Wednesday Poem

Exit Strategy

Tell me there is a way to believe it all,
an exit strategy with groggy murmurs
of nothing but rest and a quiet universe.

All I can think of is my child, asleep
in bed, dealing with whatever birthright
his dreams afford his fears, waiting to wake.

Sometimes I feel like Kepler, poised to inherit
pages of wrinkled data, but grumbling,
What a holy-fucking mess Tycho left behind.

Under the surface of the crowd’s rumble
is a song. We could have danced, you know,
to the how-not-why of these perfect heartbeats.

It’s true. You’ve not been asked to understand.
You’ve been asked to listen, and work it out.

by George Murray
from
Rush to Here
Nightwood Editions, 2007

 



Hood: Trailblazer of the Genomics Age

Luke Timmerman in Undark:

TWO WEEKS BEFORE Christmas 1999, Lee Hood appeared to have it all: A loving family. Money. Fame. Power. He counted Bill Gates, one of the world’s richest men, as a friend and supporter. Eight years earlier, Gates had given the University of Washington $12 million to lure the star biologist from Caltech in what the Wall Street Journal called a “major coup.” Hood’s assignment on arrival: build a first-of-its-kind research department at the intersection of biology, computer science, and medicine. Even at 61, the former high school football quarterback could still do 100 pushups in a row. He ran at least three miles a day. He climbed mountains. He traveled the world to give scientific talks to rapt audiences. At a time when many men slow down, Hood maintained a breakneck pace, sleeping just four to five hours a night. He owned a luxurious art-filled mansion on Lake Washington, but otherwise cared little for the finer things in life, sporting a cheap plastic wristwatch and driving an aging Toyota Camry. Those who worked closely with him said he still had the same wonder and enthusiasm for science he had as a student.

Yet here, at the turn of the millennium, Hood was miserable.

His once-controversial vision for “big science” was becoming a reality through the Human Genome Project, yet he didn’t feel like a winner. He felt suffocated. He had a new vision, a more far-sighted and expansive one that he insisted would revolutionize healthcare. But he felt the university bureaucrats were blind to the opportunity. They kept getting in his way. It was time, Hood felt, to have a difficult conversation with his biggest supporter. On a typically dark and gray December day in Seattle, Hood climbed into his dinged-up Camry and drove across the Highway 520 floating bridge over Lake Washington to meet Gates, the billionaire CEO of Microsoft. Hood shared some startling news: he had resigned his endowed Gates-funded professorship at UW. He wanted to start a new institute free from university red tape. It was the only way to fulfill his dream for biology in the 21st century.

Gates was well aware of Hood’s record of achievements and its catalytic potential. Hood had led a team at Caltech that invented four research instrument prototypes in the 1980s, including the first automated DNA sequencer. The improved machines that followed made the Human Genome Project possible and transformed biology into more of a data-driven, quantitative science. Researchers no longer had to spend several years — an entire graduate student’s career — just to determine the sequence of a single gene. With fast, automated sequencing tools, a new generation of biologists could think broadly about the billions of units of DNA.

More here.

Tuesday, July 14, 2020

The Calculus of Ought: Quantification is more than merely a means of communication and persuasion in a fragmented culture

James Davison Hunter and Paul Nedelisky in The Hedgehog Review:

There was a time not long ago when most educated people believed that science would one day explain everything—not only the workings of the physical world but also the secrets to the good life. Such confidence perhaps peaked in the early nineteenth century, when Jeremy Bentham proposed utilitarianism as a way of making happiness quantifiable and the positivist Auguste Comte sought a social physics to apply immutable scientific laws to all aspects of human life. But by the early twentieth century, that boundless faith in science had been badly shaken. Within the academy, philosopher G.E. Moore was widely thought to have refuted empirical approaches to ethics. Within the Temple of Science, the pace of new discoveries forced researchers to acknowledge how tentative and contingent their findings were. And ever newer sciences such as quantum physics made people wonder whether there was anything regular or predictable (or even ultimately material) about even the physical world. As for relying on science and the calculus of the greater good to tell us how to live our lives—particularly after the serial horrors of two world wars—that notion increasingly met with skepticism, if not outright derision. Today, most thoughtful people dismiss the old scientism as crudely reductive, and certainly irrelevant as a source of moral and ethical guidance. Except…

More here.

Emerging cases of Covid-19 reinfection suggest herd immunity could be wishful thinking

D. Clay Ackerly in Vox:

“Wait. I can catch Covid twice?” my 50-year-old patient asked in disbelief. It was the beginning of July, and he had just tested positive for SARS-CoV-2, the virus that causes Covid-19, for a second time — three months after a previous infection.

