The FBI began to monitor Pauling in 1950, when he became a contract employee of the US Navy. As Pauling involved himself more closely with the peace movement, the FBI likewise began to monitor his activities more stringently.
By 1960 Linus Pauling had become a controversial political figure. His importance in the international peace movement was cemented in 1957 when he wrote the “Appeal by American Scientists to the Governments and Peoples of the World“, a petition against nuclear bomb testing worldwide. Pauling, along with more than 13,000 other scientists throughout the world, signed this petition in an effort to curb the deleterious health effects that nuclear bomb tests were causing to humans. This effort resulted in Pauling’s receipt of a second Nobel, the Peace Prize, in 1963.Not only the FBI, but also the SISS had begun to keep tabs on Pauling’s peace work and ultimately subpoenaed Pauling in June 1960. The purpose was to investigate Pauling’s anti-Bomb petitions — how they were devised, who gathered signatures, and where the funding came from. The underlying question was: How had Pauling managed to get all those thousands of names without a large — possibly Communist — organization behind him? .
When he appeared before the committee with his lawyer at his side, Pauling answered all the members’ questions except one: a request to provide the names of everyone who had helped him circulate his petitions. Pauling, after conferring with his lawyer, refused to name names. “The circulation of petitions is an important part of our democratic process,” he told the committee. “If it is abolished or inhibited, it would be a step toward a police state. No matter what assurances the subcommittee might give me concerning the use of names, I am convinced the names would be used for reprisals against these enthusiastic, idealistic, high-minded workers for peace.” Pauling did not want the system to be curtailed “by representatives of defense industries who benefit financially from the cold war.” He knew he was risking a citation for contempt of Congress. But he was adamant. He was told in reply that the committee would give him a month to come up with the requested names.
By the time he was called back before the SISS on August 9, 1960, Pauling’s refusal to provide names to the committee had become a national issue. His petitions, he told the press, “were not Communist inspired. I inspired them.” He attacked the committee for attempting to stifle free speech. “Do you think anybody tells me what to do — with threats? I make up my mind. If I want to take a chance, I take a chance.”
His brave words masked deep concern. His refusal to cooperate with the Senate could cost him up to a year in prison. But by this time the McCarthy Era was nearing its end, and public opinion was beginning to swing away from knee-jerk support for anti-Communist witch hunts. The nation’s newspaper editorialists began writing in support of Pauling, with one calling the SISS investigation “superfluous,” and another editorialist writing “My blood tingles with pride now as I read Dr. Pauling’s refusal to bow to this bullying committee.” Pauling’s lawyer succeeded in postponing the next hearing until October, giving the Paulings time to travel and speak widely about the investigation.
Pauling was behaving more like an honored diplomat than a fellow traveler, speaking across the US and Europe, and meeting in Geneva with the American, British, and Soviet ambassadors. He attacked the SISS in every speech he gave. By the time his second appearance neared in the Fall, Pauling appeared to have marshaled public opinion behind him.
On the night of October 10, he was served with a subpoena to appear before the committee the next morning — and to bring the requested information about his petitions. The hearing room the next day was packed. He was asked again for the names of those who had helped him. “I am unwilling to subject these people to reprisals by the committee,” he said. “I could protect myself by agreeing, but I am fighting for other persons who could not make a fight themselves.” The committee counsel retreated, then turned in another direction, grilling Pauling for the remainder of the day about his affiliation with suspect groups. In the end the committee leadership, unwilling to make Pauling a martyr, backed down. Pauling never gave the names, and was never cited for contempt.
Despite Pauling’s dismissal by the committee, many articles continued to be published in newspapers and magazines around the country that decried Pauling as a communist supporter and criticized his refusal to release the names of the people who had help to collect signatures for the bomb test petition.
Although it was successful on the international level, the bomb test petition was controversial at home due to the conservative political climate at the time and the strong anti-communist sentiment prevailing during the Cold War. Pauling wished to collaborate with all citizens throughout the world on the petition, regardless of their governmental or economic system, a position that many saw as a potential threat to U.S. security. Indeed, in the eyes of some, opposition to nuclear bomb testing was equated with being a communist.
