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Geeks have a love-hate relationship with The Big Bang Theory, America's favorite sitcom. I'm a Johnny-come-lately to the show, but when I saw it I suddenly got, after years of resistance, that a "truly alien" Doctor could really work in the modern series. (And yes, I'm saying that Smith isn't THAT much more alien than his two predecessors.)
Sheldon is skagra in shada the book if he is anyone
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Maybe it's because you're new to the show and perhaps Sheldon wasn't such a caricature at first (can't remember), but I think making the Doctor more alien by making him Sheldon-like is completely the wrong way to go about it.
The Doctor doesn't need quirks and hang-ups like Sheldon has to seem alien.
I think subtlety rather than exaggeration is the key to portray the Doctor's alieness. It's in his difficulty to connect and startling outside perspective that it's important. Which is why the Moffat era began badly for me when the Doctor said "You're Scottish, fry something." It's completely out of character for him to make a joke based on a stereotype like that. He's a alien. Why would he lend credence to the more senseless aspects of human culture? This became a troubling tendency that reached its nadir with the Doctor making a crack about women in Let's Kill Hitler. Funnily enough, these are exactly the sort of comments Sheldon would make.
Sheldon acts like a jerk because he's sheltered, self-centred and immature. These are not alien qualities. The Doctor is an ancient citizen of the Universe who risks his life to save others and it would make no sense for him to act like that. The Doctor can be arrogant and have moments of egotism, but he's too wise to be like that all the time, and he cares too much about his friends to belittle them all the time like Sheldon does to his.