[entee]

While there's truth in the paradigm you advance, it's not anywhere near as binary or direct as you might me suggesting.

There's a ton of leakage and noise at most stages in biological pathways. Biology actually spends enormous amounts of effort to reduce the noise and leakage, but it's really hard to eliminate entirely.

Lets take the danger temp gene you use as an example. In bacteria that's mostly true, but even there what if we're low on nutrients? Or low on a particular nutrient? Or what if we start producing too much protein which is aggregating because the concentration is too high? Each cell is balancing all these concerns simultaneously, so even very simple biological circuits work/don't work in unexpected ways. What the OP is suggesting is that you're always concurrent with a huge number of different things going on that are far less isolated from your "process" than is traditionally the case in CS.

I agree that concurrency, mutability, scope, all that is relevant, but I think the OP's point that we don't have the theory on how those will apply in a biological context is correct.

Edit: for those interested, some papers on biological noise and the efforts cells use to reduce it:

https://arxiv.org/pdf/1610.00820.pdf https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4006352/ https://www.cell.com/molecular-cell/abstract/S1097-2765(12)0...