Epigenetic facts vs variable recombination theories
(click to enlarge)
6/14/13 Nutrient-dependent/pheromone-controlled adaptive evolution: a model
….the model represented here is consistent with what is known about the epigenetic effects of ecologically important nutrients and pheromones on the adaptively evolved behavior of species from microbes to man. Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific ‘fit’.
7/25/13
Jay R. Feierman: Variation is not nutrient availability and the something that is doing the selecting is not the individual organism. A feature of an educated person is to realize what they do not know. Sadly, you don’t know that you have an incorrect understanding [of] Darwinian biological evolution.
7/26/13
Jay R. Feierman: I am absolutely certain that if you showed this statement to any professor of biology or genetics in any accredited university anywhere in the world that 100% of them would say that “Random mutations are the substrate upon which directional natural selection acts” is a correct and true statement.
Facts:
Epigenetic modifications poster
DNA repair pathways poster
Epigenetic Dynamics in Stem Cells and Differentiation webinar
Epigenetic Editing: Permanently Modulate Gene Expression webinar
Histone modifications: a guide
Epigenetic Mechanisms in Early Mammalian Development webinar
DNA Methylation Changes During Cell Differentiation webinar
Chromatin: from nucleosomes to chromosomes
Epigenetics round-up of 2014
Changes in histone acetylation may aid memory reconsolidation in post-traumatic stress disorder
See also: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems (2014)
This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man. Species diversity is a biologically-based nutrient-dependent morphological fact and species-specific pheromones control the physiology of reproduction. The reciprocal relationships of species-typical nutrient-dependent morphological and behavioral diversity are enabled by pheromone-controlled reproduction. Ecological variations and biophysically constrained natural selection of nutrients cause the behaviors that enable ecological adaptations. Species diversity is ecologically validated proof-of-concept. Ideas from population genetics, which exclude ecological factors, are integrated with an experimental evidence-based approach that establishes what is currently known. This is known: Olfactory/pheromonal input links food odors and social odors from the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man during their development.
Theme issue ‘Evolutionary causes and consequences of recombination rate variation in sexual organisms’ (2017)
Recombination rate variation in sexual organisms is energy-dependent and RNA-mediated. Variation is biophysically constrained by the pheromone-controlled physiology of reproduction in species from microbes to humans. See: From Fertilization to Adult Sexual Behavior (1996)
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.
Theories:
Review article: Variation in recombination frequency and distribution across eukaryotes: patterns and processes
Jessica Stapley, Philine G. D. Feulner, Susan E. Johnston, Anna W. Santure and Carole M. Smadja
Phil. Trans. R. Soc. B December 19, 2017 372 20160455; doi:10.1098/rstb.2016.0455
https://rstb.royalsocietypublishing.org/content/372/1736/20160455
Review article: The impact of recombination on human mutation load and disease
Isabel Alves, Armande Ang Houle, Julie G. Hussin and Philip Awadalla
Phil. Trans. R. Soc. B December 19, 2017 372 20160465; doi:10.1098/rstb.2016.0465
https://rstb.royalsocietypublishing.org/content/372/1736/20160465
Opinion piece: Connecting theory and data to understand recombination rate evolution
