The success of Artificial Life depends on whether it will help solving the conceptual problems of biology. Biology may be viewed as the science of the transformation of organizations. And, yet, biology lacks a theory of organization. We use this as an example of the challenge that Artificial Life must meet. "If - as I believe - physics and chemistry are conceptually inadequate as a theoretical framework for biology, it is because they lack the concept of function, and hence that of organization. [...] [P]erhaps, therefore, we should give the [...] computer scientists more of a say in the formulation of Theoretical Biology." -- Christopher Longuet-Higgins, 1969 [29] 1 Life and the organization problem in biology There are two readings of "life": "life" as an embodied phenomenon and "life" as a concept. Foucault [20] points out that up to the end of the eighteenth century life does not exist: only living beings. Living beings are but a class in the series of all things in the world. T...

Assembling non-biological materials (geomaterials) into a proto-organism constitutes a bridge between nonliving and living matter. In this paper we present a simple step-by-step route to assemble a proto-organism. Many pictures have been proposed to describe this transition within the origins of life and artificial life communities and more recently alternative pictures are emerging from advances in nanoscience and biotechnology. The proposed proto-organism lends itself to both traditions and defines a new picture based on a simple idea: Given a set of required functionalities, minimize the physicochemical structures that support these functionalities, and make sure that all structures self-assemble and mutually enhance each other’s existence. The result is the first, concrete rational design of a simple physicochemical system that integrates the key functionalities in a thermodynamically favorable manner as a lipid aggregate integrates proto-genes and a proto-metabolism. Under external pumping of free energy, the metabolic processes produce the required building blocks, and only specific gene sequences enhance the metabolic kinetics sufficiently for the whole system to survive. We propose a concrete experimental implementation of the proto-organism with a

This paper gives details of Squirm3, a new artificial environment based on a simple physics and chemistry that supports self-replicating molecules somewhat similar to DNA.The self-replicators emerge spontaneously from a random soup given the right conditions.Interactions between the replicators can result in mutated versions that can out-perform their parents.We show how artificial chemistries such as this one can be implemented as a cellular automaton.We concur with [9] that artificial chemistries are a good medium in which to study early evolution.

The theory of autocatalytic binary ligation is reviewed within the context of a consistently applied Michaelis-Menten quasi-steady-state approximation to obtain explicit analytical results describing time-course data from experiments. A detailed protocol for the step-wise elucidation of a minimal set of experimental parameters is outlined. The kinetic equations are then generalized to cases of self- and cross-catalysis among an arbitrary number of different templates and applied to experiments involving just two templates. Depending on the values of various kinetic parameters such systems can display exclusionary Darwinian selection corresponding to an exponential growth law, selective coexistence or coexistence of all species characteristic of a parabolic growth law; the intermediate behaviour arises as a property of the full mechanism analysed here. Our results are applicable to the classical case of self-replicating nucleic acids and their analogues as well as to newly discovered sel...

A synthetic proto-organism could be self-assembled by integrating a lipid protocontainer with a proto-metabolic subsystem and a proto-genetic subsystem. This three-component system can use energy and nutrients either by means of redox or photo-chemical reactions, evolve its proto-genome by means of template directed replication, and ultimately die. The evolutionary dynamics of the proto-organism depends crucially on the chemical kinetics of its sub-systems and on their interplay. In this work the template replication kinetics is investigated and it is found that the product inhibition inherent in the ligation-like replication process allows for coexistence of unrelated self-replicating proto-genes in the lipid surface layer. The combined catalytic effects from the proto-genes on the metabolic production rates determine the fate of the strain proto-cell.

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We extend earlier cellular automata models of spatially extended hypercycles by including an explicit genetic component into the model. This allows us to study the sequence evolution of hypercyclically coupled molecular replicators in addition to considering their population dynamics and spatial organization. In line with previous models, that considered either spatial organization or sequence evolution alone, we find both temporal oscillations of the relative concentration of the species forming the hypercycles as well as the formation of spatial organisations including spiral waves. We also confirm the greatly increased robustness of the spatially extended hypercycle against various classes of parasites. We find the sequence evolution of each of the hypercyclically coupled populations proceeds (after an inital selection-dominated phase) in a drift-like manner that can be described by a diffusion process in sequence space. Kimura’s theory of neutral evolution is therefore applicable on long time-scales despite the fact that the hypercycle exhibits extreme periodic changes in population sizes and that are governed solely by frequency-dependent selection.

The population dynamics of macromolecules that reproduce by means of template-directed ligation of two fragments are shown to be represented by a replicator equation with a special non-linear response function. This result is obtained through detailed consideration of the mechanism of ligation autocatalysis. In contrast to treatments which involve simplification to a parabolic growth law and the expectation of global coexistence of all species, we find that strong selection can take place in such systems, even when there is slow uncatalysed synthesis of replicators. Also, systems of this type are subject to invasion by new species that have a selective advantage. An expression is derived for the survival threshold in terms of species parameters and it is shown that this threshold depends on the total concentration of all species in the system. For a plausible distribution of species parameters, the number of surviving species coexisting above the threshold increases monotonically with increasing concentration. Illustrative numerical simulations are presented.

RNA and protein molecules were found to be both templates for replication and specific catalysts for biochemical reactions. RNA molecules, although very difficult to obtain via plausible synthetic pathways under prebiotic conditions, are the only candidates for early replicons. Only they are obligatory templates for replication which can conserve mutations and propagate them to forthcoming generations. RNA based catalysts, called ribozymes, act with high efficiency and specificity on all classes of reactions involved in the interconversion of RNA molecules such as cleavage and template assisted ligation. The idea of an RNA world was conceived for a plausible prebiotic scenario of RNA molecules operating upon each other and constituting thereby a functional molecular organization. A theroretical account on molecular replication making precise the conditions under which one observes parabolic or exponential growth is presented. Exponential growth is observed in a protein assisted RNA wor...