The root is government power. When government is free to meddle in every corner of our lives and regulate the economy through taxes, regulation and subsidies, then "special interests" have every incentive to work on the politicians to preserve their turf or gain an advantage.
A tax, regulation or subsidy can make the difference between an industry's success and failure. If the government were not giving preferential tax treatment to ethanol, the corn farmers and ethanol processors would have to find something else to do because their product can't compete against regular gasoline on a level playing field.
In a real free market, a company succeeds only by making things consumers want to buy and keeping costs low enough that the market price yields a profit. Sadly, in our mixed economy, success can be achieved another way: by lobbying the government for advantages over one's competitors. The prospect of favorable government intervention creates incentives for producers and their lobbyists to strive to satisfy legislators and bureaucrats instead of consumers. The resulting competition for privileges sets the stage for the improper relationships that reformers fret about.
The irony is that the "good government" types favor big government, so they undermine their own efforts to eliminate corruption.
It is naive to think that government can hold the power to grant privileges without also setting off a mad scramble by special interests to get a piece of it. All the good-government legislation in the world cannot prevent unsavory dealings between the wielders of power and those who seek to profit by it. To think otherwise is to ignore human nature.
There is one way to rid the political system of this sort of corruption: severely restrict government power as the founders intended. Only when we eliminate the state's ability to meddle in business will business will stop meddling in government.
A genuine free market, unburdened by government interference, is the route to cleaner politics.
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