The Continuous Time Random Walk (CTRW) formalism is used to model the non-Poisson relaxation of a... more The Continuous Time Random Walk (CTRW) formalism is used to model the non-Poisson relaxation of a system response to perturbation. Two mechanisms to perturb the system are analyzed: a first in which the perturbation, seen as a potential gradient, simply introduces a bias in the hopping probability of the walker from on site to the other but leaves unchanged the occurrence times of the attempted jumps ("events") and a second in which the occurrence times of the events are perturbed. The system response is calculated analytically in both cases in a nonergodic condition, i.e. for a diverging first moment in time. Two different Fluctuation-Dissipation Theorems (FDTs), one for each kind of mechanism, are derived and discussed. * * * PG acknowledges Welch and ARO for financial support through Grants no. B-1577 and no. W911NF-05-1-025.
Extrinsic noise-induced transitions to bimodal dynamics have been largely investigated in a varie... more Extrinsic noise-induced transitions to bimodal dynamics have been largely investigated in a variety of chemical, physical, and biological systems. In the standard approach in physical and chemical systems, the key properties that make these systems mathematically tractable are that the noise appears linearly in the dynamical equations, and it is assumed Gaussian and white. In biology, the Gaussian approximation has been successful in specific systems, but the relevant noise being usually non-Gaussian, non-white, and nonlinear poses serious limitations to its general applicability. Here we revisit the fundamental features of linear Gaussian noise, pinpoint its limitations, and review recent new approaches based on nonlinear bounded noises, which highlight novel mechanisms to account for transitions to bimodal behaviour. We do this by considering a simple but fundamental gene expression model, the repressed gene, which is characterized by linear and nonlinear dependencies on external parameters. We then review a general methodology introduced recently, so-called nonlinear noise filtering, which allows the investigation of linear, nonlinear, Gaussian and non-Gaussian noises. We also present a derivation of it, which highlights its dynamical origin. Testing the methodology on the repressed gene confirms that the emergence of noise-induced transitions appears to be strongly dependent on the type of noise adopted, and on the degree of nonlinearity present in the system.
Many types of cells can sense external ligand concentrations with cell-surface receptors at extre... more Many types of cells can sense external ligand concentrations with cell-surface receptors at extremely high accuracy. Interestingly, ligand-bound receptors are often internalized, a process also known as receptor-mediated endocytosis. While internalization is involved in a vast number of important functions for the life of a cell, it was recently also suggested to increase the accuracy of sensing ligand as the overcounting of the same ligand molecules is reduced. Here we show, by extending simple ligand-receptor models to out-of-equilibrium thermodynamics, that internalization increases the accuracy with which cells can measure ligand concentrations in the external environment. Comparison with experimental rates of real receptors demonstrates that our model has indeed biological significance.
The risk of conflict is exasperated by a multitude of internal and external factors. Current mult... more The risk of conflict is exasperated by a multitude of internal and external factors. Current multivariate analysis paints diverse causal risk profiles that vary with time. However, these profiles evolve and a universal model to understand that evolution remains absent. Most of the current conflict analysis is data-driven and conducted at the individual country or region level, often in isolation. Consistent consideration of multi-scale interactions and their non-linear dynamics is missing. Here, we develop a multiplexed network model, where each city is modeled as a non-linear bistable system with stable states in either war or peace. The causal factor categories which exasperate the risk of conflict are each modeled as a network layer. We consider 3 layers: (1) core geospatial network of interacting cities reflecting ground level interactions, (2) cultural network of interacting countries reflecting cultural groupings, and (3) political network of interacting countries reflecting alliances. Together, they act as drivers to push cities towards or pull cities away from war. Using a variety of data sources that overlap consistently between 2002 − 2016, we show, that our model is able to correctly predict the transitions from war to peace and peace to war with F1 score of 0.78 to 0.92 worldwide at the city scale resolution. As many conflicts during this period are auto-regressive (e.g. the War on Terror in Afghanistan and Iraq, the Narco War across the Americas), it is important to show that we can predict the emergence of new war or new peace. Indeed, we demonstrate successful predictions across a wide range of conflict genres and we go on to perform causal discovery by identifying which model component led to the correct prediction. A variety of diverse conflict case studies were generated:
We consider a generic class of gene circuits affected by nonlinear extrinsic noise. To address th... more We consider a generic class of gene circuits affected by nonlinear extrinsic noise. To address this nonlinearity we introduce a general perturbative methodology based on assuming timescale separation between noise and genes dynamics, with fluctuations exhibiting a large but finite correlation time. We apply this methodology to the case of the toggle switch, and by considering biologically relevant log-normal fluctuations, we find that the system exhibits noise-induced transitions. The system becomes bimodal in regions of the parameter space where it would be deterministically monostable. We show that by including higher order corrections our methodology allows one to obtain correct predictions for the occurrence of transitions even for not so large correlation time of the fluctuations, overcoming thereby limitations of previous theoretical approaches. Interestingly we find that at intermediate noise intensities the noise-induced transition in the toggle switch affects one of the genes involved, but not the other one.
