Related papers: Physical foundations of biological complexity
A central biological question is how natural organisms are so evolvable (capable of quickly adapting to new environments). A key driver of evolvability is the widespread modularity of biological networks--their organization as functional,…
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…
In this paper we will try to provide a formalization of some characteristics of the development of biological systems aiming at the highest level of adequacy: justificative adequacy, that is, not only what we observe (descriptive adequacy)…
Biological systems, unlike physical or chemical systems, are characterized by the very inhomogeneous distribution of their components. The immune system, in particular, is notable for self-organizing its structure. Classically, the dynamics…
This paper is concerned with complex macroscopic behaviour arising in many-body systems through the combinations of competitive interactions and disorder, even with simple ingredients at the microscopic level. It attempts to indicate and…
The question What is Complexity? has occupied a great deal of time and paper over the last 20 or so years. There are a myriad different perspectives and definitions but still no consensus. In this paper I take a phenomenological approach,…
In this review, we discuss modularity and hierarchy in biological systems. We review examples from protein structure, genetics, and biological networks of modular partitioning of the geometry of biological space. We review theories to…
After more than a century of concerted effort, physics still lacks basic principles of spontaneous self-organization. To appreciate why, we first state the problem, outline historical approaches, and survey the present state of the physics…
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,…
The origin of life is shrouded in mystery, with few surviving clues, obscured by evolutionary competition. Previous reviews have touched on the complementary approaches of top-down and bottom-up synthetic biology to augment our…
At present, there is a great deal of confusion regarding complexity and its measures (reviews on complexity measures are found in, e.g. Lloyd, 2001 and Shalizi, 2006 and more references therein). Moreover, there is also confusion regarding…
The intuition that a long history is required for the emergence of complexity in natural systems is formalized using the notion of depth. The depth of a system is defined in terms of the number of parallel computational steps needed to…
Cooperation is a widespread natural phenomenon yet current evolutionary thinking is dominated by the paradigm of selfish competition. Recent advanced in many fronts of Biology and Non-linear Physics are helping to bring cooperation to its…
What features characterise complex system dynamics? Power laws and scale invariance of fluctuations are often taken as the hallmarks of complexity, drawing on analogies with equilibrium critical phenomena[1-3]. Here we argue that slow,…
Non-uniform rates of morphological evolution and evolutionary increases in organismal complexity, captured in metaphors like "adaptive zones", "punctuated equilibrium" and "blunderbuss patterns", require more elaborate explanations than a…
Complexity Theory is highly interdisciplinary, therefore any regularities must hold on all levels of organization, independent on the nature of the system. An open question in science is how complex systems self-organize to produce emergent…
Species coexistence is one of the central themes in modern ecology. Coexistence is a prerequisite of biological diversity. However, the question arises how biodiversity can be reconciled with the statement of competition theory, which…
The last decade has witnessed a rapid growth in understanding of the pivotal roles of mechanical stresses and physical forces in cell biology. As a result an integrated view of cell biology is evolving, where genetic and molecular features…
Biomolecules are the prime information processing elements of living matter. Most of these inanimate systems are polymers that compute their structures and dynamics using as input seemingly random character strings of their sequence,…
Why are living systems complex? Why does the biosphere contain living beings with complexity features beyond those of the simplest replicators? What kind of evolutionary pressures result in more complex life forms? These are key questions…