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Droplet formation has emerged as an essential concept for the spatiotemporal organisation of biomolecules in cells. However, classical descriptions of droplet dynamics based on passive liquid-liquid phase separation cannot capture the…
This review article provides a specific example of recombinant cell and protocell technology, moving from what is presently known to suggesting how novel application of existing methodologies could be utilized to design a complex synthetic…
Standard techniques for studying biological systems largely focus on their dynamical, or, more recently, their informational properties, usually taking either a reductionist or holistic perspective. Yet, studying only individual system…
In [N. A. Baas, Emergence, Hierarchies, and Hyper-structures, in C.G. Langton ed., Artificial Life III, Addison Wesley, 1994.] a general framework for the study of Emergence and hyper-structure was presented. This approach is mostly…
Living systems exhibit a range of fundamental characteristics: they are active, self-referential, self-modifying systems. This paper explores how these characteristics create challenges for conventional scientific approaches and why they…
The emergence of membranous compartments (protocells) with encapsulated genetic material was a crucial step life's origin and evolution. The hot spring hypothesis for the origin of life suggests that protocells could have formed in hot…
We survey some of the philosophical challenges and pitfalls within origins research. Several of these challenges exhibit circularities, paradoxes, or anthropic biases. We present origins approaches in terms of three broad categories:…
Laboratory experiments play a key role in deciphering the chemistry of the interstellar medium (ISM) and the role that product complex organic molecules (COMs) may play in the origins of life. However, to date, most studies in experimental…
Cell formation problem is among the first obstacles the designer of cellular production systems must overcome. This paper presents a critical analysis of the various criteria and constraints considered in the literature. The objective is to…
Life occurs in ionic solutions, not pure water. The ionic mixtures of these solutions are very different from water and have dramatic effects on the cells and molecules of biological systems, yet theories and simulations cannot calculate…
It is suggested that life originated in a three-step process referred to as the jigsaw model. RNA, proteins, or similar organic molecules polymerized in a dehydrated carbon-rich environment, on surfaces in a carbon-rich environment, or in…
A great number of biological organisms live in aqueous environments. Major evolutionary transitions, including the emergence of life itself, likely occurred in such environments. While the chemical aspects of the role of water in biology…
One of the main goals of Artificial Life is to research the conditions for the emergence of life, not necessarily as it is, but as it could be. Artificial Chemistries are one of the most important tools for this purpose because they provide…
The search for what differentiates inanimate matter from living things began in antiquity as a search for a "fundamental life force" embedded deep within living things - a special material unit owned only by life - later transforming to…
How do complex adaptive systems, such as life, emerge from simple constituent parts? In the 1990s Walter Fontana and Leo Buss proposed a novel modeling approach to this question, based on a formal model of computation known as $\lambda$…
Whole-cell computational models aim to predict cellular phenotypes from genotype by representing the entire genome, the structure and concentration of each molecular species, each molecular interaction, and the extracellular environment.…
This thesis is about the study of complex systems through simple models. Our work evidences the relevance of this kind of modeling in science, which provides us with a better understanding of nature at minimum cost. The fundamentals tools…
The evolution of complexity has been a central theme for Biology [2] and Artificial Life research [1]. It is generally agreed that complexity has increased in our universe, giving way to life, multi-cellularity, societies, and systems of…
A simple, heuristic formula with parallels to the Drake Equation is introduced to help focus discussion on open questions for the origins of life in a planetary context. This approach indicates a number of areas where quantitative progress…
Cells with the same genome can exist in different phenotypes. and can change between distinct phenotypes when subject to specific stimuli and microenvironments. Some examples include cell differentiation during development, reprogramming…