What’s A Gene For?

Carl Zimmer in his weblog, The Loom:

There was a time not that long ago when sequencing a single gene would be hailed as a scientific milestone. But then came a series of breakthroughs that sped up the process: clever ideas for how to cut up genes and rapidly identify the fragments, the design of robots that could do this work twenty-four hours a day, and powerful computers programmed to make sense of the results. Instead of single genes, entire genomes began to be sequenced. This year marks the tenth anniversary of the publication of the first complete draft of the entire genome of a free-living species (a nasty little microbe called Haemophilus influenzae). Since then, hundreds of genomes have emerged, from flies, mice, humans, and many more, each made up of thousands of genes. More individual genes have been sequenced from the DNA of thousands of other species. In August, an international consortium of databases announced that they now had 100 billion “letters” from the genes of 165,000 different species.

But this data glut has created a new problem. Scientists don’t know what many of the genes are for.

More here.

Brain researchers explain why old habits die hard

From Physorg.com:

HabitimageenlargedA new study in the Oct. 20 issue of Nature, led by Ann Graybiel of MIT’s McGovern Institute, now shows why. Important neural activity patterns in a specific region of the brain change when habits are formed, change again when habits are broken, but quickly re-emerge when something rekindles an extinguished habit — routines that originally took great effort to learn.

“We knew that neurons can change their firing patterns when habits are learned, but it is startling to find that these patterns reverse when the habit is lost, only to recur again as soon as something kicks off the habit again,” said Graybiel, who is also the Walter A. Rosenblith Professor of Neuroscience in MIT’s Department of Brain and Cognitive Sciences (BCS).

The patterns in question occur in the basal ganglia, a brain region that is critical to habits, addiction and procedural learning. Malfunctions in the basal ganglia occur in Parkinson’s disease, obsessive-compulsive disorder (OCD) and many neuropsychiatric disorders.

More here.

The Wider, Not Wilder, Egon Schiele

Ken Johnson in the New York Times:

EgoThe Viennese Expressionist Egon Schiele (1890-1918) had only two urgent interests: himself and his sexual fantasies. Out of such limited preoccupations and by means of a preternatural gift for drawing and graphic design, he created artworks that still burn with narcissistic yearning, erotic desire, bohemian dissent and existential anxiety.

Since the revival in the early 1970’s of his dormant reputation, he has been esteemed by fine-art lovers as one of the 20th century’s great draftsmen and he has been a romantic hero to generations of young people raised on sex, drugs and rock ‘n’ roll who would not know a Monet from a Manet.

Schiele did other things besides self-portraits and sexy pictures of young women. He made wonderful portraits of friends, relatives and lovers, painted gloomy landscapes in an amalgam of Modernist and medieval styles, and concocted lugubrious, overwrought allegories of life, love and death. But were it not for the self-portraits and erotic pictures on paper, his name would be forgotten today.

More here.

Astrology is scientific theory, courtroom told

Celeste Biever in New Scientist:

Astrology would be considered a scientific theory if judged by the same criteria used by a well-known advocate of Intelligent Design to justify his claim that ID is science, a landmark US trial heard on Tuesday.

Under cross examination, ID proponent Michael Behe, a biochemist at Lehigh University in Bethlehem, Pennsylvania, admitted his definition of “theory” was so broad it would also include astrology.

The trial is pitting 11 parents from the small town of Dover, Pennsylvania, against their local school board. The board voted to read a statement during a biology class that casts doubt on Darwinian evolution and suggests ID as an alternative.

The parents claim this was an attempt to introduce creationism into the curriculum and that the school board members were motivated by their evangelical Christian beliefs. It is illegal to teach anything with a primarily religious purpose or effect on pupils in government-funded US schools.

Supporters of ID believe that some things in nature are simply too complex to have evolved by natural selection, and therefore must be the work of an intelligent designer.

More here.

Happy 120th? Science Pushes Human Longevity

From National Geographic:

How long can humans conceivably live? In most developed countries, life expectancy has grown steadily to an average of 75 years. But scientists are exploring ways to extend lifespan to lengths that seem inconceivable now—perhaps 120 years and beyond. Ideally, future centenarians who avail themselves to life-prolonging advances won’t suffer the familiar frailties of old age. The goal is for them to retain their youthful vitality, rather than add extra years of decline. Several studies show lifespans can be stretched far beyond normal limits. In one example, Cynthia Kenyon, a professor at the University of California in San Francisco, has doubled the lifespans of simple roundworms from two weeks to a month by altering the function of a single gene, known as daf-2. Even near death, these mutated worms look better than normal worms half their age. Their bodies are smooth and plump, and they wriggle along like much younger worms.

More here.

On The Political Consequences of US bases abroad

Alex Cooley has a thoughtful piece in the latest Foreign Affairs on the political consequences of basing US troops in foreign countries. (Subscription required for full article.)

This past July, the government of Uzbekistan evicted U.S. personnel from the Karshi-Khanabad air base, which Washington had used as a staging ground for combat, reconnaissance, and humanitarian missions in Afghanistan since late 2001. The government in Tashkent gave no official reason for the expulsion, but the order was issued soon after the UN airlifted 439 Uzbek refugees from Kyrgyzstan to Romania — a move that Washington supported and Tashkent opposed. . . The showdown was the latest in a series of confrontations since a much-criticized crackdown on antigovernment demonstrators in the eastern city of Andijon last May.

These events illustrate the enduring problem that U.S. defense officials face as they try to promote democratic values abroad while maintaining U.S. military bases in nondemocratic countries. Although some in Washington acknowledge this tension, they generally argue that the strategic benefits of having U.S. bases close to important theaters such as Afghanistan outweigh the political costs of supporting unsavory host regimes. With the Pentagon now redefining the role of the U.S. military in the twenty-first century, moreover, its officials insist even more on the importance of developing a vast network of U.S. bases to confront cross-border terrorism and other regional threats. Some of them also turn the objections of pro-democracy critics around. They claim that a U.S. military presence in repressive countries gives Washington additional leverage to press them to liberalize. . .

Such arguments have merit, but they do not tell the whole story. For one thing, the political complications sometimes associated with dealing with democracies are ephemeral. For another, setting up bases in nondemocratic states brings mostly short-term benefits, rarely helps promote liberalization, and sometimes even endangers U.S. security.

Reconsidering the more troops in Iraq counterfactual

Via Crooked Timber, Mathew Yglesias and Sam Rosenfeld consider the agrument that the Iraq war was a good idea that was botched in its execution and find it wanting.

So was the Iraq War a good idea, ruined by poor implementation? Perhaps the founding myth of the incompetence argument is that the postwar mess could have been avoided had the United States deployed more troops to Iraq. “Army Chief of Staff General Eric Shinseki was ridiculed for suggesting that it would take several hundred thousand troops to secure Iraq,” wrote Senator Joe Biden in a June 2004 New Republic article. “He looks prescient today.”

Shinseki’s ballpark numbers were based on past Army experience with postconflict reconstruction. A RAND Corporation effort to quantify more precisely that experience, frequently cited by dodgers, concluded that a ratio of 20 foreigners for every 1,000 natives would have been necessary to stabilize Iraq.

The flaw in the popular “more troops” argument is strikingly easy to locate. The 20-to-1,000 ratio implies the presence of about 500,000 soldiers in Iraq. That’s far more than it would have been possible for the United States to deploy. Sustaining a given number of troops in a combat situation requires twice that number to be dedicated to the mission, so that soldiers can rotate in and out of theater. As there are only 1 million soldiers in the entire Army, a 500,000-troop deployment would imply that literally everyone — from the National Guard units currently assisting with disaster relief on the Gulf Coast to those serving in Afghanistan, Korea, and Europe to the bureaucrats doing staff work in the Pentagon and elsewhere — would be dedicated to the mission. This is plainly impossible. . .

ANOTHER LETTER FROM ZAWAHIRI TO ZARQAWI

T. A. Frank in The New Republic:

Dear Brother,

God only knows how much I would enjoy visiting you in Iraq. The only thing keeping me from packing my bags, donning a burqa, and slipping into a carrier sack on a westbound mule right now is that I’m tied up with promoting my latest book, Man Behind the Mosque: Faith, Community and Discourse in Post-Bunker-Buster Waziristan (334 pp., Madrassa Press, $28.95 Canadian). Did you happen to see me on “Charlie Rose”? I had you in mind when I sent in my threatening audiotape.

I hope the move is going well, and I would love to see a picture of your new house in Falluja. I am glad the old one had insurance, God be praised. I do hope that it has a comfortable recreation room, God permitting, and a spacious, windowless basement with good lighting for the Panasonic AG-DVC7 you were discussing.

However, I do, gracious brother, want to discuss one or two points about strategy and tactics, even as I recognize your pioneering role in decapitation research. In terms of ambition, your plan to explode every Shia in Iraq cannot be faulted for scope, but is it practicable? I worry that the Iranians and others visiting Najaf or Basra might pick up on clues, such as the absence of human life. Mind you, I sympathize entirely with your sentiments, but it might make more sense to focus primarily on the American infidels and to save the detonation of Shia for special occasions, such as birthdays.

