Sugar-coated RNAs could ‘alter the face of biochemistry as we know it’—if they’re real

Robert F. Service in Science:

Sugar isn’t just for sweets. Inside cells, sugars attached to proteins and fats help molecules recognize one another—and let cells communicate. Now, for the first time, researchers report that sugars also appear to bind to some RNA molecules, the cellular workhorses that do everything from translating DNA into proteins to catalyzing chemical reactions. It’s unclear just what these sugar-coated RNAs do. But if the result holds up, it suggests vast new roles for RNA.

The report, posted to the preprint server bioRxiv on Monday, drew immediate Twitter responses verging on the hyperbolic: “a new era is starting!!” wrote one scientist. “A brilliant example of how collaboration … can alter the face of biochemistry as we know it!” wrote another. “This is a mind-blowing result,” tweeted a third. Asked by Science for comment, scientists were somewhat more measured. “This is a profound observation that nobody anticipated,” says Mark Lehrman, a pharmacologist at the University of Texas (UT) Southwestern Medical Center in Dallas who was not involved in the work. That profound observation still spurs caution: Others aren’t yet convinced about the basic findings.

The notion that RNAs might be modified by other molecules isn’t new. Chuan He, an RNA chemist at the University of Chicago in Illinois, notes that researchers have observed some 170 different chemical modifications to RNA—a methyl group here or an acetyl group there—that, among other functions, make sure RNA winds up in one cellular compartment or another. But until now, no one had seen complex sugars modify RNAs.

More here.

Wednesday, October 2, 2019

The problem with the trolley problem

Simon Beard in Quartz:

Imagine you’re driving a trolley car. Suddenly the brakes fail, and on the track ahead of you are five workers you’ll run over. Now, you can steer onto another track, but on that track is one person who you will kill instead of the five: It’s the difference between unintentionally killing five people versus intentionally killing one. What should you do?

Philosophers call this the “trolley problem,” and it seems to be getting a lot of attention these days—especially how it relates to autonomous vehicles. A lot of people seem to think that solving this thorny dilemma is necessary before we allow self-driving cars onto our roads. How else will they be able to decide who lives or dies when their algorithms make split-second decisions?

I can see how this happened. The trolley problem is part of almost every introductory course on ethics, and it’s about a vehicle killing people. How could an “ethical” self-driving car not take a view on it, right?

However, there’s just one problem: The trolley problem doesn’t really have anything to do with the ethics AI—or even driving.

More here.

How Ergodicity Reimagines Economics for The Benefit of Us All

Mark Buchanan at berfrois:

The upshot is that a subtle and mostly forgotten centuries-old choice in mathematical thinking has sent economics hurtling down a strange path. Only now are we beginning to learn how it might have been otherwise – and how a more realistic approach could help re-align economic orthodoxy with reality, to the benefit of all.

Of particular importance, the approach brings a new perspective to our understanding of cooperation and competition, and the conditions under which beneficial cooperative activity is possible. Standard thinking in economics finds limited scope for cooperation, as individual people or businesses seeking their own self-interest should cooperate only if, by working together, they can do better than by working alone. This is the case, for example, if the different parties have complementary skills or resources. In the absence of possibilities for beneficial exchange, it would make no sense for an agent with more resources to share or pool them together with an agent who has less.

more here.

The Radical Empathy of Lana Del Rey

Quinn Roberts at the LARB:

In Rolling Stone, Greil Marcus called “Venice Bitch” the greatest California beach record of all time. To Marcus, the nine-minute rock ballad was languid and delicate, its production reminiscent of Randy Newman, the Beach Boys, the heyday of ’60s psychedelia. “It opens like a love letter,” he wrote, “prosaic, direct […] then a little more than two minutes in it begins to swirl, and you could be listening to an affair that began years ago or has yet to start.”

