Sunday, February 28, 2010

Learning From the Sin of Sodom

Nicholas Kristof, born evangelical, has long argued that his base community is more than just anti-abortion and anti-gay radicals.
World Vision, a Seattle-based Christian organization (with strong evangelical roots), now has 40,000 staff members in nearly 100 countries. That’s more staff members than CARE, Save the Children and the worldwide operations of the United States Agency for International Development — combined. …

The head of World Vision in the United States, Richard Stearns, begins his fascinating book, “The Hole in Our Gospel,” with an account of a visit a decade ago to Uganda, where he met a 13-year-old AIDS orphan who was raising his younger brothers by himself.

“What sickened me most was this question: where was the Church?” he writes. “Where were the followers of Jesus Christ in the midst of perhaps the greatest humanitarian crisis of our time? Surely the Church should have been caring for these ‘orphans and widows in their distress.’ (James 1:27). Shouldn’t the pulpits across America have flamed with exhortations to rush to the front lines of compassion?

“How have we missed it so tragically, when even rock stars and Hollywood actors seem to understand?”

Mr. Stearns argues that evangelicals were often so focused on sexual morality and a personal relationship with God that they ignored the needy. He writes laceratingly about “a Church that had the wealth to build great sanctuaries but lacked the will to build schools, hospitals, and clinics.”

In one striking passage, Mr. Stearns quotes the prophet Ezekiel as saying that the great sin of the people of Sodom wasn’t so much that they were promiscuous or gay as that they were “arrogant, overfed and unconcerned; they did not help the poor and needy.” (Ezekiel 16:49.) …

Some conservative Christians reinforced the worst view of themselves by inspiring Ugandan homophobes who backed a bill that would punish gays with life imprisonment or execution. Ditto for the Vatican, whose hostility to condoms contributes to the AIDS epidemic. But there’s more to the picture: I’ve also seen many Catholic nuns and priests heroically caring for AIDS patients — even quietly handing out condoms.

One of the most inspiring figures I’ve met while covering Congo’s brutal civil war is a determined Polish nun in the terrifying hinterland, feeding orphans, standing up to drunken soldiers and comforting survivors — all in a war zone. I came back and decided: I want to grow up and become a Polish nun.

Some Americans assume that religious groups offer aid to entice converts. That’s incorrect. Today, groups like World Vision ban the use of aid to lure anyone into a religious conversation. …

If secular liberals can give up some of their snootiness, and if evangelicals can retire some of their sanctimony, then we all might succeed together in making greater progress against common enemies of humanity, like illiteracy, human trafficking and maternal mortality.

Saturday, February 27, 2010

Why do we let the Republicans get away with it?

One of the major planks in the Republican health care "plan" is to allow companies to sell insurance "across state lines." Of course that's a terrible idea. As Paul Krugman points out.
The states with the weakest regulations — for example, those that allow insurance companies to deny coverage to victims of domestic violence — would set the standards for the nation as a whole. The result would be to afflict the afflicted, to make the lives of Americans with pre-existing conditions even harder.
But amazingly even Krugman, who devoted the column from which the preceding is extracted to pointing out how dishonest the Republicans are, lets them get away with it on this point.

Why is the proposal to sell health insurance across state lines dishonest and hypocritical? Let me count the ways.

Insurance companies can sell insurance across state lines now. There is no law in any state that says that if a company sells insurance in another state it is not allowed to sell insurance in that state. Such a law would surely be struck down by the courts. If you are a company that sells insurance in New York, California will not stop you from selling insurance in California. To pretend that's not so is simply dishonest.

So what do the Republicans have in mind, if anything. Well they don't like the idea that states want to pass laws about insurance sold in their state. They pass laws about other things that happen in their state, why not about insurance? Republicans apparently would make it impossible for states to do that. Presumably the Republican plan is that if something is legal in one state, then it should be legal in all.

But of course Republicans don't really believe that. If they did, it would be legal to sell medical marijuana in all states since it is legal in California. But it isn't, and I don't hear any Republicans arguing that it should be.

And I certainly don't hear Republicans arguing that since gay marriage is legal in some states it should be legal in all. So the Republicans are not making a principled argument about selling insurance across state lines. They are simply demagoguing.

Furthermore, who would enforce the ban against states making laws about insurance sold in their own state? The only authority that could enforce such a ban would be the Federal government. So are Republicans really arguing for more Federal power? That's a new one. Of course it's not new, and we shouldn't take any of this seriously. Republicans are simply hypocritical and dishonest. What bugs me is that we let them get away with it.

