Protocells are supposed to have played a key role in the self-organizing processes leading to the... more Protocells are supposed to have played a key role in the self-organizing processes leading to the emergence of life. Existing models either (i) describe protocell architecture and dynamics, given the existence of sets of collectively self-replicating molecules for granted, or (ii) describe the emergence of the aforementioned sets from an ensemble of random molecules in a simple experimental setting (e.g. a closed system or a steady-state flow reactor) that does not properly describe a protocell. In this paper we present a model that goes beyond these limitations by describing the dynamics of sets of replicating molecules within a lipid vesicle. We adopt the simplest possible protocell architecture, by considering a semi-permeable membrane that selects the molecular types that are allowed to enter or exit the protocell and by assuming that the reactions take place in the aqueous phase in the internal compartment. As a first approximation, we ignore the protocell growth and division dynamics. The behavior of catalytic reaction networks is then simulated by means of a stochastic model that accounts for the creation and the extinction of species and reactions. While this is not yet an exhaustive protocell model, it already provides clues regarding some processes that are relevant for understanding the conditions that can enable a population of protocells to undergo evolution and selection.
We present an agent-based model of innovation processes, based upon a theory of innovation by Lan... more We present an agent-based model of innovation processes, based upon a theory of innovation by Lane and Maxfield. The theory inspires and constrains the features of the model, thus reducing the embarasse de richessethat is one of the major methodological problems of agent-based modelling. Artefacts are produced by agents using recipes; the basic dynamics, absent innovation, is one of production
The innovation theory (briefly, 2T), which has been developed in the ISCOM project and which is p... more The innovation theory (briefly, 2T), which has been developed in the ISCOM project and which is presented in this book (Chapters 9 and 10), is based on the analysis of different case studies, spanning different time periods and different kinds of products, from the introduction of printing in the Renaissance, to key new technologies introduced in the 19th and 20th centuries, up to present-day ongoing innovation efforts.
It is shown that a two-compartment isolated fluid system, where a chemical reaction takes place c... more It is shown that a two-compartment isolated fluid system, where a chemical reaction takes place close to the surfaces of the semipermeable separating membrane, can spontaneously develop a transient concentration difference across the membrane. If the system is open to the flow of chemicals, the difference can persist in the steady state. This allows concentrating chemicals in a single compartment, which may be useful for chemical engineering purposes, and which is particular interesting in the study of the dynamics of vesicles and protocells. The phenomenon is investigated and demonstrated here with a CA model: it is also shown that, in the limiting case of infinitely fast diffusion, the results are coherent with those of a homogeneous model
This chapter introduces an agent-based model designed to investigate the dynamics of some aspects... more This chapter introduces an agent-based model designed to investigate the dynamics of some aspects of exaptation that have been discussed previously in this volume. It is strongly related to the model introduced in the previous chapter. Indeed, in the model described here, cognitive categories represent the main tools that the producers and users of artifacts employ in order to interpret their environment, as in the case discussed in Chapter 14. The main addition provided by the current model, however, is the explicit introduction of artifacts.
In this work we address the issue of designing a Boolean network such that its attractors are max... more In this work we address the issue of designing a Boolean network such that its attractors are maximally distant. The design objective is converted into an optimisation problem, that is solved via an iterated local search algorithm. This technique proves to be effective and enables us to design networks with size up to 200 nodes. We also show that the networks obtained through the optimisation technique exhibit a mixture of characteristics typical of networks in the critical and chaotic dynamical regime.
In this work we present the introduction of spatial constraints in a model of generation and diff... more In this work we present the introduction of spatial constraints in a model of generation and diffusion of innovations. The presence of spatial limitations introduces several feedbacks, whose main effects are the decrease of global diversity in favour of a higher robustness, despite the apparent minor success of the individual agents. All these features hold contemporarily, but the individuated feedbacks are able to explain their only apparently contradictory nature. None of these results is obvious, nor can it be simply deduced from the qualitative theory. Moreover, the simulations could make possible comparisons between the model behaviours and the theory claims, indicating new ways of improvement and development
We consider generic protocells models allowing linear and non-linear kinetics for the main involv... more We consider generic protocells models allowing linear and non-linear kinetics for the main involved chemical reactions. We are interested in understanding if and how the protocell division and the metabolism do synchronise to give rise to sustainable evolution of the protocell.
