The approach to predictive medicine that is taking genomics research by storm

Matthew Warren in Nature:

6.6 million — that’s how many spots on the human genome Sekar Kathiresan looks at to calculate a person’s risk of developing coronary artery disease. Kathiresan has found that combinations of single DNA-letter differences from person to person in these select locations could help to predict whether someone will succumb to one of the leading causes of death worldwide. It’s anyone’s guess what the majority of those As, Cs, Ts and Gs are doing. Nevertheless, Kathiresan says, “you can stratify people into clear trajectories for heart attack, based on something you have fixed from birth”. Kathiresan, a geneticist at Massachusetts General Hospital in Boston, isn’t alone in counting outrageously high numbers of variants. The polygenic risk scores he has developed are part of a cutting-edge approach in the hunt for the genetic contributors to common diseases. Over the past two decades, researchers have struggled to account for the heritability of conditions including heart disease, diabetes and schizophrenia. Polygenic scores add together the small — sometimes infinitesimal — contributions of tens to millions of spots on the genome, to create some of the most powerful genetic diagnostics to date. This approach has taken off thanks to a number of well-resourced cohort studies and large data repositories, such as the UK Biobank (see pages 194203 and 210), which collect vast quantities of health information alongside DNA data from hundreds of thousands of people. And some studies published in the past year or so have been able to analyse more than a million participants by combining information from such sources, increasing scientists’ ability to detect tiny effects.

Supporters say that polygenic scores could be the next great stride in genomic medicine, but the approach has generated considerable debate. Some research presents ethical quandaries as to how the scores might be used: for example, in predicting academic performance. Critics also worry about how people will interpret the complex and sometimes equivocal information that emerges from the tests. And because leading biobanks lack ethnic and geographic diversity, the current crop of genetic screening tools might have predictive power only for the populations represented in the databases.

More here.

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Thursday Poem

A Barroom View of Love

I would not want all my words
To parade around this world
In pretty costumes,

So I will tell you something
Of the barroom view of Love.

Love is grabbing hold of the great Lion’s mane
And wrestling and rolling deep into Existence

While the Beloved gets rough
and begins to maul you alive.

True Love, my dear,
Is putting the ironclad grip upon

The sore, swollen balls
Of a Divine Rogue Elephant

And
Not having the good fortune to die!
.

by Hafiz
from I Heard God Laughing
Penguin Books, 2006
translation: Daniel Ladinsky

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October 10, 2018

Why atheists are not as rational as some like to think

Lois Lee in The Conversation:

Many atheists think that their atheism is the product of rational thinking. They use arguments such as “I don’t believe in God, I believe in science” to explain that evidence and logic, rather than supernatural belief and dogma, underpin their thinking. But just because you believe in evidence-based, scientific research – which is subject to strict checks and procedures – doesn’t mean that your mind works in the same way.

When you ask atheists about why they became atheists (as I do for a living), they often point to eureka moments when they came to realise that religion simply doesn’t make sense.

Oddly perhaps, many religious people actually take a similar view of atheism. This comes out when theologians and other theists speculate that it must be rather sad to be an atheist, lacking (as they think atheists do) so much of the philosophical, ethical, mythical and aesthetic fulfilments that religious people have access to – stuck in a cold world of rationality only.

The problem that any rational thinker needs to tackle, though, is that the scienceincreasingly shows that atheists are no more rational than theists. Indeed, atheists are just as susceptible as the next person to “group-think” and other non-rational forms of cognition. For example, religious and nonreligious people alike can end up following charismatic individuals without questioning them.

More here.

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How a sunbeam split in two became physics’ most elegant experiment

Anil Ananthaswamy in Aeon:

Imagine throwing a baseball and not being able to tell exactly where it’ll go, despite your ability to throw accurately. Say that you are able to predict only that it will end up, with equal probability, in the mitt of one of five catchers. The baseball randomly materialises in one catcher’s mitt, while the others come up empty. And before it’s caught, you cannot talk of the baseball being real – for it has no deterministic trajectory from thrower to catcher. Until it becomes ‘real’, the ball can potentially appear in any one of the five mitts. This might seem bizarre, but the subatomic world studied by quantum physicists behaves in this counterintuitive way.

