How does Colonel Graff isolate Ender from his classmate in Ender's Game?
Colonel Graff isolates Ender in a variety of ways throughout the novel. He does this intentionally in order to more quickly shape Ender into the commander that Graff believes Ender can one day become. In my opinion, the best place to look for textual evidence in regards to Graff's tactics to isolate Ender is chapter 4.
Chapter 4 starts right away with Graff and an unknown person talking, and they state right from the opening paragraph that Ender has to be isolated.
With Ender, we have to strike a delicate balance. Isolate him enough that he remains creative—otherwise he'll adopt the system here and we'll lose him. At the same time, we need to make sure he keeps a strong ability to lead.
Graff doesn't waste any time isolating Ender, either. As the launch leaves Earth's gravity, Graff starts to mess around with his physical orientation. Ender is able to keep pace with the changing orientation to the point that he finds it funny. Graff asks the other children if they find it funny, and they all say, "No." Graff then insults them and says that Ender is the only intelligent kid in the group.
No you didn't. Of course you didn't. Not only stupid, but a liar too. There's only one boy on this launch with any brains at all, and that's Ender Wiggin. Take a good look at him, little boys. He's going to be a commander when you're still in diapers up there. Because he knows how to think in null gravity, and you just want to throw up.
Graff continues to insult everybody except Ender, and Graff culminates his speech by telling everybody that Ender is the best of the entire group and nobody better mess with him. This entire episode was orchestrated by Graff to make the other boys both avoid Ender and hate him at the same time.
There was silence the rest of the launch. The boy sitting next to Ender was scrupulously careful not to touch him.
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