"I know extremely few people who are recognized as Communists," Pauling wrote in 1949, "but I do belong to a number of organizations that have been described as Communist-front organizations." He saw his activities for peace and against the spread of atomic weapons as patriotic acts, and was encouraged by his own experiences to believe that Communists and non-Communists could work together to achieve laudable goals.

As anti-Communist efforts in the US continued to grow, however, the ranks of Americans who spoke in favor of collaborating with Reds thinned until Pauling was one of the few high-profile scientists unafraid to speak his mind. Almost by default, he found himself becoming a leader of the Left, hosting visiting critics of US policies, sponsoring leftist conferences, and speaking out about the way he saw the US loyalty program stifling political dissent. The press began going to him for quotes; his political activities began to receive coverage in the newspapers. In the fall of 1949, Pauling led a US delegation to an international Conference for World Peace held in Mexico City, a meeting promptly -- and, it was later shown, correctly -- criticized in the US as Communist-organized.

That did not stop Pauling. The subsequent news coverage was precisely the type of publicity that the President of Caltech, Lee DuBridge, did not want to see generated by one of his faculty members. Several of his school’s trustees, most of them businessmen and a number of them very conservative, had complained about Pauling’s public activities for years. DuBridge had defended him. When news coverage of the Mexico City conference spurred one of them to write DuBridge asking for an explanation, DuBridge replied that there was little he could do as long as Pauling’s outside activities did not affect his work as a professor. Then DuBridge tried a new tack, sending Pauling out to dinner with a local businessman who had complained about his Communist leanings. Pauling tried to turn the conversation away from politics and toward science. But afterward, the businessman wrote Pauling a note, "Remember my friendly warning: Don’t get too far out on a limb with some of these ‘questionable’ groups. Some of us have saws and can use them."