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From a chemical standpoint, there's no difference in the substance itself. However, there may be differences in what impurities are present and their relative concentrations.

One of the reasons artificial flavors tend to taste ... well, artificial ... is that they don't have the same blend of impurities as the natural substance does. Artificial vanilla flavoring is just vanillin, which is the main but not the only component in natural vanilla extract. This makes it more of a "one-note" flavor, without the subtleties present in real vanilla extract.

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