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This chapter describes and elaborates on the energy coupling processes of living systems. First, equilibrium and nonequilibrium systems are discussed, introducing living systems as open, nonequilibrium, and dissipative structures continuously interacting with their surroundings. The roles of thermodynamics and Gibbs free energy as they apply to energy coupling phenomena are then summarized, followed by a discussion of protein structures as playing a crucial role in information processes and energy couplings. The “well-informed” character of living systems and the control of free energy, or exergy, by information are also briefly discussed. Finally, using the linear nonequilibrium thermodynamic approach, energy couplings in ATP production through oxidative phosphorylation and active transport of ions by chemical pumps are discussed as a part of bioenergetics.

All biological operations require the input of energy. In contemporary organisms, energy is harvested by mechanisms that are essentially electrical. Energy transduction relies on the circulation of ions across membranes (usually protons), and on a sophisticated rotary ATP synthase to capture the energy and conserve it as ATP. This chapter begins with an overview of chemiosmotic energy transduction and then poses the question, How did LUCA make a living? Current thinking questions the traditional notion that that LUCA lived off prebiotic organic molecules, and favors geochemical processes, such as the reduction of CO2 by hydrogen gas. One possible habitat for such organisms would be mineral honeycombs laid down by hydrothermal vents. If there is any truth to this hypothesis, then chemiosmotic energy transduction will have been part of LUCA's endowment, and may have evolved under the special circumstances that prevail in those vents. Subsequent evolution will have led to the liberation of cells from their mineral cradle, and the progressive expansion of energy metabolism by the invention of both photosynthesis and respiration.

In all of biology, there is no more consequential problem than the origin of life; yet despite the expenditure of much effort and ink over the past seventy years a satisfactory answer continues to elude us. This chapter surveys the huge body of experimental and theoretical work on this problem. Topics include the primordial broth of abiotic chemicals, prebiotic synthesis of metabolites, the quest for a self-replicating ribozyme, the critical importance of energy coupling, self-organized metabolic cycles, why membranes are essential, and the importance of natural selection from the outset. The recent idea, that life arose in the interstices of mineral deposits at the margins of warm alkaline hydrothermal vents, receives special attention. Between the first proto-cells and the Last Universal Common Ancestor, all the machinery of life must have been invented. We consider the place of the RNA World, and the horrendous difficulty of envisaging the origin of translation. In the end, the origin of life remains a mystery that passes understanding.

In this chapter we discuss theories which are rigorous in their formulation but which in order to be useful need to be modified by introducing approximations of some kind. The approximations we are interested in are those which involve introduction of classical mechanical concepts, that is, the classical picture and/or classical mechanical equations of motion in part of the system. At this point, we wish to distinguish between “the classical picture,” which is obtained by classical the limit ħ → 0 and the appearance of “classical equations of motion.” The latter may be extracted from the quantum mechanical formulation without taking the classical limit—but, as we shall see later by introducing a certain parametrization of quantum mechanics. Thus there are two ways of introducing classical mechanical concepts in quantum mechanics. In the first method, the classical limit is defined by taking the limit ħ → 0 either in all degrees of freedom (complete classical limit) or in some degrees of freedom (semi-classical theories). We note in passing that the word semi-classical has been used to cover a wide variety of approaches which have also been referred to as classical S-matrix theories, quantum-classical theories, classical path theory, hemi-quantal theory, Wentzel Kramer-Brillouin (WKB) theories, and so on. It is not the purpose of this book to define precisely what is behind these various acronyms. We shall rather focus on methods which we think have been successful as far as practical applications are concerned and discuss the approximations and philosophy behind these. In the other approach, the ħ-limit is not taken—at least not explicitl—but here one introduces “classical” quantities, such as, trajectories and momenta as parameters, and derives equations of motion for these parameters. The latter method is therefore one particular way of parameterizing quantum mechanics. We discuss both of these approaches in this chapter. The Feynman path-integral formulation is one way of formulating quantum mechanics such that the classical limit is immediately visible [3]. Formally, the approach involves the introduction of a quantity S, which has a definition resembling that of an action integral [101].

The outer belt flux enhancements occur in association with high-speed coronal hole streams. We show that the southward interplanetary magnetic field (IMF) within a coronal hole stream controls the flux enhancement of the relativistic electrons. Moreover, the amplitudes of the southward IMF of Alfvénic fluctuations in a coronal hole stream are controlled by the Russell–McPherron effect and continuous substorms can be observed during such periods. Therefore, the relativistic electron flux variations are also related to the Russell–McPherron effect and prolonged substorm activity may be of great importance for these variations. During periods of prolonged substorm activity, continuous hot electron injections from the plasma sheet occur, which is free energy source that can generate whistler mode waves. In fact, continuous whistler mode wave activity is observed during the periods and these waves produce relativistic electrons by the cross-energy couplings between thermal plasma, hot electrons, and relativistic electrons via wave–particle interactions. Thus, the southward IMF controls the flux enhancement of the outer belt electrons via wave–particle interactions and prolonged substorm activities are essential to cause the accelerations of relativistic electrons.

Why after 30 years of research have we not settled the relationship between substorms and convection? Why after 30 years are there still substantially different, competing models of substorm onset? Why has the progression from phenomenological to fully quantitative understanding not occurred? Answers to such questions will probably only become clear in retrospect, after the transition to quantitative understanding has taken place; in the meantime, we can only express our individual views. In our view, there have been three central difficulties. Contradictory pictures of plasma sheet transport have been able to flourish side-by-side because this fundamentally unsteady and highly spatially structured system was and is undersampled. As a result, people can still argue about when and where tail reconnection occurs in the substorm sequence, and other issues equally fundamental. Moreover, it is still not possible to connect the substorm onset in the auroral ionosphere to an event in space. For one thing, there is the timing problem: Waves communicate events’ existence across the magnetosphere and to the auroral ionosphere within a minute or two. We are only beginning to study the magnetoionosphere system globally with the required time resolution, and until we do so, there will be a “chicken and egg” problem. Finally, two key measurements are missing. No plasma sheet signatures of auroral arcs have been identified, so we do not know when a spacecraft is connected to a potential auroral onset region. We do not yet have an accepted ionospheric diagnostic of plasma sheet reconnection and the plasmoid formation; there is no auroral data display that illustrates at a glance the relationship of plasma sheet events to the onset and expansion of the substorm. Despite all this, there is real cause for optimism. The sheer magnitude of the observational effort and the volume and diversity of the results produced over the years have finally enabled us to perceive how complex the behavior of the magnetosphere really is. As our perceptions have evolved, we have designed multi-instrument, multi-spacecraft studies of ever-increasing comprehensiveness, articulation, and resolution, which further clarified our perceptions. All this effort is beginning to pay off.