A couple of years ago, my fiancée and I wanted to try to make some home-made mozzarella cheese, but ran into a problem. In order to turn milk into cheese, you have to add a substance called "rennet," which causes the milk to coagulate, allowing you to separate the curd (mostly fats and hydrophobic proteins) from the whey (the water and soluble stuff). So what's the problem? Rennet is not that tough to find, and it's provided in most cheese-making kits you can buy (this is the one we were using). The problem: my fiancée is vegetarian, and the usual source of rennet is the lining of calf stomachs.
The part of rennet that's most important for this process is called "chymosin," which is an enzyme called a protease, whose function is to break down other proteins. In baby cows, chymosin is needed to break down the proteins in mother's milk, and that's why their stomachs are such an abundant source. Unfortunately, this also means we have to kill baby cows to make cheese, which is problematic for many reasons, not least of which is the fact that vegetarians don't want any part of that.
The good news is that there are non-animal sources of proteases that are somewhat similar to chymosin. In fact, the rennet in the cheese-making kit we found is extracted form a fungus called Rhizomucor miehei. The bad news is, those enzymes aren't quite the same as calf chymosin. They work in a similar way to coagulate milk, but the products of those enzymatic reactions are different, and could lead to different flavor profiles, and different microbial communities that colonize the aged cheese (which could further effect flavor). This isn't a problem for people messing around with making cheese at home (the cheese from the kit was delicious btw), but inconsistency in flavor is a major concern for large-scale cheese producers.
Enter genetically modified organisms: it's fairly trivial to make a bacterium or yeast cell that makes boatloads of chymosin - the exact same protein that's found in the stomachs of calves - without all of the fuss and bother attendant with raising and killing cows. This process is also much more controllable and returns a more consistent product than processing from an animal source, meaning that cheese-makers can expect very little variation in their process. In fact, chymosin produced by E. coli was the first of enzyme made with recombinant DNA technology approved for use in food... all the way back in 1991.
So here's my question: would opponents of GMO technology object to eating cheese made in this way? Avoiding it might be hard - between 80-90% of hard cheese produced in the US is made with recombinant chymosin. And what about companies like Whole Foods that are moving to label all of their products that contain GMOs, or states that are passing laws to do the same? Most regulatory agencies don't consider chymosin an ingredient. And in any case, purified chymosin from E. coli is chemically indistinguishable from that taken from calves. And the problem goes beyond cheese, the FDA has approved over 30 recombinant enzymes for use in food production, including α-amylase, which is used in the production of almost all glucose or fructose syrups.
Groups like the non-gmo project reject the use of these enzymes, but go even further. Bafflingly, they even oppose the use of recombinant proteins to make small molecule compounds like citric acid, claiming they pose "GMO risk." This term is meaningless - are they saying a chemical compound can somehow have memory of where it came from like the water sold as homeopathy?
When anti-GMO advocates deny the scientific consensus around crops like Bt-corn, it's frustrating, but still somewhat understandable. Putting foreign genes in plants so they produce a pesticide sounds scary if you don't understand genetics and the central dogma (which I admit, is not the easiest thing to wrap your head around). Even if you have some idea, you could be forgiven for being wary of a plant that's making something from a bacterium. But the objection to using purified proteins, or even chemical compounds, that are 100% identical to that from other sources, just because it's being made in a lab demonstrates the rank ignorance that characterizes the professional anti-GMO movement.