According to the press, Lana Del Rey is changing — she’s grown-up, mature. She’s over the flower-crown stuff. For me, somebody whose affair with Lana began years ago, the recent praise comes as a great surprise. It seems like it was only yesterday that Pitchfork was comparing Born to Die to “a faked orgasm […] a collection of torch songs with no fire.” The critical notion of a “before and after” Lana is ultimately unrealistic. It fails to account for the tonal and thematic consistency of her oeuvre, which she has been fortifying since 2012.

more here.

How Isaac Hayes Changed Soul Music

Emily Lordi at The New Yorker:

The meaning of Hayes’s music was similarly complex. But his seizure of musical space—literalized in the LP jacket for “Black Moses,” which unfolded to reveal a full-length portrait of Hayes in a robe, his arms outstretched—made a political statement at a time when black people were being made to feel acutely unwelcome in the public sphere: patrolled by police in their own neighborhoods, maimed and killed for being “in the wrong place at the wrong time.” Hayes took up time and space as if it were owed him, and listeners responded. “Hot Buttered Soul,” despite being what the critic Phyl Garland called “probably the strangest record hit of the year,” became the first Stax LP to go gold. It sold a million records to black consumers alone.

How exactly Hayes emerged from poverty and trauma to fashion himself so deeply at home in the world is one of the miracles of soul music. But, if the source of his confidence is mysterious, its destination is clear: Hayes’s audacious claims to space and selfhood are everywhere in hip-hop. Countless tracks, perhaps most notably Wu-Tang Clan’s “I Can’t Go to Sleep,” sample “Walk On By.”

more here.

Scientists routinely cure brain disorders in mice but not us. A new study helps explain why

Sharon Begley in STAT News:

Lab mice endure a lot for science, but there’s often one (temporary) compensation: near-miraculous recovery from diseases that kill people. Unfortunately, experimental drugs that have cured millions of mice with Alzheimer’s disease or schizophrenia or glioblastoma have cured zero people — reflecting the sad fact that, for many brain disorders, mice are pretty lousy models of how humans will respond to a drug. Scientists have now discovered a key reason for that mouse-human disconnect, they reported on Wednesday: fundamental differences in the kinds of cells in each species’ cerebral cortex and, especially, in the activity of those cells’ key genes. In the most detailed taxonomy of the human brain to date, a team of researchers as large as a symphony orchestra sorted brain cells not by their shape and location, as scientists have done for decades, but by what genes they used. Among the key findings: Mouse and human neurons that have been considered to be the same based on such standard classification schemes can have large (tenfold or greater) differences in the expression of genes for such key brain components as neurotransmitter receptors.

…Last year, scientists described neuropsychiatric drug development as “in the midst of a crisis” because of all the mouse findings that fail to translate to people. Of every 100 neuropsychiatric drugs tested in clinical trials — usually after they “work” in mice — only nine become approved medications, one of the lowest rates of all disease categories.

More here. (Note: Thanks to Dr. Abdullah Ali)

How Spiritualism invented modern art

Kelly Grovier in BBC News:

Every age invents the language that it needs. Posterity will determine what it says about our own era that we have felt compelled to craft such words and phrases as ‘defriended’, ‘photobomb’, ‘flash mob’, ‘happy slapping’ and ‘selfie’. When our forebears in the 1850s found themselves at a loss for a term to describe the new cultural phenomenon of holding seances to summon souls from the great beyond, it was a little-known writer, John Dix, who recorded the emergence of a fresh coinage: “Every two or three years,” Dix wrote in 1853, “the Americans have a paroxysm of humbug … at the present time it is Spiritual-ism”. According to the Oxford English Dictionary, Dix’s comment is the first published use of the word ‘Spiritualism’, in the sense of channelling voices and visions from an invisible realm. Despite Dix’s suggestion that Spiritualism was likely a fleeting fad (“a paroxysm of humbug”), the modern psyche had well and truly been bitten by the bug. Before long, the existence of spirits with whom it was possible to communicate in the here-and-now was being passionately investigated as plausible by everyone from the leading evolutionary scientist Alfred Russel Wallace (who was eventually convinced) to the celebrated novelist and champion of empirical deduction, Arthur Conan Doyle (who needed little persuading).

