Genes, Chance And Destiny

Lloyd Sederer in The Huffington Post:

SidAt 46, Siddhartha Mukherjee, is a man driven by questions, by puzzles in science and society. In 2011, his first book, a 600-page book on the history of cancer, The Emperor of All Maladies, won a Pulitzer Prize, among other accolades. Time magazine lists the book among the one hundred most influential books written since 1923. His new and third book, The Gene, an Intimate History, published in 2016, sets out to tackle another crucial question that sits at the edge of science and society. This book is a finalist for the UK’s top award for nonfiction writing, the Baillie Gifford Prize, putting him in competition with a Nobel Laureate. More about both books below. As technologies accelerate, so does what we know about the human genome – the complete code of DNA in our cells and bodies that orchestrates our destiny. Mukherjee knows that the prospect of understanding aspects of our genetic code is no longer ‘if’ but when and how. As that happens, he asks us to wonder, as he does himself, what will we do with these new-found powers? What does the future hold for the human genome – now that we are learning to “read” and “write” our own codes of instruction? The easy answers are their application in preventing disabling and deadly genetic diseases and mitigating the progression of many illnesses, especially cancers. But science is agnostic, it does not set social or moral boundaries. Mukherjee comments that we are creating questions for our children as we master the capacity to not only decode but also to recode the genetic building blocks of our lives. We may be cutting, splicing, and inserting different genetic sequences that make us, and our progeny, truly different, where the consequences are deeply uncertain as to whether good or bad ― or both ― will result.

I met with him at his lab and office at Columbia’s Irving Cancer Center, in Washington Heights in Northern Manhattan, on a bright September morning that itself radiated hope. He was quick to let me know that he is a cell biologist, that his work and his insistent queries, scientific and societal, are meant to answer “how and why do cells go wrong {that is, mutate and become cancer}…and conversely how do they not go wrong?”, and all the variation that exists in between. Dr. Mukherjee spends a half a day each week seeing patients in a Columbia oncology clinic. That is time where he confronts the human faces and anxieties that patients and their families endure when nature goes awry and cancer takes its toll. He also has a lab that studies stem cells, the originating, undifferentiated cells that become every other type of cell in our body, from blood and bone marrow cells (his focus), to our heart, neurons and nerves, skin, nose and toes, to name a few. Stem cells undergo radical transformations and may supply clues to understanding cellular aberration and reveal how disorders can be prevented or treated. He is a husband who spoke proudly of his wife’s accomplished artistry and a dad who wonders about the future and fate of his two daughters.

More here.

Thursday Poem

Clochard

In Paris, on a day that stayed morning until dusk,
in a Paris like –
in a Paris which –
(save me, sacred folly of description!) Clochard
in a garden by a stone cathedral
(bit built, no, rather
played upon a lute)
a clochard, a lay monk, a naysayer
sleeps sprawled like a knight in effigy.

If he ever owned anything, he has lost it,
and having lost it doesn't want it back.
He's still owed soldier's pay for the conquest of Gaul –
but he's got over that, it doesn't matter.
And they never paid him in the fifteenth century
for posing as the thief on Christ's left hand –
he has forgottenall about it, he's not waiting.

He earns his red wine
by trimming the neighborhood dogs.
He sleeps with the air of an inventorof dreams,
his thick beard swarming towards the sun.

The gray chimeras (to wit, bulldogryphons,
hellephants, hippopotoads, croakodilloes, rhinocerberuses,
behemammoths, and demonopods,
that omnibestial Gothic allegro vivace)
unpetrify

and examine him with a curiosity
they never turn on me or you,
prudent Peter,
zealous Michael,
enterprising Eve,
Barbara, Clare.
.

by Wislawa Szymborska
from View with a Grain of Sand
Harcourt Brace 1995
.

Read more »

How Vector Space Mathematics Reveals the Hidden Sexism in Language

As neural networks tease apart the structure of language, they are finding a hidden gender bias that nobody knew was there.

From the MIT Technology Review:

ImageBack in 2013, a handful of researchers at Google set loose a neural network on a corpus of three million words taken from Google News texts. The neural net’s goal was to look for patterns in the way words appear next to each other.

