Scientific Method vs Halacha vs Science vs Halacha

How does Halacha deal with the scientific method (lower-case). While dealing with science is nothing new, it seems that the scientific method still needs to be grappled with. For instance, we speak about how if something can't be seen with the naked eye it may not matter in halacha, bugs in food for instance. But what about bugs that you won't find without using the discipline of science. You may be able to see it in direct sun (or with a light-box), but perhaps you wouldn't have experimented with examining it , using the principles of evidence gathering and without the influence of the scientific method. Not to suggest that this should change anything, but it does seem like any interesting trend. Would have the copepods been an issue without the experimental methods used to understand/ discover them?