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 abc⇒Z, cde⇒Z, cfg⇒Z, ∴c⇒Z; or abc⇒ZYX, cde⇒ZW, cfg⇒ZVUT, ∴c⇒Z. The method of agreement is theoretically valid but pragmatically very weak, for two reasons:
 * almost never can we be certain that the various experiments share only one common factor. We can increase confidence in the technique by making the experiments as different as possible (except of course for the common antecedent), thereby minimizing the risk of an unidentified common variable; and
 * some effects can result from two independent causes, yet this method assumes that only one cause is operant. If two or more independent causes produce the same experimental result, the method of agreement will incorrectly attribute the cause to any antecedent that coincidentally is present in both experiments. Sometimes the effect must be defined more specifically and exclusively, so that different causes cannot produce the same effect.

It is usually safest to restate the method of agreement as: if several different experiments yield the same result, and these experiments appear to have only one antecedent factor in common, then that factor may be the cause of the observed result. Caution is needed, to assure that the antecedent and result are not both controlled by some third variable, that all relevant factors are included, and that the effect or result is truly of the same kind in all experiments. Time is a variable that often converts this method into a pitfall, by exerting hidden control on both antecedents and results. Ideally, the method of agreement is used only to spot a possible pattern, then a more powerful experimental design is employed to test the hypothesis.

Method of Difference
If a result is obtained when a certain factor is present but not when it is absent, then that factor is causal. Symbolically, abc⇒Z, ab⇒−Z, ∴c⇒Z; or abc⇒ZYXW, ab⇒YXW, ∴c⇒Z. The method of difference is scientifically superior to the method of agreement: it is much more feasible to make two experiments as similar as possible (except for one variable) than to make them as different as possible (except for one variable).

The method of difference has a crucial pitfall: no two experiments can ever be identical in all respects except for the one under investigation. Thus one risks attributing the effect to the wrong factor. Consequently, almost never is the method of difference viable with only two experiments; instead one should do many replicate measurements.

The method of difference is the basis of a powerful experimental technique: the controlled experiment. In a controlled experiment, one repeats an experiment many times, randomly including or excluding the possibly causal variable ‘c’. Results are then separated into two groups -- experiment and control, or c-variable present and c-variable absent -- and statistically compared. A statistically significant difference between the two groups establishes that the variable c does affect the results, unless: During his long imprisonment, the scientist made friends with a fly and trained it to land on his finger whenever he whistled. He decided to carry out a controlled experiment. Twenty times he whistled and held out his finger; every time the fly landed there. Then he pulled off the fly’s wings. Twenty times he whistled and held out his finger; not once did the fly land there. He concluded that flies hear through their wings.
 * the randomization was not truly random, permitting some other variable to exert an influence; or
 * some other variable causes both c and the result.