Microbes Mind Forum

Research on origins, evolution, and syntheses of life

How did self-organization and evolution give rise to complex, life-like systems and how can these dynamics inform our futures? How can we move beyond the Tragedy of the Commons as a necessary outcome of evolutionary dynamics to evolve toward sustainable futures, channeled by constraints that unleash innovative potential, designing multi-agent, problem-solving systems.

Eshel Ben-Jacob is Professor of Physics of Complex Systems and holds the Maguy-Glass Chair in Physics at Tel Aviv University. He was an early leader in the study of bacterial colonies as the key to understanding larger biological systems. He maintains that the essence of cognition is rooted in the ability of bacteria to gather, measure, and process information, and to adapt in response. For the last decade, he has pioneered the field of Systems Neuroscience, focusing first on investigations of living neural networks outside the brain and later on analysis of actual brain activity. In 2007, Scientific American selected Ben-Jacob’s invention, the first hybrid NeuroMemory Chip, as one of the 50 most important achievements in all fields of science and technology for that year. The NeuroMemory Chip entails imprinting multiple memories, based upon development of a novel, system-level analysis of neural network activity (inspired by concepts from statistical physics and quantum mechanics), ideas about distributed information processing (inspired by his research on collective behaviors of bacteria) and new experimental methods based on nanotechnology (carbon nanotubes). Prof. Ben-Jacob received his PhD in physics (1982) at Tel Aviv University, Israel. He served as Vice President of the Israel Physical Society (1999-2002), then as President of the Israel Physical Society (2002-2005), initiating the online magazine PhysicaPlus, the only Hebrew-English bilingual science magazine. The general principles he has uncovered have been examined in a wide range of disciplines, including their application to amoeboid navigation, bacterial colony competition, cell motility, epilepsy, gene networks, genome sequence of pattern-forming bacteria, network theory analysis of the immune system, neural networks, search, and stock market volatility and collapse. He has examined implications of bacterial collective intelligence for neurocomputing. His scientific findings have prompted studies of their implications for computing: using chemical “tweets” to communicate, millions of bacteria self-organize to form colonies that collaborate to feed and defend themselves, as in a sophisticated social network.

Unfortunately, Eshel Ben-Jacob died before the 2017 Nobel Prize Winners in Chemistry won for detailing how cryo-EM technology links food energy-dependent biophysically constrained pheromone-controlled changes from atoms to ecosystems. The changes link microRNAs from food to healthy longevity and the changes also link the virus-driven degradation of messenger RNA to all pathology.

See also: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

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.

See also: Biology’s Second Law

…evolution operates through the complementary principles of Darwinian natural selection (biology’s “First Law”) coupled to homeostasis (biology’s “Second Law”).

See for comparison: The new mutation theory of phenotypic evolution

The enormous amount of phenotypic diversity among different phyla or classes of organisms is a product of accumulation of novel mutations and their conservation that have facilitated adaptation to different environments. Novel mutations may be incorporated into the genome by natural selection (elimination of preexisting genotypes) or by random processes such as genetic and genomic drift. However, once the mutations are incorporated into the genome, they may generate developmental constraints that will affect the future direction of phenotypic evolution. It appears that the driving force of phenotypic evolution is mutation…

See also: Hundreds of natural-selection studies could be wrong, study demonstrates

“The methods assume that when natural selection occurs the number of nucleotide substitutions that lead to changes in amino acids is significantly higher than the number of nucleotide substitutions that do not result in amino acid changes,” he said. “But this assumption may be wrong. Actually, the majority of amino acid substitutions do not lead to functional changes, and the adaptive change of a protein often occurs by a rare amino acid substitution. For this reason, statistical methods may give erroneous conclusions.”

The extent of codon usage bias in human RNA viruses and its evolutionary origin (2003)

Revealing the determinants of codon usage bias is central to the understanding of factors governing viral evolution.

Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition

The amino acid optimality code (Fig 6) provides an alternative perspective on sequence changes between paralogs in evolution and human disease.

Role of MicroRNAs in Zygotic Genome Activation: Modulation of mRNA During Embryogenesis

The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression

In conclusion, while fescue toxicosis appeared to have little effect upon sperm miRNA expression (with the possible exception of miRNA-146a), the miRNA profile of mature ejaculated sperm may in fact have downstream consequences upon embryonic development. The potential for sperm miRNA affecting zygote development has recently been reported in the literature [18] and has interesting implications for the use of sperm miRNA profiles as indicators of potential male fertility.

Virus-driven energy theft in soil bacteria and in plants links mutations from loss of function to reduced fertility in mammals. Energy-dependent feedback loops typically prevent the virus-driven degradation of messenger RNA from linking mutations to all pathology.

See for comparison: Why does the universe exist? Physicists have found the answer and it will blow your mind

  … particles simply pop into existence, usually in pairs, from absolutely nowhere.

That explains everything?

See for a discussion attempt: Quantum Field Theory

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