The FBI under J. Edgar Hoover had been following Oppenheimer since before the war, when he showed Communist sympathies as a professor at Berkeley and had been close to members of the Communist Party, including his wife and brother. He had been under close surveillance since the early 1940s, his home and office bugged, his phone tapped and his mail opened. The FBI furnished Oppenheimer's political enemies with incriminating evidence about his Communist ties. These enemies included Lewis Strauss, an AEC commissioner who had long harbored resentment against Oppenheimer both for his activity in opposing the hydrogen bomb and for his humiliation of Strauss before Congress some years earlier; regarding Strauss's opposition to the export of radioactive isotopes to other nations, Oppenheimer had memorably categorized these as "less important than electronic devices but more important than, let us say, vitamins."
On June 7, 1949, Oppenheimer testified before the House Un-American Activities Committee, where he admitted that he had associations with the Communist Party in the 1930s. He testified that some of his students, including David Bohm, Giovanni Rossi Lomanitz, Philip Morrison, Bernard Peters and Joseph Weinberg, had been Communists at the time they had worked with him at Berkeley. Frank Oppenheimer and his wife Jackie testified before the HUAC and admitted that they had been members of the Communist Party. Frank was subsequently fired from his University of Minnesota position. Unable to find work in physics for many years, he became instead a cattle rancher in Colorado. He later taught high school physics and was the founder of the San Francisco Exploratorium.
Oppenheimer had found himself in the middle of more than one controversy and power struggle in the years from 1949 to 1953. Edward Teller, who had been so uninterested in work on the atomic bomb at Los Alamos during the war that Oppenheimer had given him time instead to work on his own project of the hydrogen bomb, had eventually left Los Alamos to help found, in 1951, a second laboratory at what would become the Lawrence Livermore National Laboratory. There, he could be free of Los Alamos control to develop the hydrogen bomb. Long-range thermonuclear "strategic" weapons delivered by jet bombers would necessarily be under control of the new United States Air Force (USAF). Oppenheimer had for some years pushed for smaller "tactical" nuclear weapons which would be more useful in a limited theater against enemy troops and which would be under control of the Army. The two services fought for control of nuclear weapons, often allied with different political parties. The USAF, with Teller pushing its program, gained ascendance in the Republican-controlled administration following the election of Dwight D. Eisenhower as president in 1952.
In 1950, Paul Crouch, Communist Party organizer for Alameda County from April 1941 to early January 1942, was the first person to accuse Oppenheimer of Communist Party ties. He testified before a Congressional committee that Oppenheimer had hosted a Communist Party meeting at his Berkeley home. The charges were widely publicized at the time. However, Oppenheimer was able to prove that he was in New Mexico at the time and Crouch over time was shown to be an unreliable informant. In November 1953, J. Edgar Hoover was sent a letter concerning Oppenheimer by William Liscum Borden, former executive director of Congress' Joint Atomic Energy Committee. In the letter, Borden stated his opinion "based upon years of study, of the available classified evidence, that more probably than not J. Robert Oppenheimer is an agent of the Soviet Union."
Strauss and Senator Brien McMahon, author of the 1946 McMahon Act, pushed Eisenhower to revoke Oppenheimer's security clearance. On December 21, 1953, Lewis Strauss told Oppenheimer that his security clearance had been suspended, pending resolution of a series of charges outlined in a letter, and discussed his resigning. Oppenheimer chose not to resign and requested a hearing instead. The charges were outlined in a letter from Kenneth D. Nichols, General Manager of the AEC. The hearing that followed in April–May 1954, which was initially confidential and not made public, focused on Oppenheimer's past Communist ties and his association during the Manhattan Project with suspected disloyal or Communist scientists. One of the key elements in this hearing was Oppenheimer's earliest testimony about George Eltenton's approach to various Los Alamos scientists, a story that Oppenheimer confessed he had fabricated to protect his friend Haakon Chevalier. Unknown to Oppenheimer, both versions were recorded during his interrogations of a decade before. He was surprised on the witness stand with transcripts of these, which he had not been given a chance to review. In fact, Oppenheimer had never told Chevalier that he had finally named him, and the testimony had cost Chevalier his job. Both Chevalier and Eltenton confirmed mentioning that they had a way to get information to the Soviets, Eltenton admitting he said this to Chevalier and Chevalier admitting he mentioned it to Oppenheimer, but both put the matter in terms of gossip and denied any thought or suggestion of treason or thoughts of espionage, either in planning or in deed. Neither was ever convicted of any crime.
Teller testified against Oppenheimer, saying that he considered him loyal, but of such questionable judgment that he should be relieved of clearance on the basis of bad decision-making. This led to outrage by the scientific community and Teller's virtual expulsion from academic science. Groves, threatened by the FBI as having been potentially part of a coverup about the Chevalier contact in 1943, likewise testified against Oppenheimer. Many top scientists, as well as government and military figures, testified on Oppenheimer's behalf. Inconsistencies in his testimony and his erratic behavior on the stand, at one point saying he had given a "cock and bull story" and that this was because he "was an idiot", convinced some that he was unstable, unreliable and a possible security risk. Oppenheimer's clearance was revoked one day before it was due to lapse anyway. Isidor Rabi's comment was that Oppenheimer was merely a government consultant at the time anyway and that if the government "didn't want to consult the guy, then don't consult him."
During his hearing, Oppenheimer testified willingly on the left-wing behavior of many of his scientific colleagues. Had Oppenheimer's clearance not been stripped then he might have been remembered as someone who had "named names" to save his own reputation. As it happened, Oppenheimer was seen by most of the scientific community as a martyr to McCarthyism, an eclectic liberal who was unjustly attacked by warmongering enemies, symbolic of the shift of scientific creativity from academia into the military. Wernher von Braun summed up his opinion about the matter with a quip to a Congressional committee: "In England, Oppenheimer would have been knighted."
In a seminar at the Woodrow Wilson Institute on May 20, 2009, based on an extensive analysis of the Vassiliev notebooks taken from the KGB archives, John Earl Haynes, Harvey Klehr and Alexander Vassiliev confirmed that Oppenheimer never was involved in espionage for the Soviet Union. The KGB tried repeatedly to recruit him, but was never successful; Oppenheimer did not betray the United States. In addition, he had several persons removed from the Manhattan Project who had sympathies to the Soviet Union.
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