Measuring Information Propagation and Processing in Biological Systems

Measuring Information Propagation and Processing in Biological Systems

Juha Kesseli (Tampere University of Technology, Finland), Andre S. Ribeiro (Tampere University of Technology, Finland) and Matti Nykter (Tampere University of Technology, Finland)
DOI: 10.4018/978-1-60566-246-6.ch009
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In this chapter the authors study the propagation and processing of information in dynamical systems. Various information management systems can be represented as dynamical systems of interconnected information processing units. Here they focus mostly on genetic regulatory networks that are information processing systems that process and propagate information stored in genome. Boolean networks are used as a dynamical model of regulation, and different ways of parameterizing the dynamical behavior are studied. What are called critical networks are in particular under study, since they have been hypothesized as being the most effective under evolutionary pressure. Critical networks are also present in man-made systems, such as the Internet, and provide a candidate application area for findings on the theory of dynamical networks in this chapter. The authors present approaches of annealed approximation and find that avalanche size distribution data supports criticality of regulatory networks. Based on Shannon information, they then find that a mutual information measure quantifying the coordination of pairwise element activity is maximized at criticality. An approach of algorithmic complexity, the normalized compression distance (NCD), is shown to be applicable to both dynamical and topological features of regulatory networks. NCD can also be seen to enable further utilization of measurement data to estimate information propagation and processing in biological networks.
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Information propagation and flow are key aspects in understanding how systems interact and function. Various information management systems can be represented as dynamical systems where information processing units (nodes) are connected with links (edges) that represent information transfer. Here we present recent results that provide insight into the general properties of this kind of systems. We focus our discussion on the context of important class of systems, namely the genetic regulatory networks that can, at very high level, be modeled as Boolean networks (Kauffman, 1993). Genetic regulatory networks process and propagate digital information stored in genome and orchestrate a specific response to various external stimuli (inputs) (Hood & Galas, 2003). What makes this class of systems the most interesting is that regulatory networks have evolved over millions of years. Thus, it can be argued that through natural selection and self organization only the most robust and evolvable network structures remain today. Understanding the information processing principles that are present in genetic regulatory networks can help us to engineer man made information processing systems that are extremely robust and take advantage of the insights that biological systems have gained over the years of evolution.

The dynamical behavior of large, complex networks of interacting elements is generally difficult to understand in detail. The existence of multiple influences on each element can give rise to exceedingly complicated dynamics even in deterministic systems. A paradigmatic case is the network of genes within a cell, where the interactions correspond to transcriptional and post-transcriptional regulatory mechanisms. The expression of a single gene may be subject to regulation by itself and up to 20 proteins expressed by other genes, and the network of such interactions has a complicated structure, including positive and negative feedback loops and nontrivial combinatorial logic.

The genetic regulatory networks may be compared with e.g. Internet traffic, which has been seen to exhibit critical dynamics (Fukuda et al., 2000; Valverde & Sole, 2002). This suggests that Internet as a self-organizing system may optimize information transfer. Internet provides an example of a man-made system of information management and processing, and thus, any insights into information processing in critical networks may have consequences in terms of information management as well. A large part of what we present in this book chapter may be seen as general in the sense that many of the precise characteristics of the network can be abstracted away, and the principles of dynamical behavior still hold.

The structure of this chapter is as follows. First, we present some background of information in genetic regulatory networks, our main object of study. In addition, the Boolean network model utilized as a simple approximation of genetic networks is presented. Our main aim in this chapter is to uncover general features of information processing in cells, and for this purpose, different measures related to global dynamics of the system are suggested. Each of the measures is able to capture an aspect of dynamical information processing in the cells. Criticality of cellular dynamics is taken to be the main focus of attention and each of the measures utilized is, in turn, shown to shed some light on this question.

After the background information, we begin by outlining the principles of basic annealed approximation. This is a technique that can be used as a first-order approximation of global dynamics. Its main drawback is that the analysis cannot take into account topological details of the networks under study. The findings presented utilizing branching process models give some support to the hypothesis that cells might have critical dynamics. Next, we discuss an application of Shannon’s information theory to genetic regulatory network models. Pairwise mutual information between states of network nodes is utilized as a dynamical measure of coordination between nodes. It is observed that critical networks maximizes this measure, thus making pairwise mutual information an interesting tool for characterizing global dynamics.

