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We know a lot, but not that much, about the multiple interactions in a biological system. Nutritionists can barely even tell us what's healthy to eat - because they don't know except by observing outcomes.
Blueberries are good for you, as an example. This is well known and uncontroversial. But why? No one really knows the answer to this. If you take vitamin supplements containing all the nutritionally equivalent constituents of the blueberry that have been identified as healthful, you still can't replicate the benefits of a handful of fresh berries.
How can we claim that something absolutely isn't disturbing some property of a complex organism that we don't even understand well enough to measure?
And though you say that scientists understand the one gene, one protein model is overly simple, that there are multiple interactions, again, they don't know what all of them are. The prediction of protein folding configurations is a "conditionally intractable", np complete problem. Genes make proteins, but which ones, and how are they shaped, and what do they do? Anyone who says they know is just making stuff up.
Maybe this frankenfood is fine, though, after all. But I don't want to have to eat it until there's real safety testing done on it.