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.

0333 Well, what if matter… er… information… consists of multiple biomolecules that are… um… modular… in so far as they… because of circumstances… simultaneously engage in a cooperative endeavor… a “love”, so to speak?

Some would say that this what if is similar to the hierarchical relation between parts and a whole.

But, would the whole be the form associated with goal or the form associated with the real initiating event?

Or, would it be the thing called “semiotic agency”?

0334 At the start of section 10.2, the author lays this ambiguous multiple metaphor onto the procrustean bed of an evolutionary paradigm, where (on a molecular level) biological parts are added to one another in a piecemeal way to an evolving system.

The author proposes a phylogenomic-based biphasic model of module creation that explains evolutionary growth in biochemical systems.  In phase one, modules nest within one another, in a provisional sort of way, until over time or suddenly, the form that is goal clarifies. Different modules start to work together as a semiotic agent. In phase two, modules working within that functioning cooperative change as semiotic agency diversifies.

0335 The second phase associates to “adaptation”.

The first phase does not have a proper name.  I suggest the term, “empedoclement”. 

An empedoclement is the inverse of an impediment.

0336 Here is an analogy.

Recently, I joined a tennis club.  I trained to play the game by enduring real initiating events and reviewing information on my performance.  Since I am so modular, different aspects of me perform independently of one another, so I did not adapt well to the circumstances. My instructor says that if I don’t think about what I am doing with each of my modules,then I could move holistically in a coordinated manner.  I will become an adept, rather than a lackluster player full of impediments.

0337 One would think that routinely training and playing tennis would lead to (perhaps slow, but) steady improvement towards the goal of being competitive.  This is a matter of adaptation.  All the facets of mind and body are modular.  Each module develops along its own trajectory. In apparent stasis, improvement is held at bay by one or two recalcitrant modules. In surprisingly fast change, two or more modules improve in tandem.  The fast change could be an empedoclement.

0338 While this analogy helps, I find it difficult to imagine that first phase, where parts are present and may afford some advantages, but no one part realizes the game that is afoot.

0339 The author offers two images as metaphors for the phylogenomic-based biphasic model.

One metaphor is a tree, where the roots represent modules, the trunk stands for the modules coalescing into matter [love] form, where matter is information and the form is a telos or an end.  

The other metaphor portrays modules themselves, which over time, interact to generate scaffolds and active sites, until a robust combination constellates.

Here is a picture of the second metaphor.

0340 The word, “constellates”, is a psychological term (actually, Jungian) that marks the coming into presence (esse_ce) of an archetypal form (essence).  The result may be called “a primordial image”.

For example, the archetype of the king may constellate in a variety of ways, including the duplicitous and the honest, the greedy and the beneficent, as well as the foolish and the wise.  Each pair of these primordial images informs us of a module within the one archetype and how that module can yield different responses to similar circumstances.

0341 But, can the word, “constellate”, also label the coming together of modules within an archetype as an empedoclement?

0342 How about a hypothetical example?

Cellulose is composed of glucose molecules that are beta-linked to one another.  Starch is composed of glucose molecules that are alpha-linked to one another.  Beta-linked polysaccharides cannot be digested.  Alpha-linked polysaccharides are easy to digest.  

0343 Imagine a bacteria that has a receptor capable of clinging to cellulose, but cannot break the beta-linkage.  It binds because exposed cellulose associates to plant damage and plant damage releases various nutrients, including alpha-linked polysaccharides.  This bacteria is an opportunist.

0344 At this point, I find it hard to predict what happens next.  A biosemiotic reality is going to unfold, but I don’t know how. 

I do know that phenomena of this biosemiotic constellation objectify the following noumenal overlay.  If I want to scientifically study this specific bacteria, then the real elements of the noumenal overlay give rise to phenomena.  Phenomena may be observed and measured.  The observations and measurements may be modeled.  The models account for the contiguities.

0345 Now, this prokaryotic bacteria is not the only living thing that can take advantage of sites of plant damage.  Wood-eating insects do the same.  They chew into wood, not because they can digest the beta-linked cellulose, but because they get… well… the same nutrients that the cellulose-binding bacteria want to feed on.

0346 Then what happens?

Wood-eating insects, who create the damage that attracts the cellulose-clinging bacteria, inadvertently ingest these bacteria, who do not create the damage that nourishes them.  Bacteria are only present to exploit a long-established relation between exposed cellulose and food.

So, when a cellulose-clinging bacteria gets ingested, it can serve as food for the termite (if it dies) or it can simply pretend that nothing significant has changed (if it lives).  Bacteria can still hold onto cellulose in the termite’s gut and compete for food with the termite’s own digestive system.

0347 The bacteria’s competition with the termite’s own capacity to digest alpha-linked polysaccharides presents a signaling error.  It is as if exposed cellulose (SV_s) no longer indicates that food is in the vicinity (SO_s) according to the ways that this bacteria interprets the world (SI_s).