As I said, though, Krugman often makes an attempt to call the Republicans on their dishonesty. The column from which I quoted was devoted to that for the most part. Krugman ended it as follows.
So what did we learn from the [health care] summit? What I took away was the arrogance that the success of things like the death-panel smear has obviously engendered in Republican politicians. At this point they obviously believe that they can blandly make utterly misleading assertions, saying things that can be easily refuted, and pay no price. And they may well be right.
And unfortunately he may well be right.

Friday, February 26, 2010

A Bigger Container

Jessica responded to my previous posting by pointing out that
"container" in this context refers back to Charlotte Joko Beck who in Everyday Zen spoke about the ABC of practice — A Bigger Container.
I looked for extracts and found this one from
We can talk about 'oneness' until the cows come home. But how do we actually separate ourselves from others? How? The pride out of which anger is born is what separates us. And the solution is a practice in which we experience this separating emotion as a definite body state. When we do, A Bigger Container is created.

What is created, what grows, is the amount of life I can hold without it upsetting me, dominating me. At first this space is quite restricted, then it’s a bit bigger, and then it’s bigger still. It need never cease to grow. And the enlightened state is that enormous and compassionate space. And how do we know where this cut-off point is? We are at that point when we feel any degree of upset, of anger. It’s no mystery at all. And the strength of our practice is how big that container gets.

This practice of making A Bigger Container is essentially spiritual because it is essentially nothing at all. A Bigger Container isn’t a thing; awareness is not a thing; the witness is not a thing or a person. There is not somebody witnessing. Nevertheless that which can witness my mind and body must be other than my mind and body. If I can observe my mind and body in an angry state, who is this 'I' who observes? It shows me that I am other than my anger, bigger than my anger, and this knowledge enables me to build A Bigger Container, to grow. So what must be increased is the ability to observe. What we observe is always secondary. It isn’t important that we are upset; what is important is the ability to observe the upset.

As the ability grows first to observe, and second to experience, two factors simultaneously increase: wisdom, the ability to see life as it is (not the way I want it to be) and compassion, the natural action which comes from seeing life as it is. We can’t have compassion for anyone or anything if our encounter with them is ensnarled in pride and anger; it’s impossible. Compassion grows as we create A Bigger Container.
A search for "Bigger Container" on the "look Inside" feature of Amazon's page for Everyday Zen lets you read the entire "A Bigger Container" chapter (pp 49 - 52) from which this extract is drawn.

Thursday, February 25, 2010

Feeling More and More | Tricycle Magazine

Tricycle has what they call their daily dharma. Today's is longer than most, but it's quite nice.
We bump up against the fact of change and impermanence as soon as we acknowledge our feelings or needs for others. Basically, we all tend to go in one of two directions as a strategy for coping with that vulnerability. We either go in the direction of control or of autonomy. If we go for control, we may be saying: “If only I can get the other person or my friends or family to treat me the way I want, then I’ll be able to feel safe and secure. If only I had a guarantee that they’ll give me what I need, then I wouldn’t have to face uncertainty.” With this strategy, we get invested in the control and manipulation of others and in trying to use people as antidotes to our own anxiety.

With the strategy (or curative fantasy) of autonomy, we go in the opposite direction and try to imagine that we don’t need anyone. But that strategy inevitably entails repression or dissociation, a denial of feeling. We may imagine that through spiritual practice we will get to a place where we won’t feel need, sexuality, anger, or dependency. Then, we imagine, we won’t be so tied into the vicissitudes of relationships. We try to squelch our feelings in order not to be vulnerable anymore, and we rationalize that dissociation under the lofty and spiritual-sounding word “detachment,” which ends up carrying a great deal of unacknowledged emotional baggage alongside its original, simpler meaning as the acceptance of impermanence.

We have to get to know and be honest about our particular strategies for dealing with vulnerability, and learn to use our practice to allow ourselves to experience more of that vulnerability rather than less of it. To open yourself up to need, longing, dependency, and reliance on others means opening yourself to the truth that none of us can do this on our own. We really do need each other, just as we need parents and teachers. We need all those people in our lives who make us feel so uncertain. Our practice is not about finally getting to a place where we are going to escape all that but about creating a container that allows us to be more and more human, to feel more and more.

