Things got worse for Pauling in 1950. At the national level, there were revelations of spying within the atomic research program, then the perjury conviction of Alger Hiss. Senator Joe McCarthy of Minnesota started generating headlines by waving lists of suspected Communists in government. The US announced it was going to develop a new type of "superbomb." The membership of the FAS shrank to half of what it had been.

Pauling responded by giving one of his finest peace speeches to a packed Carnegie Hall on February 13. In it, he called for negotiations with the USSR and advised that the National Science Foundation should set up a program to study the causes and prevention of war. "An atomic war would kill everyone, left, right, or center," he exhorted. "The world has finally come to the critical point in time at which the ultimate, irrevocable decision has to be made. This is the decision between, on the one hand, a glorious future for all humanity, and, on the other, death, devastation, and the complete destruction of civilization."

His words were greeted with loud applause. It was one of many speeches he gave in the spring of 1950, every one of them monitored by reporters for the right-wing press, California investigatory committee representatives, or FBI agents. When not monitoring his activities directly, agents were questioning his colleagues and laboratory staff. They found evidence that one of his assistants, Sidney Weinbaum, was a Communist Party member. It turned out to be true. Weinbaum, however, denied it under oath and was arrested, tried, and convicted of perjury. Pauling, who had been friends with Weinbaum for decades, further alienated the conservative trustees at Caltech by working to raise money for his employee’s defense fund. "What the Institute had at that time were some people who were just so opposed to Communism that they were almost rabid on it," remembered Arnold Beckman, then himself a trustee. "And Linus’s behavior bothered them a great deal, particularly when Sidney Weinbaum was accused and then convicted. . . . So many people thought Linus was a Communist. And Linus, being the independent character he is, didn’t do anything to mollify them."