Over the course of the ensuing century, Spiritualism blossomed into a formidable force that shaped countless milestones of cultural expression: from the ‘automatic writings’ of the Irish poet William Butler Yeats to the so-called ‘New Music’ of the avant-garde US-Austrian composer Arnold Schoenberg. In the visual arts, the spiritualist dimensions of certain painters is well established. Piet Mondrian once confessed that he “got everything” from the occultist writings of Madame Helena Blavatsky, founder of the mystical Theosophical Society, and Wassily Kandinsky published the seminal aesthetic treatise Concerning the Spiritual in Art in 1911.

More here.

Exploring the brain in a new way: Researcher records neurons to understand cognition

Jack Stump in Phys.Org:

Where is Waldo?

Whether we’re searching for Waldo or our keys in a room of clutter, we tap into a part of the frontal region of the brain when performing visual, goal-related tasks. Some of us do it well, whereas for others it’s a bit challenging. One West Virginia University researcher set out to investigate why, and what specifically this part of the brain, called the pre-supplementary motor area, does during searching.

To find out, Shuo Wang, assistant professor of chemical and biomedical engineering, took on the rare opportunity to record single neurons with electrodes implanted in epilepsy patients. He found neurons that signaled whether the target of a visual search was found and, if not, how long the patient had been searching for the item. This suggests that the pre-SMA contributes to goal-directed behavior by signaling goal detection and time elapsed since the start of a search, regardless of the task. It may be the first time scientists have identified neurons in the human pre-SMA that represent search goals, Wang said. These findings contribute to a better understanding of the cognitive aspects of disorders such as Parkinson’s disease and schizophrenia, which are linked to dysfunction of the pre-SMA, he said. Similarly, pre-SMA hyperactivity is a frequent observation in people with autism.

More here.

Wednesday Poem

Bone of My Bone Flesh of My Flesh

I can’t always refer to the woman I love,
my children’s other mother,
as my darling, my beloved,
sugar in my bowl. No.
I need a common, utilitarian word
that calls no more attention to itself
than nouns like grass, bread, house.
The terms husband and wife are perfect for that.
Hassling with PG&E
or dropping off dry cleaning,
you don’t want to say,
The light of my life doesn’t like starch.
Don’t suggest spouse—a hideous word.
And partner is sterile as a boardroom.
Couldn’t we afford a term
for the woman who carried that girl in her arms
when she was still all promise,
that boy curled inside her womb?
And today, when I go to kiss her
and she says “Not now, I’m reading,”
still she deserves a syllable or two—if only
so I can express how furious
she makes me. But
maybe it’s better this way—
no puny pencil-stub of a word.
Maybe these are exactly the times
to drag out the whole galaxy
of endearments: Buttercup,
I should say, lambkin, mon petit chou.

by Ellen Bass
from
The Human Line
Copper Canyon Press, 2007

Tuesday, October 1, 2019

What Was The Golden Age of TV?

Adam Wilson at Harper’s Magazine:

I’ll come back to The Sopranos, but first I want to discuss Bad-Good, an admittedly inelegant term for what the critic Dwight Macdonald called Midcult, which is not particularly elegant either. In his seminal 1960 essay “Masscult and Midcult,” Macdonald coined the word Masscult to describe popular forms—romance novels, Victorian Gothic architecture, the illustrations of Norman Rockwellwhich he refused to dignify by classifying as culture. Macdonald’s chief concern was protecting high culture from the degradation of the marketplace, and to this end, he considered Masscult benign, too forthright in its motives to be mistaken for anything but commerce. He found a larger threat in Midcult, which was similar to Masscult except that it “pretends to respect the standards of High Culture while in fact it waters them down and vulgarizes them.” Midcult was Masscult masquerading as art.

