It seems you don't understand the context of research projects. When you're assigned to write a program that processes data x coming group another group, it's v

It seems you don't understand the context of research projects. When you're assigned to write a program that processes data x coming group another group, it's valid to say that that input data is a 'black box' to you. That still doesn't mean that the whole research is 'black box' or somehow not 'real science'.