Amy L. Dapper and Bret A. Payseur
Phil. Trans. R. Soc. B December 19, 2017 372 20160469; doi:10.1098/rstb.2016.0469
https://rstb.royalsocietypublishing.org/content/372/1736/20160469
Review article: Coevolution between transposable elements and recombination
Tyler V. Kent, Jasmina Uzunović and Stephen I. Wright
Phil. Trans. R. Soc. B December 19, 2017 372 20160458; doi:10.1098/rstb.2016.0458
https://rstb.royalsocietypublishing.org/content/372/1736/20160458
Review article: Evolution of recombination rates between sex chromosomes
Deborah Charlesworth
Phil. Trans. R. Soc. B December 19, 2017 372 20160456; doi:10.1098/rstb.2016.0456
https://rstb.royalsocietypublishing.org/content/372/1736/20160456
Research article: Low recombination rates in sexual species and sex–asex transitions
Christoph R. Haag, Loukas Theodosiou, Roula Zahab and Thomas Lenormand
Phil. Trans. R. Soc. B December 19, 2017 372 20160461; doi:10.1098/rstb.2016.0461
https://rstb.royalsocietypublishing.org/content/372/1736/20160461
(openaccess) Review article: The consequences of sequence erosion in the evolution of recombination hotspots
Irene Tiemann-Boege, Theresa Schwarz, Yasmin Striedner and Angelika Heissl
Phil. Trans. R. Soc. B December 19, 2017 372 20160462; doi:10.1098/rstb.2016.0462
https://rstb.royalsocietypublishing.org/content/372/1736/20160462
(openaccess) Research article: The Red Queen model of recombination hot-spot evolution: a theoretical investigation
Thibault Latrille, Laurent Duret and Nicolas Lartillot
Phil. Trans. R. Soc. B December 19, 2017 372 20160463; doi:10.1098/rstb.2016.0463
https://rstb.royalsocietypublishing.org/content/372/1736/20160463
(openaccess) Research article: Background selection as null hypothesis in population genomics: insights and challenges from Drosophila studies
Josep M. Comeron
Phil. Trans. R. Soc. B December 19, 2017 372 20160471; doi:10.1098/rstb.2016.0471
https://rstb.royalsocietypublishing.org/content/372/1736/20160471
(openaccess) Review article: Recombination rate plasticity: revealing mechanisms by design
Laurie S. Stevison, Stephen Sefick, Chase Rushton and Rita M. Graze
Phil. Trans. R. Soc. B December 19, 2017 372 20160459; doi:10.1098/rstb.2016.0459
https://rstb.royalsocietypublishing.org/content/372/1736/20160459
(openaccess) Review article: Are the effects of elevated temperature on meiotic recombination and thermotolerance linked via the axis and synaptonemal complex?
Christopher H. Morgan, Huakun Zhang and Kirsten Bomblies
Phil. Trans. R. Soc. B December 19, 2017 372 20160470; doi:10.1098/rstb.2016.0470
https://rstb.royalsocietypublishing.org/content/372/1736/20160470
Research article: What drives the evolution of condition-dependent recombination in diploids? Some insights from simulation modelling
Sviatoslav R. Rybnikov, Zeev M. Frenkel and Abraham B. Korol
Phil. Trans. R. Soc. B December 19, 2017 372 20160460; doi:10.1098/rstb.2016.0460
https://rstb.royalsocietypublishing.org/content/372/1736/20160460
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RNA-mediated development
2 MIN READ
0
Healthy mutants
2 MIN READ
0
Uniquely epigenomic gene regulation
2 MIN READ
0
Rejecting pseudoscientific nonsense
6 MIN READ
1
Ignoring top-down causation
2 MIN READ
0
microRNAs, glycosylation, and genomes
4 MIN READ
0
DNA organization, structure, and function
7 MIN READ
0
Alternative splicings: epigenetics meets pharmacogenomics
4 MIN READ
0
Epigenetic regulation of aging by glycine and GnRH
5 MIN READ
0
Viruses and the human-like microbiome
3 MIN READ
0
Informing the biologically uninformed
< 1 MIN READ
0
Tweaking the story to fit the theory
5 MIN READ
0
I forgot. How do mutations cause evolution?
