Hmmm... I was trying to reduce your desription to code, but I'm not sure exactly what you're trying to describe. (I can tell you're not a programmer. :-)Your code example (A [the promoter region getting triggered] == TRUE), but is now activated when (A AND B == TRUE) would indicate a programing change and an information increase. But suppose the code was written --I'm not a programmer so forgive the incorrect syntex -- as (A == TRUE) Unless RNA = Double THEN (A AND B == TRUE)?
That would not be an increase in information.
What I was describing was the logical expression that gets evaluated when the gene (G, we'll call it) gets activated & transcribed (condition A). If originally G got transcribed & eventually produced protein P, and then later a regulatory mechanism evolved that sometimes prevented P from getting produced, that mechanism could act at one of several points: It could prevent the activator from being produced in the first place, it could prevent the activator from reaching G & starting translation, it could prevent translation into P in midstream (like the RNAi seems to do), or it could block P somehow after it's produced. Either way it's a more complex system than the one without the regulation, even if the result is less P's getting produced in the cell.
glibertarians!
But that's the point. The regulatory mechanism seems to have been there all the while in plants and animals. Now we're just recognizing it and starting to understand how to manipulate it.