In providing an answer from a body of knowledge science does allow "why" questions to be asked. Even when talking about an investigative process it is perfectly acceptable to use "why" in certain situations where the instigative process is not one which conforms to a linear process or monochronistic pattern. In fact even the Western vanity of relativity presumes a single point of initiation or single point of reference whereas it is often the case that there is more than one point of initiation and multiple perspectives are required.
Thus replacing the polychronic "why?" which allows for incomplete solutions, backtracking and modal explanations for the linear "what causes?" is simplistic, disingenuous and incomplete.