How to cram your entire genome into a tiny nucleus

Elizabeth Pennisi in Science:

DnaStretched end to end, the DNA in the nucleus of just one of your cells would be as long as you are. Now, using sophisticated statistics, imaging, and experimental data, biophysicists have a clearer idea about how all this genetic material is squished into such a tiny space. “This new work does reveal a striking, high-resolution model of the human genome,” says Job Dekker, a biologist at the University of Massachusetts Medical School in Worcester, who was not involved with the work. “It is indeed beautiful.” Over the past decade, researchers have come to realize that how our DNA is bunched into the nucleus is a miracle of packaging, with very deliberate loops and bends that bring specific parts of each chromosome into contact to help control what genes are active. “Cells have been evolving to exploit this apparently chaotic organization to efficiently store the genetic information and use it for their function,” says Marco Di Stefano, a biophysicist now at the National Centre for Genomic Analysis in Barcelona, Spain.

In the new study, he and his colleagues used statistical approaches to convert experimental data into a 3D model. Previous experiments—capturing when one bit of DNA came close to another bit of DNA—had provided only indirect information about individual connections, but the new modeling resulted in a comprehensive, biologically correct depiction (visualized above) of how our DNA fits into a nucleus. In the video, each chromosome is a different color. The model incorporated imaging data with the experimental results about DNA contacts. The analysis yielded specifics not discernable from the experimental data alone, such as showing that active genes are near the center of the nucleus and inactive ones are toward the edges, the team reports this month in Scientific Reports.

More here.

Was “Lolita” About Race?: Vladimir Nabokov on Race in the United States

Lolita

Jennifer Wilson in the LA Review of Books [h/t: Tunku Varadarajan]:

The question of miscegenation would not appear in Nabokov’s work until some 13 years later, with the scandalous 1955 publication of Lolita — a novel Nabokov knew was a “timebomb,” as he wrote to an American friend. In “On a Book Entitled Lolita,” Nabokov writes that there are only three subjects American publishers find taboo: pedophilia, atheism (which carried connotations of “godless” communism), and “a Negro-White marriage which is a complete and glorious success resulting in lots of children and grandchildren.” This invocation of American hysteria surrounding miscegenation seems jarring at first. After all, Lolita is concerned with actual sexual perversity, not what racist distortion falsely presents as sexual perversity. But a closer reading demonstrates just how central the theme of American racism is to Nabokov’s narrative.

Early on in Lolita, Humbert Humbert learns that his first wife, Valeria, relocated from Europe to the United States, where she became a subject of an ethnological experiment. The project involved research on “human and racial reactions to a diet of bananas and dates”; this vignette is emblematic of the United States’s obsession with understanding race through “science,” and is tinged with overtones of Nazi eugenicist experimentation. A forgotten target of Nabokov’s satirical eye, the United States’s obsession with racial purity and the policing sex almost exclusively toward that end, is arguably a subplot of Lolita.

Indeed, one could argue that part of why Humbert Humbert so successfully evades discovery as he takes Lolita from motel to motel is that white men, even white pedophiles, were not surveilled with the same force or regularity as black men engaged in the “sex crime” of miscegenation. The Mann Act, which made transporting girls and women across state lines for the purpose of “debauchery” illegal, looms in the background of Lolita.

More here.

A New Spin on the Quantum Brain

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Jennifer Ouellette in Quanta Magazine:

The mere mention of “quantum consciousness” makes most physicists cringe, as the phrase seems to evoke the vague, insipid musings of a New Age guru. But if a new hypothesis proves to be correct, quantum effects might indeed play some role in human cognition. Matthew Fisher, a physicist at the University of California, Santa Barbara, raised eyebrows late last year when he published a paper in Annals of Physics proposing that the nuclear spins of phosphorus atoms could serve as rudimentary “qubits” in the brain — which would essentially enable the brain to function like a quantum computer.

As recently as 10 years ago, Fisher’s hypothesis would have been dismissed by many as nonsense. Physicists have been burned by this sort of thing before, most notably in 1989, when Roger Penrose proposed that mysterious protein structures called “microtubules” played a role in human consciousness by exploiting quantum effects. Few researchers believe such a hypothesis plausible. Patricia Churchland, a neurophilosopher at the University of California, San Diego, memorably opined that one might as well invoke “pixie dust in the synapses” to explain human cognition.

