In 1965, as president, Johnson named Mr. Boyd under secretary of commerce for transportation. Mr. Boyd soon resolved to end what he regarded as wasteful federal subsidies to American merchant ships. Invited to the Oval Office to discuss his plan with Johnson and his chief domestic aide, Joseph A. Califano Jr., Mr. Boyd, according to his memoir, got into a heated dispute with the president:
“‘You don’t know what you’re talking about, Alan,’ Johnson said. ‘The merchant marine is our fourth arm of defense. If we got into another war without it, we would be totally helpless.’
“‘Mr. President,’ I said, ‘you are crazy as hell.’
“Joe seemed shocked that I would address the president in such a tone. But I had gotten to know the president, and knew he would take my comments in stride. I pointed out that American shipping companies owned hundreds of ships registered under flags of convenience. Those ships had served the United States during World War II and Korea, and they would be available in case of future need.
“ ‘All right, you bastard,’ the president shot back. ‘I know you’re right. And I also know you’re going to get us both killed politically. I’ll support you for a year. See what you can do.’”
Mr. Boyd used the year. He made his case to shipowners, the Seafarers International Union and to Congress, but got nowhere. The subsidies were too entrenched. He told the president he had failed.
“I knew you would, Alan,” Johnson had said, according to Mr. Boyd’s memoir. “But you gave it a good try.”
In 1966, Johnson revived a long-discussed idea of streamlining the nation’s fragmented transportation systems. There were 35 agencies with related responsibilities. Americans spent 20 percent of their income on transportation. Mr. Boyd led a group that studied the problems, wrote a bill to create the Department of Transportation and shepherded it through Congress.
Johnson signed the bill into law on Oct. 15, 1966, and the department began operation on April 1, 1967. Mr. Boyd, confirmed by the Senate without opposition as the first transportation secretary, picked both Democrats and Republicans as aides, insisting that transportation was nonpartisan. He plunged into airport modernization, air traffic control improvements, enforcement of auto safety standards and driver education.