Tag Archives: biology

02/22/25

Looking at Alexei Sharov and Morten Tonnessen’s Book (2021) “Semiotic Agency” (Part 24 of 24) 

0264 What do I conclude?

By the time that the authors finish Parts II and IV of Semiotic Agency, the range of applications expands into Parts I-IV of Pathways to the Origin and Evolution of Meanings of the Universe.

0265 Is such an expansion warranted?

From my examination of Parts I and III of Semiotic Agency, I may say, “Yes.  Biosemiotics entails a re-articulation of biology and the social sciences.  Biosemiotics also reveals the nature of phenomenology, cybernetics and the psychometric sciences.”

0266 The re-articulation of biology and the social sciences in the light of biosemiotics is just beginning.  In looking at Part I and III of Semiotic Agency, I could sense the breadth of the project.

0267 The problem concerns the status of the noumenon.

Natural scientists never worry about the noumenon, because the noumenon should be obvious. Indeed, triumphalist scientists want to paper over each natural noumenon with a successful model.  Social scientists observe and measure social phenomena then pull the associated noumena from holes in the ground.  Phenomenologists promote intuitive methods for guessing what a noumenon must be.  Sharov and Tonnessen re-format the triadic specifying sign-relationinto a dyadic structure amenable to empirio-schematic inquiry.  I call their discovery, “the Sharov and Tonnessen noumenal overlay”.

0268 The authors call it “semiotic agency”.

0269 Semiotic agency, depicted as a dyad (agency) within a dyad (semiotic agency), forces scientists to re-examine all that has gone before.

And, that is quite an accomplishment.

0270 The task before me remains.  A sea of biosemiosis lies before me.  The question is how to traverse the waters. How to set sail?

In order to examine Parts II and IV of Semiotic Agency (2021) and Parts I, II, III and IV of Pathways (2024) I plan to take certain steps, listed in the following script.

This script allows me to examine here and there, like a bumbling bee in a spring field, not certain about a proper path, and inadvertently pollinating along the way.

I begin by looking at the chapters on the origins of life.

02/21/25

Biosemiotics and the Origins of Life on Earth (Part 1 of 8)

0271 What does biosemiotics have to say about abiogenesis, the origin of life from non-living matter?

0272 Two texts are before me.

0273 Semiotic Agency: Science Beyond Mechanism is written by biosemioticians Alexei Sharov and Morten Tonnessen.  Semiotic Agency is published in 2021 by Springer and logs in at volume 25 of Springer’s Series in Biosemiotics.  Series editors have Razie Mah’s permission for use of the following disquisition, with attribution of said blogger.

The text is open to chapter five, titled, “Origins of Life”, and is found on pages 123-149.  This chapter closes Part II of Semiotic Agency.  The title of Part II is “Agency in Organisms and Beyond.”

0274 Pathways to the Origin and Evolution of Meaning in the Universe is edited by Alexei Sharov and George Mikhailovsky (2024, Scrivener Press, Beverly MA).

The text is open to chapter nine, titled “Chemical Origins of Life, Agency and Meaning” (pages 189-210).  This chapter opens Part II, titled “Meanings in the Evolution of Life”.  The chapter’s author is Alexei Sharov.

0275 First and foremost, chemistry-based scenarios for the origins of life have proven futile.  Why?  For one, it is difficult to imagine a chemical system constituting a semiotic agent.  Sure, a biological agent can be reduced to a chemical soup, but a chemical soup cannot unreduced to a biological being.

Is this the reason why proposals of life emerging from a primordial soup consistently fail?

0276 The key word in the above paragraph is “emerging”.

0277 So why not turn to Mariusz Tabaczek, who writes two books, titled Emergence (2019) and Divine Action and Emergence (2021) that are reviewed in Razie Mah’s blog for April and May, 2024?  These and other examinations go into Razie Mah’s two-part e-book, Comments on Mariusz Tabaczek’s Arc of Inquiry (2019-2024), available at smashwords and other e-book venues.

0278 Tabaczek criticizes Terrence Deacon, even as he translates Deacon’s conceptual apparatus into a classical Aristotelian framework.  Why?  If Deacon borrows ideas from Aristotle and re-tools them for his own approach to emergent systems, then why not articulate Deacon’s approach using Aristotle’s terms?

