Carl Zimmer in his excellent blog, The Loom:

I’ve written a few times here about the ongoing work of Joe Thornton, a biologist at the University of Oregon and the Howard Hughes Medical Institute. Thornton studies how molecules evolve over hundreds of millions of years. He does so by figuring out what the molecules were like in the distant past and recreating those ancestral forms in his lab to see how they worked. I first wrote about his work looking at how one molecule in our cells evolved from one function to another (here, here, and here). [Update: These links are now fixed.]

Most recently, I wrote in the New York Times about his latest experiment, in which he and his colleagues found that the evolution from the old function to the new one has now made it very difficult for natural selection to drive the molecule back to its old form. Its evolution has moved forward like a ratchet.

Thornton’s new work turned up last week on a web site run by the Discovery Institute, a clearinghouse for all things intelligent design (a k a the progeny of creationism). Michael Behe, a fellow at the Institute, wrote three posts (here, here, and here) about the new research, which he pronounced “great.”

This is the same Michael Behe who, when Thornton published the first half of this research, declared it “piddling.”

Why the change of heart? Because Behe thinks that the new research shows that evolution cannot produce anything more than tiny changes. And if evolution can’t do it, intelligent design can. (Don’t ask how.)

I pointed out Behe’s posts to Thornton and asked him what he thought of them. Thornton sent me back a lengthy, enlightening reply.

More here.

Rhys Blakely in The Times of London:

Courtship can be an intricate business in India, but the mothers of the northern state of Haryana have a simple message for men who call on their daughters: “No toilet, no bride.”

The slogan – often lengthened in Hindi to “If you don't have a proper lavatory in your house, don't even think about marrying my daughter” – has been plastered across villages in the region as part of a drive to boost the number of pukka facilities. In a country where more households have TV sets than lavatories, it is one of the most successful efforts to combat the chronic shortage of proper plumbing.

That is probably partly because of the country's skewed sex ratio, with 8 per cent more men than women, leading to a “bride shortage”. Woman generally have also become more vocal in their resentment at having to relieve themselves outside, giving brides more leverage in premarital bargaining.

In India it is estimated that more than 660 million people still defaecate in the open – a big cause of a host of diseases, from diarrhoea to polio. It is women, activists say, who suffer the most.

More here. [Thanks to Ruchira Paul.]

TIMOSORA, ROMANIA Like Saint Petersburg before she was operated on for her three-hundredth, the brie-colored streets and decaying facades have a dusty continuity. Against this backdrop, the Roma build their Disneyland. Forced by the Communists to settle in the ’60s, they have embraced a style of permanent renovation. Their mansions, in primary colors, stick like fingers in the dead dictator’s eye. But this provokes nothing beyond tourists snapping photos and locals shaking their heads. “How do you think they pay for them?” they ask me and then spit. Gypsy mansions are confusing. Though they are decorated with wild variation, their structural similarities are apparent. The mansion plans are essentially standardized: All rooms branch off a central corridor, and none have direct access to any others; but there the standardization ends, and this is not so surprising. Mansions are primarily structures of one-upmanship; eternal construction sites of dubious habitable value (they are often abandoned, though this could be because the settlement policies went with the Communists) that rise as barometers of personal (male) status, they are intensely decorated sheds with few interior complications.

more from Lev Bratishenko at Triple Canopy here.

In the basement of Aaron Beck’s house, nine miles northwest of downtown Philadelphia, in a dimly lit, dusty, concrete-walled room dedicated to his archives, there sits a pink plastic box containing patient notes from a 40-year-old case of psychotherapy. Beck, a professor emeritus of psychiatry at the University of Pennsylvania, has short-cropped white hair, sharp blue eyes, and, at 88, a hunched and shuffling gait. He has been a practicing psychiatrist for 59 years. Among the thousands of patients Beck has treated during this time, this case rates as persistent but uncomplicated. The patient was in his mid-40s and had a good career, a loving wife, four beautiful children, and a trove of close friends. Privately, however, he struggled with an acute tendency toward self-criticism. He was of the type that can’t help but interpret neutral events as harsh reflections on his personal worth. He was forever searching for approval, and forever anticipating disapproval. When the patient’s treatment began—the earliest notes date from the mid-1960s—the dominant psychotherapeutic approach in the United States was psychoanalysis. Sigmund Freud had made his first and only visit to this country in 1909, and in the half century that followed, his approach to mental suffering took firm hold of American psychiatry, splintering into a multitude of camps but always retaining a focus on the unconscious mind, the central feature of Freudian analysis.

more from Daniel B. Smith at The American Scholar here.

