Figure 3 - available via license: CC BY
Content may be subject to copyright.
Double-stranded DNA (dsDNA), formed by the interaction between two single strands of DNA (ssDNA), resists entropy and thus enables long term survival of the composite genetic information. The colored bars protruding horizontally from the DNA strands represent non-covalent bonding sites. Interactions between the bonding sites in dsDNA protect the joint molecule from illicit, potentially damaging interactions. DNA in the single stranded form-ssDNA-is not protected from non-physiological interactions and is thereby readily degraded. Image of ssDNA and dsDNA reproduced from 68 under fair use licensing for nonprofit and educational purposes.
Source publication
The evolution of multicellular eukaryotes expresses two sorts of adaptations: local adaptations like fur or feathers, which characterize species in particular environments, and universal adaptations like microbiomes or sexual reproduction, which characterize most multicellulars in any environment. We reason that the mechanisms driving the universal...
Context in source publication
Context 1
... paired strands of dsDNA, bound together, are relatively resistant to random damage because each strand is in constant interaction with its sister strand; the two strands can be perceived to be in continuous cooperation; essentially all potentially reactive, non-covalent bonding energy is engaged in cooperative interactions between the strands. In marked contrast to the stable dsDNA dimer, ssDNA and single stranded RNA (ssRNA) are highly susceptible to destruction; reactive bonding energy in the single-strand configuration is not quenched by physiological interactions and is available for haphazard interactions with illicit target molecules, leading to degradation ( Figure 3). Cooperative interaction explains why stable dsDNA can be recovered from mummies or woolly mammoths thousands of years old 67 , while unstable ssDNA and ssRNA survive for only days, at best. ...
Similar publications
The evolution of multicellular eukaryotes expresses two sorts of adaptations: local adaptations like fur or feathers, which characterize species in particular environments, and universal adaptations like microbiomes or sexual reproduction, which characterize most multicellulars in any environment. We reason that the mechanisms driving the universal...
Citations
... The role of entropy in evolution is a particularly sought-after problem (Bartlet, 2017;Cohen & Marron, 2020;Kondepudi et al., 2020;Pross & Pascal, 2017;Sherwin, 2018;Skene, 2015;Roach et al., 2020;Roach, 2020;Torday, 2021;Wong, 2020). Entropy measures the variety of existing possible configurations within a system. ...
... Microscopic fluctuations drive the system towards more probable states; horizontal gene transfer spreads the genetic elements (Rosenberg, 2022;Sakaue et al., 2017), dispersing potential for new functions and morphologies (Sailer & Harms, 2017) and species formation (Woods et al., 2020;Suh, 2021). Entropy increases with time (Cohen & Marron, 2020;Jennings et al., 2020), generating disorder, which has diffusional effects on gene spreading (LaBar & Adami, 2016;Sailer & Harms, 2017) without producing substantial evolutionary change. Therefore, entropic force represents microstate fluctuations of the gene pool, a trend that reverses the low entropy first phase. ...
Although Darwin's theory of biological evolution is the cornerstone of modern biology, it lacks proper physical foundations. We consider ecosystems as closed systems that only exchange energy and information, not matter with the outside. Moreover, predictable and periodic fluctuations in entropy, genetic diversity, population number, and resource availability form a cyclic process that can be analyzed via thermodynamic principles. The sun's energy input drives a reversed Carnot cycle in four phases. The first phase is low entropy, a fast-changing environment spurring genotype-phenotype plasticity. In phase 2, the growing population increases entropy, forming nutrient cycles via symbiotic, parasitic, and predator-prey relationships. In phase 3, competitive and chaotic interactions spread genetic innovations in the overpopulated, stressed ecosystem. Finally, in phase 4, extinction purges the non-evolvable genomes, but the surviving species carry the cycle's genetic innovations on which further evolutionary progression is possible. The sun's energy input is a potent driver of genetic complexity through the cyclic compression and expansion of the ecospace. Using thermodynamic principles, we show that ecosystems conserve genetic complexity. Therefore, intellectual complexity never decreases but increases or remains constant might be a new law of physics, the second law of intellect.
