Dana-Farber retractions: meet the blogger who spotted problems in dozens of cancer papers

Max Kozlov in Nature:

The prestigious Dana-Farber Cancer Institute (DFCI) in Boston, Massachusetts, acknowledged yesterday that it would seek retractions for six papers and corrections for an additional 31 — some co-authored by DFCI chief executive Laurie Glimcher, chief operating officer William Hahn and several other prominent cancer researchers. The news came after scientific-image sleuth Sholto David posted his concerns about more than 50 manuscripts to a blog on 2 January. In the papers, published in a range of journals including BloodCell and Nature Immunology, David found Western blots — common tests for detecting proteins in biological samples — where bands seemed to be spliced and stretched. He also found images of mice duplicated across figures where they shouldn’t have been. (Nature’s news team is editorially independent of its publisher, Springer Nature, and of other Nature-branded journals.)

…You recently left your 2,000th comment on PubPeer. What keeps you coming back?

I enjoy the ridiculous back and forth with the authors over e-mail. I care a lot about the animals [whose lives are taken to conduct these experiments] as well. The level of expectation we should have when we’re dealing with animals and high-profile institutions is that they’re super careful and that they get things right, so it’s frustrating when you see errors.

More here.



Thursday Poem

Musée des Beaux Arts

About suffering they were never wrong,
The Old Masters: how well they understood
Its human position; how it takes place
While someone else is eating or opening a window or just
walking dully along;
How, when the aged are reverently, passionately waiting
For the miraculous birth, there must always be
Children who did not specially want it to happen, skating
On a pond at the edge of the wood:
They never forgot
That even the dreadful martyrdom must run its course
Anyhow in a corner, some untidy spot
Where the dogs go on with their doggy life and the torturer’s horse
Scratches its innocent behind on a tree.

In Brueghel’s Icarus, for instance: how everything turns away
Quite leisurely from the disaster; the ploughman may
Have heard the splash, the forsaken cry,
But for him it was not an important failure, the sun shone
As it had on the white legs disappearing into the green
Water; and the expensive delicate ship that must have seen
Something amazing, a boy falling out of the sky,
Had somewhere to get to and sailed calmly on.

by W.H. Auden
from
Literature and the Writing Process
Prentice Hall, 1996

Nature In Los Angeles

Jenny Price at The Believer:

There are many places in L.A. you can go to think about the city, and my own favorite has become the Los Angeles River, which looks like an outsize concrete sewer and is most famous for being forgotten. The L.A. River flows fifty-one miles through the heart of L.A. County. It is enjoying herculean efforts to revitalize it, and yet commuters who have driven over it five days a week for ten years cannot tell you where it is. Along the river, the midpoint lies roughly at the confluence with the Arroyo Seco, near Dodger Stadium downtown. L.A. was founded near here in 1781: this area offers the most reliable aboveground supply of freshwater in the L.A. basin. It’s a miserable spot now, a trash-strewn wasteland of empty lots, steel fences, and railroad tracks beneath a tangle of freeway overpasses: it looks like a Blade Runner set that a crew disassembled and then put back together wrong. It’s not the most scenic spot to visit the river but may be the finest place on the river to think about L.A.

more here.

Lou Reed: The King Of New York

Hanif Abdurraqib at Bookforum:

BEYOND AN OLDER SIBLING’S headphones wringing the sweet, distorted fuzz of the Velvet Underground out and into my ears, my second most notable encounter with Lou Reed was in the pages of the Lester Bangs anthology Psychotic Reactions and Carburetor Dung, which has a whole section dedicated to Bangs and his relentless sparring with Reed. A book within a book, almost. There are two interviews that would, today, seem alarming in both their approach and the nature of their candidness, with Bangs demeaning Reed’s pal David Bowie, Reed taking the bait, Bangs shouting that Reed is full of shit. The interviews go on like this, Bangs and Reed clashing, arguing loudly, or with an on-page ferocity that occasionally veered into affection. Reed clamors on about the drugs he consumes to survive, Bangs takes Reed to task for his songwriting’s increasing laziness. Ultimately, in the essays Bangs wrote about Reed, without Reed in the room, we find that these clashes, brutal and invasive as they might have seemed in the interview form, were born out of a writer being present with a subject he admired deeply, growing frustrated that the mythology he’d made of the subject wasn’t being manifested in the person he had been so fascinated by. This frustration inspired some terribly cruel writing that eventually led to a permanent falling-out between the two.

more here.

