Fast-Evolving Human DNA Leads to Bigger-Brained Mice

Ed Yong in Not Exactly Rocket Science:

MouseEmbryo-990x609Between 5 and 7 million years of evolution separate us humans from our closest relatives—chimpanzees. During that time, our bodies have diverged to an obvious degree, as have our mental skills. We have created spoken language, writing, mathematics, and advanced technology—including machines that can sequence our genomes. Those machines reveal that the genetic differences that separate us and chimps are subtler: we share between 96 and 99 percent of our DNA.

Some parts of our genome have evolved at particularly high speed, quickly accumulating mutations that distinguish them from their counterparts in chimps. You can find these regions by comparing different mammals and searching for stretches of DNA that are always the same, except in humans. Scientists started identifying these “human-accelerated regions” or HARs about a decade ago. Many turned out to be enhancers—sequences that are not part of genes but that control the activity of genes, telling them when and where to deploy. They’re more like coaches than players.

It’s tempting to think these fast-evolving enhancers, by deploying our genes in new formations, drove the evolution of our most distinguishing traits, like our opposable thumbs or our exceptionally large brains. There’s some evidence for this. One HAR controls the activity of genes in the part of the hand that gives rise to the thumb. Many others are found near genes involved in brain development, and at least two are active in the growing brain. So far, so compelling—but what are these sequences actually doing?

To find out, J. Lomax Boyd from Duke University searched a list of HARs for those that are probably enhancers. One jumped out—HARE5. It had been identified but never properly studied, and it seemed to control the activity of genes involved in brain development. The human version differs from the chimp version by just 16 DNA ‘letters’. But those 16 changes, it turned out, make a lot of difference.

More here.

The Case of Georges Simenon

22BRADFIELD3-master315-v2Scott Bradfield at the New York Times:

In many ways, the Maigrets were a sort of comfort food — the books that Simenon wrote to recover from the physical and psychological stress of writing his better, and far less comforting, novels. In these non-Maigret “thrillers,” often referred to as the romans durs (but to most aficionados known simply as the “Simenons”), the central, usually male character is lured from the stultifying cocoon of himself — and his suburban, oppressively Francophile (and often mother-dominated) life — into a wider, vertiginous world of sexual and philosophical peril, where violence, whether it occurs or only threatens to occur, feels like too much freedom coming at a guy far more quickly than he can handle.

Even though Simenon was widely published, and translated, in his lifetime, there still seem to be some very good “serious” books — like “The Mahé Circle,” which recently received its first English translation — falling loose from forgotten cupboards and laundry hampers. That novel’s Dr. Mahé is the quintessential Simenon protagonist: Raised in a provincial village, overshadowed by a local-legend father who died showing how far he could lift and carry a horse, and hemmed in by the always disapproving eyes of his family and neighbors, he discovers his first taste of existential freedom on holiday in the Porquerolles, where he falls in love (or in fascination) with a bohemian teenage girl in a red dress.

more here.

Human rights under international law

9c3d93b8-ceed-404b-ae5c-b7c09f45db5cPhilippe Sands at the Financial Times:

In the spring of 1945, governments came together to remake the world. Within a few years a new international legal architecture was in place, constructed on the pillars of economic liberalisation, limits on the use of force and the protection of human rights. That last idea, reflected in the UN Charter, drew on various sources including Magna Carta (1215), the French Declaration of the Rights of Man and of the Citizen (1789) and the US Bill of Rights (1791). But its effect was truly novel, upending the convention that states could do more or less as they wished within their own borders.

It may seem remarkable today but, back in the 1930s, Germany was free under international law to mistreat its own citizens, even to kill them, because they were Jewish or communist or gay or disabled. This was the world that jurists such as Hersch Lauterpacht, author of the groundbreaking book An International Bill of the Rights of Man (1945), sought to banish. The hope that the individual might become “the ultimate unit of all law”, as Lauterpacht put it, would underpin the 1948 Universal Declaration of Human Rights, which proclaimed a non-binding list of “inalienable rights of all members of the human family”; it would form a basis, too, for the binding European Convention on Human Rights that followed a couple of years later.

more here.

