Today Chipotle announced that genetically-modified organisms will no longer find a place in its pantry—but taken literally, that means no more corn, a crop that has its origins in human intervention.

The company has long emphasized organic and local foods, and its decision puts it on the side of activists who question the safety of the increasingly sophisticated genetic manipulation that makes industrial agriculture more productive.

Those on the other side of the issue, including most the recent apostate from the anti-GMO ranks, science guy Bill Nye, say the evidence shows that genetically-modified crops are safe—and part of human history. Take corn, one of the founding staples of Mexican food and a key ingredient for Chipotle’s tortillas, chips and salsas. In his fascinating examination of the western hemisphere before Europeans arrived, 1491, Charles Mann describes the development of maize by indigenous peoples in Mexico six thousand years ago:

[Maize] is like the one redheaded early riser in a family of dark-haired night owls. Left untended, other cereals are capable of propagating themselves. Because maize kernels are wrapped inside a tough husk, human beings must sow the species—it essentially cannot reproduce on its own. … No known wild ancestor, no obvious natural way to evolve a non-shattering variant, no way to propagate itself—little wonder that the Mexican National Museum of Culture claimed in a 1982 exhibition that maize “was not domesticated, but created”—almost from scratch. …[Scientists] argue that modern maize was the outcome of a bold act of conscious biological manipulation—“arguably man’s first, and perhaps his greatest, feat of genetic engineering,” Nina V. Federoff, a geneticist at Pennsylvania State University, wrote in 2003. Federoff’s description, which appeared in Science, intrigued me. It makes twenty-first-century scientists sound like pikers, I said when I contacted her. “That’s right,” she said. “To get corn out of teosinte is so—you couldn’t get a grant to do that now, because it would sound so crazy.” She added, “Somebody who did that today would get a Nobel Prize! If their lab didn’t get shut down by Greenpeace, I mean.”

The anti-GMO community argues that selective breeding differs from modern genetic modification techniques, and scientists tend to retort that the only difference is the time-frame. Regardless, if you’re going by the World Health Organization definition that Chipotle cites on its website—”organisms in which the genetic material (DNA) has been altered in a way that does not occur naturally”—then any corn at all should be forbidden. Chipotle proposes to stop using only corn that has been modified with newer methods to fit the needs of agribusiness. (Incidentally, the WHO says GMO foods are generally safe.)

But this really gets at how the debate over GMOs gets both sides talking past each other. Scientists are confident that relying on genetics to encourage useful traits in foodstuffs like corn, whether that’s kernel size or resistance to herbicides, won’t hurt humans that ingest them. But beyond the health concerns, there is the issue of becoming overly reliant on certain GMOs, leading to problems like pesticide resistance and monopolies. Monsanto’s intellectual property rights over its seeds includes 90% of the soybean market. Most of Chipotle’s use of GMOs comes from the soybean oil it used in cooking, and it will now use sunflower seed oil instead.

Scientists have raised concerns about the unexpected consequences (paywall) of growing GM crops at such a large scale. Mann’s book praises the wide variety of maize species cultivated by indigenous Mexicans, and his later work goes on to trace the troubles faced by Europeans who imported another new food from the western hemisphere—the potato—and cultivated only one variety, leaving them vulnerable to a massive famine. No one should be blind to the long history of genetically modified food—good and ill.