Frame outlines the scientific method as such: “Experiment. Observe. Measure. Gradually, observed facts will accumulate into a dependable body of knowledge.” However, a page or so later he states.
The “popular understanding of the scientific method” that we mentioned earlier is really a serious oversimplification. Scientists do not just “check out the facts” by means of sense-experience. (i) Generally they use instruments, rather than their naked senses, because the senses by themselves are generally not sufficiently accurate for scientific purposes. But the instruments that scientists use interpose a great deal of human theoretical ingenuity between the observer and the things he observes. When he uses such instruments, the scientist is not only checking his theory with observations, he is also checking out his observations by means of theory-dependent instruments. (ii) Scientific work does not consist in just making and reporting observations but in analyzing and evaluating data. (iii) Scientific theories do not merely report observational data; they go beyond it. Scientific laws are usually general; they claim to hold for the entire universe. (iv) What we “see,” “hear,” “smell,” “taste,” and “feel” is influenced by our expectations. Those expectations do not come just from sense-experience but from theories, cultural experience, group loyalties, prejudice, religious commitments, and so forth. Thus there is no “purely empirical” inquiry. We never encounter “brute,” that is, uninterpreted, facts. We only encounter facts that have been interpreted in terms of our existing commitments. (v) Often, then, scientists do not recognize data that contradict their theories. But even when they do, they do not immediately accept such data as refutations of the theories in question. An apparently contradictory datum constitutes a “problem” to be solved in terms of the theory, not a refutation of it. Only when the problems multiply and alternative theories begin to look more promising will the scientist abandon his theory for another. For all of those reasons, the work of science is far more than merely “checking out the facts.” And if scientists are unable to separate theory from fact, nonscientists can hardly be expected to do so. Science does not operate by means of a pure empiricism, and certainly the rest of us cannot be expected to either.
John Frame, Doctrine of the Knowledge of God (116-117)