What it found was complex but the Google team discovered it could represent these patterns using vectors in a vector space with some 300 dimensions.

It turned out that words with similar meanings occupied similar parts of this vector space. And the relationships between words could be captured by simple vector algebra. For example, “man is to king as woman is to queen” or, using the common notation, “man : king :: woman : queen.” Other relationships quickly emerged too such as “sister : woman :: brother : man,” and so on. These relationships are known as word embeddings.

This data set is called Word2vec and is hugely powerful. Numerous researchers have begun to use it to better understand everything from machine translation to intelligent Web searching.

But today Tolga Bolukbasi at Boston University and a few pals from Microsoft Research say there is a problem with this database: it is blatantly sexist.

More here. [Thanks to Farrukh Azfar.]

Fish Can Be Smarter Than Primates

Jonathan Balcombe in Nautilus:

ScreenHunter_2249 Sep. 28 19.21Intelligence is shaped by the survival requirements that an animal must face during its everyday life, according to cognitive ecology. Some birds can remember where they buried tens of thousands of nuts and seeds, which allows them to find them during the long winter months; a burrowing rodent can learn a complex underground maze with hundreds of tunnels in just two days; and a crocodile can have the presence of mind to carry sticks on her head and float them just below an area where herons are nesting, then pounce when an unwary bird swoops down to collect nesting material.

What about the mental abilities of fishes? Notwithstanding the liberties taken by filmmakers in popular movies like The Little Mermaid, Finding Nemo, and its sequel, Finding Dory, can fishes really think?

Here’s an example of fish intelligence, courtesy of the frillfin goby, a small fish of intertidal zones of both eastern and western Atlantic shores. When the tide goes out, frillfins like to stay near shore, nestled in warm, isolated tide pools where they may find lots of tasty tidbits. But tide pools are not always safe havens from danger. Predators such as octopuses or herons may come foraging, and it pays to make a hasty exit. But where is a little fish to go? Frillfin gobies deploy an improbable maneuver: They leap to a neighboring pool.

How do they do it without ending up on the rocks, doomed to die in the sun? With prominent eyes, slightly puffy cheeks looking down on a pouting mouth, a rounded tail, and tan-gray-brown blotchy markings along a 3-inch, torpedo-shaped body, the frillfin goby hardly looks like a candidate for the Animal Einstein Olympics. But its brain is an overachiever by any standard. For the little frillfin memorizes the topography of the intertidal zone—fixing in its mind the layout of depressions that will form future pools in the rocks at low tide—while swimming over them at high tide.

More here.

Arturo Escobar: a post-development thinker to be reckoned with

Drawing on influences from Foucault to Said, the Colombian's arguments have a sophistication that often goes unrecognised.

Simon Reid-Henry in The Guardian:

MDG--Arturo-Escobar-009One response to the development impasse caused by modernisation and dependency theories was “can do” neoliberalism; another involved reflection on the very purpose of development. This took shape across “alternative” approaches including environment, gender and sustainability. All these approaches grew up alongside the neoliberal right, but most were drowned out, for a time at least, by its noisiness.

Perhaps the most distinctive new approach, however – one set on meeting the new right's noisiness with a strategic and all-encompassing silence – was the post-development thinking embodied by the work of Colombian scholar Arturo Escobar.

Escobar's ideas are best summed up in his 1995 book Encountering Development, which offered much more than an analysis of mainstream development economics or the sprawling array of development actors and institutions it spawned. It was a critique of the whole rotten edifice of western ideas that supported development, which Escobar regarded as a contradiction in terms and a sham. For Escobar, development amounted to little more than the west's convenient “discovery” of poverty in the third world for the purposes of reasserting its moral and cultural superiority in supposedly post-colonial times.

More here.

on the ‘higher’ friendship between men and women

Streeter_Happiness2Baflr30.2_34cmykGeorge Scialabba at The Baffler:

When Mill was twenty-four and already a rising intellectual star, he met Mrs. Taylor, twenty-three, the wife of a Unitarian businessman and mother of two children. John had recently come through the depression he famously described in his Autobiography, caused, he was convinced, by having starved his feelings. Harriet was brilliant, beautiful, and fearless. Both were smitten, instantly and forever. Except when one or the other was convalescing (they were both tubercular), they rarely went a day without seeing or writing each other until she died twenty-eight years later, in 1858. (For the first nineteen of those years, they met openly at her house, thanks to her remarkably enlightened husband, John Taylor, of whom there is a small commemorative medallion on display in the Harriet Taylor Room.)

