73 research outputs found
On the emergence and evolution of artificial cell signaling networks
No full textThis PhD project is concerned with the evolution of Cell
Signaling Networks (CSNs) in silico. CSNs are complex biochemical networks responsible for the coordination of cellular activities. We are investigating the possibility to build an evolutionary simulation platform that would allow the spontaneous emergence and evolution of Artificial Cell Signaling Networks (ACSNs). From a practical point of view, realizing and evolving ACSNs may provide novel computational paradigms for a variety of application areas. This work may also contribute to the biological understanding of the origins and evolution of real CSNs
Exploring evolutionary stability in a concurrent artificial chemistry
No full textMulti-level selection has proven to be an affective mean to
provide resistance against parasites for catalytic networks
(Cronhjort and Blomberg, 1997). One way to implement these multi-level systems is to group molecules into several
distinct compartments (cells) which are capable of cellular
division (where an offspring cell replaces another cell). In
such systems parasitized cells decay and are ultimately displaced by neighboring healthy cells. However in relatively small cellular populations, it is also possible that infected cells may rapidly spread parasites throughout the entire cellular population. In which case, group selection may fail to provide resistance to parasites. In this paper, we propose a concurrent artificial chemistry (AC) which has been implemented on a cluster of computers where each cell is running on a single CPU. This multi-level selectional artificial chemistry called the Molecular Classifier Systems was based on the Holland broadcast language. An attribute inherent to such a concurrent
system is that the computational complexity of the
molecular species contained in a reactor may now affect the
fitness of the cell. This molecular computational cost may
be regarded as the chemical activation energy necessary for
a reaction to occur. Such a property is often not considered
in typical Artificial Life models. Our experimental results
obtained with this system suggest that this activation energy property may improve the resistance to parasites for catalytic networks. This work highlights some of the benefits that could be obtained using a concurrent architecture on top of computational efficiency. We first briefly present the Molecular Classifier Systems, this is then followed by a description of the multi-level concurrent model. Finally we discuss the benefits of using this multi-level concurrent model to enhance evolutionary stability for catalytic networks in our AC
A molecular approach to complex adaptive systems
No full textComplex Adaptive Systems (CAS) are dynamical networks of interacting agents which as a whole determine the behavior, adaptivity and cognitive ability of the system. CAS are
ubiquitous and occur in a variety of natural and artificial systems (e.g., cells, societies, stock markets). To study CAS, Holland proposed to employ an agent-based system in which Learning Classifier Systems (LCS) were used to determine the agents behavior and adaptivity. We argue that LCS are limited for the study of CAS: the rule-discovery mechanism is pre-specified and may limit the evolvability of CAS. Secondly, LCS distinguish a demarcation between messages and rules, however operations are reflexive in CAS, e.g., in a cell, an agent (a molecule) may both act as a message (substrate) and as a catalyst (rule). To address these issues, we proposed the Molecular Classifier Systems (MCS.b), a string-based Artificial Chemistry based on Holland’s broadcast language. In the MCS.b, no explicit fitness function or rule discovery mechanism is specified, moreover no distinction is made between messages and rules. In the context of the ESIGNET project, we employ the MCS.b to study a subclass of CAS: Cell Signaling Networks (CSNs) which are complex biochemical networks responsible for coordinating cellular activities. As CSNs occur in cells, these networks must replicate themselves prior to cell division. In this paper we present a series of experiments
focusing on the self-replication ability of these CAS. Results indicate counter intuitive outcomes as opposed to those inferred from the literature. This work highlights the current deficit of a theoretical framework for the study of Artificial Chemistries
The Holland broadcast language and the modeling of biochemical networks
No full textThe Broadcast Language is a programming formalism devised by Holland in 1975, which aims at improving the efficiency of Genetic Algorithms (GAs) during long-term evolution. The key mechanism of the Broadcast Language is to allow GAs to employ an adaptable problem representation. Fixed problem encoding is commonly used by GAs but may limit their performance in particular cases. This paper describes an implementation of the Broadcast Language and its application to modeling biochemical networks. Holland presented the Broadcast Language in his book “Adaptation in Natural and Artificial Systems” where only a description of the language was provided, without any implementation. Our primary motivation for this work was the fact that there is currently no published implementation of the Broadcast Language available. Secondly, no additional examination of the Broadcast Language and its applications can be found in the literature. Holland proposed that the Broadcast Language would be suitable for the modeling of biochemical models. However, he did not support this belief with any experimental work. In this paper, we propose an implementation of the Broadcast Language which is then applied to the modeling of a signal transduction network. We conclude the paper by proposing that with some refinements it will be possible to use the Broadcast Language to evolve biochemical networks in silico
Crosstalk and the cooperation of collectively autocatalytic reaction networks
No full textWe examine a potential role of signalling crosstalk in Artificial Cell Signalling Networks (ACSNs). In this research, we regard these ACSNs as subsets of collectively autocatalytic (i.e., organizationally closed) reaction networks being able to both self-maintain and to carry out a distinct signal processing function. These signalling crosstalk phenomena occur naturally when different biochemical networks become mixed together where a given molecular species may contribute simultaneously to multiple ACSNs. It has been reported in the biological literature, that crosstalk may have effects that are both constructive
(e.g., coordinating cellular activities, multi-tasking)
and destructive (e.g., premature programmed cell death). In
this paper we demonstrate how crosstalk may enable distinct
closed ACSNs to cooperate with other. From a theoretical point of view, this work may give new insights for the understanding of crosstalk in natural biochemical networks. From a practical point view, this investigation may provide novel applications of crosstalk in engineered ACSNs
Modeling and evolving biochemical networks: insights into communication and computation from the biological domain
No full textThis paper is concerned with the modeling and evolving
of Cell Signaling Networks (CSNs) in silico. CSNs are
complex biochemical networks responsible for the coordination of cellular activities. We examine the possibility to computationally evolve and simulate Artificial Cell Signaling Networks (ACSNs) by means of Evolutionary Computation techniques. From a practical point of view, realizing and evolving ACSNs may provide novel computational paradigms for a variety of application areas. For example, understanding some inherent properties of CSNs such as crosstalk may be of interest: A potential benefit of engineering crosstalking systems is that it allows the modification of a specific process according to the state of other processes in the system. This is clearly necessary in order to achieve complex control tasks. This work may also contribute to the biological understanding of the origins and evolution of real CSNs. An introduction to CSNs is first
provided, in which we describe the potential applications
of modeling and evolving these biochemical networks in
silico. We then review the different classes of techniques to model CSNs, this is followed by a presentation of two alternative approaches employed to evolve CSNs within the
ESIGNET project. Results obtained with these methods
are summarized and discussed
The Holland broadcast language
No full textThe broadcast language is a programming formalism devised by Holland in 1975, which aims at allowing Genetic Algorithms (GAs) to use an adaptable representation. A GA may provide an efficient method for adaption but still depends on the efficiency of the fitness function used. During long-term evolution, this efficiency could be limited by the fixed
representation used by the GA to encode the problem. When a fitness function is very complex, it is desirable to adapt the problem representation employed by the fitness function.
