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We explore the emergence of cooperation in the framework of evolutionary game theory. First we introduce the cooperation problem in a novel way that we believe it have important consequences in how problem is addressed. Then we present a…

Ecological systems are emergent features of ecological and adaptive dynamics of a community of interacting species. By natural selection through the abiotic environment and by co-adaptation within the community, species evolve, thereby…

Molecular chirality is critical to biochemical function, but it is unknown when chiral selectivity first became important in the evolutionary transition from geochemistry to biochemistry during the emergence of life. Here, we identify key…

How the very first nervous systems evolved remains a fundamental open question. Molecular and genomic techniques have revolutionized our knowledge of the molecular ingredients behind this transition but not yet provided a clear picture of…

Social dilemmas are an integral part of social interactions. Cooperative actions, ranging from secreting extra-cellular products in microbial populations to donating blood in humans, are costly to the actor and hence create an incentive to…

The recent success of large foundation models in artificial intelligence has prompted the emergence of chemical pre-trained models. Despite the growing interest in large molecular pre-trained models that provide informative representations…

Competitive exclusion, a key principle of ecology, can be generalized to understand many other complex systems. Individuals under surviving pressure tend to be different from others, and correlations among them change correspondingly to the…

Many organisms live in populations structured by space and by class, exhibit plastic responses to their social partners, and are subject to non-additive ecological and fitness effects. Social evolution theory has long recognized that all of…

Each living species carries a complex DNA sequence that determines their unique features and functionalities. It is generally assumed that life started from a random pool of oligonucleotides sequences, generated by a prebiotic…

Deep generative models have been shown powerful in generating novel molecules with desired chemical properties via their representations such as strings, trees or graphs. However, these models are limited in recommending synthetic routes…

Life on earth is distinguished by long-lived correlations in time. The patterns of material organization that characterize living organisms today are contingent on events that occurred billions of years ago. This contingency is a necessary…

Introducing environmental feedback into evolutionary game theory has led to the development of eco-evolutionary games, which have gained popularity due to their ability to capture the intricate interplay between the environment and…

Many complex adaptive systems contain a large diversity of specialized components. The specialization at the level of the microscopic degrees of freedom, and diversity at the level of the system as a whole are phenomena that appear during…

A fundamental issue discussed in evolutionary biology is the transition from unicellular to multicellular organisms. Here we develop non-robust models provided in [1] and attempt to get robust models investigated how differentiation of…

While all organisms on Earth descend from a common ancestor, there is no consensus on whether the origin of this ancestral self-replicator was a one-off event or whether it was only the final survivor of multiple origins. Here we use the…

Isologous diversification theory for cell differentiation is proposed, based on simulations of interacting cells with biochemical networks and cell division process following consumption of some chemicals. According to the simulations of…

Colloidal particles can create reconfigurable nanomaterials, with applications such as color-changing, self-repairing, and self-regulating materials and reconfigurable drug delivery systems. However, top-down methods for manipulating…

For understanding the origin of life, it is essential to explain the development of a compartmentalized structure, which undergoes growth and division, from a set of chemical reactions. In this study, a hypercycle with two chemicals that…

Metabolism and evolution are closely connected: if a mutation incurs extra energetic costs for an organism, there is a baseline selective disadvantage that may or may not be compensated for by other adaptive effects. A long-standing, but to…

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…