Yes. Those are factors that you also include in your final theory. Older chemicals, variations of the environment, the stability of the source material, it is all part of the calculations. That is why when a medicine is made the factors are listed as well what happens when it encounters something odd. That's why theories always are proven as theories. Rarely do you have something in science that is stated as a fact. Facts do not exist in science, not even something as commonly given as a fact like gravity.
You still have to start with a basic idea no matter if you use science or magic. Nothing starts out purely as one or another. I can give you an example: a group of theorists took a meteorite and refined it, finding that it had unusual properties. As they worked with the material, it split into four different objects, each one encompassing an element separate from the other. They still have the same source, and thus react to each other, but their uses differ from each other. The creation of these objects is from science, yet the final forms are more of a magic.
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You still have to start with a basic idea no matter if you use science or magic. Nothing starts out purely as one or another. I can give you an example: a group of theorists took a meteorite and refined it, finding that it had unusual properties. As they worked with the material, it split into four different objects, each one encompassing an element separate from the other. They still have the same source, and thus react to each other, but their uses differ from each other. The creation of these objects is from science, yet the final forms are more of a magic.