Chipotle restaurant workers fill orders for customers Monday in Miami, Florida.
Chipotle restaurant workers fill orders for customers Monday in Miami, Florida. - 
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Chipotle has proudly announced that its menu is now entirely free of genetically-modified organisms, the result of a two-year effort. To get enough GMO-free cooking oil — in this case, sunflower-seed oil — the company had to recruit a North Dakota supplier to plant acres of non-GMO sunflowers.

However, the project has not reduced the Chipotle menu’s “GMO footprint” to zero. Far from it.  

Most genetically-modified crops end up as food for animals, including the cows, chickens and pigs that end up in Chipotle burritosThose animals mostly eat corn and soybeans, which overwhelmingly come from genetically modified seeds.

Rounding up a supply of animals raised on a GMO-free diet "would be very, very difficult to do, short of going to organic meat," company spokesman Chris Arnold says. "And if we wanted to make that switch, you’ve got another tremendous price premium and an enormous supply constraint."

Chipotle already has problems with supply. The chain maintains “humane treatment” standards for the animals that end up in its burrito bowls — but it can’t always get enough. Right now, that means no carnitas at some Chipotles.

Organic meat would be a much tougher problem. Catherine Greene, an economist with the United States Department of Agriculture, calls the supply of organic beef "extremely limited." 

As in, last time USDA ran the numbers, in 2011, it was 0.3 percent.

Even when demand goes up and price follows, supply doesn't immediately follow that. Farmers have to use organic practices for three years before they can sell the product as organic.

"That’s a pretty long time to commit to using organic production systems without tapping into the organic premium," Green says.

That’s a big disincentive, and when farmers do switch, there’s a long lag: the three-year transition period, plus the two years or more it takes to actually raise a cow for slaughter.

Meanwhile, the corn chips and tortillas at Chipotle are reliably GMO-free.

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Follow Dan Weissmann at @danweissmann