Synthetic Criticality in Cellular Brains

Cognitive networks have evolved to cope with uncertain environments in order to make reliable decisions. Such decision making circuits need to respond to the external world in efficient and flexible ways, and one potentially general mechanism of achieving this is grounded in critical states. Mounting evidence has shown that brains operate close to such critical boundaries consistent with self-organized criticality (SOC). Is this also taking place in small-scale living systems, such as cells? Here we explore a recent model of engineered gene networks that have been shown to exploit the feedback between order and control parameters (as defined by expression levels of two coupled genes) to achieve a SOC state. We suggest that such SOC motif could be exploited to generate adaptive behavioral patterns and might help design fast responses in synthetic cellular and multicellular organisms.

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Synthetic criticality in cellular brains

Journal of Physics: Complexity ◽

10.1088/2632-072x/ac35b3 ◽

2021 ◽

Vol 2 (4) ◽

pp. 041001

Author(s):

Ricard Solé ◽

Nuria Conde-Pueyo ◽

Antoni Guillamon ◽

Victor Maull ◽

Jordi Pla ◽

...

Keyword(s):

Gene Networks ◽

Cognitive Networks ◽

General Mechanism ◽

Small Scale ◽

Control Parameters ◽

Uncertain Environments ◽

Self Organized ◽

Self Organized Criticality ◽

Multicellular Organisms ◽

And Control

Abstract Cognitive networks have evolved to cope with uncertain environments in order to make reliable decisions. Such decision making circuits need to respond to the external world in efficient and flexible ways, and one potentially general mechanism of achieving this is grounded in critical states. Mounting evidence has shown that brains operate close to such critical boundaries consistent with self-organized criticality (SOC). Is this also taking place in small-scale living systems, such as cells? Here, we explore a recent model of engineered gene networks that have been shown to exploit the feedback between order and control parameters (as defined by expression levels of two coupled genes) to achieve an SOC state. We suggest that such SOC motif could be exploited to generate adaptive behavioral patterns and might help design fast responses in synthetic cellular and multicellular organisms.

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Engineering Self-Organized Criticality in Living Cells

10.20944/preprints202011.0546.v1 ◽

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.

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Self-organized criticality and the fractal scaling of a predator-prey interaction

The Paleontological Society Special Publications ◽

10.1017/s2475262200005712 ◽

1992 ◽

Vol 6 ◽

pp. 11-11

Author(s):

Richard B. Aronson

Keyword(s):

Large Scale ◽

Interactive Systems ◽

Small Scale ◽

Biological Interactions ◽

Ecological Processes ◽

The Bahamas ◽

Fractal Scaling ◽

Self Organized ◽

Predation Effects ◽

Self Organized Criticality

In many cases, it is not possible to explain evolutionary-scale patterns by analogy to ecological processes. However, in at least some cases, biological interactions appear amenable to such extrapolation. The paleobiological literature contains examples of predation, competition, and herbivory in which the dynamics are similar on multiple spatiotemporal scales.Dense populations of epifaunal, suspension-feeding ophiuroids, or brittlestar beds, are widely distributed, but they are rare and are restricted in their habitat distribution. On a small scale (meters to kilometers, hours to days), brittlestar bed distribution in the British Isles and the Bahamas is limited by predatory fishes and crabs. On an intermediate scale (tens to hundreds of kilometers, decades to centuries), predation by seastars may cause cycles of ophiuroid abundance in the western English Channel, beyond the stringent restrictions imposed by fish and crab predators. On a large scale (globally, millions to tens of millions of years), the Jurassic decline of brittlestar beds is associated with the diversification of predatory teleosts, neoselachian sharks, and decapod crustaceans.Small-scale predator-ophiuroid interactions sum to produce analogous intermediate- and large-scale interactions. Predation effects on brittlestar beds appear to be scale-independent, or fractal. Fractal scaling may be a consequence of self-organized criticality, an inherent property of large, interactive systems.

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Engineering self-organized criticality in living cells

10.21203/rs.3.rs-118874/v1 ◽

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.

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Analyses of Aggregate Fluctuation of Firm Network Based on Self-Organized Criticality Model and Control Theory

SSRN Electronic Journal ◽

10.2139/ssrn.2695275 ◽

2015 ◽

Cited By ~ 1

Author(s):

Hiroyasu Inoue

Keyword(s):

Control Theory ◽

Self Organized ◽

Self Organized Criticality ◽

And Control ◽

Aggregate Fluctuation

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Exploiting self-organized criticality in strongly stratified turbulence

Journal of Fluid Mechanics ◽

10.1017/jfm.2021.1060 ◽

2021 ◽

Vol 933 ◽

Author(s):

Gregory P. Chini ◽

Guillaume Michel ◽

Keith Julien ◽

Cesar B. Rocha ◽

Colm-cille P. Caulfield

Keyword(s):

Large Scale ◽

Ad Hoc ◽

Three Dimensional ◽

Boussinesq Equations ◽

Marginal Stability ◽

Small Scale ◽

Stratified Turbulence ◽

Self Organized ◽

Reduced Equations ◽

Self Organized Criticality

A multiscale reduced description of turbulent free shear flows in the presence of strong stabilizing density stratification is derived via asymptotic analysis of the Boussinesq equations in the simultaneous limits of small Froude and large Reynolds numbers. The analysis explicitly recognizes the occurrence of dynamics on disparate spatiotemporal scales, yielding simplified partial differential equations governing the coupled evolution of slow large-scale hydrostatic flows and fast small-scale isotropic instabilities and internal waves. The dynamics captured by the coupled reduced equations is illustrated in the context of two-dimensional strongly stratified Kolmogorov flow. A noteworthy feature of the reduced model is that the fluctuations are constrained to satisfy quasilinear (QL) dynamics about the comparably slowly varying large-scale fields. Crucially, this QL reduction is not invoked as an ad hoc closure approximation, but rather is derived in a physically relevant and mathematically consistent distinguished limit. Further analysis of the resulting slow–fast QL system shows how the amplitude of the fast stratified-shear instabilities is slaved to the slowly evolving mean fields to ensure the marginal stability of the latter. Physically, this marginal stability condition appears to be compatible with recent evidence of self-organized criticality in both observations and simulations of stratified turbulence. Algorithmically, the slaving of the fluctuation fields enables numerical simulations to be time-evolved strictly on the slow time scale of the hydrostatic flow. The reduced equations thus provide a solid mathematical foundation for future studies of three-dimensional strongly stratified turbulence in extreme parameter regimes of geophysical relevance and suggest avenues for new sub-grid-scale parametrizations.

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Engineering self-organized criticality in living cells

10.1101/2020.11.16.385385 ◽

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.

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

Behavioral and Brain Sciences ◽

10.1017/s0140525x18001188 ◽

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.

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