Massive DNA ‘Borg’ structures perplex scientists

Amber Dance in Nature:

The Borg have landed — or, at least, researchers have discovered their counterparts here on Earth. Scientists analysing samples from muddy sites in the western United States have found novel DNA structures that seem to scavenge and ‘assimilate’ genes from microorganisms in their environment, much like the fictional Star Trek ‘Borg’ aliens who assimilate the knowledge and technology of other species. These extra-long DNA strands, which the scientists named in honour of the aliens, join a diverse collection of genetic structures — circular plasmids, for example — known as extrachromosomal elements (ECEs). Most microbes have one or two chromosomes that encode their primary genetic blueprint. But they can host, and often share between them, many distinct ECEs. These carry non-essential but useful genes, such as those for antibiotic resistance.

Borgs are a previously unknown, unique and “absolutely fascinating” type of ECE, says Jill Banfield, a geomicrobiologist at the University of California, Berkeley. She and her colleagues describe their discovery of the structures in a preprint posted to the server bioRxiv1. The work is yet to be peer-reviewed.

Unlike anything seen before

Borgs are DNA structures “not like any that’s been seen before”, says Brett Baker, a microbiologist at the University of Texas at Austin. Other scientists agree that the find is exciting, but have questioned whether Borgs really are unique, noting similarities between them and other large ECEs. In recent years “people have become used to surprises in the field of ECEs”, says Huang Li, a microbiologist at the Chinese Academy of Sciences in Beijing. “However, the discovery of Borgs, which undoubtedly enriches the concept of ECEs, has fascinated many in the field.”

More here.



Oliver Muday in The Atlantic:

One morning a few weeks ago, I sent my friend a Proust text. It was a photo of a page from Swann’s Way, and it took several attempts for me to capture the near-page-length sentence in its entirety. Next to me, my 2-year-old daughter slowly guided a spoonful of oatmeal into her mouth, noticing my struggle. “Daddy, what are you doing?” she asked. The answer: being insufferable. My friend’s response shortly thereafter confirmed this: “It’s too early for me to follow this sentence.”

Proust’s work has many qualities that might recommend it for pandemic reading: the author’s concern with the protean nature of time, the transportive exploration of memory and the past, or simply the pleasure of immersing oneself in the richly detailed life of another. His novel cycle, In Search of Lost Time, also presents the attractive challenge of surmounting a massive text—multiple volumes, stretching between 3,000 and 4,000 pages, depending on the edition—and the subsequent entry into a rare and rather pretentious club of readers. All of it appealed; I wanted in. What I found was a novel so preoccupied with the minutiae of experience that I had no choice but to reappraise my own.

Before accepting that I was no different from everyone else sublimating their ambition into a “quar project,” my reading habits had changed naturally with the phases of the pandemic. Early in March, as New York City prepared for a shutdown, I felt a sense of adventure in ordering a stockpile of books along with black beans and toilet paper. My first batch included Thomas Bernhard’s Extinction and Penelope Fitzgerald’s The Beginning of Spring, works often cited for their distinctive styles of comedy (self-lacerating and wry, respectively). One night, the two novels happened to be stacked on top of each other beside my bed; I found myself haunted by the cryptic dispatch of their titles.

More here.

Sunday, July 18, 2021

On Kazim Ali’s “Northern Light”

Anjali Vaidya in the Los Angeles Review of Books:

Once upon a time, I decided to start answering the question “Where are you from?” with “The middle of the Pacific Ocean.” I never followed through, though I still think it’s a good answer. I have spent so much of my life bouncing back and forth between the United States and India that, for me, the concept of home is more like a stationary probability distribution — a phrase that I filched from a statistics paper once, and which is likely to make less sense to most people than “the middle of the Pacific Ocean.” After all, the latter at least counts as a place.

All of which is to say that the central themes of Kazim Ali’s Northern Light: Power, Land, and the Memory of Water resonated so strongly with me that I cannot pretend to be objective about how much I loved the book. I was captured by its compelling themes of global desi homelessness and what it means to love places that are not our own — what it means when none of the places we love are our own, but we belong to them anyway.

More here.

Delta Is Driving a Wedge Through Missouri

Ed Yong in The Atlantic:

The summer wasn’t meant to be like this. By April, Greene County, in southwestern Missouri, seemed to be past the worst of the pandemic. Intensive-care units that once overflowed had emptied. Vaccinations were rising. Health-care workers who had been fighting the coronavirus for months felt relieved—perhaps even hopeful. Then, in late May, cases started ticking up again. By July, the surge was so pronounced that “it took the wind out of everyone,” Erik Frederick, the chief administrative officer of Mercy Hospital Springfield, told me. “How did we end up back here again?”

