When President Bush exits the White House in January, he will leave behind a federal government in shambles.

Since his first term, Bush has pressed forward with a radical view of the executive branch. Beyond adopting autocratic positions on foreign policy and taking broad liberties to subvert the Bill of Rights, Bush has waged a quieter — and perhaps more damaging — war at home against the very agencies under his charge.

From formaldehyde-soaked FEMA trailers, tainted pharmaceuticals and politically motivated firings of U.S. attorneys, to allegations of retaliation against government whistleblowers and an exodus of career officials from key regulatory positions, the Bush administration has lorded over a highly politicized and increasingly ineffective federal bureaucracy.

Policy analysts and legal scholars paint a picture of an executive intent on controlling every aspect of the federal bureaucracy, in particular the agencies tasked with regulating industry and commerce.

Taken as a whole, the president’s rejection of international law and his consolidation of administrative oversight are representative of a decades-long effort by conservatives to implement a so-called “unitary executive theory” — a euphemism for virtually unlimited presidential power.

But for such a creation to succeed, the executive must assert its influence over all aspects of government, from the top down, through the ranks of the roughly 3 million civilian employees that today work in government jobs at more than 100 agencies and sub-agencies.

Even his detractors say this is something Bush has been especially adept at.

“Despite their ineptitude in a lot of other areas and how poor they are at governing, one of the things the Bush administration has been very good at is using administrative mechanisms to control policy outcomes,” says Rick Melberth, director of regulatory policy at the nonpartisan watchdog group OMB Watch.

Bush didn’t invent this theory, but regulatory experts say his administration has worked harder than any other to perfect it.

“I have worked on regulatory issues inside the Beltway since 1976, and have watched five presidents come and go,” says Rena Steinzor, president of the Center for Progressive Reform and a professor at University of Maryland Law School. “The Bush administration is the most hostile and aggressive toward these agencies by a couple of orders of magnitude, making the Reagan era look relatively benign.”

Steinzor says the next president will face a daunting task in putting the house back in order: “No matter who is elected in November, it will take years to repair this damage.”

The damage is evident in almost every federal agency and characterized most visibly by dwindling morale among career civil servants. None have suffered more than those in the scientific community, which has been forced to confront a growing cadre of inexperienced political appointees bent on pursuing a pro-business agenda.

An April survey conducted by the Union of Concerned Scientists found that nearly two-thirds of responding Environmental Protection Agency (EPA) scientists said they experienced political interference with their work.

“Politics is injected and elevated into decisions where science and rational judgment should prevail,” Melberth says. “Politics supersedes scientific and technical information that is critical to protecting our environment and health and safety at home and in the workplace.”

What’s more, research by political science professor David E. Lewis of Vanderbilt University shows that politicization results in lower agency competence and that political appointee-run programs earn systematically lower grades in most management areas.

Says Lewis: “Many of the politicization scandals in this administration came from cases where unqualified or inexperienced people got into key jobs … often with the power to hire others or control information flows.”

Congress seeks answers

Since the Democrats took back Congress in 2006, numerous hearings have examined the extent to which political policy has penetrated rulemaking.

Rep. Henry Waxman (D-Calif.), chair of the House Committee on Oversight & Government Reform, has been investigating the growth and influence of political appointees in federal agencies — in particular their interference with scientific research. Among the committee’s findings is that — despite Republicans’ oft-stated disdain for bloated government — the number of such appointees has actually expanded under Bush.

During his first term, federal jobs available to political appointees rose 15 percent, according to the 2004 edition of the “Plum Book,” which Congress publishes after each presidential election to list open positions.

In fact, in the first five years of the Bush administration, the total number of political appointees grew by 307 — or 12 percent — according to a 2006 report released by Waxman’s committee. At the same time, the number of Schedule C appointees — who are exempt from confirmation or qualification review — increased 33 percent during Bush’s first term.

In one of the more egregious examples, Bush appointed George Deutsch as NASA press officer in 2005. Deutsch, a then 24-year-old former Bush campaign staffer with no relevant scientific training, fell under fire almost immediately for attempting to censor the agency’s scientists. Most notably, he instructed senior scientists to refer to “the Big Bang” as a “theory,” and he tried to restrict scientists’ access to the media. He resigned in 2006 when it was revealed that he had lied on his resume about graduating from college.

But as the federal workforce has grown larger, it hasn’t gotten more done. Just the opposite: An analysis conducted by the Washington Post at the end of Bush’s first term found that since he took office, federal agencies had begun roughly one-quarter fewer regulations than President Clinton and 13 percent fewer than Bush’s father during their first terms.

Paul Light, a Brookings Institution fellow and author of A Government Ill Executed: The Decline of the Federal Service and How to Reverse It, refers to this tactic as the “thickening” of government.

