12/3/25

Looking at Igor Pilshchikov and Mikhail Trunin’s Article (2016) “The Tartu-Moscow School of Semiotics” (Part 24 of 27)

0306 Now, I proceed to the derivative interscope.

0307 The content level deals with semasiological issues.  Given the words of a literary text2af, how do we discuss2amthese words2af by way of meaning1a?

Or should I ask, “Given a signifier2af, then what is the proper signification2am?”

The literary text as semiological structuralist form2af [presents signifiers that entangle] positivist language as matter2am.

Given a positivist language as matter2am, then what corresponds to its meaning1a?

0308 Does the correspondence reflect the nature of explicit abstraction?

Does the model-regarded parole2af of the literary text2af entangle a language2am, displaying the attributes of a langue2am emerging from (and situating) the possibility of ‘positivist meaning’1a?

Given the parole2af of a literary text2afwhat does the entangled language2am corresponding to langue2am suggest by way of meaning1a?

0309 What type of confounding is this?

The single form is in red.  The originating matter is language2bm (fundament).  The entangled matter is language2am(derivative).

0310 The onamasiological question concerns whether there is a spoken parole corresponding to a particular (and perhaps, yet to be fully articulated) positivist langue.

When applied to the situation-level of the derivative interscope, the onamasiological question transforms into a cultural query, asking “Is there a presence1b to attach to the meaning1a underlying the content-level positivist langauge2am?”

0311 Say what?

Oh my.  I now proceed step by step.

0312 Step one, the literary text2af (the SOi for the semiological2a structuralist2b model2c as SVi) entangles an explicit abstraction2am consisting of a label2am emerging from (and situating) a positivist3a meaning1a.

In this entanglement, the fundament is confounded with the derivative.

0313 In step two, I compare the two content-level actualities.

In the fundament interscope, langue2am (more or less actualizing a signified1a) [substantiates] parole2af (more or less serving as a signifier1a).

In the derivative interscope, the literary text2af, that was originally substantiated by the language2bm of the mother tongue, now serves as the form2af  (perhaps, as a semiological2a structuralist2b model2c substituting for the literary text2bf) entangling an expert language2am that emerges from and situates the possibility of ‘positivist3a meaning’1a.

0314 This directly calls to mind the semasiological question, “Given a spoken word2am, then what is its meaning1a?”

In other words, what is the meaning1a (associated to signifier1a) of the explicit abstraction2am (associated to parole2af) in the derivative interscope?

0315 For the fundament, definition is regarded as implicit for the originating language2bm, specified by a text’s {langue2am [substantiates] parole2af}.

For the derivative, definition must be explicit, leading to the semasiological question.  An explicit abstraction2am (a label, parallel to parole2af) is entertained (or entangled).  However, the positivist meaning1a, which may serve as a metaphorical signifier1a for the explicit label2am resides in the domain of possibility1. An explicit abstraction2amemerges from (and situates) the potential of positivist meaning1a in the normal context of the TMS intellect3a.

0316 Step three, the derivative’s explicit abstraction2am manifests as a label2am arising (like a parole2af) from the potential of ‘positivist3a meaning’1a (serving as a metaphorical signifier1a).  The label2am (the fundament’s parole2afserves as a metaphor) emerges from a meaning1a (the fundament’s signifier1a serves as a metaphor) and its signified1acarries the potential of ‘exhibiting explicit positivist3a meaning’1a (and the fundament’s signified1a serves as a metaphor).

0317 In short, the entangled language2am seems like parole2af.

Plus, positivist meaning1a seems like a signifier1a.

The language2am of the explicit abstraction2am (the metaphorical parole2af) appears to do justice to the TMS positivist intellect3a and the potential of ‘meaning’1a (the metaphorical signifier1a).

How about a diagram of four elements of the derivative interscope?

0318 So far, step three covers the content-level elements.

0319 Once again, Saussure’s langue2am (for the fundament interscope) also serves as a metaphor for the literary text2af(for the derivative interscope).  The literary text2af (perhaps, now a semiological2a structuralist2b model2c substituting for the literary text2bf) is formally contextualized by the TMS positivist intellect3a and is alchemically enclosed in the scholar’s inquiry as a metaphorical langue1am, corresponding to the possibility of a ‘signified’1a.

