The federal government must announce the final decision by June 17 on the 1,200-kilometre pipeline that would link the Alberta oil sands with a tanker port on the B.C. coast.
The letter sent this week to Harper and several key cabinet ministers said the report by the joint review panel is "indefensible as a basis to judge in favour of the project."
It was signed by 300 scientists from universities from Newfoundland to Vancouver Island, along with colleagues from international institutions including Stanford, Cornell and Oxford.
The chief concern from the group is that the panel did not look at the increase in global greenhouse gas emissions that will result from the expansion in oil sands production.
"This isn't the fault of the panellists," said Kai Chan, an associate professor at the Institute for Resources, Environment and Sustainability at the University of British Columbia and one of the instigators of the petition. "Much more of it was really about the design of the process."
The panel was not given a mandate from the federal government to look at the larger climate change picture, he said.
It's a systemic problem, said Chan, a board member of the Canadian Parks and Wilderness Society who made a 10-minute presentation to the panel during 18-months of hearings.
"It just feels like we're ostriches sticking our heads in the ground, pretending like we care about climate change and that we're taking action on it but then not even allowing it to be a consideration on these huge projects that obviously have ramifications for climate change," he said.
The joint Canadian Environmental Assessment Agency-National Energy Board panel issued a report in December recommending approval of Northern Gateway, with 209 conditions.
Janet Holder, Northern Gateway project leader, said the panel's report is "based on sound science and fact, and included input from thousands of Canadians with a wide range of viewpoints and expertise."
"By actively seeking to undermine the work of these experts outside the JRP process, the signatories of this letter are denying the experts an opportunity to defend their work," Holder said in a statement emailed in response to a request for an interview.
The review process was one of the most comprehensive in Canadian history, she said. Eighty expert witnesses testified under oath and the panel ultimately recommended approval.
Holder did not address the issue of greenhouse gas emissions.
The scientists' letter also said the panel failed to explain its rationale for finding that the benefits of the $7-billion pipeline justify the risks.
The panel relied on information from the proponent, Calgary-based Enbridge (TSX:ENB), without external assessment of their information, it said.
And it said a finding that marine mammals will not suffer significant adverse cumulative effects contradicts government's own management plans for several endangered and at-risk species.
Chan and fellow scientists Anne Salomon, an assistant professor of resource and environmental management at Simon Fraser University, and Rick Taylor, a professor of zoology at UBC, launched a social media campaign to gather support for the letter.
Ideally, Chan said he hopes it gives Harper and his Conservative cabinet pause as they near the deadline for their decision.
"It might be completely naive but that's what we're hoping for," he said.
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