Infection and vaccine-induced neutralizing antibody responses to the SARS-CoV-2 B.1.617.1 (India’s “double mutant”) variant

Venkata-Viswanadh Edara and others at bioRxiv:

SARS-CoV-2 has caused a devastating global pandemic. The recent emergence of SARS-CoV-2 variants that are less sensitive to neutralization by convalescent sera or vaccine-induced neutralizing antibody responses has raised concerns. A second wave of SARS-CoV-2 infections in India is leading to the expansion of SARS-CoV-2 variants. The B.1.617.1 variant has rapidly spread throughout India and to several countries throughout the world. In this study, using a live virus assay, we describe the neutralizing antibody response to the B.1.617.1 variant in serum from infected and vaccinated individuals. We found that the B.1.617.1 variant is 6.8-fold more resistant to neutralization by sera from COVID-19 convalescent and Moderna and Pfizer vaccinated individuals. Despite this, a majority of the sera from convalescent individuals and all sera from vaccinated individuals were still able to neutralize the B.1.617.1 variant. This suggests that protective immunity by the mRNA vaccines tested here are likely retained against the B.1.617.1 variant. As the B.1.617.1 variant continues to evolve, it will be important to monitor how additional mutations within the spike impact antibody resistance, viral transmission and vaccine efficacy.

More here.

A sweeping new history of U.S. capitalism finds that economic gains have always been driven by the state

Justin H. Vassallo in the Boston Review:

The start of Joe Biden’s presidency has prompted an unlikely reassessment of the direction of American capitalism. Announcing a “paradigm shift” away from a policy regime that for decades has ruthlessly favored the very wealthy, Biden has invoked the New Deal to capture his vision for activist government. Alongside the expansion of the welfare state, he has promised an ambitious developmental agenda that links together infrastructure, industrial policy, and an energy transition to fight climate change. Though Biden’s resolve to execute his vision remains untested, the prospects for aggressive state intervention now seem far greater than during the Great Recession, when austerity quickly became a transatlantic phenomenon.

The most salient difference between then and now is that Biden has identified long-term investment as critical to the very preservation of democracy. Breaking from the neoliberal economists who held sway over Democratic policymaking for a generation, Biden’s vision is also a quiet disavowal of Hillary Clinton’s boast three years ago that, despite losing the 2016 presidential election to Donald Trump, she “won the places that represent two-thirds of America’s gross domestic product”—the parts of the country “that are optimistic, diverse, dynamic, moving forward.” The pandemic has only further illustrated how even the country’s most prosperous cities, once the drivers of growth in the age of globalization, are in acute need of state-led projects and egalitarian distribution.

More here.

The End of Israel’s Illusion

Shlomo Ben-Ami (former Israeli foreign minister) in Project Syndicate:

The sudden eruption of war outside and inside Israel’s borders has shocked a complacent nation. Throughout Binyamin Netanyahu’s 12-year premiership, the Palestinian problem was buried and forgotten. The recent Abraham Accords, establishing diplomatic relations with four Arab states, seemed to weaken the Palestinian cause further. Now it has re-emerged with a vengeance.

Wars can be triggered by an isolated incident, but their cause is always deeper. In this case, the trigger, the eviction of Palestinians in favor of Israeli nationalists in the Sheikh Jarrah neighborhood of East Jerusalem, touched all the sensitive nerves of the Israeli-Palestinian conflict. Israel’s occupation of East Jerusalem, its humiliating control of access to the Al-Aqsa mosque, the ever-present memory of the 1948 Nakba (the displacement of 700,000 Palestinians when Israel was founded), and the grievances of Israel’s Arab minority are all fueling the current flare-up.

It may be true that the contested real estate in Sheikh Jarrah did belong to a Jewish family before 1948. But Palestinians saw the incident as part of Israel’s unrelenting drive to “Judaize” Jerusalem, and a striking injustice, because the state of Israel was built partly on the abandoned properties of Palestinian refugees. While Jews are entitled to reclaim property they owned before Israel’s founding, Palestinians may not. Those facing eviction in Sheikh Jarrah cannot recover the homes in Jaffa and Haifa that they once owned.

More here.

