck, not brilliance. This is easier to see when tyrants lose – as they nearly all do in the end, when their luck runs out.

I. The Clownish Incompetence of Tyranny

The myth of the strategic brilliance of tyrants is driven by cognitive biases. There is the assumption that significant events must have significant agency behind them (the same bias that drives conspiracy thinking). And there is the tendency to fill in the murky mysteries of tyrants’ decision-making by projecting our own worst fears. But if you actually think it through it is rather unlikely that tyrannies would be more competent than democracies, let alone bastions of brilliance. Read more »

Means, Medians and Percentiles: Common Statistics Through an Optimization Lens

by Hari Balasubramanian

Figure from the text ‘Introduction to Statistical Learning’ by James, Witten, Hastie and Tibshirani.

Optimization – the search for the best among many – is at the heart of the statistical and machine learning models that get used so extensively these days. Take the simple concept that underlies many of these models: fitting a mathematical curve to data points, better known as regression. In the simplest two-dimensional case, the curve is a line; in three dimensions, it is a plane, as seen in the figure. Among all possible planes – there are infinitely many of them, obtained by changing the angle and orientation: imagine rotating the plane every which way – we would like the one that passes ‘closest’ to as many of the data points (shown in red) as possible. Thus regression, often called the workhorse of machine learning, is really an optimization problem.

It turns out that optimization is fundamentally connected to even basic statistical quantities. Common statistics we we now reflexively use to summarize data – means, medians and percentiles – are themselves answers to certain optimization questions. We are not used to looking at them in this way.

Let’s take the average or sample mean, which, despite its obvious limitations, everyone turns to first. Suppose we have five numbers in a sample: 3,4,5,8 and 12. The sample mean is given by the straightforward calculation:

(3+4+5+8+12)/5 = 6.4

But there is another way to think of the sample mean: as the optimal answer to the following problem. We seek to find the x that minimizes (produces the lowest value of) the sum of the squared difference between x and each observation in the sample. Mathematically, we can write the function as:

(x-3)2 + (x-4)2 + (x-5)2 + (x-8)2 + (x-12)2

At what value of x does the function have its lowest value? In the figure below, the horizontal axis shows the values that x can take (I restricted myself to the range of the data points, 3 to 12). The vertical axis shows value of the sum of squares function corresponding to each value of x.

We see that the function follows a U-shape with the lowest/best value, x=6.4, occurring at the bottom of the U. Simple high school calculus – finding that point on the continuous curve at which the derivative is 0 – will yield the same answer. In fact, the formula for the mean, adding up all the sample values and dividing by the total number in the sample, can be derived using such calculus. Read more »

Why do people care about sport?

by Emrys Westacott

Why do people care about sport? With hundreds of millions of human beings (myself included) obsessively following the world cup that is being played out in Russia, it’s a good time to reflect once again on this perennially interesting question.

Of course, it’s also true that hundreds of millions don’t give a damn about sport. I know the type: I’m closely related to a disproportionate number of them. To these people, the passion aroused by twenty-two men in shorts trying to force a ball between two sticks is a great mystery, and not something they find it easy to respect. In their view, even if they don’t say this out loud, getting all worked up over a soccer match is a) dumb, and b) good evidence that one needs to get a life. And they may be right. But that still leaves the phenomenon of sport-induced passion unexplained.

Since it is arguably the sporting event that occasions the most consuming passions, let’s focus on the world cup (although many of the points made will naturally apply to other sports also). And let’s distinguish, at the outset, between enjoyment and passion.

Why is soccer entertaining?

It isn’t so hard to understand why soccer provides enjoyable entertainment. First, and most obviously, a good match is dramatic; it has a compelling narrative. But unlike a play or a film, it is unscripted, which means the outcome is not determined in advance, and that makes a game genuinely exciting. Read more »

Behind the Oxygen Mask

by Holly Case and Lexi Lerner

Approach, The Naval Aviation Safety Review (June 1962)

What follows is part of a collaborative project between a historian and a student of medicine called “The Temperature of Our Time.” In forming diagnoses, historians and doctors gather what Carlo Ginzburg has called “small insights”—clues drawn from “concrete experience”—to expose the invisible: a forensic assessment of condition, the origins of an idiopathic illness, the trajectory of an idea through time. Taking the temperature of our time means reading vital signs and symptoms around a fixed theme or metaphor—in this case, the oxygen mask—to reveal how our everyday, recorded interactions can acquire extraordinary historical  momentum.

