PTI
Politics: Reserved For Idiots?Rajinder Puri writes in Outlook May29, 2008
One year ago the Gujjar agitation in Rajasthan -- demanding Scheduled Tribe (ST) status to get job reservation -- resulted in police firing and over 20 deaths. This weekend Gujjar-police clashes left over 30 dead. ...
One year ago the Gujjar agitation in Rajasthan resulted in police firing and over 20 deaths. This weekend Gujjar-police clashes left over 30 dead. Over 50 people have already lost their lives demanding Scheduled Tribe (ST) status to get job reservation for their community. After the Gujjar riots halted last year this scribe wrote: “Those who think the crisis has ended need to re-think. The crisis has begun.” Both government and opposition leaders have offered no solutions. They continue to parrot their stupid formulations about caste-based social justice.
The Gujjars have job reservation in the OBC quota. They seek reservation in the ST quota. They think prospects under ST quota would be better than under the OBC quota. In Rajasthan the Jats have hogged the OBC quota. The Meenas have hogged the ST quota. The Meenas are more affluent than the Gujjars. The British listed both the Meenas and the Gujjars as “criminal tribes”. The Gujjars rebelled against the British. They robbed and looted British garrisons. That is why the British classified them as a criminal tribe.
Given this history, why should Gujjars be denied ST status? Never mind that a hundred years ago the Gujjars were demanding recognition as Kshatriyas, a powerful forward caste. In the insane political context created by India’s leaders the Gujjars are also seeking “social justice”. Going down the social ladder helps folk climb up the economic ladder. So it seems is the current wisdom propagated by India’s politicians. Why don’t Dr Manmohan Singh, Arjun Singh, Laloo Yadav, Sharad Yadav, Mulayam Singh Yadav, Prakash Karat and LK Advani take up the Gujjar cause? Are Gujjar votes insufficient to counter the Meena vote, the Jat vote and the Yadav vote? Or is it that our politicians as frightened chickens simply cannot comment on an issue which like Pandora’s Box could unleash all kinds of dire possibilities?
There are over 3000 listed castes among the OBCs alone. In a caste-based reservation system is it not inevitable that such demands and grievances will never stop proliferating? VP Singh had no idea about the complexities of the issue when in pursuit of short term political advantage he recklessly unleashed the Mandal formula which itself is flawed. Dr Lohia and Charan Singh during certain periods of their political careers also favoured caste-based reservation. History tells us that both leaders were mistaken. No leader like God is above human error. However exalted their lives we will pledge blind allegiance to the mistaken policies of past icons at our own grave peril.
Caste-based reservation as a quick-fix for getting strictly limited political support has no real value. Once VP Singh took it up as a political issue his support has continuously shrunk. Today it is pathetic. The Yadav leaders are limited really to their own caste. They attempt to augment strength through tactical alliances with other castes and communities. Politics in India therefore has degenerated to tribal interaction devoid of national policy or relevance.
The most ironical aspect of this issue is that reservation on the basis of caste is unconstitutional. The Supreme Court signally failed to discharge its responsibility by failing to enunciate this. Earlier this scribe had quoted Article 16 (2) of the Constitution to assert this. There has been no convincing rebuttal from any quarter until now. If caste-based reservation is constitutional, so would religion-based or region-based reservation be constitutional?
Neither politicians nor the judiciary display the guts to address the issue courageously.The Indian establishment seems totally overwhelmed by false conventions and traditions that are in no way sanctified by law. Unless there is radical reappraisal of India’s political system and culture, the nation will continue to blunder from crisis to crisis.
Friday, May 30, 2008
Interview withNoam Chomsky by Gabriel Matthew Schivone
United States of Insecurity: Perils and Alternatives in the Post 9-11 World
Based on an interview with Noam Chomsky conducted by Gabriel Matthew Schivone via telephone and e-mail at the Massachusetts Institute of Technology, November 27, 2007 through February 11, 2008. Parts of the text have been expanded by the author. Published in Monthly Review.
A State of Insecurity in the Post-9/11 World
GMS: In a recent interview, Abdel Bari Atwan, author and editor of the London-based Arabic daily newspaper Al-Quds Al Arabi, said that President Bush is not ending terrorism nor is he weakening it, as is one of his strongest assertions in his so-called "War on Terror", but that now Al-Qa'ida has powerfully developed into more of an ideology than an organization, as Atwan describes, expanding like Kentucky Fried Chicken, opening franchises all over the world. "That's the problem," he says. "The Americans are no safer. Their country is a fortress now, the United States of Security." Is this accurate?
CHOMSKY: Except for the last sentence, it's accurate. There's good reason to think that the United States is very vulnerable to terrorist attacks. That's not my opinion, that's the opinion of US intelligence, of specialists of nuclear terror like Harvard professor Graham Allison, and former Defense Secretary Robert McNamara and others, who have warned that the probability of even a nuclear attack in the United States is not trivial. So, it's not a fortress.
One of the things that Bush hasn't been doing is improving security. So, for example, if you look at the government commission after 9-11, one of its recommendations—which is a natural one—is to improve security of the US-Canadian border. I mean, if you look at that border, it's very porous. You or I could walk across it somewhere with a suitcase holding components of a nuclear bomb. The Bush administration did not follow that recommendation. What it did instead was fortify the Mexican border, which was not regarded as a serious source of potential terrorism. They in fact slowed the rate of growth of border guards on the Canadian Border.
But quite apart from that, the major part of Atwan's comment is quite correct. Bush Administration programs have not been designed to reduce terror. In fact, they've been designed in a way—as was anticipated by intelligence analysts and others—to increase terror.
So take, say, the invasion of Iraq. It was expected that that would probably have the effect of increasing terror—and it did, though far more than was anticipated. There was a recent study by two leading terrorism experts (using RAND Corporation government data) which concluded that what they called the "Iraq effect" -- meaning, the effect of the Iraq invasion on incidents of terror in the world -- was huge. In fact, they found that terror increased about seven-fold after the invasion of Iraq. That's quite an increase—a lot more than was anticipated.
Also, the invasion increased the threat of nuclear proliferation—for very good reason. One of Israel's leading historians, Martin van Creveld, discussing the possibility of Iran developing a bomb, pointed out the obvious. He said that, after the invasion of Iraq, if Iran isn't developing a nuclear deterrent, "they're crazy" (that's his word, "crazy"). Why? Because the United States made it explicit that it is willing to invade any country it likes, as long as that country can't defend itself. —It was known that Iraq was basically defenseless. Well, that sends a message to the world. It says, "If you don't obey what the US demands, they can invade you, so you better develop a deterrent."
Nobody's going to compete with the United States in a military capacity. I mean, the US spends as much on the military as the rest of the world combined, and it's far more sophisticated and advanced. So, what they'll do is turn to weapons of the weak. And weapons of the weak are basically two: terror and nuclear weapons.
So, sure, the invasion of Iraq predictably increased the threat of terror and of proliferation, and the same is true of other actions. And we can continue. One of the major parts of the so-called "war on terror" is an effort to carry out surveillance and control of financial interactions which enter into terrorist activities. Well, yeah, that's been going on. But according to the Treasury Bureau [Office of Foreign Assets Control] that's been responsible for it, they're spending far more time and energy on possible violations on the US embargo on Cuba than they are on Al Qa'ida transactions.
Why would elites be making the United States, as you say, more vulnerable to attacks in the future? It doesn't seem reasonable, logically speaking, as educated, sensible, intelligent people, that they'd endanger themselves personally and endanger their families, in the short- or long-term, with raising the threat of terror to manifold levels now. Terror would surely threaten them personally, especially with regard to more attacks being committed inside the U.S. and throughout the world. I mean, isn't there something peculiar in this sort of behavior?
I think there's something pathological about it but it's not peculiar. I mean, if you look at it within the framework of elite perceptions, it has a kind of rationality. Short-term considerations of profit and power quite often tend to overwhelm longer term considerations of security and welfare, even for your own children.
I mean, take environmental concerns. Take, say, lead. It was known in the early 1920s by the huge corporations that were producing lead-based products that lead was poisonous. They knew it. We now know—there's been extensive discussion and revelations—and they knew it right away. But they concealed it. And they paid huge amounts of money and effort and legal maneuvers and lobbying and so on to prevent any constraints on it. Well, you know, those windowsills poisoned with lead paint are going to harm their own children, but the interests of profit overwhelmed it. And that's standard.
And take, say, tobacco. It's been known for decades, from the very beginning, that it's a very poisonous product. That didn't stop the tobacco producers from trying to get everyone possible to smoke. Make women smoke, children and others—even their own. These are conflicting demands of profit and power on the one hand, and care about even your own family on the other hand. And very commonly profit and power win out. I think it's pathological. But it's not a pathology of individuals, it's a pathology of social institutions.
When you say the common loyalty to power and profit among elites superseding any care of other human beings is a "pathology of social institutions" and not individuals, are you referring to certain values of American society?
It is not specific to American society. These are institutional properties of semi-competitive state capitalist societies.
Suppose, for example, that there are three US-based conglomerates that produce automobiles: GM, Ford, Chrysler (no longer). They were able to gain their status through substantial reliance on a powerful state, and they were able to survive the 1980s only because the president, Ronald Reagan, was the most protectionist in post-war history, virtually doubling protective barriers to save these and other corporations from being taken over by more advanced Japanese industry. But they (more or less) survive.
Suppose that GM invests in technology that will produce better, safer, more efficient cars in 20 years, but Ford and Chrysler invest in cars that will sell tomorrow. Then GM will not be here in 20 years to profit from its investment. The logic is not inexorable, but it yields very significant anti-social tendencies.
The Predatory Reach of Private Power
Since the so-called "reconstruction" throughout the wake of Hurricane Katrina in 2004, one of the policy-initiatives championed by the Bush Administration right up to the present was the dismantling of the New Orleans public school system. The New York Times reported that, of those who could return, children and families were coming back to a "much different" New Orleans with "a smaller [educational] system dominated by new charter schools", along with the termination of nearly 7000 public school employees. What are the implications of private control of public resources, such as education, in this instance, or healthcare, telecommunications, social security, etc.?
Well, there are actually two components to that, both of them leading themes of the Bush Administration's domestic policies, and of reactionary policies generally. One of them is, to put it simply, to put as many dollars as you can in the pockets of your rich friends: that is, to increase profits for the wealthy—to increase the wealth and power of concentrated, private capital. That's one driving force in the administration's policy. The other is to break down the social bonds that lead to people having sympathy and supportive feelings about one another. That contributes to transferring profit and decision-making into the hands of concentrated private power. A component of that is to undermine the normal relations—sympathy and solidarity—that people have.