Wednesday, January 24, 2024

Why the United States leads the world in airline safety

Kyra Dempsey in Asterisk:

In the aftermath of a disaster, our immediate reaction is often to search for some person to blame. Authorities frequently vow to “find those responsible” and “hold them to account,” as though disasters happen only when some grinning mischief-maker slams a big red button labeled “press for catastrophe.” That’s not to say that negligence ought to go unpunished. Sometimes there really is a malefactor to blame, but equally often there isn’t, and the result is that normal people who just made a mistake are caught up in the dragnet of vengeance, like the famous 2009 case of six Italian seismologists who were charged for failing to predict a deadly earthquake. But when that happens, what is actually accomplished? Has anything been made better? Or have we simply kicked the can down the road?

It’s often much more productive to ask why than to ask who. In some industries, this is called a “blameless postmortem,” and in aviation, it’s a long-standing, internationally formalized tradition.

More here.

Empire and Liberalism—a Saidian Reading: On Jeanne Morefield’s “Unsettling the World”

Conor McCarthy in the Los Angeles Review of Books:

Edward Said, the 20th anniversary of whose death has just passed, was one of the United States’ greatest literary critics of the last 50 years. But he was also an intellectual, a figure who transcended or stepped beyond his professional location to think and speak publicly, about matters of public import, for and to a public.

Although Said was trained and practiced as a critic-scholar, the socioprofessional category that really interested him was that of the “intellectual.” Said’s interest in intellectuals and in making himself an intellectual—a central concern of his first two books, as Timothy Brennan pointed out years ago—was what enabled him to consider the realm of culture as a major zone of political engagement. For Said, the cultural intellectual could—and should—take on the tasks set by Noam Chomsky, in his 1967 essay “The Responsibility of Intellectuals”: to “speak the truth and to expose lies.”

Said lived up to that responsibility with great seriousness. Even today, his work and positions offer and embody provocations for disciplines where their effects remain yet unfelt. The challenge of considering these resonances lies at the core of political theorist and Oxford professor Jeanne Morefield’s intriguing monograph Unsettling the World: Edward Said and Political Theory (2022). Morefield argues forcefully that although political theory has only referenced Said’s work in passing, his ideas might be used to effect a thorough reworking of the discipline.

More here.

Wednesday Poem

Invisible City

Hasn’t everyone lived in an invisible
And essentially unreal, imaginary city
With beautiful empty buildings on byways
Or sewers called canals filled with
Slopping water and huge coffins offering
Pronged upright musical clefs to the air
As the whole load staggers nobly
Toward the extraordinary, and maybe Venice
Was named for Venus, the gondola
For someone gone over the edge,
Poled politely up and down with art
By fellows in straw hats and jerseys,
Warehouses, churches, and meeting places,
A Bridge of Sighs where lovers and prisoners
Are still confused and identical as in
D.H. Lawrence’s mating of whales poem where
Archangels of bliss cross over a bull’s
Let’s call it his Bridge of Signs,
For in clandestine Venice, as if named
For Venus, although no whales, there are
Waves of blindness, or a gaudy bondage
To which one submits, and life draws
All its lumens from that bridge.

by Kenneth Rosen
from
Everyday Seductions
edited by Gary Soto
Ploughshares, Spring, 1995

Hawaii’s out-of-control, totally bizarre fight over stray cats

Benji Jones in Vox:

On a warm day last spring, dozens of protesters gathered outside a shopping center on the west side of Hawaii’s Big Island. They weren’t there to boycott a store or a pipeline or to deride a politician. They came to revolt against a new ban on feeding cats in the parking lot. “Stop starving the cats,” the protesters chanted, according to a local newspaper. The lot outside Queens Marketplace, the shopping center, is home to one of the island’s many colonies of stray, or free-ranging, cats. While there are no formal estimates, experts guess that there are hundreds, if not thousands, of these colonies across Hawaii, each comprising anywhere from a few to more than a hundred felines. Hawaii is, to put it simply, teeming with cats.

