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.

0364 According to Shannon’s information theory, which offers a mathematical model for “information” occurring in human-mediated electro-magnetic transmissions, there are five components to the whole process: (i) an information source, (ii) a transmitter, (iii) a channel, (iv) a receiver and (v) a destination that serves as an information sink.

0365 Can I draw associations to the S&T noumenal overlay?

I suppose so.

0366 The specifying sign-interpretant_3b,1b (SI_s) is like an information source (i) and the specifying sign-vehicle_2a (SV_s) associates to the transmission (ii) of something_2a that stands for information_2b (SO_s).  Maybe, I can say that the SV_s is like a transmitter (ii) and SO_s is like that transmission entering the proper channel (iii).

The SO_s is contiguous with SV_e, so a transmission in the proper channel_2b (iii) constitutes an exemplar sign-vehicle_2b(SV_e) that stands for a perspective-level actuality_2c (SO_e) (iv), according a perspective-level normal-context_3c and potential_1c (SI_e) (v).  So, the SO_e may be labeled as a receiver (iv) and the exemplar sign-interpretant_3c,1c (SI_e) associates to the information sink or destination (v).

0367 Here is a picture.

0368 Of course, my associations are both evocative and fallible.

Here are three implications (F, G, H).

0369 First (F), Shannon’s theory of communication regards biosemiotic sign-interpretants as sources (i) and receivers(iv).  These are precisely the elements in the S&T noumenal overlay that need to be explained.  Shannon’s theory places them in black boxes and treats them as givens.

What does that imply?

From the point of view of biosemiotics, I wonder, “What is Shannon’s theory actually modeling?”

0370 After all, if I go to the start of the chapter, the two crucial aspects involved in biological change, as characterized by the premoderns, correspond to sign-interpretants.

0371 Shannon’s theory of communication takes these two primordial aspects for granted, in order to concentrate on another question.

What is the channel’s capacity to carry information?

0372 What is so important about the channel_2b (iii)?

Hmmm. I see that the channel_2b corresponds to “information_2b” and to SO_s[and]SV_e.

What is that about?

Is [and] the same as [contiguity]?

Is this topic about to get fuzzy?

0370 Second (G), Shannon’s theory of communication, as depicted above, is consistent with a biosemiotic approach in regards to the sources of phenomena for communication: transmitter (SV_s) (ii), channel (SO_s [and] SV_e) (iii)  and receiver (SO_e) (iv).

Okay, so everything’s fine.

0371 Does that mean that Shannon’s theory of communication somehow is relevant to the hypothetical scenario where the... um… vehicle of a beta-linked polysaccharide_2a (SV_s) is “transmitted” then “received” as the object of glucose molecules ready to power a wood-eating insect’s metabolism (SO_e)?

In this case, does the term, “information_2b“, correspond to “the ability of a gut bacteria’s dual-modular claw and jaw apparatus to cleave the terminal glucose of a beta-linked polysaccharide”?

It makes me wonder about the meaning, the presence and the message underlying the word, “information_2b“.

There seems be a lot going in within the situation-level actuality_2b, which is where the SO_s transits into the SV_e.

0372 Third (H), Shannon’s theory of communication, expressed as an application of the S&T noumenal overlay,presents a simplification that drags the inquirer to that confounding channel_2b.

After all, the channel (iii) goes with phenomena.

In human electronic communication technology, the channel_2b can carry only so much information_2b.  Noise is the loss of information_2b.  Is “noise” information that can no longer be properly received?  Or is “noise” some lacking that makes information no longer salient?

Questions like these, as problematic as they are, seem well-cogitated compared to ones that arise when Shannon’s theory of communication is transferred from the dyadic S&T noumenal overlay to a three-level interscope containing the specifying and exemplar sign-relations.

0373 Recall the unexpected and twisted path from point 0270 to point 0300?

Now, maybe I should start getting used to that storyline.

0374 Why?

It’s the story of the evocation of thirdness by firstness.

0375 Initially, Sharov and Tonnessen’s noumenal overlay associates to the specifying sign relation.

Once the Deacon and Tabaczek interscope for emergence enters into the picture, the S&T noumenal overlayincorporates the exemplar sign relation.