Microscopic particles, governed by the laws of quantum mechanics, throw up some of the biggest questions about the nature of our underlying reality. Do we live in a universe that is deterministic – or given to chance and the rolls of dice? Does reality at the smallest scales of nature exist independent of observers or observations – or is reality created upon observation? And are there ‘spooky actions at a distance’, Albert Einstein’s phrase for how one particle can influence another particle instantaneously, even if the two particles are miles apart.

As profound as these questions are, they can be asked and understood – if not yet satisfactorily answered – by looking at modern variations of a simple experiment that began as a study of the nature of light more than 200 years ago. It’s called the double-slit experiment, and its findings course through the veins of experimental quantum physics.

More here.

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If We’re Going To Save The Planet, We’ve Got To Use The Nuclear Option

Joshua S. Goldstein and Staffan A. Qvist in the Huffington Post:

Good news and bad news arrived this week from the world’s top climate change experts. Good news: they can tell us in agonizing detail why the world should really, really keep the rise in global warming to less than 1.5 degrees Celsius. Bad news: the 132 authors of the 700-page report offer many ideas but no feasible plan for how to do that. As the International Panel on Climate Change’s co-chair put it, “One thing the report did not aspire to do is answer the question of feasibility.” So we can call it the Beach Boys Report ― “Wouldn’t it be nice…”

The 2015 Paris Agreement set an overall goal of staying below 2 degrees Celsius of global warming. However, the combination of the deal’s country-by-country goals would not accomplish that, and no major country is on track to meet its goals anyway. The 1.5 degree target is rightly even more ambitious, but also even further from the reality of energy systems in the world today.

In the first part of the 21st century, the fastest-growing energy source was coal. And energy use is going up rapidly because poor countries want to be richer ― and have a right to be. Climate goals and realities are not converging.

More here.

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A Conversation with David Bertrand

Whitney Curry Wimbish talks with David Bertrand at Music and Literature:

At the risk of not sounding patriotic, as I grew older, I came into some conflict with the aesthetic of Trinidadian jazz.

There was a generation that felt like we have to generate something that works in parallel with our idiosyncrasies. I think there was a bit of historical confusion. They were looking at jazz and thinking, “But we don’t want to sound American, we want to sound Trinidadian.” There was nothing wrong with that, but it meant it was as if there was no acknowledgement of how jazz was generated in the first place. The narrative that we all know—that jazz came out of the African-American experience, and the various frustrations that occurred parallel to that people—would eventually be shared with the rest of mankind. You’re creating music that recalls that. Trinidadian jazz wanted to present an anticolonial stance, but it did not acknowledge that jazz had originally been a response to a very similar force.

more here.

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What Was Delacroix Doing?

Jerry Saltz at New York Magazine:

Prepare to grapple with the cosmic grandiosity and optical hot-messes of that 19th-century French freak of painterly nature, Eugène Delacroix, who’s churning, turgid, crimson-tinged floridity has enkindled the respiratory systems of artists since he first debuted at the Paris Salon of 1822 — and given many others agita.

Now, at the Met, comes the first large-scale North American retrospective of his epoch-altering work. How did it alter his epoch? Delacroix’s style is so uncontained, convulsive, and atmospheric it’s hard to pigeonhole as simply Romanticism. At times I often look at his painting and mourn the death of his extraordinary comrade, Théodore Géricault, he of the 1819 Raft of the Medusa, as this artist might have made French Romanticism less flamboyant and easier to take had he not died before the age of 33. Delacroix pushed much harder, which means that his work is more demanding and hard to digest, even now, but, as a result, he is one of the most influential artists of the last two centuries.

more here.