... The natural history of the biosphere is the product of communication and interaction to obtain information and cognition. In that way, the molecular signaling is the mechanism that initiates adaptation by virtue of genetic expression (Cohen and Marron, 2020;Slijepcevic, 2021). Thus, in plants, the epigenetic control of enzymes that synthesize the molecules of secondary metabolism through DNA methylation and histone acetylation allows expression of the environmental change in biosynthetic gene clusters (BGCs) (Scherlach et al., 2021). ...
... The natural history of the biosphere is the product of communication and interaction to obtain information and cognition. In that way, the molecular signaling is the mechanism that initiates adaptation by virtue of genetic expression (Cohen and Marron, 2020;Slijepcevic, 2021). Thus, in plants, the epigenetic control of enzymes that synthesize the molecules of secondary metabolism through DNA methylation and histone acetylation allows expression of the environmental change in biosynthetic gene clusters (BGCs) (Scherlach et al., 2021). ...
Alkamides are a group of bioactive, novel, and natural secondary compounds showing broad structural variability with an important range of activities, including tingling, pungent, antioxidant, and many more activities. Plants produce multiple intracellular and systemic responses and pathways against abiotic and biotic stresses. Alkamides are helpful in increasing plant growth, root development, the architecture of the root and shoot system, and nitric oxide (NO) signal transduction pathways, and, ultimately, yield. Their chemical-signaling pathways and relations with soil, water, and minerals lead to the presentation of defense-related genes and the production of antimicrobial secondary metabolites to have a greater impact on plant physiology and metabolism. Signals produced by alkamides and NAEs are used by microorganisms for cell-to-cell communication and can be observed by plants to modulate gene expression, metabolism, and growth development. Compounds such as alkamides produced by certain growth-promoting rhizobacteria contribute to plant immunity and development.
... The role of entropy in evolution is a particularly sought-after problem (Bartlet, 2017;Cohen & Marron, 2020;Kondepudi et al., 2020;Pross & Pascal, 2017;Sherwin, 2018;Skene, 2015;Roach et al., 2020;Roach, 2020;Torday, 2021;Wong, 2020). Entropy measures the variety of existing possible configurations within a system. ...
... Microscopic fluctuations drive the system towards more probable states; horizontal gene transfer spreads the genetic elements (Rosenberg, 2022;Sakaue et al., 2017), dispersing potential for new functions and morphologies (Sailer & Harms, 2017) and species formation (Woods et al., 2020;Suh, 2021). Entropy increases with time (Cohen & Marron, 2020;Jennings et al., 2020), generating disorder, which has diffusional effects on gene spreading (LaBar & Adami, 2016;Sailer & Harms, 2017) without producing substantial evolutionary change. Therefore, entropic force represents microstate fluctuations of the gene pool, a trend that reverses the low entropy first phase. ...
Darwin's theory of biological evolution became a cornerstone of modern biology. Predictable fluctuations in entropy, genetic diversity, population number, and resource availability in ecosystems turn evolution into a cyclic process, making the ecosystem's thermodynamic analysis possible. The sun's energy input drives a closed theoretical process, the reversed Carnot cycle. The Carnot cycle is divided into four distinct phases with standard features. The first phase is a low entropy, fast-changing environment, spurring phenotypic plasticity (phase 1). In phase 2, the population growth increases entropy, forming nutrient cycles via symbiotic, parasitic, predator-prey, and other interdependent relationships. In phase 3, the overpopulated, stressed ecosystem outgrows its boundaries; competitive and chaotic interactions spread genetic innovations through horizontal gene transfer. Finally, in phase 4, extinction purges the non-evolvable genomes, but the surviving species carry the cycle's genetic innovations and make renewal possible. Therefore, compression and expansion of the ecospace by energy fluxes (i.e., ecosystem dynamics) are potent drivers of change. Thus, the Darwinian concept is a cyclic sequestering of the sun's energy into genetic complexity. The second law of intellect shows that genetic complexity either increases or remains constant; it never decreases.