Wednesday Poem

Perhaps

Perhaps these thoughts of ours
…………………. will never find an audience
Perhaps the mistaken road
…………………. will end in a mistake
Perhaps the lamps we light one at a time
…………………. will be blown out, one at a time
Perhaps the candles of our lives will gutter out
…………………. without lighting a fire to warm us

Perhaps when all the tears have been shed
…………………. the earth will be more fertile
Perhaps when we sing praises to the sun
…………………. the sun will praise us in return
Perhaps these heavy burdens
…………………. will strengthen our philosophy
Perhaps when we weep for those in misery
…………………. we must be silent about the miseries of our own

Perhaps
Because of our irresistible sense of mission
We have no choice

by Shu Ting
from
A Book of Luminous Things
translation from the Chinese, Carolyn Kizer

Burnout: Modern Affliction or Human Condition?

Jill Lepore in The New Yorker:

Burnout is generally said to date to 1973; at least, that’s around when it got its name. By the nineteen-eighties, everyone was burned out. In 1990, when the Princeton scholar Robert Fagles published a new English translation of the Iliad, he had Achilles tell Agamemnon that he doesn’t want people to think he’s “a worthless, burnt-out coward.” This expression, needless to say, was not in Homer’s original Greek. Still, the notion that people who fought in the Trojan War, in the twelfth or thirteenth century B.C., suffered from burnout is a good indication of the disorder’s claim to universality: people who write about burnout tend to argue that it exists everywhere and has existed forever, even if, somehow, it’s always getting worse. One Swiss psychotherapist, in a history of burnout published in 2013 that begins with the usual invocation of immediate emergency—“Burnout is increasingly serious and of widespread concern”—insists that he found it in the Old Testament. Moses was burned out, in Numbers 11:14, when he complained to God, “I am not able to bear all this people alone, because it is too heavy for me.” And so was Elijah, in 1 Kings 19, when he “went a day’s journey into the wilderness, and came and sat down under a juniper tree: and he requested for himself that he might die; and said, It is enough.”

To be burned out is to be used up, like a battery so depleted that it can’t be recharged. In people, unlike batteries, it is said to produce the defining symptoms of “burnout syndrome”: exhaustion, cynicism, and loss of efficacy. Around the world, three out of five workers say they’re burned out. A 2020 U.S. study put that figure at three in four. A recent book claims that burnout afflicts an entire generation. In “Can’t Even: How Millennials Became the Burnout Generation,” the former BuzzFeed News reporter Anne Helen Petersen figures herself as a “pile of embers.” The earth itself suffers from burnout.

More here.

The mysterious microbes that gave rise to complex life

Amber Dance in Nature:

Evolutionary biologist David Baum was thrilled to flick through a preprint in August 2019 and come face-to-face — well, face-to-cell — with a distant cousin. Baum, who works at the University of Wisconsin–Madison, was looking at an archaeon: a type of microorganism best known for living in extreme environments, such as deep-ocean vents and acid lakes. Archaea can look similar to bacteria, but have about as much in common with them as they do with a banana. The one in the bioRxiv preprint had tentacle-like projections, making the cells look like meatballs with some strands of spaghetti attached. Baum had spent a lot of time imagining what humans’ far-flung ancestors might look like, and this microbe was a perfect doppelgänger.

Archaea are more than just oddball lifeforms that thrive in unusual places — they turn out to be quite widespread. Moreover, they might hold the key to understanding how complex life evolved on Earth. Many scientists suspect that an ancient archaeon gave rise to the group of organisms known as eukaryotes, which include amoebae, mushrooms, plants and people — although it’s also possible that both eukaryotes and archaea arose from some more distant common ancestor.

Eukaryotic cells are palatial structures with complex internal features, including a nucleus to house genetic material and separate compartments to generate energy and build proteins. A popular theory about their evolution suggests that they descended from an archaeon that, somewhere along the way, merged with another microbe. But researchers have had trouble exploring this idea, in part because archaea can be hard to grow and study in the laboratory. The microbes have received so little attention that even the basics of their lifestyle — how they develop and divide, for example — remain largely mysterious

More here.

In Defense of Ethnoscience

Justin E. H. Smith in his Substack Newsletter:

“Ethnoscience” and “Indigenous science”, along with more fine-grained designations like “ethnomathematics”, “ethnoastronomy”, etc., are common terms used to describe both Indigenous systems of knowledge, as well as the scholarly study of these systems. These terms are contested among specialists, for reasons I will not address here. More recently they have also been swallowed up by the voracious beast that is our neverending culture war, and are now hotly contested by people who know nothing about them as well.