Mohsin Hamid’s ‘Discontent and Its Civilizations,’

La-ca-jc-mohsin-hamid-20150222-002David L. Ulin at the LA Times:

We're not accustomed to considering Pakistan with such subtlety, at least not in the United States. As such, “Discontent and its Civilizations” is at its best when Hamid takes time to deconstruct our preconceptions, as in the long essays “Why They Get Pakistan Wrong” — which reminds us that “[t]he country's annual death toll from terrorist attacks rose from 164 in 2003 to 3,318 in 2009, a level exceeding the number of Americans killed on September 11” — and “Why Drones Don't Help,” with its explication of the blowback provoked by our policies.

“To turn on one's TV's in Pakistan is to find oneself entering a world permeated with conspiracy theories,” he writes, before turning the argument on us: “Conspiracy theorists have numerous examples they can cite in support of their positions. But perhaps none is as emotionally potent as the claim that flying robots from an alien power regularly strike down from the skies and kill Pakistani citizens. In the U.S., such a claim would be science fiction or paranoid survivor cultism of the furthest fringe-dwelling kind. In Pakistan, it is real.”

more here.

Saturday Poem

The Burial of the Poet’s Daughter

—for Susie Iremonger

What an assembly of the old!
Of tangled grey hair!
Of stooped backs and rheumatism!
Of baldness, wrinkles and weak eyes!
Their youth unrecognisable now –
Experts at death this poetic band.

But at the base of the altar
Where the coffin was laid
The glass houses of sorrow!
The teeming colours of Spring!
Blue, yellow and rose!

The sisters are weeping –
Cries like an awl piercing the heart –
But high in the rafters
I hear the bell of her laughter
Silvered and beautiful.

Old age is the common fate;
She chose the opposite.

by Máire Mhac an tSaoi
from The Miraculous Parish / An Paróiste Míorúilteach
publisher: O'Brien Press / Cló Iar-Chonnacht, Dublin, 2011

Slavery and Freedom on the Minnesota Territory Frontier: The Strange Saga of Joseph Godfrey

Walt Bachman in Blackpast.org:

HutMy fascination with Joseph Godfrey arose from the investigation of a family story told to me by my grandfather when I was a teenager in Minneapolis in the 1950s. One of our ancestors, Grandpa said, had been killed in the largest Indian uprising in the American West, the U.S.-Dakota War of 1862. A stone monument marked the scene of his killing, he added, and an excellent museum in New Ulm, Minnesota, had original accounts documenting the story of his death.

…In 1836, when Godfrey was just five years old, his master decided to keep him in bondage but to sell Courtney in St. Louis, the closest slave market. Remarkably, Courtney then made her way to one of the Missouri lawyers who later represented Dred Scott. She managed to procure her freedom via the courts of a slave state even as her son remained in slavery for another decade in supposedly “free” Minnesota. In the late 1840s, a conversation with an abolitionist missionary spurred Godfrey to risk a run for freedom. Fearing that he would be taken back into slavery if he stayed in the missionary’s home, he sought refuge among a band of Dakotas whose language and customs he had learned in the fur trade. Lacking free papers, he became Minnesota’s only home-grown fugitive slave. In the mid-1850s, Godfrey married a Dakota woman and lived with his wife and son on a new Dakota reservation in southwestern Minnesota. Fort Ridgely was built nearby in 1853 to keep order as hordes of white settlers arrived in the vicinity. To Godfrey’s disquiet, army officers continued to bring slaves to the new fort right up to Minnesota’s statehood. When the 1862 war broke out, Godfrey’s options were to leave his family to seek refuge among the army whose officers had enslaved his mother, or to stay with the Dakotas who had given him refuge. His life was imperiled no matter which way he turned; he remained on the Dakota side and reluctantly accompanied the war party to Milford.

Picture: Image of Fur Trading Post Near Shakopee, Minnesota, the Last Fur Trading Post Where Josephy Godfrey was held in Slavery.

More here. (Note: One post throughout February will be dedicated to Black History Month.)

