Selective incorporation is a legal doctrine that protects the rights, immunities and privileges of U.S. citizens from state laws. It is a product of the convoluted path taken by a debate at the heart of the Constitution itself. The relationship between the individual states and the national government has been a major fault line in American legal and political thinking since the inception of the country, and was a hotly debated topic at the Philadelphia convention that produced the Constitution. In fact, the first two political parties in the United States were the federalists, who believed in a strong central government, and the anti-federalists, who did not--and insisted on a Bill of Rights limiting the government's power over individuals before they would ratify the Constitution. Today, the process of selective incorporation through the 14th Amendment is a judicial patch covering this fundamental division.
The Bill of Rights and the states
Does the Bill of Rights limit state governments, or just the federal government? In other words, does (say) the First Amendment prevent a state government from restricting freedom of the press, or establishing an official religion?
An affirmative answer might seem obvious, but it has not always been so clear. Consider, for example, that the Ninth and 10th Amendments reserve for the states all powers not granted to the national government. And, while some have asserted that the Bill of Rights was intended to enshrine certain fundamental rights that would be recognized throughout the country, others have indicated the authors of the Bill of Rights only sought to restrict the reach of the new and distant national government, secure in the ability of citizens (and their right) to control the laws of their own states without outside supervision.
The Supreme Court weighs in
The Supreme Court of the United States took the latter view in 1833 in Barron v. Baltimore, a case that has never been formally overturned. This was a case about seizing private property for public use (eminent domain), which the Takings Clause of the Fifth Amendment prevents the national government from doing without just compensation.
The Supreme Court unanimously held that the Fifth Amendment does not apply to the states, and that a state government could, in accordance with its own laws, seize private property for public use. In the decision, Chief Justice Marshall explicitly says the Bill of Rights only applies to the national government, and this holding has since been the law of the land.
Under the constitutional separation of powers, the legislative branch has sole authority to make law. If it does not agree with the Supreme Court's interpretation, it can simply change the law. That is unless the law that needs changing is the Constitution itself, in which case it can only do this through the formal amendment process--which is exactly what it did in response to Barron v. Baltimore.
The 14th Amendment explicitly protects the "privileges and immunities" of U.S. citizens from state laws. Politically, the amendment was presented as a way of securing rights (particularly the rights to vote, speak, assemble and bear arms) for the recently emancipated slaves of the post-Civil War South. But the authors of the amendment made no secret that they were also targeting the decision in Barron.
Shortly after the passage of the 14th Amendment, the Supreme Court acted again to severely limit the application of the Bill of Rights against state governments. In the Slaughterhouse Cases, in 1873, the Supreme Court rejected a very broad reading of the privileges of U.S. citizens and a general incorporation of the Bill of Rights against the states.
For a time, the law stopped here. Gradually, however, on a case-by-case basis starting in the 1920s, the Supreme Court has softened its stance and applied aspects of the Bill of Rights as part of either "due process" of law or the privileges and immunities of U.S. citizens. The result has been that, piece by piece, almost all of the first 10 amendments have been selectively incorporated to restrict state governments. Despite the prominent place of the Second Amendment, protecting the right to keep and bear arms, in the intentions of the 14th Amendment's drafters, this has been one of the final and most contentious of the American rights to be protected against state regulation.
Selective incorporation is a double-edged sword. While few believe state governments should be able to pass laws that limit the rights of free speech and trial by jury, or remove the protection against self-incrimination, the selective incorporation doctrine has empowered the Supreme Court over the states in ways the nation's founders probably never intended.
In fact, it can be and has been argued that such power is exactly what the framers of the Bill of Rights intended to avoid, and that responsibility for just state laws lies with the citizens of the states exclusively. It can be said that by turning to the Supreme Court as the final arbiter in all things related to civil rights, whether to protect gun rights or recognize same-sex marriage, we have abdicated some of our self-determination and the autonomy of our individual states.