Extrinsic noise-induced transitions to bimodal dynamics have been largely investigated in a varie... more Extrinsic noise-induced transitions to bimodal dynamics have been largely investigated in a variety of chemical, physical, and biological systems. In the standard approach in physical and chemical systems, the key properties that make these systems mathematically tractable are that the noise appears linearly in the dynamical equations, and it is assumed Gaussian and white. In biology, the Gaussian approximation has been successful in specific systems, but the relevant noise being usually non-Gaussian, non-white, and nonlinear poses serious limitations to its general applicability. Here we revisit the fundamental features of linear Gaussian noise, pinpoint its limitations, and review recent new approaches based on nonlinear bounded noises, which highlight novel mechanisms to account for transitions to bimodal behaviour. We do this by considering a simple but fundamental gene expression model, the repressed gene, which is characterized by linear and nonlinear dependencies on external parameters. We then review a general methodology introduced recently, so-called nonlinear noise filtering, which allows the investigation of linear, nonlinear, Gaussian and non-Gaussian noises. We also present a derivation of it, which highlights its dynamical origin. Testing the methodology on the repressed gene confirms that the emergence of noise-induced transitions appears to be strongly dependent on the type of noise adopted, and on the degree of nonlinearity present in the system.
Cells sense external concentrations and, via biochemical signaling, respond by regulating the exp... more Cells sense external concentrations and, via biochemical signaling, respond by regulating the expression of target proteins. Both in signaling networks and gene regulation there are two main mechanisms by which the concentration can be encoded internally: amplitude modulation (AM), where the absolute concentration of an internal signaling molecule en-codes the stimulus, and frequency modulation (FM), where the period between successive bursts represents the stimulus. Although both mechanisms have been observed in biologi-cal systems, the question of when it is beneficial for cells to use either AM or FM is largely unanswered. Here, we first consider a simple model for a single receptor (or ion channel), which can either signal continuously whenever a ligand is bound, or produce a burst in sig-naling molecule upon receptor binding. We find that bursty signaling is more accurate than continuous signaling only for sufficiently fast dynamics. This suggests that modulation based on burst...
We consider a generic class of gene circuits affected by nonlinear extrinsic noise. To address th... more We consider a generic class of gene circuits affected by nonlinear extrinsic noise. To address this nonlinearity we introduce a general perturbative methodology based on assuming timescale separation between noise and gene dynamics, with fluctuations exhibiting a large but finite correlation time. We apply this methodology to the case of the toggle switch, and by considering biologically relevant log-normal fluctuations, we find that the system exhibits noise-induced transitions. The system becomes bimodal in regions of the parameter space where it would be deterministically monostable. We show that by including higher order corrections our methodology allows one to obtain correct predictions for the occurrence of transitions even for not so large correlation time of the fluctuations, thereby overcoming limitations of previous theoretical approaches. Interestingly we find that at intermediate noise intensities the noise-induced transition in the toggle switch affects one of the genes involved, but not the other one.