The hospital is now busier than at any previous point during the pandemic. In just five weeks, it took in as many COVID-19 patients as it did over five months last year. Ten minutes away, another big hospital, Cox Medical Center South, has been inundated just as quickly. “We only get beds available when someone dies, which happens several times a day,” Terrence Coulter, the critical-care medical director at CoxHealth, told me.

More here.

How Many Numbers Exist? Infinity Proof Moves Math Closer to an Answer

Natalie Wolchover in Quanta:

In October 2018, David Asperó was on holiday in Italy, gazing out a car window as his girlfriend drove them to their bed-and-breakfast, when it came to him: the missing step of what’s now a landmark new proof about the sizes of infinity. “It was this flash experience,” he said.

Asperó, a mathematician at the University of East Anglia in the United Kingdom, contacted the collaborator with whom he’d long pursued the proof, Ralf Schindler of the University of Münster in Germany, and described his insight. “It was completely incomprehensible to me,” Schindler said. But eventually, the duo turned the phantasm into solid logic.

Their proof, which appeared in May in the Annals of Mathematics, unites two rival axioms that have been posited as competing foundations for infinite mathematics. Asperó and Schindler showed that one of these axioms implies the other, raising the likelihood that both axioms — and all they intimate about infinity — are true.

“It’s a fantastic result,” said Menachem Magidor, a leading mathematical logician at the Hebrew University of Jerusalem. “To be honest, I was trying to get it myself.”

Most importantly, the result strengthens the case against the continuum hypothesis, a hugely influential 1878 conjecture about the strata of infinities.

More here.

Cruelest Summer: What is the cost of comfort?

Andru Okun in The Baffler:

Concerns were raised about the 2020 hurricane season even before it officially began, as above-average air and water temperatures in the Gulf signaled an elevated chance of supercharged storms. When Hurricane Laura struck the southwest coast of Louisiana late last August, it carried with it 150 mile-per-hour winds and a storm surge of roughly ten feet. It was the strongest hurricane to hit Louisiana since 1856, causing around $17.5 billion in damages and killing thirty-three. Six weeks later, the same area was hit by yet another powerful hurricane that dumped fifteen inches of rain onto the storm-ravaged city of Lake Charles. Recently, climate researchers looked at over ninety peer-reviewed scientific articles on tropical cyclones and concluded that anthropogenic global warming was—to no one’s surprise—making storms more powerful. Meanwhile, Louisiana continues to heat up, with cities throughout the state experiencing up to an extra month of extreme heat when compared to fifty years ago.

As I began writing this, the New Orleans area was under an excessive heat warning, with a possibility of “feels like” temperatures nearing 110 degrees. I posted up in front of an air-conditioner—a window unit, set to 82 degrees. I’d describe it as “comfortable,” but what does that even mean? Much of Eric Dean Wilson’s new far-reaching study of air-conditioning—After Cooling: On Freon, Global Warming, and The Terrible Cost of Comfort—deals directly with this question. While it may not be a surprise to learn that Euro-American standards of comfort have been largely dictated by rich and sweaty white men, how exactly this standard was set makes for a fascinating narrative of technological innovation and environmental destruction.

…While air-conditioning became normalized in industry and education by the 1920s, Wilson notes that “the idea of air-conditioning for public and private comfort remained absurd”—even for the wealthy. Early model air-conditioners tended to be clumsy and dangerous, using toxic natural refrigerants like ammonia that could corrode copper piping and leak, thereby infusing a space with the smell of urine and potentially killing anyone who remained inside. For comfort cooling to achieve mainstream acceptance, safer, more efficient systems needed to be created.

Enter chlorofluorocarbons (CFCs), the synthetic refrigerant better known as Freon—which facilitated the widespread adoption of mechanical cooling and massively fucked up the planet in the process.

More here.

The Left Needs Free Speech

Katha Pollitt in Dissent:

People who want to deplatform a speaker or deep-six a book love to point out that the First Amendment only applies to government. But socially and culturally, the notion that people have a right to say what they think and read what they want is much broader than that. That is why common dismissals—you can still get the book online, the speaker has plenty of other ways to express herself, books go out of print all the time—sound flip.

