You can fully describe DNA transcription and neurotransmitter binding in mechanical terms too (granted there is some loss of fine detail in these models).
The scare quotes, in the sense I was using them, certainly would apply to how a cell membrane "knows" things as well. None of those systems has any sort of the self-awareness of the type we typically associate with "knowing."
I think the big question here is if the higher level knowing of conciousness is essentially something totally new (type dualism at a high level of emergence), or is the result of something entirely different, something due to the special intrinsic nature of physical symbols such as letters, DNA, etc. (substance dualism).
The latter seems harder to justify because certainly things without intrinsic meaning transmit meaning to knowers. We know the paths of old riverbeds from the paths they cut in rocks. We can tell the trajectory of a plane crash from where debris ends up. My friends and I once got caught dipping out of school to go smoke blunts at a friend's house because, when we fled out the back door upon seeing his dad coming home, someone left a freshly made cup coffee on the table.
My friend's dad knew someone had been home recently because the coffee was hot, that is, it was a system that would have tended towards thermodynamic equilibrium with its enviornment, so the additional entropy in the cup was a signal of a non-equlibrium event occuring in the house recently.
My friend's dad didn't have to be a scientist to pick this up because variance from the enviornmental entropy equilibrium is something our nervous system is specifically adapted to do (hence it tends to extinguish stimuli that are persistent, because monitoring difference from the norm is often as important as monitoring difference for ideal settings for homeostasis).
But if something as simple as heat can be a signal carrying a complex meaning, then it doesn't seem like all meaning must come from the intrinsic features of symbols. So then where does the distinction occur?
The substance dualism approach also seems to run into significant issues when it claims that computer algorithms don't process meaning because they aren't "alive." This seems strange given that they are composed of and use symbols to sustain themselves, symbols that are supposedly inheritly meaningful. The same problem pops up if biological viruses are said to not be alive. Computer viruses can also be set up in such a way that they produce novel information, mutate, undergo selection, and evolve. With the advent of the internet, and their ability to spread across a huge eco system, they are also no longer dependent on intentional human action to keep them alive.
Anyways, my objection isn't as much to the concept of some sort of dualism per say; it's such dualism creating a black box that discourages additional inquiry and that such dualism makes its cut using poorly defined definitions. If some meanings can't be described in our common physical frames, we need to try to define all the meaning that can be described in current frames to define the new frame.
I'm not sure what is meant by language and mathematics violating physical laws. Obviously, they can describe things that violate physical laws, but this is inheritly going to be true of any system that can create its own axioms. It is essentially what we should expect for any such system with limited computational power and energy limits, because it has to try to represent the world using compression.
Since algorithmic entropy is non-computable due to logical contradictions inherit in an algorithm finding the shortest possible algorithm to code Y, where Y is a given set of information, we shouldn't expect to find perfect replications of the external world in self-organizing systems. We'll find internal models full or errors and violations of how the world actually works. These errors aren't going to be selected against unless they are grave enough to stop the reproduction of the system. What we will see is selection towards better representations, not a progression to an ideal a fixed point.
The dividing line for biosemiotics is a tough issue though, right? Physics has the embarrassment of having at least 8 major interpretations of its most central theory. Biology has the similar, perhaps greater problem of having no definition of what constitutes life. Here in lies the problem. If meaning is something that only appears in life, but life is going to be defined in terms of a definition of evolution based on organisms using meaning to maximize survival value, then the definition is circular, and it seems like a viscous circle. In definitions of evolution that avoid this circularity, it seems languages and computer viruses, even crystals, may be living things (as well as biological viruses). Attempts to keep synthetic entities out often have the problem of increasingly ad hoc additions to the definition. If we're talking about a unique sort of substance dualism, we should be able to find a very neat dividing line.
For an example of the problem:
https://blogs.scientificamerican.com/brainwaves/why-life-does-not-really-exist/
The other issue is, do other, non-living, self-organizing systems not undergo evolution or other processes considered unique to life? Here there is no good answer either.
Defining evolution for non-biological systems is difficult because they are more diffuse in space and do not have a specific "individual" to use as a unit of analysis. If a phenomena reguarly reappears, is it being extinguished and a new, similar phenomena shows up later, or is the continual reoccurence one system?
Evolution might be something totally unique to life, something that can define life, but it needs a better definition to show that with any rigor.
Plenty of complex phenomena, seeming miracles of life, actually end up being described by the same mathematics that can describe phenomena in diffuse inorganic systems (earthquakes and heart cells sharing the same model for synchrony).
In terms of causes, I think there might be something missing here. There are the material causes, what biology has tended to look at. The efficient causes are actually where I might put information and meaning. The physical descriptions of systems alone does not tell you how it will interact with another system. This is where the idea of synonymity would play a role. The meaning of an interaction for the complex system is what matters (this gets to interconnectivity as a defining feature of complexity).
So, if you kick semiotics down to the efficient cause, what would be the formal cause?
I think this would be the mathematics of the system. This might be a totally wrong way to think about it, but I am very intrigued by the fact that incredibly disparate self organizing phenomena operate through extremely similar functions, and how incredibly common self similarity is. A formal cause that is tied to mathematics opens the possibility of unifying different sciences.
One example of the problems of non-living evolution and applying our current frameworks to them:
https://serendipstudio.org/exchange/gavia/essential-character-non-life-evolution
Edit: Another issue for the epistemic cut occuring at the fuzzy boundary of life are modified Wigner's friend experiments showing that the role of an observer in physics may emerge at incredibly small scales, well below scales for the simplest organic molecules. This seems like it would result in two epistemic cuts, one for observation, a second for biologically relevant meaning.
You also have people fiddling around with the possibility of evolution at these incredibly small scales, but they are less convincing (still neat
https://www.nature.com/articles/s41598-021-96048-6)