In this paper, we study the basic problem of a charged particle in a stochastic magnetic field. W... more In this paper, we study the basic problem of a charged particle in a stochastic magnetic field. We consider dichotomous fluctuations of the magnetic field where the sojourn time in one of the two states are distributed according to a given waiting-time distribution either with Poisson or non-Poisson statistics, including as well the case of distributions with diverging mean time between changes of the field, corresponding to an ergodicity breaking condition. We provide analytical and numerical results for all cases evaluating the average and the second moment of the position and velocity of the particle. We show that the field fluctuations induce diffusion of the charge with either normal or anomalous properties, depending on the statistics of the fluctuations, with distinct regimes from those observed, e.g., in standard Continuous-Time Random Walk models.
We consider the effect of non-constant parameters on the human-forest interaction logistic model ... more We consider the effect of non-constant parameters on the human-forest interaction logistic model coupled with human technological growth introduced in [1]. In recent years in fact, a decrease in human population growth rate has emerged which can be measured to about 1.7% drop per year since 1960 value which coincides with latest UN projections for next decades up to year 2100 [2]. We therefore consider here the effect of decreasing human population growth-rate on the aforementioned model and we evaluate its effect on the probability of survival of human civilisation without going through a catastrophic collapse in population. We find that for realistic values of the human population carrying capacity of the earth (measured by parameter β) this decrease would not affect previous results leading to a low probability of avoiding a catastrophic collapse. For larger more optimistic values of β instead, a decrease in growth-rate would tilt the probability in favour of a positive outcome, i.e. from 10-20% up to even 95% likelihood of avoiding collapse.
Extrinsic noise-induced transitions to bimodal dynamics have been largely investigated in a varie... more Extrinsic noise-induced transitions to bimodal dynamics have been largely investigated in a variety of chemical, physical, and biological systems. In the standard approach in physical and chemical systems, the key properties that make these systems mathematically tractable are that the noise appears linearly in the dynamical equations, and it is assumed Gaussian and white. In biology, the Gaussian approximation has been successful in specific systems, but the relevant noise being usually non-Gaussian, non-white, and nonlinear poses serious limitations to its general applicability. Here we revisit the fundamental features of linear Gaussian noise, pinpoint its limitations, and review recent new approaches based on nonlinear bounded noises, which highlight novel mechanisms to account for transitions to bimodal behaviour. We do this by considering a simple but fundamental gene expression model, the repressed gene, which is characterized by linear and nonlinear dependencies on external parameters. We then review a general methodology introduced recently, so-called nonlinear noise filtering, which allows the investigation of linear, nonlinear, Gaussian and non-Gaussian noises. We also present a derivation of it, which highlights its dynamical origin. Testing the methodology on the repressed gene confirms that the emergence of noise-induced transitions appears to be strongly dependent on the type of noise adopted, and on the degree of nonlinearity present in the system.
In this paper we afford a quantitative analysis of the sustainability of current world population... more In this paper we afford a quantitative analysis of the sustainability of current world population growth in relation to the parallel deforestation process adopting a statistical point of view. We consider a simplified model based on a stochastic growth process driven by a continuous time random walk, which depicts the technological evolution of human kind, in conjunction with a deterministic generalised logistic model for humans-forest interaction and we evaluate the probability of avoiding the self-destruction of our civilisation. Based on the current resource consumption rates and best estimate of technological rate growth our study shows that we have very low probability, less than 10% in most optimistic estimate, to survive without facing a catastrophic collapse.
A role for Wnt signaling in melanocyte specification from neural crest is conserved across verteb... more A role for Wnt signaling in melanocyte specification from neural crest is conserved across vertebrates, but possible ongoing roles in melanocyte differentiation have received little attention. Using a systems biology approach to investigate the gene regulatory network underlying stable melanocyte differentiation in zebrafish highlighted a requirement for a positive feedback loop involving the melanocyte master regulator Mitfa. Here we test the hypothesis that Wnt signaling contributes to that positive feedback. We show firstly that Wnt signaling remains active in differentiating melanocytes and secondly that enhanced Wnt signaling drives elevated transcription of mitfa. We show that chemical activation of the Wnt signaling pathway at early stages of melanocyte development enhances melanocyte specification as expected, but importantly that at later (differentiation) stages it results in altered melanocyte morphology, although melanisation is not obviously affected. Downregulation of ...
