Related papers: Neutrally Evolving Interlocking Complexity in the …
Living systems, particularly multicellular systems, often seem hopelessly complex. But recent studies have suggested that beneath this complexity, there may be unifying quantitative principles that we are only now starting to unravel. All…
Across the tree of life, populations have evolved the capacity to contend with suboptimal conditions by engaging in dormancy, whereby individuals enter a reversible state of reduced metabolic activity. The resulting seed banks are complex,…
Biological systems are notorious for complex behavior within short timescales (e.g. metabolic activity) and longer time scales (e.g. evolutionary selection), along with their complex spatial organization. Because of their complexity and…
The metabolism is the motor behind the biological complexity of an organism. One problem of characterizing its large-scale structure is that it is hard to know what to compare it to. All chemical reaction systems are shaped by the same…
Artificial neurons with arbitrarily complex internal structure are introduced. The neurons can be described in terms of a set of internal variables, a set activation functions which describe the time evolution of these variables and a set…
We introduce a minimal model for the evolution of functional protein-interaction networks using a sequence-based mutational algorithm, and apply the model to study neutral drift in networks that yield oscillatory dynamics. Starting with a…
Even when concepts similar to emergence have been used since antiquity, we lack an agreed definition. However, emergence has been identified as one of the main features of complex systems. Most would agree on the statement ``life is…
Current analyses of genomes from numerous species show that the diversity of organism's functional and behavioral characters is not proportional to the number of genes that encode the organism. We investigate the hypothesis that the…
Noise is a ubiquitous feature of the physical world. As a result, the first prerequisite of life is fault tolerance: maintaining integrity of state despite external bombardment. Recent experimental advances have revealed that biological…
The evolution of microbial and viral organisms often generates clonal interference, a mode of competition between genetic clades within a population. In this paper, we show that interference strongly constrains the genetic and phenotypic…
The major biochemical networks of the living cell, the network of interacting genes and the network of biochemical reactions, are highly interdependent, however, they have been studied mostly as separate systems so far. In the last years an…
Cellular automata are interacting classical bits that display diverse emergent behaviors, from fractals to random-number generators to Turing-complete computation. We discover that quantum cellular automata (QCA) can exhibit complexity in…
While modern physics and biology satisfactorily explain the passage from the Big Bang to the formation of Earth and the first cells to present-day life, respectively, the origins of biochemical life still remain an open question. Since…
Binding interactions between proteins and other molecules mediate numerous cellular processes, including metabolism, signaling, and regulation of gene expression. These interactions evolve in response to changes in the protein's chemical or…
Biological systems are generally complicated and/or complex. In the former approach, one sets up a model with a large number of parameters to describe the system in detail. The latter approach focuses on understanding the universal aspects…
"Evolution behaves like a tinkerer" (Francois Jacob, Science, 1977). Software systems provide a unique opportunity to understand biological processes using concepts from network theory. The Debian GNU/Linux operating system allows us to…
Microbial communities routinely have several alternative stable states observed for the same environmental parameters. Sudden and irreversible transitions between these states make external manipulation of these systems more complicated. To…
Evolutionary dynamics is often viewed as a subtle process of change accumulation that causes a divergence among organisms and their genomes. However, this interpretation is an inheritance of a gradualistic view that has been challenged at…
When a neural network can learn multiple distinct algorithms to solve a task, how does it "choose" between them during training? To approach this question, we take inspiration from ecology: when multiple species coexist, they eventually…
We explore the complex dynamical behavior of simple predator-prey models of biological coevolution that account for interspecific and intraspecific competition for resources, as well as adaptive foraging behavior. In long kinetic Monte…