The University of Maryland’s law clinic wants Perdue Farms Inc. to take charge of its chicken poop.

The environmental law clinic’s decision to represent environmental advocacy groups in a lawsuit against Perdue, a leader of the state’s poultry industry, has spurred intense discussion about academic freedom. But it has also brought up big questions of accountability in the effort to clean up the Chesapeake Bay.

The Clean Water Act citizen lawsuit, in which the clinic is representing Kathy Phillips, the executive director of the Assateague Coastal Trust, and other environmentalists, sparked anger among state legislators.

Though the defendant is Perdue as a whole, the case focuses on a small Eastern Shore farm contracted by the company to grow chickens. The suit says the farmers, Alan and Kristin Hudson, stored manure from the chickens next to a drainage ditch, funneling pollution into the Chesapeake Bay. It placed responsibility for the pollution upon Perdue, but the Hudsons still expressed worry that legal costs from the case could bankrupt their farm.

The lawsuit raises important questions about where responsibility for chicken poop lies, whether with the large company that owns the chickens or the small farmers who grow them. The answer could change the way pollution is regulated in the state.

But some Maryland lawmakers said the clinic is using government funds to attack family farmers and push a narrow agenda, bringing up a different debate about scholastic independence. State senators initially voted to withhold $250,000 from law school’s budget until it turned over information about the clinic’s clients and funding, hoping to “send a message that the law school should not target small farmers when choosing cases,” according to the Baltimore Sun.

“Small family farms on the lower Eastern Shore have survived only because of the poultry industry,” state Sen. J. Lowell Stoltzfus told the New York Times. “If we have this harassment in the courts, they’re going to go away.”

Many saw this as an assault on academic autonomy, and protests rang out across the country, from the St. Louis Post Dispatch to the National Law Journal. So when reconciling House and Senate forms of the state budget on April 6, the Maryland legislature ceded to the pressure and did not cut the law school’s funding. However, it did still request information about the clinic’s clients and finances from the past two years, meaning the debate is far from over.

Meantime, accountability for pollution, an issue that was pushed to the background by the legislative wrangling, also remains unresolved.

As Eric Hartley of the Annapolis Capital wrote in his column, the lawsuit showcases what he sees as one of the chicken industry’s biggest problems: Corporations such as Perdue own chickens, but their manure belongs to the individual farmers. So  responsibility for nutrient pollution from chicken feces reaching the bay can fall to farmers, leading to small family farms bearing responsibility in cases such as this one.

Hartley applauded the suit for taking on Perdue and trying to hold the company accountable for pollution from its chickens, tying debate over this case to the larger effort to clean up the Chesapeake Bay.