Mill insisted that everything he wrote after meeting Taylor was a joint production—she had the flashes of inspiration that he laboriously worked out. Some subsequent critics have doubted that this was true of his Logic and other philosophical writings. But it was surely true of The Subjection of Women, his powerful and influential critique of sexual inequality. Mill was already an advanced feminist when they met (which was, he later wrote, the only reason she gave him the time of day). But she enlarged his vision and kindled his indignation. The latter is perhaps the most striking feature of Mill’s treatise. Wollstonecraft’s Vindication had a conciliatory, occasionally even pleading, tone. But The Subjection of Women gave no quarter, rhetorically. The relentlessness of the prose in the cause of emancipation fits right into today’s sex-war rhetoric.

more here.

The decline of liberal democracy in Europe’s midst

10955Gábor Halmai at Eurozine:

Hungary's illiberal turn, which has significantly weakened the rule of law safeguards instituted by the 1989-1990 constitutional process, can be described as a 'constitutional counter-revolution'.[1] At the same time, it has not resulted in the restoration of either a single-party or police state structures. Rather, the Hungarian system since 2010 is better characterized as a 'democradura'.[2] In the following, I describe the elements and possible reasons for Hungary's political transformation.[3] The failure of the elite (myself included) that built liberal democracy in Hungary is one of the issues discussed. Another is why the first twenty years of regime transition did not see the emergence of greater respect for constitutional values. This would have prevented the rapid deconstruction of democracy or, at the very least, have made the collapse more difficult.

Especially after the refugee crisis, the Hungarian situation is also a test as to whether, and to what extent, the civilized world, especially Europe, can enforce global values in countries that are members of the international community, and of value-based communities such as the European Union and the Council of Europe. So far, the results by no means qualify as a success. The Hungarian government's minor concessions have been due not to the resolve of European institutions, nor to the power its value-enforcement mechanisms, but to the exigencies of Hungary's economic situation.

more here.

Two essay collections examine race relations in America

Cover00Jabari Asim at Bookforum:

All of which brings me back to Richard Wright’s suggestion, in Native Son (1940), that literature is a battleground on which blacks and whites have often fought over the very “nature of reality.” All too often, differing approaches to language reflect sharply contrasting visions of American society. For African Americans, the disparate language of our country’s racial majority has seldom been separate from customs and policies that hinder complete access to the “grand experiment” we continue to hear so much about. Into this schism steps Jesmyn Ward, whose novel Salvage the Bones won the 2011 National Book Award. In her introduction to the new anthology The Fire This Time, she finds evidence of this clash of visions in George Zimmerman’s killing of Trayvon Martin. She looks at images of the latter’s baby face and sees a child. But she recognizes that “most Americans” look at the same person and see someone quite different: “some kind of ravenous hoodlum, perpetually at the mercy of his animalistic instincts.”

Around a year after Martin’s death, Ward began the project that became The Fire This Time. She writes that she wanted to provide writers of her generation with an opportunity “to dissent, to call to account, to witness, to reckon.” Anthologies of this sort are plentiful and powerful, at least to African American readers, those most likely to engage and embrace such efforts, which include The New Negro (1925), Black Fire (1968), and Step into a World(2000). That there have been so many of these books, decade after decade, speaks to their limited utility beyond the sympathetic circles where black artists and thinkers congregate—there always have been new atrocities to respond to, clueless assessments to refute, hostilities to defend against.

more here.

Wednesday Poem

Where do we Go From Here

Through the cold glass of a winter window
where crazed weather holds my breath
to task,
a tangled canopy of tree and sky
becomes that ornately carved pediment:
Banteay Shrei in late afternoon
just south of where great rivers
are diverted by Chinese dams—
visions of yuan, mouths screaming for profit,
a world where Mao means anything.

A modern woman stands alone
in the stillness of a place
where life may not have been
that different. She tries
to untangle the skeins of power
from tradition’s weave.
Nothing moves. All things speak.
Impossible to know for sure
but these stones tell her:
pay attention.
.

by Margaret Randall
from Where do we Go from Here
Wings Press, San Antonio, TX
.

