When Chipotle announced that its menu is now GMO-free, the Internet exploded in cheers from the group of people horrified that genetic modification is going to cause all sorts of unforeseen medical problems, and righteous indignation from scientists and the people who listen to scientists.

Among the headlines from major publications: Why Chipotle Mexican Grill Going GMO-Free is Terrible News, Chipotle’s GMO gimmick is hard to swallow, and Chipotle’s junk science on GMOs.

There is plenty of support from the public, though. An analysis of social media sentiment after the fact found that 42% of responses to the announcement were positive, compared to 31% negative (the rest were neutral). So this was probably a smart marketing move for the company, if nothing else.

But Chipotle says that its decision wasn’t motivated by public opinion. It is, according to Chris Arnold, Chipotle’s communications director, part of the company’s larger commitment to its tagline, “food with integrity.” This includes animals raised without antibiotics and hormones, a commitment to organic and local produce, and dairy products free of added hormones, among other things.

“While many [have] emphasized the safety of genetically modified foods, there are many ingredients that have been proven safe to eat that [Chipotle doesn’t] have in our food, such as artificial sweeteners, flavors, and colors. We don’t think these ingredients are necessary to make our food as delicious as possible. Over the years, we have come to believe that the limited number of GMOs that were in our food were not making our food better or providing benefits to the farmers and other suppliers involved in producing our ingredients. We also found that switching to non-GMO alternatives in these cases was less expensive than initially predicted,” writes Arnold in an email.

Most of Chipotle’s other commitments have a basis in scientific fact. Ensuring that animals are raised without antibiotics, for example, is a big step in ensuring that the food system doesn’t contribute to antibiotic resistance in humans. The problem is that anti-GMO hysteria is already rampant, without much basis in fact.

When a popular chain like Chipotle removes GMOs from its food, it might be good for business, but it stokes the hysteria further. Plus, it’s something of a misdirected assurance of healthiness to consumers, who may not be paying attention to the fact that burritos contain a whole lot of calories, something which scientists know to be bad if you consume too many of them, as opposed to GMOs, which the majority of scientists say are fine.

Chipotle’s ingredients aren’t even actually GMO-free, if you want to get technical about it. While the chain’s meat and dairy products aren’t genetically modified themselves, the cows and pigs and chicken that provide them eat GMO food. It’s hard to avoid that, since the vast majority of animal feed (think: corn and soy) in the U.S contains GMO ingredients. Chipotle says that it’s working towards GMO-free animal feed, but that would likely raise costs for consumers. But the bottom line is, if you’re worried about being poisoned by GMOs, you better go vegan when you order.

The cost of its current move to GMO-free ingredients, which entailed switching out GMO soy (in flour tortillas and cooking oil) and corn (in flour and corn tortillas) to rice bran oil and sunflower oil won’t be significant, however. According to Arnold, Chipotle doesn’t expect to raise its prices at all.

So how did it make this decision? Chipotle says that it has talked with experts across the spectrum of viewpoints on the subject, including farmers, seed and chemical companies, biotech companies, soil scientists, agronomists, Chipotle suppliers, academic researchers, NGOs, and “those in the private sector representing companies that have or are taking similar positions with regard to GMOs as we have taken.” Chipotle has an ongoing dialogue with everyone it has spoken to, and Arnold says that the process “wasn’t an investigation that’s now closed.”

“We found that anyone looking to support their own perspective on GMOs could find scientific research to substantiate that perspective, which is one of the reasons the debate on the topic has been so contentious. While some scientists—often with ties to the chemical, biotech, and seed industries—claim that there is a scientific consensus on GMOs, there are many who disagree,” he writes.

And yet, a survey by the Pew Research Center finds that 88% of scientists think that GMO food is safe to eat (Only 37% of the public agrees). Arnold, on the other hand, points to a peer-reviewed study published in Environmental Sciences Europe that says there is no scientific consensus on GMO safety. To put GMO fear in perspective, 87% of scientists surveyed also said they believe that climate change is the result of human activity. The consensus is almost exactly the same for both issues.

Chipotle has emphasized repeatedly that it’s less concerned about short-term human health effects of GMOs than long-term environmental issues—such as crops that are engineered to be tolerant to herbicides like glyphosate (also known as Roundup), which hurts soil health and leads to herbicide-resistant weeds, already a major agricultural problem. “Given … the existence of credible concerns about the safety of widespread use of glyphosate, and compelling evidence that growing GMOs does not increase yields, we decided to take a cautious approach to GMOs where we have the most control: in the ingredients we cook with every day,” writes Arnold.

But according to a statement from Chipotle’s Twitter account, the sunflower oil used by the company is made with herbicide-resistant sunflowers—they just happen to have become herbicide-resistant from conventional breeding techniques instead of having new genes inserted into them in a lab. Instead of glyphosate, the sunflowers tolerate a type of herbicide called ALS inhibitors. This still leads to the same problem of superweeds, and there are more weeds today that are resistant to ALS inhibitors than to glyphosate. I asked Arnold about the company’s use of herbicide-resistant sunflowers, and his response, which talks about the danger of glyphosate but avoids answering anything about the type of herbicide that Chipotle’s sunflowers do use, is below:

“The use of herbicides and pesticides isn’t limited to GMO crops, nor is it limited to sunflowers, and not all are the same. The vast majority of the GMO crops grown in the U.S. and around the world are engineered either to be resistant to glyphosate, to produce the bt insecticidal toxin, or to display both of these traits … This March, the World Health Organization classified glyphosate as ‘probably carcinogenic to humans.’ In August of 2011, the U.S. Geological Survey (USGS) reported that glyphosate is now commonly found in the air and rain in the Midwestern U.S. during the spring and summer. Other research has found glyphosate in waterways, packaged food products, and human breast milk.”

Chipotle hasn’t done any consumer research on the decision (though it has included questions related to GMO foods on tracking studies in the past), but the company points out that other research has shown a “wariness among consumers about GMO use.” Chipotle’s decision will likely increase that wariness, justified or not.