Crispr Gene Editing Can Cause Unwanted Changes in Human Embryos

Katherine Wu in The New York Times:

A powerful gene-editing tool called Crispr-Cas9, which this month nabbed the Nobel Prize in Chemistry for two female scientists, can cause serious side effects in the cells of human embryos, prompting them to discard large chunks of their genetic material, a new study has found. Administered to cells to repair a mutation that can cause hereditary blindness, the Crispr-Cas9 technology appeared to wreak genetic havoc in about half the specimens that the researchers examined, according to a study published in the journal Cell on Thursday.

The consequences of these errors can be quite serious in some cases, said Dieter Egli, a geneticist at Columbia University and an author of the study. Some cells were so flummoxed by the alterations that they simply gave up on trying to fix them, jettisoning entire chromosomes, the units into which human DNA is packaged, Dr. Egli said. “We’re often used to hearing about papers where Crispr is very successful,” said Nicole Kaplan, a geneticist at New York University who was not involved in the study. “But with the amount of power we hold” with this tool, Dr. Kaplan said, it is crucial “to understand consequences we didn’t intend.”

More here.

Saturday Poem

Euclid

Old Euclid drew a circle
On a sand-beach long ago.
He bounded and enclosed it
With angles thus and so.
His set of solemn greybeards
Nodded and argued much
Of arc and circumference,
Diameter and such.
A silent child stood by them
From morning until noon
Because they drew such charming
Round pictures of the moon.

by Vachel Lindsay

‘Not a Novel’ by Jenny Erpenbeck

Lucy Popescu at The Guardian:

The essays explore the subjects – walls and borders, truth and silence, identity and memory and the limitations of language – present in her fiction while her autobiographical accounts give valuable context. Despite having slept through a nation’s collapse, Erpenbeck swiftly realised: “Everything that had been called the present up until then was suddenly called the past.” And so she erected another border inside herself, “made of time, between the first half of my life which was transformed into history by the fall of the wall… and the second half, which began at that same moment”. She clearly enjoyed a happy childhood. In John we learn about the lovesick schoolboy who would phone her and, refusing to reveal his identity, would quote Beatles lyrics. Years later, when Erpenbeck requested her file from the Stasi, she discovered that they had intercepted John’s daily record of who had arrived and left her apartment block. In Open Bookkeeping her mother’s death in 2008 is reduced to a poignant list of everything Erpenbeck has to find a home for, the accounts she has to close, the refunds that come in and those that don’t.

more here.

The Mystery of Charles Dickens

Robert Gottlieb at the NYT:

A.N. Wilson has been for many years one of England’s most formidable biographers, as well as an amazingly productive novelist — 23 novels under his belt, to match nearly the same number of nonfiction considerations of subjects ranging from Jesus and St. Paul to Milton, Darwin, Hitler, C. S. Lewis and the queen. (Along the way he spent seven years lecturing on medieval literature at Oxford.) His knowledge is wide, his writing fluent — one can only wonder why his name and reputation haven’t flourished here in America the way they have in his own country, where he is something of a Figure. Alas, I don’t believe that this is going to change with his latest book, “The Mystery of Charles Dickens,” which is appearing just in time for the Dickens anniversary. Here, to put it bluntly, is a highly peculiar biography — peculiar not for what it says about Dickens but for what it says about Wilson himself.

more here.

Friday, November 6, 2020

Psychologists offer tips to get through election stress

Alvin Powell in The Harvard Gazette:

Look away, America. For your own good, look away. Everything will still be there when you come back. Even once the vote counting’s done, there’ll be the recounting, and the tag-along lawsuits.

So take a walk, take a breath, take a break from the election drama unspooling at a pace better suited to a garden slug than an advanced nation’s sophisticated vote-counting system. So, psychologists say, maybe you should get off the smartphone, get back to work, and get some perspective. Though weighty issues like climate change, the economy, and the COVID pandemic also are on the table, the science of “affective forecasting” assures us that we’re lousy judges of our own future emotions on such matters.

“One of the things that happens with uncertainty is we often don’t think realistically about the outcome, and we tend to think catastrophically. So, you’re already thinking that if your candidate loses it’s going to be awful, it’s going to be unbearable, it’ll be disastrous,” said psychologist Shelley Carson, a lecturer at the Harvard Extension School and associate of the Faculty of Arts and Sciences’ Psychology Department. “We overestimate how this event — or any event — is going to affect our happiness in the future.”

More here.

The Best Science Books of 2020: The Royal Society Book Prize

Caspar Henderson in Five Books:

Let’s turn to Transcendence by Gaia Vince, who won the Royal Society science book prize back in 2015 for Adventures in the Anthropocene. What’s her latest book about?

