0403 Section 11.1 mentions codes and adaptors.

It makes me wonder about the solidity of the disciplinary language for codes.

In the above example of a bicycle lock, I ask, “Is the slot for the key an adaptor?  I suspect that the tumblers that give way in the face of key entrance are adaptors.  One particular configuration of that conformal change will no longer restrain the bolt.  Is the bolt an adaptor?  Yes, the curved bolt is precisely what binds my bicycle to the metal stand.

0404 World A is me with my bicycle key in my pocket.

World B is my bicycle locked to a public stand, like a steed awaiting my return.

0405 Section 11.2 notes several well-characterized organic codes in the biological literature.

The first is the genetic code.  The genetic code is primary.  I suppose that it is why it must be mentioned first.  I suppose that the genetic code is locked with that well-sequestered polymer, DNA.  I have a word for the potential of DNA.  I call it the “genotype”.

The second code mentioned is the DNA repair code.

That is not encouraging.

0406 Let me take a peek at this genotype business.

In order to make amino-acid proteins (world B), DNA is first transcribed into messenger-RNA.

Now, that is a story in itself.

Like how does some transcriber say, “I think that the section of DNA that I want to transcribe is located here.”, when “here”, looks like a spool of yarn that is held together with gum?

Unintended mishaps explain why the second-mentioned code stands ready-at-hand.  What a mess.

0407 So, instead of starting with DNA as world A, the author reasonably begins with m-RNA.

The code?

A nucleic acid triple (codon) located in a messenger-RNA (A) codes for a specific amino acid attached to a transfer-RNA by aminoacyl synthetase (B).

I suppose that I can say, “Codons in world A directly map amino acids in world B.”

0408 Two adaptors seem to be involved.

One, an aminoacyl synthetase attaches a specific amino-acid to a specific transfer-RNA.  The t-RNA is doubly specific.  On one hand, it is specific to an amino acid.  On the other hand, it carries the nucleic-acid complement to the codon that maps to that amino-acid.  The t-RNA complement codon hydrogen bonds to the m-RNA codon because of their complementary nucleic-acid geometries.

Two, a protein translation machine crawls along the strand of mRNA and chaperones the match between a t-RNA complementary codon and the currently exposed m-RNA codon.  If pairing is good enough, then the t-RNA’s amino acid gets added onto the forming peptide (amino-acid chain).

0409 Does this two point description fit into the idea of code and S&T’s noumenal overlay?

0410 The answer is yes.

And, that leads to this concern.

The S&T noumenal overlay seems like an afterthought.

All this nerve-wracking research in a genetics laboratory has come up with the two-point description stated above.  The rule of thumb is this: Every sentence in a senior college-level biochemistry text corresponds to a five-year doctoral thesis.  By extension, each item in the above two-point description corresponds to five or ten sentences in a biochemistry textbook.

Decades and decades of laboratory research goes into elucidating what Barbeiri calls the “genetic code”.

So what value does Barbeiri’s formalism offer?

0411 It offers a vision of the noumenon, the thing itself, that is not the same as taking this very complicated and successful model and placing it over the noumenon, as a triumphalist scientist is wont to do.

As soon as the triumphal scientist says, “The current model of the role of mRNA in peptide synthesis is the thing itself.”, then the biosemiotic connection is severed, and the research falls, like a leaf no longer connected to the tree of semiosis.

0412 The genetic code is not the only organic code mentioned in section 11.2.

Section 11.3 lists organic codes that control other organic codes.  

I wonder, “How can one code gain control over another?”

I can imagine two trajectories, starting with the following routinization of a S&T noumenal overlay.  Note how the two contiguities are replaced by codes corresponding to a sign-interpretant that operates on only one possibility.

In order to put the above figure in more familiar terms, the specificative code is habit and the exemplar code is salience.

0413 How does one code gain control of this semiotic agency?

It games it.

I have already presented the example of a wood-eating insect gaming a bacteria capable of latching onto exposed cellulose.

0414 One agent incorporates another agent into its semiotic agency.

The question is, “How?”

0415 Semiotic agency₂ is an actuality₂.  Actuality₂ belongs to Peirce’s category of secondness.  Secondness consists in two contiguous real elements.

Actuality₂ is contextualized by a normal context₃.  Normal context₃ belongs to Peirce’s category of thirdness. Thirdness is triadic.  Thirdness brings secondness into relation with firstness.

Actuality₂ is potentiated by ‘something’ in the realm of possibility₁.  The monadic realm of possibility₁ associates to firstness.

Hmmm.  One semiotic agency₂ can game another semiotic agency₂ by changing its normal context₃ and potential₁.

0416 Here is another way of looking at it.

The agent₃ of semiotic agency₂ is no longer the agent₃ that was present originally.  The new agent₃ effectively games an established semiotic agency₂ by changing its underlying signficance₁.  But, it is not an intentional change.  It is more like a subtle change in landscape that eventually alters the course of a river.