These furry strays are descended from, or are themselves, abandoned pet cats, though they’re not really abandoned. Most of them have at least one “colony manager,” a term you’ll hear in Hawaii and elsewhere for locals who provide groups of free-ranging cats with food, water, and even medical care. Sometimes colony managers (or their friends) will also build feeding stations, like the one pictured below. These are self-described do-gooders, common across the Hawaiian islands, who feed cats that don’t live with them.

More here.

Paper Trail: Firms churning out fake papers have taken to bribing journal editors

Frederik Joelving in Science:

One evening in June 2023, Nicholas Wise, a fluid dynamics researcher at the University of Cambridge who moonlights as a scientific fraud buster, was digging around on shady Facebook groups when he came across something he had never seen before. Wise was all too familiar with offers to sell or buy author slots and reviews on scientific papers—the signs of a busy paper mill. Exploiting the growing pressure on scientists worldwide to amass publications even if they lack resources to undertake quality research, these furtive intermediaries by some accounts pump out tens or even hundreds of thousands of articles every year. Many contain made-up data; others are plagiarized or of low quality. Regardless, authors pay to have their names on them, and the mills can make tidy profits.

But what Wise was seeing this time was new. Rather than targeting potential authors and reviewers, someone who called himself Jack Ben, of a firm whose Chinese name translates to Olive Academic, was going for journal editors—offering large sums of cash to these gatekeepers in return for accepting papers for publication.

More here.

Tuesday, January 23, 2024

Hamas Kidnapped My Father for Refusing to Be Their Puppet

Ala Mohammed Mushtaha in The Free Press:

On Saturday, December 30, our front door was busted down, and twenty masked men barged in and took my father, a widely respected and deeply learned imam here in Gaza.

One dragged him by his head, and another grabbed him by his beard. My younger brother tried to intervene and reason with the kidnappers, but they beat him. I have a medical condition that makes it hard for me to breathe, so all I could do was watch as the horror unfolded.

I know that if Hamas kills my father, they’ll say that the Israeli army did it. But my father was very keen that even if he died, we should make known the despicable demands they made of him. It was his last request to us, literally as he was being carried out of the door, that should he die, we should publicize the real reason for his death, and it is this:

He wouldn’t preach what Hamas told him to. He refused to tell Gazans that violent resistance, and obedience to Hamas, is the best way out of our current hell.

More here.

How to Guarantee the Safety of Autonomous Vehicles

Steve Nadis in Quanta:

Driverless cars and planes are no longer the stuff of the future. In the city of San Francisco alone, two taxi companies have collectively logged 8 million miles of autonomous driving through August 2023. And more than 850,000 autonomous aerial vehicles, or drones, are registered in the United States — not counting those owned by the military.

But there are legitimate concerns about safety. For example, in a 10-month period that ended in May 2022, the National Highway Traffic Safety Administration reported nearly 400 crashes involving automobiles using some form of autonomous control. Six people died as a result of these accidents, and five were seriously injured.

The usual way of addressing this issue — sometimes called “testing by exhaustion” — involves testing these systems until you’re satisfied they’re safe. But you can never be sure that this process will uncover all potential flaws.

More here.

Influencers: Looking beyond the consensus of the crowd

Wilfred M. McClay in The Hedgehog Review:

When we find words being used in a novel way, our countenances tend to stiffen. What’s going on here? Is this a euphemism? Is there a hidden agenda here?

But there are times when the older language seems inadequate, and in fact may mislead us into thinking that the world has not changed. New signifiers may sometimes be necessary, in order to describe new things.

Such is unquestionably the case of the new/old word influencer. At first glance, it looks harmless and insignificant, a lazy and imprecise way of designating someone as influential. But the word’s use as a noun is the key to what is different and new about it. And much as I dislike the word, and dislike the phenomenon it describes, necessity seems to have dictated that such a word be created.

More here.