We study the transport of information between two complex networks with similar properties. Both ... more We study the transport of information between two complex networks with similar properties. Both networks generate non-Poisson renewal fluctuations with a power-law spectrum 1/f^(3-\mu), the case \mu= 2 corresponding to ideal 1/f-noise. We denote by \mu_S and \mu_P the power-law indexes of the network "system" of interest S and the perturbing network P respectively. By adopting a generalized fluctuation-dissipation theorem (FDT) we show that the ideal condition of 1/f-noise for both networks corresponds to maximal information transport. We prove that to make the network S respond when \mu_S < 2 we have to set the condition \mu_P < 2. In the latter case, if \mu_P < \mu_S, the system S inherits the relaxation properties of the perturbing network. In the case where \mu_P > 2, no response and no information transmission occurs in the long-time limit. We consider two possible generalizations of the fluctuation-dissipation theorem and show that both lead to maximal i...
Physical Review E Statistical Nonlinear and Soft Matter Physics, Jan 21, 2010
Many types of cells can sense external ligand concentrations with cell-surface receptors at extre... more Many types of cells can sense external ligand concentrations with cell-surface receptors at extremely high accuracy. Interestingly, ligand-bound receptors are often internalized, a process also known as receptor-mediated endocytosis. While internalization is involved in a vast number of important functions for the life of a cell, it was recently also suggested to increase the accuracy of sensing ligand as the overcounting of the same ligand molecules is reduced. Here we show, by extending simple ligand-receptor models to out-of-equilibrium thermodynamics, that internalization increases the accuracy with which cells can measure ligand concentrations in the external environment. Comparison with experimental rates of real receptors demonstrates that our model has indeed biological significance.
Non-ergodic renewal processes have recently been shown by several authors to be insensitive to pe... more Non-ergodic renewal processes have recently been shown by several authors to be insensitive to periodic perturbations, thereby apparently sanctioning the death of linear response, a building block of nonequilibrium statistical physics. We show that it is possible to go beyond the ``death of linear response&amp;quot; and establish a permanent correlation between an external stimulus and the response of a complex
The Continuous Time Random Walk (CTRW) formalism is used to model the non-Poisson relaxation of a... more The Continuous Time Random Walk (CTRW) formalism is used to model the non-Poisson relaxation of a system response to perturbation. Two mechanisms to perturb the system are analyzed: a first in which the perturbation, seen as a potential gradient, simply introduces a bias in the hopping probability of the walker from on site to the other but leaves unchanged the occurrence times of the attempted jumps ("events") and a second in which the occurrence times of the events are perturbed. The system response is calculated analytically in both cases in a nonergodic condition, i.e. for a diverging first moment in time. Two different Fluctuation-Dissipation Theorems (FDTs), one for each kind of mechanism, are derived and discussed. * * * PG acknowledges Welch and ARO for financial support through Grants no. B-1577 and no. W911NF-05-1-025.
Extrinsic noise-induced transitions to bimodal dynamics have been largely investigated in a varie... more Extrinsic noise-induced transitions to bimodal dynamics have been largely investigated in a variety of chemical, physical, and biological systems. In the standard approach in physical and chemical systems, the key properties that make these systems mathematically tractable are that the noise appears linearly in the dynamical equations, and it is assumed Gaussian and white. In biology, the Gaussian approximation has been successful in specific systems, but the relevant noise being usually non-Gaussian, non-white, and nonlinear poses serious limitations to its general applicability. Here we revisit the fundamental features of linear Gaussian noise, pinpoint its limitations, and review recent new approaches based on nonlinear bounded noises, which highlight novel mechanisms to account for transitions to bimodal behaviour. We do this by considering a simple but fundamental gene expression model, the repressed gene, which is characterized by linear and nonlinear dependencies on external parameters. We then review a general methodology introduced recently, so-called nonlinear noise filtering, which allows the investigation of linear, nonlinear, Gaussian and non-Gaussian noises. We also present a derivation of it, which highlights its dynamical origin. Testing the methodology on the repressed gene confirms that the emergence of noise-induced transitions appears to be strongly dependent on the type of noise adopted, and on the degree of nonlinearity present in the system.
