Biology to a Physicist

Sal Giardina: apologetics revisited

March 26, 2017 Sal Giardina wrote:

“James, I appreciate your responding to my posts but I would prefer that your input would be related to the content of the post.”

My reply: If you do not want people to learn how my claims are linked to yours, please tell me that you intend to continue with apologetics rather the concept of energy as information.


… the religious discipline of defending or proving the truth of religious doctrines through systematic argumentation and discourse.[1][2][3] Early Christian writers (c. 120–220) who defended their beliefs against critics and recommended their faith to outsiders were called Christian apologists.[4] In 21st century usage, ‘apologetics’ is often identified with debates over religion and theology.

In the context of debates over religion and theology, Sal Giardina opened discussion of physics, chemistry, and the conserved molecular epigenetics of RNA-mediated cell type differentiation. Secular humanists are scared by the ghosts of their biologically uninformed past and their ongoing ignorance. Fortunately for them, Sal Giardina and others like him cannot prove anything via the use of apologetics. So far as I know, the apologeticists have never convinced anyone to believe in any of their claims.
See for example: What does DNA have to do with the Origin of Life ?
Unfortunately, you must join this “false flag” group go find this post: I’ve been banned from the group twice, but just submitted a request to re-join.
My comments: Secular humanists seem willing to believe that the origin of life could somehow lead to consciousness as a side effect.
See for example: Consciousness could be a side effect of ‘entropy’, say researchers
My comment: Serious scientists do not make such ridiculous claims. These researchers are theorists who tout meaningless pseudoscientific nonsense. Their ridiculous claims makes news when biologically uninformed journalists, like Fiona Macdonald pass the unsupported claims on to others who do not know that the theorists are touting meaningless pseudoscientific nonsense.
See also: Virus evolution and this special issue on Orgasms:  Introductory editorial to ‘Orgasm: Neurophysiological, Psychological, and Evolutionary Perspectives
My comment: Who are the people trying to convince others that virus evolution links prairie vole monogamy to the evolution of human love via organsm? One of them is James Pfaus.

In ‘The Role of Orgasm in the Development and Shaping of Partner Preferences’, Coria-Avila, Herrera-Covarrubias, Ismail, and Pfaus (2016) explore the relationship between orgasm and sexual preference-formation in animals. Of particular significance with respect to human orgasm, Coria-Avila et al. describe the pre- and post-ejaculatory factors contributing to male rats forming conditioned sexual preferences.

See this article by Rachel Feltman, who placed the ridiculous claims of Pfaus before my detailed model of nutrient-dependent pheromone-controlled biologically-based cause and effect.
What Do We Actually Know About Pheromones?

But Kohl’s products, which he likens to food spices (“They give you an extra kick!”), make some researchers roll their eyes. Dr. Jim Pfaus, professor of psychology at Concordia University in Montreal, is one of them.

See for comparison: Ecologically relevant neurobehavioral assessment of the development of threat learning
Summary: “Informed Conditioning” is linked to the differences between wolves and dogs and biophysically constrained cell type differentiation in all living genera.
See for example: A Comparison of the Sensory Development of Wolves (Canis lupus lupus) and Dogs (Canis lupus familiaris)
See also (link opens pdf): Early life experiences: enduring behavioral, neurological and endocrinological consequences

See also: Sexual Differentiation of the Brain: A Fresh Look at Mode, Mechanisms, and Meaning

…no study has yet shown an effect of manipulating the expression of a particular microRNA on a behavioral or brain sex difference. In other words, we are still awaiting the demonstration that microRNAs contribute to sexual differentiation of the brain.

Olfaction is important to humans as well, but visual stimuli are far more potent and the arousal potential of same-sex versus opposite-sex images depends on the partner preference of the observer (see for review Baum, 2006).

Michael Baum and others still make ridiculous claims about visual input compared to the epigenetic effect of food odors and pheromones on energy-dependent microRNA-mediated cell type differentiation in species from microbes to humans. That fact supports my claim that people like him are biologically uninformed.

See for comparison: Feedback loops link odor and pheromone signaling with reproduction

See also: Crosstalk between epigenetics and metabolism—Yin and Yang of histone demethylases and methyltransferases in cancer

Pioneering experiments by Allfrey and Mirsky >50 years ago identified methylation and acetylation of histones by isotope incorporation and showed that histone modification can influence whether RNA synthesis of genes is switched on or off [3].

