Physicochemical Foundations of Life that Direct Evolution: Chance and Natural Selection are not Evolutionary Driving Forces

Abstract

The current framework of evolutionary theory postulates that evolution relies on random mutations generating a diversity of phenotypes on which natural selection acts. This framework was established using a top-down approach as it originated from Darwinism, which is based on observations made of complex multicellular organisms and, then, modified to fit a DNA-centric view. In this article, it is argued that based on a bottom-up approach starting from the physicochemical properties of nucleic and amino acid polymers, we should reject the facts that (i) natural selection plays a dominant role in evolution and (ii) the probability of mutations is independent of the generated phenotype. It is shown that the adaptation of a phenotype to an environment does not correspond to organism fitness, but rather corresponds to maintaining the genome stability and integrity. In a stable environment, the phenotype maintains the stability of its originating genome and both (genome and phenotype) are reproduced identically. In an unstable environment (i.e., corresponding to variations in physicochemical parameters above a physiological range), the phenotype no longer maintains the stability of its originating genome, but instead influences its variations. Indeed, environment- and cellular-dependent physicochemical parameters define the probability of mutations in terms of frequency, nature, and location in a genome. Evolution is non-deterministic because it relies on probabilistic physicochemical rules, and evolution is driven by a bidirectional interplay between genome and phenotype in which the phenotype ensures the stability of its originating genome in a cellular and environmental physicochemical parameter-depending manner.

Non-Random Genome Editing and Natural Cellular Engineering in Cognition-Based Evolution

“…In opposition to the random genetic narrative, Auboeuf asserts that the prevailing gene-centric ‘top-down’ framework that originated in early Darwinism was premised on biased observations made on complex multicellular organisms. In contrast, Auboeuf argues that an alternative ‘bottom-up’ approach better fits the physicochemical properties of nucleic and amino acid polymers [ 180 ]. In that frame, the actual objective of selective fitness is meant to sustain a “bidirectional interplay between genome and phenotype that is directed towards genomic self-integrity” [ 180 ] (p. 1).…”

Origin of Life: The Point of No Return

“…The mechanism of Darwinian evolution is the key to understanding the initial complex that triggers the origin of life. Darwinian evolution is a well understood phenomenon in terms of genetic variations, natural selection, heredity, and mathematical modeling, as has been shown many times [6][7][8][9][10][11][12][13]. The task here is to define the minimum number of components working on the molecular level necessary for selection to occur, so these might be utilized in the further origin of life research.…”

“…In the case of functional RNAs, the "rule" is just Watson-Crick base pairing. These two components: an information carrier and a functional executive component are described as genotype and phenotype, interacting in a feedback loop that maintains the genomic stability or "guiding" the outcome from genome variations [11]. The information coming from the DNA or RNA works in tandem with the structure carried by the protein or the structural/functional RNA sequence.…”

“…Since [11,13,30,46,[81][82][83][84][85][86][87][88][89][90]. In the RNA-peptide scenarios, the information is carried by RNA (or RNA-like) polymer, but the structure comes initially from peptides and later from evolved proteins.…”

“…In fact, the issue with replication is easily solved in the RNA-peptide world, which offers the possibility for the emergence of a simple peptide capable of holding two Mg 2+ (or any suitable two-valence metal ions) at a specific distance and facilitates the beginning of enzymatic replication with a catalytic center specific for all modern DNA and RNA polymerases. Some authors advocate that the processes of replication and translation were initially the same [11,92]. In the author's opinion, this is not necessary because within the very first steps of the formation of the Darwinian complex, non-enzymatic replication of any kind (even low fidelity) would be sufficient to maintain some short sequence motifs of RNA.…”