Because if he found out that you already knew
The atom had a positive, a negative and a neutral
He'll probably salute you
Then wait till you turn your back like a coward and shoot you
This is Jay’s argument coming to a head, and the climax of his puzzling advice to follow along with government propaganda. He is saying that if you express your education and strongly oppose the government, they will publicly praise you, but behind closed doors they will add you to “No-Fly” lists, wiretap you and otherwise betray the trust you have in them.
Within this there is an interesting parallel:
“The atom had a positive, a negative and a neutral"
Jay compares the three subatomic particles (proton, electron, and neutron respectively) that make up atoms to the nuclear debate. In context, he is saying that if you recognize that are different points of view on the nuclear issue (a positive one, a negative one and a neutral one) the government will feel threatened, as they rely on the population agreeing with the point of view that they put forth, leading them to "shoot you.”
Positive Negative Neutral also refers to the Universal Law of Attraction. Jay has referenced his knowledge of this in other songs e.g. Victory Is In My Clutches
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