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President Pro Tempore is always the longest-serving member of the majority party in the Senate. I dont believe it technically has to be, but it always is. The Vice-President is considered the "President" of the Senate, and the President Pro Tempore is supposed to preside over Senate sessions in the VP's absence. Usually, neither one of them preside over Senatorial sessions, but let less-experienced Senators do it so that they can learn parliamentary procedure.
There's no way that they'd give it to her as the Junior Senator from New York. Frankly, I wish they would give it to someone like Hillary, because right now, it's Robert Byrd, and I do NOT want Byrd running the country at his age, should we reach that point in the succession.
I think that, because of the opportunities to make transformative change in our foriegn policy that will occur during the Obama administration, it would be a great move for her to accept the S.O.S. position. However, if its true that Senator Kennedy will look to her to spearhead the passage of a major health care bill in the Senate, then I would certainly understand if she wanted to focus on that instead, as health care has been a major focus of hers for years.