From Science Daily:

Melanie Rutkowski, PhD, of UVA’s Department of Microbiology, Immunology and Cancer Biology, found that disrupting the microbiome of mice caused hormone receptor-positive breast cancer to become more aggressive. Altering the microbiome, the collection of microorganisms that live in the gut and elsewhere, had dramatic effects in the body, priming the cancer to spread. “When we disrupted the microbiome’s equilibrium in mice by chronically treating them antibiotics, it resulted in inflammation systemically and within the mammary tissue,” she said. “In this inflamed environment, tumor cells were much more able to disseminate from the tissue into the blood and to the lungs, which is a major site for hormone receptor-positive breast cancer to metastasize.”

Most breast cancers — 65 percent or more — are hormone receptor positive. That means their growth is fueled by a hormone, either estrogen or progesterone. The good news is that these types of cancers are likely to respond well to hormone therapy. Predicting whether such cancers will spread beyond the breast to other parts of the body (a process called metastasis) is a major challenge within the field, and is primarily driven by clinical characteristics at the time of diagnosis. Early metastasis is affected by a variety of factors, Rutkowski explained. “One of them is having a high level of [immune] cells called macrophages present within the tissue,” she said. “There have also been studies that have demonstrated that increased amounts of the structural protein collagen in the tissue and tumor also lead to increased breast cancer metastasis.”

Having an unhealthy microbiome prior to breast cancer increased both, and the effect was powerful and sustained.

More here.

John McWhorter in the New York Times:

Justice Ruth Bader Ginsburg grew up with a solid old-school Brooklyn accent. She displays no trace of it in recordings of her work as a young litigator, but today, one can hear shades of it in her speech on and off the court. Why?

Black English is often reviled as an indication of lower intelligence, and yet ever more, advertisers seek out voice-over artists with an identifiably “Black” sound. Why?

Things like this do not surprise linguists who specialize in the intersection of language and sociology. For example, they have found that people of the lower middle class, in settings where their speech is being evaluated, tend to speak more “correctly” than even upper-middle-class or wealthy people do. Justice Ginsburg’s suppression of Brooklyn vowels was a perfect example, as is the fact that having moved into a different class since, she subconsciously feels she has less to “prove.”

Meanwhile, the Black English issue can best be explained through an experiment carried out in Montreal in the 1960s at a time when English was considered much more prestigious than French.

More here.

Jennifer Ouellette in Ars Technica:

There’s a pivotal scene in the 2012 film The Hobbit: An Unexpected Journey when Gandalf, Bilbo Baggins, and a company of dwarves are chased by orcs through a classic New Zealand landscape. For Northwestern University neuroscientist and engineer Malcolm MacIver, the scene is an excellent example of the kind of patchy landscape—dotted with trees, bushes, boxers, and rolling knolls—that may have shaped the evolution of higher intelligence in humans, compared to their aquatic ancestors. Specifically, it falls within a “Goldilocks zone”—not too sparse, and not too dense—that favors strategic thinking and planning ahead, leading to the development of “planning” circuitry in the human brain, according to MacIver’s most recent paper, published in Nature Communications.

This latest paper builds on earlier research. Back in 2017, MacIver and several colleagues published a paper advancing an unusual hypothesis: those ancient creatures who first crawled out of the water onto land may have done so because they figured out there was an “informational benefit” from seeing through air, as opposed to water. Eyes can see much farther in air, and that increased visual range could lead them to food sources near the shore. MacIver and his primary co-author, paleontologist Lars Schmitz of the Claremont Colleges, argued that this in turn drove the evolutionary selection of rudimentary limbs, enabling the first animals to move from the water onto land.

More here.

Bradley Campbell in Quillette:

When moral visions clash, it’s common for people to assume their opponents have bad motives rather than different perspectives. And it’s usually wrong. If you advocate some policy you believe will save lives, whether it’s a plan for fighting COVID-19, increasing health-care coverage, or reducing homicide, your opponents probably don’t oppose your plan because they want more people to die. They may think their own plan will save lives, or they may be concerned about other values entirely. You may very well have fundamental moral disagreements with them, but the thing you hate most about their position probably isn’t what’s driving them.

We see this in the current debates over the new social justice movement. The critics of social justice activists sometimes talk as if what’s driving the activists is a kind of oversensitivity, as if they’re the equivalent of small children having tantrums to get attention. In 2016, for example, an Iowa state legislator introduced the “Suck It up, Buttercup” bill, which would have fined universities offering counseling and “cry rooms” to students upset about the 2016 presidential election. And in 2018 then-US Attorney General Jeff Sessions, in a speech about threats to free speech on college campuses, warned that schools were creating a generation of “sanctimonious, sensitive, supercilious snowflakes.”

The social justice activists aren’t snowflakes, though; they’re not people who just haven’t learned to suck it up. Sessions and others may perceive them that way—that is, the sensitivity the activists often display may be what they object to—but surely the activists themselves and those inspired by them are driven by moral concerns, by a vision of how to improve the world. Failing to understand that leads the activists’ critics to underestimate them.

More here.

Lyn Hejinian at Cabinet:

Cyan (pronounced SIGH-ann) is the color that emanates from a calm sea not far offshore on a clear day as the blue of the sky is reflected in salt water awash over yellow sand. You can see it for yourself in postcards mailed from coastal resorts or, if you are at a resort, from a vantage point somewhere above the beach—from a cliff, say, or lacking cliffs, from atop a palm tree. Various shades of cyan form the background to the ad for Swarovski (whatever that is) on page 13 of the April 2005 issue of Gourmet magazine. To create a highly saturated cyan on your own, you might pour 1/4 cup of Arm & Hammer’s Powerfully Clean Naturally Fresh Clean Burst laundry detergent onto the whites in your next load of wash (presumably Arm & Hammer adds the pigment to its product in order to provoke association with what we imagine to be the pristine purity of tropical seas). Also, you might search for “cyan” at wikipedia.org, where a resplendent rectangle of the color is on display, along with a succinct definition: “Cyan is a pure spectral color, but the same hue can also be generated by mixing equal amounts of green and blue light. As such, cyan is the complement of red: cyan pigments absorb red light. Cyan is sometimes called blue-green or turquoise and often goes undistinguished from light blue.”

more here.

David Kordahl at The New Atlantis:

Two new books on quantum theory could not, at first glance, seem more different. The first, Something Deeply Hidden, is by Sean Carroll, a physicist at the California Institute of Technology, who writes, “As far as we currently know, quantum mechanics isn’t just an approximation of the truth; it is the truth.” The second, Einstein’s Unfinished Revolution, is by Lee Smolin of the Perimeter Institute for Theoretical Physics in Ontario, who insists that “the conceptual problems and raging disagreements that have bedeviled quantum mechanics since its inception are unsolved and unsolvable, for the simple reason that the theory is wrong.”

Given this contrast, one might expect Carroll and Smolin to emphasize very different things in their books. Yet the books mirror each other, down to chapters that present the same quantum demonstrations and the same quantum parables. Carroll and Smolin both agree on the facts of quantum theory, and both gesture toward the same historical signposts. Both consider themselves realists, in the tradition of Albert Einstein.

more here.

Steve Donoghue in The Christian Science Monitor:

Even though the year is only a little more than halfway gone, 2020 has understandably been filled with talk about the “solace” of reading. More so than in any previous year in living memory, readers have been diving into books in order to escape the harsh realities of the outside world. In her new book “Austen Years: A Memoir in Five Novels,” award-winning author Rachel Cohen writes of exactly this kind of solace-seeking. While dealing with her father’s death and the birth of her daughter, Cohen found herself in a readerly relationship with the novels of Jane Austen that was more fixed, almost more compulsory, than anything she’d previously imagined for herself. In the opening pages, she muses that “if you had told me that years were coming when I would hardly pick up another serious writer with any real concentration, that the doings of a few English families would come to define almost the entire territory of my reading imagination, and that I would reach a point of such familiarity that I would simply let Austen’s books fall open and read a sentence or two as people in other times and places might use an almanac to soothe and predict, I would have been appalled.”

Her readers will be more forgiving on that point. Many of them have likely experienced the same degree of beneficial concentration in times of stress or sorrow, whether it’s Austen or the Brontë sisters or Shakespeare. But they also won’t find anything appalling in these pages. Cohen has taken her fascination with – and personal dependence on – one great author and transmutes it into something any reader in the world will find downright marvelous.

More here.

Shawna Williams in The Scientist:

When Greg Poore was a freshman in college, he lost his grandmother to pancreatic cancer. “She . . . essentially had 33 days from diagnosis to death,” he recalls. “No one could explain why they hadn’t detected the cancer before.” Three years later, in 2016, as an MD/PhD student in Rob Knight’s lab at the University of California, San Diego, Poore began investigating microbial inhabitants of tumors—and eventually, whether he could find traces of those microbes in the blood that might be used to diagnose patients earlier.

Poore and his colleagues used machine learning to mine microbial genome and transcriptome information from a database of blood and tissue samples from more than 10,000 cancer patients as well as data the team collected on healthy controls. There were indeed distinct microbial mixes in the cancerous versus healthy tissue of individuals with cancer, the researchers found, and in the blood of healthy people compared with those with cancer. In addition, the machine learning models were able to distinguish cancers of various types—and for some cancers, different stages—using microbial DNA and RNA in tumors and DNA in the blood. The data were taken at a single point in time for each patient and don’t establish cause and effect, says Poore, but the microbial signatures could have diagnostic value.