By adapting the representation, the broadcast language may overcome the deficiencies caused by fixed problem representation in GAs.
This report describes an initial detailed specification and implementation of the broadcast language. Our first motivation is the fact that there is currently no published implementation of broadcast systems (broadcast language-based systems) available. Despite Holland presented the broadcast language in his book “Adaptation in Natural and Artificial systems”, he did not support this approach with experimental studies.
Our second motivation is the affirmation made by Holland that broadcast systems could model biochemical networks. Indeed Holland also described how the broadcast language
could provide a straightforward representation to a variety of biochemical networks (Genetic Regulatory Networks, Neural Networks, Immune system etc). As these biochemical models
share many similarities with Cell Signaling Networks (CSNs), broadcast systems may also be considered to model CSNs. One of our goals, within the ESIGNET project, is to develop an
evolutionary system to realize and evolve CSNs in Silico. Examining the broadcast language may provide us with valuable insights to the development of such a system.
In this paper, we initially review the Holland broadcast language, we then propose a specification and implementation of the language which is later illustrated with an experiment: modeling different chemical reactions
Closure in artificial cell signalling networks - investigating the emergence of cognition in collectively autocatalytic reaction networks
No full textCell Signalling Networks (CSNs) are complex biochemical networks responsible for the coordination of cellular
activities in response to internal and external stimuli. We hypothesize that CSNs are subsets of collectively autocatalytic reaction networks. The signal processing or cognitive abilities of CSNs would originate from the closure properties of these systems. We investigate how Artificial CSNs, regarded as minimal cognitive systems, could emerge and evolve under this condition where closure may interact with evolution. To assist this research, we employ a multi-level concurrent Artificial Chemistry based on the Molecular Classifier Systems and the Holland broadcast language. A critical issue for the evolvability of such undirected and autonomous evolutionary systems is to identify the conditions that would ensure evolutionary stability. In this
paper we present some key features of our system which permitted stable cooperation to occur between the different molecular species through evolution. Following this, we present an experiment in which we evolved a simple closed reaction network to accomplish a pre-specified task. In this experiment we show that the signal-processing ability (signal amplification) directly resulted from the evolved systems closure properties
Evolution of self-maintaining cellular information processing networks
No full textWe examine the role of self-maintenance (collective autocatalysis) in the evolution of computational biochemical networks. In primitive proto-cells (lacking separate genetic machinery) self-maintenance is a necessary condition for the direct reproduction and inheritance of what we here term Cellular Information Processing Networks (CIPNs). Indeed, partially reproduced or defective CIPNs may generally lead to malfunctioning or premature death of affected cells. We explore the interaction of this self-maintenance property with the evolution and adaptation of CIPNs capable of distinct information processing abilities. We present an evolutionary simulation platform capable of evolving artificial CIPNs from a bottom-up perspective. This system is an agent-based multi-level selectional Artificial Chemistry (AC) which employs a term rewriting system called the Molecular Classifier System (MCS). The latter is derived from the Holland broadcast language formalism. Using this system, we successfully evolve an artificial CIPN to improve performance on a simple pre-specified information processing task whilst subject to the constraint of continuous self-maintenance. We also describe the evolution of self-maintaining, crosstalking and multitasking, CIPNs exhibiting a higher level of topological and functional complexity. This proof of concept aims at contributing to the understanding of the open-ended evolutionary growth of complexity in artificial systems
An approach to evolving cell signaling networks in silico
No full textCell Signaling Networks(CSN) are complex bio-chemical networks which, through evolution, have become highly efficient for governing critical control processes such as immunological responses, cell cycle control or homeostasis. From a computational point of view, modeling Artificial Cell Signaling Networks (ACSNs) in silico may provide new ways
to design computer systems which may have specialized application areas.
To investigate these new opportunities, we review the key issues of modeling ACSNs identified as follows. We first present an analogy between analog and molecular computation.
We discuss the application of evolutionary techniques to evolve biochemical networks for computational purposes. The potential roles of crosstalk in CSNs are then examined. Finally we present how artificial CSNs can be used to build robust real-time control systems.
The research we are currently involved in is part of the multi disciplinary EU funded project, ESIGNET, with the central question of the study of the computational properties of CSNs by evolving them using methods from evolutionary computation, and to re-apply this understanding in developing new ways to model and predict real CSNs. This also complements the present requirements of Computational Systems Biology by providing new insights in micro-biology research
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