Take social security. Social security is based on a bond among people. If you earn a salary today—somebody your age—[young people of twenty or so] you're paying for the welfare and survival of your parents' generation. Well, okay, that's a natural feeling. If you want to increase the control of concentrated private power you have to drive that out of people's heads. You have to create the kind of people that Ayn Rand is talking about, where you're after your own welfare and you don't care what happens to anyone else. You have to think, "Why do I have to care about that disabled woman across town who doesn't have enough food to eat? I didn't do it to her. That's her problem. She and her husband didn't invest properly; she didn't work hard enough, so what do I care if she starves to death?" Well, you have to turn people into pathological monsters who think that way, if you want to ensure that unaccountable, concentrated, private power will dominate the world and enrich itself. So, these things go together.
I don't happen to have children in the local school—I did, but my kids are all grown up. So, if I were to follow this line of reasoning, I would say, "Well, why should I pay taxes? My kids don't go to school; I'm not getting anything out of it. What do I care if the kid across the street doesn't go to school?" You can turn people into pathological monsters who think like that. And eliminating the public school system is one part of it.
The public school system is a sign of solidarity, sympathy and concern of people in general—even if it doesn't benefit me, myself. There's a pathological brand of what's called Libertarianism which wants to eliminate that and turn you into a monster who cares only about yourself. And that's one aspect of undermining democracy, and undermining the attitudes that underlie democracy, namely, that there should be a concern for others and a communal way of reacting to community concerns.
Well, let's consider the elimination of the public school system altogether. Would that imply something like what we see in countries in the Third World, where those who can afford to send their children to school, do, and much of the remaining population simply does not have an education? Is this a direction private power might be moving toward in this country?
There are significant forces driving the country in that direction, quite apart from Bush-style reactionaries seeking to enrich the powerful and let the rest fend somehow for themselves.
Take the reliance for school funding on property taxes. In earlier years, when communities were not so sharply separated between rich and poor, that may have been more or less acceptable. Today it means that the wealthy suburbs have better schools than impoverished urban or rural areas. That's only the bare beginning. Suburban elites who work downtown do not have to pay the taxes to keep the city viable for them; that burden falls disproportionately on the poor. Studies of public transportation have shown that the poorer subsidize the richer and more privileged. And these measures proliferate in numerous ways.
The Iraq War: Responsibility and Resistance
Everywhere from high school and college campuses to bus stops and dinner tables, we hear a lot about what a "quagmire" and "costly mess" Iraq has become for the United States, now being blamed as a Republican war, for how the Bush Administration handled the occupation—that ‘it should've been done this or that way'—and ‘now that we're there we can't leave, it's our ‘responsibility' to fix the problem we made because it'll only get worse if we leave—those people will kill each other', and so on. What do you say to these arguments that seem to interweave with each other? And what would you suggest in terms of what some might call an ‘honorable solution'? International measures, immediate withdrawal—both?
The position of the liberal doves during the Vietnam War was articulated lucidly by historian and Kennedy advisor Arthur Schlesinger, when the war was becoming too costly for the US and they began their shift from hawk to dove. He wrote that "we all pray" that the hawks will be right in believing that the surge of the day will work, and if they are, we "may be saluting the wisdom and statesmanship of the American government" in gaining victory in a land that they have left in "wreck and ruin." But it probably won't work, so strategy should be rethought. The principles, and the reasoning, carry over with little change to the Iraq invasion.
There is no "honorable solution" to a war of aggression—the "supreme international crime" that differs from other war crimes in that it encompasses all the evil that follows, in the wording of the Nuremberg Tribunal, which condemned Nazi war criminals to death for such crimes as "pre-emptive war." We can only seek the least awful solution. In doing so, we should bear in mind some fundamental principles, among them, that aggressors have no rights, only responsibilities.
The responsibilities are to pay enormous reparations for the harm they have caused, to hold the criminals responsible accountable, and to pay close attention to the wishes of the victims. In this case, we know their wishes quite well. Poll after poll has yielded results similar to those reported by the military in December, after a study of focus groups around the country. They report that Iraqis from all over the country and all walks of life have "shared beliefs," which they enumerated: The American invasion is to blame for the sectarian violence and other horrors, and the invaders should withdraw, leaving Iraq—or what's left of it—to Iraqis.
It tells us a lot about our own moral and intellectual culture that the voice of Iraqis, though known, is not even considered in the thoughtful and comprehensive articles in the media reviewing the options available to Washington. And that there is no comment on this rather striking fact, considered quite natural.
Is there anyone saying the war was fundamentally wrong?
In the case of Vietnam, years after Kennedy's invasion, liberal doves began to say that the war began with "blundering efforts to do good" but by 1969 it was clear that it was a mistake that was too costly to us (Anthony Lewis, at the critical extreme, in the New York Times). In the same year, 70% of the public regarded the war as not "a mistake" but "fundamentally wrong and immoral." That gap between public and elite educated opinion persists until the most recent polls, a few years ago.
In the media and journals, it is very hard to find any voice that criticizes the invasion or Iraq on principled grounds, though there are some. Arthur Schlesinger, for example, took a very different position than he did on Vietnam. When the bombs started falling on Baghdad he quoted President Roosevelt's condemnation of the Japanese attack on Pearl Harbor as "a date which will live in infamy." Now, Schlesinger wrote, it is Americans who live in infamy as their government follows the path of fascist Japan. But that was a lone voice among elites.
Dissidents, of course, describe "the supreme international crime" as fundamentally wrong. I haven't seen polls about public attitudes on this question.
What about when it is that people know to undertake more serious or severe resistance efforts after the point at which "the limits of possible protest" are reached? In a letter to George Steiner in the NYR, in 1967, you gave the example of what this might look like, now 60 years ago during the Spanish Civil War, when people found it quite necessary to join international brigades to fight against the army of their own country; or, applied to Vietnam, the possible action one might undertake in such circumstances of travelling to Hanoi as a hostage against further bombing. —That's pretty far-reaching, relatively speaking, to what we see in current resistance efforts today against the war. What's your feeling about the possibilities for such methods today in relation to the Iraq war, border action, or other criminal policy in the Middle East and elsewhere? Do situations have to get worse before people or individuals might deem this sort of action necessary?
In the case of Vietnam, serious resistance began several years after Kennedy's invasion of South Vietnam. I was one of a few people trying to organize national tax resistance in early 1965, at a time when South Vietnam, always the main target, was being crushed by intensive bombing and other crimes. By 1966-67, refusal to serve in the invading army was beginning to become a significant phenomenon, along with support for resistance by organized groups, primarily RESIST, formed in 1967 (and still functioning). By then the war had passed far beyond the invasion of Iraq in destructiveness and violence. In fact, at any comparable stage, protest against the Iraq invasion considerably exceeds anything during the Indochina wars.
As for living with the victims to help them or provide them some measure of protection, that is a phenomenon of the 1980s, for the first time in imperial history, to my knowledge, in reaction to Reagan's terrorist wars that devastated Central America, one of his many horrendous crimes. The solidarity movements that took shape then have now extended worldwide, though only in limited ways to Iraq, because the catastrophe created by Cheney-Rumsfeld-Wolfowitz and the rest is so extraordinary that it is almost impossible to survive in the wreckage—the main reason why reporting is so skimpy; it is simply too dangerous, unlike earlier wars of imperial aggression.
A Question of Neutrality in the Schools
Let's talk about the role of intellectuals in all of this. Here's a question that might be relevant for students to hear especially: You've suggested that the major inducements to becoming absorbed into the ideology of the overall scholarship in this country, largely subservient to power interests, are the significant rewards in prestige and affluence, as well as access to power and authority. So, what are some of the things you've observed in your own time in the academy as a kind of source of this process in American education?
Educational institutions like universities don't exist in a social vacuum; they rely for their existence on the external resources of the society. They rely on the state and contributions from, basically, the wealthy. And the state and the wealthy sectors are very closely linked. So, the universities are in a certain social system in which they reflect a certain distribution of power. They're embedded in it. And that means the struggle for university independence—or independence of thought, and willingness to challenge—that's a hard struggle. You're struggling against social conditions that militate against it.
And it's true, what you said is correct, there are rewards and privileges that come along with conformity, but there's more to say. There are also punishments and abuse, loss of jobs, and so on, that come from challenging systems of power. Both factors operate. So, yes, there's a constant struggle to try and maintain university independence, and it's a hard one.
Sometimes it's argued that the universities should just be neutral, that they shouldn't take positions on anything. Well, there's merit in that, I would like to see that in some abstract universe, but in this universe what that position entails is conformity to the distribution of external power.
So let me take a concrete case, aspects of which are still very much alive on my own campus. Let's take some distance so we can see things more clearly. Back in the 1960s, in my university, MIT, the political science department was carrying out studies with students and faculty on counterinsurgency in Vietnam. Okay, that reflected the distribution of power in the outside society. The US is involved in counterinsurgency in Vietnam: it's our patriotic duty to help. A free and independent university would have been carrying out studies on how poor peasants can resist the attack of a predatory superpower. Can you imagine how much support that would have gotten on campus? Well, okay, that's what neutrality turns into when it's carried out—when the ideal, which is a good ideal, is pursued unthinkingly. It ends up being conformity to power.
Let's take a current case. Right now there's a lot of concern about nuclear weapons in Iran. Well, again, take my own campus, MIT. In the 1970s Iran was under the rule of a brutal tyrant who the United States and Britain had imposed by force in a military coup overthrowing the democratic government. So Iran was therefore an ally. Well, in the government, people like Henry Kissenger, Dick Cheney, Donald Rumsfeld, Paul Wolfowitz and others, were calling for Iran to develop nuclear capacities and nuclear power and so on, which means a step short of nuclear weapons. And my own university, MIT, made an arrangement with the Shah of Iran, the dictator, to train Iranian nuclear engineers. It was the 1970s. There was enormous student protest about that. But very little faculty protest, in fact, the faculty approved it. And it was instituted. In fact, some of the people now running the Iranian nuclear programs are graduates of MIT. Well, is the university neutral in those respects? No, not really; it's conforming to power interests. In this case, to go back to an earlier part of our conversation, they did conform to short-term commitments to power and profit but with long-term consequences that were quite harmful to the very same people who instituted them.
Henry Kissinger, who at least has the virtue of honesty, was asked by the Washington Post why he is now objecting to same Iranian programs that he was instrumental in instituting when he was in office back in the 70s. And he said, frankly, Well, they were an ally then. They needed nuclear power. And now they are an enemy so they don't need nuclear power.
