Much of his early work for the Bush administration focused on efforts to develop technology to prevent and fight terrorist attacks, but he also fended off objections, valid or not, that the White House was inimical to free scientific inquiry.
Soon after Bush took office in 2001, the administration withdrew support for the Kyoto Protocol, an international agreement to battle global warming. The administration also restricted the use of embryonic stem cells in scientific research, maintaining that they were derived from the destruction of human embryos.
In response to these policies, more than 60 top scientists, including 20 Nobel laureates, put Dr. Marburger on the spot in February 2004 with an open letter charging that the Bush administration had “systematically” distorted or ignored scientific findings that were in conflict with its political or ideological agenda.
Four months later, 48 Nobel Prize winners issued a similar letter excoriating the administration for its stances on climate change, stem cells and other scientific matters. Dr. Marburger was singled out as the administration’s whipping boy and was ridiculed by Harvard psychologist Howard Gardner in the bluntest possible terms.
“I actually feel very sorry for Marburger,” Gardner told NPR, “because I think he probably is enough of a scientist to realize that he basically has become a prostitute.”
Gardner later backed away slightly from his vituperative characterization, saying, “I wish I’d used it as a verb rather than as a noun.”
Dr. Marburger, who revealed during the confirmation process that he was a lifelong Democrat, said his role was to offer scientific advice to the White House, not to weigh in on policy issues.
“No one doubts stem cells are valuable to research and hold tremendous promise — on that, there’s no scientific controversy,” he said in 2001. But he added that the matter “is not going to be decided by science.”
In 2005, he acknowledged to the New York Times that “global warming exists, and we have to do something about it.”
Yet he maintained that the Bush administration had been unjustly maligned by his scientific colleagues.
“From all the evidence I can find,” he said in 2004, “it’s certainly not true that science is being manipulated by this administration to suit its policy. It’s simply not the case.”
John Harmen Marburger III was born Feb. 8, 1941, in Staten Island, N.Y. His father later became the director of public works for Prince George’s County, and the family moved to Landover Hills.
Dr. Marburger graduated from Bladensburg High School in 1958 and from Princeton University in 1962. He received a doctorate in applied physics from Stanford University in 1967 and joined the faculty at the University of Southern California as a theoretical physicist.
He helped found a center for laser studies and hosted a series of educational television programs about electronics and became the university’s dean of arts and sciences.
As president of Stony Brook from 1980 to 1994, Dr. Marburger helped build the state university on Long Island into a well-regarded center for medical and scientific research.
From 1997 until 2001, he directed the Brookhaven National Laboratory on Long Island, a federal laboratory operated for the Energy Department. Although he was a proponent of nuclear energy, Dr. Marburger shut down a nuclear reactor at Brookhaven after concern arose over traces of radiation in groundwater.
After serving in the Bush administration, he returned to Stony Brook as a research scientist. He co-edited a book about science policy this year and is the author of a textbook on quantum mechanics scheduled to be published in September.
Survivors include his wife of 46 years, the former Carol Godfrey, of Port Jefferson; two sons, John H. Marburger IV of Annandale and Alexander Marburger of Jamaica Plain, Mass.; a sister, Mary Hoffman-Habig of Edgewater; and a grandson.
While serving as Bush’s science adviser in 2004, Dr. Marburger told the New York Times: “No one will know my personal positions on issues as long as I am in this job.”
As far as anyone knows, he never made those views public.