Harris is one of the best-known militant atheists right now. You need some missionary spirit, or at least a good performance of it, if you're going to run down all religion as bad and false. And atheists are not all peace-and-love hippie sorts. Some of them are social and political conservatives, even reactionaries.
Chomsky is good about pointing out the endless hypocrisy to be found in US foreign policy. But he does seem to regard almost everything about US foreign policy as based on unrelenting bad faith. And it seems every time I encounter his arguments, I find myself wishing he conveyed a little more practical awareness that foreign policy everywhere runs on hypocrisy as well as on calculations of national interests. Most importantly, he seems to be oblivious to the fact that just plain stupidity plays a significant role in foreign policy, just as it does in the rest of human life. Not everything destructive or wrong is because of bad faith decisions.
In this particular argument, I do think Chomsky has the better point on substance, by far. One of the biggest problems in American discussion of foreign policy is that our politicians and lobby groups promote a history-begins-today view of foreign policy issues. Al-Qaida bombs the World Trade Center and the Pentagon. Al-Qaida was based in Afghanistan with the permission of the Afghan government. We attack the Afghan government and install a new one. All that makes logical sense and satisfies the "American, f**k yeah!" impulse.
In a longer view, it looks different. Afghanistan was barely mentioned in American news until 1979 when the Soviets took over. Then through the 1980s, we supported Islamic fighters who were routinely described in the US press in the most laudatory terms, brave mujaheddin freedom fighters and the like. Many of them practiced the kind of brutal warfare we see today from ISIS and other Islamic extremist groups. But little was reported about that in the US press and even less said by our political leaders. The Soviet Union was the Evil Empire, the focus of evil in the modern world, as St. Reagan put it. The brave mujaheddin freedom fighters were the enemies of the Focus Of Evil, so we armed, trained and otherwise supported them. And in the process worked with Saudi Arabia to build up an international network for funding and supplying the brave mujaheddin freedom fighters. Part of that network evolved in the 1990s to become Osama bin Laden's Al-Qaida group.
On a somewhat longer scale, both the US and Israel promoted political Islam in various ways in the Middle East as a less Soviet-friendly alternative to the Arab nationalism associated with regimes in Egypt, Iraq and Syria. But this wasn't a one-dimensional effort. It didn't stop the US and/or Israel from having friendly and supportive relations with authoritarian regimes, e.g., US and Israel with Egypt, US with Saudi Arabia, Israel with Iran during the 1980s war against Saddam Hussein's secular regime while the US favored Iraq.
Chomsky performs a valuable service in reminding people over and over about the longer history and the larger picture it creates. If there were a better awareness of such things among policymakers and the public, our foreign policy could be considerably more constructive.
The exchange with Sam Harris includes a lot of hair-splitting quibbling. But the basic point is that Chomsky is talking about an example of US military action in the Muslim world, the cruise missile bombing of the Al Shifa pharmaceutical plant by the Clinton Administration in 1998. This came in the aftermath of the bombing of the US Embassies in Kenya and Tanzania by Al Qaida. The Administration also fired cruise missiles at Al Qaida camps in Afghanistan.
James Risen reported in To Bomb Sudan Plant, or Not: A Year Later, Debates Rankle New York Times 10/27/1999
Officials throughout the Government raised doubts up to the eve of the attack about whether the United States had sufficient information linking the factory to either chemical weapons or to bin Laden, according to participants in the discussions. They said senior diplomatic and intelligence officials argued strenuously over whether any target in Sudan should be attacked.The undated Kubar: Shifa Pharmaceutical Facility GlobalSecurity.org (accessed 05/06/2015) describes:
Aides passed on their doubts to the Secretary of State, officials said. But the national security adviser, Samuel R. Berger, who played a pivotal role in approving the strike, said in an interview that he was not aware of any questions about the strength of the evidence before the attack.
In the aftermath, some senior officials moved to suppress internal dissent, officials said. Secretary of State Madeleine K. Albright and a senior deputy, they said, encouraged State Department intelligence analysts to kill a report being drafted that said the bombing was not justified.
