Once codes arise — symbolic systems that are rule-based, context-sensitive, and capable of being read — we've crossed a threshold. This isn't just more complex thermodynamics; it's the birth of agency. — Wayfarer
But biology crosses this threshold at the level of the molecule that can be read as a message. Hierarchy theory was how theoretical biologists made sense of the thermodynamical basis of life and mind for a good reason. The genetic code is the easy bit to understand. How genes can be "read/interpreted/implemented" is then what the field focuses on with biosemiosis.
So you can say "agency" is just something absolutely different in kind. But then biology can shrug its shoulders and say they see this magic property in every enzymatic reaction. Codes build the molecular machinery that can clamp chemistry in exactly the right positions so that quantum tunneling takes over and achieves an entropic step that would be "impossible" for regular classical chemistry.
You make the usual big deal that something smells about physicalism because there is this explanatory gap between the quantum and the classical realms of substantial existence. And yet – as I have repeated often enough – biophysics now spells out exactly how life, and therefore mind, exists by being able to sit right on the quasi-classical junction between these "two worlds", mining quantum uncertainty for the purpose of achieving classically stable outcomes.
The explanatory gap instead turns out to be the missing link when it comes to "agency". If quantum physics has a measurement problem because apparently measurements must be something that happen in a human head, well now biology says decoherence of thermal potentials is no big deal as your whole body is a hierarchy of decoherent action. Every part of every cell is dancing the dance of flipping quantum-level switches on entropy flows. We microregulate chemistry right at the nanoscale by "making measurements" in informational fashion.
So step one for biology was realising that life did in fact have its symbol-processing secret. Step two is reconnecting that informational story to the material world as it "truly is". And the topological change in state that is the boundary between the quantum and the classical is exactly where life and mind inserts itself into the thermally-constrained physics of the world.
Thermodynamics of course is being rewritten too. You say:
This isn't just more complex thermodynamics; — Wayfarer
But you are still thinking of thermodynamics as the science of closed systems gone to their heat death equilibrium. The formerly warm bath now forever gone cold. Biologists rely on the new science of dissipative structure and topological order – as cosmologists have also started to do.
A dissipative structure is a system that self-organises so as to be able to accelerate an entropic process. It spends energy on constructing the machinery that will then unlock, or at least waste faster, some environmental entropy gradient. This is an entirely new vision of thermodynamics. One that is more complex in the proper topological sense. Not merely just more complicated.
Collections of things can get complicated. It takes the emergence of hierarchical order to make things more complex – complicated in the causal sense and not just the constituent sense.
So the question can be asked: are you actually dealing with the problems of philosophy? I mean, the problem of agency is surely central to the question of human identity. — Wayfarer
As a natural philosopher, I look for naturalistic accounts of existence. And the great thing is that this approach allows one to explain not just what agency is but why agency needs to be treated as a transcendental property by systems of human social organisation. Transcendence is an essential myth for enabling humans to live as if they were indeed constrained by some higher authority which intends to greatly limit the scope of their personal freedoms.
This is just basic political science. All complex societies need to place even their kings under some higher transcendental principle. It could be commanding gods, it could be the rationality of a constitution, it could be the unquestionable facts of a moral logic. But no large society can exist in stable and productive fashion unless it invents for itself the top-down level of constraints – the bounding information – to which it can swear absolute fealty.
Transcendence needs to be mystical as it has to be "beyond human". With the Enlightenment, we did sort of try just believing in the transcendence of rational pragmatism. But that never really dealt with the way that the same demystifying scientific spirit was busy unlocking the Pandora's box of fossil fuel and all the runaway industrial age thermalisation that could follow. So we half started crafting the well organised society and then that project got run over by the steamrolling economic forces of manufacturing and financialisation.
Economics is about organising the wholesale entropification of the planet. Dollars are how we encode the value of all that results. Rationality opened the door for entropy and it came galloping through. Now we worship entropification in rather direct and obvious fashion. It became the transcendental principle that rules the human world.
So you say I somehow ignore the central problems of philosophy? I as usual reply that I see them as all fully figured out. And barely understood by anyone.
Which is no surprise. Entropy is in charge of the show. Pragmatic rationality had to die to allow that next step in the human condition to be fully realised. Neoliberalism finally stripped away the sensible constraints and we've been off to the races ever since.