More here.

Cracking the Code of Pre-Earthquake Signals

Friedemann Freund at Space.com:

Our Earth is a restless planet. Occasionally – quite often, in some regions of the world – the restlessness turns deadly. Of all natural hazards, earthquakes are the most feared. They are feared because they seem to strike so unpredictably. Yet, for centuries, and even millennia, people living in seismically active regions have noted premonitory signals. The historical records talk of changes of the water level in wells, of strange weather, of ground-hugging fog, of unusual behavior of animals (both domestic and wild) that seem to feel the approach of a major earthquake. With the advent of modern science and technology the list of premonitory signals has become even longer. Among them are

  1. Sporadic emissions of low to ultralow-frequency electromagnetic radiation from the ground
  2. Occasional local magnetic field anomalies reaching a strength of half a percent of the Earth’s main dipole field
  3. Changes in the lower atmosphere that are accompanied by the formation of haze and a reduction of moisture in the air
  4. Large patches, often tens to hundreds of thousands of square kilometers in size, seen in night-time infrared satellite images where the land surface temperature seems to fluctuate rapidly
  5. Passing perturbations in the ionosphere at 90 – 120 km altitude that affect the transmission of radio waves

More here.

Torment and Justice in Cambodia

Christine Stansell in Dissent Magazine:

“Something terrible happened here. And I don’t know what it is,” Bill Herod remembers thinking in his first days in Phnom Penh in 1980. He was with Church World Service, one of a group of aid workers allowed into the country after the Vietnamese overthrew the Khmer Rouge in January 1979 and put an end to the three-and-a-half-year-long nightmare of the Cambodian people. In 1980, Herod had just come from Vietnam. He had seen plenty of devastation, but this was something different, a higher order of magnitude.

In those first months, Westerners were only beginning to grasp the enormity of what the KR—as they’re always called in Cambodia—had done. In the city and the refugee camps on the Thai border, relief workers were piecing together accounts of starvation, brutal forced labor, and mass executions into some comprehension of the whole. Cambodians were stunned, largely affectless, many in a state of shock. Hospitals housed crazed, emaciated children who had been found wandering in the forests, abandoned and lost by parents fleeing KR camps as the Vietnamese approached.

Thirty years later, the extent and nature of the horror are no mysteries. Between April 1975, when the KR overthrew the despised Lon Nol regime, and January 1979, when the Vietnamese invaded, the rulers of Democratic Kampuchea killed—by murder, starvation, and forced labor—1.7 to two million people, close to a quarter of the entire population. In the torment they wreaked on a small country in such a short time, the KR ranks as possibly the most savage Communist Party to curse the twentieth century.

More here.

An American Boy in Stalin’s Russia

In Archipelago:

Editor’s note: Leon Bell, a Soviet-trained nuclear physicist who later became a world-class plant physiologist with an expertise in photosynthesis, was born in Texas in 1918, and moved with his family to Moscow in 1931. His life reflects the tragedy of the Soviet Union and the situation of an American-born Jew in Stalin’s Russia. In his unpublished autobiography the author gives an inside view of what it was like to live in constant fear and poverty in a totalitarian state. . .

Part 1

Today is December 23, 1987. I am now sixty-nine years old. You can twist that figure around anyway you wish to, but you will always get sixty-nine—there is no escape. In a year’s time (if I am still alive) I will be seventy, and that is real old age. Time is running out, and if I expect to write about my life, as daughter Natasha has asked me to, it’s time to begin.

Of course, I have my doubts whether it is worthwhile writing. I can’t write a memoir as usually understood—a narrative of the life of a person of fame or one who had experienced a particularly interesting life. I am not famous and, strictly speaking, there were no extraordinary events in my life Then why write? First of all, as I have mentioned, Natasha has asked me to, and wife Ira has supported the idea. Secondly, in my opinion just about anyone’s life can be interesting as a mirror, albeit a small one, of the times in which the person lived.

I am a person of the twentieth century, a stormy and at times, maddening, century. Possibly, in the future some people would like to know how ordinary, not widely known people lived in those times.

The Dalai Lama’s The Universe in a Single Atom

The Skpetic reprints Michael Shermer’s review of the Dalai Lama’s The Universe in a Single Atom, which seems to continue in the tradition of the Einstein-Tagore discussions about science and religion (and about Tagore’s The Religion of Man).