0279 The answer turns out to be more than academic.

Recall the Positivist’s judgment for the natural sciences?

The noumenon (the thing itself) and the model (what ought to be for the empirio-schematic judgment) are two contending sources of illumination.  Deacon stands with the model, then uses modified versions of Aristotle’s vocabulary in order to project his model onto the noumenon.  In contrast, Tabaczek stands with the noumenon, where Aristotle’s terminology is at home.  He sees Deacon’s projection from the model back onto the noumenon and does not think too highly of the imposition.

02/13/25

Biosemiotics and the Origins of Life on Earth (Part 8 of 8)

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 into the 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.

02/12/25

Looking at Gustavo Caetano-Anolles’ Chapter (2024) “Evolution of Biomolecular Communication” (Part 1 of 10)

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. 

02/1/25

Looking at Gustavo Caetano-Anolles’ Chapter (2024) “Evolution of Biomolecular Communication” (Part 10 of 10)

0388 I conclude this examination of Gustavo Caetano-Anolles’ chapter with a brief discussion on the third item appearing in section 10.3, titled, “Communication”.

0389 The first item that the author mentions is Peirce’s tradition of inquiry.  Peirce’s three categories offer a variety of ways to portray triadic relations.

Biosemiotics is all about triadic relations.  This examination has shown that secondness tends to associate to phenomena.  Thirdness and firstness tends to associate to what models need to explain.

0390 The second item that the author mentions is Shannon’s information theory.

I wonder about the implications of the virtual nested form in the realm of secondness that Shannon’s information theory generates.

What if the associations are more than mere analogy?

What if my neighbor, getting that new-fangled lumber treatment and all, is not sending me a message through a channel2b that conducts wood-eating insects that are not happy, and frankly, fed up with the wooden food-fare that my neighbor’s shed now offers?

How weird and disturbing is that?

0391 The third item that the author mentions is Chomsky’s hierarchy of formal languages.  Formal language consists of operations within a finite symbolic order.

0392 Finite symbolic order?

Think of how Charles Peirce might rebrand Ferdinand de Saussures’s key term, system of differences.

0393 Ultimately, symbols enter into a picture of the evolution of biomolecular communication.

And, when they do, they seem to associate to “a receiver2c” in Shannon’s virtual nested form in secondness.

0392 Here is a picture.

0393 But that is not all, in the evolution of biomolecular communication, symbols overflow destination2c and cascade down into the bucket that the transmitter2a works from.

The author spends sections 10.4 through 10.8 discussing the implications of this imaginary overflowing, which reminds me of a Tarot card, the ace of cups, where a hand appears out of cloud overhanging an idyllic landscape.

The hand holds a water-filled cup that overflows, in a very biomolecular-cascading fashion, from a perspective-level that associates to love.  Is love an empedoclement?  Only after the empedoclements (which are the inverse of impediments) come together, in the right sort of way, does strife arrive to both hone and diversify the new creation.

0394 Here is the cup of organic biosemiosis.

01/31/25

Looking at Alexei Sharov and Morten Tonnessen’s Book (2021) “Semiotic Agency” (Part 1 of 24)

0001 The book before me is Semiotic Agency: Science Beyond Mechanism, by biosemioticians Alexei Sharov and Morten Tonnessen.  The book is published in 2021 by Springer and logs in at volume 25 of Springer’s Series in Biosemiotics.  Series editors are Kalevi Kull, Alexei Sharov, Claude Emmeche and Donald Favareau.  These editors have Razie Mah’s permission for use of the following disquisition, with attribution of said blogger.

Points 0001 to 0226 cover Parts I and III of this book.  These Parts are titled, (I) Overview and Historiography and (III) Theoretical Considerations.  These two sections set forth the rationale for scientific inquiry into semiotic agency. 

0002 Chapter one begins with a question.

Can agency be a scientific subject?

To me, the question, “What is science?”, must be addressed.

0003 Scientific inquiry involves a judgment within a judgment.

0004 Okay, then what is a judgment?

A judgment is a triadic relation containing three elements: relation, what is and what ought to be.  When each of these three elements uniquely associates to one of Peirce’s categories, then the judgment becomes actionable.  Actionable judgments unfold into category-based nested forms.  

What am I talking about?

Consult A Primer on The Category-Based Nested Form and A Primer on Sensible and Social Construction, available at smashwords and other e-book venues.

