Those things can be just as crude as each other. Genes (and proteins) can interact in very complex ways so don't be fooled into thinking that 'direct manipulation' of specific parts means you have any idea what's going on.

As a software analogy, think about a very large and complex, undocumented code-base in a bizarre language you've never come across. Your only experimental tool is to pick a line of code, delete/modify it, and then see what happens. As you learn more, you can do refine your experiments but basically, you're still just 'poking it with a stick'.