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The 9/11 Novel That Finally Understands the Fulfillments of Faith

James Wood at The New Yorker:

In several respects, John Wray’s “Godsend” (Farrar, Straus & Giroux) appears to be a conventional specimen: a compact, tautly written novel of travel and growth, about a troubled eighteen-year-old California woman who leaves home and sets out on an arduous, sometimes terrifying journey. Formally, everything fits into place: lean dialogue, attentive description, nicely paced interiority, deft characterization—all the right contemporary rations. Wray’s publisher calls it “a coming-of-age novel like no other,” and the reader prepares for a decent chunk of Californian Bildung. But Wray’s story is in fact indecently unconventional. Our heroine leaves not for, say, New York but for a madrassa in Pakistan, and then joins the Taliban, across the border in Afghanistan. She “grows,” she comes of age, but the journey will strike most readers as a distinctly unsentimental education. “Godsend,” which begins like a recognizable combination of bildungsroman and adventure tale, becomes much stranger and more original after it arrives in Pakistan, discovering within itself a profound understanding of the demands of religious practice—of religious submission, especially—which has eluded almost every serious contemporary American novelist since 9/11. It is not only Wray’s heroine but also his novel that comes of age, steadily deepening and astounding as it develops.

more here.

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The voice of Hobsbawm: How the Marxist ideas of a British historian ended up on the bookshelves of Indian civil servants and Brazilian housewives

Emile Chabal in Aeon:

Almost all Marxists have imagined themselves to be part of a global community. More than perhaps any other modern ideology, Marxism has given its adherents a sense of being connected across regions, countries and continents. The activists, thinkers, politicians, students, workers, guerrilla fighters and party apparatchiks who, throughout the 20th century, claimed Marxist ideals for themselves rarely agreed on what Marxism was or where it was headed. But they knew that they were not alone. At its height, Marxism created a web of interconnected communities at least as powerful as the Muslim ummah, complete with its own heretics, infidels, rogue saviours and clerics.

Historically, the impetus for this came from Karl Marx and Friedrich Engels themselves. Many of the concepts they deployed – such as ‘capitalism’ and ‘class’ – were transnational in theory and in practice. Some of their best-known political slogans – above all, the final line of The Communist Manifesto (1848), popularised as ‘Workers of the world, unite!’ – explicitly invoked the global power of their prophesy. Marx and Engels were hardly the only European political thinkers in the 19th century to paint their political aspirations on a global canvas, but their ideas proved to be extraordinarily influential.

More here.

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My Great-Grandfather the Bundist

Mary Crabapple in the New York Review of Books:

During his elder years, my great-grandfather, the post-Impressionist artist Sam Rothbort, tried to paint back into existence the murdered world of his shtetl childhood. Amid the hundreds of watercolors that he called Memory Paintings, one stood out. A girl silhouetted against some cottages, her dress the same color as the crepuscular sky above. A moment before, she’d hurled a rock through one now-shattered cottage window. On the painting’s margin, her boyfriend offers more rocks.

“Itka the Bundist, Breaking Windows,” Sam captioned the work.

I may have been fifteen, seventeen, or twenty when I saw the watercolor, in my great aunt’s sunbaked living room or my mother’s apartment; I don’t recall exactly. What sticks with me is the Old World awkwardness of the heroine’s name. Itka. I turned the Yiddish syllables on my tongue. And Bundist. What was that?

This question became a thread that led me to the Bund, a revolutionary society of which my mother’s Grandpa Sam had been a member, whose story was interwoven with the agonies and triumphs of Jews in Eastern Europe, and whose name has all but been erased.

More here.

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How we can turn the tide for women in science

Ronan Thomson in Phys.Org:

For the first time in 55 years, a woman has won the Nobel Prize in physics —Prof. Donna Strickland. This win has publicly highlighted that women are still under-represented in science, particularly in physics. As a woman in , this lack of diversity is something that I encounter almost daily, and also something that we can take action to change. As an undergraduate  student, I was confronted with the lack of  in science at the National Research Council (NRC) of Canada in 2001. The first day of my summer job in NRC’s now-defunct “Women in Engineering and Science” program, I was shocked looking around the lunchroom. Where were the women? The vast majority of scientists were men!

The situation was similar in my university studies —I only ever had two female professors.

