Batch effect vs epigenetic effects

By: James V. Kohl | Published on: May 20, 2015

A reanalysis of mouse ENCODE comparative gene expression data

[awaiting peer review] was reported as:

Batch Effect Behind Species-Specific Results?


genes in the mouse heart were expressed in a pattern more similar to that of other mouse tissues, such as the brain or liver, than the human heart.

My comment: If that was an accurate representation of biologically-based cause and effect, it could not be supported by what is currently known about the biophysically constrained chemistry of nutrient-depenent pheromone-controlled cell type differentiation during the life history transitions of all invertebrates and vertebrates.
The transitions are nutrient-dependent, which explains the similarities in tissue type differentiation across species.
RNA-directed DNA methylation links nutrient-dependent RNA-mediated amino acid subtitutions to biodiversity via the fixation of the substitutions in the context of the physiology of reproduction. An accurate representation of biologically-based cause and effect links Gilad (2003) et al.,  Natural Selection on the Olfactory Receptor Gene Family in Humans and Chimpanzees to Dobzhansky (1973) via this claim: “…the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla” (p. 127).
Amino acid substitutions differentiate the cell types of all cells in individuals in all genera. That may explain why others who are currently comparing the 1973 claim and 2003 claim also have challenged what appear to be misrepresentations of biologically-based cause and effect. The misrepresentations have been framed in the context of ridiculous theories.
Simply put, others are Combating Evolution to Fight Disease rather than accepting the claim that “…genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world.” (p. 199). —  Mutation-Driven Evolution
Natural selection of food is one of two ‘conditions of life’ that Darwin tried to get others to consider before Hugo de Vries definition of mutation led population geneticists to insist on ignoring Darwin’s other ‘condition of life.’ Instead of linking biodiversity to the nutrient-dependent pheromone-controlled RNA-mediated  physiology of reproduction that links metabolic networks to genetic networks in species from microbes to man, evolutionary theorists continue to place biodiversity into the context of perturbed protein folding.
Serious scientists owe a great deal to Yoav Gilad and others who are not afraid to address the inconsistencies of theory in the context of facts. It will be interesting to see if the inconsistencies of evolutionary theory lead to healthy discussion of RNA-mediated events, since they obviously link the epigenetic landscape to the physical landscape of DNA via metabolic networks and genetic networks.
See for an example of what has been attributed to a single amino acid substitution: Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults
See also: A survey of human brain transcriptome diversity at the single cell level
Concluding paragraph:

The work presented here demonstrates the applicability of single cell RNAseq to the analysis of cellular heterogeneity of the brain, one of the most complex tissues of the human body. These results lay the groundwork for the construction of a cellular map of the human brain that can be completed through the analysis of a larger number of cells from different anatomical regions of the brain. Such a map will help us identify specific markers for neuronal, glial, and vascular subtypes that we can link with information on location, connectivity, and electrophysiological properties in an attempt to fully elucidate the cellular complexity of the human brain.

The work they presented links the Val158Met amino acid substitution to the honeybee model organism of RNA-directed DNA methylation and RNA-mediated amino acid substitutions that determine the cell types of all cells in all individuals of all species.
See: Nutrient-dependent/pheromone-controlled adaptive evolution: a model.

The honeybee already serves as a model organism for studying human immunity, disease resistance, allergic reaction, circadian rhythms, antibiotic resistance, the development of the brain and behavior, mental health, longevity, diseases of the X chromosome, learning and memory, as well as conditioned responses to sensory stimuli (Kohl, 2012).

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