Thus in his New York Times column of May 13 entitled “This Is How Wokeness Ends”, David Brooks singles out ethnomathematics as one of the “fringe absurdities” produced by the new “soft totalitarian” ideology currently taking America by storm. Two days before that, Brian Leiter declared on his widely read philosophy blog that Indigenous science is “bad science” — this in response to another philosophy blog, Figs in Winter, that had recently deemed Indigenous science “pseudoscience” (Leiter thinks this latter category is unuseful, in view of the well-known demarcation problem in the philosophy of science). Now, Brooks has made a career out of modeling ignorance for intellectually soft and complacent Americans, while Leiter is a representative of an academic discipline that, at least in principle, encourages its members to pursue broad learning and to cultivate an interest in the world around them. So, though perhaps I should be inured to this sort of thing by now, I admit I found it astonishing to come across something so aggressively ignorant and incurious as his dismissal of Indigenous science.

More here.

Sean Carroll’s Mindscape Podcast: Rachel Laudan on Cuisine, Culture, and Empire

Sean Carroll in Preposterous Universe:

For as much as people talk about food, a good case can be made that we don’t give it the attention or respect it actually deserves. Food is central to human life, and how we go about the process of creating and consuming it — from agriculture to distribution to cooking to dining — touches the most mundane aspects of our daily routines as well as large-scale questions of geopolitics and culture. Rachel Laudan is a historian of science whose masterful book, Cuisine and Empire, traces the development of the major world cuisines and how they intersect with politics, religion, and war. We talk about all this, and Rachel gives her pitch for granting more respect to “middling cuisine” around the world.

More here.

Daniel Kahneman: ‘Clearly AI is going to win. How people are going to adjust is a fascinating problem’

Tim Adams in The Guardian:

Could you define what you mean by “noise” in the book, in layman’s terms – how does it differ from things like subjectivity or error?

Our main subject is really system noise. System noise is not a phenomenon within the individual, it’s a phenomenon within an organisation or within a system that is supposed to come to decisions that are uniform. It’s really a very different thing from subjectivity or bias. You have to look statistically at a great number of cases. And then you see noise.

Some of the examples you describe – the extraordinary variance seen in sentencing for the same crimes (even influenced by such external matters as the weather, or the weekend football results), say, or the massive discrepancies in insurance underwriting or medical diagnosis or job interviews based on the same baseline information – are shocking. The driver of that noise often seems to lie with the protected status of the “experts” doing the choosing. No judge, I imagine, wants to acknowledge that an algorithm would be fairer at delivering justice?

The judicial system, I think, is special in a way, because it’s some “wise” person who is deciding. You have a lot of noise in medicine, but in medicine, there is an objective criterion of truth.

More here.

Tuesday Poem

Motherhood is for Beginners

First, realize: you’ve been drowning
for thousands of years and you know
what finally gets their attention?

The economy. Birth rates at their lowest
where you live in a country that boasts
the second highest cost of childbirth

of any industrialized nation
and your neighbor recommends
goat yoga when you lock yourself

in the car to cry. The only thing
we love more than feeding babies
is keeping them in line for bread,

their sweet legs dangling off
mama’s hip and one hand caught
like a finch in her hair. Second:

a man once told you women
who refuse to have children
are selfish, and you stared at him

like he wasn’t your husband,
like that’s not the kind of paradox
you prepared yourself for, loving

a person who thinks this way
even for one disastrous moment,
even when you know he’ll learn

how cruel this claim is long before
you write the poem to remember it.
Forgiving him takes just as much

work as it does to forgive mothers
who say the same thing, assuming
you’ll agree because your daughter

Read more »

Salman Rushdie: ‘I am stupidly optimistic – it got me through those bad years’

Hadley Freeman in The Guardian:

Poor Salman Rushdie. The one thing I am most keen to talk to him about is the one thing he absolutely, definitely does not want to discuss. “I really resist the idea of being dragged back to that period of time that you insist on bringing up,” he grumbles when I make the mistake of mentioning it twice in the first 15 minutes of our conversation. He is in his elegant, book-lined apartment, a cosy armchair just behind him, the corridor to the kitchen over his shoulder. He’s in New York, which has been his home for the past 20 years, and we are talking – as is the way these days – on video. But even through the screen his frustration is palpable, and I don’t blame him. He’s one of the most famous literary authors alive, having won pretty much every book prize on the planet, including the best of the Booker for Midnight’s Children. We’re meeting to talk about his latest book, Languages Of Truth, which is a collection of nonfiction from the last two decades, covering everything from Osama bin Laden to Linda Evangelista; from Cervantes to Covid. So why do I keep bringing up the fatwa?

