At the beginning of 2011, for instance, the FDA stunned reporters while announcing changes to its medical-device approval process. The announcement was under embargo and the agency’s press officers barred journalists seeking outside comment from sharing information about the changes with experts until the embargo lifted. The association wrote a letter of protest, pointing out that the prohibition “rewrote a long-standing compact between reporters and various public and scientific organizations,” which typically allows reporters to share embargoed material with sources while working on their stories. Members of the Right to Know Committee pressed the matter, and in June the FDA reversed course. Around the same time, HHS also finally released the list of senior media officials in each of its divisions, which the association had been requesting for about a year.

Despite these victories, and the launch of what will be ongoing quarterly conversations with hhs’s public affairs staff, Freyer is unsure how much progress has been made. “The big issue is that reporters who’ve been at this for a while remember being able to call up and talk to the people who actually knew what was going on, not just spokespeople, and that’s become increasingly difficult,” she says. “So I don’t see milestones here. It’s been an ongoing problem that we’re chipping away at.”

The Obama administration’s transparency problem not only affects access to federal scientists and highly politicized environmental and medical science. It’s also about access to government documents and databases, and basic research. In 2006, allegations emerged that an electron microscopy research group at Oak Ridge National Laboratory in Tennessee, which receives millions of dollars a year from the Department of Energy, had fabricated data. Suspecting lax oversight, freelance reporter Eugenie Samuel Reich, now a contributing correspondent for the journal Nature, filed a FOIA request for files related to the ensuing investigation, which had been initiated and organized by the lab itself. The Department of Energy rejected the request, so Reich bided her time until the 2008 presidential election ushered in a new administration. When Obama made his pledge about openness and then appointed Steven Chu and a number of other “scientists with excellent reputations” to the department, she believed there would be a “change of heart.” There wasn’t. Reich filed a lawsuit under the FOIA in 2009, which a federal district judge in Boston finally dismissed in April of this year, to her amazement.

“This record had nothing to do with national security—not even the government claims it does—so it is a very good test case of how other, non-security-related records are being handled,” Reich says. “The government’s court filings have been relentless and extraordinary, with numerous deliberate references to the need for privacy, confidentiality, and respecting the proprietary rights of government contractors.”

Curtis Brainard is the editor of The Observatory, CJR's online critique of science and environment reporting. Follow him on Twitter @cbrainard.