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Carbon nanotubes are often seen as the only alternative technology to silicon transistors. While they are the most likely short-term one, other longer-term alternatives should be studied as well. While contemplating biological neurons as an…
The improbability of a spontaneously generated self-assembling molecule has suggested that life began with a set of simpler, collectively replicating elements, such as an enclosed autocatalytic set of polymers (or protocell). Since…
A generative recurrent neural network is quickly trained in an unsupervised manner to model popular reinforcement learning environments through compressed spatio-temporal representations. The world model's extracted features are fed into…
Living organisms must respond to environmental changes. Generally, accurate and rapid responses are provided by simple, unidirectional networks that connect inputs with outputs. Besides accuracy and speed, biological responses should also…
We present a probabilistic generative model and efficient algorithm to model reciprocity in directed networks. Unlike other methods that address this problem such as exponential random graphs, it assigns latent variables as community…
Neo-Darwinian evolutionary theory explains how the appearance of purposive design in the sophisticated adaptations of living organisms can have come about without their intentionally being designed. The explanation relies crucially on the…
Recent computational experiments have demonstrated the spontaneous emergence of self-replicating programs across universal automata, artificial chemistries, and self-modifying code systems. Remarkably, these results arise without explicit…
The origin of life can be understood mathematically to be the origin of information that can replicate. The likelihood that entropy spontaneously becomes information can be calculated from first principles, and depends exponentially on the…
This paper describes a 2D particle system in which autopoietic vesicles that are able to grow, repair, and reproduce can emerge from an initial random distribution of individual components. The reproduction process also exhibits inheritance…
Evolutionary transitions occur when previously-independent replicating entities unite to form more complex individuals. Such transitions have profoundly shaped natural evolutionary history and occur in two forms: fraternal transitions…
Replica-mean-field models have been proposed to decipher the activity of neural networks via a multiply-and-conquer approach. In this approach, one considers limit networks made of infinitely many replicas with the same basic neural…
Predictive coding (PC) networks are a biologically interesting class of neural networks. Their layered hierarchy mimics the reciprocal connectivity pattern observed in the mammalian cortex, and they can be trained using local learning rules…
The rise of multicellularity in the early evolution of life represents a major challenge for evolutionary biology. Guidance for finding answers has emerged from disparate fields, from phylogenetics to modelling and synthetic biology, but…
A continuing frustration for origin of life scientists is that abiotic and, by extension, pre-biotic attempts to develop self-sustaining, evolving molecular systems tend to produce more dead-end substances than macromolecular products with…
The classical approach to protein folding inspired by statistical mechanics avoids the high dimensional structure of the conformation space by using effective coordinates. Here we introduce a network approach to capture the statistical…
The origin of cellular life can be described in terms of the transition from inorganic matter: solids, liquids and gases, to the emergence of cooperative assemblies of organic matter, DNA and proteins,capable of replication and metabolism.…
Often questions arise about old or extinct networks. What proteins interacted in a long-extinct ancestor species of yeast? Who were the central players in the Last.fm social network 3 years ago? Our ability to answer such questions has been…
Regulatory networks consist of interacting molecules with a high degree of mutual chemical specificity. How can these molecules evolve when their function depends on maintenance of interactions with cognate partners and simultaneous…
When someone mentions the name of a known person we immediately recall her face and possibly many other traits. This is because we possess the so-called associative memory, that is the ability to correlate different memories to the same…
For the vast majority of naturally occurring, small, single domain proteins folding is often described as a two-state process that lacks detectable intermediates. This observation has often been rationalized on the basis of a nucleation…