Friday, February 20, 2015

writing about war

Flickr_-_The_U.S._Army_-_Colorful_Afghan_horizon-600x399Phil Klay at The American Scholar:

From the Iliad to Generation Kill, from the satire of Catch-22 to the hagiography of The Greatest Generation, we have an abundance of war stories throughout literature to help us make sense of the past decade, and Samet proves herself adept at navigating between the truths and falsehoods of the narratives we choose to tell ourselves about war. Part literary criticism, part intellectual memoir, and part reportage of the struggles, successes, and in two cases the deaths of her former students, No Man’s Land is a moving, insightful, and refreshingly iconoclastic guide toward a more nuanced understanding of America and the military that fights for it.

Samet divides her book into three long essays that explore the challenges of homecoming, the paradoxes of preparing for war, and her ultimate vision of the virtues necessary for the modern military leader—each smoothly incorporating literature, sociology, analyses of political culture, and the reflections of her former students. Her breakdown of homecomings, for example, takes us through the appeal that motorcycles hold for veterans, T. E. Lawrence’s love-hate relationship with his own legend, Dante’s and Tennyson’s decision to send Ulysses away again from Ithaca to the thrill of the open sea, comments by political and military leaders from George Washington to Admiral Mike Mullen on the responsibilities soldiers have toward their own citizenship, and a number of other examples and texts.

more here.

Is Islam a Religion of the Book?

Omar Ali in Brown Pundits:

ScreenHunter_1016 Feb. 20 23.21Razib put up an interesting post on this topic on his blog . I think his point is that no religion is a “religion of the book”. People make the religion and they remake it as time demands. Messily and unpredictably in many cases, but still, it moves. And in this sense, Islam is no more fixed in stone by what is written or not written in it's text (or texts) than any other religion.

Someone then commented (and I urge you to read the post and the comments, and the hyperlinks, they are all relevant and make this post clearer) as follows:

“Well, if you take the Old Testament and Koran at face value, the OT is more violent. The interesting question is then why Islam ends up being more violent than Judaism or Christianity, and for that I agree you have to thank subsequent tradition and reinterpretation of the violence in the text. It appears that for whatever reason Islam has carried out less of this kind of reinterpretation, so what was originally a less violent founding text ends up causing more violence because it is being interpreted much more literally.”

I replied there, and then thought I would put that reply up as a new post here because I want to see what people think of this quick and off-the-cuff comment. THEN, I can maybe improve it in a final new post this weekend. So, without further ado, my comment:

There is an easier explanation. Islam the religion we know today (classical Islam of the four Sunni schools and it's Shia counterparts) developed in the womb of the Arab empire. It is evident that it provided a unifying ideology and a theological justification for that empire (and in the case of various Shia sects, varying degrees of resistance or revolt against that empire), but at the very least, they grew and formed together; one was not the later product of the fully formed other. Being the religion of a (very successful and impressive) imperialist project, it's “official” mature Sunni version obviously has a military-supremacist feel to it.

More here.

the importance of anxiety

GS0941473Charlie Kurth at Aeon Magazine:

Immanuel Kant suggested an even graver problem with anxiety: it is incompatible with virtue. For Kant, the virtuous individual is someone who has brought ‘all his capacities and inclinations under his (reason’s) control’; therefore, he writes in The Metaphysics of Morals(1797), the ‘true strength of virtue is a tranquil mind’. But when we’re anxious, our minds are anything but tranquil. We lack the rational control that’s distinctive of virtue: it is emotion, not reason, that determines our behaviour. That’s bad.

This picture of anxiety as a dark and pernicious force certainly has illustrious supporters. Even so, I believe that it is mistaken. It goes against the grain to say this, but anxiety can be a good thing. Indeed, I hope to persuade you that it is central to our ability to successfully navigate moral and social life. I won’t go as far as to say that we needmore of it, but we should cultivate it. Worry is important; we should get it right.

more here.

the violent jane austen

Cb1501ea-b777-11e4_1130088hPaula Byrne at the Times Literary Supplement:

