EPA protecting environment from cows?

I was just watching The Daily Show and Lisa P. Jackson, head of the EPA, was the guest. They were talking about regulating carbon dioxide and Jon said 'I emit carbon dioxide..will I be regulated?' funny, she said 'EPA is not looking to reach down into individual lives and change individual livestocks(?), nor are we going to regulate cows, that's a favorite one too' that was the only mention of animal agriculture, but I was thinking, huh, if cows were polluting the environment, you'd think the EPA would have the authority to regulate them. The factory farm, confined animal feedlot operations, produce loads of waste which ends up in our water from runoff or overuse in agriculture. The vast amounts of land it takes to produce their feed at home and worldwide has pushed animal agriculture above the entire transport sector in terms of greenhouse gas emissions. The EPA could go a long way in reducing and reversing global warming by placing environmental costs into the cost chain of animal agriculture.