Barry Magid, "No Gain," Tricycle Summer 2008
He didn't really give himself away as a therapist until the very end when he used the word container. It doesn't mean to contain in the sense of to suppress. It means to be capable of experiencing the emotion within oneself, without necessarily having to externalize it—without it having to burst out, especially in a destructive way.

Wednesday, February 24, 2010

Anecdotal evidence works

From Harvard Magazine Mar-Apr 2010
Your parents recommend taking a Caribbean cruise and tell you about a discount deal. You’ve never taken a cruise and aren’t so sure you’d enjoy it, so you dig up some information on the Web and even watch a couple of videos. You recollect the times you’ve been on ships, and your past visits to Caribbean islands—rum drinks, aqua waters. But will you really enjoy an eight-day cruise? Turns out there is a better way to answer this question: ask anyone who has just gotten off a cruise boat—a total stranger is fine. That way, you’ll be 30 to 60 percent more likely to accurately predict your own experience than by basing your decision on painstaking research and inner speculations.

Ricardo was wrong

From Harvard Magazine Mar-Apr 2010
A truism about the benefits of international trade holds that countries that specialize in producing goods that they are best at manufacturing will enjoy the greatest prosperity. But a recent study of economic complexity provides a different take on the wealth of nations. Using “network science,” a method of analysis that examines webs of connections in complex systems, Ricardo Hausmann, professor of the practice of economic development and director of Harvard’s Center for International Development, and CID research fellow CĂ©sar Hidalgo, a physicist by training, have shown that the richest countries are those with the most complex economies—and actually produce the greatest diversity of goods. “Firms and individuals specialize, countries diversify,” emphasizes Hausmann.
The reason Ricardo's truism is wrong is that he assumed a static world in which there were a given number of products and a given demand for each product. But the world isn't static. The successful countries are those that can adapt as times change and as new products become important. The most successful countries are those that invent the new important products.

Tuesday, February 23, 2010

The beast is starving. Now what?

By Paul Krugman
So the beast [i.e., government, in the Republicans' eyes] is starving, as planned. It should be time, then, for conservatives to explain which parts of the beast they want to cut. And President Obama has, in effect, invited them to do just that, by calling for a bipartisan deficit commission.

Many progressives were deeply worried by this proposal, fearing that it would turn into a kind of Trojan horse — in particular, that the commission would end up reviving the long-standing Republican goal of gutting Social Security. But they needn’t have worried: Senate Republicans overwhelmingly voted against legislation that would have created a commission with some actual power, and it is unlikely that anything meaningful will come from the much weaker commission Mr. Obama established by executive order.

Why are Republicans reluctant to sit down and talk? Because they would then be forced to put up or shut up. Since they’re adamantly opposed to reducing the deficit with tax increases, they would have to explain what spending they want to cut. And guess what? After three decades of preparing the ground for this moment, they’re still not willing to do that.

In fact, conservatives have backed away from spending cuts they themselves proposed in the past. In the 1990s, for example, Republicans in Congress tried to force through sharp cuts in Medicare. But now they have made opposition to any effort to spend Medicare funds more wisely the core of their campaign against health care reform (death panels!). And presidential hopefuls say things like this, from Gov. Tim Pawlenty of Minnesota: “I don’t think anybody’s gonna go back now and say, Let’s abolish, or reduce, Medicare and Medicaid.”

What about Social Security? Five years ago the Bush administration proposed limiting future payments to upper- and middle-income workers, in effect means-testing retirement benefits. But in December, The Wall Street Journal’s editorial page denounced any such means-testing, because “middle- and upper-middle-class (i.e., G.O.P.) voters would get less than they were promised in return for a lifetime of payroll taxes.” (Hmm. Since when do conservatives openly admit that the G.O.P. is the party of the affluent?)

At this point, then, Republicans insist that the deficit must be eliminated, but they’re not willing either to raise taxes or to support cuts in any major government programs. And they’re not willing to participate in serious bipartisan discussions, either, because that might force them to explain their plan — and there isn’t any plan, except to regain power.

But there is a kind of logic to the current Republican position: in effect, the party is doubling down on starve-the-beast. Depriving the government of revenue, it turns out, wasn’t enough to push politicians into dismantling the welfare state. So now the de facto strategy is to oppose any responsible action until we are in the midst of a fiscal catastrophe. You read it here first.

