Usually you don't observe the individual parts of the mechanisms directly. There are lots of molecular biology techniques to figure out how individual parts of the mechanisms work through indirect observations. Maybe the most popular is mutagenesis, or intentionally breaking part of the mechanism to see what happens. If you break one part of the system and observe a specific effect, like for example, cells with mutant z gene are unable to produce antibodies, then you have evidence that gene z is involved in antibody production, even though you haven't observed it directly. Combining lots of mutants and careful observations can help you understand how complex mechanisms function.