I have a background in both. Both are implemented in physical mediums. The gating and current flow are similarly physical as are magnetic field changes on disk mediums. There is a greater diversity in the brain which uses field effects ala hormones, ion movement, transmitter diffusion, and direct electrical connection. The physical/informational duality is present in both so I would suggest that the building out of the hardware using the ambient materials (i.e. trophic factor) is the more specific difference you're looking for rather than the duality.
You transition to a difference in encoding which is a significant but separate consideration. I think the thrust of your statement agrees with the science but quickly nice into speculation and undue specificity that to me reads as though you are declaring fact. Language and good communication are hard.
> The physical/informational duality is present in both
A very important distinction is that a computer has clean separation between physical data representation (magnetic bits) and physical device implementation (transistors & etc). As an analogy to a biological system I'd suggest an FPGA running a self modifying program that's also reconfiguring the FPGA on the fly. No sane engineer would design such a system (I hope).
Self modifying programs have totally been a thing. :D They were hard to reason about so fell by the wayside but still...
For ion flow through dendrites and axons, the separation of information transmission from the protein assemblies of neurons is similarly separated.
For neurotransmitters the particles are literally packed into bundles and separated from the ionic transmission that causes their release and cell boundaries at the synapse until re-up take.
For electric transmission, the electricity is definitely separate from the axon and junction.
I think the distinction is a little more in how a single computer's hardware is constrained to a (relatively) small set of finite states outside of outside modification. The brain can expand and contract the set of states that it's physical parts can enter on top of being, for better and worse, less discrete. If our computers could grow their silicon wafers and lay new circuits then we would have something similar.
Self modifying programs exist, sure, but (as you note) aren't much used. Meanwhile the "software" layer in biology is a tangled mess.
> If our computers could grow their silicon wafers and lay new circuits then we would have something similar.
Yes, that's why my analogy included reconfiguring the FPGA (ie hardware) that's running the program on the fly. You highlight a number of examples where a reasonably clear line between the biological "hardware" and "software" can be drawn at a given point in time. However, you fail to explicitly mention any of the biological mechanisms involved in reconfiguration, some of which I would consider to blur those lines!
The addition and removal of synapses over time is an obvious but fairly slow and boring example. The software is very slowly modifying the hardware by small amounts, but the two are still clearly separate.
Epigenetics is more interesting. Any number of convoluted signalling pathways feeding back on the machinery that controls gene expression, with (in some cases) heritable effects. The distinction here remains fairly clear to me at any given point in time. The proteins are the hardware, the DNA the storage, and the program is manipulating the storage so as to modify the synthesis of future hardware components. Easy enough.
... or is it? Often the quantity of some component that gets synthesized is itself used as a signal. Does synthesis being used in this manner mean that the hardware has become part of the software? How far do things have to go before the hardware can be considered to be part of the software? But things get even weirder!
> the separation of information transmission from the protein assemblies of neurons is similarly separated
Not always! Ever come across GPCR heteromerization? This happens at your synapses (among other places), more or less in real time, in response to various convoluted signalling pathways. It can change how the receptor responds to a given ligand, or even allow it to respond to entirely different ligands. So in some cases, an important part of the "logic" for the neurotransmitter response is being played out by the physical configuration of the receptors. From my perspective, it looks decidedly as though the receptor (ie hardware) has become an integral part of the software.
Other examples abound, but this comment has gotten quite lengthy so I digress.
Gene expression, signaling proteins, and protein synthesis or epigenetics in general are excellent examples both of the duality but some circumstances where the distinction gets fuzzier, particularly depending on the context and perspective you take.
I had not heard of GPCR heteromerization and will be reading more. I ended up going down the complexity and theory path more heavily and assigning my brain into business software so my knowledge of the concrete mechanisms is shallower than I'd like.
I definitely enjoyed thinking about about where to more specifically pin the difference in this context so thank you for being gracious with my making that attempt to offer a formulation. I think there's another interesting question to ask whether the duality divide matters but perhaps another day.
You transition to a difference in encoding which is a significant but separate consideration. I think the thrust of your statement agrees with the science but quickly nice into speculation and undue specificity that to me reads as though you are declaring fact. Language and good communication are hard.