Okay, he's a complete cynic, but he's an honest one, fortunately. But should universities take that position?
By Steady Drips of Water: Activism and Social Change
For the last question I'd like to talk a little about providing alternatives, for people trying to figure out things, searching for answers, seeing through propaganda, developing solidarity, initiating movements. Here's a good quote I came across that might be a good starting point, from the notable novelist E.M. Forster, writing at the beginning stages of the Second World War, in 1939, in his essay "What I Believe":
"I do not believe in Belief. But this is an age of faith, and there are so many militant creeds that, in self-defense, one has to formulate a creed of one's own. Tolerance, good temper and sympathy...in a world rent by religious and racial persecution, in a world where ignorance rules, and science, who ought to have ruled, plays the subservient pimp." He repeats: "Tolerance, good temper and sympathy—they are what matter really, and if the human race is not to collapse they must come to the front before long."
What are some of the things he's getting at here that we can discuss in terms of alternatives for the future, and social organization?
I'm often asked questions like that, in maybe a dozen emails a night or in talks and so on, and I'm always at a loss to answer. Not because I can't think of an answer, but because I think we all know the answer. There aren't any magic keys here; there are no mysterious ways of approaching things. What it takes is just what has led to progress and success in the past. We live in a much more civilized world than we did even when Forster was writing, in many respects.
Say, women's rights, or opposition to torture—or even opposition to aggression—environmental concerns, recognition of some of the crimes of our own history, like what happened to the indigenous population. We can go on and on. There's been much improvement in those areas. How? Well, because people like those working in alternative media, or those we never hear about who are doing social organizing, community building, political action, etc., engage themselves in trying to do something about it.
And the modes of engagement are not mysterious. You have to try and develop a critical, open mind, and you have to be willing to evaluate and challenge conventional beliefs—accept them if they turn out to be valid, but reject them if—as is so often the case—they turn out to just reflect power structures. And then proceed with educational and organizing activities, actions as appropriate to circumstances. There is no simple formula; rather, lots of options. And gradually over time, things improve. I mean, even the hardest rock will be eroded by steady drips of water. That's what social change comes to and there are no mysterious modes of proceeding. They're hard ones, demanding ones, challenging, often costly. But that's what it takes to get a better world.
Noam Chomsky is an Institute Professor of Linguistics at the Massachusetts Institute of Technology. Perhaps one of the most revered thinkers of the twentieth century and tireless advocate for honorable peace and social justice, he lectures and writes widely on American foreign policy and world affairs. His latest books are Interventions (City Lights) and Failed States (Metropolitan Books).
Gabriel Matthew Schivone is an editor of Days Beyond Recall Alternative Media and Literary Journal. His articles, having been translated into multiple languages, have appeared in numerous journals such as Z Magazine, Counterpunch and the Monthly Review, as well as Contre Info (France), and Caminos (Cuba). He is most recently the recipient of the 2007 Frederica Hearst Prize for Lyrical Poetry. He is also an active member of the UA Chapter of Amnesty International, Voices of Opposition (to War, Racism and Oppression), Dry River Radical Resource Center, and Students Organized for Animal Rights.
Based on an interview with Noam Chomsky conducted by Gabriel Matthew Schivone via telephone and e-mail at the Massachusetts Institute of Technology, November 27, 2007 through February 11, 2008. Parts of the text have been expanded by the author. Published in Monthly Review.
A State of Insecurity in the Post-9/11 World
GMS: In a recent interview, Abdel Bari Atwan, author and editor of the London-based Arabic daily newspaper Al-Quds Al Arabi, said that President Bush is not ending terrorism nor is he weakening it, as is one of his strongest assertions in his so-called "War on Terror", but that now Al-Qa'ida has powerfully developed into more of an ideology than an organization, as Atwan describes, expanding like Kentucky Fried Chicken, opening franchises all over the world. "That's the problem," he says. "The Americans are no safer. Their country is a fortress now, the United States of Security." Is this accurate?
CHOMSKY: Except for the last sentence, it's accurate. There's good reason to think that the United States is very vulnerable to terrorist attacks. That's not my opinion, that's the opinion of US intelligence, of specialists of nuclear terror like Harvard professor Graham Allison, and former Defense Secretary Robert McNamara and others, who have warned that the probability of even a nuclear attack in the United States is not trivial. So, it's not a fortress.
One of the things that Bush hasn't been doing is improving security. So, for example, if you look at the government commission after 9-11, one of its recommendations—which is a natural one—is to improve security of the US-Canadian border. I mean, if you look at that border, it's very porous. You or I could walk across it somewhere with a suitcase holding components of a nuclear bomb. The Bush administration did not follow that recommendation. What it did instead was fortify the Mexican border, which was not regarded as a serious source of potential terrorism. They in fact slowed the rate of growth of border guards on the Canadian Border.
But quite apart from that, the major part of Atwan's comment is quite correct. Bush Administration programs have not been designed to reduce terror. In fact, they've been designed in a way—as was anticipated by intelligence analysts and others—to increase terror.
So take, say, the invasion of Iraq. It was expected that that would probably have the effect of increasing terror—and it did, though far more than was anticipated. There was a recent study by two leading terrorism experts (using RAND Corporation government data) which concluded that what they called the "Iraq effect" -- meaning, the effect of the Iraq invasion on incidents of terror in the world -- was huge. In fact, they found that terror increased about seven-fold after the invasion of Iraq. That's quite an increase—a lot more than was anticipated.
Also, the invasion increased the threat of nuclear proliferation—for very good reason. One of Israel's leading historians, Martin van Creveld, discussing the possibility of Iran developing a bomb, pointed out the obvious. He said that, after the invasion of Iraq, if Iran isn't developing a nuclear deterrent, "they're crazy" (that's his word, "crazy"). Why? Because the United States made it explicit that it is willing to invade any country it likes, as long as that country can't defend itself. —It was known that Iraq was basically defenseless. Well, that sends a message to the world. It says, "If you don't obey what the US demands, they can invade you, so you better develop a deterrent."
Nobody's going to compete with the United States in a military capacity. I mean, the US spends as much on the military as the rest of the world combined, and it's far more sophisticated and advanced. So, what they'll do is turn to weapons of the weak. And weapons of the weak are basically two: terror and nuclear weapons.
So, sure, the invasion of Iraq predictably increased the threat of terror and of proliferation, and the same is true of other actions. And we can continue. One of the major parts of the so-called "war on terror" is an effort to carry out surveillance and control of financial interactions which enter into terrorist activities. Well, yeah, that's been going on. But according to the Treasury Bureau [Office of Foreign Assets Control] that's been responsible for it, they're spending far more time and energy on possible violations on the US embargo on Cuba than they are on Al Qa'ida transactions.
Why would elites be making the United States, as you say, more vulnerable to attacks in the future? It doesn't seem reasonable, logically speaking, as educated, sensible, intelligent people, that they'd endanger themselves personally and endanger their families, in the short- or long-term, with raising the threat of terror to manifold levels now. Terror would surely threaten them personally, especially with regard to more attacks being committed inside the U.S. and throughout the world. I mean, isn't there something peculiar in this sort of behavior?
I think there's something pathological about it but it's not peculiar. I mean, if you look at it within the framework of elite perceptions, it has a kind of rationality. Short-term considerations of profit and power quite often tend to overwhelm longer term considerations of security and welfare, even for your own children.
I mean, take environmental concerns. Take, say, lead. It was known in the early 1920s by the huge corporations that were producing lead-based products that lead was poisonous. They knew it. We now know—there's been extensive discussion and revelations—and they knew it right away. But they concealed it. And they paid huge amounts of money and effort and legal maneuvers and lobbying and so on to prevent any constraints on it. Well, you know, those windowsills poisoned with lead paint are going to harm their own children, but the interests of profit overwhelmed it. And that's standard.
And take, say, tobacco. It's been known for decades, from the very beginning, that it's a very poisonous product. That didn't stop the tobacco producers from trying to get everyone possible to smoke. Make women smoke, children and others—even their own. These are conflicting demands of profit and power on the one hand, and care about even your own family on the other hand. And very commonly profit and power win out. I think it's pathological. But it's not a pathology of individuals, it's a pathology of social institutions.
When you say the common loyalty to power and profit among elites superseding any care of other human beings is a "pathology of social institutions" and not individuals, are you referring to certain values of American society?
It is not specific to American society. These are institutional properties of semi-competitive state capitalist societies.
Suppose, for example, that there are three US-based conglomerates that produce automobiles: GM, Ford, Chrysler (no longer). They were able to gain their status through substantial reliance on a powerful state, and they were able to survive the 1980s only because the president, Ronald Reagan, was the most protectionist in post-war history, virtually doubling protective barriers to save these and other corporations from being taken over by more advanced Japanese industry. But they (more or less) survive.
Suppose that GM invests in technology that will produce better, safer, more efficient cars in 20 years, but Ford and Chrysler invest in cars that will sell tomorrow. Then GM will not be here in 20 years to profit from its investment. The logic is not inexorable, but it yields very significant anti-social tendencies.
The Predatory Reach of Private Power
Since the so-called "reconstruction" throughout the wake of Hurricane Katrina in 2004, one of the policy-initiatives championed by the Bush Administration right up to the present was the dismantling of the New Orleans public school system. The New York Times reported that, of those who could return, children and families were coming back to a "much different" New Orleans with "a smaller [educational] system dominated by new charter schools", along with the termination of nearly 7000 public school employees. What are the implications of private control of public resources, such as education, in this instance, or healthcare, telecommunications, social security, etc.?
Well, there are actually two components to that, both of them leading themes of the Bush Administration's domestic policies, and of reactionary policies generally. One of them is, to put it simply, to put as many dollars as you can in the pockets of your rich friends: that is, to increase profits for the wealthy—to increase the wealth and power of concentrated, private capital. That's one driving force in the administration's policy. The other is to break down the social bonds that lead to people having sympathy and supportive feelings about one another. That contributes to transferring profit and decision-making into the hands of concentrated private power. A component of that is to undermine the normal relations—sympathy and solidarity—that people have.
Take social security. Social security is based on a bond among people. If you earn a salary today—somebody your age—[young people of twenty or so] you're paying for the welfare and survival of your parents' generation. Well, okay, that's a natural feeling. If you want to increase the control of concentrated private power you have to drive that out of people's heads. You have to create the kind of people that Ayn Rand is talking about, where you're after your own welfare and you don't care what happens to anyone else. You have to think, "Why do I have to care about that disabled woman across town who doesn't have enough food to eat? I didn't do it to her. That's her problem. She and her husband didn't invest properly; she didn't work hard enough, so what do I care if she starves to death?" Well, you have to turn people into pathological monsters who think that way, if you want to ensure that unaccountable, concentrated, private power will dominate the world and enrich itself. So, these things go together.
