There’s a new controversy raging in Canada’s scientific community as word spreads about impending changes to the country’s major health science research organization.

In what has been called a "rebellion," emails are flying as scientists share news about a recent decision by the Canadian Institutes of Health Research's Governing Council. They say it will force scientists to shop around for matching external funds before they can access public money that used to be granted with no strings attached.

The CIHR's decisions "can only be described as top-down, secretive and disrespectful," says Fred Wien. (Patrick Callaghan/CBC)

“Part of the reason for the rebellion is that the process that the senior leadership of CIHR has used to make these decisions can only be described as top-down, secretive and disrespectful," Fred Wien, professor emeritus at Dalhousie University wrote in a letter to colleagues.

"I feel very strongly, and a majority of my colleagues feel the same way, that the interests of Canadians are not being served," said one researcher who was recently briefed on the changes.

To understand what’s going on requires a short primer on how medical research is funded in Canada.

Most of the country’s health scientists apply for funding through the Canadian Institutes of Health Research, which receives just over a billion dollars a year from Ottawa for health science research.

About half of that money is awarded through an open competition, in a process so competitive that only around 15 per cent of those who apply are successful in securing research grants.

And scientists were already upset about new rules in that open competition. It overhauled a long standing peer review process where scientists met to discuss which grants were the best candidates for funding. It also set aside almost half of the money to fund a small number of large labs or collaborations, leaving the rest of the scientists to compete for limited funding opportunities.

Many of these resource industries are the cause of many of our health problems so to get funding from them would be problematic. - Rod McCormick

Those changes had already "imposed significant anxiety and confusion among researchers," according to one letter sent to the head of CIHR.

Now, adding to that confusion, is a new series of changes that will affect the structure of the CIHR’s 13 research institutes, which specialize in areas such as aboriginal health, child health, gender studies, nutrition, and aging.

The institutes each have their own independent advisory board, and they award grants based on priorities they establish within each institute, to focus on specialized areas of research.

Or at least that’s how it used to be.

Now, in a decision making process described as "shrouded in secrecy," the CIHR is implementing changes that risk pitting one institute against the other as their budgets are cut in half.

The other half of the money is being pooled into a common fund, and to access that money the institutes will have to compete with each other, and the scientists will have to knock on doors to find matching external funding.

It’s a requirement that has raised particular concerns at the Institute for Aboriginal People’s Health, where researchers fear they have few options for finding those matching funds.

"Unfortunately for aboriginal people, we don’t really have many organizations we can leverage with," said Rod McCormick, who holds the B.C. Chair in Aboriginal Early Childhood Development at Thompson Rivers University in Kamloops, B.C. "I don’t think it’s a secret that the Harper government wants us to get our funding from resource industries. But many of these resource industries are the cause of many of our health problems so to get funding from them would be problematic."

Others have echoed that concern.

"We also came to understand that our work would require substantial investment by industry partners that we simply couldn’t attract or that would not be acceptable to Aboriginal communities," wrote Charlotte Loppie, professor at the School of Public Health and Social Policy at the University of Victoria. "We simply can’t justify why we must partner with the very industries that are harming them or their fellow nations."

The Harper government has made it clear that collaboration between federally funded scientists and the private sector is a priority, and some scientists believe the CIHR is following that directive.

"The end result of the changes will be to push scientists to commercialize and to work on research that will produce concrete results almost immediately," said a member of the one of the institute advisory boards who spoke off the record. "The changes will have the effect of shooting the future in the leg by not investing more in research that will produce results over time."

"It’s absurd to be forced to make an argument in 2014 about why a country needs to invest in long term basic science,” that source said.

In what has been described as "near unanimous negative sentiment," at least eight out of the 13 boards have written to protest the changes, which also include eliminating the individual institute advisory boards, and then bundling the institutes into four groups. The institutes are also losing dedicated staff based in Ottawa that were attached to each institute.

"Many scientists view this as a major concern because it really challenges the operating ability of the Institutes," said Bill Avison, from Western University in London, Ont.

What’s at stake, some say, is the future of health research in areas such as aboriginal health. That’s why news of the recent decision prompted outrage and anger from some of the most prominent researchers in Canada’s aboriginal research community.

"A serious rift is now developing between CIHR and the Aboriginal health community and beyond," wrote Wien, in a letter to the CIHR.

Aboriginal health research is a relatively young field of study in Canada, and for a decade the CIHR had a special fund to help indigenous students earn Masters and PhD degrees. That funding has recently been cut by CIHR, further hampering their ability to compete for research money.

"It’s not a level playing field," said McCormick. "There aren’t very many aboriginal health researchers in Canada. We don’t have the senior researchers, we don’t have the numbers that can compete against the biomedical researchers who are well established in Canada."

The funding changes have also raised concerns for the future of child health research in Canada through the Institute of Human Development, Child and Youth Health.

"We think that it threatens the viability of health research for children in this country," said Avison, chair of the Council for Canadian Child Health Research. "The agenda for children tends to get lost in the bigger picture. The other issue of course is there’s not enough money for research in this country."

Others have said they don’t understand the reason for the changes or why they’re being brought in so quickly.

"We struggle with the lack of full disclosure on WHY such changes are being mandated," wrote the chair of the advisory board for the Institute of Nutrition, Metabolism and Diabetes

The decision was made by the CIHR’s Governing Council, which is appointed by Ottawa and includes health professionals, university officials and members from the private sector.