While there’s still much we don’t understand about immunity to this new illness, a small but growing number of cases like his suggest the answer is yes.

Covid-19 may also be much worse the second time around. During his first infection, my patient experienced a mild cough and sore throat. His second infection, in contrast, was marked by a high fever, shortness of breath, and hypoxia, resulting in multiple trips to the hospital.

Recent reports and conversations with physician colleagues suggest my patient is not alone.

More here.

Recomposing The Soundscape of The Intensive Care Unit

Sally O’Reilly at Cabinet Magazine:

Sonic branding is big business. Should you be interested, you could commission the composition of a long-form anthem, a sonic logo, or the sounds your product emits during user operation. Computer and video game companies lavish much time, effort, and money on the second and third of these. For a canonic commission, there is the Windows 95 start-up sound designed by Brian Eno. A more guerilla affair was Jim Reekes’s Apple computer start-up chime, which he snuck onto a new Mac model without permission circa 1992.13 Interestingly, the sound he was so driven to replace was “absolutely the most inharmonic dissonant sound you could make”—a tritone. There are many other, less substantiated stories out there: that one-eighth of the bits of the original Sonic the Hedgehog game were taken up by the SEGA sonic logo; that the first note in the Intel logo comprises twenty sounds, one of which is an anvil being hit; that the first Facebook messenger “ding” was an F major seventh, which comprises the pitches F, A, C, and E.

more here.

The Beinart Controversy over the End of the Two-State Solution and Juan Cole On Palestinian Statelessness

Juan Cole in Informed Comment:

Peter Beinart, a professor of journalism at the City University of New York, has caused a stir in the past week with articles and interviews in which he says he has given up on the project of a Jewish state in Israel. He still likes the idea of a Jewish “homeland.” What clearly drives his position is the collapse of the two-state solution around the year 2000. By now it is clear that there cannot be a Palestinian state, what with 650,000 Israeli settlers in the Palestinian West Bank (if you count the parts of it that Israel annexed and made part of its district of Jerusalem). Not only that, but the rise of an Israeli illiberalism inside Israel proper that is determined to make the over 20% of the population that is not Jewish permanent second-class citizens underlines for him that Jewish power as now configured as a zero-sum game. Jews have rights, citizenship, and sovereignty inside Israel; non-Jews have no sovereignty even though they are Israeli citizens, and their rights are fewer.

More here.

The Barbarian at the Gate

Philip Parker at Literary Review:

Like many a subsequent empire, Rome had a highly ambivalent relationship with the outsiders it needed to fuel its commerce, stock its slave markets and man its armies. In this particular case, those outsiders were not colonised peoples but the Germanic barbarian tribes living in areas against which the waves of Roman imperialism had only lapped during the empire’s high tide, before it began to recede in the third century. The Danube basin, where Alaric grew up in the 370s, seems from Boin’s account an idyllic place: his family home bore the bucolic name Pine Tree Island and Boin conjures an image of infant Goths listening to tales of their heroic ancestor King Berig, who had led his people – perhaps understandably – out of a homeland of ‘quaking bogs’ called Scandza. Yet it was also a place of profound danger: of slave traders who kidnapped young girls in order to sell them south of the river, of ghosts and demons and, most threatening of all, of predatory Roman officials whose actions in trying to starve would-be migrants who were crossing the imperial frontier led to the first mass Gothic raids on the Balkans.

more here.

Tuesday Poem

Hummingbird

One day in a lifetime
I saw one with wings
a pipesmoke blur
shaped like half a kiss
and its raspberry-stone
heart winked fast
in a thumbnail of a breast.

In that blink it
was around a briar
and out of sight, but
I caught a flash
of its brain
where flowers swing
udders of sweet cider;
and we pass as thunderclouds or,
dangers like death, earthquake, and war,
ignored because it’s no use worrying ….

By him I mean. Responsibility
Against the threat of termination-
by war or other things
is given us as by a deity.

by Milton Acorn
from
Dig Up My Heart- Selected Poems -1952-83
McClelland & Stewart, Toronto, 1983

How Pandemics Wreak Havoc—and Open Minds

Lawrence Wright in The New Yorker:

Italy at the beginning of the fourteenth century was a conglomeration of prosperous city-states that had broken free of the feudal system. Some of them, such as Venice, formed merchant republics, which became seedbeds for capitalism. Venice and other coastal cities, including Genoa, Pisa, and Amalfi, set up trading networks and established outposts throughout the Mediterranean and as far away as the Black Sea. Other Italian cities, such as Bologna, became free communes, which meant that peasants fleeing feudal estates were granted freedom once they entered the city walls. Serfs became artisans. A middle class began to form. The early fourteenth century was robust and ambitious. Then, suddenly, people began to die.