I don't happen to have children in the local school—I did, but my kids are all grown up. So, if I were to follow this line of reasoning, I would say, "Well, why should I pay taxes? My kids don't go to school; I'm not getting anything out of it. What do I care if the kid across the street doesn't go to school?" You can turn people into pathological monsters who think like that. And eliminating the public school system is one part of it.
The public school system is a sign of solidarity, sympathy and concern of people in general—even if it doesn't benefit me, myself. There's a pathological brand of what's called Libertarianism which wants to eliminate that and turn you into a monster who cares only about yourself. And that's one aspect of undermining democracy, and undermining the attitudes that underlie democracy, namely, that there should be a concern for others and a communal way of reacting to community concerns.
Well, let's consider the elimination of the public school system altogether. Would that imply something like what we see in countries in the Third World, where those who can afford to send their children to school, do, and much of the remaining population simply does not have an education? Is this a direction private power might be moving toward in this country?
There are significant forces driving the country in that direction, quite apart from Bush-style reactionaries seeking to enrich the powerful and let the rest fend somehow for themselves.
Take the reliance for school funding on property taxes. In earlier years, when communities were not so sharply separated between rich and poor, that may have been more or less acceptable. Today it means that the wealthy suburbs have better schools than impoverished urban or rural areas. That's only the bare beginning. Suburban elites who work downtown do not have to pay the taxes to keep the city viable for them; that burden falls disproportionately on the poor. Studies of public transportation have shown that the poorer subsidize the richer and more privileged. And these measures proliferate in numerous ways.
The Iraq War: Responsibility and Resistance
Everywhere from high school and college campuses to bus stops and dinner tables, we hear a lot about what a "quagmire" and "costly mess" Iraq has become for the United States, now being blamed as a Republican war, for how the Bush Administration handled the occupation—that ‘it should've been done this or that way'—and ‘now that we're there we can't leave, it's our ‘responsibility' to fix the problem we made because it'll only get worse if we leave—those people will kill each other', and so on. What do you say to these arguments that seem to interweave with each other? And what would you suggest in terms of what some might call an ‘honorable solution'? International measures, immediate withdrawal—both?
The position of the liberal doves during the Vietnam War was articulated lucidly by historian and Kennedy advisor Arthur Schlesinger, when the war was becoming too costly for the US and they began their shift from hawk to dove. He wrote that "we all pray" that the hawks will be right in believing that the surge of the day will work, and if they are, we "may be saluting the wisdom and statesmanship of the American government" in gaining victory in a land that they have left in "wreck and ruin." But it probably won't work, so strategy should be rethought. The principles, and the reasoning, carry over with little change to the Iraq invasion.
There is no "honorable solution" to a war of aggression—the "supreme international crime" that differs from other war crimes in that it encompasses all the evil that follows, in the wording of the Nuremberg Tribunal, which condemned Nazi war criminals to death for such crimes as "pre-emptive war." We can only seek the least awful solution. In doing so, we should bear in mind some fundamental principles, among them, that aggressors have no rights, only responsibilities.
The responsibilities are to pay enormous reparations for the harm they have caused, to hold the criminals responsible accountable, and to pay close attention to the wishes of the victims. In this case, we know their wishes quite well. Poll after poll has yielded results similar to those reported by the military in December, after a study of focus groups around the country. They report that Iraqis from all over the country and all walks of life have "shared beliefs," which they enumerated: The American invasion is to blame for the sectarian violence and other horrors, and the invaders should withdraw, leaving Iraq—or what's left of it—to Iraqis.
It tells us a lot about our own moral and intellectual culture that the voice of Iraqis, though known, is not even considered in the thoughtful and comprehensive articles in the media reviewing the options available to Washington. And that there is no comment on this rather striking fact, considered quite natural.
Is there anyone saying the war was fundamentally wrong?
In the case of Vietnam, years after Kennedy's invasion, liberal doves began to say that the war began with "blundering efforts to do good" but by 1969 it was clear that it was a mistake that was too costly to us (Anthony Lewis, at the critical extreme, in the New York Times). In the same year, 70% of the public regarded the war as not "a mistake" but "fundamentally wrong and immoral." That gap between public and elite educated opinion persists until the most recent polls, a few years ago.
In the media and journals, it is very hard to find any voice that criticizes the invasion or Iraq on principled grounds, though there are some. Arthur Schlesinger, for example, took a very different position than he did on Vietnam. When the bombs started falling on Baghdad he quoted President Roosevelt's condemnation of the Japanese attack on Pearl Harbor as "a date which will live in infamy." Now, Schlesinger wrote, it is Americans who live in infamy as their government follows the path of fascist Japan. But that was a lone voice among elites.
Dissidents, of course, describe "the supreme international crime" as fundamentally wrong. I haven't seen polls about public attitudes on this question.
What about when it is that people know to undertake more serious or severe resistance efforts after the point at which "the limits of possible protest" are reached? In a letter to George Steiner in the NYR, in 1967, you gave the example of what this might look like, now 60 years ago during the Spanish Civil War, when people found it quite necessary to join international brigades to fight against the army of their own country; or, applied to Vietnam, the possible action one might undertake in such circumstances of travelling to Hanoi as a hostage against further bombing. —That's pretty far-reaching, relatively speaking, to what we see in current resistance efforts today against the war. What's your feeling about the possibilities for such methods today in relation to the Iraq war, border action, or other criminal policy in the Middle East and elsewhere? Do situations have to get worse before people or individuals might deem this sort of action necessary?
In the case of Vietnam, serious resistance began several years after Kennedy's invasion of South Vietnam. I was one of a few people trying to organize national tax resistance in early 1965, at a time when South Vietnam, always the main target, was being crushed by intensive bombing and other crimes. By 1966-67, refusal to serve in the invading army was beginning to become a significant phenomenon, along with support for resistance by organized groups, primarily RESIST, formed in 1967 (and still functioning). By then the war had passed far beyond the invasion of Iraq in destructiveness and violence. In fact, at any comparable stage, protest against the Iraq invasion considerably exceeds anything during the Indochina wars.
As for living with the victims to help them or provide them some measure of protection, that is a phenomenon of the 1980s, for the first time in imperial history, to my knowledge, in reaction to Reagan's terrorist wars that devastated Central America, one of his many horrendous crimes. The solidarity movements that took shape then have now extended worldwide, though only in limited ways to Iraq, because the catastrophe created by Cheney-Rumsfeld-Wolfowitz and the rest is so extraordinary that it is almost impossible to survive in the wreckage—the main reason why reporting is so skimpy; it is simply too dangerous, unlike earlier wars of imperial aggression.
A Question of Neutrality in the Schools
Let's talk about the role of intellectuals in all of this. Here's a question that might be relevant for students to hear especially: You've suggested that the major inducements to becoming absorbed into the ideology of the overall scholarship in this country, largely subservient to power interests, are the significant rewards in prestige and affluence, as well as access to power and authority. So, what are some of the things you've observed in your own time in the academy as a kind of source of this process in American education?
Educational institutions like universities don't exist in a social vacuum; they rely for their existence on the external resources of the society. They rely on the state and contributions from, basically, the wealthy. And the state and the wealthy sectors are very closely linked. So, the universities are in a certain social system in which they reflect a certain distribution of power. They're embedded in it. And that means the struggle for university independence—or independence of thought, and willingness to challenge—that's a hard struggle. You're struggling against social conditions that militate against it.
And it's true, what you said is correct, there are rewards and privileges that come along with conformity, but there's more to say. There are also punishments and abuse, loss of jobs, and so on, that come from challenging systems of power. Both factors operate. So, yes, there's a constant struggle to try and maintain university independence, and it's a hard one.
Sometimes it's argued that the universities should just be neutral, that they shouldn't take positions on anything. Well, there's merit in that, I would like to see that in some abstract universe, but in this universe what that position entails is conformity to the distribution of external power.
So let me take a concrete case, aspects of which are still very much alive on my own campus. Let's take some distance so we can see things more clearly. Back in the 1960s, in my university, MIT, the political science department was carrying out studies with students and faculty on counterinsurgency in Vietnam. Okay, that reflected the distribution of power in the outside society. The US is involved in counterinsurgency in Vietnam: it's our patriotic duty to help. A free and independent university would have been carrying out studies on how poor peasants can resist the attack of a predatory superpower. Can you imagine how much support that would have gotten on campus? Well, okay, that's what neutrality turns into when it's carried out—when the ideal, which is a good ideal, is pursued unthinkingly. It ends up being conformity to power.
Let's take a current case. Right now there's a lot of concern about nuclear weapons in Iran. Well, again, take my own campus, MIT. In the 1970s Iran was under the rule of a brutal tyrant who the United States and Britain had imposed by force in a military coup overthrowing the democratic government. So Iran was therefore an ally. Well, in the government, people like Henry Kissenger, Dick Cheney, Donald Rumsfeld, Paul Wolfowitz and others, were calling for Iran to develop nuclear capacities and nuclear power and so on, which means a step short of nuclear weapons. And my own university, MIT, made an arrangement with the Shah of Iran, the dictator, to train Iranian nuclear engineers. It was the 1970s. There was enormous student protest about that. But very little faculty protest, in fact, the faculty approved it. And it was instituted. In fact, some of the people now running the Iranian nuclear programs are graduates of MIT. Well, is the university neutral in those respects? No, not really; it's conforming to power interests. In this case, to go back to an earlier part of our conversation, they did conform to short-term commitments to power and profit but with long-term consequences that were quite harmful to the very same people who instituted them.
Henry Kissinger, who at least has the virtue of honesty, was asked by the Washington Post why he is now objecting to same Iranian programs that he was instrumental in instituting when he was in office back in the 70s. And he said, frankly, Well, they were an ally then. They needed nuclear power. And now they are an enemy so they don't need nuclear power.
Okay, he's a complete cynic, but he's an honest one, fortunately. But should universities take that position?
By Steady Drips of Water: Activism and Social Change
For the last question I'd like to talk a little about providing alternatives, for people trying to figure out things, searching for answers, seeing through propaganda, developing solidarity, initiating movements. Here's a good quote I came across that might be a good starting point, from the notable novelist E.M. Forster, writing at the beginning stages of the Second World War, in 1939, in his essay "What I Believe":
"I do not believe in Belief. But this is an age of faith, and there are so many militant creeds that, in self-defense, one has to formulate a creed of one's own. Tolerance, good temper and sympathy...in a world rent by religious and racial persecution, in a world where ignorance rules, and science, who ought to have ruled, plays the subservient pimp." He repeats: "Tolerance, good temper and sympathy—they are what matter really, and if the human race is not to collapse they must come to the front before long."
