Trump & Soon-Shiong secure the media (2)

By: James V. Kohl | Published on: October 29, 2024

Integrated translation and metabolism in a partially self-synthesizing biochemical network 7/11/24

(Fig. 1A). Realizing a genetic network that is controlled by in vitro production of glycine

Light-activated carbon fixation in cyanobacteria links the in vitro production of glycine across kingdoms to the patent for in vivo RNA-guided human genome engineering, and the patent for biophysically constrained miRNA-mediated protein folding chemistry: Pheromones and the luteinizing hormone for inducing proliferation of neural stem cells and neurogenesis, which links peptide synthesis at the origin of life to achiral glycine in position 6 of the gonadotropin releasing hormone (GnRH) decapeptide. See: Footprints of a Singular 22-Nucleotide RNA Ring at the Origin of Life 4/25/20 Their claims united nucleic acid scientists with clinicians to devise human therapies linked to RNA interference across kingdoms.

“We propose a model revisiting the architecture of RNA-peptide interactions at the origin of life…”

See also: In situ visualization of endothelial cell-derived extracellular vesicle formation in steady state and malignant conditions 10/22/24 Reported as: Cellular couriers: The body’s extracellular vesicles could lead to a new cancer blood test 10/28/24

“This revealed—for the first time—that there is a link between EVs in the blood and tissue damage during cancer.

Energy-dependent changes in the cargo carried by exosomes link extracellular vesicle formation to healthy longevity across kingdoms via fixation of amino acid substitutions in microtubules, effective treatment of COVID-19 with Paxlovid, and effective cancer treatment with microtubule inhibitors via autophagy.

See: [Research progress in the regulation of functional homeostasis of adipose tissue by exosomal miRNA] 10/25/24

Direct effects on energy-dependent cell type differentiation are primarily mediated by miRNAs, which are transported by exosomes, a subtype of extracellular vesicles (EVs).

The facts about effective treatment of all virus-driven diseases appear to be deliberately obfuscated in the context of Artificial Intelligence (AI) and stupid theories.

GROK AI @microRNApro continues to challenge the facts by linking the automagical emergence of energy from the cosmic void to the mathemagical evolution of people from pond scum despite the claims in Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants 11/28/12, A two-amino acid change in the hemagglutinin of the 1918 influenza virus abolishes transmission 2/3/07, 2 Cell Studies Reveal Genetic Variation Driving Human Evolution 2/14/13, Bacteria evolve over a weekend 2/26/15, and Machine-guided design of cell-type-targeting cis-regulatory elements 10/23/24

For examples:

GROK AI:

“@microRNApro…seems to be focused on discussing topics related to microRNA biology, its implications in health and disease, particularly concerning viral interactions, genetic mechanisms, and ecological adaptations.

Yes. For links to every aspect of light-matter interactions & protection from virus-driven pathology, see: Cellulose for ages 14+

A two amino acid substitution ended the 1918 Spanish influenza. One SNP, EDAR V370A was linked to protection from all virus-driven pathology during 5K years of ecological adaptations from East Asia to the North American Indians.

“…Cellulose” for ages 14+ starts with light-matter interactions at the origin of life, which were linked from miRNA abundance to all biodiversity via the 2024 Nobel Prize for Physiology or Medicine and Identification of Shemin pathway genes for tetrapyrrole biosynthesis in bacteriophage sequences from aquatic environments 10/15/24

See for comparison

GROK AI 10/15/24

How are miRNAs linked to evolution

Answer

MicroRNAs (miRNAs) play a significant role in evolution due to several reasons:

  1. Regulation of Gene Expression: miRNAs are small non-coding RNA molecules that regulate gene expression post-transcriptionally. They do this by binding to messenger RNA (mRNA), leading to either mRNA degradation or translation repression. This regulation can influence numerous biological processes, including development, cell proliferation, and differentiation, which are key elements in evolutionary processes.
  2. Genomic Plasticity: The genes that code for miRNAs are relatively small and can evolve quickly due to their short length, making them quite plastic in the genome. This plasticity allows for rapid evolutionary changes. New miRNAs can arise through mutations, duplications, or from transposable elements, providing a mechanism for evolutionary innovation.
  3. Species-Specific miRNAs: Many miRNAs are species-specific or show significant variation among closely related species. This suggests that miRNAs can contribute to species differentiation and adaptation. For instance:
    • Divergence in miRNA sequences between species can lead to changes in target recognition, potentially altering gene regulation patterns.
    • Gain or loss of miRNAs during evolution can lead to novel regulatory networks or the loss of certain regulatory pathways, influencing evolutionary trajectories.
  4. Role in Developmental Timing: miRNAs often regulate developmental timing, which is crucial for the life cycle of organisms. Changes in miRNA expression during development can lead to evolutionary changes in morphology or physiology. For example, the timing of expression of certain miRNAs in different organisms can result in different body plans or life stages.
  5. Epistatic Interactions: miRNAs can modulate complex genetic interactions, or epistasis, where the effect of one gene depends on the presence of one or more other genes. This can lead to evolutionary novelties by altering how genes interact in different species.
  6. Environmental Adaptation: miRNAs can be involved in responding to environmental changes, which is a key aspect of evolution. For example, miRNAs might be upregulated or downregulated in response to stressors, aiding in the survival and adaptation of organisms to new environments.
  7. Hybrid Viability and Speciation: miRNAs might influence hybrid viability by affecting gene regulation in ways that could either promote or hinder the success of hybrids, potentially playing roles in speciation events.
  8. Conservation Across Species: Despite their rapid evolution, some miRNAs are highly conserved across vast evolutionary distances, indicating their fundamental roles in core biological processes, showing that while miRNAs can be a source of evolutionary novelty, they also maintain crucial ancient regulatory functions.

Through these mechanisms, miRNAs contribute to the complexity and adaptability of life forms, playing a pivotal role in evolutionary biology by fine-tuning gene expression networks over time. Their study not only sheds light on how organisms evolve but also provides insights into the molecular mechanisms behind evolutionary changes.

Does the weekend resurrection of the bacterial flagellum refute every aspect of neo-Darwinian evolutionary theory?·

Oct 18

A two amino acid substitution ended the 1918 Spanish influenza. One SNP, EDAR V370A was linked to protection from all virus-driven pathology during 5K years of ecological adaptations from East Asia to the North American Indians. Why isn’t anyone discussing those facts?

Oct 19

Replying to @murraygilmanand@DrJBhattacharya

Agreed, but “Cellulose” https://kickstarter.com/projects/geniusgames/cellulose-a-plant-cell-biology-game for ages 14+ starts with light-matter interactions at the origin of life, which were linked from miRNA abundance to all biodiversity via the 2024 Nobel Prize for Physiology or Medicine and https://nature.com/articles/s41467-024-52726-3

10/15/24

How are miRNAs linked to evolution

Answer

MicroRNAs (miRNAs) play a significant role in evolution due to several reasons:

  1. Regulation of Gene Expression: miRNAs are small non-coding RNA molecules that regulate gene expression post-transcriptionally. They do this by binding to messenger RNA (mRNA), leading to either mRNA degradation or translation repression. This regulation can influence numerous biological processes, including development, cell proliferation, and differentiation, which are key elements in evolutionary processes.
  2. Genomic Plasticity: The genes that code for miRNAs are relatively small and can evolve quickly due to their short length, making them quite plastic in the genome. This plasticity allows for rapid evolutionary changes. New miRNAs can arise through mutations, duplications, or from transposable elements, providing a mechanism for evolutionary innovation.
  3. Species-Specific miRNAs: Many miRNAs are species-specific or show significant variation among closely related species. This suggests that miRNAs can contribute to species differentiation and adaptation. For instance:
    • Divergence in miRNA sequences between species can lead to changes in target recognition, potentially altering gene regulation patterns.
    • Gain or loss of miRNAs during evolution can lead to novel regulatory networks or the loss of certain regulatory pathways, influencing evolutionary trajectories.
  4. Role in Developmental Timing: miRNAs often regulate developmental timing, which is crucial for the life cycle of organisms. Changes in miRNA expression during development can lead to evolutionary changes in morphology or physiology. For example, the timing of expression of certain miRNAs in different organisms can result in different body plans or life stages.
  5. Epistatic Interactions: miRNAs can modulate complex genetic interactions, or epistasis, where the effect of one gene depends on the presence of one or more other genes. This can lead to evolutionary novelties by altering how genes interact in different species.
  6. Environmental Adaptation: miRNAs can be involved in responding to environmental changes, which is a key aspect of evolution. For example, miRNAs might be upregulated or downregulated in response to stressors, aiding in the survival and adaptation of organisms to new environments.
  7. Hybrid Viability and Speciation: miRNAs might influence hybrid viability by affecting gene regulation in ways that could either promote or hinder the success of hybrids, potentially playing roles in speciation events.
  8. Conservation Across Species: Despite their rapid evolution, some miRNAs are highly conserved across vast evolutionary distances, indicating their fundamental roles in core biological processes, showing that while miRNAs can be a source of evolutionary novelty, they also maintain crucial ancient regulatory functions.

Through these mechanisms, miRNAs contribute to the complexity and adaptability of life forms, playing a pivotal role in evolutionary biology by fine-tuning gene expression networks over time. Their study not only sheds light on how organisms evolve but also provides insights into the molecular mechanisms behind evolutionary changes.

Does the weekend resurrection of the bacterial flagellum refute every aspect of neo-Darwinian evolutionary theory?

Answer

The “weekend resurrection of the bacterial flagellum” refers to an experiment where researchers demonstrated that the bacterial flagellum, a complex cellular structure thought by some to challenge evolutionary theory due to its irreducible complexity, could evolve through evolutionary processes within a relatively short period. This experiment aimed to address the arguments typically raised by proponents of intelligent design, particularly the concept of irreducible complexity, which suggests that certain biological structures are too complex to have evolved through gradual, step-by-step evolutionary processes.

Here’s how this experiment relates to neo-Darwinian evolutionary theory:

  • Refutation of Irreducible Complexity: The experiment showed that the flagellum could indeed evolve from simpler structures, suggesting that it is not irreducibly complex. This directly challenges one of the key arguments used by proponents of intelligent design against evolutionary theory.
  • Gradual Evolution: Neo-Darwinian theory posits that evolution occurs through gradual changes where structures evolve through intermediate forms that provide selective advantages. The evolution of the flagellum in the experiment supported this by showing that flagellar components could have evolutionary histories independent of each other before coming together to form the flagellum, thus refuting the notion that all parts must be present simultaneously for functionality.
  • Modular Evolution: The flagellum shares components with other bacterial systems, like the type III secretion system, which supports the idea of modular evolution where parts of one system can be co-opted for another, a concept well within the framework of neo-Darwinian theory.
  • Evolutionary Mechanisms: The experiment used mechanisms like gene duplication, mutation, and natural selection, which are fundamental to the neo-Darwinian model of evolution.

