Should we replace "God" in the national anthem with "Flying Spaghetti Monster," as the FSM is more current and evident in today's scientific era?

First of all, I wonder if you really mean to refer to the national anthem in this question.  The word “God” does not appear in the first verse of “The Star-Spangled Banner,” which is the only verse that is usually sung and the only verse that most people even know about.  The word “God” is used in the last verse, but this is so obscure that it is unlikely that many people would care about removing it.

It seems more likely, then, that this question would be about removing “God” from our currency (Motto: In God We Trust) and/or from the Pledge of Allegiance (one nation, under God).  It is certainly possible to argue that we should remove the word “God” from these things.  However, there is no rationale under which it is logical to insert “Flying Spaghetti Monster” in place of “God.”

The case for taking “God” out of the motto and the Pledge is that those things represent an establishment of religion under the First Amendment.  In other words, when we use the word “God” in those two places, it shows that the government approves of religion.  This is unconstitutional (we can argue) because the First Amendment says that the government may not give official support to religion.

However, even if we accept this argument, there is no reason to put the Flying Spaghetti Monster in the motto or the Pledge.  If we accept the FSM as a deity, then putting it in the motto and Pledge would violate the Establishment Clause just as much as the word “God” does.  The government would be supporting Pastafarianism, which would be just as wrong as supporting Christianity.

The Supreme Court has ruled that the word “God” in the motto and Pledge does not violate the First Amendment.  It has said that “God” is used there for patriotic or ceremonial reasons and not for religious reasons.  We can invoke God in these instances because we are so used to doing so that it is hardly a religious reference.  (This is similar to the idea that I could wish you a “Merry Christmas” even if I do not believe in Christ.  I can do that simply because Christmas has become so secularized that it has lost much of its religious significance.)  This is why putting the FSM in place of “God” would not be permissible.  There is no tradition of belief in that being in our society.  There is no way in which invoking the FSM could be seen as a patriotic, secular reference.

For these reasons, it would not make sense, and would not be legal, to replace “God” with “Flying Spaghetti Monster” in things like the Pledge, the motto, or even the national anthem.