More here.

The muses are ghosts, and sometimes
they come uninvited.― Stephen King

On Ghosts

Blame it on the quartz.
Call it coffin candle,

foolish fire.  A surgery
in Gettysburgh beckons:

Limbs stacked as ricks
at a window.

Call it the staring past.
Call it schism.

Burn the wedding dress.
Call it Chinese grievance.

In Poland, ignus faatua,
“traveller’s lights,” believed

to be spirits of dead
mapmakers.  Eat your cabbage

or else they’ll draw “here”
out of sight.
.

by Lea Graham
from This End of the World: Notes to Robert Kroetsch
Apt. 9 Press, 2016; also published in Ditchpoetry.com.

Former 3QD writer, Vivek Menezes: “Huge congratulations to Zohran Mamdani, who appears to have won the Democratic primary for District 36 in the New York State Assembly (that’s Astoria + Long Island City in Queens). Son of (great) film-director Mira Nair and (great) Ugandan-Indian intellectual force Mahmood Mamdani, the 29-year-old is an exciting progressive with limitless promise. Also very cool: in his previous avatar as rapper Mr. Cardamom, he made this all-time-favourite (of mine) video featuring (the great!) Madhur Jaffrey as foul-mouthed, blunt-smoking, badass granny. Enjoy!”

https://www.youtube.com/watch?v=bCalqwsicls

Sam Leith at The Spectator:

On this week’s books podcast, my guess is Oxford University’s Professor of European Archaeology, Chris Gosden. Chris’s new book The History of Magic: From Alchemy to Witchcraft, From the Ice Age to the Present opens up what he sees as a side of human history that has been occluded by propaganda from science and religion. Accordingly, he delves back to evidence from the earliest human settlements all over the world to learn about our magical past – one thread in what he calls the ‘triple-helix’ of our cultural history. He tells me why John Dee got a bad rap, where magic wands came from – and why, unusually as an academic, he argues that magic isn’t just an anthropological curiosity but might, in fact, have something useful to teach us.

more here.

Namwali Serpell at the NYRB:

Pictures of Sun Ra often suggest chaotic hybridity: priestly futuristic costumes and sets, ancient Egypt and the planet Saturn forming a palimpsest of past and future utopias. His sound synthesized big band, swing, hard bop, reggae, Afropop, electronic music, and Walt Disney musicals. His references—expressed in his lyrics, poetry, and pamphlets—showcased this eclecticism too: Kabbalah, gnosticism, freemasonry, pan-Africanism, Zen. When he taught a course at the University of California, Berkeley in 1971, his syllabus included The Egyptian Book of the Dead; the theosophical works of Madame Blavatsky, the nineteenth-century Russian medium; Henry Dumas, a brilliant poet gunned down by New York City Transit Police in 1968. He often cited George G.M. James’s Stolen Legacy (1954), which claimed that Greek philosophy had filched its ideas from Egyptian mythology.

In Sun Ra’s various writings and interviews, he always maintained that there was a metaphysical basis for what he called his “equations”: non sequitur chains of koans and runes, of numerology and etymology.

more here.

Stan Carey in Sentence First:

My limited knowledge of Scots and Scottish English when I was young was based on caricatures in comics, particularly ‘Hot-Shot Hamish’. It was not until later that visits to Scotland, friendships with Scottish people, and books by the likes of James Kelman and Irvine Welsh gave me a proper flavour of the richness of Scots vocabulary and grammar.

Scots is a language with Germanic roots and a complicated political history. Linguistically it has been described as a continuum spanning Broad Scots and Standard Scottish English, with considerable variety in between. A common misconception is dispatched on the Spellin an Grammar page of Scots Wikipedia: ‘Scots isna juist Inglis written wi orra wirds an spellins. It haes its ain grammar an aw.’

It is wirds that are showcased in Cauld Blasts and Clishmaclavers, a new book by Robin A. Crawford, whose publisher, Elliott & Thompson, sent me a copy. The book is a marvellous compendium of a thousand Scottish words, from a’ (aa, aw) ‘all’ to yowe trummle ‘unseasonably cold weather in early summer’ – cold enough to make a yowe (ewe) trummle (tremble).

More here.

John Horgan in Scientific American:

Horgan: Neuroscientist Christof Koch has suggested that we get brain implants to keep up with machines. Does that strike you as a good idea?