In an interview with Harry Kriesler on 18 January 1983, Pauling reflected about his advocacy of nuclear disarmament:
Kriesler: Were charges made against you that you were for unilateral disarmament? In a public debate there tends to be such a distortion of views that are so different from the conventional as yours were in the fifties.
Pauling: There were some irresponsible statements about me to the effect that I was working for disarming the United States, that I was taken by Soviet propaganda, and that sort of thing. Of course, I was speaking out contrary to the official opinion. If we had had a dictatorship in this country, I might well have been accused of the crime of seditious libel, which is used in dictatorships to suppress criticism. When I was awarded the Nobel Peace Prize in 1963, Life Magazine published an editorial with the heading “A Weird Insult from Norway — The Norwegian Nobel Committee Awards the Peace Prizes.” I think that the writer of this editorial thought that it was insulting to give the peace prize to someone who advocated something that was not the official policy of the United States government.
Kriesler: And, indeed, when you circulated a 1958 petition which was signed by 2,000 American scientists, and I think 8,000 foreign scientists from 49 different countries, there was government harassment, there was harassment in the press, and charges of working for the enemy.
Pauling: I first announced that 2,000 American scientists had signed the petition asking for cessation of the testing of nuclear weapons on the atmosphere where they were liberating radioactive fallout over the whole world that would cause defective children to be born and that would damage living human beings, causing cancer and other diseases. We asked that the nations make an agreement to stop testing of nuclear weapons. At that time, the government policy was not to make this treaty, it had not yet been decided, but pretty soon it was decided to make such a treaty. I think that I got a good bit of support but some criticism also. I’d written this petition together with Barry Commoner and Ed Condon. Ed Condon is a Berkeley man who was at that time Professor of Physics at Washington University in St. Louis; Barry Commoner was Professor of Biology at Washington University. We circulated the petition. Scientists from foreign countries began to send in signed copies of the petition, so my wife and I circulated it in foreign countries and ultimately turned over 13,000 signatures of scientists to Secretary-General Dag Hammarskjöld of the United Nations.
Kriesler: Do you feel that scientists have a special moral responsibility to make known these insights and mobilize public opinion?
Pauling: Yes. I think that scientists have a special responsibility. All human beings, all citizens, have a responsibility for doing their part in the democratic process. But almost every issue has some scientific aspect to it, and this one of nuclear war, or war in general, is of course very much a matter of science. Scientists understand the problem somewhat better than their fellow citizens. I think that scientists who are able to do it, who are in the position to do it, and who have the ability to do it, should help their fellow citizens to understand what the issues are and how they look at it, and should go beyond that and express their own opinions for the benefit of their fellow citizens.
Kriesler: What about the problem of science in the Soviet Union, and the problem of science and peace movements in the Soviet Union? One can compare, for example, your career here and your harassment by the government here with the situation of Sakharov, for example, or with the suppression recently of a burgeoning peace movement there.
Pauling: I was harassed, of course, in a less blatant way when my passport was refused at the time that the Royal Society of London had arranged a conference of scientists, a two day symposium, on the biochemistry of DNA, and on my ideas. I would be the first speaker. And the second speaker was my associate Professor Cory, and then there were talks from people from many countries for the next two days. I wasn’t there because my passport was withheld from me on the grounds that it was not in the best interest of the United States. A statement was made that my anticommunist statements hadn’t been strong enough. So, I didn’t get to go and to see the X-ray photographs taken by Russell and Franklin, which I would have seen if I had gone to London on that occasion . And others. I was prevented from attending various scientific congresses. And, of course, I was threatened by the Internal Security Subcommittee of the Senate with a year in jail for contempt of Senate, when I was being harassed by the Internal Security Subcommittee.
 Footnote: Russell and Franklin’s X-rays would have shown Dr. Pauling that his research on the structure of DNA was based on a false hypothesis. By not attending the conference, Dr. Pauling was denied an opportunity to correct his ideas, leaving the field open to James Watson and Francis Crick, who received the Nobel Prize in 1962 for their discovery.