Related papers: Neutrally Evolving Interlocking Complexity in the …
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 common assumption in evolutionary thought is that adaptation drives an increase in biological complexity. However, the rules governing evolution of complexity appear more nuanced. Evolution is deeply connected to learning, where…
Enzymes are on the front lines of evolution. All living organisms rely on highly efficient, specific enzymes for growth, sustenance, and reproduction; and many diseases are a consequence of a mutation on an enzyme that affects its catalytic…
The possibility that evolutionary forces -- together with a few fundamental factors such as thermodynamic constraints, specific computational features enabling information processing, and ecological processes -- might constrain the logic of…
Protein evolution underpins life, and understanding its behavior as a system is of great importance. However, our current models of protein evolution are arguably too simplistic to allow quantitative interpretation and prediction of…
We study genetic networks that produce many species of non-coding RNA molecules that are present at a moderate density, as typically exists in the cell. The associations of the many species of these RNA are modeled physically, taking 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…
Evolutionary complexity is here measured by the number of trials/evaluations needed for evolving a logical gate in a non-linear medium. Behavioural complexity of the gates evolved is characterised in terms of cellular automata behaviour. We…
Complex systems with tightly coadapted parts frequently appear in living systems and are difficult to account for through Darwinian evolution, that is random variation and natural selection, if the constituent parts are independently coded…
A common trait of complex systems is that they can be represented by means of a network of interacting parts. It is, in fact, the network organisation (more than the parts) what largely conditions most higher-level properties, which are not…
In order to make a case for or against a trend in the evolution of complexity in biological evolution, complexity needs to be both rigorously defined and measurable. A recent information-theoretic (but intuitively evident) definition…
Biological networks have evolved to be highly functional within uncertain environments while remaining extremely adaptable. One of the main contributors to the robustness and evolvability of biological networks is believed to be their…
Many organisms exhibit branching morphologies that twist around each other and become entangled. Entanglement occurs when different objects interlock, creating complex and often irreversible configurations. This physical phenomenon is…
At odds with a traditional view of molecular evolution that seeks a descent-with-modification relationship between functional sequences, new functions can emerge {\it de novo} with relative ease. At early times of molecular evolution,…
A protein's function depends critically on its conformational ensemble, a collection of energy weighted structures whose balance depends on temperature and environment. Though recent deep learning (DL) methods have substantially advanced…
The evolution of structure in biology is driven by accretion and change. Accretion brings together disparate parts to form bigger wholes. Change provides opportunities for growth and innovation. Here we review patterns and processes that…
Through extensive studies of dynamical system modeling cellular growth and reproduction, we find evidence that complexity arises in multicellular organisms naturally through evolution. Without any elaborate control mechanism, these systems…
The ubiquity of modules in biological networks may result from an evolutionary benefit of a modular organization. For instance, modularity may increase the rate of adaptive evolution, because modules can be easily combined into new…
Biological systems, from a cell to the human brain, are inherently complex. A powerful representation of such systems, described by an intricate web of relationships across multiple scales, is provided by complex networks. Recently, several…
Continuing generation of novelty, complexity, and adaptation are well-established as core aspects of open-ended evolution. However, it has yet to be firmly established to what extent these phenomena are coupled and by what means they…