Classical, quantum and biological randomness as relative unpredictability

International audienceWe propose the thesis that randomness is unpredictability with respect to an intended theory and measurement. From this point view we briefly discuss various forms of randomness that physics, mathematics and computing science have proposed. Computing science allows to discuss unpredictability in an abstract, yet very expressive way, which yields useful hierarchies of randomness and may help to relate its various forms in natural sciences. Finally we discuss biological randomness — its peculiar nature and role in ontogenesis and in evolutionary dynamics (phylogenesis). Randomness in biology has a positive character as it contributes to the organisms' and populations' structural stability by adaptation and diversity. Abstract We propose the thesis that randomness is unpredictability with respect to an intended theory and measurement. From this point view we briefly discuss various forms of randomness that physics, mathematics and computing science have proposed. Computing science allows to discuss unpredictability in an abstract, yet very expressive way, which yields useful hierarchies of randomness and may help to relate its various forms in natural sciences. Finally we discuss biological randomness—its peculiar nature and role in ontogenesis and in evolutionary dynamics (phylogenesis). Randomness in biology has a positive character as it contributes to the organisms' and populations' structural stability by adaptation and diversity

Effects of disorder on the wave front depinning transition in spatially discrete systems

Pinning and depinning of wave fronts are ubiquitous features of spatially discrete systems describing a host of phenomena in physics, biology, etc. A large class of discrete systems is described by overdamped chains of nonlinear oscillators with nearest-neighbor coupling and subject to random external forces. The presence of weak randomness shrinks the pinning interval and it changes the critical exponent of the wave front depinning transition from 1/2 to 3/2. This effect is derived by means of a recent asymptotic theory of the depinning transition, extended to discrete drift-diffusion models of transport in semiconductor superlattices and confirmed by numerical calculations.Comment: 4 pages, 3 figures, to appear as a Rapid Commun. in Phys. Rev.

Multi Layer Analysis

This thesis presents a new methodology to analyze one-dimensional signals trough a new approach called Multi Layer Analysis, for short MLA. It also provides some new insights on the relationship between one-dimensional signals processed by MLA and tree kernels, test of randomness and signal processing techniques. The MLA approach has a wide range of application to the fields of pattern discovery and matching, computational biology and many other areas of computer science and signal processing. This thesis includes also some applications of this approach to real problems in biology and seismology

Perturbation Detection Through Modeling of Gene Expression on a Latent Biological Pathway Network: A Bayesian hierarchical approach

Cellular response to a perturbation is the result of a dynamic system of biological variables linked in a complex network. A major challenge in drug and disease studies is identifying the key factors of a biological network that are essential in determining the cell's fate. Here our goal is the identification of perturbed pathways from high-throughput gene expression data. We develop a three-level hierarchical model, where (i) the first level captures the relationship between gene expression and biological pathways using confirmatory factor analysis, (ii) the second level models the behavior within an underlying network of pathways induced by an unknown perturbation using a conditional autoregressive model, and (iii) the third level is a spike-and-slab prior on the perturbations. We then identify perturbations through posterior-based variable selection. We illustrate our approach using gene transcription drug perturbation profiles from the DREAM7 drug sensitivity predication challenge data set. Our proposed method identified regulatory pathways that are known to play a causative role and that were not readily resolved using gene set enrichment analysis or exploratory factor models. Simulation results are presented assessing the performance of this model relative to a network-free variant and its robustness to inaccuracies in biological databases

Conservation, Creation, and Evolution: Revising the Darwinian Project

There is hardly anything more central to our universe than conservation. Many scientific fields and disciplines view the law of conservation as one of the most fundamental universal laws. The Darwinian model pivots the process of evolution on variability, reproduction, and natural selection. Conservation plays a marginal role in this model and is not really universal, as the model allows exceptions to conservation, i.e. non-conservation, to play an equally important role in evolution. This anomalous role of conservation in the Darwinian model raises questions: What is the reason for this anomaly? Is conservation really universal, as we tend to believe or is it not, as the Darwinian model suggests? This contribution proposes a new model of evolution that focuses on levels of organization, rather than of species, organisms, or populations. It argues that conservation is central to evolution. Not only does this new model restores the universal status of conservation but it also makes possible to resolve some outstanding problems and controversies that continue to plague the Darwinian model. The article tries to advance the broad Darwinian project that seeks to explain the process of evolution as a product of the spontaneous processes in nature