
On the surface, he dresses and acts oddly, so that streak of individualism is always present, but it's more than a personal choice - it's a mission. There are many stories in which the Doctor is the agent of revolutionary change, overthrowing oppressive regimes across time and space. Just look at his two greatest enemies: The Daleks, a Nazi metaphor (if you don't see it, watch The Dalek Invasion of Earth), creatures obsessed with genetic purity. The Cybermen, the template for the Borg, cyborgs whose mantra is "you will be like uzzzzzzz". Autons will replace you with plastic replicas. Sontarans are a clone race, all the same. These return again and again because they are the greatest symbols of conformity in the Whoniverse.

The new series, of course, has followed into those footsteps. How could it not? More than 30 of its episodes 56 have an element of mind control built into them, and another 8 feature identity-stealing aliens. The Doctor is definitely on the side of free will, and will often win the day by convincing someone to throw off the yoke of slavery. But it's got to be their decision. None of that shoot the computer and let the chips fall where they may business Captain Kirk was always up to...
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On the other hand, though, he's also a strong defender of the status quo as well. Part of that is the general natureo f superheroing in general, and another part is the constraint against changing pre-airtime Earth history, but there's a bit more to it than that. (Any form of progress that even lightly smacks of transhumanism is invaraibly bad on this show. Change, especially change in 'what it means to be human' (to quote the Lazarus Expriment), is most often terrifying...
Ah, but what DOES it mean to be human? I think what draws the Doctor here is our sense of individuality. Threats to that get his dander up. He's not against transhumanism per se (not the way he mentions it in the Year 5 Billion episodes), but possibly sees where it leads at this point in history.
He's an agent of change, but not an amoral one. Change for the better (freedoms), not for the worst (loss of choice). In the case of Lazarus, "immortality" (even without the monster stuff) is seen as a source of stagnation. Tomorrow's post will have something about another one of the Doctor's motivations that sheds light on this.
But you make good points. No character is complete without a central paradox.
Got to disagree with Jeff, especially with the Lazarus episode.
The Doctor is more trying to prevent outcomes he knows specifically are bad but human don't - like immortality.
Look at the Five Doctors - one of the sub-themes is the realization that immortality is a curse (one of the reasons the Time Lords limit regenerations.) Those that seek it are shown as being strongly connected with the dictatorial impulses the Doctor opposes.
Immortality is just one big status quo.
Again, God blessa youse -Fr. Sarducci, ol SNL
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