Can you trust where your meat is coming from these days? 

Chipotle couldn't. The company announced this month that it would pull pork from its menu after discovering one of its producers failed to meet certain animal-welfare standards.

"This is fundamentally an animal welfare decision and it's rooted in our unwillingness to compromise our standards where animal welfare is concerned," Chris Arnold, Chipotle's communications director, told the Washington Post. 

While Chipotle has not released either the name of the supplier, nor the specific violation it found during a routine inspection, some have suggested that the violation stemmed from a producer's use of slated-floor housing and farrowing crates -- both common slaughterhouse features. Critics maintain that slated-floor housing, which allows ranchers to raise pigs indoors, and farrowing crates, which keep the sow confined to protect its piglets from being crushed to death, are inhumane.

Chipotle's move is an important indication of evolving standards of decency in the treatment of livestock. With growing public awareness, giant meat producers like Tyson Foods, Cargill, and Oscar Myer have also pledged to address consumer concern over health and ethics, and even fast food chains are hopping on emerging trends.

Our government might be the worst offender

But this issue runs deeper than a few bad apples. The problems around ethnically sourced meat seem to be ingrained in the meat production economy.

A lengthy New York Times investigation, published earlier this month, on a little-known animal research facility in Nebraska reveals the government's support of the meat industry's relentless quest for profit in spite of animal well-being or even public relations pressure. 

The facility, known as the US Meat Animal Research Center, is a taxpayer-funded outgrowth of the United States Department of Agriculture (USDA). According to the Times, the center "has one overarching mission: helping producers of beef, pork, and lamb turn a higher profit as diets shift towards poultry, fish and produce." The center was created half a century ago by Congress to consolidate the Agriculture Department's research on farm animals, and it has since worked to engineer better quality meat, fend off diseases, secure food safety measures, and prop-up American ranchers in the global marketplace.

Yet the investigation reveals that this work has come at a cost. Animals at the center have been subjected to abuses such as malnourishment, untreated illness, and experimental genetic modifications made to increase birth rates. There have also been experimental surgeries performed by "untrained, unskilled, and unsupervised staff."

At the center, pigs are birthing 14 piglets instead of eight, cows two calves instead of one, and lambs are birthing "easy care" babies with thin hair instead of fur that needs shearing. This creates bad conditions for the offspring. According to the Times, hundreds of newborn piglets are being crushed in cramped pens as their mothers roll over. Since 1985, when many of the center's most ambitious projects began, at least 6,500 animals have starved, and more than 625 have died of a painful, treatable disease of the udder called mastitis.

Will taxpayers continue bankrolling the center in light of larger industry strides?

Here's the irony: The USDA is actually the nation's chief guardian of the ethical treatment of animals. It closely monitors their treatment by private companies and private laboratories. Yet, it is not enforcing the rules at its own testing center. 

In an era of increasing public concern for the ethical treatment of animals -- even those we kill for food -- it is disconcerting that a government-run center has not acted on these larger trends. As the Times notes, "Certainly, the production of meat is a rough enterprise. Yet even against that reality––raising animals to be killed, for profit––the center stands out."

The good news is that information about this reality is coming to light. Not only are we hearing about the practices inside factory farms, but we're also understanding their effect on the environment outside the farm. 

A recent study, for example, showed that towns nearby massive cattle farms are breathing in poop and hormones carried in the air. And given that Americans' diets have been shifting away meat products that were once staples, according to USDA data, government-sanctioned animal abuse in the interest of propping up a stagnating industry doesn't help, either.

With Chipotle's announcement, along with promises by big meat producers to address cruelty concerns, the notoriously maverick meat industry seems to be moving to a more sustainable, localized, and humane food politics. Hopefully, the government will catch up and properly handle the ethical issues at its own testing center.