This is fascinating and all-encompassing view of evolution from the beginning of the human species to what we are today. It focuses particularly on evolution through fire, language, beauty and time. It’s intelligently and thoroughly researched, with an impressive body of publications and reading being covered. Gaia Vince has lived in three different countries and visited over 60. This comes through as she draws on her experience in various ways. She speaks with authority.

We are used to thinking about genes and the environment in relation to evolution, but she brings out the role of culture, and how this differentiates us from other species. It has given us a level of connectivity that has made us, so far, very successful and has made us into this superorganism, which she calls ‘Homni.’

More here.

France’s President Stands on Principle, But Stumbles in Practice

Justin E. H. Smith in Foreign Affairs:

France elected Emmanuel Macron president in 2017 as a symbolic barrier against the rising global tide of illiberal populism. Four years later, as the chaos fomented by U.S. President Donald Trump builds toward some sort of crescendo in the United States, domestic tensions in France threaten to define Macron’s leadership and legacy. The coronavirus pandemic is resurgent, leading the government to institute a strict new lockdown that will continue at least until early December; the mouvement des “gilets jaunes” (“yellow vest” protest movement) has been simmering since late 2018; and a crisis that began in 2015, when Islamist terrorists twice attacked Paris, never went away and has in fact returned with new intensity in recent months.

These problems require divergent responses, and only an exceptional leader could navigate all of them with success. Macron has acquitted himself most poorly in those domains in which symbolism rings hollow and where concrete solutions matter most. The terrorism crisis and certain dimensions of the pandemic, however, underscore the importance of symbolism, backed by principle, in the face of nihilistic attacks and unprincipled abandonment by traditional allies.

More here.

In Defense of Politics

Michael Gecan in Boston Review:

If timing is everything, I’m in trouble. As a lifelong organizer with the Industrial Areas Foundation, I made a habit of instigating trouble for those who tried to exploit the leaders in the communities I worked with, but rarely made trouble for myself.

Yet now I am choosing to write a piece defending politics a few days before a national election roils the nation and troubles the world. This is a moment when the words ‘politics’ and ‘politicians’ are usually spoken as curses, smears, charges, indictments, not as descriptions, much less as constructive activities and urgent titles.

I’m also writing in another, albeit less immediate, shadow cast by a short book of approximately 270 pages written by the late British social critic Bernard Crick, In Defence of Politics. The book was first published in 1962, when the catastrophic shadows of the holocaust alongside the horrors of totalitarian fascism and communism were still the stuff of our daytime dread and our 2:00 a.m. nightmares. I should say up front that Crick was a socialist. I am not a socialist—I never was and I never will be. Despite this obvious difference of opinion, Crick’s book remains one of the most penetrating and important critiques of ideology and ideologues. Even as Crick aligned himself with socialism, he simultaneously tried to convince his fellow socialists of the errors of their ways. I recommend his book to all of my fellow non-socialists, and even anti-socialists.

More here.

A Large Portion of the Electorate Chose the Sociopath: America will have to contend with that fact

Tom Nichols in The Atlantic:

The moment every Donald Trump opponent has been waiting for is at hand: Joe Biden seems to be taking the lead. So why am I not happy? I am certainly relieved. A Biden victory would be an infinitely better result than a Trump win. If Trump were to maintain power, our child-king would be unfettered by bothersome laws and institutions. The United States would begin its last days as a democracy, finally stepping over the ledge into authoritarianism. A win for Biden would forestall that terrible possibility.

But no matter how this election concludes, America is now a different country. Nearly half of the voters have seen Trump in all of his splendor—his infantile tirades, his disastrous and lethal policies, his contempt for democracy in all its forms—and they decided that they wanted more of it. His voters can no longer hide behind excuses about the corruption of Hillary Clinton or their willingness to take a chance on an unproven political novice. They cannot feign ignorance about how Trump would rule. They know, and they have embraced him. Sadly, the voters who said in 2016 that they chose Trump because they thought he was “just like them” turned out to be right. Now, by picking him again, those voters are showing that they are just like him: angry, spoiled, racially resentful, aggrieved, and willing to die rather than ever admit that they were wrong.

More here.

New York City’s Hart Island

Alexandra Marvar at The Believer:

Starting in the 1870s, and every year for the past fifteen years, journalists have told and retold the “hidden history” of New York City’s Hart Island, a hundred-acre city cemetery off the coast of the Bronx. Some fields are rolling and green with little white plot markers. Others are fresh brown earth, where individual coffins are buried in communal graves. Where there are not bodies, there are dry stone walls, woodlands, wetlands, and nineteenth-century brick ruins ringed by salt marshes and rubble. For over 150 years, the cemetery has been run as an extension of the prison system, difficult to visit, and this fact tends to capture the imagination.

Stories about it have often circled the same details: An island prison for the dead!Boxes of dismembered limbs and Civil War soldiers and bones all clacking together, forgotten in the dirt on a mostly barren piece of land shaped like the top of what else but a tibia bone, ever shrouded in fog, capitula and patellae protruding from its eroding edges.

more here.

