0280 Tabaczek’s re-allocates Deacon’s treatment of emergence, without the benefit of Peirce’s category-based nested form.  Razie Mah examines Tabaczek’s re-allocation using two works, A Primer on the Category-Based Nested Formand A Primer on Sensible and Social Construction.

The result in the Deacon-Tabaczek interscope for emergence.

0281 What can I say?

Obviously, a three-level interscope is a nested form composed of nested forms.

In this interscope, Deacon’s terminology is used.

To begin, consider Deacon’s labels for the three levels.

0282 On the content-level, a thermodynamic process that tends towards equilibrium (in a spontaneous sort of way)_3abrings the actuality of a contained circulation of ingredients_2a, where reagents are separated so that some of the free-energy of their reaction can be captured, into relation with (a situationally induced) displacement from equilibrium_1a.

For example, if a dam extracts the gravitational potential and kinetic energy released in a river flowing downstream, then the content-level is the adjusted spontaneous process of water flowing downstream.

0283 On the situation-level, a homeodynamic process capable of extracting the captured energy_3b brings the actuality of the embodiment of the captured energy_2b into relation with the potential of the various constraints and biases imposed on the content-level nested form_1b.

For the example of the hydroelectric dam_3b, water is channeled in such a fashion as to drive a turbine_1b that produces alternate (and sometimes, direct) voltage in a wire cable_2b.  The emergent being is electrical “current”_2b.

0284 On the perspective-level, a morphodynamic process_3c, capable of utilizing the energy captured by the emergent being_1c, generates a persisting form_2c.  The persistent form is like an end point of the emergence_2c, because it_2c not only dissipates the potential_1c of the emergent being_2b but it_2c “forms” something_2c in the process_3c.  Here, Deacon’s terminology sounds oblique and, perhaps, misleading.  The dissipative power_2c persists as a form_2c, yet “dynamic form” labels the normal context_3c.  Also, the potential of the emergent being_1c is a “simplification”, of sorts.  But, is “simplification_1c” a satisfying term?

For example, a morphodynamic process_3c takes the potential of the alternative electric voltage… or is it current?… in a wire connected (however distantly) to the aforementioned turbine_1c and performs some sort of work, such as heating my morning toast_2b.

0285 Yes, the example sounds lame.  But, with butter and apricot jam, the emergence is really quite satisfying.

0286 An example that is closer to Tabaczek’s argument sounds much less lame.

Mitochondria produce ATP from sugar and oxygen.  I breathe in order to supply oxygen to my mitochondria.  I eat toast in order to supply the sugar.

0287 Outside the body, the reaction of sugar with oxygen is called “combustion”_2a.

Inside the body, the degradation of sugar into carbon dioxide and water belongs to the Kreb’s cycle_1b.  The combination of atomic hydrogen (released by the degradation of sugar) with molecular oxygen is called the mitochondrial electron transport chain_1b.  These separated reactions both produce ATP_2b, a high-energy molecule that, given enough time, will degrade back to ADP and P_i (inorganic phosphate).

0288 ATP_2b is one of the currencies of the cell.  All sorts of biosynthetic routes and transportation mechanisms_3c within a eukaryotic cell will take the ATP, which has three covalently bound phosphates, then pop off the last phosphate_1b, and use the released energy to do biochemical or kinetic work_2c.

0289 Here is a picture of the Deacon-Tabaczek interscope for mitochondria.

0290 On the adjusted thermodynamic or content level, the normal context of orthograde reactions_3a brings the actuality of the transfer of electrons from sugar to oxygen_2a (yielding water and carbon dioxide)_2a into relation with the potential of ‘the chemistry of glucose and oxygen’_1a.  

On the homeodynamic level, the normal context of cellular matrix and mitochondria_2b bring the actuality of ATP (as an emergent being)_2b into relation with the potential of ‘the Kreb’s cycle and the mitochondrial electron-transport chain’_1b.

On the morphodynamic level, the normal context of staying alive_3c brings the actuality of biosynthesis and cellular transport_2c into relation with the potential of ‘utilizing the controlled degradation of ATP in order to do work’_1c.

0291 Now, I turn to biosemiotics.

Recall that Sharov and Tonnessen’s noumenal overlay presents the triadic specifying sign-relation (connecting situation and content levels of an interscope)…

…as a dyadic relational structure.