Many types of cells can sense external ligand concentrations with cell-surface receptors at extre... more Many types of cells can sense external ligand concentrations with cell-surface receptors at extremely high accuracy. Interestingly, ligand-bound receptors are often internalized, a process also known as receptor-mediated endocytosis. While internalization is involved in a vast number of important functions for the life of a cell, it was recently also suggested to increase the accuracy of sensing ligand as the overcounting of the same ligand molecules is reduced. Here we show, by extending simple ligand-receptor models to out-of-equilibrium thermodynamics, that internalization increases the accuracy with which cells can measure ligand concentrations in the external environment. Comparison with experimental rates of real receptors demonstrates that our model has indeed biological significance.
The risk of conflict is exasperated by a multitude of internal and external factors. Current mult... more The risk of conflict is exasperated by a multitude of internal and external factors. Current multivariate analysis paints diverse causal risk profiles that vary with time. However, these profiles evolve and a universal model to understand that evolution remains absent. Most of the current conflict analysis is data-driven and conducted at the individual country or region level, often in isolation. Consistent consideration of multi-scale interactions and their non-linear dynamics is missing. Here, we develop a multiplexed network model, where each city is modeled as a non-linear bistable system with stable states in either war or peace. The causal factor categories which exasperate the risk of conflict are each modeled as a network layer. We consider 3 layers: (1) core geospatial network of interacting cities reflecting ground level interactions, (2) cultural network of interacting countries reflecting cultural groupings, and (3) political network of interacting countries reflecting alliances. Together, they act as drivers to push cities towards or pull cities away from war. Using a variety of data sources that overlap consistently between 2002 − 2016, we show, that our model is able to correctly predict the transitions from war to peace and peace to war with F1 score of 0.78 to 0.92 worldwide at the city scale resolution. As many conflicts during this period are auto-regressive (e.g. the War on Terror in Afghanistan and Iraq, the Narco War across the Americas), it is important to show that we can predict the emergence of new war or new peace. Indeed, we demonstrate successful predictions across a wide range of conflict genres and we go on to perform causal discovery by identifying which model component led to the correct prediction. A variety of diverse conflict case studies were generated:
We consider a generic class of gene circuits affected by nonlinear extrinsic noise. To address th... more We consider a generic class of gene circuits affected by nonlinear extrinsic noise. To address this nonlinearity we introduce a general perturbative methodology based on assuming timescale separation between noise and genes dynamics, with fluctuations exhibiting a large but finite correlation time. We apply this methodology to the case of the toggle switch, and by considering biologically relevant log-normal fluctuations, we find that the system exhibits noise-induced transitions. The system becomes bimodal in regions of the parameter space where it would be deterministically monostable. We show that by including higher order corrections our methodology allows one to obtain correct predictions for the occurrence of transitions even for not so large correlation time of the fluctuations, overcoming thereby limitations of previous theoretical approaches. Interestingly we find that at intermediate noise intensities the noise-induced transition in the toggle switch affects one of the genes involved, but not the other one.
Extrinsic noise-induced transitions to bimodal dynamics have been largely investigated in a varie... more Extrinsic noise-induced transitions to bimodal dynamics have been largely investigated in a variety of chemical, physical, and biological systems. In the standard approach in physical and chemical systems, the key properties that make these systems mathematically tractable are that the noise appears linearly in the dynamical equations, and it is assumed Gaussian and white. In biology, the Gaussian approximation has been successful in specific systems, but the relevant noise being usually non-Gaussian, non-white, and nonlinear poses serious limitations to its general applicability. Here we revisit the fundamental features of linear Gaussian noise, pinpoint its limitations, and review recent new approaches based on nonlinear bounded noises, which highlight novel mechanisms to account for transitions to bimodal behaviour. We do this by considering a simple but fundamental gene expression model, the repressed gene, which is characterized by linear and nonlinear dependencies on external parameters. We then review a general methodology introduced recently, so-called nonlinear noise filtering, which allows the investigation of linear, nonlinear, Gaussian and non-Gaussian noises. We also present a derivation of it, which highlights its dynamical origin. Testing the methodology on the repressed gene confirms that the emergence of noise-induced transitions appears to be strongly dependent on the type of noise adopted, and on the degree of nonlinearity present in the system.