Fisher’s hypothesis faces the same daunting obstacle that has plagued microtubules: a phenomenon called quantum decoherence. To build an operating quantum computer, you need to connect qubits — quantum bits of information — in a process called entanglement. But entangled qubits exist in a fragile state. They must be carefully shielded from any noise in the surrounding environment. Just one photon bumping into your qubit would be enough to make the entire system “decohere,” destroying the entanglement and wiping out the quantum properties of the system. It’s challenging enough to do quantum processing in a carefully controlled laboratory environment, never mind the warm, wet, complicated mess that is human biology, where maintaining coherence for sufficiently long periods of time is well nigh impossible.

More here.

THE BOOK THAT PREDICTED TRUMP

Matt Feeney in The New Yorker:

41lPrf+lvdL._SX331_BO1,204,203,200_There’s a sort of ideal figure that conservative intellectuals conjure when they want to argue about the essence of their ideology. This figure is a dreamy quietist of peaceable disposition, who savors apolitical friendship, nurses a skeptical outlook, and looks to an anti-theoretical politics of homey tradition and humane, but chastened, sentiment to guide him. The political scientist Corey Robin argues in his 2012 book, “The Reactionary Mind,” that this ideal is more like a myth. Conservatism, Robin says, is always inherently a politics of reaction—usually also populist, often also violent. From Robin’s argument, we could predict that a conservative party would be unlikely to nominate the idealized conservative as its standard-bearer, but that it would absolutely yoke itself to a populist nut job like Donald Trump.

Robin’s argument about why this happens is a little too sweeping at times, too reliant upon convenient factoids for its historical-theoretical linkages. For example, he dubiously establishes that libertarians are secret heirs to Hobbesian absolutism by noting that the free-market economist Milton Friedman was an adviser to the Chilean dictator Augusto Pinochet. And conservative readers would surely grind their molars on seeing John Calhoun and Ronald Reagan blithely summoned as members of the same political team. By the same token, this bold and maddening connection between a notorious slavery apologist and a beloved Republican provided a polemical charge that was no doubt central in turning the book into an unexpected publishing hit among progressives still energized by the Occupy movement.

More here.

Universe Not Accelerating? New Battle Over Supernova Results

Ethan Siegel in Forbes:

Merger_accretionIn 1998, the two leading independent collaborations working to measure distant supernovae in the Universe reported the same bizarre findings: they seemed to indicate that the Universe was accelerating. The only way to explain how distant these lights appeared was if the fabric of space was expanding at a rate that wasn’t decreasing like we’d expect, and if the most distant galaxies were receding faster and faster, despite the pull of gravity. Over the next 13 years, the evidence grew stronger and stronger for this picture, and in 2011 three pioneers in the field were awarded the Nobel Prize. And then, just last week, a new study came out alleging that the supernova evidence for this picture was marginal at best. The study concludes that perhaps the Universe hasn’t been accelerating, after all.

But is that fair and correct? Certainly the news reports are claiming it is, but what does the science say? Let’s start with what the supernova data is, and what it’s told us so far.

More here.

Shahzia Sikander interviewed by Sara Christoph

From The Brooklyn Rail:

Shahziasikander-webSince moving to the U.S. from Pakistan in the mid-’90s, Shahzia Sikander has pushed through boundaries corroded by decades of multiculturalist rhetoric with an artistic practice that reimagines the connections between Eastern experiences and Western perspectives. Sikander is best known for her early mastery of Indo-Persian miniaturist painting—a radical appropriation of a craft formerly considered kitsch—but her recent work in video is immersive, animated, and monumental in scale. She sat down with Sara Christoph to discuss the paradoxes of colonialism and translation, and the narratives that frame history, in the context of today’s charged atmosphere of divisive polemics.

Sara Christoph (Rail): I’d like to begin by touching on a theme that runs through your work as an artist: the imperative of imagination. You’ve said it is something that drives you, that “art is an instinct to imagine the future.” Let’s start there: imagination as instinct, as something that even in times of great divisiveness, binds us all. How would you articulate the role of imagination in your work?

