--Sir Thomas More
Thinking scientifically involves assessing 'why is it this and not that?' Early on you need a theory or hypothesis that postulates the important variables and how they are connected. A good theory is descriptive and predictive. Often, it is well supported by past scientific work.
It should also be well supported by reason and logic. Reason and logic transcend measurement problems liable to distort results of empirical studies of complex, multivariate environments.
Due diligence is also required to identify plausible rival theories or hypotheses that raise the question of 'what else could it be?' Many individuals ignore this step, because it often requires stepping outside comfort zones to understand other perspectives that don't agree with yours. Doing so is essential, however, as it helps overcome confirmation bias that clings to pet theories. Developing plausible alternatives pits your theory in the ring against other reasonable explanations of a phenomenon.
Then the theories need to be tested. Testing could be as straightforward as applying logical tests or reason validate some theories and invalidate others. This is a desirable approach both because of its efficiency and its capacity to disentangle empirical complexity.
If empirical testing is required, then care must be taken to develop an appropriate way to measure important variables and relationships in real world contexts. This can be difficult due to the multitude of background factors that could obscure or alter findings from their true value. More often than not, empirical findings are limited or contestable because of measurement problems.
At the end of the day, logic and reason become the final arbiters, because even empirical test results must be evaluated by the mind. If the validity of one theory cannot be reasonably separated from the invalidity of other theories, then scientific progress is stalled until future study advances it.
However, it one theory stands alone after testing, then progress has been made. We know why it is this and not that.
And we are one step closer to the truth.
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