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The House and Senate are moving inexorably toward a showdown between two very different versions of the proposed Homeland Security Department. The House is almost sure to give the president almost everything he has asked for in what will be the largest, and arguably, most difficult, reorganization in modern bureaucratic history, while the Senate seems well on its way to a more focused proposal.

We prefer the Senate’s approach for two reasons. First, the Senate is headed toward a much more focused department, which will be somewhat easier to implement and manage. Bureaucratic history suggests that it is much easier to move new units to an existing department than unglue units that do not fit.

Second, the Senate does a better job at ensuring that multi-mission agencies such as the Customs Service and Coast Guard will be allowed to fulfill all their statutory responsibilities.

Unfortunately, the Senate does not give the Homeland Security secretary enough managerial flexibility to do the job. Although we believe that the House has gone too far in releasing the department from civil service protection, the Senate has not gone far enough in releasing the department from a civil service system that was designed for a workforce that has not shown up for a half century.

The administration is clearly thinking big. Having opposed a Cabinet department for most of the past year, the president surprised everyone with what is arguably the most difficult reorganization in bureaucratic history. The proposal is built on four pillars: border and transportation security, critical infrastructure protection and information analysis, emergency preparedness and response, and countermeasures for chemical, biological, radiological and nuclear attacks.

At first glance, consolidating like agencies with like functions makes perfect sense. It does not follow, however, that all of these functions all belong in the same organization. Military force and diplomacy both contribute to national security, yet no one argues for placing them in the same agency. The president’s plan would leave more than 75 agencies with homeland security responsibilities untouched.

We believe that a new Homeland Security Department should be built around three core missions: border security, critical infrastructure protection and intelligence analysis. The fact that these three functions are so closely related makes the case for reorganization compelling. And September 11 showed that these areas are our most pressing weaknesses.

The administration plan gets border security reorganization just right. Customs officers, immigration agents and agricultural inspectors should present a common face at the border. The Coast Guard, which helps secure our coasts, and the new Transportation Security Administration, which helps make our air transportation routes safe, should also join the new department.

The Homeland Security Department should also take the lead in protecting critical infrastructure. Terrorists are likely to target our food, water, energy, financial and information systems. Putting critical infrastructure protection in the new department, which could address the problem with flexibility, gives it the priority it deserves.

Terrorism analysis should form the third leg of the new department. No single federal agency currently has responsibility for assessing homeland threats and vulnerabilities. Although President Bush wants to create a terrorism assessment unit, he would give it too little authority and staff. The new department needs the capacity to examine all intelligence and law-enforcement information (including all “raw” data) pertaining to terrorist threats to the country. If that means more dollars and people, so be it.

The federal government’s emergency preparedness and response programs should be folded into the Federal Emergency Management Agency (FEMA), as the administration proposes. But FEMA itself should remain an independent agency.

Moving FEMA will almost certainly disturb its current mission, even as its current mission could disturb the new department. Floods in Texas, hurricanes in Florida and blizzards in the plains are routine occurrences with major political consequences, and could quickly preoccupy the new homeland secretary. FEMA has rebuilt itself into one of the federal government’s best-performing agencies by focusing on what it does best ? respond to natural disasters. Our rule here is simple: If it ain’t broke, don’t move it.

We also believe that the new chemical, biological, radiological and nuclear unit should be postponed. The administration’s plan oversimplifies a broader and more complex problem—how to organize the federal government’s scientific research efforts on terrorism. Congress should invite the administration to develop a new proposal next year on the broader issue of how to manage homeland security-related research and development.

Where possible, non-homeland security missions, such as the Immigration and Naturalization Service’s citizenship functions, should be kept out of the Homeland Security Department. And when non-homeland security missions, such as the Custom Service’s trade-promotion functions and the Coast Guard’s environmental protection functions must move into the new department, Congress should assure that they are not forgotten, whether by creating directorates to house multi-mission agencies or by forming oversight boards to ensure sustained attention.

This alternative Homeland Security Department is not a small reorganization. It would include 12 of the 22 agencies in the administration’s plan, employ roughly 185,000 people (compared to 200,000 in the Bush version once the Transportation Security Administration finishes hiring), and have a budget of $26 billion (compared to $37.5 billion in the president’s plan).

As such, even our more modest proposal demands management flexibility. The president was right to propose a “flexible and contemporary” personnel system for managing what will be one of the largest front-line work forces in government, but he left it to Congress to define just what the words “flexible” and “contemporary” mean. We believe the words should be defined in statute to include whistleblower protection, a performance-sensitive reward and advancement system, the right to organize and labor-market-based pay.

At the same time, we believe someone must watch the watchdog. We do not support the secretary’s unfettered freedom to reorganize the department, the proposed limits on the inspector general’s investigative and auditing authority, or the unnecessary exemption from the Federal Advisory Committee Act. Nor do we believe the new department needs the bureaucratic layering associated with 28 presidential appointees and the alter-ego minions that come with them. The new department should have the power to succeed, but not the power to oppress or obfuscate.

Comparing apples to apples, our proposal is not far from the president’s. The work force is almost as large, the responsibilities almost as great. But we believe it is best to start with a more focused mission, adding responsibilities as success allows.