Saussure’s parole2af serves as a metaphor for the language2am that is entangled by the literary text2af.  This metaphorical parole2am is both finally and efficiently related to the potential of a ‘positivist3a signifier’1a by way of definition3.

Of course, this sounds a little goofy, since an explicit abstraction2am emerges from a metaphorical signifier1a, and I am not sure what the corresponding ‘signified’1 might be.

0320 For the fundament interscope, I know that langue2am [substantiates] parole2af.

For the derivative interscope, I suspect that the literary text (semiological structuralist model)2af as metaphorical langue2am [now appears to substantiate] a language2am as a metaphorical parole2afoffering an explicit label2amallowing a positivist signifier to constellate1a.

Does that imply that the label2am (metaphorical parole2af, associated to signifier1a) precedes its meaning1a(metaphorical langue2am, associated to signified1a)?

That is a very good question.

0321 In step four, I ask, “If the explicit abstraction2am that labels a positivist meaning1a constellates the potential of ‘a signifier’1a, then what is the corresponding ‘signified1‘?”

It cannot be the literary text2af, because the literary text2af is the metaphorical langue2am that corresponds to… um… the interventional sign-object (SOi) of the structuralist3a semiological2a model2c (SVi).

If that is the case, then the corresponding signified1 may be something1b that acknowledges the presence of the entangled language2am.  Plus, it1b should show up on the situation level.

0322 Ah, I have arrived at the situation level.

If the onomasiological question concerns whether there is a spoken parole2af corresponding to a particular langue2am, then how does the question apply to a situation where the presence of a signifier1a, underlying an explicit abstraction2am, requires a corresponding situation-located signified1b?

Given the presence1b of a metaphorical signifier1a, then what technical term might label that presence1b as a signified1b?

Would such a signified1b support a referent2b as the situation-level actuality2b that virtually situates the entangled explicit abstraction2am?

0323 So maybe, the onamosiological question may be reframed by the situation-level of the derivative interscope.

Does the presence1b of a label2am associated to the entangled language2am of positivist signifiers1a in the derivative interscope serve as a signified1b that is situated by cognition2am, as a situation-level actuality2b in the normal context of cultural studies3b?

0324 Well, if that reframed question sounds plausible, then I can offer the following conclusions.

The fundament interscope operates as an empirio-schematic description of what is going on in any particular literary text.  What is going on when an author writes and a reader reads entails implicit abstraction, for the most part.  In other words, the writer conveys a text and the reader uses the same text in order to fill in the elements of a purely relational structure associated with langue.

This implicit process is the subject matter for semiology3a and structuralism3b.  These two fields of inquiry culminate ina judgment, actualized as a model2c.

The derivative interscope serves as a Positivist description of what is going on when writing and reading a particular literary text.  This description uses explicit labels2am, bearing the qualities of a metaphorical parole2af (that is, of a positivist signifier1a), that will be virtually situated by a cultural thing2b.  In short, an explicit abstraction2am (SVs) broadly stands for a cultural thing2b (SOs) in regards to cultural studies3b operating on the potential of a signified1b(virtually situating a positivist signifier1a)’ (SIs).

0325 Thus, the situation level of the derivative wrestles with onomasiological issues in a strange manner.

Given a signified1b, then what is the name of the corresponding referent2b?

Does cognition2bm, as a situation-level actuality2b in the normal context of cultural studies3b, virtually situate the presence1b of a label2am associated to the entangled language2am of positivist signifiers1a in the derivative interscope?

0326 {Cognition as matter2bm [substantiates] social and cultural interaction as form2bf} situates the presence1b of positivist3a meaning1a in the normal context of cultural studies3b.

0327 May I further transform the onomasiological question and ask, “Is the situation-level actuality of cognition2bmand social interaction2bf  the referent of an explicit abstraction2am (or label2amthat is entangled by a literary text2af?”

The answer is, “Yeah, just watch what people do after they read a particular text.”

Do actions speak louder than words?

Hmmm.

12/3/25

Looking at Igor Pilshchikov and Mikhail Trunin’s Article (2016) “The Tartu-Moscow School of Semiotics” (Part 25 of 27)

0329 The story does not stop there.

Notably, this following two-level interscope does not have a perspective level.  A perspective is required to complete a langue, a three-level interscope.

