First: check whether the issue is really important: With some exceptions (voting correctly, believing the correct afterlife and not getting sent to hell) If you aren't in a position to interact with the evidence it's probably not something you meaningfully have control over. (Most things for which it is important for you to personally understand have measurable consequences to you. Why do you need the right answer to the GMO question, what would you even do with the right answer?).
Then:
-Figure out exactly what the claims really are and try not to conflate different claims (GMOs will do what, exactly?)
-Consider the possibility that the entire premise is silly ("Is God one or trinity?" "Is she a witch?") and the "consensus" is just wrong and the debate is insane. Generate some plausible third options.
-Check if the two hypotheses seem by your perception to be of roughly equal parsimony, internal logical consistency, and compliance with known evidence, and also check the third options you generated.
-Ask the basic "so, what evidence would you need to tell the difference" questions.
-all the things you mentioned (weigh expert opinions, eliminate bad arguments, eliminate experts who use bad arguments)
-look for concrete predictable things in that area, and adjacent to that area which differ according to the two hypotheses.
-If it's a political issue, try to find out what people who might plausibly be expertish in the area yet don't seem to be invested in debating the issue think about it.
-check what known superforcasters in the field think (people who have a track record of successful predictions in that area). Superforecasters need not actually be loudly engaging with the issue, just ask.
-check if people who have different types of knowledge tend to say different things (e.g. economists vs. sociologists)
-What sorts of knowledge would you need to have to answer the question vs. what sorts of knowledge do the experts in question actually have? (You might think medical doctors are qualified to talk about the effectiveness and safety of various treatments, for example, but they aren't. You want a medical researcher for that. The only difference between a medical doctor and a witch doctor is that one was trained by a curriculum developed by medical researchers and the other wasn't.)
-check for founder effects or cultural effects biasing beliefs (Again, economists vs sociologists. Also, if theologians believe in god at higher rate than biologists it might not be because of different knowledge)
What else? I mean it's a big question, you've asked after a fairly big chunk of "rationality" there.
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No, there are practical healths risks that come from food containing substances that I don't expect. I might get too much of a certain vitamin if I don't know that it's added to my food.
Yes... but this is not an issue of GMO. This is an issue of additives. You should require information that is clearly relevant to health regardless of GMO status. GMOing is a way of adding nutrients, but we would want additives labeled regardless of how they are added.
Or, to put it another way, this is a case where the GMO change is something that should be labeled, because there is a possible effect on health. But the factor under consideration isn't that it is GMO, it is that it there is an possible effect on health.