Molecular Diagnostics: What is unprotected life? (5)
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Molecular Diagnostics (April 6 and 7, 2016)
Available on demand: Molecular Medicine in Healthcare: The Personalized Medicine Initiative
Pieter Cullis answered this question at 41:50
In the context of nutritional epigenetics and Precision Medicine, do you think RNA-mediated amino acid substitutions link changes in the microRNA/messenger RNA balance from the innate immune system to healthy longevity and/or to pathology?
Pieter Cullis Pieter Cullis answered this question at 1:01
Do you think that neo-Darwinian theories, which link mutations to evolution have prevented scientific progress towards Precision Medicine?
My comment: The links from energy-dependent changes in base pairs to the microRNA/messenger RNA balance and links from the immune system and RNA-mediated amino acid substitutions to healthy longevity and / or virus-driven energy theft and pathology are clear. I asked Pieter Cullis about neo-Darwinian theories because I consistently see attempts by theorists to link physics and chemistry from mutations to natural selection and evolution. The attempts become more ridiculous each week.
See: April 8, 2016 Ribose and related sugars from ultraviolet irradiation of interstellar ice analogs
Their theory about the origin of life in outer space can now be compared to my model of energy-dependent biodiversity on Earth. See for instance: Ultraviolet Absorption Induces Hydrogen-Atom Transfer in G⋅C Watson–Crick DNA Base Pairs in Solution
Compare ultraviolet (UV) radiation and UV absorption in interstellar ice analogs to UV absorption on Earth, which links energy-dependent base pair changes and RNA-mediated protein folding chemistry to biophysically constrained life via the physiology of reproduction in all living genera. For consistency, remember to place all claims about UV radiation and UV absorption into the context of the creation of the innate immune system, which links metabolic networks to genetic networks that ensure the physiology of reproduction in all living genera.
For instance, to establish the consistency across disciplines, start in outer space and link angstroms to ecosystems as these two groups tried to do.
See for example: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system
Does UV irradiation of interstellar ice analogs link weekend evolution of the bacterial flagellum to hominid genome evolution outside the context of UV absorption and the physiology of nutrient energy-dependent reproduction on Earth?
See also: Clustered mutations in hominid genome evolution are consistent with APOBEC3G enzymatic activity
Can you explain how UV irradiation of interstellar ice analogs and clustered mutations link enzymatic activity from weekend evolution of the bacterial flagellum to hominid genome evolution. If so, your explanation could refute claims by Einstein, Schrodinger, Dobzhansky and others who have collectively linked theories and experimental evidence of biologically-based cause and effect to de novo gene creation and the creation of the innate immune system, which links metabolic networks and genetic networks to supercoiled DNA.
The experimental evidence links supercoiled DNA to protection of organized genomes from virus-driven entropy. Alternative models that link biologically-based cause and effect could be used to refute claims about the need for the anti-entropic energy of the sun, which links energy-dependent changes in base pairs to supercoiled DNA. Do you have an alternative model that explains how all organized genomes are protected from virus-driven entropy? If so, how does your model link UV radiation and UV absorption from ecological variation to nutrient-dependent pheromone-controlled ecological adaptations in species from microbes to humans?
If there is no other model for comparison to my model, neo-Darwinists have prevented the scientific progress that should have led to the Precision Medicine Initiative from the details of molecular epigenetics we included in our section on molecular epigenetics in our 1996 Hormones and Behavior review.
From Fertilization to Adult Sexual Behavior
Molecular epigenetics.
It is now understood that certain genes undergo a process called “genomic or parental imprinting.” Early in embryonic development attached methyl groups become removed from most genes. Several days later, methyl groups are reattached in appropriate sites. Fascinatingly, some such genes reestablish methylation patterns based upon whether the chromosomal segment carrying the gene came from maternal or paternal chromosomes. These sexually dimorphic patterns are labeled genomic or parental imprinting, and these imprintings are inheritable but non-genetic modifications of specific genes (Razin and Shemer, 1995; Reik, 1989; Surani, 1991; Zuccotti and Monk, 1995).
There are at least 16 known genomic-imprintings in the human genome and each particular imprint depends upon whether the chromosome is of maternal or paternal origin (Hurst, McVean, and Moore, 1996). Furthermore, these inherited imprintings are physiologically important and are capable of sex-specific effects as evidenced in the Prader-Willi and Angelman syndromes (congenital disorders with physical and mental characteristics) derived from imprinting anomalies in a specific region of chromosome 15 (Driscoll, Waters, Williams, Zori, Glenn, Avidano, and Nicholls, 1992).