0292 A specifying sign-relation also stands within the interscope for emergence.

The specifying sign-relation stands out when ATP_2b, as an emergent being, associates to the specifying sign-object (SO_s).  then, other elements of the interscope for mitochondrial respiration fall into slots in the S&T noumenal overlay.

0293 As it turns out, the interscope for emergence also contains the exemplar sign-relation.  Well, every three-level interscope contains an exemplar sign-relation.  So maybe, that is no surprise.  The exemplar sign-relation binds the situation and perspective levels.  A situation-level actuality_2b (SV_e) stands for a perspective-level actuality_2c (SO_e) in regards to the perspective-level normal context_3c operating on a perspective-level potential_1c (SI_e).

“SV”, “SO” and “SI” label the sign-vehicle, sign-object and sign-interpretant. Subscript “s” denotes the specifying sign-relation.  Subscript “e” denotes the exemplar sign-relation.

0294 When I turn my gaze back to the S&T noumenal overlay, I note the following.

The three-level interscope depicting the production of ATP as an emergent being contains both specifying and exemplar sign relations.

The S&T noumenal overlay directly incorporates the specifying sign-relation.

When the full three-level interscope of emergence associates to the S&T noumenal overlay, the incorporation of the exemplar sign-relation becomes apparent.

0295 So, for emergence, the agency aspect of the S&T noumenal overlay should express the exemplar sign-relation.

Here is a picture.

0296 I recall that the agency aspect for the S&T noumenal overlay has simpler formulations.

Here is one that is worth comparing to the ongoing association.

0297 In mitochondrial respiration as emergence, ATP_2b is the actuality₂ on the situation_b level.  Both actuality₂ and situation_b associate to Peirce’s category of secondness.  ATP_2b is the actuality₂ on the level_b associated with actuality.  Consequently, the observation and measurement of ATP_2b in biological systems should be of interest for modeling the specifying character of [habit] as well as the exemplar character of [salience].

In this regard, ATP_2b associates to information and information displays the way that the emergent being_2b serves as both the sign-object of the specifying sign-relation (SO_s) and the sign-vehicle of the exemplar sign-relation (SV_e).

0298 The production of ATP_2b is the specifying sign-object (SO_s).

The dissipation of the energy (SO_e) embodied by ATP_2b (SV_e) represents a goal.

ATP_2b (SV_e) stands for the productive dissipation of its energy_2c (SO_e) in the normal context of dynamic form_3coperating on the potential intracellular uses of ATP_1c (SI_e).

This application of emergence, appearing in Comments on Mariusz Tabaczek’s Arc of Inquiry (2019-2024), offers a promising start to look at Sharov’s carefully formulated model for the origin of life.

0299 Here is a three-level interscope for emergence, with the specifying and exemplar sign-relations noted.

0300 Emergence enters into S&T’s noumenal overlay.

Here are the results.

0301 When Sharov and Tonnessen confront the origin of life on Earth in chapter five of Semiotic Agency, associations with Mariusz Tabaczek’s formulation of emergence are not apparent.  The focus on inquiry is on chemical self-replication rather than structures that capture thermodynamic energy_2a through an emergent_2b then dissipate the emergent’s energy_2cby building a persistent structure.

The eukaryotic cell’s metabolism of glucose and oxygen works by extracting energy released in the combustion of these reagents.

In combustion, oxygen gas directly takes electrons from glucose, without any homeodynamics.  Covalent bonds are broken.  Covalent bonds form.  Lots of free-energy is released and converted into heat.

In the eukaryotic cell, electrons produced by the oxidation of glucose (at one cellular location) are used to produce an emergent being, such as ATP, before going into the reduction of oxygen (at another cellular location), where more ATP is produced.  ATP_2b is the emergent being, whose energy is dissipated on the morphodynamic level.

0302 So, where is a scientist supposed to start, when considering abiogenesis?

Researchers into the origins of life focus on the formation of covalent bonds that constitute polymers.  Polymeric molecules are persistent structures.  But, scientists have not identified an emergent, similar to ATP, whose concentration is low yet constant, because it is produced on the homeodynamic level and used up on the morphodynamic level.  Nor have researchers identified any thermodynamic processes amenable to exploitation by a homeodynamic level.

