Thermodynamics and fractality - not enough in an electromagnetic world
Gregory O'Kelly, n/a
26 May 2011
Dr. Kurakin states, "...how exactly the apparent decrease of entropy on the planet earth is compensated by an increase in entropy somewhere else is less clear....'somewhere else' can potentially include the whole Universe..." The lack of clarity results from the inclusion of the whole universe rather than planetary or local considerations, at which clarity is more detectible. Yet this is the foundation for the universality of the discovery method he terms "self-organizing fractal theory." He writes, "...the Universe evolves from simplicity and disorder to complexity and order via self-organization, in accordance with the empirical laws of nonequilibrium thermodamics (NET)," and "...self-organizaing fractal theory (SOFT)...(which) implies the existence of universal principles governing self-organizational dynamics in a scale-invariant manner."
He does not say what these implied universal principles of nonequilibrium self-organization are, though he gives a few examples relating to the conduction of heat. These examples, e.g., Benard instability, do not escape the realm of 'classical mechanics and equilibrium thermodynamics that Dr. Kurakin insists comprises classical mechanics, despite the phase changes. Nonequilibrium thermodynamics, as well as equilibrium thermodynamics, does not extend to the world of electromagnetism. Neither is capable of field theory, a key ingredient of electromagnetism. Yet Dr. Kurakin states: (1) "...it appears that the physicochemical properties of proteins have carefully tailored by evolution to support electron transport through proteins and multi-protein complexes"; (2) "...a large body of experimental evidence demonstrates that proteins, nucleic acids, lipids and their complexes represent structured macromolecular media that enable and facilitate the capture and directed transport of electrons and protons..."; (3) "Because so many physicochemical properties of proteins, nucleic acids, and lipids appear to have been carefully tailored by evolution to satisfy the requirements of organized electron transport over large molecular distance, it is reasonable to suggest that electron flow may represent a fundamental physical force that sustains, drives, and informs all biological oranization and dynamics"; and (4) "What appears to be always and everywhere present is a continuous and rapid flow of electrons and protons through each and every living organism." This is the province of field theory, not thermodynamics or statistical mechanics, about which Dr. Kurakin has little to say.
Nevertheless, Dr. Kurakin writes, "Whether explicitly stated or tacitly implied, the phenomena studied in molecular and cell biology are traditionally interpreted and rationalized within the conceptual framework of classical physics, i.e., classical mechanics and equilibrium thermodynamics....despite the commonly accepted fact that the cell/organism (any living organization, in fact) is an open nonequilibrium system, which exists and functions only because of the incessant flow of energy/matter passing through it." That energy is not mechanical or heat energy, but is instead chemical energy, coulombs carried by electrons.
Ludwig Von Bertallanfy [Science, 1951, "The theory of open systems in physics and biology"], the founder of systems theory, wrote that non-equilibrium or open systems self-organize around a steady-state dependent upon their degree of openness. Systems theory is about thermodynamics, and reveals nothing in particular about the nature of self-organizing tendencies of open systems, unless supplemented by electrochemical considerations. Those considerations, as they occur in the allometric scaling of metabolism, are scale invariant. Bertallanfy defines metabolism as the total of the chemical processes involved in energy equilibration needed to maintain a non-equilibrium steady-state, regardless of complexity of the system. In other words the system is always moving toward equilibrium, but its openness allows it to maintain a steady-state short of it. Variations in openness influence the size, growth, development, replication, and organization of the structure. In other words the structure itself is proceeded by the chemical processes that result in it rather than determining what processes might be possible given an accidentally assembled structure.
In the allometric scaling of metabolism openness is expressed as a variable in the exponent of the biomass. Because openness is an electrochemical consideration, it is expressed as a ratio of amperes of anabolism to amperes of catabolism, where metabolic rate is expressed in watts, the power necessary to maintain the biomass short of equilibrium. This is called metabolic efficiency, where the denominator annunciates degree of openness (always changing); and the numerator gages the rate at which the open system is able to harness this openness. In his 2009 on the importance of non-equilibrium considerations in understanding life, Dr. Kurakin held that the version of Kleiber's Law favored by quarter-power scalers like Enquist and West, was seminal. This version does not include any considerations of openness, of metabolic efficiency. Dr. Kurakin does not discuss the power of quarter-power scaling in this latest attempt to account for electron flow in terms of thermodynamics.
