What is an independent agency
As stated in the post regarding the General Services Administration, an "independent agency" is not considered part of any executive departments. Independent agencies are established through laws passed by Congress. The legislation that contains the establishment of such an agency must define the agency's purpose or the goal it must work towards in addition to what areas it has the power to create laws if applicable. Outside of Congress (the legislative branch) and the Supreme Court (the Judicial Branch), the departments of the executive branch are the major operating units of the federal government. However, other agencies are set up with specific and important responsibilities to serve the people and to carry out operations that the executive departments cannot.
While an arguments can be made that an unofficial "fourth branch" may exist, the independent agencies are not considered part of it. More information regarding the three official branches of government and the unofficial "fourth branch" will be discussed in future posts. Although they are not considered as part of any executive department, the majority of them are stand alone entities of the executive branch since they exercise executive powers although they are not part of an executive department.
However, a few of them are part of the legislative branch under Congress. These include the Government Accountability Office (formerly known as the General Accounting Office), the Library of Congress, the Congressional Research Service, and the Government Printing Office. The purpose of each of these agencies very widely. Some have been set up to regulate sectors of the economy while others contain special services for either the government or the people-- you guys out there. In most cases, Congress has created various agencies to deal with matters and issues that have become too complex for ordinary legislation to take care of.
The President appoints the commissioners or board members while the Senate confirms them. This is similar to that of Cabinet positions that head the executive departments. However, unlike Cabinet positions, they often serve staggered terms and may stay in their respective position even if there is anew administration. Since some commissioners, board members, or directors can stay for longer than four years, most Presidents will not have the opportunity to appoint all of the heads of the independent agencies. In many cases, there are provisions that limit the President's authority to remove commissioners or directors. However, the President can do so for an inability to do the job, neglect of duty, some form of wrongdoing, or other good reasons. In every case, the President must get confirmation from Congress for whoever he nominates for the position.
In addition, laws that contain the establish of an agency usually have a requirement of bipartisan membership n the board or commission. Therefore, the President is not allowed to simply fill a vacancy with a member of his own political party.
There are hundreds of commissions and agencies currently active in the federal government.
For more information regarding the President's involvement in nominating commission members in a independent agency, check out the wikipedia entry.