When Kristi Miller walked into the Cohen Commission hearings two years ago, she had a security guard and a communications handler with her to keep the media away.

It was a strange moment. Here was one of British Columbia's top scientists, the author of a groundbreaking fish-health study in Science magazine, about to testify at a public inquiry, and she wasn't allowed to speak to reporters.

The result of the decision by the federal Department of Fisheries and Oceans to muzzle Dr. Miller of course only inflamed speculation about what she had found in her groundbreaking research into salmon diseases.

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This time around, the DFO is trying a different approach and is allowing the head of molecular genetics to speak openly about the research she's doing.

And it's a good thing, too, because the unmuzzled Dr. Miller is a thoughtful, tough-minded, independent researcher who's clearly dedicated to pursuing science without any political agenda.

In other words, she is just what's needed if British Columbia is ever to get past the long-running, emotional debate over whether fish farms are spreading diseases to wild salmon.

In an interview, Dr. Miller was asked whether the research she's undertaking with Brian Riddell, of the Pacific Salmon Foundation, will finally answer the big questions. Are farms spreading disease and if they are, how serious is it?

"It is designed with that intention," she said. "We are intending to include large sample sizes from wild fish, hatchery fish and aquaculture fish. And we have been working with industry in developing an agreement to obtain those fish."

Getting access to large samples of farmed fish is a key to the success and credibility of the study. It means that at the end of the project, the researchers will have full genomic disease profiles for hatchery, wild and farmed salmon, which will allow them to analyze how diseases flow between those different populations.

Dr. Miller said it will be relatively easy to determine what microbes and combinations of microbes the salmon have, as each fish sampled will be tested for 45 microbes known to be associated with salmon diseases globally.

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It will be a much tougher challenge to figure out where those diseases came from. Did they go from farmed fish to wild fish? Or was it the reverse? And what role did the fish raised in federal hatcheries play in spreading or magnifying diseases?

"The harder question is the one on transmission – and ultimately that is where we want to go. But you know, that will take a variety of different approaches to really nail that one," said Dr. Miller.

What about infectious salmon anemia? Will she search for ISA, a virus that is controversial because it is associated with farmed fish and which, if found on the West Coast, might point to aquaculture operations in Scotland or Norway?

"It is our intention to have ISA as one of the microbes on the chip," said Dr. Miller, referring to the tests she will be running. "Basically any microbe that you've heard about in the news will be on our chip."

So Dr. Miller isn't going to shy away from controversy.

Should fish farmers be worried about her research?

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No, because she will be able to resolve the troubling question about what role, if any, farms play in disease transmission. She can absolve the innocent. And if she finds farms responsible, she will open the way for new management approaches. Fish in farms or hatcheries can be treated for disease microbes – but only if you know they are infected.

Treating wild fish is another matter, but as Dr. Miller notes, if you know what is ailing the fish, and how many are sick, you can predict survival rates and set effective fishing targets.

In other words, she's going to give fisheries managers a solid scientific base from which to make important policy decisions. And that's exactly what British Columbians want.

It's a wonder this scientist wasn't allowed to speak a lot sooner.