Transformation of matter in living organisms during growth and evolution

Toward the Relational Formulation of Biological Thermodynamics

Classical thermodynamics employs the state of thermodynamic equilibrium, characterized by maximal disorder of the constituent particles, as the reference frame from which the Second Law is formulated and the definition of entropy is derived. Non-equilibrium thermodynamics analyzes the fluxes of matter and energy that are generated in the course of the general tendency to achieve equilibrium. The systems described by classical and non-equilibrium thermodynamics may be heuristically useful within certain limits, but epistemologically, they have fundamental problems in the application to autopoietic living systems. We discuss here the paradigm defined as a relational biological thermodynamics. The standard to which this refers relates to the biological function operating within the context of particular environment and not to the abstract state of thermodynamic equilibrium. This is defined as the stable non-equilibrium state, following Ervin Bauer. Similar to physics, where abandoning the absolute space-time resulted in the application of non-Euclidean geometry, relational biological thermodynamics leads to revealing the basic iterative structures that are formed as a consequence of the search for an optimal coordinate system by living organisms to maintain stable non-equilibrium. Through this search, the developing system achieves the condition of maximization of its power via synergistic effects.

SARS-CoV-2 strain wars continues: Chemical and thermodynamic characterization of live matter and biosynthesis of Omicron BN.1, CH.1.1 and XBC variants

SARS-CoV-2 has during the last 3 years mutated several dozen times. Most mutations in the newly formed variants have been chemically and thermodynamically characterized. New variants have been declared as variants under monitoring. The European Centre for Disease Prevention and Control has suggested the hypothesis that the new BN.1, CH.1.1 and XBC variants could have properties similar to those of VOC. Thermodynamic properties of new variants have been reported in this manuscript for the first time. Gibbs energy of biosynthesis, as the driving force for viral multiplication, is less negative for the new variants than for the earlier variants. This indicates that the virus has evolved towards decrease in pathogenicity, which leads to less severe forms of COVID-19.

Ghosts of the past: Elemental composition, biosynthesis reactions and thermodynamic properties of Zeta P.2, Eta B.1.525, Theta P.3, Kappa B.1.617.1, Iota B.1.526, Lambda C.37 and Mu B.1.621 variants of SARS-CoV-2

From the perspectives of molecular biology, genetics and biothermodynamics, SARS-CoV-2 is the among the best characterized viruses. Research on SARS-CoV-2 has shed a new light onto driving forces and molecular mechanisms of viral evolution. This paper reports results on empirical formulas, biosynthesis reactions and thermodynamic properties of biosynthesis (multiplication) for the Zeta P.2, Eta B.1.525, Theta P.3, Kappa B.1.617.1, Iota B.1.526, Lambda C.37 and Mu B.1.621 variants of SARS-CoV-2. Thermodynamic analysis has shown that the physical driving forces for evolution of SARS-CoV-2 are Gibbs energy of biosynthesis and Gibbs energy of binding. The driving forces have led SARS-CoV-2 through the evolution process from the original Hu-1 to the newest variants in accordance with the expectations of the evolution theory.

Biothermodynamics of Viruses from Absolute Zero (1950) to Virothermodynamics (2022)

Biothermodynamics of viruses is among the youngest but most rapidly developing scientific disciplines. During the COVID-19 pandemic, it closely followed the results published by molecular biologists. Empirical formulas were published for 50 viruses and thermodynamic properties for multiple viruses and virus variants, including all variants of concern of SARS-CoV-2, SARS-CoV, MERS-CoV, Ebola virus, Vaccinia and Monkeypox virus. A review of the development of biothermodynamics of viruses during the last several decades and intense development during the last 3 years is described in this paper.

Why doesn't Ebola virus cause pandemics like SARS-CoV-2?

Ebola virus is among the most dangerous, contagious and deadly etiological causes of viral diseases. However, Ebola virus has never extensively spread in human population and never have led to a pandemic. Why? The mechanistic biophysical model revealing the biothermodynamic background of virus-host interaction) could help us to understand pathogenesis of Ebola virus disease (earlier known as the Ebola hemorrhagic fever). In this paper for the first time the empirical formula, thermodynamic properties of biosynthesis (including the driving force of virus multiplication in the susceptible host), binding constant and thermodynamic properties of binding are reported. Thermodynamic data for Ebola virus were compared with data for SARS-CoV-2 to explain why SARS-CoV-2 has caused a pandemic, while Ebola remains on local epidemic level. The empirical formula of the Ebola virus was found to be CH_1.569O_0.3281N_0.2786P_0.00173S_0.00258. Standard Gibbs energy of biosynthesis of the Ebola virus nucleocapsid is -151.59 kJ/C-mol.

