President Harry Truman famously remarked about his successor, “He’ll sit here, and he’ll say, ‘Do this! Do that!’ And nothing will happen. Poor Ike — it won’t be a bit like the Army. He’ll find it very frustrating.” Donald Trump ascended to the presidency with far less experience than General Eisenhower. He also took over a government that is much larger. All signs indicate that he, as Truman predicted about Eisenhower, is very surprised at the limits of his ability to control the executive branch.

In the past few weeks, there have been a number of times when executive agencies have taken actions directly contrary to the wishes of the president. Most prominently, last week the Mueller investigation of Russian interference in the 2016 presidential election produced a series of revelations that implicate those close to the president. President Trump Donald John TrumpOmar fires back at Trump over rally remarks: 'This is my country' Pelosi: Trump hurrying to fill SCOTUS seat so he can repeal ObamaCare Trump mocks Biden appearance, mask use ahead of first debate MORE tweets continuously about Mueller and “witch hunts” and even appointed an acting Attorney General supposedly hostile to the investigation. Yet Mueller carries on.

Right before Thanksgiving, the Trump Administration issued the National Climate Assessment which laid bare the dangers to the United States of man-made climate change. Trump denied the conclusions of the report, a strange reaction for a president regarding a report from the executive branch of government.

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Finally, while the President has gradually walked back his condemnation of Mohammed bin Salman of Saudi Arabia for his potential involvement in the murder of journalist Jamal Khashoggi, the CIA had a different response. They issued a report tying bin Salman to the murder.

Supporters of the president bemoan the “deep state,” in each of these cases. Steve Bannon Stephen (Steve) Kevin BannonJuan Williams: Swamp creature at the White House Engineers say privately funded border wall is poorly constructed and set to fail: report Bannon and Maxwell cases display DOJ press strategy chutzpah MORE called for its deconstruction in the early days of the administration. But there is no grand conspiracy out there to buck the president or make him look foolish. It is just the government working the way it was designed over the past century.

Most importantly, agencies like the CIA and the EPA don’t just work for the president. In our system of government, they also work for the body that created them and exercises oversight over them, the U.S. Congress. Failure to follow the will of Congress on the part of agencies leads first to unpleasant hearings on Capitol Hill, and then perhaps riders on budget bills, Congressional investigations, or reduced funding for your agency.

Executive branch agencies also have to worry about the third branch of government, the judiciary. In other words, they have to follow the law. The National Climate Assessment was written pursuant to a law passed in the early 1990s. Failure to follow the law results in embarrassment for agencies, and the wasting of valuable resources. The Trump Administration has learned this the hard way as many of their attempts at deregulation have been halted by the courts.

None of this is to say that agency officials (or the “deep state”) don’t have their own policy preferences. They do. Prosecutors like to see their targets behind bars whether they are presidential advisers or alleged drug kingpins. Those who work in environmental agencies place a value higher on environmental protection than on other consequences of economic activity.

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But their preferences are a minor contributor to President Trump’s difficulty in controlling the agencies that report to him. A much bigger problem for the president are the laws written by Congress (and signed by previous presidents) that direct those agencies to behave in certain ways, and the courts charged with making sure agencies follow those laws.

President Trump is fighting the law, not the deep state, when he complains about agency actions. And, as the song tells us, when you fight the law, the law usually wins.

Stuart Shapiro is professor and director of the Public Policy Program at the Bloustein School of Planning and Public Policy at Rutgers University, and a member of the Scholars Strategy Network. Follow him on Twitter @shapiro_stuart.