Here is a picture of what I am talking about.

0330 What fills the void of the perspective level?

Before 1989, Lotman has a ready-at-hand perspective level that satisfies any Soviet authority who may be asking.

Who is going to argue with the following?

Certainly not a poorly educated rube with a rubber stamp.

0331 What does this imply?

Those summer schools in Estonia must have been amazing.

On the one hand, international and intellectual “students” are free to play, because the perspective level is missing.  Discourse consists of sensible construction, because the missing perspective level is… um… somehow benevolent.

Benevolent?

No rubber-stamper is going to argue with the prior figure.

0332 Marxism is the ideological currency of the USSR before 1989.  The value of that currency begins to decline after 1968.  But that does not mean… you know… that one can directly deceive the ones who are charged with supervision of intellectual giants like Juri Lotman and his cohorts.

The mantra is “appease, not deceive”.

0333 At the same time, the missing perspective level is benevolent in a complete different fashion.

The gathering scholars study a civilization that converts to Christianity through the charisma of Saints Cyril and Methodius, and other saints (depending on the nation), in the 800s AD.  Cyril translates the Bible.  The Cyrillic alphabet (the raw material of the written words under investigation) is forged at this time.

0334 Most importantly, these missionaries hail from Byzantium.  They grow up on the Greek side of the formerly “Roman Empire”.  They are familiar with Aristotle.

In contrast, in the West, familiarity with Aristotle is… um… lost… then regained.  In the 600s, Boethius, who intends to translate classical Greek philosophy into Latin, croaks.  Aristotle does not get translated into Latin.  In the 1200s, the Crusaders bring Greek and Arabic texts from the Levant.  Aristotle finally gets translated and Saint Thomas Aquinas “baptizes” Aristotle’s philosophy, amidst controversy.

0335 Differences between Slavic and Western civilizations show up in subtle ways.  Hylomorphic structures occupy almost every slot for actuality in the above figures.  Westerners would put a single word into each slot.  They would not ideate the hylomorphe that expresses Peirce’s category of secondness.

0336 Appease.

Don’t deceive.

Confound.

Don’t confront.

There is a rubber-stamper who needs answers to questions like, “Comrade, does your theory reveal how material arrangements [substantiate] humans conditions2c?”

12/2/25

Looking at Igor Pilshchikov and Mikhail Trunin’s Article (2016) “The Tartu-Moscow School of Semiotics” (Part 26 of 27)

0337 Sections seven and eight (7 & 8) offer three ideations that dwell within the ambiguity depicted above.

Section seven (7) first discusses Poldmae’s theory of verse.

0338 Jaak Poldmae (1942-1979) considers poetry in the Slavic and German civilizations.  To me, it looks like his interest in metrics goes with the signifier and his interest in poetics associates to the signified.  Once these substitutions are made, the following derivative interscope is readily completed from the authors’ brief description of verse theory.

0339 While Poldmae may come unnervingly close to the old formalist habit of finding the literary devices, the above interscope is not a mere collection of mechanisms.  Verse theory is an organic whole.  Plus, the perspective-level category-based nested form looks like a clone of Marxist theory.

0340 To me, this begs the question, asking, “What happened to the content and situation levels of Marxist theory?”

Did they somehow deplete themselves?

Plus, the rubberstamper is uncharacteristically uninterested, because Poldmae asserts that poetry2c somehow corresponds to… or reveals… or depicts… the human condition2c.

Isn’t that what any Slav already appreciates?

0341 Section seven (7) next discusses the phenomenon… er… model substituting for the noumenon (?)… of intertextuality.  Intertextuality delocalizes the poet, because the poet produces a text in relation to other (prior) texts.  In a sense, a contemporary poet joins the conversation of other poets.  The contemporary poet responds to the poetics and the metrics of… what?… civilization, past and present?

0342 Uh oh, remember Saints Cyril and Methodius?

Where did they come from?

The Byzantine civilization is a fusion of Greek and Jewish civilizations, made possible by the Christianization of the Roman Empire.

0343 Unlike America, Russia is not made of new cloth.  The Slavic civilization is cut from old cloth, over and over again, in a theodrama that the American Empire simply wants to ignore.

Oh, I should say, “the USSA”?

