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Health Canada set out to drive a Canadian-made stop-smoking aid from the market after a complaint from Pfizer Canada Inc., a pharmaceutical company that makes competing products, a judge has found.

In its first few months on the market, a lozenge called Resolve, billed as a natural way to stop or reduce smoking, sold more than 250,000 cartons across Canada, according to its manufacturer, The Winning Combination Inc. (TWC) of Winnipeg. Then Pfizer wrote Health Canada a letter saying the product posed health risks. (That same year – 2007 – Pfizer sought and obtained Health Canada approval for a quit-smoking prescription medication, Champix.)

What followed, according to a scathing ruling from Federal Court Justice James Russell, was a process in which a lone bureaucrat, Robin Marles, set up roadblocks to Resolve while other Health Canada officials stood by or supported his efforts. At every stage, as the company tried to make its case for a licence to sell Resolve, Dr. Marles, the director of Health Canada's clinical trials bureau, denied it any fairness, Justice Russell said. (Under Health Canada rules at the time, a company could sell a natural health product while its application for a licence was under consideration.)

Checks and balances "were abandoned and those with the authority and responsibility to make the decision simply followed Dr. Marles' directions, whose directing mind appears to have lost all sense of objectivity and procedural fairness as he attempted to shore up his own misperceived conclusions," Justice Russell wrote in his 68-page ruling this month.

The result: Resolve was wrongly banned from the market for eight years, he said. Rather than send the matter back to Health Canada to rethink whether Resolve meets its standards – the normal course for this situation, he said – he ordered Health Canada to approve a natural-health-product licence within 30 days.

"To simply return the matter for reconsideration to a system that has shown itself to be so dysfunctional might simply plunge TWC back into the quagmire and trigger more litigation," he said. The judge did not criticize Pfizer.

Shazad Bukhari, chief executive officer of The Winning Combination, said the company did not receive fair treatment from Health Canada. "The sense of fair play you would expect and you hope the government would provide isn't always the case," he said in an interview.

Dr. Marles would not comment when reached by phone.

A spokeswoman for Health Canada said the department is appealing the court's decision. "The department remains committed to a fair and impartial review of all health product licence applications," she said.

Pfizer said it had been beyond reproach. "Pfizer Canada always conducts itself appropriately," a spokesman said by e-mail after receiving a copy of the ruling from The Globe and Mail. "There is absolutely no conclusion or statement in the court decision to indicate otherwise."

Justice Russell said that after Pfizer complained to Health Canada in mid-2007, the government claimed Resolve contained a substance drawn from passionflower, and would be harmful. The company showed independent lab tests confirming the product contained no passionflower, and Health Canada ultimately accepted that it was not harmful.

Next, the judge said, Health Canada said Resolve was not a natural health product, defined as one whose key ingredient occurs in nature, or is a synthetic version of a natural product. Instead, it said, Resolve was a drug, and would need a more thorough process to prove its effectiveness.

"Dr. Marles has conceded that he had no evidence that the active ingredient in Resolve was not a [natural health product]. All he had was his own opinion," Justice Russsell wrote. "And yet Dr. Marles actively sought to have the Active Ingredient delisted … without giving any notice to TWC that classification was a problem."

Then came a "reconsideration," at the company's request, in which Health Canada retained an expert – Dr. Marles's former postdoctoral supervisor. The reconsideration came to the same conclusion – that the key ingredient was not natural. But the ruling said the expert had done a faulty search of a database, and missed convincing evidence that it was natural.

Finally, accepting that Resolve was a natural product and not a drug, Health Canada said it would need conclusive evidence it was effective – a standard that it had not applied to any other natural health products, or even to drugs, Justice Russell found.

Even in its handling of the court case, Health Canada allowed Dr. Marles to serve as its front man, the source of all evidence about how it handled Resolve.

"He is an advocate for himself. Health Canada remains firmly in the hands of Dr. Marles and is apparently unwilling to provide the court with reliable factual evidence from others in the system who were involved," Justice Russell wrote in the ruling. Health Canada never should have fought to uphold Dr. Marles's conduct in court, the judge said.

So reprehensible was the government's conduct, he said, that Health Canada must pay The Winning Combination's legal costs, which Mr. Bukhari estimates at $1-million. The company laid off 15 employees, at a time when it had just 35, and its suppliers laid off more, Mr. Bukhari said, adding that the company now has 100 employees, and plans to launch Resolve in Europe, Australia, South Africa and elsewhere.

Pfizer's quit-smoking prescription medication, Champix, was described in a Canadian Medical Association Journal article in 2011 as being linked to an increased risk of cardiovascular problems. Health Canada has published warnings, but has allowed it to be sold.