In this paper, we reject commonly accepted views on fundamentality in science, either based on bottom-up construction or top-down reduction to isolate the alleged fundamental entities. We do not introduce any new scientific methodology, but rather describe the current scientific methodology and show how it entails an inherent search for foundations of science. This is achieved by phrasing metaphysical assumptions into falsifiable statements and define as fundamental those that survive empirical tests. The ones that are falsified are rejected, and the (...) corresponding philosophical concept is demolished as a prejudice. Furthermore, we show the application of this criterion in concrete examples of the search for fundamentality in quantum physics and biophysics. (shrink)