Television began as a strictly Masscult medium, and for most of its history remained indisputably so. In the Forties, the soap opera came to TV from radio as an instrument for selling cleaning products to housewives. The shows were produced by retail brands such as Procter and Gamble, and product promotions were woven directly into their story lines.

more here.

Serotonin By Michel Houellebecq

Houman Barekat at Literary Review:

That an author so notoriously sex-obsessed should concern himself with something as wholesome as ‘happiness’ looks, at first sight, like something of a contradiction. But Houellebecq was never really a hedonist. While often gratuitously graphic, his sex scenes are notably listless: related in blandly functional prose, they are conspicuously devoid of eroticism or joy. What some have interpreted as licentiousness could in fact be seen as the inverted prudery of the repressed social conservative. In Houellebecq’s fiction the libido, whether waxing or waning, is a problem to be overcome.

In an essay published in Harper’s earlier this year, Houellebecq praised Donald Trump’s protectionist economic policies, describing his administration as a ‘necessary ordeal’, a corrective to the free market fundamentalism that has dominated Western politics for so long. His disaffected protagonists embody the impulse, common to Left and Right alike, to halt the juggernaut of unfettered globalisation.

more here.

A World Without Children

Samuel Scheffler in The Point:

My wife and I never spent much time talking about whether we wanted to have children. It was clear to both of us that we did, and our only concern was that we might not be able to. Yet if you had asked me why I wanted to have children, I would not have had anything very articulate to say. Nor did that fact bother me. Having children just seemed like the natural next step, and I felt no need to have or give reasons.

For increasing numbers of people in developed countries, things are not so simple. The decision whether to have children is regarded as an important lifestyle choice. Many people choose not to have children, and they bristle at the description of themselves as “childless.” The preferred description is “childfree,” which suggests the absence of a burden (compare “carefree”) rather than a form of privation (compare “homeless,” “jobless” or “friendless”). Marketers regard two-career couples without children—or DINKS (dual-income, no kids), in the slang expression—as an attractive target demographic.

More here.

Sean Carroll’s Mindscape Podcast: Will Wilkinson on Partisan Polarization and the Urban/Rural Divide

Sean Carroll in Preposterous Universe:

The idea of “red states” and “blue states” burst on the scene during the 2000 U.S. Presidential elections, and has a been a staple of political commentary ever since. But it’s become increasingly clear, and increasingly the case, that the real division isn’t between different sets of states, but between densely- and sparsely-populated areas. Cities are blue (liberal), suburbs and the countryside are red (conservative). Why did that happen? How does it depend on demographics, economics, and the personality types of individuals? I talk with policy analyst Will Wilkinson about where this division came from, and what it means for the future of the country and the world.

More here.

Is the United States on the brink of a revolution?

Serbulent Turan in The Conversation:

Of course, every revolution is unique and comparisons between them do not always yield useful insights. But there are a few criteria we identify in hindsight that are usually present in revolutionary explosions.

First, there’s tremendous economic inequality.

Second, there’s a deep conviction that the ruling classes serve only themselves at the expense of everyone else, undermining the belief that these inequalities will ever be addressed by the political elite.

Third, and somewhat in response to these, there is the rise of political alternatives that were barely acceptable in the margins of society before.

More here.

The Arc of Life: Roger Penrose

Stephen Hawking once said of his long-time friend and collaborator Roger Penrose: “although I’m regarded as a radical, I’m definitely a conservative compared to Roger”. Roger Penrose has made ground-breaking contributions to the fields of quantum gravity, general relativity, and cosmology. In this interview with filmmaker David Malone, Penrose looks back on his life’s work and shares new ideas on the subjects of logic and consciousness.