0376 Initially, Sharov and Tonnessen’s noumenal overlay belongs to what is of the Positivist’s judgment.  It belongs to firstness.  Yet, it touches base with secondness, in so far as its own dyadic structure serves as a guide for discerning what should be regarded as phenomena and what is in need of being modeled.

This makes sense, in so far as biosemiotics is the study of the relational thing that all biological entities have in common.

0377 I mean really, how is a biologist going to examine a sample of the relational thing that all biological entities have in common?

Hey, who left a biosemiotic slide in the microscope?

Is it Shannon?

Let me take a look.

0378 Yeah, it’s Shannon’s alright.  It has information theory written all over it.

But now, the associations are even more evocative.

0379 The two tendencies that the premoderns identified, the force of life and the influence of circumstances, now associate to normal contexts and potentials.  The stuff of strife (situation-level) and love (perspective-level) associate to both thirdness and firstness.  These are the things that biosemiotics is supposed to account for.

0380 Shannon’s information theory fixates on the virtual nested form in the realm of actuality.

0381 The perspective-level actuality_2c of a receiver_2c virtually brings the situation-level actuality_2b of a channel_2b into relation with the potential of a content-level information transmitter_2a.

Yes, these actualities manifest phenomena that can be observed and measured.  Shannon’s information theory assists in modeling those observations and measurements.  But, do those models tell me about the situation- and perspective-level normal contexts and potentials?  Do they tell me about the specifying and exemplar sign-interpretants?

If they do not, then is Shannon’s information theory biosemiotic?

0382 Does Shannon’s information theory offer a metaphor for biosemiotics?

And, how weird and disturbing would that analogy be?

0383 Consider the hypothetical that exemplifies the author’s biphasic depiction of evolutionary growth.

Here is a picture.

0384 According to Shannon’s information theory, I should focus on the virtual nested form in the realm of actuality.

The perspective-level actuality_2c of free glucose to the insect’s body_2c virtually brings the situation-level actuality_2b of the functionality of the claw and jaw combination achieved by bacteria in the insect’s gut_2b into relation with the potential of the content-level actuality_2a of glucose bound within the cellulose that the insect has eaten_2a.

0385 My exterminator says that he recommends a new product.

Apparently, investigators at the Molecular Biology Department at the University of Slidell, in Louisiana, hatched a scheme for treating lumber with dilute concentrations of hydrofluoric acid.  They patented the process.

0386 Apparently, the fluoride replaces a hydroxy group on the beta-linked polysaccharides of wood, here and there.  The fluoride causes the claw part of the jaw and claw to not let go.  Apparently, one fluoride on one beta-linked polysaccharide can gum up the operations of a whole bacteria and the bacteria dies, which is no big deal, until the wood-eating insect’s gut digests the bacteria and frees that one fluoride-labeled beta-linked polysaccharide back into the gut, for another bacteria to pick up to digest.

In short, bacteria-killing fluoride-labeled beta-linked polysaccharides start to build up in the wood-eating insect’s gut and the insect gets less glucose, even as it continues to eat the treated wood.  This is no good.  So, the wood-eating insects move on.

Yes, the treated wood_2a transmits a message into a channel within the wood-eating insect’s gut_2b so the insect itself receives a signal to move on_2c.

0387 What a sales pitch.  The explanation offers a specific mechanism for deterring wood-eating insects.  Plus, it fits a budget.

The economy of the exterminator’s proposal, along with the promised robustness of treatment and flexibility in application, convinced my neighbor to use the processed wood for his new shed, which replaces his old, well-infested, one.

I suspect that my neighbor secretly hopes that the wood-eating insects simply move over to my lot.  It is as if my neighbor_2a transmits a message into a channel consisting of a trail of wood-eating insects to my untreated wood shed_2bthat signals to me that I better build a new shed with treated lumber_2c.

0012 Okay, the Positivist’s judgment uses the empirio-schematic judgment as a tool for generating models.  For this reason, what ought to be belongs to secondness.

