scholarly journals Engineering self-organized criticality in living cells

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Blai Vidiella ◽  
Antoni Guillamon ◽  
Josep Sardanyés ◽  
Victor Maull ◽  
Jordi Pla ◽  
...  
Keyword(s):  
Critical Point ◽  
Gene Network ◽  
Feedback Loop ◽  
Living Cells ◽  
Brain Dynamics ◽  
E Coli ◽  
Order And Disorder ◽  
Self Organized ◽  
Self Organized Criticality ◽  
Dynamical Fluctuations

AbstractComplex dynamical fluctuations, from intracellular noise, brain dynamics or computer traffic display bursting dynamics consistent with a critical state between order and disorder. Living close to the critical point has adaptive advantages and it has been conjectured that evolution could select these critical states. Is this the case of living cells? A system can poise itself close to the critical point by means of the so-called self-organized criticality (SOC). In this paper we present an engineered gene network displaying SOC behaviour. This is achieved by exploiting the saturation of the proteolytic degradation machinery in E. coli cells by means of a negative feedback loop that reduces congestion. Our critical motif is built from a two-gene circuit, where SOC can be successfully implemented. The potential implications for both cellular dynamics and behaviour are discussed.

scholarly journals Engineering Self-Organized Criticality in Living Cells

2020 ◽  
Author(s):  
Blai Vidiella ◽  
Antoni Guillamon ◽  
Josep Sardanyes ◽  
Victor Maull ◽  
Nuria Conde ◽  
...  
Keyword(s):  
Critical Point ◽  
Gene Networks ◽  
Collective Intelligence ◽  
Living Cells ◽  
Intracellular Traffic ◽  
E Coli ◽  
Order And Disorder ◽  
Self Organized ◽  
Molecular Noise ◽  
Self Organized Criticality

Complex dynamical fluctuations, from molecular noise within cells, collective intelligence, brain dynamics or computer traffic have been shown to display noisy behaviour consistent with a critical state between order and disorder. Living close to the critical point can have a number of adaptive advantages and it has been conjectured that evolution could select (and even tend to) these critical states. One way of approaching such state is by means of so-called self-organized criticality (SOC) where the system poises itself close to the critical point. Is this the case of living cells? It is difficult to test this idea given the enormous dimensionality associated with gene and metabolic webs. In this paper, we present an alternative approach: to engineer synthetic gene networks displaying SOC behaviour. This is achieved by exploiting the presence of a saturation (congestion) phenomenon of the ClpXP protein degradation machinery in E. coli cells. Using a feedback design that detects and then reduces ClpXP congestion, a {\em critical motif} is built from a two-gene network system, where SOC can be successfully implemented. Both deterministic and stochastic models are used, consistently supporting the presence of criticality in intracellular traffic. The potential implications for both cellular dynamics and designed intracellular noise are discussed.

scholarly journals Engineering self-organized criticality in living cells

2020 ◽  
Author(s):  
Blai Vidiella ◽  
Antoni Guillamon ◽  
Josep Sardanyes ◽  
Victor Maull ◽  
Nuria Conde ◽  
...  
Keyword(s):  
Critical Point ◽  
Gene Networks ◽  
Collective Intelligence ◽  
Living Cells ◽  
Intracellular Traffic ◽  
E Coli ◽  
Order And Disorder ◽  
Self Organized ◽  
Molecular Noise ◽  
Self Organized Criticality

Abstract Complex dynamical fluctuations, from molecular noise within cells, collective intelligence, brain dynamics or computer traffic have been shown to display noisy behaviour consistent with a critical state between order and disorder. Living close to the critical point can have a number of adaptive advantages and it has been conjectured that evolution could select (and even tend to) these critical states. One way of approaching such state is by means of so called self-organized criticality (SOC) where the system poises itself close to the critical point. Is this the case of living cells? It is difficult to test this idea given the enormous dimensionality associated with gene and metabolic webs. In this paper we present an alternative approach: to engineer synthetic gene networks displaying SOC behaviour. This is achieved by exploiting the presence of a saturation (congestion) phenomenon of the ClpXP protein degradation machinery in E. coli cells. Using a feedback design that detects and then reduces ClpXP congestion, a critical motif is built from a two-gene network system, where SOC can be successfully implemented. Both deterministic and stochastic models are used, consistently supporting the presence of criticality in intracellular traffic. The potential implications for both cellular dynamics and designed intracellular noise are discussed.