Genomic-imprinting is also manifest in specific parts of the X-inactivation region’s related XIST gene. Here male- and female-specific methyl-group patterns participate in X-inactivation in females and also in the preferential inactivation of the paternal X in human placentae of female concepti (Harrison, 1989; Monk, 1995). This process indicates that tissues of the early conceptus can sense and react differentially to epigenetic sexual dimorphisms on the female conceptus’ own two X chromosomes. Furthermore, variations of X-inactivation patterns often account for traits discordance in monozygotic twin females. In other words, they are often found to have nonidentical patterns of X-inactivation, yielding differing expression of noticeable X-linked traits (Machin, 1996).
Pollard (1996) has hypothesized that sexual orientation may be encoded within imprinted genes. In a manner that also challenges the Gn–H–B paradigm she posits that genomic imprinting, as a preconception event, enables a gene to be “able to switch through different states of potential activity from the incomplete to the fully penetrant state resulting in a continuum of orientations ranging from asexual, through graded bisexual to homosexual” (p. 269). And she envisions these modifications to be potentially prompted by social environmental events.
Yet another kind of epigenetic imprinting occurs in species as diverse as yeast, Drosophila, mice, and humans and is based upon small DNA-binding proteins called “chromo domain” proteins, e.g., polycomb. These proteins affect chromatin structure, often in telomeric regions, and thereby affect transcription and silencing of various genes (Saunders, Chue, Goebl, Craig, Clark, Powers, Eissenberg, Elgin, Rothfield, and Earnshaw, 1993; Singh, Miller, Pearce, Kothary, Burton, Paro, James, and Gaunt, 1991; Trofatter, Long, Murrell, Stotler, Gusella, and Buckler, 1995). Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans (Adler and Hajduk, 1994; de Bono, Zarkower, and Hodgkin, 1995; Ge, Zuo, and Manley, 1991; Green, 1991; Parkhurst and Meneely, 1994; Wilkins, 1995; Wolfner, 1988). That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.
A potential ramification of epigenetic imprinting and alternative splicing may be occurring in Xq28, a chromosomal region implicated in homosexual orientation (Brook, 1993; Hu, Pattatucci, Patterson, Li, Fulker, Cherny, Kruglyak, and Hamer, 1995; Turner, 1995). Xq28 contains one of the X chromosome’s two pseudoautosomal regions (PARs), adjoins the telomere, and has various means of gene expression control (D’Esposito, Ciccodicola, Gianfrancesco, Esposito, Flagiello, Mazzarella, Schiessinger, and D’Urso (1996). Xq28, therefore, is a chromosomal region that has many of the heterochromatic and telomeric characteristics that participate in sexual determination and behavior in other species.
—————-
See also, our introduction to RNA-mediated cell type differentiation in the context of the nutrient-dependent pheromone-controlled “conditions of life,” which Darwin placed before natural selection in the context of important considerations for any additional theories.
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Stress-perturbed mitochondrial dysfunction (2)
5 MIN READ
0
Behavioral Immune System model
4 MIN READ
0
Let there be anti-entropic light (3)
6 MIN READ
0
Theorists can’t understand biology
6 MIN READ
0
Neuroplasticity
4 MIN READ
0
Too complex for the Complex Biological Systems Alliance
4 MIN READ
0
Virus, transposon and plasmid evolution
< 1 MIN READ
0
RNA central and RNA-mediated.com
6 MIN READ
0
Skip the politics; embrace the facts
5 MIN READ
0
Human pheromone deniers: What’s next?
5 MIN READ
0
Mystery machine vs model (2)
2 MIN READ
0
Xist-ing on planet Earth
2 MIN READ
0
Preventing genomic entropy
4 MIN READ
0
Supercoiled DNA constrains virus-driven genomic entropy
2 MIN READ
0
Let there be anti-entropic light (2)
4 MIN READ
0
Mechanisms of stress: from genes to cancer
9 MIN READ
0
Theorists have not seen the light
4 MIN READ
0
A 5-10K comparison of design principles to evolution
3 MIN READ
0
Alternative pre-mRNA splicing and ecological adaptation
7 MIN READ
0
Multi-omic analysis features (SNPs, miRNA)
3 MIN READ
0
Somatic hypermutation vs RNA-mediated events
2 MIN READ
0
New anti-entropic microbes
3 MIN READ
0
Genome sequencing, cadherins, and quantum consciousness
6 MIN READ
0
“New” quantum biology. Pirating the old
3 MIN READ
0
Cell types, SNVs, CNVs, and chromosomes
3 MIN READ
0
RNA-mediated permanent symbioses
11 MIN READ
0
Is life the balance between quantum and classical physics?
