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When a federal commission investigating the collapse of Fraser River sockeye stocks heard recently that a Fisheries and Oceans scientist who has done groundbreaking research was being silenced, it gave Jeffrey Hutchings a bad case of déjà vu.

"Your recent articles on DFO's muzzling of Dr. Kristi Miller remind me of similar attempts by DFO to stifle the imparting of science from government scientists to other scientists and to the Canadian public," he wrote in an e-mail.

Prof. Hutchings, a widely respected fisheries scientist, holds the Canada Research Chair in Marine Conservation & Biodiversity at Dalhousie University, in Halifax. In 1997, he, Carl Walters from the Fisheries Centre at the University of British Columbia and Richard Haedrich, Department of Biology at Memorial University of Newfoundland, set off a media firestorm with a paper that ripped DFO for suppressing controversial science.

Writing in the Canadian Journal of Fisheries and Aquatic Sciences, they outlined two cases – the collapse of Atlantic cod stocks and the diversion of the Nechako River, in B.C. – in which they maintained research was stifled because it didn't conform to political agendas.

They argued that, on the East Coast, DFO silenced scientists who warned Atlantic cod stocks had been devastated not by seal predation, but from overfishing. And, in the West, they stated that DFO rejected research that showed an Alcan plan to divert the Nechako River would damage Chinook stocks.

In both cases, they wrote, hard-working scientists had their findings suppressed by DFO managers who didn't want to see research that clashed with political goals.

"We contend that political and bureaucratic interference in government fisheries science compromises the DFO's efforts to sustain fish stocks," Mr. Hutchings and his colleagues wrote.

When the article came out, it created headlines, sparking a national debate on the role of science within government. DFO officials denied stifling any researchers. But the article, quoting internal DFO memos, showed scientists had been "explicitly ordered … not to discuss 'politically sensitive' matters … with the public, irrespective of the scientific basis."

Earlier this month, the Cohen Commission of Inquiry Into the Decline of Sockeye Salmon in the Fraser River, saw an e-mail by Dr. Miller in which she complained about being kept away from a workshop because her DFO masters "fear that we will not be able to control the way the disease issue could be construed in the press."

Dr. Miller, who suspects a virus is killing millions of sockeye salmon in the river, had a paper published in the prestigious journal Science earlier this year. But she has not been allowed to talk to the press about it.

"By preventing Dr. Miller from speaking to the media and from participating in non-DFO controlled meetings/workshops, DFO is inhibiting science," Mr. Hutchings said in his e-mail. "This action, so evidently lacking in openness and transparency, is regrettably consistent with the objective of controlling the information that public servants are permitted to disseminate to the public."

Dr. Miller's situation also inspired Alan Sinclair, a retired DFO scientist, to write: "Your recent article reporting that DFO put a gag order on Dr. Kristi Miller's research on disease in sockeye salmon is very disturbing. Unfortunately, this sort of thing is all too common in DFO and other Federal Ministries with large science components. I encourage you to follow up on this and make Canadians more aware of what's going on."

But following up while Dr. Miller is locked away from the press won't be easy. She isn't due to testify before the Cohen Commission for several months. Until then, Canadians can only wonder what she discovered – and why she was silenced.