Re-reading the youthful writings, one is struck again and again by the violence. A group of characters threaten murder by dagger, which shall be “steeped in your hearts blood”. A sister poisons another sister and is “speedily raised to the gallows” for her perfidy. A child bites off her mother’s fingers. There is also notable violence against the self. One young heroine inadvertently enters into an engagement with two gentlemen in the space of a single evening and kills herself by plunging into the river. Another is addicted “to the bottle”, and drinks herself half to death. In “Love and Freindship”, the two heroines, indulging in a bout of sensibility, are momentarily distracted by a road accident. They see “Two Gentlemen most elegantly attired but weltering in their blood”. When the heroines discover that the gentlemen are in fact their husbands, they respond like characters in a sentimental novel: “Sophia shrieked and fainted on the Ground – I ran instantly mad”. Sophia faints for so long that she catches cold, develops a fever and dies. Her final advice is not to faint but to run mad: “Beware of swoons, dear Laura . . . . A frenzy fit is not one quarter so pernicious; it is an exercise to the Body and if not too violent, is I dare say conducive to Health in its consequence”.

Critics have long seen “Love and Freindship” as an embryo version of Sense and Sensibility. Both works, of course, are attacks on the novel of sensibility. Austen’s first published novel establishes the type of novelist she is not.

more here.

The Wrong Objections to the Many-Worlds Interpretation of Quantum Mechanics

Sean Carroll in Preposterous Universe:

Sean_carroll_biopic-smallLongtime readers know that I’ve made a bit of an effort to help people understand, and perhaps even grow to respect, the Everett or Many-Worlds Interpretation of Quantum Mechanics (MWI) . I’ve even written papers about it. It’s a controversial idea and far from firmly established, but it’s a serious one, and deserves serious discussion.

Which is why I become sad when people continue to misunderstand it. And even sadder when they misunderstand it for what are — let’s face it — obviously wrong reasons. The particular objection I’m thinking of is:

MWI is not a good theory because it’s not testable.

It has appeared recently in this article by Philip Ball — an essay whose snidely aggressive tone is matched only by the consistency with which it is off-base. Worst of all, the piece actually quotes me, explaining why the objection is wrong. So clearly I am either being too obscure, or too polite.

I suspect that almost everyone who makes this objection doesn’t understand MWI at all. This is me trying to be generous, because that’s the only reason I can think of why one would make it. In particular, if you were under the impression that MWI postulated a huge number of unobservable worlds, then you would be perfectly in your rights to make that objection. So I have to think that the objectors actually are under that impression.

An impression that is completely incorrect.

More here.

A Curious Case of Writer’s Block

Irvin D. Yalom in the New York Times:

Writers-blockDr. Yalom, I would like a consultation. I’ve read your novel “When Nietzsche Wept,” and wonder if you’d be willing to see a fellow writer with a writing block.

No doubt Paul sought to pique my interest with his email. And he succeeded: I’d never turn away a fellow writer. As for the writing block, I felt blessed by not having been visited by one of those creatures and I was keen to help him tackle it.

Ten days later Paul arrived for his appointment. I was startled by his appearance. For some reason I had expected a frisky, tormented, middle-aged writer, yet entering my office was a wizened old man, so stooped over that he appeared to be scrutinizing the floor. Almost able to hear his joints creaking, I took his heavy battered briefcase, held his arm and guided him to his chair.

“All I know about you comes from your short email,” I said. “You wrote that you were a fellow writer, you’ve read my Nietzsche novel, and you have a writing block.”

“Yes,” he said. “And I’m requesting a single consultation. That’s all. I’m on a fixed income and can’t afford more.”

“I’ll do what I can,” I said. “Tell me what I should know about the block.”

“I have to go back to my grad school days,” he began. “I was in philosophy at Princeton writing my doctorate on the incompatibility between Nietzsche’s ideas on determinism and his espousal of self-transformation. But I couldn’t finish. I kept getting distracted by such things as Nietzsche’s extraordinary correspondence, especially by his letters to his friends and fellow writers like Strindberg.”

More here. [Thanks to Laura Claridge.]