Cells sense external concentrations and, via biochemical signaling, respond by regulating the exp... more Cells sense external concentrations and, via biochemical signaling, respond by regulating the expression of target proteins. Both in signaling networks and gene regulation there are two main mechanisms by which the concentration can be encoded internally: amplitude modulation (AM), where the absolute concentration of an internal signaling molecule en-codes the stimulus, and frequency modulation (FM), where the period between successive bursts represents the stimulus. Although both mechanisms have been observed in biologi-cal systems, the question of when it is beneficial for cells to use either AM or FM is largely unanswered. Here, we first consider a simple model for a single receptor (or ion channel), which can either signal continuously whenever a ligand is bound, or produce a burst in sig-naling molecule upon receptor binding. We find that bursty signaling is more accurate than continuous signaling only for sufficiently fast dynamics. This suggests that modulation based on burst...
We consider a generic class of gene circuits affected by nonlinear extrinsic noise. To address th... more We consider a generic class of gene circuits affected by nonlinear extrinsic noise. To address this nonlinearity we introduce a general perturbative methodology based on assuming timescale separation between noise and gene dynamics, with fluctuations exhibiting a large but finite correlation time. We apply this methodology to the case of the toggle switch, and by considering biologically relevant log-normal fluctuations, we find that the system exhibits noise-induced transitions. The system becomes bimodal in regions of the parameter space where it would be deterministically monostable. We show that by including higher order corrections our methodology allows one to obtain correct predictions for the occurrence of transitions even for not so large correlation time of the fluctuations, thereby overcoming limitations of previous theoretical approaches. Interestingly we find that at intermediate noise intensities the noise-induced transition in the toggle switch affects one of the genes involved, but not the other one.
In this paper, we study the basic problem of a charged particle in a stochastic magnetic field. W... more In this paper, we study the basic problem of a charged particle in a stochastic magnetic field. We consider dichotomous fluctuations of the magnetic field where the sojourn time in one of the two states are distributed according to a given waiting-time distribution either with Poisson or non-Poisson statistics, including as well the case of distributions with diverging mean time between changes of the field, corresponding to an ergodicity breaking condition. We provide analytical and numerical results for all cases evaluating the average and the second moment of the position and velocity of the particle. We show that the field fluctuations induce diffusion of the charge with either normal or anomalous properties, depending on the statistics of the fluctuations, with distinct regimes from those observed, e.g., in standard Continuous-Time Random Walk models.
We consider the effect of non-constant parameters on the human-forest interaction logistic model ... more We consider the effect of non-constant parameters on the human-forest interaction logistic model coupled with human technological growth introduced in [1]. In recent years in fact, a decrease in human population growth rate has emerged which can be measured to about 1.7% drop per year since 1960 value which coincides with latest UN projections for next decades up to year 2100 [2]. We therefore consider here the effect of decreasing human population growth-rate on the aforementioned model and we evaluate its effect on the probability of survival of human civilisation without going through a catastrophic collapse in population. We find that for realistic values of the human population carrying capacity of the earth (measured by parameter β) this decrease would not affect previous results leading to a low probability of avoiding a catastrophic collapse. For larger more optimistic values of β instead, a decrease in growth-rate would tilt the probability in favour of a positive outcome, i.e. from 10-20% up to even 95% likelihood of avoiding collapse.
Extrinsic noise-induced transitions to bimodal dynamics have been largely investigated in a varie... more Extrinsic noise-induced transitions to bimodal dynamics have been largely investigated in a variety of chemical, physical, and biological systems. In the standard approach in physical and chemical systems, the key properties that make these systems mathematically tractable are that the noise appears linearly in the dynamical equations, and it is assumed Gaussian and white. In biology, the Gaussian approximation has been successful in specific systems, but the relevant noise being usually non-Gaussian, non-white, and nonlinear poses serious limitations to its general applicability. Here we revisit the fundamental features of linear Gaussian noise, pinpoint its limitations, and review recent new approaches based on nonlinear bounded noises, which highlight novel mechanisms to account for transitions to bimodal behaviour. We do this by considering a simple but fundamental gene expression model, the repressed gene, which is characterized by linear and nonlinear dependencies on external parameters. We then review a general methodology introduced recently, so-called nonlinear noise filtering, which allows the investigation of linear, nonlinear, Gaussian and non-Gaussian noises. We also present a derivation of it, which highlights its dynamical origin. Testing the methodology on the repressed gene confirms that the emergence of noise-induced transitions appears to be strongly dependent on the type of noise adopted, and on the degree of nonlinearity present in the system.
