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He does this so it looks like he is drinking whiskey. This gives people a reason that he doesn't change his ways. People think he can't change.
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Raymond says that Scout has not even seen the world yet. He says "You don't know that your pa's not a run-of-the-mill man" insisting that he might be like the rest of Macomb and might have a prejudice against blacks.
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Atticus is showing how harsh society was and shows that one little incident with a black man could ruin your reputation forever.