Babies Have a Microbial Window of Opportunity

Finlay et al in Scientific American:

BabyUntil very recently, whenever we thought of microbes — especially around babies — we considered them only as potential threats and were concerned with getting rid of them, and it is no surprise why. In the past century, most human communities have experienced the benefits of medical advances that have reduced the number and the degree of infections we suffer throughout life. These advances include antibiotics, antivirals, vaccinations, chlorinated water, pasteurization, sterilization, pathogen–free food, and even good old-fashioned hand washing. The quest of the past 100 years has been to get rid of microbes — “the only good microbe is a dead one.” This strategy has served us remarkably well; nowadays, dying from a microbial infection is a very rare event in developed countries, whereas only 100 years ago 75 million people died worldwide over a span of two years infected with H1N1 influenza virus, also known as the Spanish flu. At first glance, our war on microbes along with other medical advances has truly paid off. The average life span in the US in 1915 was 52 years, approximately 30 years shorter than it is today. For better or for worse, there are almost four times more humans on this planet than only 100 years ago, an incredibly accelerated growth in our historic timeline. Evolutionarily speaking, we have hit the jackpot. But at what price?

More here.

High Hitler: how Nazi drug abuse steered the course of history

Rachel Cooke in The Guardian:

ScreenHunter_2249 Sep. 27 18.34The German writer Norman Ohler lives on the top floor of a 19th-century apartment building on the south bank of the river Spree in Kreuzberg, Berlin. Visiting him there is a vertiginous experience. For one thing, he works – and likes to entertain visitors – in what he calls his “writing tower”, a flimsy-seeming, glass-walled turret perched right on the very edge of the roof. (Look down, if you dare, and you will see his little boat moored far below.) For another, there is the fact that from this vantage point it is possible to discern two Berlins, one thrusting and breezy, the other spectral and grey. To our left, busy with traffic, is the Oberbaum Bridge, where there was once a cold war checkpoint, and beyond it the longest remaining section of the Berlin Wall, its doleful length rudely interrupted by the block of luxury flats that went up in 2013. As for the large building immediately opposite, these days it’s the home of Universal Music. Not so very long ago, however, it was the GDR’s egg storage facility.

Does all this press on Ohler as he sits at his desk, the light bouncing off the screen of his laptop? Is it ghostly sometimes? “Yes, it is strange,” he says, smiling at my giddiness. But then he has long believed in a certain kind of time travel. “I remember the 90s. The wall had just come down, and I was experimenting with party drugs like ecstasy and LSD. The techno scene had started up, and there were all these empty buildings in the east where the youth [from east and west] would meet for the first time. They were hardcore, some of those guys from the east – they didn’t understand foreigners at all – and the ecstasy helped them to lose some of their hatred and suspicion. Sometimes, then, you could step into a room, and you could just see the past. Of course, it’s not like that now. I don’t take drugs any more. But I can remember it, and maybe that was why I was able to write this book.”

The book in question is The Total Rush – or, to use its superior English title, Blitzed – which reveals the astonishing and hitherto largely untold story of the Third Reich’s relationship with drugs, including cocaine, heroin, morphine and, above all, methamphetamines (aka crystal meth), and of their effect not only on Hitler’s final days – the Führer, by Ohler’s account, was an absolute junkie with ruined veins by the time he retreated to the last of his bunkers – but on the Wehrmacht’s successful invasion of France in 1940.

More here.

A non-probabilistic quantum theory produces unpredictable results

Lisa Zyga in Phys.org:

ConstructortQuantum measurements are often inherently unpredictable, yet the usual way in which quantum theory accounts for unpredictability has long been viewed as somewhat unsatisfactory. In a new study, University of Oxford physicist Chiara Marletto has developed an alternative way to account for the unpredictability observed in quantum measurements by using the recently proposed theory of superinformation—a theory that is inherently non-probabilistic. The new perspective may lead to new possibilities in the search for a successor to quantum theory.