0302 In section 5.5 of Semiotic Agency and sections 9.4 and 9.5 of Pathways, Alexei Sharov presents a replicator-niche coupling model.  Several items are required: water, oil, pigments (in oil), light, and two complementary molecules that are separate in water, yet combine to form an active site when they attach to the surface of an oil droplet.

0304 Here is a picture.

0305 Let me start with the oil droplet.

Water tends to drive alkanes out of solution.  That is why alkanes form oil droplets in water.  These droplets are not really stable, because they are not held together because of mutual attraction, but are held in place by the fact that each water molecule networks with other water molecules so well that, if a molecule does not participate in water’s hydrogen-bond networks, it gets driven out of solution. That also applies to the pigment, which is oil-soluble and not water-soluble.

0306 What about the polymers?

Parts of complementary polymers are soluble in water.  Other parts are not as soluble.  So, parts are driven out of water and parts are pulled back into water.  These molecules collect on the surface of the oil droplet, then couple with one another, with the pigment and with an alkane, which is part of the oil droplet.

0307 There are no oxygen molecules in the picture.  Today, the Earth’s atmosphere is around 20% oxygen and 80% nitrogen.  In the early Earth’s atmosphere, reduced carbon compounds make the smaller fraction and nitrogen makes the large fraction.  More or less.  No scientist can go back in time and measure the composition of the atmosphere of the early Earth.

Reduced carbon in the atmosphere goes with the alkanes in the oil.  Much of the light of the early sun is absorbed by the carbon-rich atmosphere, but some makes it down to pigments in the oil droplet.  The pigment and complementary polymers conjoin in two locations in the figure below.

0308 Then, what happens?

The pigment absorbs a photon and becomes an electronically excited pigment.

Then, the energy captured by this pigment initiates a chemical reaction, where the alkane is oxidized to a fatty acid.  Oxidation releases electrons.  One among many possible oxidations is pictured above.  With a little more oomph, that carboxylic acid would pop off as carbon dioxide.  However, this reaction stops as an alkane chain with a carboxylic acid at the terminus.  I call this molecule a “fatty acid”.

In the following figure, the two processes are depicted as two dyads.  Each dyad exhibits the structure of reagents [turn into] products.

0309 Now, theoretically a reduction reaction is close at hand.  If the oil droplet is near a chemical that can accept the electrons, then a coordinated reduction can take place.  For example, the hydrogen ions and the electrons can combine to form 3H₂(g).  Or, atmosphere nitrogen (N₂) can be reduced to ammonia, 2NH₃.

0310 What happens next?

The fatty acid serves as the emergent being_2b, because the carboxylic-acid side tends to favor the water and the alkane side stays in the oil droplet.

0311 In short, fatty acid is the emergent being_2b that has the potential of stabilizing oil droplets_1c, allowing them to “feed off” or “absorb” oil from less stable oil droplets_2c.

0312 Does Sharov’s scenario, as far as it goes, fit the Deacon-Tabaczek interscope?

Indeed, it does.

0313 Does this interscope associate to the S&T noumenal overlay?

Yes, it does.

0314 Well, so far so good.

Nevertheless, there is a long way to go to get to a prokaryotic cell (as noted in sections 5.8-5.10 of Semiotic Agency and 9.6-9.8 of Pathways).

For example, prokaryotic cells replicate themselves through cell division.  But, the replication is nothing like this oil droplet example.  That is because DNA plays a role in prokaryotic cell division.  Biologist call this type of replication, “template based”.

Also, there is the issue of the cell membrane.  The cell membrane is a lipid bilayer, consisting of phosphorylated fatty acids.  In other words, fatty acids may stabilize an oil droplet.  Once those fatty acids have a phosphate attached to them, then their phosphates love water so much that the alkane-portion of the molecule is excluded from the water so strongly that a bilayer is stable.

0315 Also, there is the formalization of pigments that capture sunlight in order to produce energy-rich sugar molecules.  Today, photosynthesis absorbs carbon dioxide (gas) and releases oxygen (gas).  In the early Earth, photosynthesis does the same.

Here is the balanced chemical reaction.