What are some of the things he's getting at here that we can discuss in terms of alternatives for the future, and social organization?
I'm often asked questions like that, in maybe a dozen emails a night or in talks and so on, and I'm always at a loss to answer. Not because I can't think of an answer, but because I think we all know the answer. There aren't any magic keys here; there are no mysterious ways of approaching things. What it takes is just what has led to progress and success in the past. We live in a much more civilized world than we did even when Forster was writing, in many respects.
Say, women's rights, or opposition to torture—or even opposition to aggression—environmental concerns, recognition of some of the crimes of our own history, like what happened to the indigenous population. We can go on and on. There's been much improvement in those areas. How? Well, because people like those working in alternative media, or those we never hear about who are doing social organizing, community building, political action, etc., engage themselves in trying to do something about it.
And the modes of engagement are not mysterious. You have to try and develop a critical, open mind, and you have to be willing to evaluate and challenge conventional beliefs—accept them if they turn out to be valid, but reject them if—as is so often the case—they turn out to just reflect power structures. And then proceed with educational and organizing activities, actions as appropriate to circumstances. There is no simple formula; rather, lots of options. And gradually over time, things improve. I mean, even the hardest rock will be eroded by steady drips of water. That's what social change comes to and there are no mysterious modes of proceeding. They're hard ones, demanding ones, challenging, often costly. But that's what it takes to get a better world.
Noam Chomsky is an Institute Professor of Linguistics at the Massachusetts Institute of Technology. Perhaps one of the most revered thinkers of the twentieth century and tireless advocate for honorable peace and social justice, he lectures and writes widely on American foreign policy and world affairs. His latest books are Interventions (City Lights) and Failed States (Metropolitan Books).
Gabriel Matthew Schivone is an editor of Days Beyond Recall Alternative Media and Literary Journal. His articles, having been translated into multiple languages, have appeared in numerous journals such as Z Magazine, Counterpunch and the Monthly Review, as well as Contre Info (France), and Caminos (Cuba). He is most recently the recipient of the 2007 Frederica Hearst Prize for Lyrical Poetry. He is also an active member of the UA Chapter of Amnesty International, Voices of Opposition (to War, Racism and Oppression), Dry River Radical Resource Center, and Students Organized for Animal Rights.
Wednesday, May 21, 2008
genetic mapping of India
Frontline
Volume 25 - Issue 11 :: May. 24-Jun. 06, 2008
INDIA'S NATIONAL MAGAZINE
from the publishers of THE HINDU
SCIENCE
Genetic landscape
R. RAMACHANDRAN
The Indian Genome Variation Consortium is carrying out a unique study to provide a comprehensive genetic mapping of India as a whole.
K.K. MUSTAFAH
The billion-plus people of India today comprise 4,963 communities, which include several thousands endogamous groups, speak in 325 functioning languages and write in 25 different scripts.
HISTORIANS and anthropologists have over the years provided us with a fairly good understanding of the peopling of India, its evolution over centuries to its current diverse compositional fabric, its population groupings in terms of geography, language, culture and ethnicity as well as its characteristically unique societal stratification and hierarchies. The billion-plus people of India today comprise 4,693 communities, which include several thousands of endogamous groups, speak in 325 functioning languages and write in 25 different scripts. Now, as a result of what is perhaps the largest multi-institutional research effort (at least in biology) in this country, we have a genetic basis to this unparalleled diversity.
The IGVC
This research effort began about five years ago under the name of the Indian Genome Variation Consortium (IGVC). It has involved many Indian anthropologists and over 150 scientists drawn from six laboratories of the Council of Scientific and Industrial Research (CSIR); the Indian Statistical Institute (ISI), Kolkata; and The Centre for Genomic Application (TCGA), an institution in New Delhi set up in the public-private-partnership (PPP) mode by the CSIR and the Chatterjee Group of Kolkata. The six CSIR institutes are the Institute of Genomics and Integrative Biology (IGIB), Delhi, the nodal institution for the consortium; the Central Drug Research Institute (CDRI), Lucknow; the Indian Institute of Toxicology Research, or IITR (formerly the Industrial Toxicology Research Centre), Lucknow; the Institute of Microbial Technology (IMTECH), Chandigarh; the Indian Institute of Chemical Biology (IICB), Kolkata; and the Centre for Cellular and Molecular Biology (CCMB), Hyderabad. (Interestingly, the letters in the acronym of the PPP institute – T, C, G, A – also stand for the molecules called bases in nucleotides, the fundamental structural units of deoxyribonucleic acid, or DNA, whose ordering or sequence in DNA codes for genetic information.)
Many studies in the population genetics of the Indian people have been carried out in the past, primarily from an anthropological perspective, but most of them have been limited to certain identified population groups. This study, however, is unique because the genetic information generated is of biomedical relevance. To obtain population-specific genetic information, genes were selected on the basis of their established, or suggested but not proven, linkages to certain common diseases and disorders. The study thus becomes significant from the perspective of pharmacogenetics, or genetic-information-based medicine.
The IGVC was launched as a response to the International HapMap Consortium launched in 2002 to map global genomic diversity. The HapMap study, which cost $100 million, covered 45 Japanese, 45 Chinese, 90 Caucasian and 90 African individuals. Significantly, it failed to cover India. Even if it had, a population sample of the order of 45 would hardly have captured the diversity that is evident in a population that accounts for one-sixth of the world population. Besides HapMap, there are other genetic databases on worldwide populations – such as dbSNP (2001), Celera (2002) and HGVBase (2004) – and on specific populations – such as the Japanese JSNP (2002) – in the public domain. The Indian subcontinent is not represented in any of these as well.
The independent Indian effort has already provided considerable genetic insight into the people(s) of India. Its conceptually different approach focussed on a smaller set of apparently “functional” genes – because of the suggested disease linkages – and was carried out at about 1/20th the cost of the HapMap study (Rs.25 crore as of date). “The budget was significantly scaled down from the original proposal of Rs.113 crore based on a HapMap-like approach,” says Samir K. Brahmachari, Director-General of the CSIR and former Director of the IGIB.
Project aim
The aim of the IGVC project is to obtain data on about 1,000 such genes in 15,000 individuals drawn from different sub-populations so as to provide a comprehensive genetic mapping of the country as a whole. This could serve as the template for identifying reference sub-populations or groups predisposed to specific diseases. Appropriate medical intervention could then target these populations.
In the first phase, the results derived from a study of 55 populations, involving 75 genes and 405 genetic markers (random mutations that serve as milestones), have been published as a paper authored by 151 scientists in the April issue of Journal of Genetics, a high-impact journal of the Indian Academy of Sciences (IAS). The second phase of this mammoth effort is already on, and data on 4,000 genetic markers from over 1,000 genes from 26 of the 55 populations have been gathered and are undergoing analyses.
The paper points out that earlier studies carried out elsewhere by mapping isolated populations, considered important to the understanding of the genetic underpinnings of diseases, had met with limited success because the lack of genetic homogeneity in outbred populations meant that the results could not be validated across the populations. It becomes difficult to get a proper gene-disease linkage map by sampling in such genetically heterogeneous populations. Notwithstanding the overall genetic diversity that one obtains in India, the existence of large families and the high levels of endogamy and population stratification provide “a unique source for dissecting complex disease etiology and pathogenesis”, the authors note.
It is this situation that the work has sought to exploit. “The premise that populations in India are more endogamous than our original perception was actually suggested by our work on SCA12 [spinocerebellar ataxia 12, a neurological disorder],” says Brahmachari. “What we found was that the disorder was associated predominantly with a single kind of allele [variant of a gene], and every patient came from the same community,” he adds.
Even as the study reiterates well-known historical and anthropological elements about the Indian population, it has revealed a remarkable feature of the genetic profile: that there are clusters of populations showing significant genetic differences between them in the frequencies of disease-associated genetic markers and that there is a strong association between the geographic/linguistic profiles in the country and these clusters or groups. That is, Brahmachari says: “From a linguistic map, we have built a genetic map for disease risk.”
The basic approach of the IGVC was to study the genetic variation across population groups on the basis of data on what are called Single Nucleotide Polymorphisms (or SNPs, pronounced “snips”) in the genes that are known to be markers for certain diseases. SNPs constitute the simplest of mutations that a gene undergoes and involve a change, by the alteration of the base molecule (A, T, C or G) at its free end, in one among the string of nucleotides that make up the gene.
In contrast, earlier population genetics studies on Indian populations generally used mitochondrial DNA (mtDNA), the DNA of certain self-replicating organelles present in the cytoplasm of the cell and inherited from the mother; the Y-chromosome; and, occasionally, limited markers from the genomic DNA. As Mitali Mukerji of the IGIB, one of the lead authors of the paper, points out, in mtDNA, which is “uniparentally transmitted”, there is no possibility of crossovers and genetic recombinations – exchange of DNA sequences in the genes between chromosome pairs – and other accidental variations that can occur during chromosome duplication as cells divide (mitosis).
Similarly, unlike autosomes, or non-sex chromosomes, the Y-chromosome does not have a homologous pair (having the same genetic loci) and, therefore, cannot reflect genetic recombinations that can occur by the exchange of segments across identical loci.
“Such [mtDNA-based] studies,” she says, “can at best reveal the origins or ancestry of populations by tracing the communities that females have married into and how societies have intermingled and not the relevant fine structure or stratification in the populations. The bulk of our genome is in the autosomes where there is adequate mixing.”
A population genetics study that merely looks at the gene flow and infers who is related to whom and ends up with a phylogenetic (evolutionary descent) tree, “is too expensive to use public money on”, feels Brahmachari. “Our objective,” he says, “was to see how much is the variation in the genes with important pathways or is suggestive of such associations in populations and whether there is any population stratification revealed on that basis.” Databases such as the Online Mendelian Inheritance in Man (OMIM), maintained by the National Centre for Biotechnology Information (NCBI) at Johns Hopkins University, were used to identify established gene-disease associations.
As the paper states, the first phase of the IGVC effort set out to answer the following five questions: (i) Are the frequencies of SNPs putatively associated with diseases similar across populations and can clusters of populations that have similar frequencies be identified? (ii) Do these clusters correlate with ethnic, linguistic and geographic divisions? (iii) What is the nature and extent of genetic differentiation within and among such clusters? (iv) How are Indian populations related to the HapMap populations? and (v) Does a subset of all the SNPs considered suffice to distinguish between ethnic groups? By answering the above affirmatively, the first results of the project have shed new and important light on the genetic profile of India, which, as will be described in Part 2 of this report, can have significant public health implications.