0344 The term “intertextuality” is a beautiful Platonic term, offered by Julie Kristeva, a French linguist, that serves to cover over the perspective-level actuality of the following three-level interscope, in such a manner as to comport with the actuality2c of Marxist theory3c.

0345 To appreciate the rhizomic character of intertextuality, an inquirer may consider Razie Mah’s blog for August 2025, titled Looking at Slavoj Zizek’s Book (2024) “Christian Atheism”.

Zizek is a philosopher, not a poet, but he sounds like a poet some of the time.  He writes like a poet, even though he doesn’t know it.  Only a poet would make “Christ”, the adjective, and our human condition, the noun.  Isn’t that what the story of the Garden of Eden tells us?  We have been kicked out of the Garden because we can now challenge God Himself.  Now, outside of His Domain, we are “a-” (“without”) “-theists” (“God”).

Does Zizek suggest that Christian Atheism can stand in for… material arrangements2c?

0346 As if to confirm, Zizek concludes with a reflection on Alexandr Blok’s poem, The Twelve, written in 1918, depicting Christ as a holy ghost leading twelve Red Guards on their patrol of revolutionary Petrograd.   Of course, Soviet authorities later replaced the word, “Christ”, with “sun”, because they were too embarrassed to substitute in “material arrangements”.

0347 Zizek aside, intertextuality and verse theory both cohere to the reality of Lotman’s and Jakobson’s legacy.  Plus, they do not cross the line that Lotman’s derivative interscope tunnels under.

11/28/25

Looking at Dennis Venema and Scot McKnight’s Book (2017) “Adam and the Genome” (Part 2 of 22)

0008 Adam and the Genome divides into two parts.  Each part is about 100 pages long.

0009 In the first half, Dennis Venema, a biologist versed in genetics, lays out the case for the impossibility of a bottleneck in human evolution.  Adam and Eve cannot be the first anatomically modern humans.

In the second half, Scot McKnight, an evangelical theologian familiar with ancient Near East literature, lays out the case against a historical Adam.  No early Jewish or Christian writer, including the preacher Paul, regarded Adam and Eve as the biological ancestors of all humans, the parents of the species, whose DNA is sown into all living human beings.

0010 By “early” I mean before Augustine (around 400AD).  McKnight does not elaborate how Augustine wrote the dramatic script calling for a historical Adam who is literally the father of all sinners.

Augustine’s script has been performed on stage for over one and one-half thousand years.  What a run.

0011 The current examination separates the two halves.  I consider each half in a very different manner.

0012 My metaphor goes like this:  Each half is like a curtain, lowered in order to conclude the continued enactment of Augustine’s drama.

0013 Evangelicals have seen the play a thousand times.  Eve is called “the mother of all living”.  The serpent fooled her.  Adam went along.  Then, they had children, spreading their fallen natures to us all.

No wonder Evangelicals yearn for a biological historical Adam, a literal father of all living, that will prove the so-called “rational” BG(il)L zealots wrong.  They know Augustine’s play by heart.  Why can’t the show continue?

0014 Venema and McKnight theatrically lower these two curtains, one on either side of the stage.

They declare, “The play cannot go on.  There is no biological historical Adam and Eve, from which all human DNA descends (with modification).  Plus, the Genesis stories are similar to the literature of the ancient Near East.  The Bible must be read in context.”

0015 Ah, but God’s grace is like a diva.  If she cannot be on stage, she will take to the curtains.  Read these comments and you will see.  The curtains come alive.

11/26/25

Looking at Dennis Venema and Scot McKnight’s Book (2017) “Adam and the Genome” (Part 3 of 22)

0016 Dr. Venema tells a great story.  He was raised as an evangelical, suspicious of modern evolutionary biology.  He became a geneticist.  The turning point came when he started doing research in the lab.

Research led to further study, eventually forcing him to confront the ideological roadblocks placed by his church’s tradition.  He came to the conclusion that Galileo might be right.  If there are two books, Darwinian evolution belongs to the book of nature.  The theory has been tested over and over again.

0017 The theory of descent with modification yields counterintuitive truths.

For example, who would have thought that animals with backbones and four limbs descended from fish?  As it turns out, the ancestors are not just any type of fish.  The ancestral fish are lobe-finned lung fish.

