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?
When you claim that it 'evolved' and that 'evolutionary relationships' can be inferred from it.
"The study of evolution and evolutionary relationships is as subject to empirical tests, observation, and falsification as any physics experimentation."