The population groups in the study were classified as Isolated (tribal) Populations (IPs), Large Populations (LPs), which were mostly caste groups with a population strength of more than 10 million, and Special Populations (SPs), essentially religious groups apart from the dominant Hindu group, which were also nearly all large populations. Some of the IPs were also large. “This classification ensured that there was maximum genetic variation between the tribals and the large populations,” says Brahmachari.
For sampling, given the fact that there are basically four linguistic groups in the country – Austro-Asiatic (AA), Tibeto-Burman (TB), Indo-European (IE) and Dravidian (DR) – and six broad geographical regions – south, west, central, north, east and north-east – at least two IPs and two LPs were selected from each language-geography grid so that population and ethnic diversity would be adequately represented. (This gave each selected group a three-character label of language-geographic zone-population category.) The 55 population groups selected included 26 LPs, 23 IPs and six SPs (see Table 1).
A representative set of 75 genes spread across nearly all the chromosomes (excluding the Y-chromosome) was identified for the study. The genes are known to be associated with drug response, cancer and aging, eye diseases, allergy and asthma, susceptibility to infections, neuro-psychiatric problems, and metabolic and cardiovascular disorders (see Table 2). “Genes on which maximum biochemical and molecular biological information was available were chosen. This also ensured that nearly the entire gamut of biomolecular functions and biological processes were covered by the genes,” says Brahmachari.
A minimum of 50 samples from LPs and 25 samples from IPs were collected. From an initial number of 2,014 unrelated samples, quality control reduced the number to 1,871, comprising 1,240 males and 631 females (see Table 3). The sampling does reveal an apparent bias towards populations of the north, which account for as many as 44 per cent of the samples.
“Yes, the south has not been covered very well,” admits Mukerji. “This was basically because the north is fairly homogeneous and the south comparatively heterogeneous. We have now collected all the information on the admixtures in southern populations, particularly in the IE and AA tribals. The fine structuring of the population has to be captured, which is being done in the second phase with more samples,” she adds. “The new results are not very different, which indicates that there was not any significant bias due to sampling,” Brahmachari points out, however.
Since the study was primarily focussed on disease-related functional polymorphisms, the SNPs suggestive of such associations had to be first identified. For this a “discovery panel” of 43 samples was drawn up from geographically and ethnically diverse populations. By sequencing the candidate gene loci from these samples, a total of 170 novel and 560 reported SNPs were identified. Application of certain selection criteria brought the number down to 601, and when these were validated on the larger complete sample set, only 405 met the criterion of being from the non-sex chromosomes. A bi-directional sampling on the panel of 43 samples enabled the discovery of the novel SNPs.
The identification of SNPs was done by the automated high throughput sequencing technique (HTST), widely used in post-genomics biological research, which can easily locate these. Such a facility exists at the TCGA. “For sequencing genes, some of the design was done at the IGIB and some here, but we did all the quality controls and high-throughput screening for SNPs and genotyping,” says K. Narayanasamy of the TCGA. Genotyping refers to determining the genotype, or the genetic constitution of an individual, in this case, the limited set of SNPs in the sample.
“While the throughput we achieved on the Sequenom platform of about 50,000 genotypes a day was perhaps a little lower than what one can achieve with the latest equipment; in terms of accuracy it was most accurate,” Narayanasamy adds. “For the second phase, for which we have already sequenced over 1,000 genes and screened them at about five to six SNPs per gene, we used this as well as a comparatively higher-throughput platform, Ilumina, and the concordance between the two platforms is excellent,” he says.
A larger number of genetic markers from a set of populations than most studies have to deal with also meant that a more careful data analysis had to be done. “It meant that the data had to be carefully curated and quality controls applied consistently,” says Partha Majumder of the ISI, another lead author of the paper, under whose guidance much of the statistical analysis was carried out. “To make comparisons, the techniques used were fairly standard. Only that they had to be adapted suitably for the larger dimensional problem at hand,” he adds.
Data analysis basically involved computation of the frequencies of genetic variation (allele frequencies) of all autosomal loci, and these were systematically compared between pairs of population to determine how far each population was genetically separated from another, that is, determining the “genetic distance” or the extent of “genetic differentiation”, as it is termed. It was found that the differentiation was statistically significant in most cases, and as the paper notes, in those few cases where it was not statistically significant, it remains to be determined whether it was an artefact of the small sample sizes.
Genetic diversity
However, the comparison on the basis of a few loci alone revealed a very high degree of differentiation, which was comparable in magnitude to that observed among continental populations. This is a clear demonstration of the genetic diversity in the country. Significantly, maximum differentiation was found among tribal populations in the different linguistic regions. A significant observation of the study is that while on a pan-India level the extent of differentiation among linguistic or geographic groups was not statistically significant, grouping by ethnicity (caste and tribe) revealed a higher degree of differentiation between caste groups and tribal groups, which is indicative of the “antiquity and isolation of the tribal compared to the caste populations”.
Analysis of genetic distances within geographic regions or ethno-linguistic groups has revealed some interesting features. While Dravidian-speaking LPs and IPs did not show statistically significant differentiation, the Indo-European-speaking LP and IP groups are significantly differentiated. Also, there is significant differentiation within both Indo-European- speaking tribes and Dravidian-speaking tribes, pointing to a relatively greater degree of isolation and non-mixing. The same, however, cannot be said of caste groups, which is indicative of a more recent formation of such societal groups. Interestingly,
Dravidian-speaking tribal people and the tribal people who speak Austro-Asiatic languages did not show any significant degree of genetic separation. “From the above results,” observe the authors, “it is clear that pooling populations without considering ethnicity and linguistic affiliations that contribute to population stratification can result in false inferences in genetic association studies.”
Different statistical methods were employed to obtain a slightly different perspective of the country’s genetic profile: namely, to study the genetic affinities of populations and see how the population clustered genetically across the country and to see how this correlated with the linguistic groupings (see map). The first major cluster comprised Austro-Asian IPs and Dravidian IPs, consistent with the earlier observation of lower genetic differentiation between them. The second cluster included Tibeto-Burman-speaking populations, irrespective of their geographical region of habitat. This cluster also consisted of three Indo-European-speaking IPs and two LPs. The majority of these populations reside in the Himalayan belt, the paper notes. There were a larger number of smaller clusters that predominantly consisted of Indo-European-speaking LPs and SPs.
The Dravidian-speaking LPs and IPs formed a separate cluster, predominantly located in the south. The clustering also reveals that there seems to be considerable diversity among Indo-European-speaking populations in different geographical locations. Besides, within the Indo-European-speaking populations, LPs and SPs (largely Muslims) were found to have a strong genetic affinity, which basically implies that Hindus and Muslims of the north are essentially the same people. Similarly, affinity was also observed between Tibeto-Burman-speaking IPs and SPs.
“Thus,” infer the authors, “although there are no clear geographical grouping of populations, ethnicity (tribal/non-tribal) and language seem to be the major determinants of genetic affinities between populations of India.” On the basis of the observed stratification of the Indian population, the paper cautions conventional population genetics studies to correct for this stratification “if cases and controls are drawn from populations that belong to different clusters”. This observation, therefore, has the implication that careful sampling of the populations is necessary to capture the entire genetic spectrum of the country.
Besides disease-linked genetic mapping of Indian populations, an objective of the study was to look at the ancestry of the diverse populations and their relatedness from that perspective. This, in the parlance of population genetics, is determined by looking at what is called “Linkage Disequilibrium (LD)”. Majumder explains this as follows: “Even if two SNPs are not close to each other, there is a statistical association between them when the ancestry is short. This is because sufficient time has not elapsed for genetic recombinations that would disturb this association to occur. They stay together over a period of time. LD is basically a measure of this.” However, according to him, the analysis of SNPs in Indian populations shows that the extent of LD was not high enough. This basically implies that the population groups are of ancient descent and despite that, there are pockets of homogeneity in the Indian population.
An interesting corollary outcome of the study is the finding that the IPs are relatively unadmixed, unlike the LPs. An analysis conceived by Majumder found that it was possible to identify a small number of SNPs that can serve as signatures of population ancestry. “If there are two populations and we had a small bunch of alleles, I wanted to see if there is a useful way of differentiating the populations based on these,” says Majumder.
Keystone SNPS
The answer turned out to be yes, perhaps not too surprising given the extent of differentiation seen between different sub-populations. A small set of 12 SNP loci, which Majumder has called “Keystone SNPs”, is enough to identify a population with unknown ethnicity as predominantly tribal or predominantly caste with 100 per cent accuracy! The accuracy dropped when unknown linguistic lineage or geographical lineage had to be determined. “Though there are a few Keystone SNPs that have strong medical linkage, I would not draw any larger conclusion from this until there is clearly proven linkages for the entire set, which we do not have,” Majumder says.
Global perspective
The study also investigated what the genetic variations in Indian populations reveal when viewed from a global perspective. This was done by carrying out a comparison with the genetic profiles of the HapMap populations by porting what are called Tag SNPs from the HapMap populations onto the Indian populations.
Interestingly, it was found that all the HapMap populations, except those of African descent (YRI), namely, the Chinese (CHB), the Japanese (JPT) and the Caucasian (CEU), were well represented among the Indian population. The isolated populations of the Himalayan belt are closest to the Chinese and Japanese and separate from the rest of the populations. The YRI, on the other hand, lay statistically farther away from the Indian populations and closest to the single outlying population group (from the 55) labelled as OG-W-IP. As expected, the CEU was found to be closest to the Indo-European-speaking LPs, the majority of whom are in the north. Again, as expected, the Austro-Asiatic-speaking and Dravidian-speaking populations were distinct from the HapMap populations. Interestingly, however, the mean statistical association of these Tag SNPs was higher in Indian populations than in the HapMap populations themselves. This is perhaps a reflection of the inherent urban bias in the HapMap samples, which were drawn from Beijing, Tokyo, and so on.
“A pertinent question is how robust is our genetic map because ideally genetic affinities should be inferred from a random set of neutral loci and not from a biased set based on disease linkage,” says Brahmachari.
A statistical analysis, after a proper statistical filtering of the loci, showed that the correlation between affinities with 405 and the reduced set of 332 was very high, establishing the robustness of the findings, Brahmachari points out.