“Among the various exploits, vital or destructive, which oxygen can perform, we varnish makers are interested above all in its capacity to react with certain small molecules such as those of certain oils, and of creating links between them, transforming them into a compact and therefore solid network.”   —Primo Levi, The Periodic Table (1975)

“[A]t 40,000 ft, people have as little as 18 seconds of ‘useful consciousness’ time if they are starved of oxygen. […] [T]he risks of hypoxia–oxygen starvation–are all the greater as people may not realise they are suffering until they can no longer breathe and fall unconscious …”   —Lizzie Porter, “What happens when a plane loses cabin pressure?The Telegraph (Feb. 3, 2016)

“‘Put on your own mask before helping someone else.’ […] I believe this is a metaphor for life.”  Paul Dodd,The Metaphor of the Airplane Oxygen Mask,”  Modern Enlightenment [blog] (May 16, 2015) 

***

E. Everling, “Eine vereinfachte Atmungsmaske für Freiballon-Hochfahrten” [A simplified breathing mask for high-altitude hot air balloon ascents], Deutsche Luftfahrer-Zeitschrift (Feb. 16, 1916)
“Following a two-hour gradual ascent to 5,000 meters, he started his nitrogen experiment. He had to inhale pure nitrogen […] While on the ground this experiment could always be done without ill effects, now after taking just one breath, Mr. Steyrer went from feeling perfectly fine to turning purple and fainting against the edge of the [balloons] basket. Two breaths from the oxygen bottle were enough to revive him.”   Illustrierte Aeronautische Mitteilungen [Illustrated Aeronautical Memoranda], (Nov. 17, 1909)

“Before the oxygen apparatus was used I used to suffer a great deal from flying at high altitudes. […] I used to get this palpitation of the heart and headache when I would fly over 16,000 feet; I would also feel ‘rotten and done up,’ […]”     Air Service Medical, War Department, Air Service Division of Military Aeronautics (1919) Read more »

Sunday, July 1, 2018

Friedrich Nietzsche: The truth is terrible

Brian Leiter in the Times Literary Supplement:

The German philosopher Friedrich Nietzsche (1844–1900) pursued two main themes in his work, one now familiar, even commonplace in modernity, the other still under-appreciated, often ignored.  The familiar Nietzsche is the “existentialist”, who diagnoses the most profound cultural fact about modernity: “the death of God”, or more exactly, the collapse of the possibility of reasonable belief in God. Belief in God – in transcendent meaning or purpose, dictated by a supernatural being – is now incredible, usurped by naturalistic explanations of the evolution of species, the behaviour of matter in motion, the unconscious causes of human behaviours and attitudes, indeed, by explanations of how such a bizarre belief arose in the first place. But without God or transcendent purpose, how can we withstand the terrible truths about our existence, namely, its inevitable suffering and disappointment, followed by death and the abyss of nothingness?

Nietzsche the “existentialist” exists in tandem with an “illiberal” Nietzsche, one who sees the collapse of theism and divine teleology as tied fundamentally to the untenability of the entire moral world view of post-Christian modernity.

More here.

Rising seas: ‘Florida is about to be wiped off the map’

Elizabeth Rush in The Guardian:

In 1890, just over six thousand people lived in the damp lowlands of south Florida. Since then the wetlands that covered half the state have been largely drained, strip malls have replaced Seminole camps, and the population has increased a thousandfold. Over roughly the same amount of time the number of black college degree holders in the United States also increased a thousandfold, as did the speed at which we fly, the combined carbon emissions of the Middle East, and the entire population of Thailand.

About 60 of the region’s more than 6 million residents have gathered in the Cox Science Building at the University of Miami on a sunny Saturday morning in 2016 to hear Harold Wanless, or Hal, chair of the geology department, speak about sea level rise. “Only 7% of the heat being trapped by greenhouse gases is stored in the atmosphere,” Hal begins. “Do you know where the other 93% lives?”

A teenager, wrists lined in aquamarine beaded bracelets, rubs sleep from her eyes. Returns her head to its resting position in her palm. The man seated behind me roots around in his briefcase for a breakfast bar. No one raises a hand.

“In the ocean,” Hal continues. “That heat is expanding the ocean, which is contributing to sea level rise, and it is also, more importantly, creating the setting for something we really don’t want to have happen: rapid melt of ice.”

More here.

Ordinary Faithfulness: Stanley Cavell, 1926–2018

Larry Jackson in n + 1:

EARLY IN THE MORNING on April 10, 1969, four hundred police stormed into University Hall, Harvard’s main administration building. In under twenty minutes they forced out three hundred students using billy clubs and mace, dragging many occupants out by their hair. Nearly two hundred were arrested, and forty-one were seriously injured.

The previous day, three hundred members of Students for a Democratic Society (SDS) had occupied the building and issued demands. Three of them dealt with the SDS campaign to end the campus Reserve Officers’ Training Corps (ROTC) program, which, they claimed, made the university an accessory to genocide in Vietnam. The other three addressed rising rents and planned evictions in Harvard-owned housing in Cambridge and Roxbury.

After “the bust,” as it came to be known on campus, thousands of students—radical and moderate alike—voted to boycott classes in protest. Harvard went on strike.

Philosopher Stanley Cavell, the Walter M. Cabot Professor of Aesthetics and the General Theory of Value at Harvard, who died on June 19at age 91, published his first book, Must We Mean What We Say?, during the strike. 

More here.