At this point, the reader may see a method to the madness of the seventeenth century mechanical philosophers.  Truncated material and efficient causes permit the construction of mathematical and mechanical models, based on observations and measurements of phenomena.  Final and formal causes cannot be regarded as data, since they are metaphysical.  Metaphysical causalities cannot be regarded as physical.

Mathematical and mechanical formula represent the physical world as models (what ought to be, secondness).  Disciplinary language (relation, thirdness) couches these formula (what ought to be, secondness) in terminology that applies to observations and measurements of phenomena (what is, firstness).  Phenomena belong to firstness (the realm of possibility) because they have the potential to be observed and measured.

0013 In regards to what is, a dyadic relational structure belongs to the category of firstness.

What is the nature of this dyad, a noumenon [&] its phenomena?

0014 When an Aristotelian approaches a thing, the first abstraction sees the thing in terms of matter and form.  Typically, matter raises questions in regards to material and formal causalities.  Form raises questions in regards to efficient and final causalities.

Aristotle’s hylomorphe is a premier example of Peirce’s category of secondness.  Secondness consists of two contiguous real elements.  The contiguity, which is placed in brackets for proper notation, should signify the… um… how one real element accounts for the other real element.

Here is a picture of Aristotle’s hylomorphe and Peirce’s category of secondness.

0015 Yes, both these figures associate to Peirce’s category of secondness, the realm of actuality.

Now, according to the Positivist’s judgment, the noumenon (the thing itself) and its phenomena (the observable and measurable facets of the noumenon) belong to the category of firstness.

Here is a picture of a slogan that may be attributed to the German philosopher, Immanuel Kant (1724-1802 AD), even though he may never have actually said it.

0016 Isn’t that how philosophy operates?

A lifetime of dedicated thinking gets alchemically distilled into a slogan propounded by people who claim to be dedicated to philosophy, but are only gossips spreading unwarranted attributions.

0017 Well, maybe not “unwarranted”.

How so?

Kant’s slogan makes a crucial point.

No matter how many observations and measurements of phenomena that one makes, the resulting model does not fully objectify the thing itself.

0018 Kant’s slogan is anathema for any scientist who is convinced that science is the only reliable way to approach reality.

But, scientists are a hearty sort, even when wounded by technically appropriate statements that are anathema.  One hundred years after Kant (and I suspect, even during Kant’s lifetime), triumphalist scientists have a response-at-hand.  The noumenon is a philosophical construct.  Therefore, it may be regarded as the first approximation to a successful model, which can be objectified as its phenomena.  Since the model belongs to secondness in both the Positivist’s and empirio-schematic judgments, the model is more actual than the noumenon.  So, the model should replace the noumenon.

0019 If a model overlays the noumenon, then the apparent contradiction resolves.

Isn’t that cathartic?

0020 Well, it is good enough for scientists who are not much interested in philosophy.

How so?

To start, how can a mathematical or mechanical model be the source of the phenomena that is observed and measured in order to generate… um… itself, through the medium of a scientific disciplinary language?

0021 Okay, what about a college-level physics or chemistry or biology laboratory?

Have you ever noticed that some students (especially the one’s susceptible to philosophical inquiry) find each laboratory perplexing, as an instructor leads the class through a recipe that demonstrates that the principles behind the recipe are as real as well… any thing that you’d find in nature?

The laboratory recipe allows one to generate the phenomena that need to be observed and measured (please correctly fill out the experiment’s fact sheet) in order to validate that the model [can be objectified as] its phenomena.

And, the instructor never mentions Kant’s slogan, because the instructor has excluded philosophy so rigorously that things themselves can be replaced by scientific mathematical and mechanical models.

0022  From the point of view of a college instructor, the model (overlaying the noumenon) can be objectified as its phenomena.

The instructor does not realize that the phenomena have changed. They are not the observable and measurable facets of things that one encounters in nature.  They are recipes for generating observations and measurements in a laboratory.  A subtle change in the nature of the noumenon (it is now a model) changes the phenomena.  In this case, the phenomena become so routine that college sophomores can handle the equipment necessary to encounter the model overlaying the noumenon.