0018 The fossil record does not stand mute.  Several fossils are difficult to assign the label “lung-fish” or “amphibian”.  These date to the proper epoch, long, long ago.

0019 Whales are a more recent example.  They are mammals, so they must have started as land creatures.  Somehow, they adapted to the deep blue sea.  What a change.

0020 Now, I turn to the category-based nested form, wondering, “How does Darwin’s classical idea of descent with modification work?” 

Amphibian land creatures are very different from their ancestral lung fish.  Whales are amazingly different from any bear or hippo-like ancestor.  Water-born fish adapt to the land.  Land animals adapt to the sea.

0021 The word “niche” applies to an actuality, independent of the species, that the species adapts to.  The actuality is real.  Like land and sea, a niche is independent of the adapting species.  The original species experiences this actuality as potential.  The land and sea offer the potentials of new habitats.  These potentials constitute the niche that the species adapts to.

Here, descent is assumed.  Emphasis falls on the phrase “with modification”, because natural selection operates on phenotypic variations.

0022 Is there a certain “logic” to the Darwinian paradigm?

Two actualities stand out: adaptation and the actuality underlying the niche.  They are related as situation and content, respectively.  Two nested forms are required to model the classical Darwinian idea of descent with modification.

0023 Two nested forms?

The nested form is a purely relational structure, following the logic of Charles Peirce.  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.

0024 Here is a diagram for adaptation, as portrayed in the preceding discussion.

0025 The normal context of natural selection3b brings the actuality of an adaptation2b into relation with a niche1b.

0026 A niche1b expresses the potential of an actuality independent of the adapting species1b.  The niche1b emerges from (and situates) a content-level actuality2a.  For ancestral water-dwelling lung fish, the actuality2a was land.  For the ancestors of the whale, the actuality2a was sea.

11/25/25

Looking at Dennis Venema and Scot McKnight’s Book (2017) “Adam and the Genome” (Part 4 of 22)

0027 According to classical Darwinism, adaptations2b are explained through natural selection.  The niche1b accounts for modifications.  Descent is assumed.

0028 At the time of Darwin, no one knew much about descent with modification.  Darwin simply contended that the babes of a breeding pair would have similar traits to the parents.  This much is obvious from animal breeding hobbies.

0029 Today, biologists know so much about the mechanism of descent that the niche is taken for granted.

Yes, the assumptions have been reversed.

0030 Venema explains descent with the analogy of a mother tongue over time.  Spoken words change over generations.  The English speaker of today would not understand the English speaker of 400 years ago.

Word spelling also changes over time.  Treuthe went to truthe, then to trueth, then to truth.  That ain’t no lie.

0031 Thus, spoken and written words show descent with modification over the centuries.  Each subpopulation of speakers shifts word locution one way or another.  Isolation between two subpopulations eventually produces two different – closely related – languages.

0032 How does this explain descent with modification?

0033 Ah, this is Dr. Venema’s area of expertise.  His writing is wonderful.  Read his own words.  Especially, note the passages where he assumes the niche.  The niche may be land, sea, as well as gunk in a waste pond.  For a virus, a niche may be… say… bacteria. 

0034 Now, I go back to the diagrams.

How does the role of DNA fit into descent with modification, as depicted by category-based nested forms?

0035 What are the actualities?

0036 DNA is one actuality.

DNA is like a book containing genes.  Genes are recipes for proteins.  Proteins build the body of a cell.

DNA also instructs the “reader” how to read the book.

DNA does not get rid of old recipes.  Old recipes merely become unreadable through various substitutions, deletions, insertions and so on.  New recipes may derive from old recipes.  They may be fashioned, whole cloth, by new instructions.

0037 Let me say this in another way.

The genotype is the potential of a DNA book, complete with recipes and reading instructions.

The phenotype is the viral, cellular, or multicellular body that a DNA book is responsible for.

0038 The “body”, or the phenotype, is the second actuality.

Here is a picture of the content and situation levels for the science of genetics

0039 The normal context of the biological body3b brings the actuality of the phenotype2b into relation with the genotype1b.