Physical contact matters

Momentary touches … — whether an exuberant high five, a warm hand on the shoulder, or a creepy touch to the arm — can communicate an even wider range of emotion than gestures or expressions, and sometimes do so more quickly and accurately than words.

“It is the first language we learn,” said Dacher Keltner, a professor of psychology at the University of California, Berkeley, and the author of “Born to Be Good: The Science of a Meaningful Life” (Norton, 2009), and remains, he said, “our richest means of emotional expression” throughout life.

The evidence that such messages can lead to clear, almost immediate changes in how people think and behave is accumulating fast. Students who received a supportive touch on the back or arm from a teacher were nearly twice as likely to volunteer in class as those who did not, studies have found. A sympathetic touch from a doctor leaves people with the impression that the visit lasted twice as long, compared with estimates from people who were untouched. Research by Tiffany Field of the Touch Research Institute in Miami has found that a massage from a loved one can not only ease pain but also soothe depression and strengthen a relationship.

In a series of experiments led by Matthew Hertenstein, a psychologist at DePauw University in Indiana, volunteers tried to communicate a list of emotions by touching a blindfolded stranger. The participants were able to communicate eight distinct emotions, from gratitude to disgust to love, some with about 70 percent accuracy.

“We used to think that touch only served to intensify communicated emotions,” Dr. Hertenstein said. Now it turns out to be “a much more differentiated signaling system than we had imagined.”
We all knew that at some level. It's probably more difficult today, though, with so much emphasis on possible harassment.

Friday, February 19, 2010

Pain and suffering

This op-ed piece discusses how animals (presumably including humans) experience pain. It says that there are two components to pain: sensation and suffering. It is possible to turn off the suffering without turning off the sensation. (This is important so that an animal can feel a stimulus that it should avoid, such as a hot surface, even if the stimulus does not cause what we traditionally think of as pain.)

It then argues that since we can engineer animals so that they do not suffer when subjected to the conditions common factory farms, we should do it—not change the farms but change the animals so that they don't feel bad.

Seems like a very strange argument. Whether or not factory farms are ethical ways to treat animals, the argument seems to be saying that torture is ok as long as the victim doesn't suffer.

Along the way the claim is made that morphine works because it competes with the part of the brain that feels bad about pain, i.e., the part of the brain that suffers. When the suffering receptors are blocked by morphine, they are unable to respond to pain—hence no suffering.

The whole thing is an interesting description of how the brain works. I was unaware of it. Nor did I know we were so certain about this mechanism. It's strange to learn about it in such a strange op-ed piece, though.

The brain, it turns out, has two separate pathways for perceiving pain: a sensory pathway that registers its location, quality (sharp, dull or burning, for example) and intensity, and a so-called affective pathway that senses the pain’s unpleasantness. This second pathway appears to be associated with activation of the brain’s anterior cingulate cortex, because people who have suffered damage to this part of the brain still feel pain but no longer find it unpleasant. (The same is true of people who are given morphine, because there are more receptors for opiates in the affective pain pathway than in the sensory pain pathway.)

Neuroscientists have found that by damaging a laboratory rat’s anterior cingulate cortex, or by injecting the rat with morphine, they can likewise block its affective perception of pain. The rat reacts to a heated cage floor by withdrawing its paws, but it doesn’t bother avoiding the places in its cage where it has learned the floor is likely to be heated up.

Recently, scientists have learned to genetically engineer animals so that they lack certain proteins that are important to the operation of the anterior cingulate cortex. Prof. Min Zhuo and his colleagues at the University of Toronto, for example, have bred mice lacking enzymes that operate in affective pain pathways. When these mice encounter a painful stimulus, they withdraw their paws normally, but they do not become hypersensitive to a subsequent painful stimulus, as ordinary mice do.

Wednesday, February 17, 2010

Biological curiosities - CSWiki

I just posted the following on the Biological curiosities page of the CS wiki. It comments on a story that talks about how viruses (phages) help anthrax bacteria survive.
I would love to see a diagram that shows the various entities and processes involved. There are at least 4 levels: phage, bacterium, earthworm, and mammal. What is the role of each and when is that role played out? I gather from the article that it's not even as simple as that since different phages change how anthrax acts under various conditions.

This is a beautiful example of a complex system that we are beginning to understand. It would be very useful as an illustration of how complex systems function.