We try again. I want to do better because, really, he’s a lot of fun to chat to. Given his success and his history, pomposity should be a given, paranoia would be understandable. But this thoughtful man with an easy giggle is neither, as happy to talk about Field Of Dreams (“A very good film!”) as he is about Elena Ferrante, of whom he’s a fan. Also, Rushdie, 73, tells me, that since he recovered from Covid last spring, he’s been working on his first play. “Ooh, that’s exciting,” I say. “What’s it about?”

“Helen of Troy. It’s written in verse, and she’s interesting because all we really know about her is that she ran off with Paris. But who is she? Why does she do what she does? How does she feel about the consequences of her actions?”

More here.

The 1,000-Year Secret That Made Betta Fish Beautiful

Annie Roth in The New York Times:

For centuries, humans have been captivated by the beauty of the betta. Their slender bodies and oversized fins, which hang like bolts of silk, come in a variety of vibrant colors seldom seen in nature. However, bettas, also known as the Siamese fighting fish, did not become living works of art on their own. The betta’s elaborate colors and long, flowing fins are the product of a millennium of careful selective breeding. Or as Yi-Kai Tea, a doctoral candidate at the University of Sydney who studies the evolution and speciation of fishes, put it, “quite literally the fish equivalent of dog domestication.”

A new study, uploaded in April to the preprint service BioRxiv, shows through genome sequencing that humans began domesticating bettas at least 1,000 years ago. The millennium of careful selection gave rise to the stunning diversity of domestic betta fishes alive today, but also caused both wild and domestic betta fish to undergo vast genetic changes. By studying the genes of these fish, the study’s authors argue, scientists can learn a great deal about how domestication alters the genes of wild animals.

Mr. Tea, who was not involved in the analysis, praised the research for being “the first major study to tease apart the genetic basis for this remarkable phenomenon” in fish, he said.

More here.

Clearing the Decks

by Scott F. Aikin and Robert B. Talisse

Here’s a reasonable rule for critical discussion: all views for consideration should receive the same degree of scrutiny.  Subjecting one account to a low level of critical evaluation, but another to a higher level, is not only unfair, but it clearly risks incorrect outcomes. In retrospect, it is easy to see how such a shift can occur, especially when the claims on offer are controversial and when one sees some in the conversation as adversaries or allies. When a person we despise says something, we might even positively want them to be wrong. So, when they say something anodyne, like the sky is blue, we may be motivated to reply in the following fashion:

Oh yeah?  Well, sometimes, it’s red, purple, and yellow. That’s called sunset. And sometimes, it’s grey.  That’s called overcast. Oh, and sometimes, it’s just black.  That’s called night. Nice job overgeneralizing from sunny and cloudless days, you jerk.

You get the picture. Yet when a friendly interlocutor offers up the sky is blue, we tend to treat it with the modest degree of scrutiny that it calls for – as a general statement, with many exceptions. No problem.

One reason why the shift in critical scrutiny is hard to detect in situ is that it happens over time and with a background assumption about the exchange established in the process. This overall pattern we call the clearing the decks fallacy. Here’s how it unfolds. Step 1: Subject your opponents to the highest degree of scrutiny. Step 2: Once it is clear that the opponent’s views cannot satisfy that degree of scrutiny, conclude that they are nonviable and unsalvageable. Step 3: Pronounce your own view, but in a way that assumes that the appropriate degree of scrutiny has greatly diminished (after all, the opposition has been refuted). Step 4: If objections do appear, reply with a reminder of Step 2 – that the alternatives have been eliminated, so objections that must be based on their assumptions are undercut. It’s a neat dialectical strategy: one clears the decks of one’s opposition by adopting an unforgiving critical stance, but then one proceeds as if those same standards are inappropriate when it comes time to articulate one’s own view. In short, one applies demanding standards to clear the decks of one’s opposition, but then retracts those standards when presenting one’s own position once the opposition has been eliminated. Two features of the clearing the decks fallacy deserve emphasis. Read more »

Do Mention It

Editor’s Note: This essay once mentions a well-known racial slur. Indeed, much of the essay is about the usefulness of maintaining a distinction between using a word and merely mentioning it, and argues that mentions of even taboo words should be allowed, so it would be self-defeating to resort to euphemism in this case.

by Gerald Dworkin

For the past year or so there have been a considerable number of cases of teachers or authors or journalists who have been threatened with sanctions, had sanctions imposed, or lost their positions, because of articles they wrote or statements they made as part of their occupations. Many of these cases involved the appearance of the N-word in their speech or written work. Here are some of them.

