CHILTON, Wis. — An eastern Wisconsin judge ruled against factory farms about whether they can be required to obtain state permission before dumping pollutants. The state Department of Natural Resources had begun requiring permits to protect the state’s waters. But the Wisconsin Manufacturers and Commerce, the state’s largest business lobby, sued on behalf of the Wisconsin Dairy Alliance and the Venture Dairy Cooperative.  Calumet County Circuit Judge Carey Reed ruled that pre-emptory permits are within the regulatory jurisdiction of state to protect lakes, streams and drinking water.