“Despite the president’s promise to bring business-like thinking to the federal government, the Bush administration has overseen, or at least permitted, a significant expansion of both the height and width of the federal hierarchy,” Light says. “There have never been more layers at the top of government, nor more occupants at each layer.”

For Bush, the slowing of the federal machine has been less about manipulating regulatory output and more about sabotaging the machine itself.

Rep. Danny Davis (D-Ill.), who chairs the subcommittee that oversees the federal workforce, says that while he respects the authority of the executive branch to follow and implement certain policy initiatives, the Bush administration may have crossed an ethical line.

“We’ve been particularly concerned that some of the scientific community is being co-opted by political manipulation, and that policy is being presented as fact,” Davis says.

At the end of July, Rep. John Conyers (D-Mich.) — chair of the House Judiciary Committee — held a hearing to take inventory of what he called the Bush “imperial presidency.” He noted a laundry list of administration shenanigans: improper politicization of the Justice Department and the U.S. attorneys’ offices; misuse of executive branch authority (including unitary executive theory); misuse of presidential regulatory authority; and improper retaliation against administration critics.

A brief history of the unitary executive

The modern concept of a unitary executive was formalized during President Reagan’s first term, largely through the efforts of then-Attorney General Ed Meese. At its heart, the theory asserts the supremacy of the executive branch and the role of president as chief executive officer with unilateral authority over the workings of the regulatory functions of government.

Reagan codified this so-called “centralized regulatory review” through two sweeping executive orders that essentially gave the White House the power over regulatory policy — from inception to planning to final implementation.

In 1981, Reagan issued Executive Order No. 12291, which gave the newly created Office of Information and Regulatory Affairs (OIRA) the power to review all federal regulations, and introduced cost-benefit analysis and risk assessment to the regulatory process. A division of the Office of Management and Budget (OMB) — the executive agency charged with overseeing all federal agencies — OIRA became a liaison between regulatory officials and the Office of the President.

At the start of his second term, Reagan issued another executive order, No. 12498, that took centralized review even further, requiring regulatory agencies to submit an annual statement of “policies, goals and objectives” to ensure agency plans were in line with administration objectives.

OMB Watch’s Melberth says that under Reagan, the agency became known as a “black hole” where proposed regulation disappeared, never to be seen again.

“The power to coordinate information collection and to review proposed final regulations in a policy office of the White House made OMB the equivalent of a political censor over agency actions,” he says.

Melberth, a former law professor, says it got worse during George H.W. Bush’s presidency, when regulatory review was placed under the authority of the Council on Competitiveness, which Melberth describes as a “highly centralized reviewing authority, cloaked in secrecy.”

When Bill Clinton took office in 1993, Melberth says Clinton eased some of the restrictions of the previous Republican administrations, issuing Executive Order 12866, which limited centralized review to the most significant rules. Clinton also mandated that each agency head appoint a regulatory policy officer who would report directly to the agency head, a relationship that would undergo significant changes during the second Bush administration.

When Bush was elected president in 2000, conservatives saw an opportunity to put the unitary executive back in place. In January 2001, Robert Moffit, director of the conservative Heritage Foundation’s Center for Health Policy Studies and a former Reagan OMB official, was finishing a policy paper articulating the bureaucratic vision of a unified executive. The president must “protect his right to select appointees based not only on their managerial prowess but also on their commitment to his policy agenda and their ability to advance, articulate and defend it,” Moffit wrote.

In a list of objectives, Moffit insisted that Bush should resist advice to leave careerists in top spots during the first days of his administration; increase the number of Schedule C (nonconfirmed) appointments; hire noncareer personnel on the basis of their commitment to his policy agenda; and protect his appointive power against congressional encroachments.

Lastly, Moffit suggested the administration review noncareer-to-career conversions in order to prevent Clinton appointees from integrating into career positions. Ironically, as Bush prepares to leave office, his own appointees are reportedly engaged in exactly this behavior.

Bush quickly put this plan into action. In 2002, he made changes to Clinton’s Executive Order 12866, giving more oversight authority to the OMB. In a congressional report that year, OIRA referred to itself as “the gatekeeper for new rulemakings.”

Throughout his tenure, Bush has used legal sleights-of-hand to apply the unitary executive and circumvent legislative authority, such as issuing “signing statements,” which are written comments issued by a president at the time of signing legislation that signal his intent to ignore certain aspects of it. He rejected long-held international standards on the treatment of detainees. And he showed utter disregard for the Bill of Rights, exemplified by his domestic spying program that authorized the National Security Agency to eavesdrop on U.S. citizens and foreign nationals in the United States.