... The world is not an aggregation of things, but rather a symphony of relationships between many participants that are altered by the interaction. (Weber, 2017, p. 29) An emerging view of evolution suggests that evolution of living systems is about survival-of-the-fitted-those entities that resist entropic destruction-rather than survival-of-the-fittestthe entities with the greatest reproductive success (Cohen and Marron, 2020). That is, survival requires a living entity to be integrated within biological and material networks to convert entropic disorganization into organization amid universal properties of energy, entropy, and interactions (Schrodinger, 2012;Friston, 2013;Ramstead et al., 2018). ...
Intersubjectivity refers to one person’s awareness in relation to another person’s awareness. It is key to well-being and human development. From infancy to adulthood, human interactions ceaselessly contribute to the flourishing or impairment of intersubjectivity. In this work, we first describe intersubjectivity as a hallmark of quality dyadic processes. Then, using parent-child relationship as an example, we propose a dyadic active inference model to elucidate an inverse relation between stress and intersubjectivity. We postulate that impaired intersubjectivity is a manifestation of underlying problems of deficient relational benevolence, misattributing another person’s intentions (over-mentalizing), and neglecting the effects of one’s own actions on the other person (under-coupling). These problems can exacerbate stress due to excessive variational free energy in a person’s active inference engine when that person feels threatened and holds on to his/her invalid (mis)beliefs. In support of this dyadic model, we briefly describe relevant neuroimaging literature to elucidate brain networks underlying the effects of an intersubjectivity-oriented parenting intervention on parenting stress. Using the active inference dyadic model, we identified critical interventional strategies necessary to rectify these problems and hereby developed a coding system in reference to these strategies. In a theory-guided quantitative review, we used this coding system to code 35 clinical trials of parenting interventions published between 2016 and 2020, based on PubMed database, to predict their efficacy for reducing parenting stress. The results of this theory-guided analysis corroborated our hypothesis that parenting intervention can effectively reduce parenting stress if the intervention is designed to mitigate the problems of deficient relational benevolence, under-coupling, and over-mentalizing. We integrated our work with several dyadic concepts identified in the literature. Finally, inspired by Arya Nagarjuna’s Buddhist Madhyamaka Philosophy, we described abstract expressions of Dependent Origination as a relational worldview to reflect on the normality, impairment, and rehabilitation of intersubjectivity.
... Due to advances in the appreciation of biochirality, the intuitive perception of the link between bio-molecular chirality and brain laterality and asymmetry of cognitive function is gradually replaced by a system of experimental facts [35][36][37][38][39]. The evolution of biological symmetry is evident in the animal proteome, cell signaling, and body/brain morphology, originating, mainly, due to the changes in the gene regulatory networks (GRNs) [39][40][41]. The human genome contains ∼25,000 protein-coding genes, which are differentially expressed, in response to the various intracellular and extracellular cues. ...
Chirality is a universal phenomenon, embracing the space–time domains of non-organic and organic nature. The biological time arrow, evident in the aging of proteins and organisms, should be linked to the prevalent biomolecular chirality. This hypothesis drives our exploration of protein aging, in relation to the biological aging of an organism. Recent advances in the chirality discrimination methods and theoretical considerations of the non-equilibrium thermodynamics clarify the fundamental issues, concerning the biphasic, alternative, and stepwise changes in the conformational entropy associated with protein folding. Living cells represent open, non-equilibrium, self-organizing, and dissipative systems. The non-equilibrium thermodynamics of cell biology are determined by utilizing the energy stored, transferred, and released, via adenosine triphosphate (ATP). At the protein level, the synthesis of a homochiral polypeptide chain of L-amino acids (L-AAs) represents the first state in the evolution of the dynamic non-equilibrium state of the system. At the next step the non-equilibrium state of a protein-centric system is supported and amended by a broad set of posttranslational modifications (PTMs). The enzymatic phosphorylation, being the most abundant and ATP-driven form of PTMs, illustrates the principal significance of the energy-coupling, in maintaining and reshaping the system. However, the physiological functions of phosphorylation are under the permanent risk of being compromised by spontaneous racemization. Therefore, the major distinct steps in protein-centric aging include the biosynthesis of a polypeptide chain, protein folding assisted by the system of PTMs, and age-dependent spontaneous protein racemization and degradation. To the best of our knowledge, we are the first to pay attention to the biphasic, alternative, and stepwise changes in the conformational entropy of protein folding. The broader view on protein folding, including the impact of spontaneous racemization, will help in the goal-oriented experimental design in the field of chiral proteomics.