Schneider: It depends upon the larger social and political setting. Several large research projects are currently trying to put AI inside the brain and peripheral nervous system. They aim to hook you to the cloud without the intermediary of a keyboard. For corporations doing this, such as Neuralink, Facebook and Kernel, your brain and body is an arena for future profit. Without proper legislative guardrails, your thoughts and biometric data could be sold to the highest bidder, and authoritarian dictatorships will have the ultimate mind control device. So, privacy safeguards are essential.

I have other worries as well.

More here.

Agnes Callard in the New York Times:

The Greek philosopher Aristotle did not merely condone slavery, he defended it; he did not merely defend it, but defended it as beneficial to the slave. His view was that some people are, by nature, unable to pursue their own good, and best suited to be “living tools” for use by other people: “The slave is a part of the master, a living but separated part of his bodily frame.”

Aristotle’s anti-liberalism does not stop there. He believed that women were incapable of authoritative decision making. And he decreed that manual laborers, despite being neither slaves nor women, were nonetheless prohibited from citizenship or education in his ideal city.

Of course Aristotle is not alone: Kant and Hume made racist comments, Frege made anti-Semitic ones, and Wittgenstein was bracingly upfront about his sexism. Should readers set aside or ignore such remarks, focusing attention on valuable ideas to be found elsewhere in their work?

More here.

Incident

We weren’t there when it happened.
We were on our way to another city,
another life,
under a changing sky that moved with us.
We crossed fields of green then yellow,
towns of suspicious people and impassive crows,
and not once did we miss our home
or feel nostalgia for the past.
That’s how the journey was:
at night silence,
in the morning mist.
Once I found a tin button in my pocket
and played at holding it under the sun,
throwing glimmerings onto the tall crops.
Later it was a used coin
and we had free passage at every checkpoint.
The plains of Europe are our witnesses.
They also know that something happened,
although we never saw it.
We were on our way to another country,
another life,
with neither flamboyant luggage
nor room for memories.
Everything opened before us,
now silence and later mist.

by Jordi Doce
from: We were not there
publisher: Shearsman, Swindon, 2019
translation: 2019, Lawrence Schimel

Original Spanish after “Read More”
.
Read more »

Ruth Williams in The Scientist:

Studies of blood samples from four rheumatoid arthritis patients collected over years has led to the discovery of an RNA profile that predicts an imminent flare-up of symptoms, according to a report in the New England Journal of Medicine today (July 15). The transcriptional signature also indicates that a type of fibroblast previously linked to the disease becomes enriched in the blood before migrating to the joints to wreak havoc. “The work is clearly a breakthrough in how patients with [rheumatoid arthritis] might be managed in the future,” Lawrence Steinman of Stanford University writes in an email to The Scientist. If such an RNA test were commercially developed, then “via a home test involving a mere finger stick, markers that precede a flare [would be] identified. This would allow the individual to consult with their physician and take necessary measures to avert such a flare,” continues Steinman, who studies autoimmune diseases but was not involved in the study.

Rheumatoid arthritis, in which the body’s immune system attacks the joints to cause swelling, stiffness, and pain, exhibits a waxing and waning of symptoms, as do many other autoimmune diseases. Even with treatment to suppress certain immune cells or cytokines, it is common for a patient to experience a couple of relapses each year, says study author Dana Orange, a clinical rheumatologist and researcher at Rockefeller University in the laboratory of Robert Darnell. Relapses in the disease are debilitating and can make life hard to plan, explains Orange. Patients “just don’t know when they are going to be blind-sided and incapacitated with a flare,” she says. Orange, Darnell, and colleagues therefore sought a way to predict such occurrences. Being a dynamic molecule, RNA “lends itself to profiling changes over time,” says Darnell, whose research focuses on RNA regulation in autoimmune and other diseases. “What we wanted to do,” he says, “was to design a study where we could have the RNA before a patient gets sick with a flare . . . to try and get signatures of what might be the antecedents.”

To this end the team recruited patients, via an ad in a newspaper, who were willing to collect tiny samples of their own blood—a few drops via a finger stick—each week and keep diaries of their symptoms. The patients also had clinical evaluations once a month. The team then sequenced the messenger RNA content of a selection of the blood samples—those representing baseline conditions and the weeks immediately prior to, during, and after a flare—to see whether and how the transcriptomes varied with the waxing and waning of symptoms. A total of 162 samples, taken from four patients over the course of one to four years, were sequenced and analyzed computationally. When they looked at the weeks preceding a flare up, “what jumped out was that something changed from the baseline,” says Darnell.  Two weeks prior to a relapse, the team detected a change in the RNA profile that was consistent with an increased abundance of immune cells. “That gave us a hint that we were on the right track and that was exciting,” says Darnell,  “but the big excitement came when we were looking at week -1.”

“There was a unique set of genes that were unexpected—they had signatures of stem cells and mesenchymal cells,” Darnell continues, and “it was not clear exactly what to make of that.”

More here.