The Administration's initial characterization of the Al Shifa pharmaceutical plant, based on intelligence assembled primarily by CIA, which concluded that the Al Shifa plant was involved in the manufacture of chemical-warfare materials, was based on a soil sample which disclosed the presence of a chemical precursor of VX nerve gas.The 9/11 Commission Report (2004) describes the Al Shifa attacks this way:
Subsequently, however, independent experts questioned whether this chemical would be present in the soil of a chemical weapons facility, and noted that the chemical was also a pesticide residue. As to the initial claim that the facility did not produce commercial pharmaceuticals, it was subsequently revealed that the facility was in fact one of the primary pharmaceutical production facilities in Sudan, and was in fact a showplace routinely toured by schoolchildren who watched the plant's employees package and bottle medicines. Westerners who had either toured the plant or participated in its construction reported no evident restrictions on their movement, and no evidence of chemical weapons production activities. Many CIA analysts believe that, while there is evidence tying Al Shifa to chemical weapons at some point in the past, the evidence cited by the Administration did not represent the most compelling information on the facility.
By the early hours of the morning of August 20, President Clinton and all his principal advisers had agreed to strike Bin Ladin camps in Afghanistan near Khowst,as well as hitting al Shifa.The President took the Sudanese tannery off the target list because he saw little point in killing uninvolved people without doing significant harm to Bin Ladin. The principal with the most qualms regarding al Shifa was Attorney General Reno. She expressed concern about attacking two Muslim countries at the same time. Looking back, she said that she felt the “premise kept shifting. ...This article from The Nonproliferation Review Fall 1998 is particularly interesting in that it recounts the various reasons to doubt the chemical-weapons justification for the attack soon after the attack itself, Chemical Weapons in the Sudan: Allegations and Evidence by Michael Barletta1.
Much public commentary turned immediately to scalding criticism that the action was too aggressive. The Sudanese denied that al Shifa produced nerve gas, and they allowed journalists to visit what was left of a seemingly harmless facility. President Clinton,Vice President Gore, Berger, Tenet, and Clarke insisted to us that their judgment was right, pointing to the soil sample evidence.No independent evidence has emerged to corroborate the CIA’s assessment. (pp. 117-118)
Timothy Noah wrote about the case in Khartoum Revisited, Part 2 Slate 03/31/2004:
Why did the CIA end up being fixated on Al-Shifa? The best guess Chatterbox has seen is set forth in an October 1998 piece by the murdered Wall Street Journal reporter Daniel Pearl. Pearl suggested that a man named Mubarak Fadl Al Mahdi put the word out that Al-Shifa was mixed up with chemical weapons in order to hurt the plant's owner, Salah Idris, who was a political enemy of Mahdi's. Mahdi admitted to Pearl that he'd made it his business to collect information about the plant after Idris bought it. Pearl further reported that after the bombing, Mahdi issued a communiqué that said Al-Shifa had harbored "Iraqi scientists and technicians" and that most pharmaceutical plants in Sudan weren't "manned by foreign experts." (Mahdi denied having said anything about this before the bombing, and U.S. intelligence officials denied that they'd relied on anyone with a motive to hurt Idris.)So while not everyone may agree that the Al Shifa missile strike was as clearly reckless and heedless of life as Chomsky implies in his exchange with Harris, the point he is making is a valid one: people in the United States need to have a better understanding of how our country's actions look to the rest of the world.
It is possible that we'll one day learn Al-Shifa was a legitimate bombing target. Most of the information about this incident is still classified. ... But based on the evidence available now, Al-Shifa looks very much like the fiasco we thought it was then. The Sudan bombing is a blot on the Clinton presidency, and a blot it ought to remain.
Chomsky took some flack after the 9/11 attacks for talking about how an attack that was perceived as a relatively minor incident in the United States could look far more horrible to others. Sam Harris in this exchange is trying to beat Chomsky up for the same thing, trying to make Chomsky look guilty of a favorite conservative accusation, moral equivalence. As Chomsky says here, "'moral equivalence' [is] the term that has been regularly used, since Jeane Kirkpatrick, to try to undercut critical analysis of the state one defends."