However, stating that this experiment “refutes every aspect” of neo-Darwinian evolutionary theory would be an overstatement. Here’s why:

  1. Neo-Darwinian Theory’s Breadth: Neo-Darwinian theory encompasses a wide range of evolutionary processes, including speciation, genetic drift, sexual selection, and more. The bacterial flagellum experiment mainly addresses the argument of complexity and the feasibility of evolving complex structures, not the entirety of evolutionary theory.
  2. Other Challenges: There are other criticisms and questions regarding evolutionary theory, like the rate of evolutionary change, the role of epigenetics, neutral theory versus selection, and the origin of life itself, which this experiment does not directly address.
  3. Continuing Scientific Inquiry: Science, including evolutionary biology, thrives on continuous questioning, testing, and refinement. While this experiment provides strong evidence against specific claims of irreducible complexity, it does not close the book on all evolutionary inquiries or debates.
  4. Integration with Modern Synthesis: Modern evolutionary biology integrates neo-Darwinian principles with genetics, molecular biology, and other fields, forming what is sometimes called the extended evolutionary synthesis or modern synthesis. The flagellum experiment fits into this broader understanding but doesn’t negate the need for or invalidate other aspects of evolutionary theory.

In summary, while the experiment significantly undermines the argument of irreducible complexity regarding the bacterial flagellum, it does not refute every aspect of neo-Darwinian evolutionary theory. Instead, it reinforces certain aspects of evolutionary theory by demonstrating that complex biological structures can indeed evolve through known evolutionary mechanisms. Evolutionary theory remains a dynamic scientific field, continually being tested and expanded upon with new evidence.

Does natural selection for energy-dependent codon optimality link the emergence of energy from the cosmic void to the origin of life and all biodiversity via the physiology of reproduction?

Answer

The concept you’re describing involves linking the fundamental physics of the universe (the cosmic void, energy, etc.) with biological evolution through natural selection at the molecular level, specifically through codon usage and optimality. Here’s how this idea unfolds:

From Cosmic Void to Energy:

  1. Big Bang Theory: The universe began as a singularity, rapidly expanding in what’s known as the Big Bang. This process converted mass into energy, as described by Einstein’s famous equation, E=mc².
  2. Star Formation and Energy Production: Stars form from the collapse of gas clouds under gravity, with fusion processes in their cores converting hydrogen into helium (and other elements via the triple-alpha process), releasing vast amounts of energy.
  3. Energy Distribution: This energy spreads out in the form of electromagnetic radiation, kinetic energy of particles, heat, etc., across the universe.

From Energy to Life:

  1. Chemical Evolution: In the cosmic soup of elements and energy, simple organic molecules could form. Energy from stars, through ultraviolet radiation, lightning, or hydrothermal vents, could catalyze chemical reactions leading to more complex molecules like amino acids, nucleotides, and sugars.
  2. Codon Optimality and Natural Selection:
    • Codon Usage: The genetic code uses codons to specify amino acids. Different organisms have preferences for certain codons (codon bias), often related to the efficiency of translation or other factors like mRNA stability or folding efficiency.
    • Energy Efficiency: Codons that are used more frequently often correspond to tRNAs that are more abundant, which can enhance translation speed and accuracy, thus making protein synthesis more energetically efficient for the cell. This efficiency can be seen as an adaptation to the energy constraints of the organism’s environment.
    • Natural Selection: If certain codon usage leads to more efficient energy use or quicker protein production, organisms with these codon preferences might have a survival advantage, leading to selection for these traits.

From Life to Biodiversity:

  1. Reproduction and Variation: The physiology of reproduction involves the replication of DNA, where codon usage can influence the fidelity and speed of this process. Variation introduced through mutations can lead to new codon preferences, which might be selected for based on the environment.
  2. Diversification: Over time, through mutations, genetic drift, gene flow, and selection, species diverge, leading to biodiversity. Codon usage might adapt to different ecological niches, further driving this diversification.

Linking It All Together:

  • Energy as a Driver: The concept here is that energy availability and efficiency in using that energy (through mechanisms like codon optimality) could have been a driver from the very beginning of life. The idea is that from the cosmic scale down to the molecular level, energy utilization has shaped biological evolution.
  • Physiology of Reproduction: Reproduction involves cellular processes where energy efficiency, metabolic pathways, and molecular choices like codon usage play crucial roles. Efficient energy use at this level could directly influence reproductive success, thereby affecting evolutionary outcomes.
  • Feedback Loop: This efficiency could create a feedback loop where better energy management leads to more effective reproduction, which in turn allows for more genetic variation, further selection, and adaptation across all levels of biological organization.