0348 The specifying sign-relation fails because the bacteria clings to cellulose inside the wood-eating insect’s gut, but this no longer indicates that alpha-linked polysaccharides are available for food.

0349 Then what happens?

Well, phase one ends in this hypothetical scenario when the two independent biomolecular capacities that are innate in the bacteria, the ability to latch onto cellulose and the ability to cleave glucose from alpha-linked polysaccharides, get bound to one another.  Now, a beta-linked polysaccharide chain may be held by the latching molecule and be conformationally distorted enough that a terminal glucose can be cleaved by the original cleaving enzyme.

0350 The bacteria lives off some of the glucose that it liberates.  But, the potential source of glucose has changed from the starchy alpha-linked polysaccharides that both insect gut and bacteria digest to include previously undigestible beta-linked polysaccharides now available to the bacteria.  Indeed, the bacteria release more glucose into the gut than what is available from alpha-linked polysaccharides.

The insect already has pathways for transporting glucose from the gut to the body.

The insect uses the free glucose for its own metabolism.  All it needs to do is eat more wood and keep transporting liberated glucose out of its gut, so there is no build-up of soluble glucose in the gut and the bacteria keep that beta-link cleaving pathway operating.

0351 In terms of the S&T noumenal overlay, a beta-linked polysaccharide in the claws and jaws of the “holder” and “cleaver” biomolecules is like an emergent being.

0352 Now, natural selection enters the picture.  Bacteria with the innovation prosper.  Bacteria with improvements on the innovation prosper even more.

Plus, the wood-eating insect comes under natural selection as well.

0353 Phase two of diversification follows.

0354 At this point, I must remind myself that this scenario is hypothetical.

It is a fiction that is more than a confection (an elaborate frivolous construction), even though it contains a confection (a compounding of two things).

To some, this confection (sugary delicacy) may taste implausible.

But, it offers the curious flavor of an empedoclement.

0355 The sign-elements associated to the S&T noumenal overlay conveys the new message.

For the specifying sign, exposed cellulose in the wood-eating insect’s gut_2a (SV_s) stands for the emergent being of a conformationally-distorted beta-linked polysaccharide held in the jaws of a cleaving enzyme_2b (SO_s) in regards to bacterial self-governance_3b operating on potential courses of action_1b (SI_s).

For the exemplar sign, the emergent being of a beta-linked polysaccharide bound to “the claws and jaws” of new complex_2b (SV_e) stands for a seemingly endless source of glucose from ingested cellulose_2c (SO_e) in regards to what certain bacteria in the insect’s gut_3c are capable of doing_1c (SI_e).

0356 Each of the sign-vehicles and the sign-objects have observable and measurable facets that will eventually go into scientific models.  The scientific models will assist in accounting for each of the sign-interpretants.

Biosemiotic research may be conducted after phase one is complete.

Biosemiotic research can never tell whether phase one is proceeding.

This is the way of empedoclement.

0357 It seems that the wood-chewing insect, so empowered, would go berserk and start to eat every living plant.

Like ripples in still water, biosemiotic waves propagate.

If these wood-chewing insects go after a living plant, then all that plant needs to do is develop a toxin that poisons those little beta-linkage breaking bacteria.  Problem solved.

Okay, so these new insects are not invulnerable?

0358 Tell that to the exterminator.

The exterminator facing a wood-eating insect infiltration, knows that certain principles apply.  He assesses signs.  Is communication (section 10.3) an issue here?  I suppose that depends on who is doing the talking and who is receiving the message.

0359 Peirce’s definition of a sign as a triadic relation is crucial for biosemiotics.  So, are Peirce’s three categories.  Even before getting to a question of communication, there is a character to the S&T overlay that embodies the relational structure of specifying and exemplar sign-relations.

Here is a picture.

0360 These sign-elements, in turn, represent locations in a three-level interscope.  An interscope is a category-based nested form composed of category-based nested forms.  Each nested form exhibits a normal context₃, actuality₂ and potential₁. Then, the nested forms compose the three levels of content_a, situation_b and perspective_c.

See A Primer on the Category-Based Nested Form and A Primer on Sensible and Social Construction, by Razie Mah, available at smashwords and other e-book venues.

0361 I will not show a picture of the three-level interscope.

Instead, here is how the elements of the three-level interscope correspond to elements in the S&T noumenal overlay.

0362 For the specifying sign-relation, a content-level actuality_2a (SV_s) stands for a situation-level actuality_2b (SO_s) in regards to a situation-level normal context_3b and potential_1b (SI_s).

For the exemplar sign-relation, the situation-level actuality_2b (SV_e) stands for a perspective-level actuality_2c (SO_e) in regards to a perspective-level normal context_3c and potential_1c (SI_e).

0363 In terms of communication, I can imagine that the SV_s is like a transmission sent and the SO_e is like the transmission received.