In this paper we afford a quantitative analysis of the sustainability of current world population... more In this paper we afford a quantitative analysis of the sustainability of current world population growth in relation to the parallel deforestation process adopting a statistical point of view. We consider a simplified model based on a stochastic growth process driven by a continuous time random walk, which depicts the technological evolution of human kind, in conjunction with a deterministic generalised logistic model for humans-forest interaction and we evaluate the probability of avoiding the self-destruction of our civilisation. Based on the current resource consumption rates and best estimate of technological rate growth our study shows that we have very low probability, less than 10% in most optimistic estimate, to survive without facing a catastrophic collapse.
A role for Wnt signaling in melanocyte specification from neural crest is conserved across verteb... more A role for Wnt signaling in melanocyte specification from neural crest is conserved across vertebrates, but possible ongoing roles in melanocyte differentiation have received little attention. Using a systems biology approach to investigate the gene regulatory network underlying stable melanocyte differentiation in zebrafish highlighted a requirement for a positive feedback loop involving the melanocyte master regulator Mitfa. Here we test the hypothesis that Wnt signaling contributes to that positive feedback. We show firstly that Wnt signaling remains active in differentiating melanocytes and secondly that enhanced Wnt signaling drives elevated transcription of mitfa. We show that chemical activation of the Wnt signaling pathway at early stages of melanocyte development enhances melanocyte specification as expected, but importantly that at later (differentiation) stages it results in altered melanocyte morphology, although melanisation is not obviously affected. Downregulation of ...
We study the transport of information between two complex networks with similar properties. Both ... more We study the transport of information between two complex networks with similar properties. Both networks generate non-Poisson renewal fluctuations with a power-law spectrum 1/f^(3-\mu), the case \mu= 2 corresponding to ideal 1/f-noise. We denote by \mu_S and \mu_P the power-law indexes of the network "system" of interest S and the perturbing network P respectively. By adopting a generalized fluctuation-dissipation theorem (FDT) we show that the ideal condition of 1/f-noise for both networks corresponds to maximal information transport. We prove that to make the network S respond when \mu_S < 2 we have to set the condition \mu_P < 2. In the latter case, if \mu_P < \mu_S, the system S inherits the relaxation properties of the perturbing network. In the case where \mu_P > 2, no response and no information transmission occurs in the long-time limit. We consider two possible generalizations of the fluctuation-dissipation theorem and show that both lead to maximal i...
Physical Review E Statistical Nonlinear and Soft Matter Physics, Jan 21, 2010
Many types of cells can sense external ligand concentrations with cell-surface receptors at extre... more Many types of cells can sense external ligand concentrations with cell-surface receptors at extremely high accuracy. Interestingly, ligand-bound receptors are often internalized, a process also known as receptor-mediated endocytosis. While internalization is involved in a vast number of important functions for the life of a cell, it was recently also suggested to increase the accuracy of sensing ligand as the overcounting of the same ligand molecules is reduced. Here we show, by extending simple ligand-receptor models to out-of-equilibrium thermodynamics, that internalization increases the accuracy with which cells can measure ligand concentrations in the external environment. Comparison with experimental rates of real receptors demonstrates that our model has indeed biological significance.
Non-ergodic renewal processes have recently been shown by several authors to be insensitive to pe... more Non-ergodic renewal processes have recently been shown by several authors to be insensitive to periodic perturbations, thereby apparently sanctioning the death of linear response, a building block of nonequilibrium statistical physics. We show that it is possible to go beyond the ``death of linear response&amp;quot; and establish a permanent correlation between an external stimulus and the response of a complex
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Papers by Gerardo Aquino