I'm thinking that you are using a definition of 'empirical' that allows plenty of room for imposing philosophical beliefs on the results.
As opposed to "depending upon experience or observation alone, without using scientific method or theory, especially as in medicine."
Those who control the meaning of terms, control the debate.
Empirical means based on observation. Learning to make empirical observations is part of that scientific "indoctrination" that all scientists must learn as part of the process of becoming scientists. There is no room for the imposition of philosophical beliefs onto the results of one's research.
Either my PCR experiment shows that a particular gene is expressed, or it doesn't. Where is the philosophical belief in that?