The Wallace debacle in the 1948 election showed that the political middle in America was shifting to the right, away from FDR’s legacy, away from world cooperation and social liberalism, and toward a more militant anti-Communism. While FDR was alive, Pauling would have been considered a fairly typical New Dealer, perhaps to the left end of the Party, but in step with millions of others. Now Pauling found himself increasingly isolated on what was becoming the far left fringe. Fear was driving politics. But Pauling continued to speak out for hope, assailing atomic weapon development, arguing for world cooperation, and critiquing government programs like the loyalty oaths that he saw threatening freedom of expression. He was a brave man. He was also about to be taught a lesson.

Late in 1947, the FBI, its files fattened with material from the Tenney Committee in California, reviewed Pauling’s group affiliations and tagged him for further investigation. J. Edgar Hoover himself looked at Pauling’s file. But further action was hamstrung by a simple fact: Pauling was not a government employee. He worked for a private university, using privately donated research moneys. Government employees were subject to government investigation. Private citizens made far less easy targets. On a trip to England in 1948, Pauling was approached by a representative of the Assistant Naval Attaché for Research, who asked him if he might do a small service for his country by letting the Navy know his impressions of the laboratories he visited, nothing that would break confidences, just general observations of the state of British science. For this service, the government would pay him fifty dollars per day. Pauling agreed, signed a contract -- and immediately became subject to the federal loyalty program. The FBI started investigating in earnest.