Why skin cells are skin cells and not neurons

Excerpt: “…we’re using this approach to identify how the epigenome changes when plants are exposed to challenging environmental conditions, such as drought or high temperature, and how these changes might prime the plants for greater tolerance of subsequent exposures.”

My comment: The ‘approach’ is DNA methylation at a time when RNA sequencing has since revealed how the epigenetic landscape becomes the physical landscape of DNA in the organized genomes of species from microbes to man. Simply put, nutrient-dependent RNA-mediated events alter genetic networks and metabolic networks, which is how changes in the microRNA/messenger RNA balance are linked from thermodynamic cycles of protein biosynthesis and degradation to cell type differentiation and biodiversity during the life history transitions of all species.

For comparison, no evolutionary events have been described that link mutations and/or natural selection to the evolution of biodiversity via the biophysically-constrained chemistry of protein folding. Instead, nutrient stress and social stress cause perturbed thermodynamic cycles, which lead from mutations to diseases and disorders. Pathology does not lead to increasing organismal complexity via ecological speciation, which is the only speciation that occurs in all genera.

Clearly, drought may prime plants for greater tolerance to subsequent ecological variation via nutrient-dependent amino acid substitutions that stabilize the genome. Plant species and animal species that are not primed by their natural genetic engineering to diversify become extinct. The same molecular mechanisms that enable this priming are obviously conserved from their origins in microbes.  The molecular biology of cell type differentiation does not change when examined in different species. However, it must be examined in the context of RNA-mediated events before the similarities can be used to explain the difference between theories about evolution and facts about how ecological variation leads to ecological adaptations in microbes and other primates. For example, “…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.” (Dobzhansky, 1973)

See also: From Fertilization to Adult Sexual Behavior ” 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.”

Ecological speciation is not just about sex differences in cell types. Experimental evidence of biologically-based cause and effect has since revealed that all cell type differences arise in the context of alternative splicing techniques of pre-mRNA.  See for details: Alternative RNA Splicing in Evolution. .”…alternative splicing may be the critical source of evolutionary changes differentiating primates and humans from other creatures such as worms and flies with a similar number of genes.”

In the question and answer portion of this video, Ryan Lister predicts that the importance of RNA sequencing will overshadow what has been learned from DNA sequencing.

For insight on links from physics and chemistry to the molecular biology of RNA-mediated cell type differentiation, see also:

Additional resources for refutation of ridiculous theories about mutations and evolution:

Global Epigenomic Reconfiguration During Mammalian Brain Development

There’s a model for that!

Nutrient-dependent/pheromone-controlled adaptive evolution: a model

Without acknowledging the model, except indirectly by including many of the same works I have reference in my published works, we now see that Ryan Lister has co-authored:

Epigenomics and the control of fate, form and function in social insects

Excerpt: “De novo DNA methylation is critical for developmental divergence of female larvae towards the honeybee worker caste and is progressive [49,51]. Additionally transition between behavioural castes is associated with changes in DNA methylation and histone modifications [21,40]. However, the precise mechanisms linking the epigenome to control of gene expression, and in particular alternative splicing are not yet understood. In addition, the role of miRNAs and epigenome-modifying compounds such as 10HDA in royal jelly raises the possibility that nutrition may have a significant and direct role in directing patterns of epigenomic control during developmental caste determination. Unlocking these processes will not be without challenges, however the honeybee provides a powerful and tractable model for such studies.

My comment: For a broader-based overview of how the model links invertebrates to vertebrates via the conserved molecular mechanisms of cell type differentiation, see:

Epigenomics and the concept of degeneracy in biological systems

Excerpt: “The emerging view is that a proper choice of splicing events is regulated by a coordinated action of many components including RNA polymerase II, ribonucleoprotein particles, hundreds of auxiliary proteins, chromatin factors, DNA methylation and histone modifications [46,52]. Elaborate manners of regulation, such as interacting DNA-methylation and histone modification systems, are likely to be the hallmarks of the epigenetic code. The combinatorial utilization of flexible epigenomic modifications, together with gene splicing, post-translation protein modification and RNA editing has ample potential to generate functional diversity from a fixed genotype (Figure 1). In contrast to only 64 codon combinations in the genetic code, the number of possible ‘ciphers’ in the epigenetic code or the level of degeneracy could be many orders of magnitude higher [53]. This high level of degeneracy provides virtually unlimited coding potential to ensure both developmental buffering and flexibility to deal with random external factors.”

See also:

Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors

Excerpt: “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, and diseases of the X chromosome (Honeybee Genome Sequencing Consortium, 2006). Included among these different aspects of eusocial species survival are learning and memory, as well as conditioned responses to sensory stimuli (Maleszka, 2008; Menzel, 1983).”

My comment: For a teaser on what is coming next in the context of links from the epigenetic landscape to RNA-directed DNA methylation and RNA-mediated events that differentiate all cell types of all individuals of all species, see:

‘Treasure in saliva’ may reveal deadly diseases early enough to treat them

Excerpt: “RNA, widely known as a cellular messenger that makes proteins and carries out DNA’s instructions to other parts of the cell, is now understood to perform sophisticated chemical reactions and is believed to perform an extraordinary number of other functions, at least some of which are unknown.”

My comment: The known functions of RNA in RNA-mediated cell type differentiation via amino acid substitutions have been detailed in blog posts here. They can be found by searching for the term:

RNA-mediated