... top of page AUTHORS. Search for Alessandro Filisetti Search for Roberto Serra Search for Marc... more ... top of page AUTHORS. Search for Alessandro Filisetti Search for Roberto Serra Search for Marco Villani Search for Alex Graudenzi Search for Rudolf M. Füchslin Search for Irene Poli. ... 11. DTGillespie. Exact stochastic simulation of coupled chemical reactions. ...
ABSTRACT Since real networks are noisy systems, in this work we investigate the dynamics of a det... more ABSTRACT Since real networks are noisy systems, in this work we investigate the dynamics of a deterministic model of gene networks affected by small random fluctuations. In this case jumps among different attractors are possible, thereby leading to an asymptotic dynamics different from that of the underlying deterministic model. The significance of the jumps among attractors is discussed. A key control parameter of this phenomenon is the size of the network, a fact that could lead to interesting consequences for the theories of natural and artificial evolving systems.
ABSTRACT The dynamics of genetic regulatory networks are often affected by stochastic noise, due ... more ABSTRACT The dynamics of genetic regulatory networks are often affected by stochastic noise, due to the small number of molecules involved in some reactions. The role of these fluctuations is analyzed in a discrete model of gene regulatory networks, i.e. that of noisy random Boolean networks. By relating the asymptotic states of the noisy system to the different cell types, we show how the main features of the important process of cell differentiation can be described by assuming that the noise level changes as differentiation proceeds. Differentiation is seen as a series of transitions from an asymptotic state in which the system can wander among many states under the action of noise to other asymptotic states in which the system can reach fewer and fewer states. This model easily describes the fact that multi-potent cells can stochastically differentiate along various routes. We show here that the process can also be controlled (as it happens in the embryo growth) so that it is possible to determine the final fully differentiated state of the cell. This is achieved by forcing some genes, which are called here “swithces”, to take constant values, in a way which mimicks the influence of external signals, and by simoultaneously varying the noise level in the cell.
Random boolean networks (RBN) have been proposed more than thirty years ago as models of genetic ... more Random boolean networks (RBN) have been proposed more than thirty years ago as models of genetic regulatory networks. Recent studies on the perturbation in gene expression levels induced by the knock-out (i.e. silencing) of single genes have shown that simple RBN models give rise to a distribution of the size of the perturbations which is very similar in different model network realizations, and is also very similar to the one actually found in experimental data concerning a unicellular organism (S.cerevisiae). In this paper we present further results, based upon the same set of experiments, concerning the correlation between different perturbations. We compare actual data from S. cerevisiae with the results of simulations concerning RBN models with more than 6000 nodes, and comment on the usefulness and limitations of RBN models.
The dynamical features of Random Boolean Networks (RBN) are examined, in the case where a scale-f... more The dynamical features of Random Boolean Networks (RBN) are examined, in the case where a scale-free distribution of outgoing connectivities is introduced. RBN are known to display two major dynamical behaviours, depending upon the value of some model parameters, In the ”ordered” regime the number of attractors is a growing polynomial function of the number of nodes N, while in the ”chaotic” regime the growth is exponential. We present here a modification of the classical way of building a RBN, which maintains the property that all the nodes have the same number of incoming links, but which gives rise to a scale-free distribution of outgoing connectivities. Because of this modification, the dynamical properties are deeply modified: the number of attractors is much smaller than in classical RBN, their length and the duration of the transients are shorter. Perhaps more surprising, the number of different attractors is almost independent of the network size, over almost three order of magnitudes. Besides pertaining to the study of the dynamics of nonlinear networks, these results may have interesting biological implications.
