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.

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 selection_3b brings the actuality of an adaptation_2b into relation with a niche_1b.

0026 A niche_1b expresses the potential of an actuality independent of the adapting species_1b.  The niche_1b emerges from (and situates) a content-level actuality_2a.  For ancestral water-dwelling lung fish, the actuality_2a was land.  For the ancestors of the whale, the actuality_2a was sea.

0027 According to classical Darwinism, adaptations_2b are explained through natural selection.  The niche_1b 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 body_3b brings the actuality of the phenotype_2b into relation with the genotype_1b.

0040 The genotype_1b is the potential inherent in DNA_1b.  DNA_2a is an actuality that defines the species_2a.

0041 So, the key phrase is descent with modification.

0042 DNA_2a goes with descent_b.

The actuality underlying the niche_2a accounts for relevance of the term, with modification_b.

0043 Phenotype_2b emerges from (and situates) genotype_1b.

Adaptation_2b emerges from (and situates) niche_1b.

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 niche_2a.

0045 Venema fuses the two situational actualities, phenotype_2b and adaptation_2b, into a single actuality.  

Phenotype_2b and adaptation_2b are two actualities that unite to form one: descent with modification_2-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.

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.

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 niche_1b.  The 95% S bacteria constitute an actuality independent of the virus_2a, offering the potential of exploitation in the normal context of natural selection_3b.

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.