The bottom-up approach of physics starts from material building blocks plus physical laws. Yet it is insufficient and incompetent in a biological context to produce a model that explains such elementary biological processes as the bending of a finger. There are not physical equations that can determine the time-dependent behavior of my finger which I will intend to bend in the next moment, even if it would be possible to give all the positions of the elementary particles in the initial state. Actually, there is more to nature than elementary particles plus physical laws. Besides complexity, biological behavior also enters to the scene.
In physics, any problem can be regarded as definite only if the boundary conditions representing the connection of the system are given; otherwise the differential equations cannot be solved. These conditions in physics are usually external. In contrast, in living organisms the changes initiated within the organism by the living organism itself govern behavior. This means that in biology the internal and time-dependent conditions are decisive. The same body can behave very differently within the same conditions.
It is a general view that life can perfectly well emerge from the laws of physics plus accidents (cf. Gell-Mann, 1995). Indeed it seems that physics can describe any phenomenon by boundary conditions (describing the initial state) plus the laws of physics, with the qualification that the source of all occasional physical indetermination is chance. Actually, any physical state can be reached from a previous state with the help of chance. Nevertheless, biological behavior shows a remarkably consequent character that profoundly differs from the physical case, as the example of a living bird dropped from the Pisa tower indicates. The characteristic property of the trajectory of a living bird dropped from a height is that it regains, approximately, its original height. In general, biological behavior leads to the regeneration of the distance of the organism from thermodynamic equilibrium.
Thermodynamic systems are defined as consisting of statistically independent subsystems (Landau and Lifshitz, 1959). Now the Second Law of thermodynamics tells us that all isolated thermodynamic systems will develop towards equilibrium (ibid., section 8). Systems in thermodynamic equilibrium have independent, separable subsystems and so they manifest chance (e.g., thermal fluctuations) and necessity (the systems consisting of a large number of separable subsystems are governed by the determinate laws of physics). They cannot show organized changes, since their interactions are statistically independent and chaotic (ibid., section 1).
"Thermodynamics is the study of the macroscopic consequences of myriads of atomic coordinates, which, by virtue of the statistical averaging, do not appear explicitly in a macroscopic description of a system" (Callen, 1960, 7). In terms of complexity science, the random interactions of independent subsystems have no lawful algorithmic complexity representing the algorithmic complexity of the laws of nature (in the followings, shortly: algorithmic complexity), since their effects can be averaged out. In contrast, living organisms manifest an extremely high algorithmic and genetic complexity. Therefore the - let us use that term for the moment in a biological context - "subsystems" of living organisms do not form a pure thermodynamic system, and so their interactions cannot be averaged out to thermodynamic parameters like temperature or entropy only. In respect of biological behavior, living organisms are not thermodynamic systems. In living organisms, after averaging out all statistically chaotic interactions, something remains, and this something has a fundamental importance in understanding biological organization. It seems inevitable to allow that the non-randomness of living organisms' subsystems is directly related to their observed, profoundly non-physical behavior. Actually, living organisms do not have subsystems comparable to the ones of a thermodynamic system, since biological organization extends from the level of the whole organism downwards to the level of molecules and beyond. This means that systematic dependences exist between the entities existing at the molecular, submolecular and supramolecular levels of biological organization. These systematic dependences represent systematic interactions and couplings.
It seems to be clear that if a systematic coupling exists between the subsystems in a way that determines the behavior of these subsystems, we indeed leave the realm of physical systems and enter to the field of cybernetics. It is important to keep in mind that the behavior of living organisms is much subtler governed than cybernetic machines. The non-random mechanical couplings between the components make it possible to show definite functions manifested in refrigerators and airplanes. Actually, the behavior of living organisms is also characteristically non-random. Their mechanical couplings (like that of the bones of an athlete) are originated in subtle biological couplings, determining the contraction of its muscles. These subtle, non-random biological couplings act between the myosin and ATP molecules, between the muscular cells and the global organism of the athlete. At the deepest level, biological couplings are related to couplings between thermodynamically downhill (exergonic) and uphill (endergonic) biochemical reactions. (Green and Reible, 1975; Purves et al., 1992, 1, 137) For the sake of precision, we note that thermodynamically downhill processes are defined here on the global level with the thermodynamic state variable extropy, while endergonic and exergonic reactions are qualified at the level of individual biochemical reactions.
The basic fact of life is the avoidance of thermodynamic equilibrium, which corresponds to death. Living organisms live by utilizing their nonequilibrium energies. Their functions require high-level forms of energy at their input and low-level forms of energy at their output. Thermodynamic aspects of living organisms are accompanied by equilibration or downhill processes. In order to avoid equilibrium, living organisms must continuously realize thermodynamically uphill processes compensating the downhill ones. Life in this respect is the consequent activity against thermodynamic equilibrium. Therefore, living organisms have a fundamental characteristic in compensating the equilibration downhill processes by uphill ones. The regular appearance of uphill processes may seem as contradicting the Second Law, but only when ignoring the simultaneous downhill processes. Most of these downhill processes also serve in useful biological roles, for example, dissipating "low quality" thermal radiation. This dissipation is required to balance the incoming high quality energy; and the low quality (e.g. lower temperature) of the output thermal radiation offers a net gain of useful energy for the organism. Definitely, only with the help of biological couplings between the subsystems can the organism make its biological behavior so different from the physical.
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