Atoms to ecosystems is not almost a molecular ecology
In Kohl (2012) I wrote:
Among different bacterial species existing in similar environments, DNA uptake (Palchevskiy & Finkel, 2009) appears to have epigenetically ‘fed’ interspecies methylation and speciation via conjugation (Fall et al., 2007; Finkel & Kolter, 2001; Friso & Choi, 2002). This indicates that reproduction began with an active nutrient uptake mechanism in heterospecifics and that the mechanism evolved to become symbiogenesis in the conspecifics of asexual organisms (Margulis, 1998).
Now Elizabeth Howell, Astrobiology Magazine Date: asks
Excerpt: “…you have almost a molecular ecology,” Fellermann said. “Every species and strand, they service each other’s reactants and products and catalysts.”
My comment: I have since added more details about how symbiogenesis how every species interacts. I’ve placed the details into the context of the molecular ecology in an invited review of nutritional epigenetics. The review is based on the molecular epigenetics section in our 1996 Hormones and Behavior review and other published works.
See: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
Abstract: “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.”
Claims that we “almost have a molecular ecology” have been repeatedly replaced by a model of the biophysically constrained chemistry of protein folding that links RNA-mediated amino acid substitutions to cell type differentiation in all cells of all individuals of all species. No one claims that the model is an inaccurate representation of biologically-based cause and effect, although biologically uninformed researchers have asked me to include some pseudoscientific nonsense that fits into the context of their ridiculous theories.
Instead, I build from examples of biologically-based cause and effect. The examples link nutrient-dependent amino acid substitutions, which are are fixed in the DNA of organized genomes via the physiology of reproduction. Other examples were included in Nutrient-dependent/pheromone-controlled adaptive evolution: a model
In the past 1.5 years there have been many more examples of amino acid substitutions that differentiate cell types via interactions between viral microRNAs and the nutrient-dependent pheromone-controlled microRNA/messenger RNA balance. The finely-tuned balance obviously links thermodynamic cycles of nutrient-dependent protein biosynthesis and degradation to cell type differentiation in species from microbes to man via their pheromone-controlled physiology of reproduction.
A recent report links light-induced amino acid substitutions from plants to unicelluar algae and to a multicellular sea slug. FISH Labeling Reveals a Horizontally Transferred Algal (Vaucheria litorea) Nuclear Gene on a Sea Slug (Elysia chlorotica) Chromosome
That makes it easier to link microRNAs from crustaceans to insects via the conserved molecular mechanisms we detailed in 1996 that linked insects to mammals, including primates. Dobzhansky (1973) also linked amino acid substitutions to cell type differentiation. “…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.”
The conserved molecular mechanisms of RNA-directed DNA methylation and RNA-mediated amino acid substitutions that differentiate cell types are now perfectly clear to anyone who has not continued to ignore what Dobzhansky knew 50 years ago. In “Biology, molecular and organismic” he wrote: “the only worthwhile biology is molecular biology. All else is “bird watching” or “butterfly collecting.” Bird watching and butterfly collecting are occupations manifestly unworthy of serious scientists!”