The trickster microbes that are shaking up the tree of life

Traci Watson in Nature:

Every mythology needs a good trickster, and there are few better than the Norse god Loki. He stirs trouble and insults other gods. He is elusive, anarchic and ambiguous. He is, in other words, the perfect namesake for a group of microbes — the Lokiarchaeota — that is rewriting a fundamental story about life’s early roots. These unruly microbes belong to a category of single-celled organisms called archaea, which resemble bacteria under a microscope but are as distinct from them in some respects as humans are. The Lokis, as they are sometimes known, were discovered by sequencing DNA from sea-floor muck collected near Greenland1. Together with some related microbes, they are prodding biologists to reconsider one of the greatest events in the history of life on Earth — the appearance of the eukaryotes, the group of organisms that includes all plants, animals, fungi and more.

The discovery of archaea in the late 1970s led scientists to propose that the tree of life diverged long ago into three main trunks, or ‘domains’. One trunk gave rise to modern bacteria; one to archaea. And the third produced eukaryotes. But debates soon erupted over the structure of these trunks. A leading ‘three-domain’ model held that archaea and eukaryotes diverged from a common ancestor. But a two-domain scenario suggested that eukaryotes diverged directly from a subgroup of archaea. The arguments, although heated at times, eventually stagnated, says microbiologist Phil Hugenholtz at the University of Queensland in Brisbane, Australia. Then the Lokis and their relatives blew in like “a breath of fresh air”, he says, and revived the case for a two-domain tree.

More here.

Tuesday, May 14, 2019

Why falsificationism is false

Philippe Lemoine in Nec Pluribus Impar:

Karl Popper

Karl Popper famously defended the view, known as falsificationism, that what distinguishes science from non-science is falsifiability. On this view, a theory is scientific if and only if it’s falsifiable, at least in principle. What this means for a theory to be falsifiable is that one can think of a possible observation that would be inconsistent with the theory. For instance, since Newton’s law of universal gravitation implies that every particle exerts a force of attraction on every other particle, it would be falsified if we observed a particle that repels another particle. Since it’s at least conceivable that we could observe this, Newton’s law of universal gravitation is falsifiable and therefore scientific. Popper wants to contrast this with theories like psychoanalysis, which according to him can be reconciled with any conceivable observation, hence is not scientific.

I have often been struck, when talking to scientists, by the influence that Popper seems to have among them. I would go as far as saying that, in many scientific fields, falsificationism has become the official philosophy of science. It’s drummed into the heads of scientists when they’re in graduate school and, with a few exceptions, they never learn anything else about philosophy of science and spend the rest of their career thinking that Popper’s conception of science is still the gold standard. In fact, however, not only is falsificationism not the gold standard, but it never was.

More here.

Sean Carroll’s Mindscape Podcast: Kate Darling on Our Connections with Robots

Sean Carroll in Preposterous Universe:

Most of us have no trouble telling the difference between a robot and a living, feeling organism. Nevertheless, our brains often treat robots as if they were alive. We give them names, imagine that they have emotions and inner mental states, get mad at them when they do the wrong thing or feel bad for them when they seem to be in distress. Kate Darling is a research at the MIT Media Lab who specializes in social robotics, the interactions between humans and machines. We talk about why we cannot help but anthropomorphize even very non-human-appearing robots, and what that means for legal and social issues now and in the future, including robot companions and helpers in various forms.

More here.

A Thousand Small Sanities: The Moral Adventure of Liberalism by Adam Gopnik

Peter Conrad in The Guardian:

Adam Gopnik cherishes the metropolitan exclusivity that populists hate.

Liberalism has become a tricky and even dirty term, which may be why it is banished to the subtitle of Adam Gopnik’s supremely intelligent but tortuous polemical essay. American leftwingers nowadays avoid the adjective and prefer to call themselves “progressive”.