Bologna was a stronghold of medical teaching. The city’s famous university, established in 1088, is the oldest in the world. “What they had we call scholastic medicine,” Pomata told me. “When we say ‘scholastic,’ we mean something that is very abstract, not concrete, not empirical.” European scholars at the time studied a number of classical physicians—including Hippocrates, the Greek philosopher of the fifth century B.C. who is considered the father of medicine, and Galen, the second-century Roman who was the most influential medical figure in antiquity—but scholastic medicine was confounded with astrological notions. When the King of France sought to understand the cause of the plague, the medical faculty at the University of Paris blamed a triple conjunction of Saturn, Jupiter, and Mars in the fortieth degree of Aquarius, which had occurred on March 20, 1345.

…Before arriving in Italy, the rampaging contagion had already killed millions of people as it burned through China, Russia, India, Persia, Syria, and Asia Minor. It was said that there were entire territories where nobody was left alive. The source of the disease was sometimes thought to be “miasma,” or air that was considered unhealthy, such as sea breezes. Paradoxically, there was also a folk belief that attendants who cleaned latrines were immune, which led some people to confine themselves for hours a day amid human waste, absorbing the presumed medicinal odors.

More here.

New ‘Liquid Biopsy’ Shows Early Promise in Detecting Cancer

Francis Collins in NIH Director’s Blog:

Early detection usually offers the best chance to beat cancer. Unfortunately, many tumors aren’t caught until they’ve grown relatively large and spread to other parts of the body. That’s why researchers have worked so tirelessly to develop new and more effective ways of screening for cancer as early as possible. One innovative approach, called “liquid biopsy,” screens for specific molecules that tumors release into the bloodstream.

Recently, an NIH-funded research team reported some encouraging results using a “universal” liquid biopsy called CancerSEEK [1]. By analyzing samples of a person’s blood for eight proteins and segments of 16 genes, CancerSEEK was able to detect most cases of eight different kinds of cancer, including some highly lethal forms—such as pancreatic, ovarian, and liver—that currently lack screening tests. In a study of 1,005 people known to have one of eight early-stage tumor types, CancerSEEK detected the cancer in blood about 70 percent of the time, which is among the best performances to date for a blood test. Importantly, when CancerSEEK was performed on 812 healthy people without cancer, the test rarely delivered a false-positive result. The test can also be run relatively cheaply, at an estimated cost of less than $500.

Cancers arise when gene mutations occur in individual cells, dysregulating their normal growth and allowing them to divide without the usual restraints. As the clump of cancer cells expands, some die and bits of their mutated DNA can end up in the bloodstream. Liquid biopsies then search the blood for those bits of DNA carrying mutations associated with cancer. In 2016, the FDA approved the first liquid biopsy test for detecting a single mutation in patients with non-small cell lung cancer for use in guiding treatment decisions of people already known to have this type of cancer [2]. But developing a liquid biopsy test that could screen apparently healthy people for a variety of early cancers has proven a much greater challenge.

More here.

Sunday, July 12, 2020

The Novels of Tension Between Freedom and Disaster

Tim Parks in the New York Review of Books:

After I wrote about novels characterized by their focus on belonging—the concern with being in or out of a certain community, worthy or unworthy of its membership—a reader suggested I should have included Mark Twain in my list, mentioning The Adventures of Tom Sawyer and The Adventures of Huckleberry Finn. It’s true that Twain is wonderfully attuned to the communities he describes, their speech and customs. But what drives the plot of Huckleberry Finn is the desire for freedom, Huck’s desire, Jim’s desire. The suffocating shirt collar is rejected for the great outdoors. Liberty trumps belonging at every turn. Twain rubs this in with his account of the feud between the Grangerford and Shepherdson clans, two families obsessed by belonging and family identity to the exclusion of all other values. Huck’s instinct is to hightail it out of there.

But a free life is a precarious life, precarious as the river with its flotsam of corpses and criminals. A man striking for freedom might occasionally reflect he had been safer with his chains. Here is a source of inner conflict. Independent and free on their raft, Huck and Jim are entirely unprotected, from man or nature. At the end of the book, Huck realizes some accommodation must be made with community, for the security and opportunities it offers; but by that point, he has established an inner independence.

More here.

Why Do Authoritarians Win?