Protocells are supposed to have played a key role in the self-organizing processes leading to the... more Protocells are supposed to have played a key role in the self-organizing processes leading to the emergence of life. Existing models either (i) describe protocell architecture and dynamics, given the existence of sets of collectively self-replicating molecules for granted, or (ii) describe the emergence of the aforementioned sets from an ensemble of random molecules in a simple experimental setting (e.g. a closed system or a steady-state flow reactor) that does not properly describe a protocell. In this paper we present a model that goes beyond these limitations by describing the dynamics of sets of replicating molecules within a lipid vesicle. We adopt the simplest possible protocell architecture, by considering a semi-permeable membrane that selects the molecular types that are allowed to enter or exit the protocell and by assuming that the reactions take place in the aqueous phase in the internal compartment. As a first approximation, we ignore the protocell growth and division dynamics. The behavior of catalytic reaction networks is then simulated by means of a stochastic model that accounts for the creation and the extinction of species and reactions. While this is not yet an exhaustive protocell model, it already provides clues regarding some processes that are relevant for understanding the conditions that can enable a population of protocells to undergo evolution and selection.
We present an agent-based model of innovation processes, based upon a theory of innovation by Lan... more We present an agent-based model of innovation processes, based upon a theory of innovation by Lane and Maxfield. The theory inspires and constrains the features of the model, thus reducing the embarasse de richessethat is one of the major methodological problems of agent-based modelling. Artefacts are produced by agents using recipes; the basic dynamics, absent innovation, is one of production
The innovation theory (briefly, 2T), which has been developed in the ISCOM project and which is p... more The innovation theory (briefly, 2T), which has been developed in the ISCOM project and which is presented in this book (Chapters 9 and 10), is based on the analysis of different case studies, spanning different time periods and different kinds of products, from the introduction of printing in the Renaissance, to key new technologies introduced in the 19th and 20th centuries, up to present-day ongoing innovation efforts.
It is shown that a two-compartment isolated fluid system, where a chemical reaction takes place c... more It is shown that a two-compartment isolated fluid system, where a chemical reaction takes place close to the surfaces of the semipermeable separating membrane, can spontaneously develop a transient concentration difference across the membrane. If the system is open to the flow of chemicals, the difference can persist in the steady state. This allows concentrating chemicals in a single compartment, which may be useful for chemical engineering purposes, and which is particular interesting in the study of the dynamics of vesicles and protocells. The phenomenon is investigated and demonstrated here with a CA model: it is also shown that, in the limiting case of infinitely fast diffusion, the results are coherent with those of a homogeneous model
This chapter introduces an agent-based model designed to investigate the dynamics of some aspects... more This chapter introduces an agent-based model designed to investigate the dynamics of some aspects of exaptation that have been discussed previously in this volume. It is strongly related to the model introduced in the previous chapter. Indeed, in the model described here, cognitive categories represent the main tools that the producers and users of artifacts employ in order to interpret their environment, as in the case discussed in Chapter 14. The main addition provided by the current model, however, is the explicit introduction of artifacts.
In this work we address the issue of designing a Boolean network such that its attractors are max... more In this work we address the issue of designing a Boolean network such that its attractors are maximally distant. The design objective is converted into an optimisation problem, that is solved via an iterated local search algorithm. This technique proves to be effective and enables us to design networks with size up to 200 nodes. We also show that the networks obtained through the optimisation technique exhibit a mixture of characteristics typical of networks in the critical and chaotic dynamical regime.
In this work we present the introduction of spatial constraints in a model of generation and diff... more In this work we present the introduction of spatial constraints in a model of generation and diffusion of innovations. The presence of spatial limitations introduces several feedbacks, whose main effects are the decrease of global diversity in favour of a higher robustness, despite the apparent minor success of the individual agents. All these features hold contemporarily, but the individuated feedbacks are able to explain their only apparently contradictory nature. None of these results is obvious, nor can it be simply deduced from the qualitative theory. Moreover, the simulations could make possible comparisons between the model behaviours and the theory claims, indicating new ways of improvement and development
We consider generic protocells models allowing linear and non-linear kinetics for the main involv... more We consider generic protocells models allowing linear and non-linear kinetics for the main involved chemical reactions. We are interested in understanding if and how the protocell division and the metabolism do synchronise to give rise to sustainable evolution of the protocell.