Deplatforming a speaker who has been chosen through the accepted university channels, or attacking Powell’s Books for selling Andy Ngô’s Unmasked: Inside Antifa’s Radical Plan to Destroy Democracy, means you lose the high ground. Now you look just like your enemies. And what have you won, really? Powell’s doesn’t put Ngô’s books on the shelves, but it sells it online. Charles Murray gets to look like the victim of a mob at Middlebury. Josh Hawley, like Woody Allen, takes his book to another publisher.

When you ban a book or shut down a speaker, what you’re really saying is that you need to protect people from ideas you disagree with.

More here.

The secret lives of Neanderthal children

Rebecca Sykes in BBC News:

In any normal summer, Spain’s famous Playa de la Castilla – a perfect 20km (12 mile) long stretch of sand backed by the Doñana nature reserve and close to the resort of Matalascañas, Huelva – would have been covered by the footprints of visiting tourists. But in June 2020 with international flights banned due to Covid-19, the beach was uncharacteristically quiet. Two biologists – María Dolores Cobo and Ana Mateos – who were strolling along the peaceful beach, nonetheless found many footprints. These, however, were made by a very different kind of visitor.

As savage storms and then powerful spring tides earlier in the year had lashed Spain’s south-west coast, huge waves scoured away the sand at the base of 20m (65ft) dunes, revealing an enormous area of rock covering some 6,000 sq m (1.5 acres). Its surface was pocked with indentations which the pair of biologists recognised as footprints: a jumble of hooves, claws and paws preserved in the rock. But when the two women looked closer, among the criss-crossing animal tracks were other prints that looked startlingly human. What’s more, their position at the bottom of the cliff layers meant they had to have been left in the distant past.

More here.

Sunday Poem

Exit Strategy

Tell me there is a way to believe it all,
an exit strategy with groggy murmurs
of nothing but rest and a quiet universe.

All I can think of is my child, asleep
in bed, dealing with whatever birthright
his dreams afford his fears, waiting to wake.

Sometimes I feel like Kepler, poised to inherit
pages of wrinkled data, but grumbling,
What a holy-fucking mess Tycho left behind.

Under the surface of the crowd’s rumble
is a song. We could have danced, you know,
to the how-not-why of these perfect heartbeats.

It’s true. You’ve not been asked to understand.
You’ve been asked to listen, and work it out.

by George Murray
from 
The Rush to Here
Nightwood Editions, 2007

Saturday, July 17, 2021

We Don’t Know, But Let’s Try It

Simon Torracinta in Boston Review:

This spring the United States embarked on a grand experiment. The American Rescue Plan, signed into law on March 11, appropriated $1.9 trillion in public spending—on top of $2.2 trillion for the CARES Act a year prior—to accelerate recovery from the dramatic economic shock of the pandemic. Combined, these measures amount to a fiscal stimulus of unprecedented scale.

Economists in the Biden administration and the Federal Reserve are bullish that this intervention will enable a rapid return to the boom times—or at least what passed for them—that preceded March 2020. They believe that running the economy “hot,” without much slack in unemployment, will extend the fruits of recovery to historically marginalized populations in the labor market and stimulate greater productive investment. Meanwhile, prominent skeptics like Larry Summers, himself a former Treasury secretary, have sounded the alarm about what they see as the significant risks and early signs of inflation, as existing capacity strains to meet the torrent of renewed demand. Implicitly, these admonitions conjure up the specter of the wage-price spirals of the 1970s.

Given the economic landscape since 2008—ultra-low interest rates, reduced worker power, low labor force participation rates—the prospects of this scenario seem rather dim. But the truth is that we don’t really know what will happen. The scale of the experiment and the sheer number of moving parts conspire to make forecasters even more uncertain than usual. Every new piece of economic data is scrutinized for augurs of the future, and entire news cycles turn on the finer points of microchip and lumber supply chains or used car sales.

Although uncertainty presents a persistent headache for central bankers and investors, it has a longstanding place in economic theory.

More here.

A Miniaturist Goes Large

Photography by Casey Kelbaugh, June 17, 2021

Molly Crabapple in the New York Review of Books:

The first thing you see when you walk into “Extraordinary Realities,” Pakistani-American artist Shahzia Sikander’s major retrospective at the Morgan Library, is an Indian Devata dancer, gently resting her knee on the shoulder of Aphrodite. Cast in bronze, nearly life-sized, Promiscuous Intimacies (2020) is Sikander’s first sculpture, and her two women only have eyes for each other. Aphrodite toys with the Devata’s necklace. The Devata curves around Aphrodite like a snake.

