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.

11/18/25

Looking at Dennis Venema and Scot McKnight’s Book (2017) “Adam and the Genome” (Part 9 of 22)

0082 Perhaps, intelligent design corresponds to the fact that an intersection lies at the heart of evolutionary biology.

0083 Phenotype2H and adaptation2V are two mutually exclusive, contradictory and complementary actualities.  They intersect to form one actuality: descent with modification2.

0084 No matter how fully one accounts for descent with modification.  There is always room for a miracle.

0085 Also, there is room to ignore a miracle.

Intersections are funny that way.

0086 Intersections are introduced in the chapter on message in How to Define the Word “Religion”.  Intersectionsconvey the message underlying the word.

0087 A primal example of a religious message is the intersection of action and thought. 

0088 First of all, action and thought each has its own nested form.

0090 If these two actualities are two independent ways of describing what is good and what is evil, then they may fuse into one – contradiction and complement filled – actuality.

0091 I diagram the following intersection in a particular manner.  There are other variations.  When I depict an intersection, I try to place the more celestial normal context on the vertical axis and the more mundane normal contexton the horizontal axis.  To me, the following configuration is particularly evocative.

Here is the intersection of action2 and thought2.

0092 The message is clear.  Thought2V and action2H are two contradicting and complementing actualities.  They constitute one contradiction-filled actuality2: what is good and what is evil.  Thought2V cannot be divorced from action2H.  Action2H cannot be isolated from thought2V.

0093 A mystery binds thought2V and action2H.

The mystery cannot be resolved without destroying the completeness of what is good and what is evil.  As soon as one axis disappears, the mystery vanishes.

To me, that is the character of religious messages.

A religious message violates the rules of non-contradiction because its contradictions can never be resolved.  Two actualities intersect.

Would it not be interesting if a history of civilization was written with this intersection in mind?

11/17/25

Looking at Dennis Venema and Scot McKnight’s Book (2017) “Adam and the Genome” (Part 10 of 22)

0094 Furthermore, I can compare the intersection of what is good and what is evil with the message of descent with modification.  

0095 For reading ease, here is the intersection at the heart of evolutionary biology.

Note that the Latin word, species, means “kind”.  A species can be an individual, a biological species, or a biological genus.

0096 Even though these two messages express vastly different content, they share the same mysterious relational structure.

0097 Is it creepy to think that what a species is shares the same relational structure as what is good and what is evil?

0098 It gets more creepy. 

Look at the first chapter of Genesis.

Note how God’s thoughts are also actions.

Note how the six days express the creation of kinds in various ways.

0099 Now, let me consider the two intersections presented so far.

The elements compare (as allegories of one another) according to their locations in the intersection, leading to all sorts of suggestions.

0100 Let me start by comparing the normal contexts.

Natural selection3H is like body3H.  Body development3V is like mind3V.

Can I say that another way?

Body development (and biological inheritance)3V as the normal context for the phenotype2V parallels mind3V as the normal context for thought2V.

Natural selection3H as the normal context for adaptation2H parallels the body3H as the normal context for action2H.

0101 What does this suggest?

Well, to start, the first comparison calls to mind the concept of intelligent design where ‘something thoughtful’ is contained in DNA2a.  Okay, make that the genotype1V.  DNA2a parallels what undergirds the phenotype2V.  Phenotype2V parallels thought2V.  Genotype1V parallels conscience1V.  So, is there an actuality2a that undergirds conscience2V in the same way that DNA2a undergirds genotype1V?

Here is a comparison.

I know that the actuality underlying the genotype1V is DNA2a.

What about conscience1V?

0102 It makes me wonder.

What about modern scientific manipulations of animals and plants through selective breeding and now, genetic engineering?

The human body3H  is the normal context where human actions2H perform operations that alter the DNA2a of living organisms3V.

If we were disembodied minds2V, would we do these things?

We stand in the place of gods3V when altering2H the genotypes1V of species.

Where is our conscience1V?

