Artificial Chemistries (ACs) are symbolic chemical metaphors for the exploration of Artificial Life, with specific focus on the origin of life. In this work we define a P system based artificial graph chemistry to understand the principles leading to the evolution of life-like structures in an AC set up and to develop a unified framework to characterize and classify symbolic artificial chemistries by devising appropriate formalism to capture semantic and organizational information. An extension of P system is considered by associating probabilities with the rules providing the topological framework for the evolution of a labeled undirected graph based molecular reaction semantics.
Due to recent advances in synthetic biology and artificial life, the origin of life is currently a hot topic of research. We review the literature and argue that the two traditionally competing "replicator-first" and "metabolism-first" approaches are merging into one integrated theory of individuation and evolution. We contribute to the maturation of this more inclusive approach by highlighting some problematic assumptions that still lead to an impoverished conception of the phenomenon of life. In particular, we argue that the new consensus has so far failed to consider the relevance of intermediate timescales. We propose that an adequate theory of life must account for the fact that all living beings are situated in at least four distinct timescales, which are typically associated with metabolism, motility, development, and evolution. On this view, self-movement, adaptive behavior and morphological changes could have already been present at the origin of life. In order to illustrate this possibility we analyze a minimal model of life-like phenomena, namely of precarious, individuated, dissipative structures that can be found in simple reaction-diffusion systems. Based on our analysis we suggest that processes in intermediate timescales could have already been operative in prebiotic systems. They may have facilitated and constrained changes occurring in the faster- and slower-paced timescales of chemical self-individuation and evolution by natural selection, respectively.
Formalizing self reproduction in dynamical hierarchies is one of the important problems in Artificial Life (AL) studies. We study, in this paper, an inductively defined algebraic framework for self reproduction on macroscopic organizational levels under dynamical system setting for simulated AL models and explore some existential results. Starting with defining self reproduction for atomic entities we define self reproduction with possible mutations on higher organizational levels in terms of hierarchical sets and the corresponding inductively defined `meta' - reactions. We introduce constraints to distinguish a collection of entities from genuine cases of emergent organizational structures.
We provide a framework for experimentation at https://mbuliga.github.io/quinegraphs/ic-vs-chem.html#icvschem with two artificial chemistries: directed interaction combinators (dirIC, defined in section 2) and chemlambda. We are interested if these chemistries allow for artificial life behaviour: replication, metabolism and death. The main conclusion of these experiments is that graph rewrites systems which allow conflicting rewrites are better than those which don't, as concerns their artificial life properties. This is in contradiction with the search for good graph rewrite systems for decentralized computing, where non-conflicting graph rewrite systems are historically preferred. This continues the artificial chemistry experiments with chemlambda, lambda calculus or interaction combinators, available from the entry page at https://chemlambda.github.io/index.html and described in arXiv:2003.14332.
Concepts similar to emergence have been used since antiquity, but we lack an agreed definition of emergence. Still, emergence has been identified as one of the features of complex systems. Most would agree on the statement "life is complex". Thus, understanding emergence and complexity should benefit the study of living systems. It can be said that life emerges from the interactions of complex molecules. But how useful is this to understand living systems? Artificial life (ALife) has been developed in recent decades to study life using a synthetic approach: build it to understand it. ALife systems are not so complex, be them soft (simulations), hard (robots), or wet (protocells). Then, we can aim at first understanding emergence in ALife, for then using this knowledge in biology. I argue that to understand emergence and life, it becomes useful to use information as a framework. In a general sense, emergence can be defined as information that is not present at one scale but is present at another scale. This perspective avoids problems of studying emergence from a materialistic framework, and can be useful to study self-organization and complexity.