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 energy2a through an emergent2b then dissipate the emergent’s energy2cby 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. ATP2b 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.
The fatty acid serves as the emergent being2b, 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 being2b that has the potential of stabilizing oil droplets1c, allowing them to “feed off” or “absorb” oil from less stable oil droplets2c.
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.
0316 Oxygen gas is a byproduct of photosynthesis. Over billions of years, the continual release of oxygen transforms the atmosphere of the Earth.
The ubiquity of oxygen gas in today’s atmosphere makes experimental research into the chemistry of the early Earthdifficult. Today, the reaction that Sharov suggests, the oxidation of an alkane to a fatty acid, would require elaborate precautions. Why? Even a trace amount of oxygen would directly react with the light-absorbing pigment.
0317 So, what am I saying?
Well, research is difficult.
0318 Also, as soon as one gets to the earliest forms of life on Earth, such as photosynthetic prokaryotes, the “genomic complexity” (nominally, the length of DNA that belongs to only functional genes) is already high. If one plots the genomic complexity of (1) prokaryotes, such as bacteria, (2) single-celled eukaryotes, such as amoebas, (3) multicellular water animals, such as fish (4) invertebrate land animals, such as worms, and (5) vertebrate land animals, such as mammals, versus time for first fossil evidence, one gets the following graph.
0319 On one hand, Sharov concludes that the genomic complexity doubles every 340 million years since the start of the Earth.
On the other hand, Sharov points out that, if one projects the line down to zero genomic complexity, the intersection occurs a little over 9 billion years ago. But, the Earth is only 4.5Byr.
Fortunately, the universe is around 15 billion years old.
0320 If the early Earth is seeded, then biologists already have a label, “panspermia”.
All other planets and moons in the solar system should be similarly seeded.
So, future space exploration may provide an answer.
If it turns out that the early Earth is seeded through panspermia, then research into the origins of life (in general) becomes even more difficult.
0321 Now, I conclude.
Sharov and Tonnessen’s noumenal overlay characterizes biosemiotics.
The Deacon-Tabaczek interscope characterizes emergence.
Both relational structures apply to inquiry intothe origin of life on Earth.
This examination demonstrates how the two relational structures relate to one another and constitute complementary approaches for further inquiries into the origins of life.
0322 But, what I have learned concerns more than the topic of the origin of life.
This is significant.
Sharov and Tonnessen’s noumenal overlay may “expand” to include the entire D-T interscope, which includes both the specifying and the exemplar sign-relations.
0322 By extension, the S&T noumenal overlay associates to any three-level interscope, containing two sign-relations,according to the comparison in the following figure.
0323 The topic of the origin of life on Earth turns into a valuable insight into biosemiotics, emergence, and two sign-relations.
0324 The text before me is chapter ten in Pathways to the Origin and Evolution of Meanings in the Universe (2024, edited by Alexei Sharov and George E. Mikhailovsky, pages 217-243). The author hails from the Evolutionary Bioinformatics Laboratory at the Department of Crop Sciences and Carl R. Woese Institute for Genomic Biology, at the University of Illinois, Urbana, Illinois, USA. The author and editors have permission to use and reprint this commentary.
From prior examinations, I propose that Alexei Sharov’s and Morten Tonnessen’s 2021 book, Semiotic Agency, formulates a noumenal overlay for the diverse field of biosemiotics. All manifestations of semiotic agency are unique. Each is a subject of inquiry on its own. Yet, they have one relational structure in common. Here is a picture of that dyadic actuality.
0325 Biosemiotics is not divorced from science. Scientists observe and measure phenomena, then build models based on those observations and measurements. The real elements in the above figure support phenomena. The contiguities (in brackets) call for models.
0326 So, what about communication mediated by biomolecules?
0327 In the introduction (section 10.1), the author reminds the reader of two premodern views of biological behaviorsand how they change over time. One is the force of life (in French, le pouvoir de vie), which tends to increase complexity. The other is the influence of circumstances (in French, l’influence des circonstances), which tends to select for… um… survivors.
These premodern views fit nicely into the contiguities in the above relational structure. Each dyad can be compared to Aristotle’s hylomorphe of matter [substance] form, allowing the following comparison.
0328 The force of life tends towards the many.
The influence of circumstances tends toward the few.. or rather… one goal.
Surely, my assignments are confusing, because the force of life is singular and circumstances tend to vary. Also, real initiating events can vary. But, goals tend to rule out alternatives.
0329 The author then draws upon a recently translated papyrus scroll, attributed to Empedocles. Empedocles speaks of two opposing forces, one capable of growing things together from the many and one capable of growing things apart. The former is labeled, “love”, the latter, “strife”.
0330 I wonder, “How does this ancient distinction fit into the schema pictured above?”
Here is my suggestion.
I have a 50:50 chance of being correct.
0331 Strife goes with the force of life, tending towards the many. Love goes with the influence of circumstances and tends towards a singular goal.
Both are substances and reflect (however distantly) Aristotle’s exemplar: matter [substance] form.
In the above figure, the real initiating event is like an form that conjures matter (information). At the same time, that matter (information) substantiates another form (goal). This conjured matter (information [love]goal) encompasses the presence that accounts for semiotic agency as a thing.
0332 What does that imply?
As [strife] acquires information, [love] moves closer to its goal.
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?
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.
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 (SVs) no longer indicates that food is in the vicinity (SOs) according to the ways that this bacteria interprets the world (SIs).
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 gut2a (SVs) stands for the emergent being of a conformationally-distorted beta-linked polysaccharide held in the jaws of a cleaving enzyme2b (SOs) in regards to bacterial self-governance3b operating on potential courses of action1b (SIs).
For the exemplar sign, the emergent being of a beta-linked polysaccharide bound to “the claws and jaws” of new complex2b (SVe) stands for a seemingly endless source of glucose from ingested cellulose2c (SOe) in regards to what certain bacteria in the insect’s gut3c are capable of doing1c (SIe).
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 contenta, situationb and perspectivec.
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 actuality2a (SVs) stands for a situation-level actuality2b (SOs) in regards to a situation-level normal context3b and potential1b (SIs).
For the exemplar sign-relation, the situation-level actuality2b (SVe) stands for a perspective-level actuality2c (SOe) in regards to a perspective-level normal context3c and potential1c (SIe).
0363 In terms of communication, I can imagine that the SVs is like a transmission sent and the SOe is like the transmission received.