But Melberth says that when it comes to regulatory matters, the Bush administration’s masterstroke was its ability to open doors to elite, corporate interests with little regard for the consequences.

“One of the things this administration is going to be most known for is that they provided a lot of special access for business interests,” Melberth says. “They’ve allowed an unprecedented level of involvement by private interests in creating political policy with regard to regulation, with regard to rules — their energy policy, their greenhouse gas policy, all of that.”

In January 2007, Bush tightened his grip on the federal bureaucracy when he issued Executive Order 13422, which made three particularly worrisome changes to the Clinton-era document.

First, the order mandated that a regulatory policy officer (RPO) approve all new regulations. Second, it made these RPOs presidential appointees. (They were previously chosen by the agency head.) And third, the new language requires agencies to identify the “specific market failure” that any new regulation will address.

In other words, before a new regulation can be adopted, it must be shown that free market forces are somehow failing to address the problem, and then an administration policy officer must approve it.

By controlling regulatory officers, Brookings’ Light says the Bush administration has put a “political watchdog” on the inside. With the stroke of a pen, Bush has effectively usurped control of all government rulemaking.

Less than four months after signing Executive Order 13422, Bush appointed Susan Dudley as head of OIRA during a congressional recess in April. (The consumer group Public Citizen had spent the previous year fighting the appointment, decrying Dudley as an “anti-regulation zealot.”)

Dudley’s background made her a strange choice. Prior to her nomination, she directed the Regulatory Studies Program at the Mercatus Center, a free-market think tank that advocates limited government regulation. In a 2005 Mercatus policy brief, Dudley referred to regulations as “a hidden tax on Americans.”

The think tank — which receives funding from ExxonMobil — has been criticized for downplaying the risks associated with global warming. Several months after Dudley’s appointment, Mercatus issued a white paper defending Executive Order 13422.

Seven months before her recess appointment, Public Citizen, together with OMB Watch, issued a 68-page report on Dudley, highlighting positions she has taken against the Occupation Safety & Health Administration (OSHA), the EPA and the Securities & Exchange Commission (SEC).

“Not since OIRA was created … has there been a less appropriate nominee,” Gary D. Bass, OMB Watch executive director, said in the report.

Untangling the knot

Whoever takes over the White House will face the monumental task of undoing some 30 years of bureaucratic layering that has seen the number of political appointees grow from 400 in 1961, to roughly 3,000 today. In a recent article for the Politico, Light warned that unless the next president begins fixing government, he will preside over “a string of meltdowns that will make the federal response to Hurricane Katrina look like a minor mistake.”

Many legal scholars, including Frederick Schwarz Jr., senior counsel of NYU Law School’s Brennan Center for Justice, say the problems extend beyond the Bush administration. They argue that the executive branch needs a complete overhaul.

Schwarz recommends establishing an investigatory commission — similar to the Church Committee of the ’70s that looked into illegal intelligence activities — to begin the process of unraveling the bureaucracy.

Vanderbilt’s Lewis agrees. He says the first thing a new president should do is commission a study of the federal personnel system to recommend how best to keep flexibility while also maintaining control and fairness.

“I would promote more career professionals into key positions. Not enough use is being made of civil servants,” says Lewis. “The civil service was created to provide expert and continuous management of government. The increase in appointees has hurt both the cultivation of expertise and the continuity of management.”

Unfortunately, what was already an unwieldy machine before Bush took office has since been completely broken. And by many accounts, in its last months, the administration is seeking to make it worse.

Some appointees are scrambling to push through last-minute regulation changes. At the end of July, the Washington Post reported on the Labor Department’s effort to push through rules making it harder to regulate workers’ on-the-job exposure to chemicals and toxins.

Others are working their way into career positions. Known as “burrowing,” this has some legislators worried. In a recent letter to Attorney General Michael Mukasey, Sens. Charles E. Schumer (D-N.Y.) and Dianne Feinstein (D-Calif.) urged officials at the Justice Department to ensure that political appointees not improperly fill jobs intended for nonpartisan professionals.

“We don’t need ideological stowaways undermining the work of the next administration,” Schumer wrote.

Their concerns are well-founded. On July 28, the Justice Department Inspector General concluded an investigation that found agency political appointees — including former aide Monica Goodling — engaged in misconduct and broke civil service laws by hiring and firing agency personnel based on political philosophy.

Whether Sens. John McCain (R-Ariz.) or Barack Obama (D-Ill.) have the political will to reform the federal bureaucracy remains to be seen. For her part, University of Maryland’s Steinzor believes things can only get better.

“The history of these issues demonstrates that, at some point, the pendulum reaches a limit in its rightward swing,” she says. “I think that point passed about two years ago, and that it has already begun to swing back. How long it will take to traverse the arc is the real question.”