Who’s Afraid of Impeachment? On Presidential Investigation and a 2020 Backlash

Anthont Dimaggio in Counterpunch:

There has been quite a bit of prophesizing among pundits in the news media, on the right and elsewhere, and even among some on the left with which I’ve spoken, in which critics confidently maintain that impeachment is a “gift” to Trump, dividing the nation, but mobilizing and energizing Trump’s base, thereby handing the election to Trump. These claims are almost entirely based on fear and conjecture, not on actual evidence. If we look back to the limited history of this country’s use of impeachment against presidents in modern times, there is little evidence to draw from one way or another, and certainly no cases that are equivalent to this one, in terms of telling us how impeachment will impact an election that is so far into the future – an entire year from now.

Conceding the uncertainty associated with the inquiry against Trump, available evidence suggests there is little reason to be engaging in fearmongering on impeachment. Going back to the looming impeachment of Richard Nixon following the emergence of the Watergate scandal, we see no evidence that the removal strategy harmed Democrats. Republicans lost 49 seats in the House in 1974, while losing another 5 in the Senate. Gerald Ford’s reputation – as measured by his job approval rating – quickly nosedived following his pardon of Nixon, and Jimmy Carter won the 1976 election, defeating Ford, while Democrats gained a seat in the House of Representatives, while losing one seat in the Senate. In other words, there were no observable repercussions for the Democrats for forcing Nixon from office.

More here.

These Ants Use Germ-Killers, and They’re Better Than Ours

Carl Zimmer in The New York Times:

As a microbiologist, Massimiliano Marvasi has spent years studying how microbes have defeated us. Many pathogens have evolved resistance to penicillin and other antimicrobial drugs, and now public health experts are warning of a global crisis in treating infectious diseases. These days, Dr. Marvasi, a senior researcher at the University of Florence in Italy, finds solace in studying ants. About 240 species of ants grow underground gardens of fungi. They protect their farms against pathogens using powerful chemicals secreted by bacteria on their bodies. Unlike humans, ants are not facing a crisis of antimicrobial resistance. Writing in the journal Trends in Ecology and Evolution, Dr. Marvasi and his colleagues argue that fungus-farming ants could serve as a model for drug development. It’s not just that they have antimicrobials — it’s how they use their drugs.

Fungus-farming ants bring leaves or other debris to gardens in their nests, where certain kinds of fungi thrive. The fungi — which can flourish nowhere else — grow into dense webs that the ants feed to their larvae. But the crops are also attractive to a parasitic fungus called Escovopsis. It attacks the gardens and starves the ants. “It’s a war between the ants and the pathogens for the same food,” Dr. Marvasi said. The ants have powerful allies in this war: bacteria that live on their thoraxes. Worker ants coat eggs with certain strains of these bacteria. As an ant matures, it feeds its personal supply of bacteria with secretions from glands on its thorax. The bacteria pay the ants back for this special care by making powerful antimicrobials that kill Escovopsis, protecting the gardens from destruction.

The fact that bacteria make antimicrobials is hardly surprising. The ones that doctors prescribe today were mostly discovered in the soil, made by microbes. What is surprising is that the chemicals used by the ants work so well.

More here.

Tuesday Poem

Praying the Hours At Elkhorn Slough

God. Ocean. Sunrise.
Whatever I am sitting here between,
hello.

Sea otter profile:
backcurved, hooking the tide.

Nothing so distinctive
–so joyfully learned, wondrously greeted
every salt-gift sighting.

Lowtide wader talk.
Coyote brush sun-scented
and the seals hauled out.

My low tide too
but the breeze coming up says
wake. Pray

with one foot
steady-placed, and then
the other.

Something has died. And the pleasant smell
of chaparral cannot hope to cover it up.

The chaparral must die and so must I
–would we not also wish
to leave something behind?

At the last, four notes
ascending their purple staff:
marsh-water-dune-sky.

After the last
……… silent owl-rise.

by Tara K. Shepersky
from
Echotheo Review
9/18/19