scholarly journals Engineering self-organized criticality in living cells

2020 ◽  
Author(s):  
Blai Vidiella ◽  
Antoni Guillamon ◽  
Josep Sardanyés ◽  
Victor Maull ◽  
Nuria Conde-Pueyo ◽  
...  
Keyword(s):  
Critical Point ◽  
Gene Networks ◽  
Collective Intelligence ◽  
Living Cells ◽  
Intracellular Traffic ◽  
E Coli ◽  
Order And Disorder ◽  
Self Organized ◽  
Molecular Noise ◽  
Self Organized Criticality

Complex dynamical fluctuations, from molecular noise within cells, collective intelligence, brain dynamics or computer traffic have been shown to display noisy behaviour consistent with a critical state between order and disorder. Living close to the critical point can have a number of adaptive advantages and it has been conjectured that evolution could select (and even tend to) these critical states. One way of approaching such state is by means of so called self-organized criticality (SOC) where the system poises itself close to the critical point. Is this the case of living cells? It is difficult to test this idea given the enormous dimensionality associated with gene and metabolic webs. In this paper we present an alternative approach: to engineer synthetic gene networks displaying SOC behaviour. This is achieved by exploiting the presence of a saturation (congestion) phenomenon of the ClpXP protein degradation machinery in E. coli cells. Using a feedback design that detects and then reduces ClpXP congestion, a critical motif is built from a two-gene network system, where SOC can be successfully implemented. Both deterministic and stochastic models are used, consistently supporting the presence of criticality in intracellular traffic. The potential implications for both cellular dynamics and designed intracellular noise are discussed.

Complexity and Criticality

2020 ◽  
pp. 42-50
Author(s):  
Helmut Satz
Keyword(s):  
Complex System ◽  
Complex Systems ◽  
Critical Point ◽  
Correlation Length ◽  
Critical Behavior ◽  
Scale Free ◽  
Self Organized ◽  
Self Organized Criticality ◽  
Free Behavior

Complex systems and critical behavior in complex system are defined in terms of correlation between constituents in the medium, subject to screening by intermediate constituents. At a critical point, the correlation length diverges—as a result, one finds the scale-free behavior also observed for bird flocks. This behavior is therefore possibly a form of self-organized criticality.

scholarly journals The emergence of integrated information, complexity, and consciousness at criticality

2019 ◽  
Author(s):  
Sina Khajehabdollahi ◽  
Pubuditha M. Abeyasinghe ◽  
Adrian M. Owen ◽  
Andrea Soddu
Keyword(s):  
Phase Transition ◽  
Ising Model ◽  
Critical Point ◽  
Critical Systems ◽  
Dynamical Phase ◽  
Self Organized ◽  
Self Organized Criticality ◽  
Ancient Problem ◽  
Emergence Of Complexity ◽  
Integrated Information

