Related papers: Biology is a constructive physics
With the number of sequenced genomes now over one hundred, and the availability of rough functional annotations for a substantial proportion of their genes, it has become possible to study the statistics of gene content across genomes. Here…
Research in quantitative evolutionary genomics and systems biology led to the discovery of several universal regularities connecting genomic and molecular phenomic variables. These universals include the log-normal distribution of the…
Complex systems throughout Nature display structures and functions that are built and maintained, at least in part, by optimal energies flowing through them--not specific, ideal values, rather ranges in energy rate density below which…
This review is an introduction to theoretical models and mathematical calculations for biological evolution, aimed at physicists. The methods in the field are naturally very similar to those used in statistical physics, although the…
In this paper we derive a statistical law of Life. It governs the probability of death, or complementary of survival, of the living organisms. We have deduced such a law coupling the widely used Weibull statistics, developed for describing…
Zipf's law in its basic incarnation is an empirical probability distribution governing the frequency of usage of words in a language. As Terence Tao recently remarked, it still lacks a convincing and satisfactory mathematical explanation.…
Evolutionary biology shares many concepts with statistical physics: both deal with populations, whether of molecules or organisms, and both seek to simplify evolution in very many dimensions. Often, methodologies have undergone parallel and…
We discuss the relevance of studying ecology within the framework of Complexity Science from a statistical mechanics approach. Ecology is concerned with understanding how systems level properties emerge out of the multitude of interactions…
One of the classical questions in evolutionary biology is how evolutionary processes are coupled at the gene and species level. With this motivation, we compare the topological properties (mainly the depth scaling, as a characterization of…
Systems evolving according to the standard concept of biological or technological evolution are often described by catalytic evolution equations. We study the structure of these equations and find a deep relationship to classical…
Zipf's law describes the empirical size distribution of the components of many systems in natural and social sciences and humanities. We show, by solving a statistical model, that Zipf's law co-occurs with the maximization of the diversity…
With the number of fully-sequenced genomes now well over a hundred it has become possible to start investigating if there are any quantitative regularities in the genetic make-up of genomes. In (physics/0307001), I originally showed that…
The rank-size plots of a large number of different physical and socio-economic systems are usually said to follow Zipf's law, but a unique framework for the comprehension of this ubiquitous scaling law is still lacking. Here we show that a…
Quantitative linguistics has provided us with a number of empirical laws that characterise the evolution of languages and competition amongst them. In terms of language usage, one of the most influential results is Zipf's law of word…
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 has fascinated quantitative and physical scientists for decades: how can the random process of mutation, recombination, and duplication of genetic information generate the diversity of life? What determines the rate of evolution?…
In the present article the recent works to formulate laws in Darwinian evolutionary dynamics are discussed. Although there is a strong consensus that general laws in biology may exist, opinions opposing such suggestion are abundant. Based…
"Epigenetic Tracking" is a model of systems of biological cells, able to generate arbitrary 2 or 3-dimensional cellular shapes of any kind and complexity (in terms of number of cells, number of colours, etc.) starting from a single cell. If…
We axiomatize the molecular-biology reasoning style, show compliance of the standard reference: Ptashne, A Genetic Switch, and present proof-theory-induced technologies to help infer phenotypes and to predict life cycles from genotypes. The…
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)…