Friday Poem

It’s Our Dance
—for Lorna

Every Sunday
I play Nina Simone’s
‘My baby just cares for me’
& with a different flower
in your hair every week
you spring out from the bar
& I leave the mixing desk
& we dance with our hangovers,
yes we dance around the bar
& last week we ended up
outside briefly on Lewes Road
in the petrol hazes
& we even waltzed
out to the beer garden
& everybody smiles
when we dance together
to ‘My baby just cares for me’
& for a few precious minutes
it’s as if we have all swallowed the moon
& everyone is lighter
& the world might not ever end.

by Brendan Cleary
from Face
publisher: Pighog, Brighton, 2013

Do our languages skew toward happiness?

Eoin O'Carroll in The Christian Science Monitor:

SmileAre humans inherently happy, sad, or somewhere in between? A new study suggests that, at least when it comes to our vocabulary, we tend to look on the bright side of life. A team of mathematicians, computer scientists, and linguists at the University of Vermont and the MITRE Corporation combed through 10 languages' literature, movie subtitles, music lyrics, and, of course, Web pages and social media feeds, collecting an estimated 100 billion words from Twitter alone. The team used this data – from 24 types of sources in all – to draw up lists of the 10,000 most common words in each language. Then, the researchers had native speakers of each language rate their emotional response to each word on a 9-point scale, from saddest to happiest. For each of the 10,000 words of each language, the scientists collected 50 ratings, for a total of about 5 million scores.

The result? Every source averaged above 5. Our words, which the study's authors describe as “the atoms of human language,” reveal a “universal positivity bias.” “In every source we looked at,” said UVM mathematician Peter Dodds in a press release, “people use more positive words than negative ones.” All of the languages seemed to skew positive, but some did so more than others. In descending order of happiness, they are: Spanish, Portuguese, English, Indonesian, French, German, Arabic, Russian, Korean, and Chinese.

More here.

David Jones Peck (1826-1855): First black man to graduate from an American medical school

From Blackpast.org:

DavidjonespeckHe was born to John C. and Sarah Peck in Carlisle, Pennsylvania around 1826. John Peck was a prominent abolitionist and minister who founded the local African Methodist Episcopal (AME) Church in Carlisle. Peck was also a barber and wigmaker. John and Sarah Peck moved to Pittsburgh in the early 1830s where they established the first school for black children in the area. David was one of their first students. Between 1844 and 1846 David Peck studied medicine under Dr. Joseph P. Gaszzam, an anti-slavery white doctor in Pittsburgh. He then entered Rush Medical College in Chicago in 1846, three years after the institution opened. After he graduated in 1847, Peck toured the state of Ohio with William Lloyd Garrison and Frederick Douglass promoting abolitionist ideals. His status as the first black graduate of a medical college was used by abolitionists to promote the idea of full black citizenship and was implicitly an attack on slavery. In 1849 Peck established his practice in Philadelphia. He lived in and worked from a red brick row house with his wife, Mary E. Peck, whom he married on July 24, 1849. Peck's medical practice, however, was not successful. Few doctors recognized his status, referred patients to him, or consulted with him.

Peck closed his medical practice in Philadelphia in 1851 and was preparing to travel to California when Martin Delany, an old friend and fellow Pittsburgh abolitionist, persuaded him instead to participate in an emigration project that would resettle U.S. free blacks in Central America. Delany, Peck, and other black emigrants moved to Nicaragua in 1852, settling on the east coast of the nation. The emigrants established San Juan Del Norte with Delaney as the mayor and commander of the militia. Peck practiced medicine and became the town physician. In 1854 he joined the Liberal side in the Nicaraguan Civil War and was killed by cannon fire in the town of Granada in January 1855. Dr. Peck was buried in the town square of the city of Granada.

More here. (Note: One post throughout February will be dedicated to Black History Month.)

Thursday, February 19, 2015

Fundamental theories of nature aren’t allowed to hide information

Giulio Chiribella in Nautilus:

ScreenHunter_1015 Feb. 20 09.13Let’s play a game. You get a box with two compartments and one ball. The ball could be in either compartment with equal probability, and my job is to guess which one. Ok, it’s not the most exciting game, but at least it’s fair. My odds are 50/50.

But suppose I know that your box was produced in a factory where a conveyor belt brought boxes to a cannon, which shot balls into one compartment or another depending on a coin toss. The coin toss was done once a day, and all the boxes produced on the same day have the ball in the same compartment. If I managed to get a box that was produced on the same day as yours, I would be able to win the game with certainty. So much for being fair.