The continuity of life and its evolution, we proposed, emerge from an interactive group process manifested in networks of interaction. We term this process survival of the fitted. Here, we reason that survival of the fitted results from a natural computational process we term natural autoencoding. Natural autoencoding works by retaining repeating biological interactions while non-repeatable interactions disappear. (i) We define a species by its species interaction code, which consists of a compact description of the repeating interactions of species organisms with their external and internal environments. Species interaction codes are descriptions recorded in the biological infrastructure that enables repeating interactions. Encoding and decoding are interwoven. (ii) Evolution proceeds by natural autoencoding of sustained changes in species interaction codes. DNA is only one element in natural autoencoding. (iii) Natural autoencoding accounts for the paradox of genome randomization in sexual reproduction-recombined genomes are analogous to the diversified inputs required for artificial autoencoding. The increase in entropy generated by genome randomization compensates for the decrease in entropy generated by organized life. (iv) Natural autoencoding and artificial autoencoding algorithms manifest defined similarities and differences. Recognition of the importance of fittedness could well serve the future of a humanly livable biosphere.
During the COVID-19 pandemic, many statistical and epidemiological studies have been published, trying to predict the future development of the SARS-CoV-2 pandemic. However, it would be beneficial to have a specific, mechanistic biophysical model, based on the driving forces of processes performed during virus-host interactions and fundamental laws of nature, allowing prediction of future evolution of SARS-CoV-2 and other viruses. In this paper, an attempt was made to predict the development of the pandemic, based on biothermodynamic parameters: Gibbs energy of binding and Gibbs energy of growth. Based on analysis of biothermodynamic parameters of various variants of SARS-CoV-2, SARS-CoV and MERS-CoV that appeared during evolution, an attempt was made to predict the future directions of evolution of SARS-CoV-2 and potential occurrence of new strains that could lead to new pandemic waves. Possible new mutations that could appear in the future could lead to changes in chemical composition, biothermodynamic properties (driving forces of new virus strains) and biological properties of SARS CoV-2 that represent a risk for humanity.
Dynamical systems, i.e., systems that progress along time according to fixed rules, exhibit many special phenomena like the emergence of interesting patterns, bifurcation of behavior, the appearance of chaos despite determinism and boundedness, and sensitive dependence on initial conditions. Such phenomena are encountered in diverse fields, such as fluid dynamics, biological population analysis and economic and financial operations. The study of dynamical systems, their properties, and the mathematical and computerized tools for dealing with them, are often designated as part of advanced curricula in physics or mathematics. Consequently, many computer science students, perhaps the majority thereof, graduate without ever being exposed to such concepts. We argue that with the pervasiveness of dynamical systems and manifestation of their properties in the real world, these concepts should be introduced early on; in undergraduate studies in computer science and related fields, and perhaps even in high school. Available introductory courses demonstrate that only a minimal foundation of knowledge in mathematics is needed for the basic understanding of the key ideas. Such an introduction would deepen one’s understanding of the world and highlight important capabilities and limitations of mathematical and software tools for analysis, simulation, testing and verification of complex systems. In turn, this can lead to enhancement and enrichment of languages, tools and methodologies for dealing with dynamical systems, and of research in computer science and software engineering in general.
The term "thermoeconomics" denotes a paradigm shift in our understanding of the role of energy in living systems, and in evolution. It is based on the proposition that energy in biological evolution can best be defined and understood, not in terms of the Second Law of Thermodynamics but in terms of such economic criteria as productivity, efficiency, and especially the costs and benefits (or "profitability") of various mechanisms for capturing and utilizing energy to build biomass and do work. Thus, thermoeconomics is fully consistent with contemporary evolutionary theory. Functional criteria provide a better explanation of the advances (and recessions) in bioenergetic technologies in evolution than does any formulation derived from the Second Law.
