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Self-organization plays a key role in specifying the cellular architecture.

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Most proteins are functionally promiscuous and interact opportunistically.

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Directed movement occurs in the absence of design by generating order out of chaos.

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The non-genetic heterogeneity of cell populations implies that every cell is unique.

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Physics, not engineering, proves most helpful in understanding cellular complexity.

It has become customary to conceptualize the living cell as an intricate piece of machinery, different to a man-made machine only in terms of its superior complexity. This familiar understanding grounds the conviction that a cell’s organization can be explained reductionistically, as well as the idea that its molecular pathways can be construed as deterministic circuits. The machine conception of the cell owes a great deal of its success to the methods traditionally used in molecular biology. However, the recent introduction of novel experimental techniques capable of tracking individual molecules within cells in real time is leading to the rapid accumulation of data that are inconsistent with an engineering view of the cell. This paper examines four major domains of current research in which the challenges to the machine conception of the cell are particularly pronounced: cellular architecture, protein complexes, intracellular transport, and cellular behaviour. It argues that a new theoretical understanding of the cell is emerging from the study of these phenomena which emphasizes the dynamic, self-organizing nature of its constitution, the fluidity and plasticity of its components, and the stochasticity and non-linearity of its underlying processes.

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Several modern theories of the essence of life exist.

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These were developed essentially independently of one another.

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They include some common themes, notably the idea of closure.

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All lack a system of regulation to prevent uncontrolled growth.

Most attempts to define life have concentrated on individual theories, mentioning others hardly at all, but here we compare all of the major current theories. We begin by asking how we know that an entity is alive, and continue by describing the contributions of La Mettrie, Burke, Leduc, Herrera, Bahadur, D’Arcy Thompson and, especially, Schrödinger, whose book What is Life? is a vital starting point. We then briefly describe and discuss (M, R) systems, the hypercycle, the chemoton, autopoiesis and autocatalytic sets. All of these incorporate the idea of circularity to some extent, but all of them fail to take account of mechanisms of metabolic regulation, which we regard as crucial if an organism is to avoid collapsing into a mass of unregulated reactions. In a final section we study the extent to which each of the current theories can aid in the search for a more complete theory of life, and explain the characteristics of metabolic control analysis that make it essential for an adequate understanding of organisms.

The origins, evolution and functioning of the Biosphere have occupied humankind for as long as recorded history has existed. In this paper we examine the claims of thermodynamics to be the framework within which we can understand the evolution, functioning and development of the Biosphere, exploring the evidence from ecology, molecular science and evolutionary biology, and particularly focussing upon the maximum entropy production principle (MEPP), and its explanatory potential in terms of many of the logistic relationships found within the Biosphere. We introduce the genetic entropy paradox, where the DNA increases in terms of internal information entropy, as the genetic code is continuously randomized through mutation, and yet this leads to increasing external entropy production, as increasingly more complicated structures and functions are produced in the form of new protein morphologies and metabolic pathways (again determined by the bioenergetic context). We suggest that the central dogma acts as a form of entropy exchange mechanism, but at the core of this is change in information entropy, which increases within the genetic code, and decreases within the organism. This would appear to be a truly unique event, and highlights a key interaction between two levels of organization within the Biosphere, the genome and the proteome, in terms of entropy production. The Biosphere is seen as being composed of a series of self-organizing sub-groups, each maximizing entropy production within the constraints of time, feedback and system constraints. The entropic production of the Biosphere is thus an emergent property.