On the Criticality of Adaptive Boolean Network Robots.

Systems poised at a dynamical critical regime, between order and disorder, have been shown capable of exhibiting complex dynamics that balance robustness to external perturbations and rich repertoires of responses to inputs. This property has been exploited in artificial network classifiers, and preliminary results have also been attained in the context of robots controlled by Boolean networks. In this work, we investigate the role of dynamical criticality in robots undergoing online adaptation, i.

A third transition in science?

Since Newton, classical and quantum physics depend upon the 'Newtonian paradigm'. The relevant variables of the system are identified. For example, we identify the position and momentum of classical particles.

Quantum aspects of the brain-mind relationship: A hypothesis with supporting evidence.

If all aspects of the mind-brain relationship were adequately explained by classical physics, then there would be no need to propose alternatives. But faced with possibly unresolvable puzzles like qualia and free will, other approaches are required. In alignment with a suggestion by Heisenberg in 1958, we propose a model whereby the world consists of two elements: Ontologically real Possibles that do not obey Aristotle's law of the excluded middle, and ontologically real Actuals that do.

The hiatus between organism and machine evolution: Contrasting mixed microbial communities with robots.

Mixed microbial communities, usually composed of various bacterial and fungal species, are fundamental in a plethora of environments, from soil to human gut and skin. Their evolution is a paradigmatic example of intertwined dynamics, where not just the relations among species plays a role, but also the opportunities - and possible harms - that each species presents to the others. These opportunities are in fact affordances, which can be seized by heritable variations and selection.

Quantum Gravity If Non-Locality Is Fundamental.

I take non-locality to be the Michelson-Morley experiment of the early 21st century, assume its universal validity, and try to derive its consequences. Spacetime, with its locality, cannot be fundamental, but must somehow be emergent from entangled coherent quantum variables and their behaviors. There are, then, two immediate consequences: (i).

Attractor-Specific and Common Expression Values in Random Boolean Network Models (with a Preliminary Look at Single-Cell Data).

Random Boolean Networks (RBNs for short) are strongly simplified models of gene regulatory networks (GRNs), which have also been widely studied as abstract models of complex systems and have been used to simulate different phenomena. We define the "common sea" (CS) as the set of nodes that take the same value in all the attractors of a given network realization, and the "specific part" (SP) as the set of all the other nodes, and we study their properties in different ensembles, generated with different parameter values. Both the CS and of the SP can be composed of one or more weakly connected components, which are emergent intermediate-level structures.

Constraint Closure Drove Major Transitions in the Origins of Life.

Life is an epiphenomenon for which origins are of tremendous interest to explain. We provide a framework for doing so based on the thermodynamic concept of work cycles. These cycles can create their own closure events, and thereby provide a mechanism for engendering novelty.

Emergence of Organisms.

Since early cybernetics studies by Wiener, Pask, and Ashby, the properties of living systems are subject to deep investigations. The goals of this endeavour are both understanding and building: abstract models and general principles are sought for describing organisms, their dynamics and their ability to produce adaptive behavior. This research has achieved prominent results in fields such as artificial intelligence and artificial life.

Dynamics of a birth-death process based on combinatorial innovation.

A feature of human creativity is the ability to take a subset of existing items (e.g. objects, ideas, or techniques) and combine them in various ways to give rise to new items, which, in turn, fuel further growth.

Theory of chemical evolution of molecule compositions in the universe, in the Miller-Urey experiment and the mass distribution of interstellar and intergalactic molecules.

Chemical evolution is essential in understanding the origins of life. We present a theory for the evolution of molecule masses and show that small molecules grow by random diffusion and large molecules by a preferential attachment process leading eventually to life's molecules. It reproduces correctly the distribution of molecules found via mass spectroscopy for the Murchison meteorite and estimates the start of chemical evolution back to 12.

Average Fitness Differences on NK Landscapes.

The average fitness difference between adjacent sites in a fitness landscape is an important descriptor that impacts in particular the dynamics of selection/mutation processes on the landscape. Of particular interest is its connection to the error threshold phenomenon. We show here that this parameter is intimately tied to the ruggedness through the landscape's amplitude spectrum.

Systems Pharmacogenomic Landscape of Drug Similarities from LINCS data: Drug Association Networks.

Modern research in the biomedical sciences is data-driven utilizing high-throughput technologies to generate big genomic data. The Library of Integrated Network-based Cellular Signatures (LINCS) is an example for a large-scale genomic data repository providing hundred thousands of high-dimensional gene expression measurements for thousands of drugs and dozens of cell lines. However, the remaining challenge is how to use these data effectively for pharmacogenomics.