Having thus established that the results of the first phase are on terra firma (which the early second phase results also seem to indicate), the IGVC project is perhaps all set to enter the third phase and attempt to answer the next-level question, which could have public health implications: namely, can one identify populations “at risk” for complex disorders, poor drug response and predisposition to infectious diseases?•
Volume 25 - Issue 11 :: May. 24-Jun. 06, 2008
INDIA'S NATIONAL MAGAZINE
from the publishers of THE HINDU
SCIENCE
Genetic landscape
R. RAMACHANDRAN
The Indian Genome Variation Consortium is carrying out a unique study to provide a comprehensive genetic mapping of India as a whole.
K.K. MUSTAFAH
The billion-plus people of India today comprise 4,963 communities, which include several thousands endogamous groups, speak in 325 functioning languages and write in 25 different scripts.
HISTORIANS and anthropologists have over the years provided us with a fairly good understanding of the peopling of India, its evolution over centuries to its current diverse compositional fabric, its population groupings in terms of geography, language, culture and ethnicity as well as its characteristically unique societal stratification and hierarchies. The billion-plus people of India today comprise 4,693 communities, which include several thousands of endogamous groups, speak in 325 functioning languages and write in 25 different scripts. Now, as a result of what is perhaps the largest multi-institutional research effort (at least in biology) in this country, we have a genetic basis to this unparalleled diversity.
The IGVC
This research effort began about five years ago under the name of the Indian Genome Variation Consortium (IGVC). It has involved many Indian anthropologists and over 150 scientists drawn from six laboratories of the Council of Scientific and Industrial Research (CSIR); the Indian Statistical Institute (ISI), Kolkata; and The Centre for Genomic Application (TCGA), an institution in New Delhi set up in the public-private-partnership (PPP) mode by the CSIR and the Chatterjee Group of Kolkata. The six CSIR institutes are the Institute of Genomics and Integrative Biology (IGIB), Delhi, the nodal institution for the consortium; the Central Drug Research Institute (CDRI), Lucknow; the Indian Institute of Toxicology Research, or IITR (formerly the Industrial Toxicology Research Centre), Lucknow; the Institute of Microbial Technology (IMTECH), Chandigarh; the Indian Institute of Chemical Biology (IICB), Kolkata; and the Centre for Cellular and Molecular Biology (CCMB), Hyderabad. (Interestingly, the letters in the acronym of the PPP institute – T, C, G, A – also stand for the molecules called bases in nucleotides, the fundamental structural units of deoxyribonucleic acid, or DNA, whose ordering or sequence in DNA codes for genetic information.)
Many studies in the population genetics of the Indian people have been carried out in the past, primarily from an anthropological perspective, but most of them have been limited to certain identified population groups. This study, however, is unique because the genetic information generated is of biomedical relevance. To obtain population-specific genetic information, genes were selected on the basis of their established, or suggested but not proven, linkages to certain common diseases and disorders. The study thus becomes significant from the perspective of pharmacogenetics, or genetic-information-based medicine.
The IGVC was launched as a response to the International HapMap Consortium launched in 2002 to map global genomic diversity. The HapMap study, which cost $100 million, covered 45 Japanese, 45 Chinese, 90 Caucasian and 90 African individuals. Significantly, it failed to cover India. Even if it had, a population sample of the order of 45 would hardly have captured the diversity that is evident in a population that accounts for one-sixth of the world population. Besides HapMap, there are other genetic databases on worldwide populations – such as dbSNP (2001), Celera (2002) and HGVBase (2004) – and on specific populations – such as the Japanese JSNP (2002) – in the public domain. The Indian subcontinent is not represented in any of these as well.
The independent Indian effort has already provided considerable genetic insight into the people(s) of India. Its conceptually different approach focussed on a smaller set of apparently “functional” genes – because of the suggested disease linkages – and was carried out at about 1/20th the cost of the HapMap study (Rs.25 crore as of date). “The budget was significantly scaled down from the original proposal of Rs.113 crore based on a HapMap-like approach,” says Samir K. Brahmachari, Director-General of the CSIR and former Director of the IGIB.
Project aim
The aim of the IGVC project is to obtain data on about 1,000 such genes in 15,000 individuals drawn from different sub-populations so as to provide a comprehensive genetic mapping of the country as a whole. This could serve as the template for identifying reference sub-populations or groups predisposed to specific diseases. Appropriate medical intervention could then target these populations.
In the first phase, the results derived from a study of 55 populations, involving 75 genes and 405 genetic markers (random mutations that serve as milestones), have been published as a paper authored by 151 scientists in the April issue of Journal of Genetics, a high-impact journal of the Indian Academy of Sciences (IAS). The second phase of this mammoth effort is already on, and data on 4,000 genetic markers from over 1,000 genes from 26 of the 55 populations have been gathered and are undergoing analyses.
The paper points out that earlier studies carried out elsewhere by mapping isolated populations, considered important to the understanding of the genetic underpinnings of diseases, had met with limited success because the lack of genetic homogeneity in outbred populations meant that the results could not be validated across the populations. It becomes difficult to get a proper gene-disease linkage map by sampling in such genetically heterogeneous populations. Notwithstanding the overall genetic diversity that one obtains in India, the existence of large families and the high levels of endogamy and population stratification provide “a unique source for dissecting complex disease etiology and pathogenesis”, the authors note.
It is this situation that the work has sought to exploit. “The premise that populations in India are more endogamous than our original perception was actually suggested by our work on SCA12 [spinocerebellar ataxia 12, a neurological disorder],” says Brahmachari. “What we found was that the disorder was associated predominantly with a single kind of allele [variant of a gene], and every patient came from the same community,” he adds.
Even as the study reiterates well-known historical and anthropological elements about the Indian population, it has revealed a remarkable feature of the genetic profile: that there are clusters of populations showing significant genetic differences between them in the frequencies of disease-associated genetic markers and that there is a strong association between the geographic/linguistic profiles in the country and these clusters or groups. That is, Brahmachari says: “From a linguistic map, we have built a genetic map for disease risk.”
The basic approach of the IGVC was to study the genetic variation across population groups on the basis of data on what are called Single Nucleotide Polymorphisms (or SNPs, pronounced “snips”) in the genes that are known to be markers for certain diseases. SNPs constitute the simplest of mutations that a gene undergoes and involve a change, by the alteration of the base molecule (A, T, C or G) at its free end, in one among the string of nucleotides that make up the gene.
In contrast, earlier population genetics studies on Indian populations generally used mitochondrial DNA (mtDNA), the DNA of certain self-replicating organelles present in the cytoplasm of the cell and inherited from the mother; the Y-chromosome; and, occasionally, limited markers from the genomic DNA. As Mitali Mukerji of the IGIB, one of the lead authors of the paper, points out, in mtDNA, which is “uniparentally transmitted”, there is no possibility of crossovers and genetic recombinations – exchange of DNA sequences in the genes between chromosome pairs – and other accidental variations that can occur during chromosome duplication as cells divide (mitosis).
Similarly, unlike autosomes, or non-sex chromosomes, the Y-chromosome does not have a homologous pair (having the same genetic loci) and, therefore, cannot reflect genetic recombinations that can occur by the exchange of segments across identical loci.
“Such [mtDNA-based] studies,” she says, “can at best reveal the origins or ancestry of populations by tracing the communities that females have married into and how societies have intermingled and not the relevant fine structure or stratification in the populations. The bulk of our genome is in the autosomes where there is adequate mixing.”
A population genetics study that merely looks at the gene flow and infers who is related to whom and ends up with a phylogenetic (evolutionary descent) tree, “is too expensive to use public money on”, feels Brahmachari. “Our objective,” he says, “was to see how much is the variation in the genes with important pathways or is suggestive of such associations in populations and whether there is any population stratification revealed on that basis.” Databases such as the Online Mendelian Inheritance in Man (OMIM), maintained by the National Centre for Biotechnology Information (NCBI) at Johns Hopkins University, were used to identify established gene-disease associations.
As the paper states, the first phase of the IGVC effort set out to answer the following five questions: (i) Are the frequencies of SNPs putatively associated with diseases similar across populations and can clusters of populations that have similar frequencies be identified? (ii) Do these clusters correlate with ethnic, linguistic and geographic divisions? (iii) What is the nature and extent of genetic differentiation within and among such clusters? (iv) How are Indian populations related to the HapMap populations? and (v) Does a subset of all the SNPs considered suffice to distinguish between ethnic groups? By answering the above affirmatively, the first results of the project have shed new and important light on the genetic profile of India, which, as will be described in Part 2 of this report, can have significant public health implications.
The population groups in the study were classified as Isolated (tribal) Populations (IPs), Large Populations (LPs), which were mostly caste groups with a population strength of more than 10 million, and Special Populations (SPs), essentially religious groups apart from the dominant Hindu group, which were also nearly all large populations. Some of the IPs were also large. “This classification ensured that there was maximum genetic variation between the tribals and the large populations,” says Brahmachari.
For sampling, given the fact that there are basically four linguistic groups in the country – Austro-Asiatic (AA), Tibeto-Burman (TB), Indo-European (IE) and Dravidian (DR) – and six broad geographical regions – south, west, central, north, east and north-east – at least two IPs and two LPs were selected from each language-geography grid so that population and ethnic diversity would be adequately represented. (This gave each selected group a three-character label of language-geographic zone-population category.) The 55 population groups selected included 26 LPs, 23 IPs and six SPs (see Table 1).
A representative set of 75 genes spread across nearly all the chromosomes (excluding the Y-chromosome) was identified for the study. The genes are known to be associated with drug response, cancer and aging, eye diseases, allergy and asthma, susceptibility to infections, neuro-psychiatric problems, and metabolic and cardiovascular disorders (see Table 2). “Genes on which maximum biochemical and molecular biological information was available were chosen. This also ensured that nearly the entire gamut of biomolecular functions and biological processes were covered by the genes,” says Brahmachari.
A minimum of 50 samples from LPs and 25 samples from IPs were collected. From an initial number of 2,014 unrelated samples, quality control reduced the number to 1,871, comprising 1,240 males and 631 females (see Table 3). The sampling does reveal an apparent bias towards populations of the north, which account for as many as 44 per cent of the samples.
“Yes, the south has not been covered very well,” admits Mukerji. “This was basically because the north is fairly homogeneous and the south comparatively heterogeneous. We have now collected all the information on the admixtures in southern populations, particularly in the IE and AA tribals. The fine structuring of the population has to be captured, which is being done in the second phase with more samples,” she adds. “The new results are not very different, which indicates that there was not any significant bias due to sampling,” Brahmachari points out, however.