3 MIN READ
0
Anti-entropic containment of energy: symbiosis 1.0
5 MIN READ
0
The “great filter” is an epigenetic trap
4 MIN READ
0
Atomic-resolution of cell type signaling
4 MIN READ
0
Information and communication
2 MIN READ
0
Ecology replaces the extended evolutionary synthesis
4 MIN READ
0
The stability of organized genomes (3)
3 MIN READ
0
Viruses, amino acids, and somatic cell types (3)
9 MIN READ
0
Viruses, amino acids, and somatic cell types (2)
5 MIN READ
0
Becoming biologically informed (3)
3 MIN READ
0
Easy editing: Reinventing our RNA world
3 MIN READ
0
Riding the wrong direction
3 MIN READ
0
RNA-mediated gene duplication, fixation, and ecological adaptation
6 MIN READ
0
MicroRNA – controlled ecological adaptations
5 MIN READ
0
“New” epigenetic mechanism for lifelong learning?
3 MIN READ
0
Iron, ferritin, thyroxine
2 MIN READ
0
RNA-mediated development
2 MIN READ
0
Alternative splicings: epigenetics meets pharmacogenomics
4 MIN READ
0
Epigenetic regulation of aging by glycine and GnRH
5 MIN READ
0
Pattern recognition: biogeochemical structure and function
5 MIN READ
0
Informing the biologically uninformed
< 1 MIN READ
0
Batch effect vs epigenetic effects
3 MIN READ
0
Vitamin B3 and DNA repair
4 MIN READ
0
Bees and primates automagically evolve
3 MIN READ
0
Ignoring systems complexity (it’s too complicated)
3 MIN READ
0
Five years of Ferguson
2 MIN READ
0
Virus-driven cancer treatment and prevention
2 MIN READ
0
A special issue on nutritional epigenetics
5 MIN READ
0
Retinoic acid + one receptor regulate the genome
3 MIN READ
0
Epigenetics: microRNAs effect an integrative pathway
4 MIN READ
0
Protein isoforms do not evolve
3 MIN READ
0
From gut bacteria to breast milk and back
5 MIN READ
0
Chance mutations — not natural selection
5 MIN READ
0
Viruses in gut microbes
4 MIN READ
0
MicroRNAs and the exposome
5 MIN READ
0
Thermodynamics and protein folding landscapes
2 MIN READ
0
Feedback loops link insects to human brains
2 MIN READ
0
Mutisensory integration: watching the paradigm shift
12 MIN READ
0
Nutrient-dependent microRNAs control cell types
6 MIN READ
0
Life: conserved ion and amino acid transporters
3 MIN READ
0
Too many targets for theories
3 MIN READ
0
Creating nothing but a theory
4 MIN READ
0
Epigenetic switch links MicroRNAs to RNA-protein interactions
4 MIN READ
0
Questions about life’s diversity
21 MIN READ
0
Virus-driven origin of life
2 MIN READ
0
Luis P. Villarreal tells it like it is
3 MIN READ
0
RNA-directed gene choice
5 MIN READ
0
What about birds?
5 MIN READ
0
Implicating microRNAs in cancer
2 MIN READ
0
RNA-mediated repurposing in microbes and adaptations in primate brains
2 MIN READ
0
Imagining that data historically supports evolutionary theory
7 MIN READ
0
What if Darwin was not still dead?
2 MIN READ
0
How fast can evolutionary theory be changed?
5 MIN READ
0
Quantum Superpositions: let there be light
4 MIN READ
0
Quantum entanglement, mass, and biomass
4 MIN READ
0
Constrained evolution is ecological adaptation
5 MIN READ
0
A single amino acid substitution differentiates cell types of E. coli
3 MIN READ
0
Models by evolutionary biologists are not models
2 MIN READ
0
Jumping back: Science or Pseudoscience? (2)
2 MIN READ
0
Jumping back: Science or Pseudoscience?
6 MIN READ
0
The key to science: experimental evidence
5 MIN READ
0
Intelligent viruses and cancers?
10 MIN READ
0
We need pattern recognition, not proclamations
3 MIN READ
0
From deep time into real time: What evolutionary processes?
10 MIN READ
0
It’s cell type differention, not cell fate determination (2)
3 MIN READ
0
Evolutionary theorists justify fear of the Ebola viruses
2 MIN READ
0
RNA-mediated genetic engineering (Part 3)
< 1 MIN READ
0
RNA-mediated genetic engineering (Part 2)
3 MIN READ
0
Physics, Chemistry, and Molecular biology (PCMb)
2 MIN READ
0
RNA-directed DNA methylation and RNA-mediated events
5 MIN READ
1
Seemingly futile cycles are not thermodynamically futile
3 MIN READ
0
Probable changes in connectivity
2 MIN READ
0
Can epigenetic inheritance occur without concurrent changes in morphology AND behavior?
3 MIN READ
0
A molecular visualizer of worthwhile molecular biology
2 MIN READ
0
RNA-mediated ecological adaptation is not evolution
2 MIN READ
0
Insect homology and diversity attributed to mutations
2 MIN READ
0
Cell-type differentiation
2 MIN READ
0