The unpredictability observed in quantum experiments is one of the unique features of the quantum world that sets it apart from classical physics. One prominent example of quantum unpredictability is the double-slit experiment: When sending a stream of particles (such as photons or electrons) through two small slits in a plate, the individual particles are detected at different locations on a screen behind the plate. Although it's possible to predict the probability of a particle impacting at a certain location, it's not possible to predict specifically where any individual particle will end up.

Traditionally, this apparent probabilistic behavior that is observed in experiments has been accounted for in by using the Born rule. In 1926, the German physicist Max Born developed this rule to determine the probability of finding a quantum object at a certain location—or more generally, the probability that any measurement on a quantum system will produce a particular observed outcome, depending on the quantum state of the object.

The Born rule is a unique part of quantum theory in that it is the only stochastic, or randomly determined, element in quantum theory. The Born rule has basically been added by fiat on top of a theory that is otherwise deterministic.

More here. [Thanks to Farrukh Azfar.]

The earliest known Arabic short stories in the world have just been translated into English for the first time

Robert Irwin in The Independent:

The_History_of_Ali_BabaThe Ottoman sultan Selim the Grim – having defeated the Mamluks in two major battles in Syria and Egypt – entered Cairo in 1517.

He celebrated his victory by watching the crucifixion of the last Mamluk sultan at the Zuwayla Gate. Then he presided over the systematic looting of Cairo’s cultural treasures. Among that loot was the content of most of Cairo’s great libraries. Arabic manuscripts were shipped to Istanbul and distributed among the city’s mosques. This is probably how the manuscript of Tales of the Marvellous and News of the Strange ended up in the library of the great mosque of Ayasofya.

There it lay unread and gathering dust, a ragged manuscript that no one even knew existed, until 1933 when Hellmut Ritter, a German orientalist, stumbled across it and translated it into his mother tongue. An Arabic edition was belatedly printed in 1956.

In the 1990s, when I was working on my book The Arabian Nights: A Companion, I came across references to this story collection and, since it sounded very like The Arabian Nights (or, to give it its correct title, The Thousand and One Nights), I thought I ought to have a look at it. The stories in Tales of the Marvellous were indeed as fantastic and exotic as those in the Nights, and I felt as other scholars might feel if they had come across a missing part of The Canterbury Tales or a lost play by Shakespeare.

The stories are very old, more than 1,000 years old, yet most of them are quite new to us. Some years later, I suggested to Malcolm Lyons, the translator of a recent edition of the Nights, that having completed that mighty task, he might consider translating Tales of the Marvellous.

More here.

A museum’s misguided attempt to rescue the past

1.-The-Met-Breuer-side_photograph-by-Ed-Lederman-996x1024Rachel Poser at Harper's Magazine:

The Breuer building, a mean pile of granite and concrete that squats darkly on a corner of Manhattan’s Upper East Side, was built as a kind of monument to the Metropolitan Museum’s long-standing distaste for contemporary art. In 1929, the Met refused Gertrude Vanderbilt Whitney’s gift of more than five hundred contemporary American works by the likes of Edward Hopper, George Bellows, and John Sloan. The Met’s refusal precipitated the founding of the Whitney Museum, which outgrew its row houses on West 8th Street and some time later commissioned Marcel Breuer, a Hungarian architect who had been part of the Bauhaus, to design what is commonly described as an inverted Babylonian ziggurat as its new home. Built in a neighborhood otherwise known for its Beaux-Arts and Renaissance Revival mansions, the Breuer opened in 1966 to near-universal derision. (Ada Louise Huxtable, though herself a fan, said at the time that the Breuer was “the most disliked building in New York.”)

Housed just half a mile from the Met on 5th Avenue, the Whitney served for a generation as a kind of poor relation to America’s largest and most visited museum, which for most of its history has preferred European traditionalism to the gut punches of the avant-garde. Early in their careers, Jackson Pollock and Louise Bourgeois joined sixteen other American artists, who would become known as the Irascibles, to write an open letter, calling the Met “notoriously hostile to advanced art.” The museum’s stance was unchanged as late as 1999, when its director sided with Mayor Rudy Giuliani, an irascible of another sort, in his condemnation of a contemporary show at the Brooklyn Museum that featured supercharged works such as Mark Quinn’s Self, a frozen cast of the artist’s head made from ten pints of his own blood.

more here.