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I agree with you to some extent that there is a small but real possibility of some backfiring. Honestly, I believe that he is making the right choice here in demonstrating that he can effectively counter a high-profile misinformation attack. It shows good leadership skills in that he will not just be bowled over by fictional rumors.
Furthermore, I appreciate the avenue that the Obama camp has taken in addressing rumors head-on. The typical DNC method of 'ignore-it-and-hope-it-goes-away' strategy almost always fails. I think that a multi-pronged approach would serve Mr. Obama the best...
a) the website is a great idea for those who are searching for the truth and are content with a general refuting statement from the candidate
b)for the independents or skeptics, I would suggest (on the Obama website) that they simply provide a big old link to the debunking website in order to give them a straight path to follow to read truth and cut thru speculation.
c)the toughest demographic to reach, for Obama, will be the underinformed voters. Typically, these are people living in economically depressed areas where national news is akin to science fiction - it doesn't speak to them. The things that matter, for the most part, are local and deal with the very real hardships they are facing. They don't have either the time or the luxury to go searching for information...they worry about paying the electric bill, buying groceries, and budgeting for gas. They don't care what Leonardo is driving or who Paris is dating...
To silence the rumors in these areas, all they have to do is go there and speak the truth. If he makes a few strategic trips to these areas and denounces all this crap face-to-face, the people will believe him.