Omicron BA.2.75 Sublineage (Centaurus) Follows the Expectations of the Evolution Theory: Less Negative Gibbs Energy of Biosynthesis Indicates Decreased Pathogenicity

SARS-CoV-2 belongs to the group of RNA viruses with a pronounced tendency to mutate. Omicron BA.2.75 is a subvariant believed to be able to suppress the currently dominant BA.5 and cause a new winter wave of the COVID-19 pandemic. Omicron BA.2.75 is characterized by a greater infectivity compared to earlier Omicron variants. However, the Gibbs energy of the biosynthesis of virus particles is slightly less negative compared to those of other variants. Thus, the multiplication rate of Omicron BA.2.75 is lower than that of other SARS-CoV-2 variants. This leads to slower accumulation of newly formed virions and less damage to host cells, indicating evolution of SARS-CoV-2 toward decreasing pathogenicity.

Space Biomedicine: A Unique Opportunity to Rethink the Relationships between Physics and Biology

Space biomedicine has provided significant technological breakthroughs by developing new medical devices, diagnostic tools, and health-supporting systems. Many of these products are currently in use onboard the International Space Station and have been successfully translated into clinical practice on Earth. However, biomedical research performed in space has disclosed exciting, new perspectives regarding the relationships between physics and medicine, thus fostering the rethinking of the theoretical basis of biology. In particular, these studies have stressed the critical role that biophysical forces play in shaping the function and pattern formation of living structures. The experimental models investigated under microgravity conditions allow us to appreciate the complexity of living organisms through a very different perspective. Indeed, biological entities should be conceived as a unique magnification of physical laws driven by local energy and order states overlaid by selection history and constraints, in which the source of the inheritance, variation, and process of selection has expanded from the classical Darwinian definition. The very specific nature of the field in which living organisms behave and evolve in a space environment can be exploited to decipher the underlying, basic processes and mechanisms that are not apparent on Earth. In turn, these findings can provide novel opportunities for testing pharmacological countermeasures that can be instrumental for managing a wide array of health problems and diseases on Earth.

Omicron BA.2.75 Subvariant of SARS-CoV-2 Is Expected to Have the Greatest Infectivity Compared with the Competing BA.2 and BA.5, Due to Most Negative Gibbs Energy of Binding

Omicron BA.2.75 may become the next globally dominant strain of COVID-19 in 2022. The BA.2.75 sub-variant has acquired more mutations (9) in spike protein and other genes of SARS-CoV-2 than any other variant. Thus, its chemical composition and thermodynamic properties have changed compared with earlier variants. In this paper, the Gibbs energy of the binding and antigen-receptor binding rate was reported for the BA.2.75 variant. Gibbs energy of the binding of the Omicron BA.2.75 variant is more negative than that of the competing variants BA.2 and BA.5.

Thermodynamics of Soil Microbial Metabolism: Applications and Functions

The thermodynamic characterization of soils would help to study and to understand their strategies for survival, as well as defining their evolutionary state. It is still a challenging goal due to difficulties in calculating the thermodynamic state variables (enthalpy, Gibbs energy, and entropy) of the reactions taking place in, and by, soils. Advances in instrumentation and methodologies are bringing options for those calculations, boosting the interest in this subject. The thermodynamic state variables involve considering the soil microbial functions as key channels controlling the interchange of matter and energy between soil and the environment, through the concept of microbial energy use efficiency. The role of microbial diversity using the energy from the soil organic substrates, and, therefore, the who, where, with whom, and why of managing that energy is still unexplored. It could be achieved by unraveling the nature of the soil organic substrates and by monitoring the energy released by the soil microbial metabolism when decomposing and assimilating those substrates. This review shows the state of the art of these concepts and the future impact of thermodynamics on soil science and on soil ecology.

Standard Thermodynamic Properties, Biosynthesis Rates, and the Driving Force of Growth of Five Agricultural Plants

Elemental composition of Gossypium hirsutum L. (cotton), Oryza sativa L. (Asian rice), Phaseolus vulgaris L. (common bean), Saccharum spp. L. (sugarcane), and Zea mays L. (corn) was used to calculate their empirical formulas (unit carbon formulas) and growth stoichiometry. The empirical formulas were used to find standard enthalpy of formation, standard molar entropy, standard Gibbs energy of formation, and standard molar heat capacity. A comparison was made between thermodynamic properties of live matter of the analyzed plants and other unicellular and multicellular organisms. Moreover, the growth process was analyzed through standard enthalpy, entropy, and Gibbs energy of biosynthesis. The average standard Gibbs energy of biosynthesis was found to be +463.0 kJ/C-mol. Thus, photosynthesis provides energy and carbon for plant growth. The average intercepted photosynthetic energy was found to be 15.5 MJ/C-mol for the analyzed plants. However, due to inefficiency, a great fraction of the intercepted photosynthetic energy cannot be used by plants. The average usable photosynthetic energy was found to be -2.3 MJ/C-mol. The average thermodynamic driving force for growth is -1.9 MJ/C-mol. Driving forces of growth of C3 and C4 plants were compared. It was found that C4 plants have a greater driving force of growth than C3 plants, which reflects the greater efficiency of C4 photosynthesis. The relationship between the driving force and growth rates was analyzed by determining phenomenological L coefficients. The determined phenomenological coefficients span two orders of magnitude, depending on plant species and environmental conditions. The L coefficient of P. vulgaris was found to be lower than that of other plants, due to additional energy requirements of nitrogen fixation.