... top of page AUTHORS. Search for Alessandro Filisetti Search for Roberto Serra Search for Marc... more ... top of page AUTHORS. Search for Alessandro Filisetti Search for Roberto Serra Search for Marco Villani Search for Alex Graudenzi Search for Rudolf M. Füchslin Search for Irene Poli. ... 11. DTGillespie. Exact stochastic simulation of coupled chemical reactions. ...
ABSTRACT Since real networks are noisy systems, in this work we investigate the dynamics of a det... more ABSTRACT Since real networks are noisy systems, in this work we investigate the dynamics of a deterministic model of gene networks affected by small random fluctuations. In this case jumps among different attractors are possible, thereby leading to an asymptotic dynamics different from that of the underlying deterministic model. The significance of the jumps among attractors is discussed. A key control parameter of this phenomenon is the size of the network, a fact that could lead to interesting consequences for the theories of natural and artificial evolving systems.
ABSTRACT The dynamics of genetic regulatory networks are often affected by stochastic noise, due ... more ABSTRACT The dynamics of genetic regulatory networks are often affected by stochastic noise, due to the small number of molecules involved in some reactions. The role of these fluctuations is analyzed in a discrete model of gene regulatory networks, i.e. that of noisy random Boolean networks. By relating the asymptotic states of the noisy system to the different cell types, we show how the main features of the important process of cell differentiation can be described by assuming that the noise level changes as differentiation proceeds. Differentiation is seen as a series of transitions from an asymptotic state in which the system can wander among many states under the action of noise to other asymptotic states in which the system can reach fewer and fewer states. This model easily describes the fact that multi-potent cells can stochastically differentiate along various routes. We show here that the process can also be controlled (as it happens in the embryo growth) so that it is possible to determine the final fully differentiated state of the cell. This is achieved by forcing some genes, which are called here “swithces”, to take constant values, in a way which mimicks the influence of external signals, and by simoultaneously varying the noise level in the cell.
Random boolean networks (RBN) have been proposed more than thirty years ago as models of genetic ... more Random boolean networks (RBN) have been proposed more than thirty years ago as models of genetic regulatory networks. Recent studies on the perturbation in gene expression levels induced by the knock-out (i.e. silencing) of single genes have shown that simple RBN models give rise to a distribution of the size of the perturbations which is very similar in different model network realizations, and is also very similar to the one actually found in experimental data concerning a unicellular organism (S.cerevisiae). In this paper we present further results, based upon the same set of experiments, concerning the correlation between different perturbations. We compare actual data from S. cerevisiae with the results of simulations concerning RBN models with more than 6000 nodes, and comment on the usefulness and limitations of RBN models.
The dynamical features of Random Boolean Networks (RBN) are examined, in the case where a scale-f... more The dynamical features of Random Boolean Networks (RBN) are examined, in the case where a scale-free distribution of outgoing connectivities is introduced. RBN are known to display two major dynamical behaviours, depending upon the value of some model parameters, In the ”ordered” regime the number of attractors is a growing polynomial function of the number of nodes N, while in the ”chaotic” regime the growth is exponential. We present here a modification of the classical way of building a RBN, which maintains the property that all the nodes have the same number of incoming links, but which gives rise to a scale-free distribution of outgoing connectivities. Because of this modification, the dynamical properties are deeply modified: the number of attractors is much smaller than in classical RBN, their length and the duration of the transients are shorter. Perhaps more surprising, the number of different attractors is almost independent of the network size, over almost three order of magnitudes. Besides pertaining to the study of the dynamics of nonlinear networks, these results may have interesting biological implications.
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Papers by Marco Villani