The lesson is clear: Whether or not our game is fair depends on whether or not the ball in your box is correlated with some other system in my possession. In order to be sure that I don’t cheat, you need to collect all the systems that are correlated with your box and keep them safely in your control. But how can you be confident that you’ve collected all of them? The strongest guarantee is that your systems are in what physicists call a “pure state,” which means that nothing else can be correlated with it, and that you have maximal knowledge of your systems. A “mixed state,” on the other hand, gives you only partial knowledge, and some essential information can hide elsewhere.

And just like that, we have come to an idea at the heart of quantum mechanics, called the Purification Principle.

More here.

Greek Finance Minister Yanis Varoufakis: How I became an erratic Marxist

Before he entered politics, Yanis Varoufakis, the iconoclastic Greek finance minister at the centre of the latest eurozone standoff, wrote this searing account of European capitalism and and how the left can learn from Marx’s mistakes.

Yanis Varoufakis in The Guardian:

ScreenHunter_1014 Feb. 19 19.44In 2008, capitalism had its second global spasm. The financial crisis set off a chain reaction that pushed Europe into a downward spiral that continues to this day. Europe’s present situation is not merely a threat for workers, for the dispossessed, for the bankers, for social classes or, indeed, nations. No, Europe’s current posture poses a threat to civilisation as we know it.

If my prognosis is correct, and we are not facing just another cyclical slump soon to be overcome, the question that arises for radicals is this: should we welcome this crisis of European capitalism as an opportunity to replace it with a better system? Or should we be so worried about it as to embark upon a campaign for stabilising European capitalism?

To me, the answer is clear. Europe’s crisis is far less likely to give birth to a better alternative to capitalism than it is to unleash dangerously regressive forces that have the capacity to cause a humanitarian bloodbath, while extinguishing the hope for any progressive moves for generations to come.

For this view I have been accused, by well-meaning radical voices, of being “defeatist” and of trying to save an indefensible European socioeconomic system. This criticism, I confess, hurts. And it hurts because it contains more than a kernel of truth.

I share the view that this European Union is typified by a large democratic deficit that, in combination with the denial of the faulty architecture of its monetary union, has put Europe’s peoples on a path to permanent recession. And I also bow to the criticism that I have campaigned on an agenda founded on the assumption that the left was, and remains, squarely defeated. I confess I would much rather be promoting a radical agenda, the raison d’être of which is to replace European capitalism with a different system.

Yet my aim here is to offer a window into my view of a repugnant European capitalism whose implosion, despite its many ills, should be avoided at all costs. It is a confession intended to convince radicals that we have a contradictory mission: to arrest the freefall of European capitalism in order to buy the time we need to formulate its alternative.

More here.

Why Do Luna Moths Have Such Absurdly Long Tails?

Ed Yong in Not Exactly Rocket Science:

Luna-moth-990x704You don’t need a field guide to recognise a luna moth. This large insect, found throughout the eastern half of North America, is unmistakeable. It has a fuzzy white body, red legs, feathery yellow antennae, and huge lime-green wings that can stretch up to 4.5 inches across. And at the end of its hindwings are a pair of long, streaming tails that can double the moth’s length.

In 1903, an entomologist named Archibald Weeks suggested that the tails direct predators away from the moth’s body. “Again and again may predator bat or bird, in an effort to capture a moth or butterfly, successively tear away sections of the tails, of which a sacrifice can be readily afforded, without disabling it or retarding its flight,” he wrote.

He was roughly right. More than a century on, Jesse Barber from Boise State University has shown that the luna moth’s tails are the equivalent of eyespotson fish and butterflies. These distinctive markings are typically found on dispensable body parts like tails and outer wings. They serve to draw a predator’s attention away from more vulnerable regions; better to lose a tail than a head.

Eyespots are visual defences, and bats—the main nemeses of moths—are not visual hunters. They find their prey with sonar—they make high-pitched squeaks and visualise the world using the rebounding echoes. To divert a bat, you need something that makes distracting echoes.

More here.