Dr. Kurakin notes "...degree of order and the rate of energy/matter flow are co-defining in far-from-equilibrium systems, large-scale conductivity is an emergent property of organization (an ordered whole) rather than of component parts. Properties of parts are only compatible with and, in fact, are often selected and/or reinforced by the emergent properties of the organizational whole." This phenomenon is expressed in allometric scaling by the value for metabolic efficiency (the variable in the exponent of biomass annunciating degree of openness of the system) being determined by the whole and applying to all the parts. Large-scale conductivity is seen in the development of nerves and the nervous system.
Dr. Kurakin speaks of an 'electron gradient' as a key force (or pressure) driving electron flow. This pressure is voltage, electrical voltage, not entropic pressure resulting from gradients of particle concentration, the standard model of bioelectricity that treats thermodynamics and electromagnetism as commensurable and mutually substitutable, as Peter Mitchell, Alan Hodgkin, Andrew Huxley, and John Eccles believed. Dr. Kurakin suggests electron transfer is related to the flux of charge and matter. This explanation embodies two properties of batteries. In the first case the battery is a rechargeable battery able to capture, because of a voltage pressure, an electrical field, in the reversal of a catabolic chemical reaction within. This is in essence the generation of negative entropy. This is how life started.
In the second case, that of matter, the battery is non-rechargeable, and must have new chemicals introduced that may, in turn, be catabolized for energy content, as in digestion or any form of heterotrophism. In the first case we have a secondary cell, and in the second case we have a primary cell, two different types of batteries. The aggregation of secondary cells driven by fluctuations in metabolic efficiency resulted in the evolution of biomass that had primary cell capabilities. These capabilities were at first limited to the effectiveness of the tidal flow of water bearing nutrients, and later occurred as stomachs with capillary delivery of substance to the individual cells and organelles of the emerging structure. At this point the fractality Dr. Kurakin holds dear may have had some influence on the evolution of the structure. But such fractality does not extend to attempts to understand the origins of life. Only appeal to secondary cells can do that. In other words fractality might have something to do the equilibration of energy flux through the organism (as it concerns movement of matter for strictly local catabolic breakdown), but reveals little pertinent to the forces and pressures behind the origins of life and self-organization of the organism. These things can only be understood in terms of thermodynamics and electromagnetism as they act upon aggregations of organic molecules.
Competing interests
I have no competing interests or financial stake in this paper or the ideas herein presented.
Theoretical Biology and Medical Modelling
Thermodynamics and fractality - not enough in an electromagnetic world
26 May 2011
Dr. Kurakin states, "...how exactly the apparent decrease of entropy on the planet earth is compensated by an increase in entropy somewhere else is less clear....'somewhere else' can potentially include the whole Universe..." The lack of clarity results from the inclusion of the whole universe rather than planetary or local considerations, at which clarity is more detectible. Yet this is the foundation for the universality of the discovery method he terms "self-organizing fractal theory." He writes, "...the Universe evolves from simplicity and disorder to complexity and order via self-organization, in accordance with the empirical laws of nonequilibrium thermodamics (NET)," and "...self-organizaing fractal theory (SOFT)...(which) implies the existence of universal principles governing self-organizational dynamics in a scale-invariant manner."
He does not say what these implied universal principles of nonequilibrium self-organization are, though he gives a few examples relating to the conduction of heat. These examples, e.g., Benard instability, do not escape the realm of 'classical mechanics and equilibrium thermodynamics that Dr. Kurakin insists comprises classical mechanics, despite the phase changes. Nonequilibrium thermodynamics, as well as equilibrium thermodynamics, does not extend to the world of electromagnetism. Neither is capable of field theory, a key ingredient of electromagnetism. Yet Dr. Kurakin states: (1) "...it appears that the physicochemical properties of proteins have carefully tailored by evolution to support electron transport through proteins and multi-protein complexes"; (2) "...a large body of experimental evidence demonstrates that proteins, nucleic acids, lipids and their complexes represent structured macromolecular media that enable and facilitate the capture and directed transport of electrons and protons..."; (3) "Because so many physicochemical properties of proteins, nucleic acids, and lipids appear to have been carefully tailored by evolution to satisfy the requirements of organized electron transport over large molecular distance, it is reasonable to suggest that electron flow may represent a fundamental physical force that sustains, drives, and informs all biological oranization and dynamics"; and (4) "What appears to be always and everywhere present is a continuous and rapid flow of electrons and protons through each and every living organism." This is the province of field theory, not thermodynamics or statistical mechanics, about which Dr. Kurakin has little to say.
