DNA is a tool but exactly how that tool affects the system is largely a guess, as of now. When I was a kid Lyellian stuff ruled but it flunked because the premise didn’t match the results, the death of many reputations.
We know what it does, we know how it does what it does.
Just how complex the regulatory mechanisms are (make this protein now, that protein later, modify this protein by splicing out this region of RNA thusly, etc) we are still learning; but there is not some ‘great and secret show’ going on with DNA that we have no idea about, although there most likely are ways of regulating how when and where the DNA makes the protein that presently we have little idea of (much as micro RNA’s are changing our ideas of how transcription is regulated).