That lack of diversity was something I grew accustomed to. A resident at Perimeter Institute for my Ph.D. studies, I was often the only woman in the room at scientific meetings or seminars. My office was shared with four male students, and there were some jokes that I had been assigned “the secretary’s desk” and remarks about the colour of my T-shirt. I was the only woman in the room for my Ph.D. defence at the University of Waterloo in 2007. When I became a faculty member in 2010, I was thrilled to be one of four women physics professors —more than 20 per cent of physics faculty at Carleton University. This bucked the trend among physics faculty members at many universities (and this continues, as we now have five women physics professors at Carleton). But as I started teaching, the lack of  among undergraduate physics students was striking: a class of 50 students with only three women, another with no women, in my first year of teaching. As a researcher, the lack of women as invited and keynote speakers at scientific conferences continues to be discouraging. There are certainly women giving excellent conference presentations, but they are too often overlooked when it comes to invited and keynote speakers lists. An invited or keynote speaker entry on a CV indicates respect and recognition of excellence; omission of women hinders their careers.

More here.

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October 9, 2018

Delete Your Social Media Account Now!

Harper Simon talks to Jaron Lanier at the LARB:

You brought up this other question of why is it so important for people to leave, and the thing I want to say is that, because of addiction and because of network effects, I realize that only a small minority of people can do it, and I don’t know how many I have influenced to get off of there. I don’t have a means of measuring that. But here’s what I would say: there have been times before, recently and even in America, when society had to confront mass addiction that had a commercial component.

I’m thinking of Mothers Against Drunk Drivers. And I’m thinking of the public smoking of cigarettes. In both of those cases, there were industries that relied on mass addiction, but somehow or other, a rational conversation gradually created a change. In neither case was the substance totally outlawed, but its role in society was vastly changed.

more here.

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Buying Rest in an Era of Damaged Sleep

Sophie Haigney at The Baffler:

We really are sleeping less. As Crary writes, in the early twentieth century, adults slept an unthinkable ten hours every night on average. A generation ago, people were tucking in for eight hours. Today, the average North American adult sleeps a paltry six-and-a-half hours every night. This is often blamed on our devices, which do play a major role. But Crary argues that, interrelatedly, the forces of twenty-first-century capitalism have shown an obsessive enthusiasm for destroying sleep.

Sleep, he argues, is a last frontier, something that unlike every other strand of modern life has not yet been commodified. This is because sleep is perfectly pointless and therefore useless. “The stunning, inconceivable reality is that nothing of value can be extracted from it,” Crary writes.

more here.

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Why Charles Aznavour’s Global Fame Never Reached American Shores

Franz Nicolay at The Paris Review:

When he passed away this week at the age of ninety-four, the singer, songwriter, and actor Charles Aznavour was still touring. He was a living link to the golden age of French chanson. As a young man, he had been maligned as short and ugly, an immigrant with a hoarse voice, but he became a protégée of Édith Piaf, and then a global star in his own right. While his success in the anglophone world never equaled his renown in other countries, he was, by any reckoning, one of the twentieth century’s most popular entertainers, often referred to as the French Sinatra (Aznavour sang with Sinatra on the latter’s Duets record). He sang in five languages, appeared in at least thirty films, wrote somewhere in the vicinity of a thousand songs, and sold hundreds of millions of records worldwide.

“I am popular because I am like everybody in France,” he told Lillian Ross in 1963. “My face is the face of anybody. My voice is the voice of anybody. My face is the face of their hope.”

more here.

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Tuesday Poem

What It Was Like

If you want to know what
it was like, I’ll tell you
what my tío told me:
There was a truck driver,
Antonio, who could handle a
rig as easily in reverse as
anybody else straight ahead:

Too bad he’s a Mexican was
what my tío said the
Anglos had to say
about that.

And thus the moral:

Where do you begin if
you begin with if
you’re too good
it’s too bad?

by Leroy Quintana
from El Coro
Uniniversity of Massachusetts Press, 1997

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The Book of Humans – a pithy homage to our species

Robin McKie in The Guardian:

In 2017, scientists in Australia observed some striking avian behaviour. A handful of kites and falcons in the outback were seen picking up burning sticks from bush fires. The birds would then carry these smoking embers in their beaks to areas of dry grass and drop them. New fires were set off, triggering frenzied evacuations by small animals – which were promptly snatched from above by the waiting raptors. Such actions are extraordinary, says Adam Rutherford, a science writer and broadcaster. “It is, as far as I am aware, the only documented account of deliberate fire-starting by an animal other than a human. These birds are using fire as a tool.” Indigenous Australians occasionally deliberately start fires in order to flush out game, he notes. Did they learn the habit from birds? “Or maybe it is just a good trick and only us and the raptors have worked it out.” Either way, it is clear humans are not the only ones who see fire as a means for getting what they want – and that is key to Rutherford’s examination of what it means to be human. In what way, exactly, are we exceptional as a species? Science has continually chipped away at the notion of human specialness, the idea of our being “the paragon of animals”. Prowess at pyrotechnics is just the latest “human-only” attribute that has since been revealed to have animal exponents.