Shahzia Sikander: When I think of the idea of the postcolonial, the rhetoric of imagination seems so much more buoyant, so full of visual possibilities, specifically as a foil to the notion of the exile. I think of it as a soaring and empowering space that is free from constraints. And if you’re thinking in terms of inter-connectivity, imagination is what ties all of us together.

More here.

WHAT AN UGLY CHILD SHE IS

Ferrante-Ugly-Child-826Elena Ferrante at The New Yorker:

I read “Madame Bovary” in the city of my birth, Naples. I read it laboriously, in the original, on the orders of a cold, brilliant teacher. My native language, Neapolitan, has layers of Greek, Latin, Arabic, German, Spanish, English, and French—a lot of French. Laisse-moi (“leave me alone”) in Neapolitan is làssame and sang (“blood”) is ’o sanghe. It’s not so surprising if the language of “Madame Bovary” seemed to me, at times, my own language, the language in which my mother appeared to be Emma and said laisse-moi. She also said le sparadrap (but she pronounced it ’o sparatràp), the adhesive plaster that had to be put on the cut I’d gotten—while I read and was Berthe—when I fell contre la patère de cuivre.

I understood then, for the first time, that geography, language, society, politics, the whole history of a people, were for me in the books that I loved and which I could enter as if I were writing them. France was near, Yonville not that far from Naples, the wound dripped blood, the sparatràp, stuck to my cheek, pulled the stretched skin to one side. “Madame Bovary” struck with swift punches, leaving bruises that haven’t faded. All my life since then, I’ve wondered whether my mother, at least once, with Emma’s words precisely—the same terrible words—thought, looking at me, as Emma does with Berthe: C’est une chose étrange comme cette enfant est laide! (“It’s strange how ugly this child is”).

more here.

Thomas De Quincey and the Making of a Murderer

Efd1f0de6df70171d7e4729a047a7670de24d82aColin Dickey at The New Republic:

Artistic considerations of death and mayhem were De Quincey’s bread and butter. De Quincey, she writes, “gorged on scenes of violence,” but unlike others he was able to transmute this passion into high art, particularly in his Macbeth essay and the satiric tour-de-force, “On Murder Considered as One of the Fine Arts. “Everything in this world has two handles,” the anonymous narrator tells the assembled Society of Connoisseurs in Murder. “Murder, for instance, may be laid hold of by its moral handle (as it generally is in the pulpit, and at the Old Bailey); and that, I confess, is its weak side; or it may also be treated aesthetically, as the Germans call it—that is, in relation to good taste.” Long before Hollywood began catering to our innate fascination with murder, De Quincey was, like no one else before him, plumbing the depths of our darkest humanity, eschewing morality in favor of that second handle. “It was De Quincey who legitimized the luxurious excitement of murder,” Wilson reminds us, “just as he legitimized, in his most famous work, Confessions of an English Opium-Eater, the pleasure of opiates.”

It is that most famous work, the opium essay, which has paradoxically stood in the way of properly appreciating De Quincey’s many other contributions to literature. InRebecca Solnit’s biography of Eadweard Muybridge, she describes how the photographer “undermined his vast output of good work with his great work.” Had he never done his excellent Yosemite studies, he might have been known for his less ambitious San Francisco cityscapes, and the Yosemite photos, in turn, have been all-but-forgotten by the later motion studies that changed the world.

more here.

William Kentridge’s ‘Right into Her Arms’

Hard01_3821_01Jeremy Harding at The London Review of Books:

The most recent of William Kentridge’s works on display in Thick Time at the Whitechapel Gallery (until 15 January) is called Right into Her Arms. It’s also one of the best. A raised stage, three metres long, about a metre high, is dressed with a flimsy backdrop of beige, brown, grey; here and there are torn swatches of yellow, green and maroon. At first we seem to see an austere Kurt Schwitters collage from the early 1920s. Close up, we discover unadorned cardboard, plain or coloured card. The wings of the stage are decorated with pages from a dictionary. Front of stage are two rectangular, mobile panels, MDF or cork, decorated like the rest and attached to a guide rail that runs along the top of the proscenium. They are driven left and right by an electric motor, or angled, or made to pirouette through 360 degrees. Mostly they trundle to and fro; on occasion they whizz or flounce; once or twice they cross.