0417 So, coded semiotic agency₂ finds itself within the domain of a new agent₃ and potential₁ and the new domain is going to “game” the semiotic agency₂.

0418 Options?

Well, the original code can go out of business, to be replaced by semiotic agency₂ from the new management_3,1.

The original code can continue to operate irrespective of the semiotic agency₂ that the new management_3,1 is actualizing.  In this case, the new management_3,1 may use the original code as a functional component within a more comprehensive semiotic agency₂.

The original code that manifests as a functional component within a more comprehensive semiotic agency₂ may start to change, in response to its new normal context₃ and potential₁, through empedoclements.

0419 In short, modularity and hierarchy among semiotic agencies₂ may also be regarded as modularity and hierarchy among agents₃ and their significance₁.

Thus, the title of Prinz’s chapter is accounted for.

0420 Section 11.4 lists topics in neural codes.

Section 11.5 raises the question as to whether meaning is in or from codes.

Section 11.6 wonders how interpretation delivers meaning.

These sections all flow from Barbieri’s insights into the all-encompassing nature of codes.

And, codes are all-encompassing because the Sharov and Tonnessen’s noumenal overlay is all-encompassing.

0421 For neural codes, consider a human agent who sees an object on a sunny day.

Specular reflection of photons from a solid thing (SV_s) in the external world (A) stands for a thing with matter and form (SO_s) in regards to the functioning of pattern-recognizing specifiers in my occipital lobe (SI_s).

A thing with matter and form (SV_e) stands for an exemplar of ‘what it is’ (SO_e) in my world (B) according to specialized exemplar-recognizing modules outside of my occipital lobe (SI_e).

0422 I can ask, “How do I experience this?”

I can ask, “What is happening?”

A juxtaposition between the category-based nested form containing semiotic agency₂ and the content-level of the scholastic interscope for how humans think (appearing in Razie Mah’s blog for October, 2023, titled, Looking at John Deely’s Book (2010) “Semiotic Animal”) provides an interesting answer.

Does a comparison work?

0423 A human agent₃ asks, “What is happening?”

What is happening₃ is a content-level normal context_3a.

It_3a makes me wonder about the possibility that ‘something’ is happening_1a.

A neural code-based S&T noumenal overlay_2c presents an impression_2a of an exemplar sign-object_2c (SO_e).

The potential of vision_1a offers the possibility of identifying what it_2a (SV_s) is_1a.

So, maybe, in the above figure, the entire lower nested form fits into the actuality₂ of semiotic agency₂.

0424 Here is another example for neural codes.

0425 In the specifying sign-relation, formant frequencies uttered by a vocal tract (parole) (SV_s) in the external world (A) stands for a spoken word (langue, an item in a mental system of differences) (SO_s) in regards to rapid associations between parole and langue that occurs in specialized regions of the brain (SI_s).

In the exemplar sign-relation, a spoken word (langue) (SV_e) stands for an exemplar of ‘meaning, presence and message’ (“m.p.m.”; SO_e) in my world (B) according to definition (SI_e).

0426 Definition?

Is a definition₃ a normal context₃ like the content-level question, “What is happening?_3a“

Consider the following juxtaposition.

0427 The author provides one illustration, titled, “Box 1”, listing various definitions of words in classic dictionary style.  For the past few centuries, encyclopedists have labored to keep track of and pin down the meanings of spoken words.  The effort is crucial to constructing and maintaining scientific disciplinary languages.

0428 Consequently, I can imagine a similarity between the human agent₃ engaged in definition₃ and the stance of a human agent₃ asking the question, “What is happening?”_3a.

0429 But, there is a difference, as well.

The problem is that the former normal context may be called, “explicit abstraction”, and the latter may be called, “implicit abstraction”.

The difference between the potential of meaning, presence and message₁ and the possibility that ‘it is something’_1acannot be swept under the cognitive table.  One is counter-intuitive and the other is intuitive.

0430 I can take that lesson all the way to the core term in this chapter.

Barbieri’s signature book is titled, Code Biology: A New Science of Life (2015, Springer Dordecht).

0444 Still, the writing of Abir Igamberdiev stands before me.

So, let me run through how Aristotle’s four causes play out in the category-based nested form.

I start with material and efficient causalities.

0445 Material causes point to the contiguity between the two real elements.  If the elements are matter and form (as in Aristotle’s exemplar), then the material cause introduces some sort of contiguity between the two.  For example, molten bronze flows into a plaster hollow (created by covering a wax figure with plaster then melting the wax).  For Peirce, the contiguity expresses the character of scientific cause and effect.  An observable cause [produces] a measurable effect.  For chemistry, reagents [react and turn into] products.  Chemical notation is iconic in this regard.

0446 Efficient causes point to actuality₂ emerging from (and situating) possibility₁.

For example, in chemistry, spontaneous chemical reactions release free energy (heat and entropy).  A change in thermodynamic potential supports spontaneous chemical reactions.  With a special apparatus, one can measure the heat produced by a chemical reaction by recording the temperature increase of a water bath.  Efficient and instrumental causes support observations and measurements that contribute to scientific modeling of the contiguity between reagents and products.