And just what kind of “moral adventure” does Gopnik have in mind? Amoral options abound: liberality sounds spendthrift and libertinism is certainly decadent. Delacroix envisaged Liberty as a bare-breasted free spirit storming the revolutionary barricades; Bartholdi, designing the statue in New York harbour, dressed her in a ballgown, gave her a spiked crown and made her balefully scowl. Is she a permissive mistress or an antiquated matron whose torch looks like a bludgeon?

These are more than semantic queries, because Gopnik alerts us to an emergency. “Gangster-style authoritarianism” threatens the US, Russia, Hungary, Brazil, the Philippines and Saudi Arabia, while our own lying Brexiters prate about national grandeur and use “parliamentary proceduralism”, as Gopnik shrewdly says, to “corrupt and co-opt potential resistance”. Can liberal values be revived to save us?

More here.

Joe Biden may resurface a long-held dream: a White House laser-focused on cancer

Lev Facher in The New York Times:

WASHINGTON — Barely five months after his son’s death from brain cancer, a bereaved Vice President Joe Biden announced to the nation he would not run for president in 2016 — and immediately pinpointed his deepest regret. “If I could be anything, I would have wanted to be the president that ended cancer,” he said in a Rose Garden address in October 2015. “Because it’s possible.” Biden’s announcement that he will run for president in 2020, however, has resurfaced his dream: a White House that makes cancer a signature issue, backed by a politician whose life was so publicly upended by the disease. With much of the early debate in the Democratic primary centering on health care, Biden’s stint as cancer-advocate-in-chief and orchestrator of the Obama administration’s “cancer moonshot” could give him the opportunity to make the disease, its treatments, and his own grief central to the presidential election.

After leaving office, Biden structured his cancer-fighting efforts in a way that could suit a possible campaign. The Biden Cancer Initiative — the pillar of Biden’s policy work since leaving office — raised $10 million in the year following its incorporation. The nonprofit did not accept contributions from pharmaceutical companies, in an effort both to preserve independence and avoid the political pitfalls associated with an increasingly vilified drug industry. The Bidens have fostered collaboration between stakeholders “at the foundation level, the patient advocacy level, the scientific level, and the government level,” said Dr. Elizabeth Jaffee, a Johns Hopkins researcher who sits on the Biden Cancer Initiative’s board.

More here.

Gabriel García Márquez in 1950s Paris

Gabriel García Márquez at Lit Hub:

When I arrived in Paris, I was nothing but a raw Caribbean. I am most grateful to that city, with which I have many old grudges, and many even older loves, for having given me a new and resolute perspective on Latin America. The vision of the whole, which we didn’t have in any of our countries, became very clear here around a safe table, and one ended up realizing that, in spite of being from different countries, we were all crew members of the same boat. It was possible to travel all around the continent and meet its writers, its artists, its disgraced or budding politicians, just by making rounds of the crowded cafés of Saint-Germain-des-Prés. Some didn’t arrive, as happened to me with Julio Cortázar—whom I already admired for the wonderful stories of Bestiario—and for whom I waited for almost a year in the Old Navy café, where someone had told me he often went. I finally met him fifteen years later, also in Paris, and he was still as I’d imagined him since long ago: the tallest man in the world, who never decided to grow old. The faithful copy of that unforgettable Latin American who, in one of his short stories, liked to walk through the misty dawns to go and watch the guillotine executions.

more here.

Archie Butt, The Titanic, Related Matters….

Will Stephenson at The Believer:

To President William Howard Taft, the most notable casualty of the Titanic was a person named Archibald Butt. “He was like a member of my family,” Taft said in his eulogy, “and I feel his loss as if he had been a younger brother.” Reading this, I feel a tinge of competitiveness with Taft, because Butt was a member of my family—he was my great-grandfather’s cousin. In the hallway bathroom of my childhood home, we had a framed Butt family crest he’d purchased and mailed home from Europe: a lion holding a broken spear. It always got a laugh, the solemnity of the image relative to the apparent stupidity of the surname: Butt. It seemed obviously ironic, like a poster you’d buy at a gas station.

