If these molecules, and genes themselves, do not function like a computer, then how do they function?
Direct physical contact. The molecules, I think, are enzymes. Enzymes catalyze chemical reactions by binding other molecules in their "active site". They're fairly selective in terms of what molecules can "fit" in the site, like a key inside a lock.
If you think of a DNA strand being read inside the cell, there's an enzyme called RNA polymerase running down the strand like the tab on a zipper, spitting out an RNA copy of the DNA it's reading like a ticker-tape machine.
So imagine you wanted to send a simple signal to stop that process. If you introduced an enzyme keyed to bind to the strand of DNA at a specific place (determined by gene sequence), then the big chunk of enzyme stuck to the DNA would block the RNA polymerase, like a glob of chewing gum stuck in your zipper.
Like I said it's almost too simple to be called "signalling." It's a signal the same way that throwing a wrench in the gears is a "signal" for the machine to stop.
Another analogy. You're driving down the road. I want you to stop. I send you a "signal" by driving a dump truck into the middle of the intersection and leaving it there.
You crash into it and stop. Did I just send you a "signal?" What I did was almost too direct to use that term, don't you think? And wouldn't it be irrelevant to talk about the "medium", or the "protocol", or the "encoding mechanism"? I mean, I didn't send you a secret code that said "stop", I actually
physically stopped you by direct physical contact.
Signalling molecules, I think, work the same way, if I recall my genetics correctly. (I'm no biochemist yet.) They're enzymes that tell a cell (for instance) to stop producing a certain protein product by getting in the nucleus and directly blocking the transcription of a specific gene, like a monkey wrench in the works.
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