William E. Scheuerman in the Boston Review:

Democracy seems in bad shape these days. In contrast, its global political rivals appear to be prospering and gaining confidence in their ability to offer a viable alternative. Commenting gleefully a few weeks after Donald Trump’s election, Vladimir Putin celebrated “the degradation of the idea of democracy in western society in the political sense of the word.” Su Changhe, a Chinese scholar who has praised his country’s successes under President-for-life Xi Jinping, offers approval that “Western democracy is already showing signs of decay.” Sheik Mohammed bin Rashid Al Maktoum, ruler of Dubai and United Arab Emirates (UAE) Prime Minister, hopes that his government will soon be “closer to its people, faster, better and more responsive” than western democracy. Since the UAE’s version of democracy is deeply rooted in local society, he claims, that dream is already being realized.

Of course, autocrats always tout their achievements, or insist that their regimes rest on the will of the people. Even Nazi Germany claimed popular legitimacy, a racist and anti-Semitic Volks-sovereignty. Soviet apologists and fellow travelers labeled Stalin’s Eastern European vassal states “people’s democracies.” The contemporary narrative seems depressingly familiar. Even so, the specter of powerful autocratic states that parasitically mimic democracy, while in reality eviscerating its core, should alarm us. Are democracy’s rivals indeed gaining ground? And, what precisely is different this time?

More here.

Q&A: Idan Landau and Noam Chomsky on Skepticism

From the Columbia University Press blog:

Idan Landau: This book develops many ideas and themes that your readers will recognize from your earlier works. Still, I sense a new, or at least a more pronounced thread of skepticism running through it—especially as regards the limits of human cognition. “Mysteriansim” is a form of skepticism, so it is no wonder that one encounters Hume in these pages much more often that one did in your earlier writings. I wonder about the roots of this shift: Is it a natural perspective one gains with old age (Ecclesiastes-style wisdom)? Or is it a well-directed response to the over-optimism you see in certain branches of theoretical cognitive science? Jerry Fodor, perhaps, has gone through a similar process of “disenchantment” with the prospects of the cognitive enterprise between his Modularity of Mind (1983) and The Mind Doesn’t Work That Way (2000). Certain things you say may strike some as a defeatist position, which cannot inspire truly groundbreaking work. After all, if we wouldn’t constantly try to push against our limits, how would we know where they are?

Noam Chomsky: We should certainly push against our limits, just as the sciences have done, with remarkable results, since lowering their aspirations as the import of Newton’s discoveries set in. What for me at least is the most important part of WKC is the first chapter: the review of work that has tried “to push against our limits.” The results discussed were not considered within the realm of possibility only a few years ago. And going farther back, we may recall that a prevailing structuralist doctrine in the fifties was the “Boasian thesis” mentioned in chapter 1, holding that with marginal exceptions, languages can differ arbitrarily and that each new one must be studied without preconceptions.

My own concern with “problems and mysteries” (in the organism-relative sense that I am using) is not recent. In print, it goes back to an essay in a 1976 collection in memory of my close friend Yehoshua Bar-Hillel (“Problems and Mysteries in the Study of Human Language,” in Language in Focus, ed. A. Kasher)—topics that we had discussed privately well before.

More here.

Emasculated

Luke Brown in TLS:

When Philip Roth died in 2018 an era of unpalatable writing by men about men seemed to close. Roth, who often wrote about antagonistic relationships, was dogged by accusations of misogyny for his portrayals of women. Carmen Callil, the founder of Virago resigned from the judging panel of the Man Booker International Prize in 2011 when it was given to Roth: “he goes on and on and on about the same subject. It’s as though he’s sitting on your face and you can’t breathe”.

Roth wrote regularly about betrayal: by wives and daughters, and by friends and brothers and Cold War foreign policy and the voting public and antisemites and Puritanism and medicine, by one’s own spine, prostate, penis and heart. But it was for the focus on the penis that Roth was best known, for his willingness to portray masculinity in the unflattering light of desire. In the course of his most extreme and nihilistic novel about lust, Sabbath’s Theatre (1995), Mickey Sabbath remembers the taped phone sex (transcribed word for word) with one of his students that lost him his job, steals a pair of his friend’s daughter’s knickers and tells his wife while trying to seduce her that “there is no punishment too extreme for the crazy bastard who came up with the idea of fidelity”. The novel is shocking in its accumulating vision, though some of the depraved things Sabbath does are simply the result of following the kind of commonplace urges generally kept in check by the male super ego.

When the superego fails, restrictions must be imposed from without. There is a pressure now to avoid the unflattering light, to the extent that you might conclude from reading many recently successful male literary authors that they have “solved the problem of sex”: their male characters have idealized sex drives, or ones we know little about. Meanwhile female writers have taken up the gauntlet, presenting sexual relationships that are real and complex, in which goodness is difficult. Many of us male writers have ceased to describe ourselves honestly, and no longer seem able to present a world in which reconciliation with women is fraught.

Heterosexual male desire has been linked so closely to abuses of power for so long that the two seem inextricable.

More here.