Related papers: Combinatory Chemistry: Towards a Simple Model of E…
By uncovering the contrast between Artificial Intelligence and Natural-born Intelligence as a computational process, we define closed computing and open computing, and implement open computing within chemical reactions. This involves…
For over half a century, computer-aided structural elucidation systems (CASE) for organic compounds have relied on complex expert systems with explicitly programmed algorithms. These systems are often computationally inefficient for complex…
The role of historical contingency in the origin of life is one of the great unknowns in modern science. Only one example of life exists--one that proceeded from a single self-replicating organism (or a set of replicating hyper-cycles) to…
This paper explores a novel connection between a thermodynamic and a dynamical systems perspective on emergent dynamical order. We provide evidence for a conjecture that Hamiltonian systems with mixed chaos spontaneously find regular…
Natural selection favors the more successful individuals. This is the elementary premise that pervades common models of evolution. Under extreme conditions, however, the process may no longer be probabilistic. Those that meet certain…
A theory of aging based on the principles of the kinetics of chemical reactions and the rules of natural selection of organisms is proposed. The theory is based on a hypothesis that the biochemical processes in the organism can be described…
Aggregation-diffusion equations are foundational tools for modelling biological aggregations. Their principal use is to link the collective movement mechanisms of organisms to their emergent space use patterns in a concrete mathematical…
(Bi)multi-partite interaction patterns are commonly observed in real world systems which have inhibitory and excitatory couplings. We hypothesize these structural interaction pattern to be stable and naturally arising in the course of…
Background: The idea that autocatalytic sets played an important role in the origin of life is not new. However, the likelihood of autocatalytic sets emerging spontaneously has long been debated. Recently, progress has been made along two…
We present chemlambda (or the chemical concrete machine), an artificial chemistry with the following properties: (a) is Turing complete, (b) has a model of decentralized, distributed computing associated to it, (c) works at the level of…
We propose a generic model of eco-systems, with a {\it hierarchical} food web structure. In our computer simulations we let the eco-system evolve continuously for so long that that we can monitor extinctions as well as speciations over…
We develop a formal model of the emergence of self-constructing objects (e.g. heteropolymers with autocatalytic capability) in an open system, which don't contain such objects initially. The objects are constructed from subunits (e.g.…
At odds with a traditional view of molecular evolution that seeks a descent-with-modification relationship between functional sequences, new functions can emerge {\it de novo} with relative ease. At early times of molecular evolution,…
Chemical systems are interpreted through the species they contain and the reactions they may undergo, i.e., their chemical reaction network (CRN). In spite of their central importance to chemistry, the structure of CRNs continues to be…
Computational techniques are required for narrowing down the vast space of possibilities to plausible prebiotic scenarios, since precise information on the molecular composition, the dominant reaction chemistry, and the conditions for that…
We are often interested in decomposing complex, structured data into simple components that explain the data. The linear version of this problem is well-studied as dictionary learning and factor analysis. In this work, we propose a…
Combinatory logic shows that bound variables can be eliminated without loss of expressiveness. It has applications both in the foundations of mathematics and in the implementation of functional programming languages. The original…
Artificial swarm systems have been extensively studied and used in computer science, robotics, engineering and other technological fields, primarily as a platform for implementing robust distributed systems to achieve pre-defined…
Presented in this paper is a derivation of a 2D catalytic reaction-based model to solve combinatorial optimization problems (COPs). The simulated catalytic reactions, a computational metaphor, occurs in an artificial chemical reactor that…
Natural selection explains how life has evolved over millions of years from more primitive forms. The speed at which this happens, however, has sometimes defied formal explanations when based on random (uniformly distributed) mutations.…