The self-organizing fractal theory as a universal discovery method: the phenomenon of life

Abstract

A universal discovery method potentially applicable to all disciplines studying organizational phenomena has been developed. This method takes advantage of a new form of global symmetry, namely, scale-invariance of self-organizational dynamics of energy/matter at all levels of organizational hierarchy, from elementary particles through cells and organisms to the Universe as a whole. The method is based on an alternative conceptualization of physical reality postulating that the energy/matter comprising the Universe is far from equilibrium, that it exists as a flow, and that it develops via self-organization in accordance with the empirical laws of nonequilibrium thermodynamics. It is postulated that the energy/matter flowing through and comprising the Universe evolves as a multiscale, self-similar structure-process, i.e., as a self-organizing fractal. This means that certain organizational structures and processes are scale-invariant and are reproduced at all levels of the organizational hierarchy. Being a form of symmetry, scale-invariance naturally lends itself to a new discovery method that allows for the deduction of missing information by comparing scale-invariant organizational patterns across different levels of the organizational hierarchy.An application of the new discovery method to life sciences reveals that moving electrons represent a keystone physical force (flux) that powers, animates, informs, and binds all living structures-processes into a planetary-wide, multiscale system of electron flow/circulation, and that all living organisms and their larger-scale organizations emerge to function as electron transport networks that are supported by and, at the same time, support the flow of electrons down the Earth's redox gradient maintained along the core-mantle-crust-ocean-atmosphere axis of the planet. The presented findings lead to a radically new perspective on the nature and origin of life, suggesting that living matter is an organizational state/phase of nonliving matter and a natural consequence of the evolution and self-organization of nonliving matter.The presented paradigm opens doors for explosive advances in many disciplines, by uniting them within a single conceptual framework and providing a discovery method that allows for the systematic generation of knowledge through comparison and complementation of empirical data across different sciences and disciplines.

Figure 1

The Benard instability. Establishing an increasing vertical temperature gradient (ΔT) across a thin layer of liquid leads to heat transfer through the layer by conduction (organizational state #1). Exceeding a certain critical value of temperature gradient (ΔT_C) leads to an organizational state transition within the liquid layer. As a result of the transition, conduction is replaced by convection (organizational state #2) and the rate of heat transfer through the layer increases in a stepwise manner. Organizational state #2 (convection) is a more ordered state (higher negative entropy) than organizational state #1 (conduction). The more ordered state requires and, at the same time, supports a higher rate of energy/matter flow through the system. For this reason, the transitions between organizational states in nonequilibrium systems tend to be all-or-none phenomena. As a consequence, nonequilibrium systems are inherently quantal, absorbing and releasing energy/matter as packets. Organizational state #2 (convection) will relax into organizational state #1 (conduction) upon decreasing the temperature gradient (not shown). The Benard instability is an example of a nonequilibrium system illustrating a number of universal self-organizational processes shared by all nonequilibrium systems, including living cells and organisms (see discussion in the text). Reproduced from [8].

Figure 2

A linear, nonequilibrium model of biological organization and dynamics. The SOFT-NET theory conceptualizes biological organization and dynamics in terms of nonequilibrium electron transport chains that support and, at the same time, are supported by electrons moving between redox centers along electron gradients. Electron flow/circulation is organized by and, at the same time, organizes intervening macromolecular media residing in an aqueous environment (see details in the text). Two major forms of electron transport and the corresponding organization of a linear electron transport chain are shown: A) fast electron transport through and by means of highly organized macromolecular media (e.g., proteins, lipids, nucleic acids, and their complexes) and B) relatively slow electron transport by means of the same disorganized chain components diffusing in the aqueous phase. Two consecutive "zoom-ins" (in A) reveal the multiscale complexity of alternative and, thus, competing pathways of electron flow. The apparent complexity is greatly simplified, however, by the fact that electron flow is organized in a self-similar (i.e., scale-invariant) manner, with pathways making up higher-order pathways making up yet higher-order pathways and so forth. Within each hierarchical level in the organization of electron flow, individual pathways are similarly clustered into families of related pathways, with the overall electron flow being dynamically, competitively, and highly unevenly partitioned among alternative pathways and pathway families. C) The model is brought closer to reality by introducing orthogonal flow of chain components passing through a steady-state organization of the electron transport chain. Filled (●) and empty (○) circles denote redox centers with excess and deficit of electrons, correspondingly. Dotted line (-·-·-·) denotes electron transfer. Geometrical shapes with complementary features are animate media.

Figure 3

Electron relay in the class I ribonucleotide reductase (RNR). Each enzymatic turnover of RNR is accompanied by the transfer of an electron from the active site cysteine (Cys439) to a long-lived tyrosyl radical (Tyr122) stabilized by a diiron center. Cys439 and Tyr122 reside in different subunits of the enzyme and are separated by a formidable distance of approximately 3.5 nm. Intervening residues (Tyr730, Tyr731, Tyr356, and Trp48) relay the electron by forming transient amino acid radicals and thus function as "stepping stones" for a tunneling electron. The electron relay chain greatly outperforms unistep tunneling in terms of the rate of electron flow it can support. If unistep tunneling alone were responsible for electron transfer from Cys439 to Tyr122, the estimated waiting time for a single ET event would be hours or years. However, a single turnover actually occurs in approximately 200 ms [270].

Figure 4

Plasma lamp. The SOFT-NET theory postulates scale-invariance of the self-organizational dynamics of energy/matter at all levels of the organizational hierarchy, from elementary particles through cells and organisms to the Universe as a whole. The presented analysis of empirical data, together with the inferences made on the basis of scale symmetry, suggest that electrons moving between ionized centers in far-from-equilibrium conditions are responsible for key properties of living matter. The plasma lamp conveniently illustrates some of the physical processes and self-organizational patterns that appear to be shared by proteins, cells, organisms, living planets, and plasmas. It should also be mentioned that the hydrated electron was recently proposed to have a similar spatial organization [271]. The image is courtesy of Luc Viatour [272]; see also [260] for more details on plasmas.