AbstractUsing the critical Ising model of the brain, integrated information as a measure of consciousness is measured in toy models of generic neural networks. Monte Carlo simulations are run on 159 random weighted networks analogous to small 5-node neural network motifs. The integrated information generated by this sample of small Ising models is measured across the model parameter space. It is observed that integrated information, as a type of order parameter not unlike a concept like magnetism, undergoes a phase transition at the critical point in the model. This critical point is demarcated by the peaks of the generalized susceptibility of integrated information, a point where the ‘consciousness’ of the system is maximally susceptible to perturbations and on the boundary between an ordered and disordered form. This study adds further evidence to support that the emergence of consciousness coincides with the more universal patterns of self-organized criticality, evolution, the emergence of complexity, and the integration of complex systems.Author summaryUnderstanding consciousness through a scientific and mathematical language is slowly coming into reach and so testing and grounding these emerging ideas onto empirical observations and known systems is a first step to properly framing this ancient problem. This paper in particular explores the Integrated Information Theory of Consciousness framed within the physics of the Ising model to understand how and when consciousness, or integrated information, can arise in simple dynamical systems. The emergence of consciousness is treated like the emergence of other classical macroscopic observables in physics such as magnetism and understood as a dynamical phase of matter. Our findings show that the sensitivity of consciousness in a complex system is maximized when the system is undergoing a phase transition, also known as a critical point. This result, combined with a body of evidence highlighting the privelaged state of critical systems suggests that, like many other complex phenomenon, consciousness may simply follow from/emerge out of the tendency of a system to self-organize to criticality.

scholarly journals Author Correction: Engineering self-organized criticality in living cells

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Blai Vidiella ◽  
Antoni Guillamon ◽  
Josep Sardanyés ◽  
Victor Maull ◽  
Jordi Pla ◽  
...  
Keyword(s):  
Living Cells ◽  
Self Organized ◽  
Self Organized Criticality

Problem behavior in autism spectrum disorders: A paradigmatic self-organized perspective of network structures

2019 ◽  
Vol 42 ◽  
Author(s):  
Lucio Tonello ◽  
Luca Giacobbi ◽  
Alberto Pettenon ◽  
Alessandro Scuotto ◽  
Massimo Cocchi ◽  
...  
Keyword(s):  
Autism Spectrum Disorder ◽  
Problem Behaviors ◽  
Autism Spectrum ◽  
The Self ◽  
Network Structures ◽  
Self Organized ◽  
Critical Equilibrium ◽  
Self Organized Criticality ◽  
Acute Agitation ◽  
Spectrum Disorders

AbstractAutism spectrum disorder (ASD) subjects can present temporary behaviors of acute agitation and aggressiveness, named problem behaviors. They have been shown to be consistent with the self-organized criticality (SOC), a model wherein occasionally occurring “catastrophic events” are necessary in order to maintain a self-organized “critical equilibrium.” The SOC can represent the psychopathology network structures and additionally suggests that they can be considered as self-organized systems.

Self-Organized Criticality in the Autowave Model of Speciation

2020 ◽  
Vol 75 (5) ◽  
pp. 398-408
Author(s):  
A. Y. Garaeva ◽  
A. E. Sidorova ◽  
N. T. Levashova ◽  
V. A. Tverdislov
Keyword(s):  
Self Organized ◽  
Self Organized Criticality

Modeling Extinction

2003 ◽  
Author(s):  
M. E. J. Newman ◽  
R. G. Palmer
Keyword(s):  
Evolutionary Biology ◽  
Large Scale ◽  
Competitive Exclusion ◽  
Applied Mathematics ◽  
Santa Fe ◽  
New Approach ◽  
Self Organized ◽  
Self Organized Criticality ◽  
Extinction Events ◽  
Mass Extinction Events

Developed after a meeting at the Santa Fe Institute on extinction modeling, this book comments critically on the various modeling approaches. In the last decade or so, scientists have started to examine a new approach to the patterns of evolution and extinction in the fossil record. This approach may be called "statistical paleontology," since it looks at large-scale patterns in the record and attempts to understand and model their average statistical features, rather than their detailed structure. Examples of the patterns these studies examine are the distribution of the sizes of mass extinction events over time, the distribution of species lifetimes, or the apparent increase in the number of species alive over the last half a billion years. In attempting to model these patterns, researchers have drawn on ideas not only from paleontology, but from evolutionary biology, ecology, physics, and applied mathematics, including fitness landscapes, competitive exclusion, interaction matrices, and self-organized criticality. A self-contained review of work in this field.

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