Sapiens? The Origins And Obsolescence Of An Epithet

Hunter Dukes at Cabinet Magazine:

By the 1758 edition of Systema naturae, when Linnaeus first endowed humans with the specific epithet sapiens, the maxim “know thyself” had blossomed into a creed that wed introspection with observation. “The first step of wisdom,” he wrote, is to observe “those marks imprinted on [natural bodies] by nature, to distinguish them from each other, and to affix to every object its proper name.” Far from the oblivion of childhood innocence, and decades away from the cognitive decay that would return the natural world to indistinction before his eyes, Linnaeus once more worries about the cost of forgetting. “If the name be lost, the knowledge of the object is lost also; and without these, the student will seek in vain for the means to investigate the hidden treasures of nature.”

It was perhaps this capacity for linguistic stewardship, and the threat posed to knowledge by cultural aphasia, that led Linnaeus to classify his species as sapient. After all, he thought, there are hardly any meaningful physical qualities that separate us from other primates.

more here.

Lindsay Hunter Is Redrawing the Boundaries of Crime Fiction

Stephen Patrick Bell interviews Lindsay Hunter at The Millions:

Lindsay Hunter: As I was drafting this novel, I was thinking of it as almost a shattered windshield, or a crazy quilt. Something made of shards but that, together, was a whole thing. Initially, I had Jackie in both first- and third-person narration. I wanted readers to have access to her story, the way she’d tell it, but also glimpse a more objective truth about her. I thought that was pretty clever. Huge red flag for a writer, when we think we’re clever. As I revisited the novel in the editing process, this fell flat. It just seemed like I’d forgotten to choose a perspective. I chose to stay with first person because I needed people to get really, really close to Jackie. Uncomfortably close. I wanted readers to see her. Jackie is, in my opinion, a reliable narrator. She just chooses what to tell you. She gets as close as she can to facing herself, but she never quite goes all the way. That kind of narrator was huge for this novel. She was truthful, but the truth she was telling just wasn’t the whole story. What she isn’t telling you, what you don’t see, that kept me obsessed as I wrote. That’s what keeps me obsessed when I think of crimes like this, the people involved in them, the aftermath.

more here.

Blood: The Science, Medicine and Mythology of Menstruation

Kate Womersley in The Guardian:

The doctor who taught me about human reproduction at medical school was in fact a veterinarian. More is known about a sheep’s rhythms than a woman’s, he said, setting the tone in our first tutorial, presumably because ewes drive a healthy profit. I was disappointed. I felt that menstruation and pregnancy shouldn’t be narrated to us like they would be for any other animal. These aren’t just biological events, but experiences coloured by memory and anticipation. What about days of frantic maxi pad changes in school cubicles that go unspoken between girls, some as young as eight, unpredictably timed yet reliably painful? Periods are a muddled burden: a monthly shame as well as a relief.

If millennials have been undernourished with information about their bodies, then previous generations were almost starved of it. A flush of coverage has arisen out of this embarrassed silence, such as Emma Barnett’s Period and BBC Radio 4’s series 28ish Days Later. Dr Jen Gunter’s Blood takes an unapologetically scientific approach to the menstrual cycle, written for anyone who wants to understand its often mystified ways and what medicine can do to help. Perhaps Gunter’s resolve to reduce stigma around women’s health was a reaction to her own upbringing in Canada, with a mother who thought tampons were “evil”.

More here.

Can autoimmune diseases be cured? Scientists see hope at last

Cassandra Willyard in Nature:

Back in 2001, immunologist Pere Santamaria was exploring a new way to study diabetes. Working in mice, he and his collaborators developed a method that uses iron oxide nanoparticles to track the key immune cells involved in the disorder.

But then Santamaria, who is at the University of Calgary in Canada, came up with a bold idea. Maybe he could use these particles as a therapy to target and quiet, or even kill, the cells responsible for driving the disease — those that destroy insulin-producing islet cells in the pancreas. It seemed like a far-fetched idea, but he decided to try it. “I kept doing experiment after experiment,” he says. Now, more than two decades later, Santamaria’s therapy is on the cusp of being tested in people. It’s not alone. Researchers have been trying for more than 50 years to tame the cells that are responsible for autoimmune disorders such as type 1 diabetes, lupus and multiple sclerosis. Most of the approved therapies for these conditions work by suppressing the entire immune response. This often alleviates symptoms but leaves people at elevated risk of infections and cancers.

More here.