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Finally, the writ of habeas corpus is used in our common-law legal system to demand that a neutral judge decide whether someone has been lawfully detained. Particularly in times of war, or even in response to threats against national security, the government has held suspected enemy agents without access to civilian courts, often without access to lawyers or a defense, seeking instead to try them before military tribunals or detain them indefinitely without trial. For example, during the Civil War, President Abraham Lincoln detained suspected Confederate saboteurs and sympathizers in Union-controlled states and attempted to have them tried in military court s, leading the Supreme Court to rule in Ex parte Milligan that the government could not bypass the civilian court system in states where it was operating.

Ex parte Milligan , 71 U.S. 2 (1866).

During World War II, the Roosevelt administration interned Japanese Americans and had other suspected enemy agents—including U.S. citizens—tried by military courts rather than by the civilian justice system, a choice the Supreme Court upheld in Ex parte Quirin ( [link] ).

Ex parte Quirin , 317 U.S. 1 (1942); See William H. Rehnquist. 1998. All the Laws but One: Civil Liberties in Wartime . New York: William Morrow.
More recently, in the wake of the 9/11 attacks on the World Trade Center and the Pentagon, the Bush and Obama administrations detained suspected terrorists captured both within and outside the United States and sought, with mixed results, to avoid trials in civilian courts. Hence, there have been times in our history when national security issues trumped individual liberties.

A photo of a group of people in a military commission, seated in chairs around a number of tables arranged in a U shape.
Richard Quirin and seven other trained German saboteurs had once lived in the United States and had secretly returned in June 1942. Upon their capture, a military commission (shown here) convicted the men—six of them received death sentences. Ex parte Quirin set a precedent for the trial by military commission of any unlawful combatant against the United States. (credit: Library of Congress)

Debate has always swirled over these issues. The Federalists    reasoned that the limited set of enumerated powers of Congress, along with the limitations on those powers in Article I , Section 9, would suffice, and no separate bill of rights was needed. Alexander Hamilton , writing as Publius in Federalist No. 84, argued that the Constitution was “merely intended to regulate the general political interests of the nation,” rather than to concern itself with “the regulation of every species of personal and private concerns.” Hamilton went on to argue that listing some rights might actually be dangerous, because it would provide a pretext for people to claim that rights not included in such a list were not protected. Later, James Madison , in his speech introducing the proposed amendments that would become the Bill of Rights, acknowledged another Federalist argument: “It has been said, that a bill of rights is not necessary, because the establishment of this government has not repealed those declarations of rights which are added to the several state constitutions.”

American History from Revolution to Reconstruction and Beyond, “Madison Speech Proposing the Bill of Rights June 8 1789,” http://www.let.rug.nl/usa/documents/1786-1800/madison-speech-proposing-the-bill-of-rights-june-8-1789.php (March 4, 2016).
For that matter, the Articles of Confederation had not included a specific listing of rights either.

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Source:  OpenStax, American government. OpenStax CNX. Dec 05, 2016 Download for free at http://cnx.org/content/col11995/1.15
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