If there is one central, recurring mistake the United States makes when dealing with the rest of the world, it is to assume that creating political stability is easy. We overthrew Saddam Hussein's regime in Iraq, and then cavalierly dismantled the entire structure of the Iraqi state, sure that we could simply set up a new one. We toppled the Taliban in Afghanistan and were confident that with foreign aid, elections and American know-how, we would build a new, modern Afghan nation. After all, the governments we were helping to set up—democratic, secular and inclusive—were so much better than the ones that preceded them. We should have paid more attention to the words of a wise man who opened one of his pioneering studies by declaring that "the most important distinction among countries concerns not their form of government but their degree of government."

Look around. So many of the world's problems—from terrorists in Waziristan to the devastating AIDS epidemic in Africa to piracy in Somalia—are caused or made worse by governments that are unable to exercise real authority over their lands or people. That was the central insight of Samuel P. Huntington, the greatest political scientist of the last half-century, who died on Christmas Eve.

Huntington is most famous for "The Clash of Civilizations," but his scholarly reputation properly rests on his earlier work. His analysis of political order had immediate, real-world applications. While studying the topic, he was asked by Lyndon Johnson's administration to assess the progress of the Vietnam War. After touring the place he argued, in 1967 and 1968, that America's strategy in South Vietnam was fatally flawed. The Johnson administration was trying to buy the people's support through aid and development. But money wasn't the key, in Huntington's view. The segments of South Vietnam's population that had resisted the Viet Cong's efforts had done so because they were secure within effective local communities structured around religious or ethnic ties. The United States, however, wanted to create a modern Vietnamese nation and so refused to reinforce these "backward" sources of authority. This 40-year-old analysis describes our dilemma in Afghanistan today.

Huntington noticed a troubling trend. Sometimes, progress American style—more political participation or faster economic growth—actually created more problems than it solved. If a country had more people who were economically, politically and socially active and yet lacked effective political institutions, such as political parties, civic organizations or credible courts, the result was greater instability. That has been the story of parts of the Third World over the past three decades. Think of Pakistan, whose population has gone from 68 million in 1975 to 165 million today, while its government has proved ill equipped to tackle the basic tasks of education, security and social welfare.

Living through change, people have often stuck with their oldest and most durable source of security: religion. That was the most important message of "The Clash of Civilizations." While others were celebrating the fall of communism and the rise of globalization, he saw that with ideology disappearing as a source of human identity, religion was returning to the fore.

My own relationship with that particular work is complicated. Huntington asked me to comment on a draft of the essay while I was his graduate student. I told him that while I disagreed with central elements of it, the essay was riveting and thought-provoking. A few months later, as the new managing editor of Foreign Affairs, I helped publish it. I still think he got some important things wrong, but much in that essay is powerful and prescient.