Tuesday, February 16, 2010

Phineas Gage

From The Scientist
On September 13, 1848, a 25-year-old railroad worker named Phineas Gage triggered an explosion that propelled a 3 foot 7 inch iron rod straight through his skull, destroying a good portion of his brain. Luckily, the iron missed the critical blood vessels and parts of the brain necessary for survival, but the injury spurred dramatic behavioral changes and made Gage’s accident one of the most important contributions to modern neurology.

“This was the first case when doctors made a definite connection between an injury to the brain and a change in personality,” says Malcolm Macmillan, a professor of behavioral science at the University of Melbourne in Australia and an expert on Gage. Linking the damage in Gage’s prefrontal cortex to his sudden erratic behavior was one of the first clues that the prefrontal cortex was responsible for personality expression and decision making.

Because Gage made public appearances and worked after the injury, Macmillan hypothesized that his personality change must have been “a temporary one” and “that he made a good psychosocial recovery.” Macmillan found further support for this theory when, in 2008, photographers Jack and Beverly Wilgus from Massachusetts revealed an image of Gage holding the pole that had shot through his brain. The picture, which they had possessed for 30 years but only recently identified as Gage, displays a handsome, proud, and confident-looking man.

“The image suggests that Phineas had adapted to his disfigurement and was not ashamed to display it,” writes Macmillan in an email. Gage’s mental improvement suggests that it’s possible for the brain to recover some of its function after an injury, he adds, although the details of Gage’s recovery remain a mystery.
This is indeed a very famous incident. From what I've read about Gage, his mental changes did not diminish, but he was able to function reasonably well.

Sunday, February 14, 2010

Lessig's Change Congress

Support it here.

Lost generation.

Watch the whole thing. It's only a minute 44 seconds.

Adding DNAv4 to DNAv3

From New Scientist
Jason Chin at the University of Cambridge and his colleagues have now redesigned the cell's machinery so that it reads the genetic code in quadruplets. …

To achieve this, the team had to redesign three pieces of the cellular machinery that make proteins.

But they didn't stop there. The team went on to prove their new genetic code works by assigning two "unnatural" amino acids to their quadruplet codons, and incorporated them into a protein chain.

"It's the beginning of a parallel genetic code," says Chin.

What's more, they've shown that these amino acids can react with each other to form a different kind of chemical bond to those which usually hold proteins together in their three-dimensional shape.

The normal kind of bonds – disulphide bonds – can be broken by changes in heat and acidity, causing proteins to lose their 3D structure. This, for instance, is why egg whites change colour and texture when cooked: as the albumen in the whites loses its structure, its physical appearance is transformed.

But the bonds created between Chin's new amino acids are stronger – and so could allow proteins to work in a much wider range of environments. This could help make drugs that can be taken orally without being destroyed by the acids in the digestive tract, for instance.

But that's just the beginning. In the longer term it might be possible to create cells that produce entirely new polymers, such as plastic-like materials. Organisms made of these cells could incorporate the stronger polymers and become stronger or more adaptable as a result.
Here's how The puts it.
Scientists have developed a new genetic language using a ribosome that can read instructions that are 4 base pairs long [rather than the three that are found in nature], enabling the construction of designer proteins containing a variety of unnatural elements, according to a study published online today (February 14) in Nature. …

[Using 3 base pairs there is only] one spare codon to work with. [As a result] scientists have largely been restricted to incorporating only one such unit per protein.

To overcome this limitation, synthetic biologist Jason Chin of the Medical Research Council Laboratory of Molecular Biology in Cambridge, UK, and his colleagues decided to devise a system that could read codons that are 4 base pairs long. Such a system could "open the door to what will be [the] truly revolutionary possibility [of creating] genetically coded polymers comprised of up to 256 [unique] building blocks."

The problem was that normal ribosomes -- which translate 3-base codons into any of the 22 naturally occurring amino acids -- don't read such quadruplet codons, at least not usually. Furthermore, the team couldn't simply manipulate the existing ribosomes, as they are responsible for producing all of the cell's proteins that are required for its survival; altering this system could quickly cause a cellular collapse. Their solution: make a whole new ribosome.

A few years ago, the researchers created the new ribosome, known as an orthogonal ribosome, by altering the region that recognizes the ribosome-binding sequence of the messenger RNA (mRNA). They then created special mRNAs with complementary binding regions to this new sequence, which the orthogonal ribosome selectively bound to and read, leaving natural mRNAs to be recognized only by the natural ribosomes.

