Lawmaking is not just a process by which Congress passes a bill and the president signs it. Much of it relies on federal agencies. Their rulemaking, which accounts for 90 percent of all federal laws, is how much policymaking in the United States actually occurs. An incompetent, understaffed bureaucracy bodes poorly for effective governing.

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Staffing key agency posts is already a difficult task. Officials in President Bill Clinton’s administration describe the appointment process as “chaotic,” “emotional” and “overwhelming,” according to David Lewis’s research. It looks as though Trump’s team is a living testament to these challenges.

Research on presidential appointments around transitions shows that, first, presidents attempt to control agencies they don’t trust by appointing loyal partisans to middle-management positions. The key question is then whether these loyalists also have the requisite qualifications and experience.

As Marissa Golden argues, career bureaucrats — those not appointed by the president — are willing to work with political appointees, but the quality of the appointees matters.

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When presidents do appoint qualified people, some bureaucrats may leave because of ideological differences with their new boss, but not because of any deeply held concerns about the mission of the agency. But appointing less-qualified loyalists is a different matter. When presidents seek to politicize agencies via purely patronage appointments, agencies will suffer much more. Many career bureaucrats, believing that their efforts will be wasted under incompetent leadership pursuing objectionable goals, leave the agency for good.

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The challenge confronting Trump is that many qualified appointees — such as Republicans who served under George W. Bush — publicly opposed Trump during the election. As a result, Trump’s transition team is having difficulty filling national security jobs.

Similarly, careerists in the Education Department and the Justice Department, observing the published lists of possible Cabinet appointees, are considering leaving en masse. A week before the election, a survey of federal workers found that only 65 percent would commit to serving under a Trump administration. The actual number is likely to be higher, but empty posts in the bureaucracy are still a cause for concern.

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A large-scale exodus of career bureaucrats has serious consequences for policy outcomes. For example, according to work by Anthony Bertelli and David Lewis, the Federal Emergency Management Agency under Bush suffered from high turnover as a result of appointed executives and the inexperienced leadership of Michael Brown. In the months immediately before Hurricane Katrina in 2005, 17 of 46 FEMA policy positions were empty.

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Another example involves the CIA. In 2004, as David Lewis describes, the Bush administration and congressional Republicans viewed the CIA as “dysfunctional” and a “rogue agency.” Bush appointed Porter Goss as CIA director with a clear mandate to hire loyal partisans to get the agency in line. Goss and his appointees told career CIA employees that they needed to support the administration and then froze out those who disagreed. Mass resignations quickly followed — among them 20 top managers, including the director of central intelligence and the executive director.

Bureaucratic agencies are pivotal actors in American policymaking. For his presidency to succeed, Trump’s transition team must reach out to qualified public servants and forgo any desire for revenge. It needs to limit turnover of career bureaucrats as much as possible.

If his administration fails at this, a wave of unqualified partisans entering the bureaucracy could damage some of our government’s most resilient institutions.

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Josh McCrain is a doctoral student in political science at Emory University.