“Jody was only a little boy, ten years old, with hair like dusty yellow grass and with shy polite gray eyes, with a mouth that worked when he thought.” (Steinbeck, 4) -The Red Pony
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Work here is used in the general sense of move or shape. The boy is fidgeting with his mouth—biting or pursing his lips, or moving his tongue absentmindedly—while he thinks.