0040 The genotype1b is the potential inherent in DNA1b.  DNA2a is an actuality that defines the species2a.

11/24/25

Looking at Dennis Venema and Scot McKnight’s Book (2017) “Adam and the Genome” (Part 5 of 22)

0041 So, the key phrase is descent with modification.

0042 DNA2a goes with descentb.

The actuality underlying the niche2a accounts for relevance of the term, with modificationb.

0043 Phenotype2b emerges from (and situates) genotype1b.

Adaptation2b emerges from (and situates) niche1b.

0044 The fossil record contains clues to the phenotypes in any particular lineage.  The fact that DNA retains unused recipes provides clues to the genotypes in any particular lineage.  All new features gained by new species remodel already existing features of the originating species.

The fossil record also contains clues to the environment that a species adapts to.  Presumably, these clues indicate an actuality underlying the niche2a.

0045 Venema fuses the two situational actualities, phenotype2b and adaptation2b, into a single actuality.  

Phenotype2b and adaptation2b are two actualities that unite to form one: descent with modification2-combined.

0046 For example, consider the features that distinguish bats from mice.

If one examines the DNA of the bat and closely related species, one finds that their DNA differs in such a way as to explain the building of the bat body as opposed to a closely related mouse-type body.  Random mutations in DNA occur every so often, so the researcher can estimate the time distance to a common ancestor between the bat and a closely related species.

0047 If one examines caves or other locations where both bats and mice dwell, one might find fossil intermediates between bats and mice.  That would require a lot of luck and a keen eye.

0048 What does this tell us about research into the evolution of the bat?

Well, the DNA of bats and closely related species is readily available.  The likelihood of finding fossils of ancestral mouse populations that adapted to flight is incredibly small, even though caves are ideal places for fossil formation.

0049 What would I do?

Of course, I would concentrate on the DNA story and take the niche story for granted.

0050 This is what Venema does with human evolution.

11/22/25

Looking at Dennis Venema and Scot McKnight’s Book (2017) “Adam and the Genome” (Part 6 of 22)

0051 I continue to roll with Venema’s text.  I’m ignoring the niche.  Rather, I am simply assuming that a niche is operating.

In chapter 3, Venema convincingly lowers the curtain on Augustine’s concept that Adam and Eve are the biological ancestors of all humans.  He does so on the basis of DNA alone.

0052 DNA “remembers”, but not completely.  Insertions, deletions and substitutions sometimes occur as DNA is copied.  DNA is copied whenever a cell divides.  Chromosomal pairs are sorted into single chromosomes when a sperm or egg is formed.  Sperm and egg are united in the formation of a fertilized egg.

What does this imply?

The range of variation within the DNA of a species reflects the size of the breeding population.  If a breeding populationpasses through a severe bottleneck, then the result would be less variability in DNA in subsequent generations.

0053 Venema shows that, for human DNA, the breeding populations never fell below several thousand.  If they had, human DNA (at present) would show the typical pattern of a genetic bottleneck.

If that is not enough, during the Paleolithic, anatomically modern humans engaged in hanky-panky with two closely related species, the Neanderthal and the Denisovan.

0054 How else to explain the appearance of their DNA in some human subpopulations?

0055 Venema forecloses on the historical Adam imagined by Saint Augustine, where Original Sin passes from one generation to the next, through that hanky-panky business mentioned above.

0056 If there is a historical Adam and Eve, they are not the parents of all anatomically humans, living during the Paleolithic, over 50,000 years ago.

11/21/25

Looking at Dennis Venema and Scot McKnight’s Book (2017) “Adam and the Genome” (Part 7 of 22)

0057 In the next chapter, Venema notes that something remains.

0058 What about intelligent design?

0059 For me, the question should be: What about the niche?

0060 Advocates of intelligent design argue that DNA mutation alone cannot account for the dramatic changes found in the fossil record.

For example, the Cambrian Period starts with new body designs and highly modified versions of earlier body designs.

Another example is the immune system, which is very complex.

0061 Venema argues that these examples can be explained through methods other than simple mutation, such as insertion and doubling.

However, simple mutations remain foundational, because…

0062 …simple mutations produce evolution directly observed in the laboratory.

Here is an example:

0063 Imagine a culture composed of 1% of bacteria with receptor R and 99% with receptor S.  The culture is then infected with a virus that latches onto receptor-R bacteria but cannot infect S bacteria.