And is this the metaphysical project you want to support? Of course not. But then it is not a genie that can be put back in the bottle by a return to the mystic transcendent principle of some earlier agricultural social order where it was just empires of wheat rather than corporations of oil that the entropic bonanza driving the show.
And once you admit something like "desire" into the lexicon — even metaphorically — you're no longer in a purely entropic domain. — Wayfarer
As I say, if I have to wave a specific banner, it would be dissipative structure. That is thermodynamics as a semiotician and hierarchy theorist would recognise it.
As Marcello Barbieri argues, the emergence of biological codes — such as the genetic code — was not merely an incremental extension of chemical complexity but an ontological leap. — Wayfarer
And yet it was Barbieri who correctly focused in on the ribosome as the precise connection between the biological information and its entropic consequences. The molecular machine that makes the molecular machinery.
In stunning self-confirming fashion, the ribosome itself recapitulates the evolution of biosemiosis. The most primitive parts of a ribosome are made out of RNA. And then as it learnt how to start sculpting the proteins it was producing, it added on the simple strands, them the more complex twists, that turned the ribosome from a rudimentary constraining tunnel made of RNA to a fantastic bit of precision engineering with a large collection of proteins components that could add enzymatic steps like splicing and proof-reading the protein strands it was producing.
So you might want to keep finding great gaps in knowledge that speak to there being "two totally different things". But science progresses fast. And biosemiosis cashed out in a big way when we discovered that biology is basically about classical machinery that is able to regulate quantum potentiality for its own private purpose. Life can live on the edge of critical instability – the quasi-classical realm where classical stability is "half-melted" and it cost next to nothing to tip a chemical reaction in some other direction.
Physical existence came with the quasi-classical possibility to be switched on and off in a mechanical fashion. And being possible, this is what had to happen. Systems of switching evolved.
RNA was in at the start as a dual-purpose deal. It was both the code and the structural material – and a bit shit at both. But once a feedback loop got started, these two functions were properly split apart and became the actually separated worlds of DNA and proteins. Coding as informational constraint and building material as structural constraint became divided in terms of the chemistry best suited to serving those functions. A vague causal division became a physically decisive one. The ribosome became its own fossil record that tracked this evolutionary change.
Codes linking signs to meanings are not derivable from physical laws alone. That’s what makes them novel — and marks the boundary between life and non-life, mechanism and meaning. — Wayfarer
How could information regulate matter unless there was this epistemic cut?
What you are quibbling over is to what extent this is also a true ontological cut – as the conventions of realism/idealism, or mind/world, would seem to require of folk who like to consider themselves card-carrying philosophers.
I as usual just argue that holism rules. And that holism itself depends on the ontological fruitfulness of dichotomies. That is symmetry breakings and the topological transitions that symmetry-breaking brings.
If you want to understand semiosis, this is why it winds up back at the triadicity of Peircean logic and hierarchical causality. You start with the "oneness" of vagueness, extract the "twoness" of the dichotomy that can part its waters on complementary fashion, and then watch how it grows to form the causally-balance wholeness that is a state of stable hierarchical order.
You can't keep advancing a semiotic argument here and yet fail to see that semiosis itself puts the dichotomy at the heart of everything. For the physical realm to take a further step up in its topological order, it had to discover the Hegelian "other" which was its own negation. Just by being "the physical" it already spoke to the possibility of "the immaterial".
The task then is not to get strung up in the usual Hegelian simplicity about how the "immaterial" ought to be cashed out. Science's job has been to show how physics is way less material than Newtonianism might have conceived of it, and how life and mind are also way less "spiritual" than the Catholic Church – as an instrument of agriculture-age social power – liked to look at it.
And as I keep saying, biosemiosis can tell you all about how the epistemic cut is actually implemented in everyday flesh and blood terms. It ain't an ontological-level dualism. It is just a very highly developed epistemic dualism. A cut that forced events like RNA's primitive level of functionality being handed over to a proper coding machinery, coupled to a proper structural material, leaving RNA to act as the shuttling messenger between the two sides of this dichotomised equation.
Incredible as it might seem, all the mysteries have just evaporated over the past 20 years when it comes to life and mind science. Natural philosophy – as the systems science legacy of Aristotelean metaphysics – got it right. We won.
:razz: