It is sometimes easy to forget that the Secretary of Agriculture is a politician who, as an appointed head of a Cabinet-level Department, reports directly to the President of the United States. (S)he is in the regrettable position of having to please the politically powerful while also heading an agency dealing in science. But the missions of politics and science are nearly irreconcilable.
Secretary of Agriculture Edward Madigan, for example, pulled the plug on the planned 1991 unveiling of the Food Pyramid amidst intense lobbying by meat and dairy industry advocates, just two weeks after he was appointed to the post (Sims, 248) by President George Herbert Walker Bush (i.e., W's Papa). The Pyramid was revised to include an emphasis on meat and dairy consumption, and re-released one year later. This revision was motivated by political forces, not by objective science. Before Madigan took office, the Pyramid had already undergone peer-review both inside and outside the USDA (Ibid.)
But don't let me paint then-Secretary Madigan as a bad guy.
It is unreasonable to expect someone to be unbiased if the very existence of his job depends on him being biased in favor of the edicts of the President. Political appointees who serve at the pleasure of the President but refuse to do his bidding are in the wrong line of work, and must always be aware that defying the President’s political agenda can result in their immediate termination. Former U.S. Surgeon General Joycelyn Elders knows this well, having lasted only fifteen months before being forced to resign amidst her public disagreement about masturbation with President Clinton and a powerful Republican-majority Congress.
Sims, Laura S. The Politics of Fat: Food and Nutrition Policy in America. Armonk, NY: M.E. Sharpe, 1998.