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Today we elect a new president. Whoever he is, his most pressing issue will be the intersection of religion, especially militant Islam, and international affairs. Our physical security and public diplomacy not only demand candor and nuanced analysis regarding religion and realpolitik, they demand institutional change within our government.

Unfortunately, we Americans just don’t seem to get it. In the first part of 2003, for example, the Coalition Provisional Authority issued its plan for elections and the turn-over of sovereignty in Iraq. On June 28, 2003, Grand Ayatollah Sistani, the senior cleric in Iraq, issued a fatwa against this plan, calling it undemocratic. It was not until mid-November that U.S. policy-makers realized how important Sistani was to a peaceful transition; then Administrator Paul Bremer soon came home for “emergency consultations.” (See, for example, “Sensing Shiites Will Rule Iraq, U.S. Starts to See Friends, Not Foes,” by Steven R. Weisman, New York Times, November 20, 2003, Page A1; “How Cleric Trumped U.S. Plan for Iraq,” by Rajiv Chandrasekaran, Washington Post, November 26, 2003. Page A1; and “Forget Vietnam,” by Sydney J. Freedberg Jr., National Journal, November 21, 2003.) We lost a year in Iraq for many reasons, but foremost among them was our inability to understand the role religion plays in realpolitik.

Recently, the Atlantic Monthly published an article on “Forensic Theology” revealing the work of a few analysts, “pioneers,” the article calls them‚ who have been working since the 1990s to better understand the theology behind the religious edicts, or fatwas, of militant Islamic clerics. (See Stephen Grey, “Follow the Mullahs,” The Atlantic Monthly, November 2004.) As encouraging as this news is, it does make you wonder; if we have been at war with variants of radical Islam, Shi’a and Sunni, since the capture of our embassy in Tehran in 1979, why has it taken so long to finally examine their theology in some kind of systematic manner?

To be fair, since 9/11, our government has naturally focused its domestic and international attention on physical security, promising gates, guards and guns against the terrorist threat. Initially paramount, this focus nonetheless reacts to the symptom not the cause. If we want to avoid merely hacking at the leaves of evil, to paraphrase Thoreau, we must begin to strike at the root‚ a radical root that is simultaneously ideological and theological.

In many ways, militant Islam is an ideology, with characteristics that are conceptually no different than other radical ideologies like communism or fascism. It provides a simple and ordered explanation of the world and who the enemy is. It acts as a catalyst, motivating its followers against the enemy, while painting a portrait of a better world absent the enemy. Understanding militant Islam as an ideology is useful because it helps us name the dynamics at play and to recognize and predict the associated patterns.

Yet militant Islam is also rooted in theology, a theology that contains the seeds of militant Islam’s defeat. Working with Muslims to better understand, promote, and institutionalize the best of the Islamic faith‚ as we have recently witnessed in Afghanistan’s new constitution‚ is the only answer we have. It is incumbent upon Muslims and U.S. policymakers alike to know Islam at its theological best, not its ideological worst.

But here’s the rub: we don’t know how to think like this. The U.S. government, as most policymakers will tell you, is not outfitted‚ organizationally and, more importantly, conceptually‚ to fight a multi-generational war that is both ideological and theological. In this context, I would like to offer some practical recommendations that, if nothing else, get this conversation going.

First and foremost, the U.S. government needs to re-consider its Counterterrorism Strategy and its efforts to “diminish” terrorism. From using public diplomacy to explain the war against the terrorists to integrating religious freedom into operational strategies (instead of wielding it as a punitive club), the U.S. government needs to develop holistic, tangible strategies and measures of effectiveness.

Second, as a near-term stop-gap, a special assistant to the president for religion and religious freedom, serving on the National Security Council, should be identified and appointed. The roles and expectations of appropriate officials in each of the major U.S. agencies should also be adjusted. For example, the Assistant Secretary of Defense for Special Operations/Low Intensity Conflict should have religion/religious freedom assigned to his portfolio.

Third, we must incorporate new curricula at entry-, mid- and top-level schools for U.S. officials. We cannot expect American policymakers and implementers to instinctively understand religion and religious freedom around the world. We must prepare them through education and training.

Finally, there needs to be a one-stop-shopping place where U.S. agencies can go for these issues. There does not now exist an analytical focal point for religion and religious freedom at the operational or strategic level of our government. A “center of excellence” for these issues would serve as a living repository of lessons learned that any U.S. agency might reference for its own global operations. It could also offer timely assessments of the potentially positive and negative implications of a given religion across a range of issues and regions. This kind of analysis would, in turn, lead to new models and measures of effectiveness for gauging religion and U.S. policy in international affairs.

These are not easy changes. They force Americans to talk about the two topics they have been taught since childhood not to talk about in polite conversation: “religion and politics.” Religion is politics in most of the world. Ignoring this fact will only hamper our ability to deal comprehensively with extremely complex issues. But talk we must, and then act. Early in his term‚ as part of the first-100-days agenda‚ the next president should take the lead in this kind of conversation about religion and realpolitik, and implement the changes we urgently need.