My great-grandfather was Jeremiah Butt, who ran a Schlitz beer outpost in southern Georgia and died at a Lutheran conference in Nashville when my father was four. A heart attack, while he was eating breakfast. 

more here.

Bad Girls: The Rebels and Renegades of Holloway Prison

Mary Hannity at the LRB:

Between 1906 and 1914 hundreds of suffragettes were imprisoned and force-fed in Holloway. They turned their resistance to prison rules into a political programme. Suffragette prisoners were held separately and forbidden from communicating, but if one of them smashed a window to protest against poor air quality, for instance, the others would follow suit. They documented their treatment and smuggled out letters and diaries. The WSPU rented a house nearby, and used it as a base to communicate with the prisoners – and to throw bombs and bottles at the prison. Suffragettes were greeted on release by applauding crowds. The governor resigned. ‘If you are not a rebel before going into Holloway, there is no reason to wonder at your being one when you come out,’ wrote Edith Whitworth, secretary of the Sheffield branch of the WSPU. The imprisonment of middle-class women, which was unusual, helped draw public attention to the treatment of incarcerated women in general, and the suffragettes agitated for improved prison conditions. Davies gives ample attention to their use of Holloway as an icon of struggle: a Holloway flag was waved on suffragette marches; Christmas cards were produced with an illustration of the prison (‘Votes and a Happy Year’); there were Holloway diaries, demonstrations, songs and poems (‘Oh, Holloway, grim Holloway/With grey, forbidding towers!/Stern are the walls, but sterner still/Is woman’s free, unconquered will’).

more here.

You’ve heard of ‘organs on a chip.’ Now ‘tissue chips in space’ test conditions in microgravity

Shraddah Chakradhar in Stat:

An unusual bit of cargo was aboard the latest Space X mission to restock the International Space Station with essential supplies in the early hours of Saturday morning. Usually, these SpaceX launches carry clothes or equipment that astronauts aboard the ISS may need to fix minor issues. But this latest launch also included tiny structures — about as big as a USB drive — containing human cells and known colloquially known as “organs on chips” were launched into space as part of a new experimental program from the National Institutes of Health’s National Center for Advancing Translational Sciences. These tissue chips are designed, with the help of pumps and other fluidics, to mimic the function of an organ. They’re used to study a wide range of diseases as well as test potential treatments. Most of the experiments with tissue chips have been confined to Earth. But in December, the first of five teams funded by the NCATS program launched an organ chip containing immune cells into space. The chips from the four other teams — roughly 50 chips in total — were packed into shoebox-sized boxes, along with all the material to help keep them going and sent along on a space capsule called Dragon. And if all goes to plan, the ISS will capture the capsule this morning. Over the next few weeks, the teams behind these tissue chips are hoping to learn all about what space — specifically, microgravity in space — does to human cells. I chatted with Lucie Low, the program manager of Tissue Chips in Space, to learn more about the mission. This interview has been condensed and lightly edited.

What types of chips are going into space? And what conditions are they hoping to provide information about?

There’s a kidney kit that’s looking at osteoporosis and the formation of kidney stones. We also have a knee joint kit that will look at osteoarthritis. Then there’s a blood-brain barrier kit to look at neurodegenerative disease. And finally, a lung kit to look at the impact of pathogens on lungs.

More here.

Tuesday Poem

Otherwise

I got out of bed
on two strong legs.
It might have been
otherwise. I ate
cereal, sweet,
milk, ripe, flawless
peach. It might
have been otherwise.
I took the dog uphill
to the birch wood.
All morning I did
the work I love.

At noon I lay down
with my mate. It might
have been otherwise.
We ate dinner together
at a table with silver
candlesticks. It might
have been otherwise.
I slept in a bed
in a room with paintings
on the walls, and
planned another day
just like this day.
But one day, I know,
it will be otherwise.