See also: Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”

The synthesis of RNA in isolated thymus nuclei is ATP dependent.

If you knew nothing about the energy-dependent de novo creation of nucleic acid precursors, you still could start from the energy-dependent creation of RNA and link RNA-directed DNA methylation to all biophysically constrained biologically-based cause and effect in all living genera to their physiology of pheromone-controlled reproduction in the context of learning and memory at the cellular level of intracellular and extracellular communications.

See also: Experience-Dependent Accumulation of N6-Methyladenosine in the Prefrontal Cortex Is Associated with Memory Processes in Mice
My comment: The conserved molecular mechanisms of experience-dependent learning and memory have been linked from energy-dependent RNA-mediated cell type differentiation to all biodiversity via quantised energy and all subsequent levels of examination the must begin with the origins of information, the sun’s anti-entropic virucidal energy.

See for comparison:  Ultraviolet Absorption Induces Hydrogen-Atom Transfer in G⋅C Watson–Crick DNA Base Pairs in Solution

My comment: Femtosecond blasts of UV light link the sun’s virucidal energy to RNA-mediated DNA repair in all living genera. People who do not know that should simply admit that they biologically uninformed. Most of them are theorists who know nothing about anything that must be linked from angstroms to ecosystems. They should not antagonize those who are biologically informed serious scientists. Serious scientists publish experimental evidence in reports such as this one.

UV-Induced Charge Transfer States in DNA Promote Sequence Selective Self-Repair


The sequences have been selected according special charge distributions and lifetimes of excimer states previously characterized by femtosecond infrared spectroscopy.(3a, 3c, 3d) With these selected sequences we demonstrate that repair occurs when the intrastrand charge transfer leads to a suitably charged nucleotide adjacent to the lesion.

My comment: The sequences cannot be selected outside the context of natural selection for energy-dependent codon optimality, which is the basis for the control of hydrogen-atom transfer in DNA base pairs in solution. Control is manifested in the measurement of pH.

See: Control of pH responsive peptide self-association during endocytosis is required for effective gene transfer


Coulombic interactions between the histidine residues modulate protonation and subsequent conformational transitions required for peptide mediated gene transfer activity and are an important factor to consider in future peptide design.

My comment: Coulomb barrier:The Coulomb repulsion which tends to keep positively charged bombarding particles out of the nucleus. Specifically, the Coulomb potential associated with this force.

Energy-dependent Coulombic interactions link autophagy to polycombic ecological adaptations for comparison to what happens when virus-driven energy theft is linked to the hecatombic evolution of all pathology.

See also: Coulombic interactions between partially charged main-chain atoms not hydrogen-bonded to each other influence the conformations of alpha-helices and antiparallel beta-sheet. A new method for analysing the forces between hydrogen bonding groups in proteins includes all the Coulombic interactions (published in 1995)

See for comparison: Jonas Edward Salk (October 28, 1914 – June 23, 1995) was an American medical researcher and virologist. He discovered and developed one of the first successful polio vaccines.

My comment: The fact that Jonas Edward Salk died in the same year that information about Coulombic interactions was published exemplifies the fact that we still need people like Salk to lead the way towards more scientific progress.

Is everyone who could do that already dead? Have people like Sal Giardina and other apologeticists replaced them. Will any of the works from the early 1990s to 1964 be resurrected before all of humanity is irreversibly impacted?

See for example: Biology, molecular and organismic (1964)

The notion has gained some currency that the only worthwhile biology is molecular biology. All else is “bird watching” or “butterfly collecting.” Bird watching and butterfly collecting are occupations manifestly unworthy of serious scientists! I have heard a man whose official title happens to be Professor of Zoology declare to an assembly of his colleagues that “a good man cannot teach zoology. A good man can teach, of course, only molecular biology.

Such pronunciamentos can be dismissed as merely ridiculous. They are, however, caricatures of opinions entertained by some intelligent and reasonable people, whose views deserve an honest and careful consideration and analysis. Science must cope with new problems that arise and devise new approaches to old problems. Some lines of research become less profitable and less exciting and others more so.