The show, which lasts 11 minutes, consists of a recorded montage of images, still and moving, beamed onto this protean set from a projector: ink splashes, ink and charcoal drawings, fragments of libretto and video outtakes, all retrieved from the workshop of ideas, materials and players that Kentridge put together for his production of Lulu, performed at the Met last year and coming to ENO on 9 November. Right into Her Arms restages the conception, design and history of the production as a kinetic notebook, full of surprise and comedy. As the panels go this way and that, the projected images are refracted across two, sometimes three planes. The little play reaches its climax over a soundtrack of Webern and Schoenberg and a recital by Kentridge of passages from Schwitters’s sound poem Ursonate.

more here.

The Road to Oxiana: the greatest travel book of the 20th century

Robert McCrum in The Guardian:

AfghanAccording to Robert Byron’s Oxford contemporary Evelyn Waugh – never the most reliable witness – the future author of The Road to Oxiana used to delight in shouting “Down with abroad”. Typical in striking a pose, Byron was an aggressive Oxford aesthete of the “Brideshead generation”, a homosexual wanderer whose precocious career as a travel writer and art historian can be traced through a succession of prewar gems. (Robert Byron by James Knox, published by John Murray in 2003, remains the principal biographical source.) Byron wrote The Station, aged 22, after a visit to Mount Athos on a mule, Fortnum & Mason saddlebags bursting with a soda siphon and chicken in aspic. This was followed by The Byzantine Achievement (1929) and The Birth of Western Painting (1930). In 1933, the publication of First Russia, Then Tibet confirmed Byron’s reputation as a traveller and connoisseur. In the same year, accompanied by his friend Christopher Sykes, but tormented by his unrequited love for Desmond Parsons, Byron set out on a journey to Persia and Afghanistan, by way of Jerusalem, Damascus and Baghdad, in search of the origins of Islamic architecture. After many vicissitudes, The Road to Oxiana (the remote northern borderland of Afghanistan) became the record of his 11-month journey, a fabulous and intoxicating weave of surreal vignettes, journal entries and odd playlets. In these gorgeous pages, poetry, gossip and scholarship become braided into an exotic tapestry that dazzles as much today as it did on publication. As many critics have noted, unlike his contemporaries, such as Peter Fleming and Norman Douglas, Byron has not dated.

An enthusiastic literary critical response ranged from Graham Greene, who admired Byron’s demotic, conversational brilliance, to the rivalrous Evelyn Waugh, who had to concede the book’s high spirits, via the Sunday Times, which linked Byron to his namesake (no relation) and declared him “the last and finest fruit of the insolent humanism of the 18th century”. Today, widely considered to be Byron’s masterpiece, The Road to Oxiana stands as perhaps the greatest travel book of the 20th century.

More here.

Beyond Trump vs Clinton: A scientist’s guide to the US election

Lauren Morello in Nature:

Nature-us-election-31-oct-2016-NEW1The presidential race between Hillary Clinton and Donald Trump is dominating the discussion about the upcoming US election, but it’s not the only contest to watch on 8 November. Choices that voters make will influence other levels of government — and some of these decisions will steer the course of science and science policy.

Will Congress change hands?

Winning the White House is only half the battle for the next president. The political balance of the two houses of Congress — the US House of Representatives and the Senate — can determine whether a president’s policies become law or die on the vine. The Republican Party currently controls both houses. But on 8 November, all 435 seats in the House of Representatives are up for grabs, as are 34 of the 100 seats in the Senate. Although the House seems likely to remain in Republican hands, a Democratic take-over of the Senate is possible. That would benefit Clinton — a Democrat — if she prevails over Trump: the latest polls suggest she has a narrow lead. A Democratic Senate would be more likely to back her funding and policy priorities, such as increasing science spending and fighting climate change, and to approve her nominees for government posts at NASA, the National Science Foundation (NSF) and other agencies key to science. And if the Senate ends up split with 50 Democrats and 50 Republicans, the vice-president — who is also president of the Senate — would break the tie, handing control to the party that wins the White House.