0447 Material and instrumental causes are familiar to scientists.  They fall under the label, “physics”.  

The other two causes are ignored and disparaged by scientists.  They fall under the label, “metaphysics”.  Metaphysics introduces the normal context and potential as “causes”.

0448 Formal causes concern the ways that a normal context₃ contextualizes its actuality₂.  Typically, formal causes are confounded with material causes.  If material causes do not satisfy a formal requirement, then the actuality₂ may fail.  Indeed, when one thinks about it, the only material causes that are relevant tend to be those that are entangled with formal causes.

Final causes concern the potential underlying the coherence of the entire category-based nested form.  The firstness that supports efficient causes is instrumental.  Instrumental of what?  Oh, instrumental of efficacy.  Okay, there must be another potential, a more substantial potential, that explains why efficient causes are instrumental.  Thirdness brings secondness into relation with thirdness.  Firstness potentiates the operations of thirdness.  Final causes are often framed in terms of “intentionality” and “purpose”.

0449 Surely, all four of Aristotle’s causes are in play when one encounters a thing or event. 

Understanding teases out all four causes.

Scientific inquiry does not seek understanding.

Science seeks the truth to be found in models of observations and measurements of phenomena.

Scientific inquiry seeks utility and control.

Of what?

The noumenon or the model?

0450 Scientific inquiry starts with the inorganic world, where the normal context is not apparent.  Seventeenth century mechanical philosophers want to reduce inanimate things to mechanistic models.  This can only be done by using material causes shorn of formal causes and efficient causes shorn of final causes to build mathematical and mechanical models.

0451 Later, the biologically inclined heirs of the mechanical philosophers strive to reduce animate things to mechanistic models.

Later, the socially inclined heirs of the mechanical philosophers strain to reduce social and psychological things to mechanistic models.

Later, the psychometrically inclined heirs of the mechanical philosophers convert what people are willing to say into data, in order to build opportunities for empirio-normative domination.

0452 What does this imply?

Scientists have been elucidating the physical foreground of semiotic agency for four-hundred years, while at the same time remaining oblivious to its metaphysical background.  It’s funny in a horrifying sort of way.  Perhaps, we may be forgiven, for we know not what we do.  Without the causes associated to Aristotle’s metaphysics, we cannot even ascertain what an agent is.

Here is a picture, once again.

0453 An agent₃ brings semiotic agency₂ into relation with the potential of ‘final causality’₁.

Without the potential of teleology₁, the agent₃ cannot be recognized as the normal context for semiotic agency₂.

0454 In section 12.2, Igamberdiev introduces two distinctive terms.

To me, “ontolon” labels the coming together of a triadic relation.  A triadic relation is an ontological whole.  Ontology encompasses thirdness, secondness and firstness.  A single category-based nested form is an ontolon.

To me, “vortex” labels the swirling coming-to-fruition of a model, in conjunction with disciplinary language and the observations and measurements of phenomena.  In short, “vortex” labels an empirio-schematic judgment, as a triadic relation constellating in what ought to be (and secondness) in the Positivist’s judgment.

0455 In sum, Igamberdiev’s terms label the two sources of illumination in the Positivist’s judgment.

Uh-oh, where is the ontolon?

0456 Ontolons associate to noumena.

Vortexes associate to phenomena.

0457 Sharov and Tonnessen’s noumenal overlay identifies what phenomena can objectify the noumenal overlay.

Remember, triumphal science places a successful model over the noumenon, in order to create the situation where a model (veiling the noumenon) [can be objectified as] its phenomena.  Sharov and Tonnessen’s noumenal overlayperforms the same catharsis.  Yet, the performance cannot be complete, because Sharov and Tonnessen’s noumenal overlay is… um… noumenal.  Indeed, it contains what every biological system has in common: the specifying and exemplar sign-relations.

0458 The phenomena that Sharov and Tonnessen’s noumenal overlay identify may be observed and measured by biologists.

Why?

Humans recognize noumena.  That is one of the human adaptations into our niche of triadic relations.

So, sign-vehicles and sign-objects constitute phenomena that humans may observe (and on occasion, measure).  That data may then go into models (vortexes) that account for the contiguities in the S&T noumenal overlay.  These models do not overwrite the noumenon, they fill in the noumenon.  So, “vortex” is an excellent word that describes the way models fill in the elements of the noumenon that need to be explained.  Models enrich our appreciation of material and efficient causalities that are not divorced from formal and final causalities.

0459 What does this imply?

Sharov and Tonnessen’s noumenal overlay explains the character of what is for the biosemiotic version of the Positivist’s judgment.   S&T’s overlay [can be objectified by] its phenomena.

Yet, the nested form of agent₃ (an ontolon) cannot be fully objectified by the same phenomena.

Why?

Agent₃ is the normal context₃ and ‘final causalities’₁ is the potential₁ for all semiotic agencies₂.

Ah, now I see the ontolon and the vortex.