Links from the creation of nucleic acid precursors to entropy and mutation-driven evolution are still being addressed by apologeticists who know nothing about physics, chemistry, or molecular epigenetics.
See also:  Biblical Creation / Entropy
See for comparison: What is life when it is not protected from virus driven entropy (6 minutes)
I think most people can understand the concept of Creation by God of all biophysically constrained life on Earth. If not, they should be told about the examples, since all examples show that all organisms must eat or die. If they die, they do not reproduce, which means they never became an extant species. Instead, the individuals and/or species became part of the fossil record or they became nothing recognizable to serious scientists as anything more than dirt.
See also:
See also: Virus Documentary | Discovering & Understanding Viruses || How Viruses Work ? (60 minutes)

My comment: Terra Firma is the battlefield mentioned in the video (a village in central Brazil). Stephen Morse, virologist at Rockefeller is fighting on the side of virus-driven entropy, which he attributes to emergence and evolution. For example, His book, Emerging Viruses (Oxford University Press) was selected by “American Scientist” for its list of “100 Top Science Books of the 20th Century”.

My comment: According to the book, our innate immune system emerged and evolved to become the source of all pathology. If the innate immune system is referred to as our “immune system” the word innate changes to evolved, and mutations are linked to evolution in the context of ridiculous neo-Darwinian theories. That is how emerging viruses are automagically linked to all healthy longevity via polycombic ecocological adaptation and to all pathology via hecatombic evolution.
We have come full circle back to the definitions that are used and discussed in Polycombic ecological adaptation as a science, not a theory (2):
See also:  The Human Virome

For comparison, see: Mutation-Driven Evolution


Mutation… includes nucleotide substitution, insertion/deletion, segmental gene duplication, genomic duplication, changes in gene regulatory systems, transposition of genes, horizontal gene transfer, etc.

My comment: The definition above links mutations to any change in any genome. It does not link virus-driven energy theft toi mutations and all pathology.


Single nucleotide substitutions or indels [insertions/deletions] can lead to several hemoglobin variants owing to amino acid replacements, while molecular defects [mutations] in either regulatory or coding regions of the human HBA2, HBA1, HBB or HBD genes can minimally or drastically reduce their expression, leading to α-, β- or δ-thalassemia, respectively.

My comment: The facts about nutrient energy-dependent single nucleotide substitutions and RNA-mediated amino acid substitutions link hemoglobin variants to healthy longevity and the facts link molecular defects to the pathology of α-, β- or δ-thalassemia, respectively.

See for comparison: Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution

The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.

See also: Peptides design based on transmembrane Escherichia coli’s OmpA protein through molecular dynamics simulations in water-dodecane interfaces
See for comparison: Understanding abundance and diversity using ghosts and goblins: a spooky ecology lesson!

If we wanted to compare the diversity of two forests, we would want to look at climate, elevation, drainage, available nutrients, proximity to human disturbance, soils, etc. Diversity can be impacted by a slew of factors. While this is a fun and rather ridiculous example of how species counts and diversity works, the leap to how this can inform ecology, management, and conservation is clear.

My comment: The fact that nothing known about virus-driven energy theft is included in their comparisons makes the most important of all comparisons irrelevant to their claims about how climate, elevation, drainage, available nutrients, proximity to human disturbance, soils, etc. link ecological variation to polycombic ecological adaptation via the physiology of reproduction in all living genera.
See for comparison: An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells

G540A supports virus replication in mammalian cells while retaining replication ability in avian cells. Host splicing regulator, SF2, interacts with this ESE to regulate splicing of NEP/NS1 mRNA and G540A substitution affects SF2–ESE interaction. The NS1 protein directly interacts with SF2 in the nucleus and modulates splicing of NS mRNAs during virus replication.

Reported as: Single nucleotide change responsible for allowing H7N9 flu to jump from birds to humans found
The identification of the G540A links the single nucleotide polymorphism (SNP) from a biomarker in fowl infected with a flu variant to what was reported as mutation.
Researchers assumed that “…the mutation played a role in allowing the virus to spread between humans once it made the leap from an avian source.”
As usual, they found no evidence to support that ridiculous claim. That ridiculous claim is among many others that theorists thought could be used to link mutations to evolution via mathematical models instead of facts about nutrient energy-dependent pheromone-controlled biophysically constrained RNA-mediated cell type differentiation.

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