4 MIN READ
0
One amino acid substitution, genes, and brain activity
3 MIN READ
0
Batch effect vs epigenetic effects
3 MIN READ
0
Bee-birthed epigenetics and primate cell types
5 MIN READ
0
Scientists lose. A sci-fi author gains credibility
2 MIN READ
0
Vitamin B3 and DNA repair
4 MIN READ
0
Ignoring systems complexity (it’s too complicated)
3 MIN READ
0
Virus-driven cancer treatment and prevention
2 MIN READ
0
The microbiome, pharmacogenetics, and privacy
< 1 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
Tissue type variation and expression of genes
< 1 MIN READ
0
Chance mutations — not natural selection
5 MIN READ
0
Viruses in gut microbes
4 MIN READ
0
How to find a “holy grail” under your nose
3 MIN READ
0
Tet3 regulation of nutrient-dependent cell type differentiation
4 MIN READ
0
Pathology constrains X-linked evolution
2 MIN READ
0
DNA Methylation and organized genomes (2)
10 MIN READ
0
DNA Methylation and organized genomes
7 MIN READ
0
Genetic chimerism and ecological adaptation
4 MIN READ
0
A genetic variant refutes neo-Darwinism
6 MIN READ
0
MicroRNAs and memory
< 1 MIN READ
0
Methylation maintains cell type differences (2)
2 MIN READ
0
Methylation maintains cell type differences
3 MIN READ
0
Creating nothing but a theory (2)
4 MIN READ
0
Creating nothing but a theory
4 MIN READ
0
Viruses and ecologically adapted animals
2 MIN READ
0
The quantum / classical RNA-mediated ‘tipping point’
3 MIN READ
0
Epigenetic effects of soil bacteria on plants
< 1 MIN READ
0
Epigenetic switch links MicroRNAs to RNA-protein interactions
4 MIN READ
0
Quantum correlations/pseudoscience
3 MIN READ
0
Correctly modeling ecological adaptation
4 MIN READ
0
Behavior (4): All responses are RNA-mediated in birds
4 MIN READ
0
Questions about life’s diversity
21 MIN READ
0
UV-light mutations and gene loss (not gain)
5 MIN READ
0
RNA-directed gene choice
5 MIN READ
0
Epigenetics Skeptism
5 MIN READ
0
Assembling yourself: Molecular self / other recognition
4 MIN READ
0
What about birds?
5 MIN READ
0
RNA directed DNA methylation and cell types
4 MIN READ
0
Implicating microRNAs in cancer
2 MIN READ
0
Reverse phosphorylation
7 MIN READ
0
RNA-mediated repurposing in microbes and adaptations in primate brains
2 MIN READ
0
From 3-D to epigenetically-effected 4-D genome make-up
5 MIN READ
0
Let there be anti-entropic light (1)
11 MIN READ
0
An epigenetic trap (the prequel)
5 MIN READ
0
Imagining that data historically supports evolutionary theory
7 MIN READ
0
Atheism: Arrogant, useless, and divisive ignorance
7 MIN READ
0
The anti-entropic force of "Nature"
2 MIN READ
0
Nutritional epigenetics, exercise, and immune system integrity
4 MIN READ
0
Military combat training to fight disease
3 MIN READ
0
Atoms to ecosystems is not almost a molecular ecology
3 MIN READ
0
RNA-mediated epigenetic modification via DNA-methylation
4 MIN READ
0
The biologically-based origin of the mammalian placenta (2)
6 MIN READ
0
Sneaking up from behind
4 MIN READ
0
An epigenetic trap (the sequel)
10 MIN READ
0
Environment epigenetically shapes the immune system
3 MIN READ
0
Beneficial microbes kill beneficial mutations
4 MIN READ
0
A single amino acid substitution differentiates cell types of E. coli
3 MIN READ
0
Unconstrained evolutionary innovability
4 MIN READ
0
Mutagenesis: Replacing facts with theories
5 MIN READ
0
ISHE's human ethology group
2 MIN READ
0
Amino acid homeostasis for a Happy New Year!
6 MIN READ
0
From Hydra to humans vs a Lakatosian research program
4 MIN READ
0
Unified nutritional and molecular mechanisms
9 MIN READ
0
Communication, not mutations
2 MIN READ
0
Models by evolutionary biologists are not models
2 MIN READ
0
The future of physics predicts no future for evolutionary theory
3 MIN READ
0
Chemical ecology and RNA-mediated control of DNA loops
< 1 MIN READ
0
Atoms to ecosystems: Evolutionary theory vs the coelacanth
6 MIN READ
0
Jumping back: Science or Pseudoscience? (2)
2 MIN READ
0
Single-cell level assay of protein biosynthesis and degradation
2 MIN READ
0
Glycine and GnRH: Am I being pedantic?
4 MIN READ
0
Extensive molecular evidence vs ridiculous theories
2 MIN READ
0
Meaningful dialogue, anonymous fools and idiot minions
4 MIN READ
0
Epigenetic pharmacology and RNA-mediated transciptional landscapes
3 MIN READ
0
Sackler Colloquium: Effects or AFFECTS on Behavior
2 MIN READ
0
Thermodynamic constraints and ecological adaptations sans evolution
6 MIN READ
0
Eliminating correlations from evolutionary ecology
6 MIN READ
0
RNA-mediated species specificity
2 MIN READ
0
Ecological adaptations reported as evolution in insects and mammals
4 MIN READ
0
There’s a model for that!