Well, the virus kills all the R bacteria and that is that.

0064 Okay.  Let me try that again, starting with 5% R bacteria and 95% S bacteria.

This time, the virus passes through enough generations that one mutated virus latches onto the S receptor.  Now, the virus can further adapt to the presence of the S-receptor.  The S-receptor bacteria start to die.

At the end of this petri-dish wipe-out, the virologists isolate the virus to see how it has changed.  As it turns out, the latching protein changed by 5 amino acids, meaning that its original DNA underwent at least 5 separate mutations.

0065 Note how the virologist plays god.  The virologist defines a niche1b.  The 95% S bacteria constitute an actuality independent of the virus2a, offering the potential of exploitation in the normal context of natural selection3b.

0066 Here is an example of gene doubling.

Two different species of fruit flies express different suites of transport proteins.  One has a single transport protein, deriving from a DNA-site labeled eclair.  The other has two transport proteins, eclair and p24.  The second recipe came from a doubling of the eclair DNA.  Then, the second copy underwent mutations, resulting in the second recipe for a transport protein, p24.

0067 Next, entire chromosomes may double.  Or they may break and connect to other chromosomes. 

Large-scale gene duplications go a long way in explaining huge changes in phenotype.  For example, animals with backbones came from animals with spinal cords without backbones.

0068 Finally, here is an example of the activation of a completely new recipe.

Nylon is an industrial polymer.  In the 1970’s, Japanese scientists discover a bacteria that lives off of nylon in an industrial waste pond.  The bacteria do so with a completely novel enzyme, which the scientists labeled nylonase.

0069 Venema concludes that intelligent design adds no explanatory value.  Living forms have inherent creativity in their DNA.  Simple mutations, gene duplication, and similar mechanisms account for descent with modification.

0070 Maybe, changes in genotype is the same as intelligent design.

Or, maybe, intelligent design is the niche.

11/19/25

Looking at Dennis Venema and Scot McKnight’s Book (2017) “Adam and the Genome” (Part 8 of 22)

0071 Each story about a change of genotype potentiating a new phenotype also is a story about an adaptation into a niche.

For the nylonase-producing bacteria, the niche is a waste pond full of industrial polymers.

For animals with backbones, the niche could be related to protection and movement.

For the fruit fly example, the niche may consist of proteins or molecules that were not previously transported.  The transport protein related to p24 may be receptive to changes in an environment that is independent of the species.

For the S-receptor virus, the niche was a petri dish filled with lots of S bacteria.

0072 In all these examples, genetic changes would not have been of value if the phenotype did not exhibit an adaptive advantage.   Genetic changes may have occurred.  But, they would not have been remembered by later generations.

0073 What does this mean?

Phenotype2b and adaptation2b are two actualities produced by independent methods of inquiry.  They inherently contradict one another.  They also inherently complement. 

0074 They intersect and form one actuality: descent with modification.

Here is my diagram of the intersection of adaptation2b and phenotype2b.

0075 Intersections are curious beings.

Classical Darwinism constitutes the horizontal axis.  It assumes some type of inheritance, but does not know how it works.

Neo-Darwinism constitutes the vertical axis.  It assumes the niche, and does not know how it works.

0076 Alone, neither classical nor neo-Darwinism can provide a full explanation of descent with modification.

Likewise, descent with modification cannot be reduced to one or the other nested form.

0077 Indeed, a miracle lies hidden within each intersection.

0078 On one hand, consider the virologists who find the right mix of R and S bacteria to observe the R-killing virus evolve to the S-killing virus.  They do not know whether other mutations would have produced an S-latching virus. They can only account for the genetic changes retrospectively (that is, after the event).  They could not have predicted what mutations would do the trick.

So, the genetic part is like a miracle.

0079 These scientists precisely define the niche.  The resulting gene changes are what (miraculously) happen to occur.

0080 On the other hand, consider the geneticists who isolate the chromosomal changes between chordates without backbones and chordates with backbones.  They may understand the DNA-altering mechanisms involved in these changes, but they cannot prospectively re-enact the niche that rewarded the phenotypes as adaptations.

So, the niche part is like a miracle.

0081 These scientists delineate the genetic changes.  But, they have no idea how to reconstitute the niche.  The niche is what (miraculously) happened to occur.