JBS Haldane: The Man Who Knew Almost Everything

Ray Monk at The New Statesman:

JBS Haldane – “Jack” to his family and friends – was once described as “the last man who might know all there was to be known”. His reputation was built on his work in genetics, but his expertise was extraordinarily wide-ranging. As an undergraduate at Oxford, he studied mathematics and classics. He never gained any kind of degree in science, but he could explain the latest work in physics, chemistry, biology and a host of other disciplines. He could recite great swathes of poetry in English, French, German, Latin and Ancient Greek. A big man (another description of him is “a large woolly rhinoceros of uncertain temper”), he was unafraid to take anyone on in a fight and, equally, could drink anyone under the table.

In his lifetime (he died in 1964 at the age of 72), Haldane was very well known because of his journalism, his appearances on the radio, his bestselling books of popular science and his promotion of communism. Today, what most people know about him is often confined to the probably apocryphal story that, when asked what his studies of nature had taught him about the Creator, he replied that He has “an inordinate fondness for beetles”.

more here.

Thursday, November 5, 2020

The left just got crushed

Damon Linker in The Week:

When every legally cast vote has been counted, Joe Biden will probably have prevailed in enough states to claim victory in the presidential race, perhaps even ending up with a few more Electoral Votes than Donald Trump managed to earn four years ago. That means Trump will probably be out, defeated in his bid for re-election.

But this is not a moment for Democrats to celebrate.

In the expectations game, the Democratic Party whiffed and whiffed badly. The Biden campaign and its allies managed to drive up turnout — but so did Trump. Republicans put up a hell of a fight, and not just, or even mainly, in the battle for the White House. Democrats have almost certainly failed to win a Senate majority, and so far they have lost some ground in the House as well (while still on track to maintain control of the lower chamber of Congress).

That means that Biden is on track to be a weak, ineffectual president governing at the mercy of Mitch McConnell’s Machiavellian machinations.

More here.

The World’s Worst Public Transport System (in Karachi) Attempts to Modernize

Faseeh Mangi at Bloomberg:

Karachi ranks as having the worst public transport system globally, according to a 2019 study by car-parts company Mister Auto that looked at 100 major cities. It serves about 42% of Karachi’s commuters, relying on decades-old, overcrowded buses that use the roof as a second deck for passengers at times. Roads are filled with potholes, not all traffic signals are automated, and it’s common to see drivers running red lights.  And yet the former capital is home to Pakistan’s main ports and the regional headquarters for companies such as Standard Chartered Plc and Unilever Plc, helping it generate half of the nation’s tax revenue.

Those funds, however, get distributed to other parts of the country. The city’s outgoing mayor Waseem Akhtar said last year he had only 12% administrative control of the city and a lack of funds. The army controls the wealthier areas of Karachi, while the rest is divided among the provincial and federal governments that don’t get along.

“Karachi, despite its importance, is a political orphan,” said Arsalan Ali Faheem, a consultant at DAI, a Bethesda, Maryland-based company that advises on development projects.

More here.

The genomic revolution gives us an opportunity to bend the mortality curve of cancer

Joshua J. Ofman and Azra Raza in Scientific American:

Improving early cancer detection may be the only way to really put a dent in the cancer mortality curve; however, early cancer detection is suffering from a common ailment in medicine and public health: the streetlight effect. We are looking for five cancers “over here” under the streetlight where we have early detection tests, but about 70 percent of cancer deaths are occurring “over there,” in the dark, where we aren’t even looking. Some may assume that we aren’t screening for these cancers because we don’t have treatments, but a review of practice guidelines and the literature shows that nearly all early cancers have effective treatments, even if watchful waiting is recommended for some, such as nonaggressive early prostate cancers.

Patients don’t get to choose which cancer they get. So, what if we transition away from screening for individual cancers, and start screening individuals for all possible cancers? What if we dramatically improved overall cancer detection? What if we shifted to tracking the cancer detection rate (CDR) in the population?

More here.

Thursday Poem

“Levity in low times is not a bad thing”
 …………….………—Ignora Angstorm

Portrait of Lady

Your thighs are appletrees
whose blossoms touch the sky.
Which sky? The sky
where Watteau hung a lady’s
slipper. Your knees
are a southern breeze — or
a gust of snow. Agh! what
sort of man was Fragonard?
—As if that answered
anything. — Ah, yes. Below
the knees, since the tune
drops that way, it is
one of those white summer days,
the tall grass of your ankles
flickers upon the shore—
Which shore?
the sand clings to my lips—
Which shore?
Agh, petals maybe. How
should I know?
Which shore? Which shore?
—the petals from some hidden
appletree — Which shore?
I said petals from an appletree.

by William Carlos Williams