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Many people refused to believe the Lancet report in 2004 from a group of American and Iraqi public-health scientists who surveyed homes across the country and found that about 100,000 additional Iraqi deaths had taken place since the coalition invasion in March 2003. Several government ministers were deployed to destroy the credibility of the findings and, in large part, they succeeded. But now their denials have come back to haunt them, for the figures from Iraq have been confirmed by a further study.

The same team from Johns Hopkins University worked with Iraqi doctors to visit over 1,800 homes in Iraq, selected randomly to make sure that no bias could creep in to their calculations.

They identified more than 12,000 family members and tracked those who had died over an interval that spanned both pre- and post-invasion periods. The Iraqi interviewers spoke fluent English as well as Arabic, and they were well trained to collect the information they were seeking. They asked permission from every family to use the data they wanted. And they chased down death certificates in over four out of five cases to make sure that they had a double check on the numbers and causes of death given to them by family members.

All of these checks and balances mean that the 650,000 additional Iraqi casualties they report since the invasion is the most reliable estimate we have of civilian deaths. Most of these deaths have been of men aged 15 to 44.

Not only do we have a better understanding of the toll our invasion has had on the country; we also understand better just how those deaths have come about. Before the invasion only a tiny proportion of deaths were due to violence. But since the invasion over half of all deaths have been due to violent causes. It is our occupation and our continued presence in Iraq that is fuelling this violence. Claims that the terrorist threat was always there are simply disproved by these findings.

The nature of these causes has changed too. Early on in the post-invasion period deaths were made worse by aerial bombing. But now gunshot wounds and car bombs are having a far greater effect. Far from our presence in Iraq stabilising the chaos or alleviating the rate at which casualties are mounting, we seem to be making the situation worse. In each year since the invasion, the mortality rates due to violence have increased.

The total figure of 650,000 is truly staggering. It represents 2.5% of the entire Iraqi population. In 2004 The Lancet was criticised for publishing a number that seemed to have a high degree of uncertainty. The best estimate then was 98,000 deaths. But the uncertainty meant that it could have been as low as 8,000 or as high as 194,000.

In the latest study there is also a large degree of uncertainty, but even the lowest possible figure it gives for the number of deaths - 400,000 - makes clear just how terrible our intervention in Iraq has been. The highest possible figure is more than 900,000. Looking at these numbers, we have to concede that we have created a humanitarian disaster of unprecedented proportions for a foreign policy that was supposed to protect civilian populations, not subject them to ever-greater harm.

Why is this Lancet estimate so much higher than the figures put out by President Bush or the Iraq Body Count website? They put the number of casualties in the tens of thousands, not the hundreds of thousands. To be fair, Iraq Body Count does not claim to publish accurate absolute numbers of deaths. Instead, their figures are valuable for measuring trends. But the reason for the discrepancy between these lower estimates and the new figure of 650,000 deaths lies in the way the number is sought. Passive surveillance, the most common method used to estimate numbers of civilian deaths, will always underestimate the total number of casualties. We know this from past wars and conflict zones, where the estimates have been too low by a factor of 10 or even 20.

Only when you go out and knock on the doors of families, actively looking for deaths, do you begin to get close to the right number. This method is now tried and tested. It has been the basis for mortality estimates in war zones such as Darfur and the Congo. Interestingly, when we report figures from these countries politicians do not challenge them. They frown, nod their heads and agree that the situation is grave and intolerable. The international community must act, they say. When it comes to Iraq the story is different. Expect the current government to mobilise all its efforts to undermine the work done by this American and Iraqi team. Expect the government to criticise the Lancet for being too political. Expect the government to do all it can to dismiss this story and wash its hands of its responsibility to take these latest findings seriously.

But if we were talking about the risk of smoking to the population, and published research demonstrating the effect of tobacco on mortality, few would dispute the message or the importance of scientists and medical journals in being actively engaged in a public debate. For Iraq, violence is the public-health priority right now. It is a proper subject for science and it is a proper subject for a medical journal to comment on.

So what is the right conclusion from this work? How should this latest research inform public policy? First, Iraq is an unequivocal humanitarian emergency. Civilians are being harmed by our presence in Iraq, not helped. That should force us to pause and ask what we are doing and why. There is no shame in saying that we have got the policy wrong. Moreover, we have a legal obligation under the Geneva conventions to do all we can to protect civilian populations. These findings show not only that are we not adhering to this legal obligation, but also that we are progressively subverting it year on year.

And finally, we can truthfully say that our foreign policy - based as it is on 19th-century notions of the nation-state - is long past its sell-by date. We need a new set of principles to govern our diplomacy and military strategy - principles that are based on the idea of human security and not national security, health and wellbeing and not economic self-interest and territorial ambition.

The best hope we can have from our terrible misadventure in Iraq is that a new political and social movement will grow to overturn this politics of humiliation. We are one human family. Let's act like it.

· Richard Horton is the editor of the Lancet

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