It seems like almost every aspect of science has an opposite in religion and vice versa. Science is a search for truth, and Bokononism is nothing but "foma." Likewise, the scientific documents are completely incomprehensible to the secretaries in the Research Laboratory who transcribe them, and Bokononism is the one real comfort to the people of San Lorenzo.
I especially like how the contrast stands out in the characters of Felix Hoenikker and Bokonon. Felix is typically described as "innocent," yet his inventions, the atom bomb and ice nine, literally bring about more death and suffering than anything else in the history of the world. Bokonon on the other hand is hunted as a criminal, and though everything is technically a charade, he is still forced to live alone in the jungle, and executions on the hook still happen (even if they are rarer than they seem). His brainchild, Bokononism, has brought to the island a degree of happiness and contentment that they would not have had otherwise: a massive contrast to the effects of Hoenikker's scientific breakthroughs. The "saint" Felix lived to be amused, always had to be looked after and taken care of, and did not give a moment's thought to anyone else. The "bad man" Bokonon brings amusement, takes care of the spiritual needs of the islanders, and devotes his life to the religion he created where man is the one sacred thing.