Related papers: A Probabilistic Framework for Quantifying Biologic…
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…
Selection is central to biological evolution, yet there has been no general experimental framework for quantifying selection in chemical systems before life. Here we demonstrate that selection in a prebiological chemical system can be…
Context dependence is central to the description of complexity. Keying on the pairwise definition of "set complexity" we use an information theory approach to formulate general measures of systems complexity. We examine the properties of…
The physiological tradition of biological research analyzes biological systems using reduced descriptions much as an engineer uses a 'black box' description of an amplifier. Simple models have been used by physiologists for a very long…
Mapping conformational heterogeneity of macromolecules presents a formidable challenge to X-ray crystallography and cryo-electron microscopy, which often presume its absence. This has severely limited our knowledge of the conformations…
Over the past two decades, enormous advances in the detection of exoplanets have taken place. Currently, we have discovered hundreds of earth-sized planets, several of them within the habitable zone of their star. In the coming years, the…
Biologists and physicists have a rich tradition of modeling living systems with simple models composed of a few interacting components. Despite the remarkable success of this approach, it remains unclear how to use such finely tuned models…
The universal concept of complexity by the dynamic redundance paradigm and the ensuing concept of extended dynamic fractality (physics/9806002) are applied here to higher levels of complexity corresponding to living systems. After recalling…
Assembly Theory (AT) was developed to help distinguish living from non-living systems. The theory is simple as it posits that the amount of selection or Assembly is a function of the number of complex objects where their complexity can be…
The ultimate goal of astrobiology is to determine the distribution and diversity of life in the universe. But as the word "biosignature" suggests, what will be detected is not life itself, but an observation implicating a particular process…
As urban critic Jane Jacobs conceived, a city is essentially the problem of organized complexity. What underlies the complexity refers to a structural factor, called living structure, which is defined as a mathematical structure composed of…
One of the most compelling problems in science consists in understanding how living systems process information. After all, the way they process information defines their capacities to learning and adaptation. There is an increasing…
Parameter inference and uncertainty quantification are important steps when relating mathematical models to real-world observations, and when estimating uncertainty in model predictions. However, methods for doing this can be…
Biological systems reach organizational complexity that far exceeds the complexity of any known inanimate objects. Biological entities undoubtedly obey the laws of quantum physics and statistical mechanics. However, is modern physics…
Network or graph structures are ubiquitous in the study of complex systems. Often, we are interested in complexity trends of these system as it evolves under some dynamic. An example might be looking at the complexity of a food web as…
Nature has found one method of organizing living matter, but maybe other options exist -- not yet discovered -- on how to create life. To study the life "as it could be" is the objective of an interdisciplinary field called Artificial Life…
The path toward the emergence of life in our biosphere involved several key events allowing for the persistence, reproduction and evolution of molecular systems. All these processes took place in a given environmental context and required…
Systems biology models are useful models of complex biological systems that may require a large amount of experimental data to fit each model's parameters or to approximate a likelihood function. These models range from a few to thousands…
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…
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…