Biological Systems: Complexity and Artificial Life


by

Jacques Ricard

DOI: 10.2174/97816080581361140101
eISBN: 978-1-60805-812-9, 2014
ISBN: 978-1-60805-813-6



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The exponential increase in computing power in the late twentieth century has allowed researchers to gather, process and analyze large...[view complete introduction]

Table of Contents

Preface

- Pp. i-ii (2)

Jacques Ricard

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The Vision of Classical Molecular Biology and its Limits

- Pp. 3-14 (12)

Jacques Ricard

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Biological Systems, Identity, Organization and Communication

- Pp. 15-34 (20)

Jacques Ricard

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Emergence of Information in Biological Systems

- Pp. 35-58 (24)

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Non-Equilibrium, Enzyme Reactions, Self-Organization and Dynamic Properties

- Pp. 59-67 (9)

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Enzyme Activity within the Living Cell

- Pp. 68-98 (31)

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Thermodynamics of Energy Conversion within the Cell

- Pp. 99-125 (27)

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Driving Unfavorable Molecular Motions within the Cell

- Pp. 126-141 (16)

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Physics of Metabolic Oscillations

- Pp. 142-169 (28)

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Biochemical Networks

- Pp. 170-183 (14)

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Non-Equilibrium Dynamics, Biological Systems and Time-Arrow

- Pp. 184-195 (12)

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Some Philosophical Implications of the Concept of Biological System

- Pp. 196-201 (6)

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Subject Index

- Pp. 202-205 (4)

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Preface

For many years biology has been rooted in a reductionist attitude probably derived from Descartes philosophy that consists in splitting the problems into simple elements that should help solve these problems. These elements are specific macromolecules, namely nucleic acids and proteins. For many years it was, explicitly or implicitly, postulated that major biological problems could be solved from the knowledge of structure and function of nucleic acids and proteins. The term “molecular biology” clearly implied that it is possible to reduce biological problems to molecular entities. In fact many difficulties arise when one attempts at reducing biological problems to biomolecules. The main reason for this difficulty is that any living organism is a complex system.

The concept of complex system has played a major role in contemporary science, particularly in biology and social sciences. Complex systems display a number of features that are stated below [1,2].

Complex systems are made up of a large number of elements in interaction.

Such systems are not disordered but display a certain degree of order and organization.

These systems display nonlinear effects and feedback loops.

From a thermodynamic viewpoint, a complex system usually operates away from thermodynamic equilibrium and requires both matter and energy to maintain its organization.

A complex system is in a dynamic state and possesses a history. Its present state is determined by its past behaviour.

The interactions between the elements of the system take place over a short range and are therefore local. These features and others have already been mentioned earlier [1].

It is therefore possible to point out the differences between molecular and systems biology. As briefly pointed out above, molecular biology attempts at understanding properties of a living organism from the individual properties of some type of biomolecules such as DNA, RNA and proteins. Systems biology explains the global properties of the living organisms from the dynamic properties of systems of biomolecules. But a system, a network, of biomolecules can be more than a simple set of macromolecules. It involves multiple interactions between its elements and display the emergence of novel properties, that is properties that are “novel” relative to the individual properties of the elements of the system. Put in other words, such systems display emergence of properties that are not borne by any individual element of the global system. It is evident then that the global properties of these systems can only be studied with the help of mathematics which then appears an unavoidable aspect of systems biology. In this line, it becomes possible to approach some aspects of biological problems through the use of simple mechanistic models of living systems and this approach can be considered some kind of systems biology.

Many biological problems can now be studied trough the concept of system. Two books have been devoted to these problems [2, 3] and it is therefore useful, to use some of these problems as a material to approach this field of complexity and systems biology.



Acknowledgements

The author wishes to thank his wife Käty for her constant support as well as Robin Coombes for carefully reading his manuscript.

Conflict Of Interest

The author confirm that, as far as he knows, the book content does not posses any conflict of interest.

References

[1] Cilliers, P. Complexity and Postmodernism (1998), Routledge, London and New York.

[2] Ricard, J. Biological Complexity and the Dynamics of Life Processes.(1999), Elsevier, Amsterdam, Lausanne, New York.

[3] Klipp, E, Liebermeister, W, Wierling, C, Kowald, A. Lehrach, H. and Herwig, R.(2010), Systems Biology, Wiley-Blackwell.

Jacques Ricard
Honorary Director of the Jacques Monod Institute
CNRS, Paris cedex 5,
France
E-mail: Jkricard@aol.com

List of Contributors

Author(s):
Jacques Ricard
Honorary Director of the Jacques Monod Institute
CNRS
Universities Paris 6 and Paris 7
Paris cedex 5
France




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