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The former commissioner of the Minnesota Pollution Control Agency (MPCA) took the stand Wednesday on the second day of an extraordinary hearing into whether the regulator suppressed serious concerns about PolyMet Mining's critical water permit.

John Linc Stine defended his handling of concerns that the U.S. Environmental Protection Agency's office in Chicago had with the permit.

Stine initially denied that a phone conversation he had with the head of the EPA's Chicago office in March 2018 was about PolyMet and the water-quality permit for the company's proposed $1 billion copper-nickel mine project.

But on further questioning by a lawyer for mine opponents and after reviewing e-mails referring to the exchange, Stine acknowledged that he discussed PolyMet with Cathy Stepp, then head of the EPA Region 5 office. That office oversees Minnesota's enforcement of the federal Clean Water Act. The public-comment period on the water-quality permit MPCA had published for PolyMet was soon closing and the agency had to respond to hundreds of comments.

"My concern was over the efficient use of staff resources," Stine testified. "I asked Ms. Stepp to consider whether it would be possible to comment at a later time when we could prepare a draft, a revised draft permit so that their comments could address the most up-to-date information."

He'd never made such a request on any other permit, he said.

"This was simply an efficiency matter on your part?" asked William Pentelovitch, an attorney for several opponents.

"That's correct," said Stine.

The phone call is a hot point on the list of "procedural irregularities" that the MPCA stands accused of, with the allegations the focus of an evidentiary hearing in Ramsey County District Court ordered by the Minnesota Court of Appeals. The MPCA has also been accused of destroying or failing to preserve evidence, known legally as spoliation.

Stine was also grilled about the MPCA's document retention policies in an effort to show that the agency did not follow the rules on preserving e-mails and other public documents related to the development of PolyMet's permit.

And he was shown a copy of a letter he and Tom Landwehr, who was then commissioner of the state Department of Natural Resources, wrote in 2015 to then-state Attorney General Lori Swanson, requesting permission to hire outside legal experts to help with PolyMet. The hard-rock mine project — the state's first — presents "unprecedented environmental and human health questions," they wrote, and they needed help in the "likely event of a legal challenge."

The letter is part of the evidence opponents are using to try to show that the MPCA knew it would face litigation but did not put a litigation hold on agency documents until last summer.

Stine's appearance capped a second day of testimony by former EPA official Kevin Pierard, who was chief of the water-quality permitting branch in EPA's Chicago office. Livestreamed from New Mexico, Pierard has been testifying that the MPCA's request for the EPA to not file its written comments on the draft permit was very unusual.

On Wednesday, Pierard was cross-examined by lawyers for the MPCA and PolyMet in an effort to show that the MPCA did nothing improper related to comments on the permit, and had the authority to craft its own protocols on permit writing. The EPA had ample time to review PolyMet's draft permit and file written comments and did not, they said.

The lawyers also worked to show that nothing in state law or regulations made it wrong for the EPA to submit written comments during the public comment period, or prohibited the MPCA from listening to the EPA read its criticisms of the PolyMet permit over the phone to state regulators, as Pierard did in April 2018 after the close of the public comment period.

Stine's testimony continues Thursday.