Nevertheless, Dr. Kurakin writes, "Whether explicitly stated or tacitly implied, the phenomena studied in molecular and cell biology are traditionally interpreted and rationalized within the conceptual framework of classical physics, i.e., classical mechanics and equilibrium thermodynamics....despite the commonly accepted fact that the cell/organism (any living organization, in fact) is an open nonequilibrium system, which exists and functions only because of the incessant flow of energy/matter passing through it." That energy is not mechanical or heat energy, but is instead chemical energy, coulombs carried by electrons.
Ludwig Von Bertallanfy [Science, 1951, "The theory of open systems in physics and biology"], the founder of systems theory, wrote that non-equilibrium or open systems self-organize around a steady-state dependent upon their degree of openness. Systems theory is about thermodynamics, and reveals nothing in particular about the nature of self-organizing tendencies of open systems, unless supplemented by electrochemical considerations. Those considerations, as they occur in the allometric scaling of metabolism, are scale invariant. Bertallanfy defines metabolism as the total of the chemical processes involved in energy equilibration needed to maintain a non-equilibrium steady-state, regardless of complexity of the system. In other words the system is always moving toward equilibrium, but its openness allows it to maintain a steady-state short of it. Variations in openness influence the size, growth, development, replication, and organization of the structure. In other words the structure itself is proceeded by the chemical processes that result in it rather than determining what processes might be possible given an accidentally assembled structure.
In the allometric scaling of metabolism openness is expressed as a variable in the exponent of the biomass. Because openness is an electrochemical consideration, it is expressed as a ratio of amperes of anabolism to amperes of catabolism, where metabolic rate is expressed in watts, the power necessary to maintain the biomass short of equilibrium. This is called metabolic efficiency, where the denominator annunciates degree of openness (always changing); and the numerator gages the rate at which the open system is able to harness this openness. In his 2009 on the importance of non-equilibrium considerations in understanding life, Dr. Kurakin held that the version of Kleiber's Law favored by quarter-power scalers like Enquist and West, was seminal. This version does not include any considerations of openness, of metabolic efficiency. Dr. Kurakin does not discuss the power of quarter-power scaling in this latest attempt to account for electron flow in terms of thermodynamics.
Dr. Kurakin notes "...degree of order and the rate of energy/matter flow are co-defining in far-from-equilibrium systems, large-scale conductivity is an emergent property of organization (an ordered whole) rather than of component parts. Properties of parts are only compatible with and, in fact, are often selected and/or reinforced by the emergent properties of the organizational whole." This phenomenon is expressed in allometric scaling by the value for metabolic efficiency (the variable in the exponent of biomass annunciating degree of openness of the system) being determined by the whole and applying to all the parts. Large-scale conductivity is seen in the development of nerves and the nervous system.
Dr. Kurakin speaks of an 'electron gradient' as a key force (or pressure) driving electron flow. This pressure is voltage, electrical voltage, not entropic pressure resulting from gradients of particle concentration, the standard model of bioelectricity that treats thermodynamics and electromagnetism as commensurable and mutually substitutable, as Peter Mitchell, Alan Hodgkin, Andrew Huxley, and John Eccles believed. Dr. Kurakin suggests electron transfer is related to the flux of charge and matter. This explanation embodies two properties of batteries. In the first case the battery is a rechargeable battery able to capture, because of a voltage pressure, an electrical field, in the reversal of a catabolic chemical reaction within. This is in essence the generation of negative entropy.
This is how life started.
In the second case, that of matter, the battery is non-rechargeable, and must have new chemicals introduced that may, in turn, be catabolized for energy content, as in digestion or any form of heterotrophism. In the first case we have a secondary cell, and in the second case we have a primary cell, two different types of batteries. The aggregation of secondary cells driven by fluctuations in metabolic efficiency resulted in the evolution of biomass that had primary cell capabilities. These capabilities were at first limited to the effectiveness of the tidal flow of water bearing nutrients, and later occurred as stomachs with capillary delivery of substance to the individual cells and organelles of the emerging structure. At this point the fractality Dr. Kurakin holds dear may have had some influence on the evolution of the structure. But such fractality does not extend to attempts to understand the origins of life. Only appeal to secondary cells can do that. In other words fractality might have something to do the equilibration of energy flux through the organism (as it concerns movement of matter for strictly local catabolic breakdown), but reveals little pertinent to the forces and pressures behind the origins of life and self-organization of the organism. These things can only be understood in terms of thermodynamics and electromagnetism as they act upon aggregations of organic molecules.
Competing interests
I have no competing interests or financial stake in this paper or the ideas herein presented.