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The present view of biological phenomena is based on a biochemical paradigm that development of living organisms is defined by information stored in a molecular form as some genetic code. However, new discoveries indicate that biological…
Our knowledge of how individual cells self-organize to form complex multicellular systems is being revolutionized by a data outburst, coming from high-throughput experimental breakthroughs such as single-cell RNA sequencing and spatially…
A continuous route from a disordered soup of simple chemical feedstocks to a functional protocell -- a compartment that metabolizes, grows, and propagates -- remains elusive. Here, we show that a homogeneous aqueous chemical mixture…
The study of origins of life on Earth and the search for life on other planets are closely linked. Prebiotic chemical scenarios can help prioritize planets as targets for the search for life as we know it and can provide informative priors…
The molecular biology revolution of the last seventy five years has transformed our view of living systems. Scientific explanations of biological phenomena are now synonymous with the identification of the genes, proteins, and signaling…
This note presents a minimal approach to the origin of life, following standard ideas. We pay special attention to the point of view of non-equilibrium statistical mechanics, and in particular to detailed balance. As a consequence we…
Composition is a powerful principle for systems biology, focused on the interfaces, interconnections, and orchestration of distributed processes to enable integrative multiscale simulations. Whereas traditional models focus on the structure…
The complex physicochemical structures and chemical reactions in living organism have some common features: (1) The life processes take place in the cytosol in the cells, which, from a physicochemical point of view is an emulsion of…
Can prelife proceed without cell division? A recently proposed mechanism suggests that transient compartmentalization could have preceded cell division in prebiotic scenarios. Here, we study transient compartmentalization dynamics in the…
Epigenetic Tracking is a mathematical model of biological cells, originally conceived to study embryonic development. Computer simulations proved the capacity of the model to generate complex 3-dimensional cellular structures, and the…
This work is an attempt for a state-of-the-art survey of natural and life sciences with the goal to define the scope and address the central questions of an original research program. It is focused on the phenomena of emergence, adaptive…
Achieving advanced machine intelligence remains a central challenge in AI research, often approached through scaling neural architectures and generative models. However, biological systems offer a broader repertoire of strategies for…
If human societies are so complex, then how can we hope to understand them? Artificial Life gives us one answer. The field of Artificial Life comprises a diverse set of introspective studies that largely ask the same questions, albeit from…
With the completion of human genome mapping, the focus of scientists seeking to explain the biological complexity of living systems is shifting from analyzing the individual components (such as a particular gene or biochemical reaction) to…
A modeling formalism is proposed for the description and study of living and life-like systems. It provides an abstract conceptual model framework for real life and evolution of biological organisms. It is proposed, that this model…
With unprecedented advances in genetic engineering we are starting to see progressively more original examples of synthetic life. As such organisms become more common it is desirable to be able to distinguish between natural and artificial…
Metabolic networks perform some of the most fundamental functions in living cells, including energy transduction and building block biosynthesis. While these are the best characterized networks in living systems, understanding their…
All aspects of our society, including the life sciences, need a mechanism for people working within them to represent the concepts they employ to carry out their research. For the information systems being designed and developed to support…
Despite great advances in our understanding of the formation of the Solar System, the evolution of the Earth, and the chemical basis for life, we are not much closer than the ancient Greeks to an answer of whether life has arisen and…
Multicellular self-organization drives development in biological organisms, yet a comprehensive theory is lacking as basic properties of cells can complicate common approaches. Framing such properties by dynamic graphs led to new…