"Now you've got two ribosomes -- one reading a new message and [the] normal ribosome" reading the old messages, Chin explained. "That's the basis of how you would write a parallel genetic code in the cell."

With the two ribosomes systems working independently, the researchers could then manipulate the orthogonal ribosome without disrupting normal cellular function. In the present study, they did just that, inducing mutations in the ribosome where the tRNA and mRNA molecules interact in hopes of creating a ribosome that could read quadruplet codons with comparable efficiency and accuracy to that of natural protein synthesis.

To test their mutated ribosomes, the team put them in bacterial cultures growing on a medium containing antibiotics, and provided the cells with an antibiotic resistance gene that included a 4-base codon. Ribosomes that could read the quadruplet codon successfully produced the antibiotic resistance protein, and survived even in the presence of high concentrations of the antibiotic. Those that couldn't read the quadruplet, couldn't create the protein to protect themselves from the antibiotic and died as a result. "In the end we get cells that are surviving this selection pressure," Chin said, and in those cells are ribosomes that can successfully read quadruplet codons.

The new ribosome can still read triplet codons as well, Chin added, but it preferentially reads the 4-base sequences. In this way, the ribosome can still incorporate natural amino acids as well as modified units attached to the amber codon.

But now with the ability to read the quadruplet codons, scientists can easily create proteins with more than one unnatural unit. Using the amber codon and a quadruplet codon to code for two different unnatural amino acids, the researchers generated a protein, synthesized by the new ribosome, that contained both unnatural units.
In many ways this is similar to the move from IPv4 to IPv6 in Internet addressing. (See here and here). It creates a much collection of potential addresses, which therefore can refer to a much larger space of things. In the Internet case the things are distinct items that can have their own internet address. In the DNA case the things are proteins that DNA can be interpreted as referring to.

Wednesday, February 10, 2010


By Timothy Egan in the Opinionator Blog -
Look at the cities with stable and recovering home markets. On [the Pacific] coast, San Francisco, Portland, Seattle and San Diego come to mind. All of these cities have fairly strict development codes, trying to hem in their excess sprawl. Developers, many of them, hate these restrictions. They said the coastal cities would eventually price the middle class out, and start to empty.

It hasn’t happened. Just the opposite. The developers’ favorite role models, the laissez faire free-for-alls — Las Vegas, the Phoenix metro area, South Florida, this valley — are the most troubled, the suburban slums.

Come see: this is what happens when money and market, alone, guide the way we live.

Sunday, February 07, 2010

Obama to Hold Bipartisan Summit on Health Care

President Obama said Sunday that he will convene a half-day, bipartisan health care summit at the White House on Feb. 25 to be broadcast on television, so Americans can see Democrats and Republicans try to break the deadlock on health care legislation.
Fantastic! The challenge will be to make it something other than Republican grandstanding. He will have to show the country that he is serious about both health care and about bi-partisan cooperation and that the Republicans are serious about neither.

Here, for example, is what the leader of the Republicans said.
Senator Mitch McConnell of Kentucky, the Republican leader, said he welcomed the bipartisan meeting on health care and called on the president to begin the dialogue “by shelving the current health spending bill.”

“The fact is Senate Republicans held hundreds of town halls and met with their constituents across the country last year on the need for health care reform, outlining ideas for the step-by-step approach that Americans have asked for,” Mr. McConnell said in a statement. “And we know there are a number of issues with bipartisan support that we can start with when the 2,700-page bill is put on the shelf.”
Obama said that he does not intend to start from scratch but that he is interested in listening to (and incorporating) any good ideas presented by Republicans. It will be up to him to ensure that the meeting stays focused and operates as a working session to discuss specific issues and that it not get dragged into the kind of demagoguery the Republicans thrive on.

I hope he succeeds. I suspect that this step will improve his public ratings. His critics will argue that his rating are improved (if they are) because he is reaching out to Republicans. I don't think so. If there is an improvement, it will be because he is seen as finally taking some action. In this case the action is putting it to the Republicans: put up or shut up. After that challenge is met, we can then move on and actually get a bill passed.

A molecular millisecond

By Brian Hayes
In the living cell, biological macromolecules do not sit immobile like bronze statues. They are machines with moving parts; they continually flex and wiggle, mesh and then disengage, spin, flap, bend, stretch; all day long they do a hyperkinetic hokey-pokey.