Richard Brody in The New Yorker:

It is, on its surface, a simple movie—it tells the story of a young unmarried mother who is about to go on vacation with her family and wants her child’s father to visit before she leaves—but it is told with a visual poetry, a sense of behavioral nuance, a sense of place, and a sculpting of space and time that are rare in movies anywhere, let alone an American independent film made for a pittance. “Hamilton” has received some terrific reviews, and can be downloaded or streamed from Amazon, but hasn’t gotten the release or the attention it deserves.

In the PM newsroom, across from faded purple and brown-striped cubicles where reporters sit amid tacked-up centerfolds and layouts for the day’s cover story of a gun-shot man discarded in a ditch, two men, a photographer and assistant editor, listen to the strains of a narcocorrido drifting from a police scanner. The vague shrill discord of accordions and a brass band echoes in the glass office until a burst of distortion shatters the ill-begotten melody and imposes a staticky silence. They know in the expanding quiet that someone will die tonight. When and where the execution will happen they cannot say yet. Perhaps in five minutes on a dirt lane beneath power lines heavy with dangling sneakers; perhaps in an hour in a van swerved to a stop, the spewed rocks and dust still unsettled even after the gunfire has ceased and neighbors come to peer with accustomed caution through barred windows; perhaps after nightfall on the stony ground of a hill beneath sheets of laundry that when billowed by winds will rise like theatrical curtains to display the vast expanse of Juárez—its gated homes where dogs bark and loll in the heat, its tree-lined streets where kids play pick-up soccer games, and the dirt lanes stretching toward barbed wire fences that block entrance to the state of Texas just beyond the muddy band of the Rio Bravo.

more from J. Malcolm Garcia at VQR here.

From The Telegraph:

He was the second man I fell in love with, was Mr. Rochester. The first was Rhett Butler but that was only because I met him first. Dashing, charming and incredibly sexy as Butler is, Mr. Rochester – and his great dane, Pilot – walked into my life, and blew him out of the water forever. So it comes as no surprise to me that when surveyed by Mills and Boon, the nation's readers voted Charlotte Bronte's Mr Rochester the most romantic character in literature. The true hero, you see, has to have more than charm and dash. Those things are all very well, and fine for having a flirtation with, but if he is to get a real hold of your heart, then he must hurt it a bit, make it bruise and bleed. True, heart-stopping, emotion-wrenching, all consuming hero-power comes from a whole range of qualities, not all of them instantly, or even ongoingly, lovable. And Mr. Rochester (isn't it funny how seldom he is referred to as Edward) has unlovable qualities in spades.

But, reader, I loved him (to paraphrase Miss Bronte).

More here.

Great Big Tree

May I be a great big tree
so big I can’t see those taking shelter under me,
a deep green conical figure wrapped in serenity
Just as I dangle my bare feet in the water
may my roots joyfully draw
from an unknown subterranean current

May I be such a great big tree
that those who look at me
will naturally feel peace and repose

Yet may my luxuriating branches and leaves
whisper to a breeze like stray hair
May they awaken before anyone else in the rosy glow of morning
May their blue shadows be cast on earth
spreading like a trailing lace skirt
May my thoughts be kind
May my thoughts be refreshing
The tree will not move
The tree will not speak
yet may it be a ladder heavenly children ascend and descend

If someone comes and rests by me at the height of day
I will provide deep shadow and infinite comfort