This book is “not an attempt to unite science and spirituality,” he explains, “but an effort to explore two important human disciplines for the purpose of developing a more holistic and integrated way of understanding the world.”

He begins his exploration by equating science with the worldview of “scientific materialism,” which “seems to be a common unexamined presupposition” that includes “a belief in an objective world, independent of the contingency of its observers. It assumes that the data being analyzed within an experiment are independent of the preconceptions, perceptions, and experience of the scientist analyzing them.” Well, not quite. Most working scientists do make this assumption when conducting their experiments, but they are well aware that their preconceptions can color their analysis and interpretation. Reality exists, we can agree. Getting an accurate reading on reality is another matter entirely.

The Dalai Lama’s other bugbear is scientific reductionism, and here I feel he has set up something of a straw man.

The view that all aspects of reality can be reduced to matter and its various particles is, to my mind, as much a metaphysical position as the view that an organizing intelligence created and controls reality.

This view, he fears, leads to nihilism, and with it the loss of subjective purpose and meaning.

The danger then is that human beings may be reduced to nothing more than biological machines, the products of pure chance in the random combination of genes, with no purpose other than the biological imperative of reproduction.

The link between breast cancer and genetics

From The Village Voice:Breast

She triumphed over breast cancer 12 years ago, but Ivis Febus-Sampayo stared it in the face again this January when a genetics test revealed she carried a specific gene mutation, which put her chances of developing a cancerous lump in her breast at a roughly estimated, and frightening, 45 percent. A 50-year-old wife and mother of two boys, Febus-Sampayo took aggressive action against the deadly disease. She went under the knife and preemptively had her ovaries removed, narrowing the likelihood of a malignant growth in her breast. With early detection of tumors directly linked to cancer survival rates, Febus-Sampayo has regular mammograms and oncologist visits. Additionally, she has an annual breast MRI (magnetic resonance imaging), recommended only for high-risk patients. While MRIs have been shown to find tumors when they are smaller and easier to treat, misreading the findings can result in false alarms and numerous painful biopsies.

Credit the field of genetics with giving Febus-Sampayo the heads-up about her genetic risks.

More here.

Peregrine swoops to photo prize

From BBC News:Bird_2

A swirling image of a peregrine falcon sweeping into a flock of starlings has won Manuel Presti this year’s Wildlife Photographer of the Year award. The Italian caught the action scene, titled Sky Chase, high above a city park in Rome. “Sky chase is a powerful image and, like it or not, it’s one that you will never forget,” said Mark Carwardine, one of this year’s judges. The competition has become one of the most prestigious in world photography. It is organised by BBC Wildlife Magazine and London’s Natural History Museum. This year brought 17,000 entries from over 55 countries.

More here.

Soldiers of the Hidden Imam

Timothy Garton Ash in the New York Review of Books:

Early this autumn, as today’s Iranian rulers defied the new Rome by pressing ahead with their nuclear program, I traveled for two weeks through what is now the Islamic Republic of Iran. In the year of their Lord 1384, I talked to mullahs armed with laptops, regime supporters in the religious hotbed of Qom, and Islamic philosophers highly critical of the regime. I met intellectuals of all stripes, artists, farmers, politicians, and businesspeople. Most memorably, I had long, intense conversations with some of the young Iranians who make up the majority of the country’s population. I see their earnest faces before me as I write, especially those of the women, framed in the compulsory Islamic head scarf, the hijab, which they somehow manage to convert into an accessory of grace and quiet allure.

More here.

Noam Chomsky selected world’s top intellectual

Is the world’s top public intellectual a brilliant expositor of linguistics and the US’s duplicitous foreign policy? Or a reflexive anti-American, cavalier with his sources?”

Robin Blackburn and Oliver Kamm, examine the cases for and against Chomsky in Prospect:

PictureThe huge vote for Noam Chomsky as the world’s leading “public intellectual” should be no surprise at all. Who could match him for sheer intellectual achievement and political courage?
Very few transform an entire field of enquiry, as Chomsky has done in linguistics. Chomsky’s scientific work is still controversial, but his immense achievement is not in question, as may be easily confirmed by consulting the recent Cambridge Companion to Chomsky. He didn’t only transform linguistics in the 1950s and 1960s; he has remained in the forefront of controversy and research.

More here.

Three friends and readers of 3 Quarks Daily were also on the list of winners: Richard Dawkins came in at number 3, while Daniel Dennett and Steven Pinker were numbers 24 and 26. Congratulations to them and all the others from all of us at 3QD.