Molecular Diversity Required for the Formation of Autocatalytic Sets.

Systems chemistry deals with the design and study of complex chemical systems. However, such systems are often difficult to investigate experimentally. We provide an example of how theoretical and simulation-based studies can provide useful insights into the properties and dynamics of complex chemical systems, in particular of autocatalytic sets.

Criticality Distinguishes the Ensemble of Biological Regulatory Networks.

The hypothesis that many living systems should exhibit near-critical behavior is well motivated theoretically, and an increasing number of cases have been demonstrated empirically. However, a systematic analysis across biological networks, which would enable identification of the network properties that drive criticality, has not yet been realized. Here, we provide a first comprehensive survey of criticality across a diverse sample of biological networks, leveraging a publicly available database of 67 Boolean models of regulatory circuits.

Systematic drug perturbations on cancer cells reveal diverse exit paths from proliferative state.

During a cell state transition, cells travel along trajectories in a gene expression state space. This dynamical systems framework complements the traditional concept of molecular pathways that drive cell phenotype switching. To expose the structure that hinders cancer cells from exiting robust proliferative state, we assessed the perturbation capacity of a drug library and identified 16 non-cytotoxic compounds that stimulate MCF7 breast cancer cells to exit from proliferative state to differentiated state.

Prebiotic network evolution: six key parameters.

The origins of life likely required the cooperation among a set of molecular species interacting in a network. If so, then the earliest modes of evolutionary change would have been governed by the manners and mechanisms by which networks change their compositions over time. For molecular events, especially those in a pre-biological setting, these mechanisms have rarely been considered.

Prolegomenon to patterns in evolution.

Despite Darwin, we remain children of Newton and dream of a grand theory that is epistemologically complete and would allow prediction of the evolution of the biosphere. The main purpose of this article is to show that this dream is false, and bears on studying patterns of evolution. To do so, I must justify the use of the word "function" in biology, when physics has only happenings.

Gene-pair expression signatures reveal lineage control.

The distinct cell types of multicellular organisms arise owing to constraints imposed by gene regulatory networks on the collective change of gene expression across the genome, creating self-stabilizing expression states, or attractors. We curated human expression data comprising 166 cell types and 2,602 transcription-regulating genes and developed a data-driven method for identifying putative determinants of cell fate built around the concept of expression reversal of gene pairs, such as those participating in toggle-switch circuits. This approach allows us to organize the cell types into their ontogenic lineage relationships.

Searching the clinical fitness landscape.

Widespread unexplained variations in clinical practices and patient outcomes suggest major opportunities for improving the quality and safety of medical care. However, there is little consensus regarding how to best identify and disseminate healthcare improvements and a dearth of theory to guide the debate. Many consider multicenter randomized controlled trials to be the gold standard of evidence-based medicine, although results are often inconclusive or may not be generally applicable due to differences in the contexts within which care is provided.

A stochastic model of autocatalytic reaction networks.

Autocatalytic cycles are rather widespread in nature and in several theoretical models of catalytic reaction networks their emergence is hypothesized to be inevitable when the network is or becomes sufficiently complex. Nevertheless, the emergence of autocatalytic cycles has been never observed in wet laboratory experiments. Here, we present a novel model of catalytic reaction networks with the explicit goal of filling the gap between theoretical predictions and experimental findings.

Required levels of catalysis for emergence of autocatalytic sets in models of chemical reaction systems.

The formation of a self-sustaining autocatalytic chemical network is a necessary but not sufficient condition for the origin of life. The question of whether such a network could form "by chance" within a sufficiently complex suite of molecules and reactions is one that we have investigated for a simple chemical reaction model based on polymer ligation and cleavage. In this paper, we extend this work in several further directions.

Dynamical properties of a boolean model of gene regulatory network with memory.

Classical random Boolean networks (RBN) are not well suited to describe experimental data from time-course microarray, mainly because of the strict assumptions about the synchronicity of the regulatory mechanisms. In order to overcome this setback, a generalization of the RBN model is described and analyzed. Gene products (e.

Approaches to the origin of life on Earth.

I discuss briefly the history of the origin of life field, focusing on the "Miller" era of prebiotic synthesis, through the "Orgel" era seeking enzyme free template replication of single stranded RNA or similar polynucleotides, to the RNA world era with one of its foci on a ribozyme with the capacity to act as a polymerase able to copy itself. I give the history of the independent invention in 1971 by T. Ganti, M.