We cannot completely predict the body and behavior of the phenotypes2V that we potentiate1V.  When unintended consequences occur, some3V will ask, “What were ‘we’ doing2H?”

But, ‘we’ does not include those of us who stand in the place of gods3V or have the power to ignore what is good and what is evil2 because ‘we’ were born3H that way3V.

0103 Shall I make another… hmmm… “thought provoking” comparison?

0104 Conscience1V compares to genotype1V.

0105 What does this parallel inspire me to imagine?

Let me ask, “Why do no other species that we observe engage in introspection?”

Well, what do we do when we engage in introspection?

Okay, we try to figure out what went wrong, among other things.

Do other animals introspect about what went wrong?

No, during an incident, an animal knows that something is going wrong.  An animal learns from what happened.  But, animals never seem to dwell (or introspect) on events in their lives.

It makes me wonder whether animals exhibit an intersection between thought2 and action2.  Maybe, thought2b virtually situates action2a.  Maybe, action2b situates thought2a.

It makes me wonder about what phenotypic structures2V are responsible for human thought2V.

It also makes me wonder whether something broke between the Lebenswelt that we evolved in and our current Lebenswelt.

11/15/25

Looking at Dennis Venema and Scot McKnight’s Book (2017) “Adam and the Genome” (Part 11 of 22)

0106 What about disposition1H and niche1H?

Good grief.  This comparison sounds almost deterministic.

Here is a picture.

Of course, the disposition of a species1H should parallel the potential of something independent of the adapting species1H.

Does that include the human religious disposition1H?

Okay, then what is The Human Niche?

Oh my, Razie Mah wrote a masterwork with exactly that title.

0107 These parallels (and there are many more) illustrate the following claim: Those who abandon Christianity because Adam and Eve cannot be the biological ancestors of all humans do not simply lose their religion.  They gain an alternate religion.

In terms of message, an alternate religion manifests an alternate intersection.

In the United States, from 1967 to 2017 AD, that religion is Big Government (il)Liberalism.

Some would say, “Bigilib.”

0108 Dominic Burbidge, an administrator for the Programme for the Foundation of Law and Constitutional Government at the University of Oxford, wrote a serious piece on contemporary universities for the Witherspoon Institute.  His article is titled: Listening: An Antidote to the Modern University’s Incoherence.

I find the article hilarious.

0109 Here is his argument in a nutshell:  The modern university consists in three disparate academic traditions: the University of Rationalism, the University of Subjectivism and the University of Revolution.  He proposes a fourth university in order to balance these three traditions.  He calls this fourth (proposed) institution: the University of Listening.

0110 Here is my interpretation:  The modern university is a single actuality that we call the University of Rationalism.

Within this university, two contradicting and complementary styles flourish.

The so-called University of Subjectivism engages in inquiry2 that emerges from (and situates) the potential of the individual person, “me”1.

The so-called University of Revolution channels inquiry2 into the potential of a counter-truth (to a prevailing truth, already established by the (old-school) University of Rationalism, or even better, founded on Christian doctrine)1.

In short, the new University of Rationalism redefines the term, “rational”.

Are you listening to me?

0111 Burbidge did not mention the normal contexts for these growing academic traditions.  I will label these normal contexts, “S” and “R”.

0112 Here are the two nested forms.

0113 The normal contexts may now be named.

Normal context S3 is personal fulfillment3.

Normal context R3 is furtherance of the collective3.

0114 The inquiry of subjectivism and the inquiry of revolution coalesce into the single actuality of the (new school of the) University of Rationalism.

0115 Here is the resulting intersection.

0116 Oh, do I need to say that this is all found How To Define The Word “Religion”, by Razie Mah, available at smashwords and other e-book venues?

To teach the course, take a look at Razie Mah’s blog for December 2023.

Okay, what else does this imply?

This intersection describes the message underlying the religion of BG(il)L.

That is not enough, what else?