0005 Here is a diagram of judgment as a triadic relation.

A relation (belonging to one category) brings what ought to be (belonging to another category) into relation with what is (belonging to the one remaining category).  Peirce’s three categories are firstness, secondness and thirdness.  Firstness is the monadic realm of possibility.  Secondness is the dyadic realm of actuality.  Thirdness is the triadic realm of normal contexts, mediations, judgments, sign-relations, and so forth.

0006 If scientific inquiry involves a judgment within a judgment, then the larger judgment is called the Positivist’s judgment.  A positivist intellect (relation, thirdness) brings an empirio-schematic judgment (what ought to be,secondness) into relation with the dyad, a noumenon [and] its phenomena (what is, firstness).

Here is a diagram.

0007 In regards to the relation, the positivist intellect has a rule.  Metaphysics is not allowed.

0008 What is “metaphysics”?

Aristotle proposes four causes: material, efficient, formal and final.  The first two are (more or less) physical.  The second two are (more or less) metaphysical.  So, the second two causes are ruled out in the seventeenth century by the mechanical philosophers of northern Europe.

0009 Of course, ruling out formal and final causes truncates material and efficient causalities.  Imagine a material cause (such as the flow of ink onto a piece of paper) without its formal cause (the piece of paper will then be folded and put into an envelope).  Imagine an efficient cause (the role of glue in sealing an envelope) without its final cause (the envelope will be put in the mail).

So, the rule of the positivist intellect has the effect of truncating physical material and efficient causalities from their metaphysical companion causalities.  The positivist intellect is assigned to the category of thirdness, the realm of normal contexts.

0010 In regards to what ought to be, the empirio-schematic judgment belongs to the category of secondness (the realm of actuality), even though it obviously belongs to the category of thirdness, because judgments are triadic relations.  In other words, to think in terms of the Positivist’s judgment, one must disregard the obvious and regard the empirio-schematic judgment as an exercise in the realm of actuality, if that makes any sense.

0011 It may help to consider the empirio-schematic judgment as a tool for producing scientific models.  Disciplinary language (relation, thirdness) brings mathematical and mechanical models (what ought to be, secondness) into relation with observations and measurements of phenomena (what is, firstness).

Here is a picture.

These figures are initially constructed in Comments on Jacques Maritain’s Book (1935) Natural Philosophy, by Razie Mah, available at smashwords and other e-book venues.

01/6/25

Is Biosemiotics Scientific? (Part 1 of 4)

0201 The book before me is Semiotic Agency: Science Beyond Mechanism, by biosemioticians Alexei Sharov and Morten Tonnnessen.  The book is published in 2021 by Springer and logs in at volume 25 of Springer’s Series in Biosemiotics.  The editors of this series have Razie Mah’s permission for use of following disquisition, with attribution of said blogger.

Part III concerns theoretical considerations, addressing the headliner question.

Here is a list of the chapters, along with their titles.

Each title labels a labor of biosemioticians.

0202 So far, from Part I, Sharov and Tonnessen propose a philosophical dyad that serves as an overlay for the noumenon of biosemiotics.  The authors’ proposed noumenon constitutes what is for the Positivist’s judgment and contains what all biosemiotic phenomena have in common.

This is significant.

0203 The Positivist’s judgment is constructed, starting in the 1600s, by mechanical philosophers.  Mechanical philosophers aim to bracket out metaphysics, in favor of models based on observations and measurements.

So, what is science?

0204 Comments on Jacques Maritain’s Book (1935) “Natural Philosophy” shows that the scholastic ideation of three styles of abstraction comes close to a satisfying answer.  But, no one can capitalize on that answer until a hidden knot is unraveled.  A knot?  Two judgments are entangled.  This becomes clear when the abstractions are pictured as elements of judgment.

0205 The following diagram of the Positivist’s judgment is a satisfying way to portray what the mechanical philosophers created in the 1600s and what Kant corrected in the late 1700s.

In 2025, no definition of science compares to this diagram.

0206 In the Positivist’s judgment, the positive intellect (relation, thirdness) brings the empirio-schematic judgment (what ought to be, secondness) into relation with the dyad, a noumenon [cannot be objectified as] its phenomena (what is, firstness).

In the empirio-schematic judgment, disciplinary language (relation, thirdness) brings mathematical and mechanical models (what ought to be, secondness) into relation with observations and measurements of phenomena (what is,firstness).

