In theory, fracking can be done safely and cleanly. In practice, the firms that do the work of pumping chemically treated water into the ground to crack shale and free natural gas have made an environmental mess. The political backlash is now making it difficult for the Obama administration to sell its plan to move the nation toward greater use of cleaner energy.

The administration's ongoing woes were evident in August, when U.S. energy secretary Ernest J. Moniz addressed an audience at Columbia University. Hecklers hounded him as pro-fracking. They have a point. Fracking plays a big role in the White House's all-of-the-above energy policy. Natural gas would serve as a bridge to a low-carbon future, full of electricity from sunshine, wind and fission, as well as fossil fuels.

The White House has been trying to shrink emissions from coal-fired power plants, which emit more carbon dioxide than comparable power plants using other fuels. In September the Obama administration mandated cuts in CO2 emissions from coal plants, after previously announcing up to $8 billion in new loans for “clean coal” projects. These include investments in carbon capture and storage, which would deposit CO2 deep underground, where it would not contribute to climate change. Despite the sweeteners, the coal industry has not taken kindly to these policies, which have been derided, Moniz said, as “tantamount to a war on coal.”

If clean coal stalls and fracking opponents succeed in slowing the flow of natural gas, electricity will have to come from somewhere else. Nuclear power, another source that figures prominently in the administration's plans, faces stiff economic headwinds from cheap natural gas and strong public opposition in light of the ongoing Fukushima disaster. If two new nuclear reactors now under construction in Vogtle, Ga.—the first built in the U.S. in more than three decades—go over budget that would “seriously cloud the future” for U.S. nuclear power, Moniz said. And any shortfall in natural gas and nuclear would most likely come from coal—not the clean kind.