Jane Kenyon
from The Academy of American Poems

Sunday, May 12, 2019

Dialectics of Enlightenment

Kwame Anthony Appiah in the New York Review of Books:

Justin E.H. Smith

How enlightened was the Enlightenment? Not a few critics have seen it as profoundly benighted. For some, it was a seedbed for modern racism and imperialism; the light in the Enlightenment, one recent scholar has suggested, essentially meant “white.” Voltaire emphatically believed in the inherent inferiority of les Nègres, who belonged to a separate species, or at least breed, from Europeans—as different from Europeans, he said, as spaniels from greyhounds. Kant remarked, of something a Negro carpenter opined, that “the fact that he was black from head to toe was proof that what he said was stupid.” And David Hume wrote, in a notorious footnote, that he was “apt to suspect” that nonwhites were “naturally inferior to the whites,” devoid of arts and science and “ingenious manufactures.”

The more general critiques take up larger intellectual currents in the eighteenth century. The era’s systematic forays into physical anthropology and human classification laid the foundation for the noxious race science that emerged in the nineteenth century. So did the rise of materialism: it became harder to argue that our varying physical carapaces housed equivalent souls implanted by God. A heedless sense of universalism, in turn, might encourage the thought that the more advanced civilizations were merely lifting up those more backward when they conquered and colonized them.

More here.

A celebration of curiosity for Feynman’s 100th birthday

Tom Siegfried in Science News:

Feynman was born 100 years ago May 11. It’s an anniversary inspiring much celebration in the physics world. Feynman was one of the last great physicist celebrities, universally acknowledged as a genius who stood out even from other geniuses.

In 1997 I interviewed Nobel laureate Hans Bethe, a Cornell University physicist who worked with Feynman during World War II on the atomic bomb project at Los Alamos (and later on the Cornell faculty). “Normal” geniuses, Bethe said, did things much better than other people but you could figure out how they did it. And then there were magicians. “Feynman was a magician. I could not imagine how he got his ideas,” Bethe told me. “He was a phenomenon. Feynman certainly was the most original physicist I have seen in my life, and I have seen lots of them.”

More here.

Justin E. H. Smith speaks about Irrationality

From The Philosopher’s Zone:

Justin E. H. Smith

In 1944, Theodor Adorno and Max Horkheimer published their famous claim that “Enlightenment reverts to mythology” – meaning that any rational order sooner or later collapses into irrationality. Seven decades later, with Brexit roiling the UK, a reality TV showman in the White House and batty conspiracy theories spreading like a plague, it seems that Adorno and Horkheimer were right on the money. How did we get here? Is human society fated to be irrational? And why is the alt-right having all the crazy fun these days?

Listen to the podcast here.

Can the World’s Largest Democracy Endure Another Five Years of a Modi Government?

India’s Prime Minister Narendra Modi waves towards his supporters during a roadshow in Varanasi, India, April 25, 2019. REUTERS/Adnan Abidi TPX IMAGES OF THE DAY

Aatish Taseer in Time:

Populists come in two stripes: those who are of the people they represent (Erdogan in Turkey, Bolsonaro in Brazil), and those who are merely exploiting the passions of those they are not actually part of (the champagne neo-fascists: the Brexiteers, Donald Trump, Imran Khan in Pakistan). Narendra Modi belongs very firmly to the first camp. He is the son of a tea seller, and his election was nothing short of a class revolt at the ballot box. It exposed what American historian Anne Applebaum has described as “unresolvable divisions between people who had previously not known that they disagreed with one another.” There had, of course, been political differences before, but what Modi’s election revealed was a cultural chasm. It was no longer about left, or right, but something more fundamental.

The nation’s most basic norms, such as the character of the Indian state, its founding fathers, the place of minorities and its institutions, from universities to corporate houses to the media, were shown to be severely distrusted. The cherished achievements of independent India–secularism, liberalism, a free press–came to be seen in the eyes of many as part of a grand conspiracy in which a deracinated Hindu elite, in cahoots with minorities from the monotheistic faiths, such as Christianity and Islam, maintained its dominion over India’s Hindu majority.