0207 Immanuel Kant (1724-1804) forces natural scientists to concede that they investigate the observable and measurable facets of the thing itself.   Plus, their observations and measurements cannot fully objectify the subject of inquiry.

0208 Over the next two centuries (1800s and 1900s),  scientists promote their successful models, saying, “Our models are more illuminating than the thing itself.  Indeed, our models can take the place of the noumenon.  Once that happens, then our models can be objectified by their phenomena.  Observations and measurements validate the successful model.”

The academic laboratory sciences are born.  For example, a chemistry laboratory and its accompanying lecture belong to the laboratory science of chemistry.  In contrast, the science of chemistry is the study of natural processes, that is, things themselves.  The key to science is to make an observation and then explain it.  The model is an explanation, rather than the thing itself.

01/2/25

Is Biosemiotics Scientific? (Part 4 of 4)

0222 With that said, here is a quick wrap-up of the four chapters in Part III.

For chapter six, Sharov and Tonnessen’s noumenal overlay conceptualizes semiotic agency.

For chapter seven, semiotic agency is considered an actuality2.  In order to understand an actuality2, the actuality2 must have a normal context3 and potential1.

0223 Here is the nested form for semiotic agency2.

Semiotic agency2 presents a sign-relation as a dyadic actuality.  This is shown in Part I.

Semiosis2 does not occur without an agent3 and the possibility of ‘significance’1.

0224 For chapter eight, the evolution of agents3 and the possibility of ‘significance’1 proceeds in tandem with the evolution of semiotic agency2.

0225 For chapter nine, phenomenology serves as a precursor to biosemiotics, just as the social sciences of the nineteenth and twentieth centuries serve as intimations of phenomenology.

0226 Without a doubt, Sharov and Tonnessen build upon the insights of philosophers writing a century earlier, as seen in two of Razie Mah’s e-books: Comments on Jacques Maritain’s Book (1935) Natural Philosophy and Comments on Nicholas Berdyaev’s Book (1939) Spirit and Reality.  Both Maritain and Berdyaev are interested in understanding the nature of scientific inquiry.  And now, their works inform biosemioticians.

05/19/21

Looking at Chris Sinha’s Essay (2018) “Praxis, Symbol and Language” (Part 1 of 5)

0001 Chris Sinha, writing from Hunan University, publishes another article on human evolution.  The journal is Interaction Studies (volume 19(2), 2018, pages 239-255).  The complete title is “Praxis, Symbol and Language: Developmental, Ecological and Linguistic Issues”.

The title of Razie Mah’s commentary is Comments on Chris Sinha’s Essay (2018) “Praxis, Symbol and Language”. The commentary is found at the smashwords website under the series: Buttressing the Human Niche.  Other vendors also sell the e-commentary.

0002 This blog complements the commentary.

0003 Sinha’s article covers from the start of the Homo genus, around two million years ago, to the speciation of Homo sapiens, around two-hundred thousand years ago. That is a lot of territory.

Several issues intertwine.  One is individual development (devo).  Another is a transition in natural selection (evo) from ecology-driven adaptations (eco) to adaptations driven by social interactions (socio).

0004 Sinha loves terminology.  He searches for a EcoEvoDevoSocio framework.

05/18/21

Looking at Chris Sinha’s Essay (2018) “Praxis, Symbol and Language” (Part 2 of 5)

0005 What about Sinha’s EcoEvoDevoSocio framework?

0006 The outer terms, “eco” and “socio”, signify a broad arc of human evolution.

Adaptation by a line of apes starts with ecological adaptations.  For example, bipedalism is evolutionarily ancient.

However, the fact that bipedalism frees the hands for communicative gestures creates new opportunities.  A truly human niche appears.  One hominin can intentionally gesture to another.  The other hominin can interpret that gesture.

0007 The frontpiece of the title captures Sinha’s EcoSocio vision.  The praxis (or habits) of intentional manual-brachial gestures for communication proceeds from signaling to functional representation.

Functional representation metaphorically runs around the symbol, defined as a sign-relation whose sign-object depends on conventions, habits, laws and so forth.  The more that intentional manual-brachial gestures act as words, the more symbolic they become.

In this way, hominins become symbol-ready and capable of engaging in language.