So what is left? What behaviours uniquely define our species? The usual list includes speech, tool-making, culture, as well as art and fashion. We are masters and mistresses of all, but none are exclusive human attributes. Crows make and use tools; apes can be taught sign language; dolphins and birds have been observed adopting habits through cultural transmission; chimps have been seen using styles of headwear “just to be in with the in-crowd”, as Rutherford puts it.

That leaves war and sex, both popular human pastimes. But is either peculiar to our species? Sex certainly occupies a titanic amount of our time and interest. One study has indicated that in Britain alone roughly 900,000,000 acts of heterosexual intercourse take place every year. (That’s about 100,000 an hour, if you are interested.) Yet only 0.1% of these bouts of British bonking results in a conception – and that is a very, very low rate of reproduction. Our species has almost, but not quite, decoupled sexual intercourse from its replication, it seems. But that still does not make us unique. Bonobo apes turn out to be even more genitally obsessed and sexually motivated than humans. All have intercourse several times a day, usually with different partners.

That leaves us with war. Again we seem infatuated with violence.

More here.

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Coal Is Killing the Planet. Trump Loves It.

The Editorial Board at The New York Times:

If we keep burning coal and petroleum to power our society, we’re cooked — and a lot faster than we thought. The United Nations scientific panel on climate change issued a terrifying new warning on Monday that continued emissions of greenhouse gases from power plants and vehicles will bring dire and irreversible changes by 2040, years earlier than previously forecast. The cost will be measured in trillions of dollars and in sweeping societal and environmental damage, including mass die-off of coral reefs and animal species, flooded coastlines, intensified droughts, food shortages, mass migrations and deeper poverty.

The worst impacts can be avoided only by a “far-reaching and unprecedented” transformation of the global energy system, including virtually eliminating the use of coal as a source of electricity, the panel warned. Yet President Trump, who has questioned the accepted scientific consensus on climate change, continues to praise “clean beautiful coal” and has directed his Environmental Protection Agency to reverse major strides undertaken by the Obama administration to reduce greenhouse gas emissions from coal-fired power plants. This is unbelievably reckless. In addition to undermining the fight against climate change, the president’s efforts to prop up the dirtiest of all fuels will also exact a significant toll on public health, on the hearts and lungs of ordinary Americans.

More here.

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Can we be held morally responsible for our actions? Yes, says Daniel Dennett; No, says Gregg Caruso

Daniel Dennett and Gregg Caruso in Aeon:

Caruso: [Dan,] you have famously argued that freedom evolves and that humans, alone among the animals, have evolved minds that give us free will and moral responsibility. I, on the other hand, have argued that what we do and the way we are is ultimately the result of factors beyond our control, and that because of this we are never morally responsible for our actions, in a particular but pervasive sense – the sense that would make us truly deserving of blame and praise, punishment and reward. While these two views appear to be at odds with each other, one of the things I would like to explore in this conversation is how far apart we actually are. I suspect that we may have more in common than some think – but I could be wrong. To begin, can you explain what you mean by ‘free will’ and why you think humans alone have it?

Dennett: A key word in understanding our differences is ‘control’. [Gregg,] you say ‘the way we are is ultimately the result of factors beyond our control’ and that is true of only those unfortunates who have not been able to become autonomous agents during their childhood upbringing. There really are people, with mental disabilities, who are not able to control themselves, but normal people can manage under all but the most extreme circumstances, and this difference is both morally important and obvious, once you divorce the idea of control from the idea of causation. Your past does not control you; for it to control you, it would have to be able to monitor feedback about your behaviour and adjust its interventions – which is nonsense.

More here.

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