Individual House and Senate races — and retirements — are set to change the political landscape for US science agencies in subtler ways.

More here.

The media’s extermination of Bernie Sanders, and real reform

Thomas Frank in Harper's Magazine:

ScreenHunter_2340 Nov. 01 18.10All politicians love to complain about the press. They complain for good reasons and bad. They cry over frivolous slights and legitimate inquiries alike. They moan about bias. They talk to friendlies only. They manipulate reporters and squirm their way out of questions. And this all makes perfect sense, because politicians and the press are, or used to be, natural enemies.

Conservative politicians have built their hostility toward the press into a full-blown theory of liberal media bias, a pseudosociology that is today the obsessive pursuit of certain nonprofit foundations, the subject matter of an annual crop of books, and the beating heart of a successful cable-news network. Donald Trump, the current leader of the right’s war against the media, hates this traditional foe so much that he banned a number of news outlets from attending his campaign events and has proposed measures to encourage more libel lawsuits. He does this even though he owes his prominence almost entirely to his career as a TV celebrity and to the news media’s morbid fascination with his glowering mug.

His Democratic opponent hates the press, too. Hillary Clinton may not have a general theory of right-wing media bias to fall back on, but she knows that she has been the subject of lurid journalistic speculation for decades.

More here. [Thanks to Eric Chaffee.]

Hesperine for David Berger

by Kazim Ali

Begin with the dining room custodian at the university who smashed the stained glass window because we are actually going to change history

Imagine then in the suburbs of Cleveland a sculpture of steel rings broken in halves but opening up away from the bullet-written history of the burning helicopter toward the open sky

Seems possible because there is a bridge between relativity and quantum mechanics that no physicist has yet ascertained

Imagining neither a conditional future if the past was different nor forging ahead from the broken but something newer that bridged that loss

For example what if a painter who left the canvas entirely and instead looked at all the extant surfaces in the already man-made and man-frayed world

History then as fragile as stained glass and yet writes new narratives that shape every movement forward

Both ways of understanding the behavior of matter cannot both be true yet somehow they still behave as true on the lived-in planet

David Berger at 27 deciding to move across the world to Israel to train and compete in the Olympics, 1972 Munich

Continue reading the poem here.

Israel Proves the Desalination Era Is Here

Rowan Jacobsen in Scientific American:

4C28277C-621D-415F-BE5BC1CA30CC5FA7Ten miles south of Tel Aviv, I stand on a catwalk over two concrete reservoirs the size of football fields and watch water pour into them from a massive pipe emerging from the sand. The pipe is so large I could walk through it standing upright, were it not full of Mediterranean seawater pumped from an intake a mile offshore.

“Now, that’s a pump!” Edo Bar-Zeev shouts to me over the din of the motors, grinning with undisguised awe at the scene before us. The reservoirs beneath us contain several feet of sand through which the seawater filters before making its way to a vast metal hangar, where it is transformed into enough drinking water to supply 1.5 million people.

We are standing above the new Sorek desalination plant, the largest reverse-osmosis desal facility in the world, and we are staring at Israel’s salvation. Just a few years ago, in the depths of its worst drought in at least 900 years, Israel was running out of water. Now it has a surplus. That remarkable turnaround was accomplished through national campaigns to conserve and reuse Israel’s meager water resources, but the biggest impact came from a new wave of desalination plants.

More here.

Truth After Trump

Justin E. H. Smith in the Chronicle of Higher Education:

Photo_78978_landscape_650x433In his essay “On Bullshit,” precirculated for years as samizdat and published by Princeton University Press in 2005, the philosopher Harry G. Frankfurt identifies and analyzes a previously neglected species of untruth. It is of the same genre of lying, but unlike its better-known relative it does not seek simply to pass off a falsehood as true. Instead, the bullshitter is the person who no longer considers truth as the anchor of discourse, who speaks without regard for the truth, and who, finally, is unconcerned about whether his interlocutor knows he is speaking untruths or not. “When an honest man speaks,” Frankfurt explains, “he says only what he believes to be true.” For the liar, it is “indispensable that he considers his statements to be false.” But the bullshitter’s eye, Frankfurt argues, “is not on the facts at all, as the eyes of the honest man and of the liar are, except insofar as they may be pertinent to his interest in getting away with what he says. He does not care whether the things he says describe reality correctly. He just picks them out, or makes them up, to suit his purpose.”