1. In a course at the Rutgers Law School last Fall, a student was curious about why a defendant in a case was charged with conspiracy to murder, when he had not been directly involved in the shooting. So he looked up the case and found that the defendant had shouted that he was going to  return to the scene where the shots were fired, but first, “I’m going back to Trenton to get my niggers.”  This clarified for the student why the defendant might be charged with conspiracy to murder.

The professor of the course has asserted that she did not hear the word spoken during a videoconference session, which three students had attended after the criminal law class.

As the NY Times reported: “In early April, in response to the incident, a group of Black first-year students at Rutgers Law began circulating a petition calling for the creation of a policy on racial slurs and formal, public apologies from the student and the professor.”

At the height of a ‘racial reckoning,’ a responsible adult should know not to use a racial slur regardless of its use in a 1993 opinion,” states the petition, which was signed by law school students and campus organizations across the country.

“We vehemently condemn the use of the N-word by the student and the acquiescence to its usage,” the petition says.

To date the Professor has not apologized for her conduct and has not been sanctioned. Read more »

Oceans of Life

by Adele A Wilby

Marine biologist Helen Scales’ book, The Brilliant Abyss: True Tales of Exploring the Deep Sea, Discovering Hidden Life and Selling the Seabed is a triumph. The four major sections in the book, ‘Explore’, ‘Depend’, ‘Exploit’ and ‘Preserve’ are indicators of the breadth of issues addressed in the book: the variety of  life forms in the different levels of the oceans; the significance of the oceans to life on the planet; the various ways in which human activity exploits the oceans resources, and concludes with her ideas about how to prevent the ocean from becoming just another area of resources of the planet for exploitation by human beings.

Most of us would have, at some point, looked out across an ocean enthralled by the natural beauty that it projects. However, anybody who has travelled on the ocean would also be aware of the vagaries of the moods that the oceans are capable of and wondered at their awesome power and potential, making them worthy of respect and caution when entering their watery domains. But it is quite extra-ordinary to realise that the beautiful vista of a mirror glass reflection on an utterly calm ocean or the wild raging of it waters is only a fraction of the oceans’ breadth and depth.  As Scales tells us, the oceans take up seven tenths of the surface of the earth. The diverse topological structures and life on land are interesting enough, but the ‘expanses of the deep seabed, the abyssal plains and seamounts, canyons and trenches, plus all the water above them, constitute the single biggest living space on the planet’, a vast reserve of life being and waiting to be discovered and understood. Read more »

Three Poets from Small Presses: All the things of the world on fire

by David Oates

Small poetry presses are the gold dust of the publishing world, glittering yet easy to miss. And of enduring cumulative value.

Of course the Big Five publishers will pick up suitably salable, already-famous, sure-thing poets. Penguin Random House publishes Terrance Hayes, and that’s a damn good thing, a Black poet of subtlety and immediacy; and Amanda Gorman, poet of the recent presidential inauguration; and Mary Oliver, who straddles the line between “accessible” and serious with an uncanny ease and a following most working poets cannot even imagine.

Meanwhile, as my previous essay here at 3QD proposed, the small presses do the nearly-invisible work of finding and developing new poets, and giving mid-career poets their next book or two, and taking risks with weird and strange and occasionally awful poets too. They do this the way ants collect morsels in the woods: because it is their nature.

(Fans of mixed metaphors may ask: So, are these ants collecting gold dust?  And I reply: They are.)

In this essay, three books from contemporary poets whose work I admire. I read them to refresh my sense of the glorious possibilities of language. And to feel that while our public discourse may be as vicious as ever – perhaps even a little worse than the (miserable) average – yet in these small books from small presses, language may be transformative, life-giving, full of surprise and truth and therefore, hope. Read more »