Johnson was born in 1931 in Phoenix, Arizona. He earned a B.A. degree in Economics in 1953 and a M.A. and a Ph.D. in political science in 1957 and 1961 respectively. All of his degrees were from the University of California, Berkeley. During the Korean War, Johnson served as a naval officer in Japan. He taught political science at the University of California from 1962 until he retired from teaching in 1992. He was best known early in his career for scholarship about China and Japan.

Johnson set the agenda for ten or fifteen years in social science scholarship on China with his book on peasant nationalism. His book MITI and the Japanese Miracle, on the Japanese Ministry of International Trade and Industry was the preeminent study of the country's development and created the subfield of what could be called the political economy of development. He coined the term "developmental state." As a public intellectual, he first led the "Japan revisionists" who critiqued American neoliberal economics with Japan as a model; their arguments faded from view as the Japanese economy stagnated in the mid-90s and beyond. During this period, Johnson acted as a consultant for the Office of National Estimates, part of the CIA, contributing to analysis of China and Maoism.

Johnson was elected a Fellow of the American Academy of Arts and Sciences in 1976. He served as Director of the Center for Chinese Studies and Chair of the Political Science Department at Berkeley, and held a number of important academic posts in area studies. He was a strong believer in the importance of language and historical training for doing serious research. Late in his career he became well known as a critic of "rational choice" approaches, particularly in the study of Japanese politics and political economy.

Johnson is today best known as a sharp critic of American imperialism. His book Blowback (2000) won a prize in 2001 from the Before Columbus Foundation, and was re-issued in an updated version in 2004. Sorrows of Empire, published in 2004, updated the evidence and argument from Blowback for the post-9/11 environment and Nemesis concludes the trilogy. Johnson was featured as an expert talking head in the Eugene Jarecki-directed film Why We Fight, which won the 2005 Grand Jury Prize at the Sundance Film Festival. In the past, Johnson has also written for the Los Angeles Times, the London Review of Books, Harper’s Magazine, and The Nation

Johnson sees that the enforcement of American hegemony over the world constitutes a new form of global empire. Whereas traditional empires maintained control over subject peoples via colonies, since World War II the US has developed a vast system of hundreds of military bases around the world where it has strategic interests. A long-time Cold Warrior, he applauded the collapse of the Soviet Union: "I was a cold warrior. There's no doubt about that. I believed the Soviet Union was a genuine menace. I still think so." But at the same time he experienced a political awakening after the collapse of the Soviet Union, noting that instead of demobilizing its armed forces, the US accelerated its reliance on military solutions to problems both economic and political. The result of this militarism (as distinct from actual domestic defense) is more terrorism against the US and its allies, the loss of core democratic values at home, and an eventual disaster for the American economy. The books of the trilogy are:

• Blowback: The Costs and Consequences of American Empire

Chalmers Johnson summarizes the intent of Blowback in the final chapter of Nemesis.

"In Blowback, I set out to explain why we are hated around the world. The concept "blowback" does not just mean retaliation for things our government has done to and in foreign countries. It refers to retaliation for the numerous illegal operations we have carried out abroad that were kept totally secret from the American public. This means that when the retaliation comes - as it did so spectacularly on September 11, 2001 - the American public is unable to put the events in context. So they tend to support acts intended to lash out against the perpetrators, thereby most commonly preparing the ground for yet another cycle of blowback. In the first book in this trilogy, I tried to provide some of the historical background for understanding the dilemmas we as a nation confront today, although I focused more on Asia - the area of my academic training - than on the Middle East."

• The Sorrows of Empire: Militarism, Secrecy, and the End of the Republic

Chalmers Johnson summarizes the intent of The Sorrows of Empire in the final chapter of Nemesis.

"The Sorrows of Empire was written during the American preparations for and launching of the invasions and occupations of Afghanistan and Iraq. I began to study our continuous military buildup since World War II and the 737 military bases we currently maintain in other people's countries. This empire of bases is the concrete manifestation of our global hegemony, and many of the blowback-inducing wars we have conducted had as their true purpose the sustaining and expanding of this network. We do not think of these overseas deployments as a form of empire; in fact, most Americans do not give them any thought at all until something truly shocking, such as the treatment of prisoners as Guantanamo Bay, brings them to our attention. But the people living next door to these bases and dealing with the swaggering soldiers who brawl and sometimes rape their women certainly think of them as imperial enclaves, just as the people of ancient Iberia or nineteenth-century India knew that they were victims of foreign colonization."

• Nemesis: The Last Days of the American Republic.

Chalmers Johnson summarizes the intent of the book Nemesis.

“In Nemesis, I have tried to present historical, political, economic, and philosophical evidence of where our current behavior is likely to lead. Specifically, I believe that to maintain our empire abroad requires resources and commitments that will inevitably undercut our domestic democracy and in the end produce a military dictatorship or its civilian equivalent. The founders of our nation understood this well and tried to create a form of government — a republic — that would prevent this from occurring. But the combination of huge standing armies, almost continuous wars, military Keynesianism, and ruinous military expenses have destroyed our republican structure in favor of an imperial presidency. We are on the cusp of losing our democracy for the sake of keeping our empire. Once a nation is started down that path, the dynamics that apply to all empires come into play — isolation, overstretch, the uniting of forces opposed to imperialism, and bankruptcy. Nemesis stalks our life as a free nation.”

Johnson released his fourth book concerning American imperialism, Dismantling the Empire: America's Last Best Hope, in August 2010. The book was published by Metropolitan Books.

• A National Intelligence Estimate on the United States by Chalmers Johnson (from Harper's Magazine)
• Empire v. Democracy: Why Nemesis Is at Our Door by Chalmers Johnson
• Blowback Chalmers Johnson essay from The Nation
• Cold Warrior in a Strange Land Tom Engelhardt interviews Chalmers Johnson
• Can We End the American Empire Before It Ends Us? By Chalmers Johnson, Tomdispatch.com. Posted May 17, 2007.
• Three Good Reasons to Liquidate Our Empire by Chalmers Johnson, The Huffington Post

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