One need not have heard of Frankfurt, or have grasped his precise technical meaning of bullshit, to associate it with the Republican nominee for president. But is a Frankfurtian analysis sufficient to understand this election?

More here.

Raising the spirit of American radicalism

Beck_FearLoveB32.4_63cmyk-838x386Jessa Crispin at The Baffler:

It was not, at one time, considered so remarkable that a candidate for the United States presidency talked to the dead. That the candidate was a former prostitute and an advocate for free love was more worrying. What’s more, her vice-presidential pick was a former slave; that was likely the surest sign that Victoria Woodhull was not going to be the next American president.

It was the election of 1872, and Woodhull stood as the nominee for the newly organized Equal Rights Party, with Frederick Douglass as her VP. (There’s no real evidence to show that Douglass agreed to this arrangement, and he certainly did not campaign with her.) Women might not have had the right to vote, but they could run for office, and Woodhull felt that the presidency was her destiny.

In the end, the first woman to seek the White House received no electoral college votes, and her party made the ballot in only twenty-two states. Her enemies pounced on her utopian call for sexual freedom for both men and women, and stirred up the fear of miscegenation that white voters felt, with only minimal prompting, at the sight of a white woman consorting with a black man. Meanwhile, Woodhull’s history of working as a clairvoyant and her vocal support of Spiritualism were not much of a hindrance to her campaign. Go figure.

more here.

Jonathan Swift: The Reluctant Rebel

51TTYueNZzL._SY344_BO1,204,203,200_Freya Johnston at Literary Review:

‘Would we have liked to live with him?’ asked Thackeray, contemplating Swift, a question he immediately ducked by supplying a long list of other writers with whom we might prefer to spend our time. Samuel Johnson, similarly recoiling from the evidence of Swift’s character as manifested in his works, thought him ‘a man of rigorous temper’, whose ‘vigilance of minute attention’ must have made him unbearable. Even his best friends, on whose testimony Johnson relied, depicted him as cold, frugal, petulant and severe.

None of this would have surprised the man himself. In his autobiographical ‘Verses on the Death of Dr Swift’ (1731), he imagined widespread indifference to his demise and posthumous distortions of his name. The poem gives neither his vilest enemies nor his closest friends much credit for the sincerity or persistence of their feelings. Instead, it is the public Swift who endures, the man who unmasked cheats and frauds, who stood up for the financial and constitutional independence of Ireland, and who left his money

To build a House for Fools and Mad:
And shew’d by one satiric Touch,
No Nation wanted it so much:
That Kingdom he hath left his Debtor,
I wish it soon may have a Better.

more here.

Black Stories Matter

Criticism_freedman_defender_webSamuel G. Freedman at VQR:

During the summer of 2013, shortly after George Zimmerman was acquitted of the fatal shooting of an unarmed black teenager named Trayvon Martin, word leaked out that a juror was already shopping around a prospective book about the case. One particular Twitter user, Genie Lauren, was so outraged that she logged on to condemn the literary agent who was representing the juror. As Lauren later explained, “I didn’t think it was right that someone would make money off of this tragedy.” Almost immediately, thousands of other people began tweeting at the agent, a protest petition circulated online, and the book project was dropped.

By some readings of recent history, this episode marked the emergence of Black Twitter, a term that refers to the concentrated, effective, and proudly parochial use of the social-media platform by African Americans. In the years since the Zimmerman trial, Black Twitter has been an information-sharing and opinion-shaping phenomenon for everything from the BET Awards to the Michael Brown killing in Ferguson, Missouri. Black Twitter, of course, gave birth to the hashtag that became a slogan that became a movement: #BlackLivesMatter.

more here.