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When Martin first goes to work for Dr. Pickerbaugh in the Department of Public Health, he looks forward to getting a fresh start in the new city of Nautilus. But he quickly realizes that Pickerbaugh is full of super-annoying enthusiasm. He's more chipper than a kindergarten teacher on the first day of school. He thinks that the best cure-all is for people to live upstanding Christian lives, and he's willing to distort science in whatever way he needs in order to make this happen. As he says at one point, "No matter what methods we use, if we can get people to have more fresh air and cleaner yards and less alcohol, we're justified" (21.2.6).
Martin, on the other hand, is committed to scientific truth at all costs and he thinks Pickerbaugh's approach to public health is total idiocy. But what really creeps Martin out is the way that Pickerbaugh manipulates his social power in order to gain money and fame for himself: "… more dismaying was the slimy trail of the dollar which he beheld in Pickerbaugh's most ardent eloquence" (21.2.16).
Unfortunately, it's people like Pickerbaugh who get ahead in the world, while truth-tellers like Martin get scorned and chased out of town for being too honest.