It is a popular misconception that the clause “separation of church and state” exists in the Constitution. That exact phrase was coined by Jefferson in a letter to a church (1), but the principle is one that has been upheld by the Supreme Court because of its constitutional basis in the First Amendment. The First Amendment has two religious clauses: the Establishment Clause and the Free Exercise clause. “Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof…” (2). The former merely states that the government shall not endorse an official religion, while the latter obviously allows one to practice his or her own religion.
While the Supreme Court has dealt mainly with cases concerning prayer and the displaying of religious icons in public places, there have been several cases in federal and lower courts dealing with the question of whether religious models of the origin of life should be taught in schools. Historically, the question has been whether to allow evolution to be taught in schools, but evolution has typically prevailed after the Supreme Court ruled in Epperson v. Arkansas (3) that any bans on teaching evolution in school violated the Establishment Clause (of course, the controversy of evolution v. creationism originated with the famous Scopes Trial of 1925). Recently there has been a controversy surrounding the federal case of Kitzmiller v. Dover Area School District regarding the validity of teaching intelligent design in schools as an alternative to creationism (4).
While I am not going to debate to what extent intelligent design resembles or does not resemble creationism, I am in agreement with the U.S. District Court for the Middle District of Pennsylvania, which ruled that teaching intelligent design violates the Establishment Clause of the First Amendment (4). Intelligent design, after all, does assume the existence of a supernatural "designer" and has no basis in scientific fact. Evolution may be called a theory, but there is a consensus in the scientific community about its validity (theory is a misleading term at times; technically gravity is a theory too, but no one will challenge its validity).
It is true that by teaching intelligent design, the state, through the school, would seem to be endorsing religion. But at the same time, doesn't the free speech clause of the First Amendment hold priority over the other clauses? Shouldn't teachers have the academic freedom to teach alternative theories, especially since the subject matter concerned is also endorsed by the parents of students? These parents are the ones who are mostly paying for their kids' education, and they did not send their kids off to school to learn material that they do not approve of. In the Kitzmiller v. Dover case, of course, it was the opposite way around; teachers and parents objected to the school board's endorsement of intelligent design, but I believe that in most cases the former assumptions hold true.
I personally believe that it is in the students' best interests to learn a scientific theory instead of a religious one in a science class. In a religious studies class, students should be free to learn all about the Bible, but there is no and can be no scientific evidence for intelligent design or creationism because they involve proving the existence of a Creator himself, a formidable task many philosophers have attempted (and failed, in my opinion, for it is a matter of faith). Furthermore, it is not the interests of the parents or teachers that the Establishment Clause is protecting in this case. It is protecting the minority from the tyranny of the religious majority. This case illustrates the basic principles of the separation of church and state; that is, protecting nonbelievers and those of different faiths from the proselytizing of one religious sect's views.
And while the marketplace of ideas may lead students to truth eventually if they are given choices of what theories to accept, imagine the controversy that would occur in other subjects if theories not held by the consensus of academics were taught. If a Communist or Fascist interpretation of history were taught in an American history class, I am sure that not many would be keen on accepting this alternative "theory" of history.