5 MIN READ
0
Biologists puzzled by evolved RNAs and decaying DNA
6 MIN READ
0
SNPs and millions of small variations in the human genome
3 MIN READ
0
More than a bag of chemicals?
2 MIN READ
0
Achiral GnRH: no prophesy, just prediction
9 MIN READ
0
Nothing new under the sun, except pseudoscientific nonsense
6 MIN READ
0
Intelligent viruses and cancers?
10 MIN READ
0
De novo DNA methylation?
3 MIN READ
0
RNA eclipses the importance of DNA to cell type differentiation
4 MIN READ
0
We need pattern recognition, not a prologue
6 MIN READ
0
Pharmacogenomics
3 MIN READ
0
A model of MHC 'evolution'
2 MIN READ
0
From deep time into real time: What evolutionary processes?
10 MIN READ
0
In theory, or supported by experimental evidence?
5 MIN READ
0
It’s cell type differention, not cell fate determination (2)
3 MIN READ
0
Are evolutionary theorists 'nob ends'?
5 MIN READ
2
ALPHA GENOMIX
7 MIN READ
2
No excuses: Creation and the meaning of organismal complexity
7 MIN READ
0
Nutrient-dependent gene duplication in plants (but not animals?)
4 MIN READ
0
Evolutionary theorists and evolutionary theists live under rocks
< 1 MIN READ
0
No understanding of biodiversity
2 MIN READ
0
Eliminating evolutionary theory
3 MIN READ
0
Behavioral ecology: please continue to believe in our fantasies
3 MIN READ
0
2014 and 2004 Nobel Prize in Medicine
3 MIN READ
0
How much good can be attributed to social science theories?
< 1 MIN READ
0
RNA-mediated genetic engineering (Part 3)
< 1 MIN READ
0
RNA-mediated events are not a matter of faith
2 MIN READ
0
Color vision refutes the evolutionary dogma of gene duplication
4 MIN READ
0
RNA-mediated cell type differentiation and behavior
3 MIN READ
0
Different physical locations and different molecular mechanisms of health and disease
2 MIN READ
0
Metabolism, fixation, health or neurodegerative disorder
2 MIN READ
0
Physics denied; pseudoscientific nonsense accepted
2 MIN READ
0
Epigenetically-effected metabolic shifts and ecological adaptations
3 MIN READ
0
Evolving DNA before RNA
4 MIN READ
0
Stop evolutionary theorists. Kill cancers
3 MIN READ
0
De novo gene Creation sans evolution of genes via mutations
4 MIN READ
0
Seemingly futile cycles are not thermodynamically futile
3 MIN READ
0
Probable changes in connectivity
2 MIN READ
0
Genotype, observed phenotype, and distinctly disordered behaviors
3 MIN READ
0
Is the problem an internet echo or Feierman's ethics?
2 MIN READ
0
RNA-mediated ecological adaptation is not evolution
2 MIN READ
0
Drunks and Monkeys: Pseudoscientific nonsense
2 MIN READ
0
Behavior is receptor-mediated
10 MIN READ
0
Nutrition, pheromones and cancer (2)
2 MIN READ
0
Darwinian theories vs Darwin's facts
2 MIN READ
0
Jay R. Feierman
3 MIN READ
0
Pheromone-controlled thermodynamics and cancer
2 MIN READ
0
Evolution: innovations may have non-adaptive origins (sans mutations)
2 MIN READ
0
Pheromones and cancer
4 MIN READ
0
A flawed model: no tripartate synapse in the adult brain
3 MIN READ
0
Comparative, developmental, neurobehavioral, sexual dimorphisms
< 1 MIN READ
0
Thinking about what we know (or not)
2 MIN READ
0
Epigenetic effects on chromatin and regulatation of gene expression (in Archaea?)
2 MIN READ
0
CB Nemeroff: Off Restriction
< 1 MIN READ
0
Pheromones and a realistic model of sexual differentiation
3 MIN READ
0