Since the study was primarily focussed on disease-related functional polymorphisms, the SNPs suggestive of such associations had to be first identified. For this a “discovery panel” of 43 samples was drawn up from geographically and ethnically diverse populations. By sequencing the candidate gene loci from these samples, a total of 170 novel and 560 reported SNPs were identified. Application of certain selection criteria brought the number down to 601, and when these were validated on the larger complete sample set, only 405 met the criterion of being from the non-sex chromosomes. A bi-directional sampling on the panel of 43 samples enabled the discovery of the novel SNPs.
The identification of SNPs was done by the automated high throughput sequencing technique (HTST), widely used in post-genomics biological research, which can easily locate these. Such a facility exists at the TCGA. “For sequencing genes, some of the design was done at the IGIB and some here, but we did all the quality controls and high-throughput screening for SNPs and genotyping,” says K. Narayanasamy of the TCGA. Genotyping refers to determining the genotype, or the genetic constitution of an individual, in this case, the limited set of SNPs in the sample.
“While the throughput we achieved on the Sequenom platform of about 50,000 genotypes a day was perhaps a little lower than what one can achieve with the latest equipment; in terms of accuracy it was most accurate,” Narayanasamy adds. “For the second phase, for which we have already sequenced over 1,000 genes and screened them at about five to six SNPs per gene, we used this as well as a comparatively higher-throughput platform, Ilumina, and the concordance between the two platforms is excellent,” he says.
A larger number of genetic markers from a set of populations than most studies have to deal with also meant that a more careful data analysis had to be done. “It meant that the data had to be carefully curated and quality controls applied consistently,” says Partha Majumder of the ISI, another lead author of the paper, under whose guidance much of the statistical analysis was carried out. “To make comparisons, the techniques used were fairly standard. Only that they had to be adapted suitably for the larger dimensional problem at hand,” he adds.
Data analysis basically involved computation of the frequencies of genetic variation (allele frequencies) of all autosomal loci, and these were systematically compared between pairs of population to determine how far each population was genetically separated from another, that is, determining the “genetic distance” or the extent of “genetic differentiation”, as it is termed. It was found that the differentiation was statistically significant in most cases, and as the paper notes, in those few cases where it was not statistically significant, it remains to be determined whether it was an artefact of the small sample sizes.
Genetic diversity
However, the comparison on the basis of a few loci alone revealed a very high degree of differentiation, which was comparable in magnitude to that observed among continental populations. This is a clear demonstration of the genetic diversity in the country. Significantly, maximum differentiation was found among tribal populations in the different linguistic regions. A significant observation of the study is that while on a pan-India level the extent of differentiation among linguistic or geographic groups was not statistically significant, grouping by ethnicity (caste and tribe) revealed a higher degree of differentiation between caste groups and tribal groups, which is indicative of the “antiquity and isolation of the tribal compared to the caste populations”.
Analysis of genetic distances within geographic regions or ethno-linguistic groups has revealed some interesting features. While Dravidian-speaking LPs and IPs did not show statistically significant differentiation, the Indo-European-speaking LP and IP groups are significantly differentiated. Also, there is significant differentiation within both Indo-European- speaking tribes and Dravidian-speaking tribes, pointing to a relatively greater degree of isolation and non-mixing. The same, however, cannot be said of caste groups, which is indicative of a more recent formation of such societal groups. Interestingly,
Dravidian-speaking tribal people and the tribal people who speak Austro-Asiatic languages did not show any significant degree of genetic separation. “From the above results,” observe the authors, “it is clear that pooling populations without considering ethnicity and linguistic affiliations that contribute to population stratification can result in false inferences in genetic association studies.”
Different statistical methods were employed to obtain a slightly different perspective of the country’s genetic profile: namely, to study the genetic affinities of populations and see how the population clustered genetically across the country and to see how this correlated with the linguistic groupings (see map). The first major cluster comprised Austro-Asian IPs and Dravidian IPs, consistent with the earlier observation of lower genetic differentiation between them. The second cluster included Tibeto-Burman-speaking populations, irrespective of their geographical region of habitat. This cluster also consisted of three Indo-European-speaking IPs and two LPs. The majority of these populations reside in the Himalayan belt, the paper notes. There were a larger number of smaller clusters that predominantly consisted of Indo-European-speaking LPs and SPs.
The Dravidian-speaking LPs and IPs formed a separate cluster, predominantly located in the south. The clustering also reveals that there seems to be considerable diversity among Indo-European-speaking populations in different geographical locations. Besides, within the Indo-European-speaking populations, LPs and SPs (largely Muslims) were found to have a strong genetic affinity, which basically implies that Hindus and Muslims of the north are essentially the same people. Similarly, affinity was also observed between Tibeto-Burman-speaking IPs and SPs.
“Thus,” infer the authors, “although there are no clear geographical grouping of populations, ethnicity (tribal/non-tribal) and language seem to be the major determinants of genetic affinities between populations of India.” On the basis of the observed stratification of the Indian population, the paper cautions conventional population genetics studies to correct for this stratification “if cases and controls are drawn from populations that belong to different clusters”. This observation, therefore, has the implication that careful sampling of the populations is necessary to capture the entire genetic spectrum of the country.
Besides disease-linked genetic mapping of Indian populations, an objective of the study was to look at the ancestry of the diverse populations and their relatedness from that perspective. This, in the parlance of population genetics, is determined by looking at what is called “Linkage Disequilibrium (LD)”. Majumder explains this as follows: “Even if two SNPs are not close to each other, there is a statistical association between them when the ancestry is short. This is because sufficient time has not elapsed for genetic recombinations that would disturb this association to occur. They stay together over a period of time. LD is basically a measure of this.” However, according to him, the analysis of SNPs in Indian populations shows that the extent of LD was not high enough. This basically implies that the population groups are of ancient descent and despite that, there are pockets of homogeneity in the Indian population.
An interesting corollary outcome of the study is the finding that the IPs are relatively unadmixed, unlike the LPs. An analysis conceived by Majumder found that it was possible to identify a small number of SNPs that can serve as signatures of population ancestry. “If there are two populations and we had a small bunch of alleles, I wanted to see if there is a useful way of differentiating the populations based on these,” says Majumder.
Keystone SNPS
The answer turned out to be yes, perhaps not too surprising given the extent of differentiation seen between different sub-populations. A small set of 12 SNP loci, which Majumder has called “Keystone SNPs”, is enough to identify a population with unknown ethnicity as predominantly tribal or predominantly caste with 100 per cent accuracy! The accuracy dropped when unknown linguistic lineage or geographical lineage had to be determined. “Though there are a few Keystone SNPs that have strong medical linkage, I would not draw any larger conclusion from this until there is clearly proven linkages for the entire set, which we do not have,” Majumder says.
Global perspective
The study also investigated what the genetic variations in Indian populations reveal when viewed from a global perspective. This was done by carrying out a comparison with the genetic profiles of the HapMap populations by porting what are called Tag SNPs from the HapMap populations onto the Indian populations.
Interestingly, it was found that all the HapMap populations, except those of African descent (YRI), namely, the Chinese (CHB), the Japanese (JPT) and the Caucasian (CEU), were well represented among the Indian population. The isolated populations of the Himalayan belt are closest to the Chinese and Japanese and separate from the rest of the populations. The YRI, on the other hand, lay statistically farther away from the Indian populations and closest to the single outlying population group (from the 55) labelled as OG-W-IP. As expected, the CEU was found to be closest to the Indo-European-speaking LPs, the majority of whom are in the north. Again, as expected, the Austro-Asiatic-speaking and Dravidian-speaking populations were distinct from the HapMap populations. Interestingly, however, the mean statistical association of these Tag SNPs was higher in Indian populations than in the HapMap populations themselves. This is perhaps a reflection of the inherent urban bias in the HapMap samples, which were drawn from Beijing, Tokyo, and so on.
“A pertinent question is how robust is our genetic map because ideally genetic affinities should be inferred from a random set of neutral loci and not from a biased set based on disease linkage,” says Brahmachari.
A statistical analysis, after a proper statistical filtering of the loci, showed that the correlation between affinities with 405 and the reduced set of 332 was very high, establishing the robustness of the findings, Brahmachari points out.
Having thus established that the results of the first phase are on terra firma (which the early second phase results also seem to indicate), the IGVC project is perhaps all set to enter the third phase and attempt to answer the next-level question, which could have public health implications: namely, can one identify populations “at risk” for complex disorders, poor drug response and predisposition to infectious diseases?•
Sunday, May 18, 2008
Peter Berger on evangelicals
alt.religion.christian.episcopal
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jwsheffield@satx.rr.com
Newsgroups: alt.religion.christian.episcopal
From: "jwsheffi...@satx.rr.com"
Date: Sun, 18 May 2008 15:29:31 -0700 (PDT)
Local: Sun, May 18 2008 6:29 pm
Subject: Swiming Upstream, Boston U. Prof. Berger project looks at `evangelical intelligentsia’
For decades, Boston University sociologist Peter Berger says, American
intellectuals have looked down on evangelicals.
Educated people have the notion that evangelicals are "barefoot people
of Tobacco Road who, I don't know, sleep with their sisters or
something," Berger says.
It's time that attitude changed, he says.
"That was probably never correct, but it's totally false now and I
think the image should be corrected," Berger said in a recent
interview.
Now, his university's Institute on Culture, Religion and World Affairs
is leading a two-year project that explores an "evangelical
intelligentsia" which Berger says is growing and needs to be better
understood, given the large numbers of evangelicals and their
influence.
"It's not good if a prejudiced view of this community prevails in the
elite circles of society," said Berger, a self-described liberal
Lutheran. "It's bad for democracy and it's wrong."
http://www.kendallharmon.net/t19/
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jwsheffield@satx.rr.com
Newsgroups: alt.religion.christian.episcopal
From: "jwsheffi...@satx.rr.com"
Date: Sun, 18 May 2008 15:29:31 -0700 (PDT)
Local: Sun, May 18 2008 6:29 pm
Subject: Swiming Upstream, Boston U. Prof. Berger project looks at `evangelical intelligentsia’
For decades, Boston University sociologist Peter Berger says, American
intellectuals have looked down on evangelicals.
Educated people have the notion that evangelicals are "barefoot people
of Tobacco Road who, I don't know, sleep with their sisters or
something," Berger says.
It's time that attitude changed, he says.
"That was probably never correct, but it's totally false now and I
think the image should be corrected," Berger said in a recent
interview.
Now, his university's Institute on Culture, Religion and World Affairs
is leading a two-year project that explores an "evangelical
intelligentsia" which Berger says is growing and needs to be better
understood, given the large numbers of evangelicals and their
influence.
"It's not good if a prejudiced view of this community prevails in the
elite circles of society," said Berger, a self-described liberal
Lutheran. "It's bad for democracy and it's wrong."
http://www.kendallharmon.net/t19/
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