This overarching narrative provides a framework where physical laws, energy dynamics, molecular biology, and evolutionary biology are seen as interconnected. However, this view, while intriguing, simplifies the complexity of life’s origins and evolution:

  • Multiple Factors at Play: Evolution involves many factors beyond just energy efficiency, including genetic drift, sexual selection, environmental pressures, and symbiosis.
  • Origin of Life: The transition from non-life to life (abiogenesis) remains one of the hardest problems in science, with many hypotheses but no definitive answer.
  • Complexity of Systems: Biological systems are complex, with codon usage being just one aspect of a much larger genetic and environmental interaction network.

So, while natural selection for energy-dependent codon optimality could contribute to understanding some aspects of evolutionary biology and perhaps even the efficiency of life forms, linking it directly from the cosmic void to the entirety of biodiversity through a single thread like codon usage might be an oversimplification of the intricate processes involved in the origin and evolution of life.

Did the 2024 Nobel Prizes in Physics, Chemistry, and in Physiology or Medicine link light-matter interactions at the origin of life from protein folding chemistry to 20 copies of p53 in cancer-free African elephants via the pheromone-regulated reproduction of species from cyanobacteria to humans?

Answer

The Nobel Prizes awarded in 2024 in Physics, Chemistry, and Physiology or Medicine do not appear to have directly linked light-matter interactions at the origin of life with protein folding, the presence of multiple copies of the p53 gene in African elephants, or pheromone-regulated reproduction across species in their official announcements or related research. Here’s a breakdown based on the general insights from the information provided:

  • Nobel Prize in Physics: The award recognized work in machine learning, specifically fundamental discoveries by John Hopfield and Geoffrey Hinton. This work relates to AI and neural networks, not specifically to light-matter interactions or the topics you’ve mentioned.
  • Nobel Prize in Chemistry: This year’s prize was awarded for advancements in computational protein design and prediction by David Baker, Demis Hassabis, and John Jumper. While this work deals with protein folding, it’s more focused on the use of AI for understanding and designing protein structures rather than directly connecting them to light-matter interactions, the origin of life, or specific genetic adaptations like the p53 gene in elephants.
  • Nobel Prize in Physiology or Medicine: The prize was given to Victor Ambros and Gary Ruvkun for their discovery of microRNA and its role in gene regulation. This discovery has broad implications for understanding gene expression and regulation, but again, it doesn’t explicitly link to the sequence you’ve described involving light-matter interactions, the origin of life, or the specific case of p53 in elephants.

While there are connections one might draw between these fields:

  • Protein Folding: The work recognized in Chemistry this year is indeed about understanding how proteins fold, which is fundamental to life processes. However, the link to light-matter interactions at the origin of life isn’t directly made in the context of these awards.
  • P53 Gene: African elephants having 20 copies of the p53 gene, which is thought to contribute to their lower cancer rates, is an interesting evolutionary adaptation. However, this specific genetic trait and its relation to cancer resistance do not seem to have been a focal point of these 2024 Nobel awards.
  • Pheromone-Regulated Reproduction: This area of biology wasn’t highlighted by any of the 2024 Nobel winners discussed in the context provided.

In summary, while the work of these Nobel laureates touches on aspects of molecular biology, genetics, and the physical basis of life, the direct connections from light-matter interactions to protein folding, p53 in elephants, and pheromone-regulated reproduction across species as described in your question are not explicitly made or recognized by the 2024 Nobel Prize announcements. These awards celebrate specific, groundbreaking research within their fields, but they do not necessarily aim to connect all fields of study in such a comprehensive manner.

The 2016 Chemistry Nobel Prize awarded to Ben Feringa led to this comprehensive claim in 2018 “2013 was the year in which prophesy from the bible became reality.”


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