The two sex bombs, archetypal respectively for East and West, expose the inanity of the categories. These avatars might be citizens of a single world—one where Alexander’s armies marched through the monsoon-soaked Punjab, where the inhabitants of the Indian city of Nysa claimed Dionysus as their founder, and where a statue of Lakshmi is hidden beneath the lava of Pompeii. Their separation only made sense according to the logic of newer empires. Here in the Morgan Library, they are wrapped together in love. Supremely self-confident and disdainful of all borders, the pair are the perfect guardians for a show in which Sikander blows open the form of miniature painting.

More here.

‘Walking the Invisible’ by Michael Stewart

Anita Sethi at The Guardian:

Stewart travels through the north of England, across moors and meadows, up mountains and through cities and villages and along coastal paths. He also voyages into the inner lives of the Brontës, showing how external place shaped their internal landscapes, how the wild fuelled their imagination.

He begins his walks in the Brontë birthplace, Thornton, in west Yorkshire, where Patrick spent his “happiest days” before the untimely death of his wife Maria and two eldest daughters. He also follows part of the Pennine Way to the ruin of Top Withens, thought to have inspired Emily’s farmhouse location of Wuthering Heights. He captures how for Emily “the moors were a place of awe and fascination. It was a land that was alive with a terrible destructive beauty.” These engaging present-tense walks include an excellent account of recreating the walk that Mr Earnshaw took in 1771 when he travelled from Wuthering Heights to Liverpool – Stewart ventures via Littleborough and Manchester with his dog Wolfie, and has some hair-raising wild camping experiences.

more here.

‘Pessoa’ Is Definitive And Sublime

Parul Sehgal at the NYT:

He published a few books that went mostly unnoticed, but there were rumors of a trunk in his room stuffed with his true life’s work. After his death in 1935, the trunk was discovered, brimming with notes and jottings on calling cards and envelopes, whatever paper appeared to be handy. They were authored not only by Pessoa but by a flock of his personas (“heteronyms,” he called them): a doctor, a classicist, a bisexual poet, a monk, a lovesick teenage girl. Among his writings was a sheaf of papers that would become his masterpiece: “The Book of Disquiet,” a mock confession in sly, despairing aphorisms and false starts — “The active life has always struck me as the least comfortable of suicides.” In total, Pessoa created dozens of heteronyms, most complete with biographies, bodies of work, reviews and correspondence. He was awed, and a little afraid of his mind, its “overabundance.” What relation did it bear to a family history of nervous instability?

Mammoth, definitive and sublime, Richard Zenith’s new biography, “Pessoa,” gives us a group portrait of the writer and his cast of alternate selves — along with a perceptive reading of what it meant for Pessoa to multiply (or did he fracture?) like this.

more here.

What is the Doomsday Clock and why should we keep track of the time?

Ian Lowe in Kurzweil AI:

It made headlines recently when the Doomsday Clock was shifted on January 26, 2017 from three minutes to midnight to a new setting of two and a half minutes to midnight.* That is the nearest the clock has been to midnight for more than 50 years. The body responsible for the clock said the probability of global catastrophe is very high, and the actions needed to reduce the risks of disaster must be taken very soon. It should be an urgent warning to world leaders. The idea of a Doomsday Clock was conceived by the editorial staff of the Bulletin of the Atomic Scientists, which was founded by many of the scientists who worked on the Manhattan Project.

When that publication graduated from being an internal newsletter among the nuclear science community to being a formal magazine in 1947, the clock appeared on the cover. The magazine’s founders said the clock symbolised the urgency of the nuclear dangers that we — and the broader scientific community — are trying to convey to the public and political leaders around the world.

The clock was [initially] set at seven minutes to midnight. Two years later, with the news that a nuclear weapon had been tested by the USSR, the communist state centered on modern Russia, the clock was moved to 11.57. In 1953, the USA first tested the hydrogen bomb, a fusion weapon much more powerful than the fission bombs that had destroyed Hiroshima and Nagasaki. The USSR followed a few months later and the clock was advanced to 11.58 with a warning there was a real chance that from Moscow to Chicago, atomic explosions will strike midnight for Western civilization.

Then there was a period of modest progress. It gradually became apparent that the new weapons were so powerful that only a deranged leader would consider using them against a similarly armed enemy, given the inevitability of catastrophic retaliation. In 1963, after they had been continuously testing more and more deadly weapons, the USA and the USSR signed the Partial Test Ban Treaty, which prohibited atmospheric testing. The clock was moved back to 11.48.

It was a false dawn.

More here.