The Chicago Sun-Times called for a boycott of BP today in response to a permit the oil giant received in late June to significantly increase the amount of toxic waste it dumps into Lake Michigan every year.

“If BP insists on dumping more pollutants into our lake, it’s time for us to stop pumping its gas into our tanks,” reads the paper’s editorial. “We’re calling for an all-out boycott of BP gas.”

“Tens of thousands” of Chicagoans have protested the permit, which allows BP’s refinery in Whiting, Indiana, twenty miles from Chicago on the south shore of the lake, to discharge 54 percent more ammonia and 35 percent more suspended solids into the water annually. The facility also received an exemption from meeting tough limits on mercury pollution for the next five years. BP contends that it needs the permit (the first it has received since 1990) for a $3.8 billion expansion that will enable the refinery, already the largest in the Midwest, to process more heavy Canadian crude oil. The company has attempted to justify the expansion by pointing out that it will create eighty permanent jobs and 2,000 construction jobs; that its discharges meet or beat state and federal emissions standards; and that it will invest $150 million to improve its onsite wastewater treatment facility.

Since the Indiana Department of Environmental Management approved the permit in June, however, there has been what local newspapers variously describe as a “blitzkrieg,” “firestorm,” “avalanche,” and “groundswell” of protest from around Lake Michigan. But the opposition has been fiercest in Chicago, where mayor Richard Daley and others have threatened legal action to block the permit, and are leaning on the federal Environmental Protection Agency to reverse its statement that the new pollution limits would not violate the Clean Water Act. In late July, the U.S. House of Representatives approved a resolution urging Indiana to reconsider the permit.

The Sun-Times boycott comes just one day after BP and Indiana regulators for the first time “softened their defense” of the permit, saying they would review suggestions from Chicago officials, the EPA, and environmental groups about technologies that could reduce the Whiting refinery’s pollution. Mayor Daley has urged his constituents to hold off on the boycott pending a “credible, independent” evaluation ordered by Indiana governor Mitch Daniels this week. But local newspapers have been adamant in their opposition to allowing more toxic waste.

The Sun-Times has now published three editorials railing against BP’s new permit. “Even if the giant oil company proves that the extra waste it will be dumping is no threat to aquatic life or humans,” the paper wrote in July, “we must have zero tolerance for the release of any additional pollution into our precious lake waters.”

Lake Michigan supplies most of the region’s drinking water and is popular for fishing and other forms of outdoor recreation. Although BP denies that increasing its toxic discharges will “damage” the environment or harm individuals, all of the effluents covered in the permit pose hazards. Ammonia and suspended solids have received the lion’s share of attention - ammonia can cause algal blooms that kill fish, and suspended solids can work their way into the food chain via the aquatic life that swim in polluted water. A third and even more toxic effluent, for which BP received a discharge exemption, has received much less attention. Mercury, one of the most strictly regulated environmental toxins, can cause brain and nervous system damage in even low dosages. The new permit allows the Whiting refinery to continue dumping two pounds into the lake annually until 2012, when it must meet federal standards that will drop the limit 8/100th of a pound.

Both the Sun-Times and the Chicago Tribune have done an impressive job covering the various and far-flung protests that erupted after the permit was granted, but only the latter has given any significant attention to the environmental science behind BP’s toxic waste. In late July, the Tribune published an excellent investigation highlighting the “little-noticed” mercury exemption contained in BP’s permit. Reporter Michael Hawthorne points out that the Whiting refinery is only one of two polluters that still dump mercury into Lake Michigan, but he also gives respectable balance to the story by pointing out that the amount released is small compared to that which falls into the water from air pollution. In addition, Hawthorne provides a thorough review of all the other nasty chemicals coming out of the refinery.

Curtis Brainard writes on science and environment reporting. Follow him on Twitter @cbrainard.