I have now seen a remarkable performance of that molecular dance. In a talk at Harvard earlier this week David E. Shaw showed two videos, each portraying about a millisecond in the life of a single protein molecule. A millisecond may not sound like much, but the video was created by computing atomic motions at roughly one step per femtosecond. That’s 1012 steps in all. (If you included all the steps in the video, and displayed them at 60 frames per second, the show would go on for 500 years.) …

Watching them in the lecture hall, I was so bedazzled that I neglected to note the identity of the molecules. One was an ion channel, a protein that spans the width of a membrane and controls the passage of some specific ion (potassium, I think, in this case). We watched the six polypeptide strands twisting closed like the blades of a camera iris, shutting off the channel. Another simulation showed an even more dramatic reconfiguration. For many microseconds of biological time, and perhaps half a minute of wall-clock time, the protein sat nervously quivering and fidgeting, hunched up in a compact globule, with occasional minor adjustments to various loops and corners. And then suddenly the whole molecule opened up like a flower blooming; a moment later it closed again. If I understand correctly what Shaw was telling us, the existence of this alternative state had been known from experimental evidence, but the transformation had never been seen before. And, as he remarked early in the talk, “seeing what it looks like” brings a level of understanding that would be hard to achieve by more analytic methods.

Ethical behavior

By Andrew Olendzki in Removing the Thorn | Tricycle Magazine.
According to the Buddha, the human world is protected by twin guardians, two forces in the mind that watch over and guide moral behavior. The first guardian of the world is hiri, a word that connotes conscience, moral intuition, and self-respect. It refers to that within the human psyche that knows the difference between right and wrong, between what is noble and ignoble, between what is worthy of respect and what is not. Each of us has within us an innate moral compass, and it is the view of the Buddhist tradition that religion is not the source of this but rather a form by which it is given expression. The second guardian of the world is ottappa, which comprises such notions as social conscience, a cultural or collective sense of morality, and respect for the opinions and the rights of others.

Buddhism teaches that anything we do that is wholesome will be done with the support and guidance of these two inner guardians. Conversely, everything we do that is unwholesome can only be done when these moral guides are disregarded. So if there is something morally reprehensible occurring in an individual or in a society, it means that we lack sufficient clarity of awareness of what we are doing. It means we are temporarily blinded by our greed, hatred, or delusion, or by some combination of the three, such that we refuse to attend openly to the deeds we are committing. When attention has been brought to bear on the matter—in sufficient amounts, with sufficient intensity, and with sufficient honesty—we will naturally shy away from doing harm to ourselves, to others, and to both.
This distinguishes Buddhism from religions that insist that the only reason people behave ethically is fear of God's punishment.

This is also consistent with current theories of evolutionary biology that explain how individual behaviors and societal norms evolve and are maintained.

Friday, February 05, 2010

Ancient dialect extinct after last speaker dies

One of the world's oldest dialects, which traces its origins to tens of thousands of years ago, has become extinct after the last person to speak it died on a remote Indian island.

Boa Sr, the 85-year-old last speaker of 'Bo,' was the oldest member of the Great Andamanese tribe, R.C. Kar, deputy director of Tribal Health in Andaman, told Reuters on Friday.

She died last week in Port Blair, the capital of Andaman and Nicobar Islands, which were hit by a devastating tsunami in 2004.

'With the death of Boa Sr and the extinction of the Bo language, a unique part of human society is now just a memory,' said Stephen Corry, director of Survival International, an organization that supports tribes worldwide."
See also The Hindu where the picture is captioned "JNU professor Anvita Abbi with Boa, one of the last surviving speakers of the unique Great Andamanese languages"

Tuesday, February 02, 2010

Philips Uday mini solar lantern

Philips Uday mini solar lantern
4-5 hours of bright white light per solar charge
Looks ugly; sounds great. What does it take to give it a full charge?


Monday, February 01, 2010

The psychology of power: Absolutely

From The Economist reporting on studies of how people with power behave.
People with power that they think is justified break rules not only because they can get away with it, but also because they feel at some intuitive level that they are entitled to take what they want. This sense of entitlement is crucial to understanding why people misbehave in high office. In its absence, abuses will be less likely. The word “privilege” translates as “private law”. If Dr Lammers and Dr Galinsky are right, the sense which some powerful people seem to have that different rules apply to them is not just a convenient smoke screen. They genuinely believe it.