Al Armendariz, the top Environmental Protection Agency official in the oil-rich Southwest region, resigned from his post, effective today. It's the latest twist in the never-ending and increasingly ugly fracking fracas. A two-year old video had surfaced last week (and since pulled) featuring Armendariz comparing his “philosophy of enforcement” to Roman conquerors, who would find “the first five guys they saw and they’d crucify them. And then you know that town was really easy to manage for the next few years.”

Certainly, it’s incumbent upon regulators to apply the best standards of science in unmasking wrongdoers. But crucify? Especially on an issue in which politics play such a large role? Unfairly or not, these comments raise troubling questions about the degree to which the EPA is committed to independent scientifically grounded oversight, or whether personal or political agendas will drive policy.

Facts v hysteria

What’s really going on here from a science and political perspective? The unfolding fiasco has hardened the ideological battle lines over shale gas development, which has emerged as a politically charged litmus test issue. Hydraulic fracking, the central technique commonly used with almost no controversy for decades to extract deep reserves of oil and gas, is now a line in the sand, dividing stalwarts from both parties.

Until ten years ago, when fracking and horizontal drilling opened the way to exploit deep reserves, Texas was not even on the shale gas map. Then the Barnett shale was found buried deep in a 5,000 square mile area centered in North Texas, which includes the Dallas-Fort Worth urban sprawl. Parker County, west of Forth-Worth, is now a major flash point.

Citing pictures of flaming tap water, hard-edged Democrats claim fracking is at best a dangerous unknown with limited economic benefits and at worst an environmental and health disaster in the making perpetrated by energy plutocrats. In contrast, Republicans portray shale gas, in Texas and elsewhere, as a growth engine, which it’s proving to be, and a way to lower energy costs, which it’s doing. But they also contend that the environmental consequences are minimal, which is still an unanswered question. Republicans are out to savage the President and demonize his energy policies at all cost. So it wasn’t surprising that they leveraged Armendariz’s video slip, portraying it as a window into the Administration “true” anti-energy views. Oklahoma State Republican Senator James Inhofe announced to great applause on the right that he was going to investigate whether Obama’s EPA is trying to block hydraulic fracturing. In response, blue shade politicos and bloggers are accusing the GOP and industry of being on a “witch hunt.”

As is President Obama’s style, the White House played both ends against the middle. He often voices vague support for the industry but it’s almost always accompanied by equally vague environmental saber rattling. Last January, during his State of the Union address, the president unveiled his "all of the above" approach to domestic energy development, which includes shale gas, but he offered no specifics. In this case, the Administration at first gingerly backed away from the EPA administrator’s comments. A spokesman trotted out an apology from Armendariz and said his characterization of the agency’s enforcement strategy was “entirely inaccurate.” On Sunday, EPA Administrator Lisa Jackson accepted his resignation.

Is this an isolated case? Political appointees run the EPA. In three high profile instances, including the latest Texas Fracking Crucifixion, Obama’s EPA has exhibited a disturbing pattern of flipping and flopping between anti-industry and pro-environmental policies. The net effect appears to be the subjugation of the EPA’s scientific mission to crude political calculation.

Pavillion, Wyoming

Last December, the EPA stirred an international anti-fracking storm when it announced it had found a direct link between fracking and ground­wa­ter contamination in Pavillion, Wyoming, at the center of the Green River shale formation. Responding to demands by local anti-drilling activists, the EPA made what it now acknowledges was a cursory review of the local drinking water wells and concluded post haste that fracking had “likely” caused the pollution.

Oops. Further review revealed that the agency had used questionable evaluation technologies. Its test wells were drilled deeper than area drinking water and were not properly flushed to avoid contamination by the drilling chemicals used by the EPA. Its own data—including details not revealed in the draft report—indicated the agency’s conclusions relied in part on improperly analyzed water samples from private wells. Acknowledging its sloppiness and haste, the EPA backtracked. Just last month it suspended its peer review process of its original findings and said it would test Pavillion again using more scientifically grounded procedures.