On a stormy day
I will be even greater, more stalwart
I will firmly anchor my roots in the great earth and will not sway
Yet my sap will flow smoothly
even my incised wounds will issue forth a refreshing scent
Soon I will whisper a smiling song
When night arrives I will dissolve into darkness
unbeknownst to people
may the song alone become invisible ripples

by Kiyoko Nagase

translation: Takako Lento
from Ooi naru jyumoku; Publisher
Sakurai Shorten, Tokyo, 1947

From MSNBC:

Newsweek may call Dawkins “the angry evolutionist,” but in his latest book, Dawkins at least makes an attempt to lower the temperature. He reserves his harshest words for “history-deniers” who refuse to accept the evidence for evolution, comparing them to Holocaust-deniers or hypothetical “ignoramuses” who insist the Roman Empire never existed because they weren't around to see the Caesars. Dawkins traces the investigation step by step, including the fossil record and the latest DNA evidence as well as the small-scale changes we see in bacteria, dog breeds and even the size of elephant tusks. All the clues point to nature as the perpetrator of biological change, using “weapons” such as climate and predation. Some mysteries are still unsolved, however. Dawkins cited four of his favorites last week during a talk at the University of Washington:

The origin of life: It might surprise some of Dawkins' critics to hear that he offers no explanation for what kick-started life in the first place. “That is a complete mystery,” he said. Scientists have plenty of suspects to check out, however.

The origin of sex: Dawkins said scientists are also puzzling over “what sex is all about” – in evolutionary theory, that is. After all, sexual reproduction isn't strictly necessary for the evolutionary process to do its thing. Some researchers surmise that sex arose to help weed out harmful mutations or provide more options for propagation.

The origin of consciousness: Where does subjective consciousness come from? Dawkins sees this as the “biggest puzzle” facing biology. Scientists have their ideas, and one of the latest ideas is that consciousness serves as the Wi-Fi network for an assortment of “computers” inside your brain.

The rise of morality: What drives us to do good, even for people we don't even know? The expectation of reciprocity provides a partial explanation, but “it doesn't account for the extremely high degree of moral behavior that humans show,” Dawkins said. He surmises that altruism might have arisen as a “mistaken misfiring” of neural circuits involved in calculating the mutual give and take among kin.

More here.

3QD friend, Hadi Ghaemi of the International Campaign for Human Rights in Iran, over at PBS Frontline (via Andrew Sullivan):

More than a hundred detainees have been on trial for the past two months in what have been widely condemned by human rights organizations as “show trials” without minimal adherence to standards of due process and fair trials. The defendants are a mixture of well-known personalities, regular street protesters, and a small group who were detained before the election and accused of connections with opposition groups.

The inclusion of the latter group, arrested in April 2009, well before the June 12 election, in trials connected with post-election unrest has been somewhat of a mystery until now. The first set of death sentences was issued against this group, which includes three people accused of having communications with a small pro-Monarchist group known as Anjoman Padeshahi Iran and one person accused of making contacts with the Mojahedin-e Khalq Organization.

It appears the prosecutor intentionally threw these cases in among the post-election defendants to establish a precedent for bringing the charge of Moharebeh [“taking up arms against God”] in the mass indictments. By condemning these four defendants to death, the Judiciary has set the stage for justifying further execution sentences against ordinary protesters as well as well known politicians, journalists, and dissidents who are also on trial.

The four defendants sentenced to death are not guilty of any violent actions and their indictments clearly state that the Intelligence Ministry arrested them “before they could engage in any action.” Even under the existing laws, they could not be sentenced to death in fair trials. However, by using them as a front in a public relations ploy to justify death sentences in post-election trials, the government is pursuing two goals. First, the government is aiming to instill fear among reform-oriented Iranians, and raising the cost of participation in further protests, by signaling its power and determination to apply the death penalty at will. The second intent is to lay the groundwork for further political executions by desensitizing the broader population to state-sponsored violence.

Over at Artlog:

How do you feel about making something horrific aesthetically appealing? Do you feel conflicted in any way by making a profit off of a terrible reality

Khan: Most of my artistic practice is hardly ever about making a profit. When I make wall paintings, it feels like a non-precious act, knowing the work is living only for a certain time in a certain setting. On the other hand, making work in this vain forces the message of the work to be extremely precious in it’s limited existence. I suppose I’m using institutions and galleries as a forum for discourse. Of course there is the market, both through my gallery and through art fairs, which has helped me grow as a young artist…I don’t denounce that either; I think it’s flattering to have a collector want your artistic voice in their respective collection.