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Editorial Advisory Board
Table of Contents
Chapter 1
Teemu Saarelainen
The amount of information surrounding us is ever increasing. Usable information is our most valuable asset both in our professional and personal... Sample PDF
Open Formats, Open Information and Future Trends in Software Engineering
Chapter 2
Chia-Chu Chiang
Documents are perfectly suited for information exchange via the Internet. In order to insure that there are no misunderstandings, information... Sample PDF
Engineering Information Into Open Documents
Chapter 3
Dwayne Rosenburgh
This chapter presents a look at the decision-making methods used by real-life, collegial, high-achieving, technical teams and organizations. One may... Sample PDF
Decision-making as a Facilitator of High-achievement in Non-hierarchical Technical Environments
Chapter 4
Khaled Ahmed Nagaty
The purpose of this chapter is to discuss the relationship between three entities: hierarchical organization, information management and human... Sample PDF
Hierarchical Organization as a Facilitator of Information Management in Human Collaboration
Chapter 5
Christine B. Glaser, Amy Tan, Ahmet M. Kondoz
Managing information collaboratively in an open and unbounded environment without an information management application influenced and challenged... Sample PDF
An Intelligent Information Management Tool for Complex Distributed Human Collaboration
Chapter 6
Lobna Hsairi, Khaled Ghédira, Adel M. Alim, Abdellatif BenAbdelhafid
In the age of information proliferation, openness, open information management, interconnectivity, collaboration and communication advances... Sample PDF
R2-IBN: Argumentation Based Negotiation Framework for MAIS-E2 model
Chapter 7
Pauli Brattico, Mikko Maatta
Automatic natural language processing captures a lion’s share of the attention in open information management. In one way or another, many... Sample PDF
Natural Language Parsing: New Perspectives from Contemporary Biolinguistics
Chapter 8
Sune Lehmann
A network structure of nodes and links is an informative way to study information systems. The network representation is valuable because it encodes... Sample PDF
Structures in Complex Bipartite Networks
Chapter 9
Juha Kesseli, Andre S. Ribeiro, Matti Nykter
In this chapter the authors study the propagation and processing of information in dynamical systems. Various information management systems can be... Sample PDF
Measuring Information Propagation and Processing in Biological Systems
Chapter 10
Yacine Benahmed, Sid-Ahmed Selouani, Habib Hamam
In the context of the prodigious growth of network-based information services, messaging and edutainment, we introduce new tools that enable... Sample PDF
Natural Human-System Interaction Using Intelligent Conversational Agents
Chapter 11
Marko Helén, Tommi Lahti, Anssi Klapuri
The purpose of this chapter is to introduce tools for automatic audio management. The authors present applications which are already available for... Sample PDF
Tools for Automatic Audio Management
Chapter 12
Susmit Bagchi
Due to the advancement of hardware technologies and mobile communication systems, the mobile devices are transforming into multimedia devices... Sample PDF
PUM: Personalized Ubiquitous Multimedia
Chapter 13
Edgar Jembere, Matthew O. Adigun, Sibusiso S. Xulu
Human Computer Interaction (HCI) challenges in highly dynamic computing environments can be solved by tailoring the access and use of services to... Sample PDF
Personalisation in Highly Dynamic Grid Services Environments
Chapter 14
Josef Makolm, Silke Weiss, Doris Ipsmiller
Efficient and effective knowledge management plays an increasingly important role in knowledge intensive organizations. The research project... Sample PDF
DYONIPOS: Proactive Support of Knowledge Workers
Chapter 15
Juhana Kokkonen
In this chapter the open-source based collaboration model of Finnish Wikipedia is examined from the perspective of user culture, which is the... Sample PDF
User Culture, User-System Relation and Trust – The Case of Finnish Wikipedia
Chapter 16
Cristina Melchiors, Lisandro Zambenedetti Granville, Liane Margarida Rockenbach Tarouco
The use of information management tools in open and unbounded operational environments demands an efficient and robust communication infrastructure... Sample PDF
P2P-Based Management of Collaboration Communication Infrastructures
Chapter 17
John Tsiligaridis
The problem of server performance in a contemporary, rapidly developed and multi-discipline environment is examined. Multiple requests in a very... Sample PDF
A Framework for Semi-Autonomous Servers in the Wireless Network Environment
Chapter 18
Rakesh Biswas, Kevin Smith, Carmel M. Martin, Joachim P. Sturmberg, Ankur Joshi
This chapter discusses the role of open health information management in the the development of a novel, adaptable mixed-platform for supporting... Sample PDF
Open Information Management in User-driven Health Care
Chapter 19
Michael Losavio, Adel Elmaghraby, Deborah Keeling
The global interconnected information space offers unprecedented ways of accessing and analyzing information. New infringements of the rights of... Sample PDF
Information Management: Jurisdictional, Legal and Ethical Factors
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