This is just a quick hit-and-run post – so much more I would love to discuss – but in brief, I distinguish between the scientific method, which relates to observable fact, and the mythic metaphors scientists use to describe what the scientific method has established.
For example, we can endlessly replicate the process used to determine that water boils at 212º Fahrenheit (100º Celsius). That imports useful information that is not a metaphor (stick your hand in the boiling water, and you will experience intense pain every time – certainly doesn’t feel like a metaphor).
On the other hand, when scientists generally fall back on metaphors to convey what they have learned to the general public – whether it’s Isaac Newton’s “God as a watchmaker ” metaphor, or particle physics’ description of the wave-particle paradox. Metaphors aim at understanding, while the scientific method serves as the nuts-and-bolts approach that builds that understanding.