What is the experience of painting these scenes like for you? Is it therapeutic in any way? What is the process that you go through while working on your art?

Khan:Surprisingly, very therapeutic. One could go crazy thinking of all the injustice and violent acts (of all sorts, not just car bombs) taking place currently, not just in the Middle East, but all over the world. As artists, we live within this public and we are allowed to have a voice or stance. With my work, I suppose it is a way to get a sense of aggression out. My process usually starts with a conceptual idea. Then I gather reference material…often times, I shoot my own. After that, I spend most of the time in the studio working.

See here. [H/t: Jessie Morgan Owens]

Though Europe thrives, its writers and politicians are preoccupied with death. The mass killings of European civilians during the 1930s and 1940s are the reference of today’s confused discussions of memory, and the touchstone of whatever common ethics Europeans may share. The bureaucracies of Nazi Germany and the Soviet Union turned individual lives into mass death, particular humans into quotas of those to be killed. The Soviets hid their mass shootings in dark woods and falsified the records of regions in which they had starved people to death; the Germans had slave labourers dig up the bodies of their Jewish victims and burn them on giant grates. Historians must, as best we can, cast light into these shadows and account for these people. This we have not done. Auschwitz, generally taken to be an adequate or even a final symbol of the evil of mass killing, is in fact only the beginning of knowledge, a hint of the true reckoning with the past still to come. The very reasons that we know something about Auschwitz warp our understanding of the Holocaust: we know about Auschwitz because there were survivors, and there were survivors because Auschwitz was a labour camp as well as a death factory.

more from Timothy Snyder at Eurozine here.

But soon he discovered one of those newfangled iPhone applications, entitled Brushes, which allows the user digitally to smear, or draw, or fingerpaint (it’s not yet entirely clear what the proper verb should be for this novel activity), to create highly sophisticated full-color images directly on the device’s screen, and then to archive or send them out by e-mail. Essentially, the Brushes application gives the user a full color-wheel spectrum, from which he can choose a specific color. He can then modify that color’s hue along a range of darker to lighter, and go on to fill in the entire backdrop of the screen in that color, or else fashion subsequent brushstrokes, variously narrower or thicker, and more or less transparent, according to need, by dragging his finger across the screen, progressively layering the emerging image with as many such daubings as he desires.[2] Over the past six months, Hockney has fashioned literally hundreds, probably over a thousand, such images, often sending out four or five a day to a group of about a dozen friends, and not really caring what happens to them after that. (He assumes the friends pass them along through the digital ether.) These are, mind you, not second-generation digital copies of images that exist in some other medium: their digital expression constitutes the sole (albeit multiple) original of the image.

more from Lawrence Weschler at the NYRB here.

Fame came early to Charles Dickens, and friends and enemies alike recorded their memories and hoarded his letters, so that we now have one of the richest and most alluring of literary archives to mine. Most of his manuscripts and proofs survive, as do more than 15,000 letters, many of incomparable wit and vivacity. We know the games Dickens played as a boy, what he wore (bright colours, flashy waistcoats), what he liked to drink (the cellar-book survives), the cases he reported as a young lawyer’s clerk, the names of his father’s creditors and the books he read at the British Museum Reading Room. In later life, he couldn’t buy a pair of silk stockings in Hull without the fact being recorded for posterity and scholars deducing whose legs they were intended for.

more from John Bowen at the TLS here.

