His tenure was marred by controversy regarding his defense of the administration against allegations from over two dozen Nobel Laureates, amongst others, that scientific evidence was being suppressed or ignored in policy decisions, including those relating to stem cell research and global warming.

[1][3] From 1988 to 1994, Marburger chaired Universities Research Association, the organization that operated Fermilab and oversaw construction of the ill-fated Superconducting Super Collider,[3] an experience that is credited with convincing him of the influence government had in how science is carried out.

He had never been to a public hearing prior to his participation in the Shoreham commission, and he said that he had initially expected that the issues could be resolved by examining scientific data and establishing failure probabilities.

Marburger's conduct on the committee was praised by activists on both sides of the debate, with his focus on listening to all viewpoints and his ability to not take disagreements personally being especially noted.

Rather than directly oppose the activists, Marburger created policies that improved the environmental management of the lab as well as community involvement and transparency.

[3][5] The tritium leak, combined with other disclosures about improper handling and disposal of hazardous waste, had caused Secretary of Energy Federico Peña to fire the lab's previous manager, Associated Universities, Inc.

Upon starting as the laboratory's director, Marburger noted the increased importance of health and environmental concerns since the beginning of the Cold War, stating that "getting the people at Brookhaven to understand that won't be simple, and there may be some disagreement on how we should do it, but that's my job.

"[8] Marburger set up a permanent community advisory council and met with local environmental groups to increase communication between them and the laboratory's management.

Marburger also called the report's conclusions illusory and the result of focusing on unrelated incidents within a vast government apparatus, and attributed the controversy as being related to the upcoming elections.

It was noted that Marburger enjoyed close personal relationships with President Bush, White House Chief of Staff Andrew Card and Office of Management and Budget Director Joshua Bolten, attesting to his active involvement within the administration.

[16][17] Marburger responded to criticism of his support for Bush administration policies in 2004, stating "No one will know my personal positions on issues as long as I am in this job.

"[1] However, in February 2005, in a speech at the annual conference of the National Association of Science Writers, he stated, "Intelligent design is not a scientific theory....

"[13] On the other hand, Robert P. Crease, a colleague of Marburger at Stony Brook University, characterized him as someone who "[went] to the White House as a scientist, not an advocate.

He refused to weigh in on high-profile, politically controversial issues, but instead set about fixing broken connections in the unwieldy machinery by which the government approves and funds scientific projects....