Dimock, Pennsylvania

A similar saga played out in Dimock, Pennsylvania in the heart of the Marcellus shale region. Residents were convinced that drilling by Cabot&Gas Oil had polluted their home water. In 2008, lawyers representing activists alleged that fracking had caused widespread contamination. The Pennsylvania Department of Environmental Protection (DEP) tested the water and found that it met federal safety standards. In response to the brouhaha, the EPA evaluated the drinking water and last November reaffirmed that it was safe. Then, three months later, the agency reversed course, saying it would take “immediate action,” that a clean up was needed and industry was likely at fault.

Why the sudden reversal? Despite no new data, the EPA appeared to have caved to political pressure from advocacy groups, which had viciously attacked its prior finding. The EPA suddenly demanded new testing of wells at 60 homes. Oops. Not surprisingly, with no new science in play, in March, the EPA again confirmed that the drinking water is safe.

Parker County, Texas

The dust up in Parker County is the coup de grace to EPA’s credibility on the shale gas front. That’s the region formerly under Armendariz’s purview. Range Resources, a Forth Worth based natural gas company, is developing that area. A local resident, Steve Lipsky, was featured in viral videos lighting his water on fire a la the misleading anti-fracking propaganda film “Gasland,” which featured a Colorado resident lighting his drinking; only later did the truth emerge that the film's director was well aware that the contamination was caused by naturally occurring methane.

Because of the media blitz inflamed by that video and a full court press by national activists who were hopeful they finally had their anti-fracking smoking gun, the EPA launched an investigation in October 2010 and sampled Lipsky’s well. Two months later, in early December, Armendariz sent what appeared to be a gleeful and thoroughly partisan email to virulently anti-shale gas blogger Sharon Wilson (known as Texas Sharon), Tom "Smitty" Smith of Public Citizen and other activists.

“We're about to make a lot of news," Armendariz boasted. Apparently, he had found the company he wanted to crucify, and that he tried to do a few days later. He issued an endangerment order based on his determination that Range Resources had caused or was contributing to the contamination of drinking water wells. The EPA ordered the company to step in immediately to stop the contamination, provide drinking water and provide methane gas monitors to the homeowners.

“We are worried about the families’ safety,” he said. “It was incumbent for us to act quickly.” Armendariz also took a partisan shot at the state Railroad Commission and Texas politicos, mostly Republicans, damning them for not protecting local water supplies, adding that the EPA was "very concerned" that natural gas could migrate into the home through water lines, leading to a fire or explosion.”

Oops. The EPA had stepped in it again. In March 2011, a review by state regulators and independent testimony from Mark McCaffrey, an MIT-educated petroleum geochemist with Weatherford Laboratories, provided geological evidence that the gas, couldn’t be from the Barnett Shale Formation, as Lipsky and activists, who had not done thorough testing, believed. As in Colorado (in the “Gasland” film) and in Pavillion, it was found that the water had been polluted by natural methane for decades. In Texas, a nearby public water system, Lake Country Acres, had signs on its water storage tanks that read, "No Open Flame," dating to around 1995. Both countries produced gas years before Range drilled its wells.

Even EPA's own geochemist had warned that gas-bearing formations other than the Barnett Shale needed to be ruled out before the agency fingered Range. According to McCaffrey, gas seeping into Range's wells would "have to migrate through the cement and take a right-hand turn and create pressure in the Strawn that would somehow push back half a mile to get into the Lipsky’s' water well." The Commission noted that the EPA had ignored many of its own standard investigatory procedures in what they concluded was a rush to judgement that circumvented standard investigatory processes. It called the EPA’s order against Range “unprecedented,” finding that the company was “not responsible for methane contamination of wells,” and voted unanimously to clear Range of water contamination. The EPA went silent.

One year later, the EPA  dropped its 15-month old emergency order. As for Armendariz, the regulator may have fantastic credentials, care deeply about the public’s trust and the environment, yadda, yadda, yadda, but he is a partisan. He serves no one well, even his own cause. Fairly or not, his quote will be used by hard-edged Republicans throughout the political season to demagogue and bludgeon environmentalists.

As an isolated incident, the Armendariz fiasco would be easy to dismiss. But it’s now one of three disturbing cases. It’s fair to wonder whether his comments are the proverbial tip of the iceberg—that he is one of many dedicated anti-shale gas activist administrators at the agency who put partisan zeal ahead of science. For a government that needs to strike a balance between innovation and environmental protection, that may be the most troubling news of all.

Jon Entine is senior fellow at the Center for Health&Risk Management and STATS at George Mason University.