Moronic Artificial Intelligence (6)

By: James V. Kohl | Published on: November 9, 2024

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Earlier today, 11/8/24, I came home to an example (pictured below) of how quantum coherence must be linked to coherently organized biology via energy-dependent biophysically constrained protein folding chemistry, or from virus-driven energy theft to the degradation of mRNA, which intelligent serious scientists have linked to extinction in the wild of these “Angel Trumpets.”

For more facts about biophysically constrained protein folding chemistry compared to extinctions via stupid theories of mathemagically evolved biodiversity, see also” Gene Regulation and Epigenetics: How Science Works 10/5/24. Unfortunately, the author does not start with God’s Creation of light-matter interactions at the origin of life and he does not link the ATP-dependent Creation of RNA in regulatory T cells to miRNA-mRNA interactions and/or fixation of amino acid substitutions in microtubules to Vibrations in Microtubules (1997) but he does parrot our claims in the molecular epigenetics section of From Fertilization to Adult Sexual Behavior (1996).

“The present book is subdivided into 16 chapters: following two introductory chapters,
four chapters take a view on gene regulation from the perspective of transcription
factors, and four further look on it from the angle of chromatin and non-coding RNA
(ncRNA). Then three chapters explain the impact of epigenetics from the standpoint
of health and the three last chapters from the view of diseases.”

The Human Genome and Its Variations “Genome-wide genotyping and whole genome sequencing allows the study and analysis of complex diseases, such as T2D (type 2 diabetes) and cardiovascular disease (CVD), on the basis of dozens to hundreds of genetic variants, such as single nucleotide variants (SNVs) and copy number variations (CNVs).”

Gene Expression and Chromatin “Tissue- and signal-specific gene expression is the central mechanism to control the general properties of a cell and its response to environmental perturbations.”

The Basal Transcriptional Machinery “…genome-wide analysis showed that the majority of human genes use alternative binding sites for GTFs. Diversity and complexity of the human transcriptome are based on that most genes have multiple TSS regions and that the TSS of many genes is not a single defined nucleotide.”

Transcription Factors and Signal Transduction “…a central characteristic of life, the response to molecules of the extracellular environment, is mediated by signal transduction cascades that mostly start with an extracellular signaling molecule and end with an activated transcription factor, i.e., with a change in gene expression.”

A Key Transcription Factor Family: Nuclear Receptors “…endocrine hormones, such as estradiol and testosterone, while others are metabolites of dietary compounds, such as fatty acids and cholesterol. Both types of lipids are of large physiological impact in health and disease, such as metabolic control and the modulation of immunity. This made nuclear receptors especially attractive for both basic and applied research.

Genome-Wide Principles of Gene Regulation “…we will discuss epigenetic NGS methods used for the genome-wide assessment of accessible chromatin, histone modifications, transcription factor binding and 3D chromatin structure. The integration of these new data types provides further insight on the mechanistic and the human genome’s functional landscape. In this way, we will obtain a genome-wide understanding of gene regulation and epigenetics.”

DNA Methylation “DNA methylation is performed by DNA methyltransferases (DNMTs) and primarily results in 5mC within CpGs. It is a prominent epigenetic mechanisms, which has an impact on genome stability, gene expression and development.”

Histone Modifications “Histone modifying enzymes, such as HATs, HDACs, KMT and KDMs, either add or remove posttranslational modifications to histone proteins and in this way change the functional profile of the epigenome.”

Chromatin Remodeling and Organization “chromatin modification and remodeling machineries allow the transition from a repressed state to an active state. Chromatin remodeling factors are multiprotein complexes that use the energy of ATP hydrolysis, in order to remodel or remove nucleosomes regulating the exposure of genomic DNA to transcription factors.”

Regulatory Impact of ncRNA “…miRNAs are small ncRNAs that regulate posttranscriptionally the expression of most protein-coding genes. They share many similarities together with transcription factors and therefore are useful for different regulatory processes.”

Epigenetics in Development “…embryogenesis is the period, where epigenetics has the largest impact. Epigenetics directs the programing of PGCs, induced pluripotency as well as the function of adult stem cells in tissue homeostasis. These key examples demonstrate the impact of epigenetics on the organization of our body in health and disease. Epigenetic regulation is also critical for the normal development and functioning of our brain. Dynamic DNA and histone methylation as well as their demethylation at specific gene loci play a fundamental role in learning, memory formation and behavioral plasticity. Thus, the epigenome of neurons allows a molecular explanation for long-term memories.

Epigenetics and Aging The progressive decline in the function of cells, tissues and organs associated with aging is affected by both genetic and epigenetic factors, i.e., there are characteristic epigenome-wide changes during aging acting as epigenetic clocks over years and decades.

Epigenetics and Immunity “…metabolism and inflammation are linked via gene regulatory actions of transcription factors and epigenetic programming affecting basically all common diseases.”

Epigenetics and Disease “…diseases are largely preventable by an appropriate lifestyle. We will elaborate the relation of phenotypes, genetic predisposition, epigenetic programming and lifestyle decisions of dietary choices and physical activity.

Cancer Epigenetics “…cancer is not only a genetic but also an epigenetic disease. The mechanistic bases of cancer epigenomics are specific genetic, environmental and metabolic stimuli that disrupt the homeostatic balance of chromatin, which then either becomes very restrictive or permissive.”

Nutritional Epigenetics “….nutritional molecules can influence the activity and biological function of both transcription factors like nuclear receptors as well as chromatin modifying enzymes.”

Nutrient-dependent Pheromone-Controlled Ecological Adaptations: From Angstroms to Ecosystems (4/18/18)

AI Overview “Nutrient-dependent Pheromone-Controlled Ecological Adaptations: From Angstroms to Ecosystems” refers to a theoretical model that proposes how nutrient availability can directly influence an organism’s pheromone production, which in turn shapes its behavior and ecological adaptations across different scales, from the molecular level (angstroms) to entire ecosystems; essentially suggesting that an organism’s diet and the resulting pheromones it emits can drive significant changes in its population dynamics and interactions within its environment.

If my model was a “theoretical model,” it would not be directly linked to the 2024 Nobel Prize in Physiology or Medicine for the discovery of microRNA and its role in post-transcriptional gene regulation via its recapitulation in Top-down causation and quantum physics 10/23/18

See for comparison The massed-spaced learning effect in non-neural human cells 11/7/24, and/or the snake-centric theory of primate evolution from pond scum.