From The Guardian:

Life in the Wild is an exploration of the extraordinary diversity of the animal kingdom through photographic portraits of mammals, birds, reptiles, fish and invertebrates. It features the work of Thomas Marent, who has devoted his life to capturing the beauty of the natural world, and the acclaimed team of underwater cameramen, Scubazoo, who have filmed for the BBC, National Geographic and Animal Planet

Leafy sea dragon

The leafy sea dragon (Phycoduras eques) is a rare and stunning animal named after the leaf-like projections that cover its body. This remarkable camouflage means it has no natural enemies – except man. It has a long, pipe-like snout for feeding, primarily eating crustaceans, including plankton and mysids. However, although it will also eat shrimp and other small fish, it has no teeth, which is rare among animals with this diet. Leafy seadragons are found only in the waters of Australia from the southern to the western shoreline.

Peruvian grasshopper

Acrid chemicals in the body of this Peruvian grasshopper (Aplatacris colorata) act as a defence against insect-eating predators. The grasshopper's vivid pattern of warning colours advertises the fact that it has a noxious taste and, since most of its enemies are birds that hunt by sight, the warning is very effective. Any bird that tries to eat one of these grasshoppers is unlikely to make the same mistake twice. The concentrated toxins in the insect's body are made from chemicals in its food plants.

More here.

Carlo Strenger in The Guardian:

For some reasons it seems to be anathema to say that there might be an intrinsic reason for the correlation between educational level and the rejection of religion: atheism takes training, and is more difficult. We accept that in medicine, physics and mathematics, but, for reasons of political correctness, it is very much considered a faux pas to say the old 19th-century thing: it takes education to develop a worldview based on science. It would be even more outrageous to say that the reasons for choosing atheism over religion might actually be valid, as the so-called new atheists have dared to claim. It seems that it has become something of a class-thing (not necessarily socio-economic, but of belonging to the politically-correct elite) to bash Dawkins, Dennett and Hitchens.

Let's look at some facts and arguments, then. According to the Pew survey, 85% of humanity is religious in some way, and that's probably a low estimate, since nobody knows the true figures about China. This doesn't mean that religion is true (it can't, because religions contradict each other), but that there are strong cognitive and motivational factors that give religions an evolutionary advantage in the market of ideas. A scientific worldview is cognitively and emotionally more difficult, and hence at a disadvantage.

More here. [Thanks to Nikolai Nikola.]

From Scientific American:

For decades the cell nucleus has been a black box of biology—scientists have understood little about its structure or the way it operates. But thanks in part to new visualization technologies, biologists have recently begun probing the architecture of the nucleus in real time. And they are discovering that this architecture appears to change as we age or fall ill or as our needs shift. In fact, the structure of nuclear components—chromosomes, RNA, protein complexes and other small bodies—could be as biologically important as the components themselves.

…Chromosomes position themselves carefully relative to one another, too. Mouse olfactory cells contain the genes for 1,300 types of smell receptors, but only one of the genes turns on in each cell. In a 2006 paper researchers used fluorescent tags to show that a receptor gene becomes expressed only if it comes into physical contact with a specific part of chromosome 14. The idea is that “these two chromosomes come together in three-dimensional space, they kiss, and that’s how you get your regulation” of genetic activity, Misteli says. Chromosome “kissing” also appears to play a role in determining which X chromosome gets turned off in female cells, because only one copy is usually active.

More here.

Sean Carroll responds to this NYT article, which I posted a couple of days ago, in Cosmic Variance:

A recent essay in the New York Times by Dennis Overbye has managed to attract quite a bit of attention around the internets — most of it not very positive. It concerns a recent paper by Holger Nielsen and Masao Ninomiya (and some earlier work) discussing a seemingly crazy-sounding proposal — that we should randomly choose a card from a million-card deck and, on the basis of which card we get, decide whether to go forward with the Large Hadron Collider. Responses have ranged from eye-rolling and heavy sighs to cries of outrage, clutching at pearls, and grim warnings that the postmodernists have finally infiltrated the scientific/journalistic establishment, this could be the straw that breaks the back of the Enlightenment camel, and worse.

Since I am quoted (in a rather non-committal way) in the essay, it’s my responsibility to dig into the papers and report back. And my message is: relax! Western civilization will survive. The theory is undeniably crazy — but not crackpot, which is a distinction worth drawing. And an occasional fun essay about speculative science in the Times is not going to send us back to the Dark Ages, or even rank among the top ten thousand dangers along those lines.

More here.