Modi’s victory was an expression of that distrust. He attacked once unassailable founding fathers, such as Nehru, then sacred state ideologies, such as Nehruvian secularism and socialism; he spoke of a “Congress-free” India; he demonstrated no desire to foster brotherly feeling between Hindus and Muslims. Most of all, his ascension showed that beneath the surface of what the elite had believed was a liberal syncretic culture, India was indeed a cauldron of religious nationalism, anti-Muslim sentiment and deep-seated caste bigotry.

More here.

Sunday Poem

At an Early Age a Boy Discovers
the Pleasures and Perils of Double o

—for Jo Sodano

Put these silly identical twins
………………………… o and o
….……….in a word and it goes goofy,
but endearing. Buffoon.
………………………… Booby. Nincompoop.

….……….Your mother’s not crazy
just a little loony. That’s not shit
………………………… in your pants
….……….but poopy.
And add one more o to lose
………………………… and you’re loose
….……….and ashamed
of nothing but ready
………………………… for everything: Cookie!
….……….Snookie! Whoopie! Booze!
Floozies!
Words only too willing
………………………… to pooh-pooh
….……….the alphabet’s great aspirations,
that silly goose. How far
………………………… would you get with a girl
….……….if seduce were spelled
sadoos? What conclusions
………………………… would a philosopher
….……….dedoos? What if
there were nothing loopy
………………………… in the language, no
….……….va-va voom! No magic
broom. No swooping wings?
………………………… no dark lagoon?
…………. No fingernail
moon? No freedom to ooh
………………………… and ahh, to swoon?
….……….Nothing too
gorgeous for words?
………………………… Too, you small extremist,
….……….pipsqueak, adverb always
piping up, Too much?
………………………… There’s never
….……….too much!

Christopher Bursk
from
The First Inhabitants of Arcadia
University of Arkansas Press, 2006

Marcus Aurelius – the Unemotional Stoic?

Massimo Pigliucci in iai:

The title of this essay may sound redundant: aren’t all Stoics unemotional, making it their business to go through life with a stiff upper lip? Actually, no, and neither was Marcus, whose 1,898th birthday falls on April 26th of this year. It is true that he wrote in the Meditations, his personal philosophical diary: ‘When you have savouries and fine dishes set before you, you will gain an idea of their nature if you tell yourself that this is the corpse of a fish, and that the corpse of a bird or a pig; or again, that fine Falernian wine is merely grape-juice, and this purple robe some sheep’s wool dipped in the blood of a shellfish; and as for sexual intercourse, it is the friction of a piece of gut and, following a sort of convulsion, the expulsion of mucus.’ (VI.13)

These don’t exactly sound like the musings of someone who delights in gourmet food or drinks (Falernian was the best wine an ancient Roman could buy), not to mention someone with a romantic bent. But Marcus was deploying a technique that modern psychologists call ‘reframing,’ and a good case can be made that he wrote the above precisely in order to help himself temper his own far too emotional attachment to things that are best seen in a slightly cooler light. Do not get so overexcited about your dinner courses — he tells himself — remember that food is for nutrition, and that one doesn’t need exotic fauna to enjoy a savoury meal. When you get too cocky about being the emperor, just bring back to mind that the purple of which you are so proud is derived from crustacean blood. And try not to go overboard with this sex thing; after all, you’ve already had 14 children!

So the most famous philosopher-king in history was not attempting to suppress emotions (which the Stoics, good psychologists that they were, recognised is both impossible and undesirable), but rather to question them when they take a disruptive form. In fact, one overall goal of Stoic training was to shift out emotional spectrum, so to speak, from negative ‘passions’ like fear, anger and hatred to positive ones, like love, joy and a sense of justice.

More here.