Our phenotype2V entails the innate expectation of “religion” characterized by meaning, presence and message.  Meaning goes with social construction (as opposed to sensible construction).  Presence associates to three nested tiers: societyC, organizationB and individual in communityA. Message includes the intersection.

Now, admittedly, there is a twist.  Our current Lebenswelt is not the same as the Lebenswelt that we evolved in.  More on that later.

11/14/25

Looking at Dennis Venema and Scot McKnight’s Book (2017) “Adam and the Genome” (Part 12 of 22)

0117 Right now I am discussing our current Lebenswelt.

For example, in 2017, various elites in Washington D.C. hosted a March for Science.  Here, practitioners of subjective and revolutionary inquiries… or should I say?… experts on capitalism and socialism claimed to “support science”.  

In short, the protesters claimed the mantle of rationalism.  But, really, they claimed the ideologies of capitalism and socialism formatted in the style of scientific discourse.

See Original Sin and the Post-Truth Condition, by Razie Mah, available at smashwords and other e-book venues for that… um… creative fusion.

Rationalism is now the single actuality encompassing the inquiries of subjectivism and revolution.  This is a mystery.  It is also a religious message.  The federal government has established a religion.

0118 Our civilization used to think that the term, “rational”, means “reasonable”.  “Rational” also meant “without passion”.  Now, rational inquiry means anything but religious.

Rational inquiry became more and more anti-religious… er… anti-Christian when Big Government (il)Liberalism increased in sovereign power in the United States, before, during and after the so-called Cold War (1945-1989 AD).

0119 That is not all.

So-called progressives consolidated sovereign power in all branches of the federal government.  They infiltrated every institution that received advantage from the federal government.  They divinized organizational objectives demanding federal action.

The message of subjectivism and revolutionary inquiry is this: The Progressive religion offers personal fulfillment and the furtherance of the collective, by being rational, where “rational” is defined as anything but “religious”… where “religious”… means “Christian”.

Amen!

0120 What about Burbidge’s proposal of a new academic tradition, the University of Listening?

Here is where I attain pure hilarity.

0121 Clearly, BG(il)Ls have redefined the word “rational”.  Rational used to mean reasonable or without passion.  Now, it means not religious.  Also, it means “scientific”, if you catch my drift.  That is the only way that subjectivity and revolution fit under the one roof of so-called “rationality”.  Trust the science.  Science is rational.

0122 Does that mean that the word “rational” is really no longer appropriate?

Let me shout from my megaphone, “The contradicting and complementing universities of subjectivism and revolutionought to throw off their old singular actuality.“

But, what new word needs to be forged in order to replace the old single actuality of the University of Rationalism?

0123 I want to coin a new word for the single actuality composed of the two intersecting actualities.

The word should sound like “university”.

So, I propose the term “you listen to me” collapsed into the spoonerism “ulistentome”.

0124 Here is the intersection that I advocate.

0125 I propose that the term university be replaced by ulistentome.

Also, the word college should give way to harangue.

Seminary should become hope for salvation.

0126 Three academic institutions stand out in Boston.  These are Harvard Ulistentome, Boston Harangue and the Gordon-Conwell Theological Hope for Salvation.  The first two are BG(il)L.  I am not sure about the third, explaining why I suggest the label: hope for salvation.

0127 Here is an assignment for the Christian student who would abandon faith in Jesus, the Messiah, when Adam and Eve are no longer the biological parents of the entire human species.

Compare these three messages (or intersections): descent with modification (or species), what is good and what is evil, and ulistentome.  Compare similar elements within these three relational structures.  See how they resonate.  Savor the ironies.  See how they illuminate one another.

0128 These resonances, ironies and illuminations ripple across the curtain that Venema lowers on Augustine’s drama of the story of Adam and Eve.  There is more to descent with modification than meets the eye.  Evangelicals may no longer be able to watch Augustine’s drama, but the curtain has come alive.  Evolutionary biology contains a religious message in the intersection of adaptation and phenotype.

Evolutionary biology manifests a mystery.