CONTENTS (TABLE DES MATIÈRES)
Preface
Forword to Volume I
* * * * *
PART I : MATERIALS AND METHODS
IN BIOLOGICAL DYNAMICS
Introduction to Part I
Chapter I : Macromolecular
Components and Interactions in Living Organisms
I. Structure of nucleic acids
II. Structure of proteins
1. Description of protein structure
2. Theory of the conformation of biological macromolecules
3. Molecular conformation and
biological activity
III. Molecular
interactions in proteins: proteinligand interactions
1. Thermodynamic theory of
molecular interactions
2. The cooperative effect

a. The concept of cooperativity

b. Cooperativity and
fhe binding polynomial

c. An illustration of
the cooperative effect
Chapter II : The Internal
Chemistry of Cells
I. Catalytic
function of the enzymic reaction
1. HenriMichaelisMenten Equations:
equilibrium conditions
2. BriggsHaldane Equations: Quasistationary
state conditions
3. The mathematical viewpoint: the pseudosteady
state hypothesis
II. Regulatory
function of the enzymic reaction
III. Molecular interactions and the active site
concept
IV. Coupled chemical reactions:
reactiondiffusion equations
1. General
equation for a chemical transformation
2. The physics of diffusion:
Fick's equation
3. The mathematics of a reactionaldiffusional
system
4. An autocatalytic reaction
Chapter
III : Methods in Biological Dynamics
I. Biology
and complexity
II. Relational theories
1. Rosen's
theory of abstract biological systems
2. Delattre's theory of transformation
systems
III.
Thermodynamic theory
1. Principles
of equilibrium thermodynamics
2. The entropy production term.
Consequence in the linear field: nonequilibrium
stationary states
in the neighbourhood of equilibrium
3. Nonlinear thermodynamics
of chemical reactions: nonequilibrium stationary
states far from equilibrium

a.
The universal criterion of evolution

b.
The GlansdorffPrigogine functional

c.
Physical interpretation

d.
Network thermodynamics

a.Characteristics
of an element in a chemical network

b. Bond graphs
IV.
Thom's theory of elementary catastrophes
Summary of Part
I
* * * * *
PART II :
THE MOLECULAR ORGANISATION OF LIVING MATTER
Introduction to Part II
Chapter
IV : Organisation of Biological Systems
I.
A formal definition of selforganisation
1. Organisation
2. Selforganisation
II.
Biological organisation and information theory
1. Von Foerster’s
selforganising system
2. The YockeyAtlan theory of
selforganisation
III.
A theory of the functional organisation of formal
biological systems some concepts and definitions
1. Introduction
to the functional organisation of biological systems
2. The problem of representation
in biology

a.
Notions of system, structure, function and evolution

a
. System: general considerations

b
. Structure and system

g
. Function

d
. Evolution

b.
A representation of physiological systems: the
hypothesis of associative

functional
selforganisation

a
. Biological structure and systems

b
. The hypothesis of associative selforganisation

g
. The physiological system as a hierarchical
system.

c.
Functional interactions, levels of organisation
3. Mathematical
representation of the functional organisation
4. Dual representations: (N,a)
and (y,r)
IV.
Spatial organisation in the cell : concept of structural
discontinuity
1. On the
existence of nonlocal interactions: The concept
of the active site reexamined
2. Enzyme organisation: microcompartmentation
and the example of "channelling"

a.
Introduction to the problem of enzyme organisation

b.
Relation with physiology and physiological consequences

c.
Definitions of channeling on biophysical bases

a
. Metabolic organisation

b
. Application of Curie’s principle of
symmetry

g
. The respective roles of diffusion and reaction

d
. How should the diffusion process be characterised
in order to account for the existence of molecular
channels in the absence of a physical limit
such as a membrane ?
3. On the
functional organisation in a biological structure:
the example of enzyme organisation

a.
Definition of a metabolic pathway as a structural
unit

a
. Michaelis enzymatic reactions: metabolic
flux and transport between the local medium
and the bulk phase

b
. Stability of the dynamics of a step in
the metabolic chain

g
. Stability of a metabolic pathway with allosteric
control of production
4. A paradigm
for the creation of functional interactions: the
selfassociation hypothesis

a.
The structural unit and the physiological function

b.
The selfassociation hypothesis

c.
On the nature of a break in the selfassociation

a
. A break in the functional interaction of
the metabolic pathway

b
. Basic mechanisms of the association
5. Functional
association between two metabolic pathways defined
as structural units 168

a.
A general and generative schema of the association

b.
Mathematical study of the dynamics in a u_{2}units:
a specific system

c.
Mathematical study of the dynamics in a u_{2}units:
a general dynamical system
6. The paradigm
of selfassociation applied to the enzyme organisation:
role of local and bulk phase
Chapter V : The ReplicationTranslation Apparatus
I.
The 'central dogma' of molecular biology
1. Genes
and chromosomes
2. Replication, transcription
and translation
3. Computational methods of determining
the sequencing properties of DNA
II.
Information theory and the genetic code
1. Measurement
of the quantity of information in the genetic code
2. The genetic code
III.
Chemical dynamics of heredity
1. Generalities
2. DNA replication
3. Protein synthesis
IV.
Topological, structural and functional implications
of nucleicacid chains
1. Topological
concepts in DNA replication and structural consequences

a. Topological
findings

b.
Experimental data
2. Topology
and protein biosynthesis
V.
The hierarchical organisation of the replicationtranslation
apparatus
Chapter
VI : Molecular Evolution and Organisation
I.
Evolution of selfinstructing information carriers
1. Phenomenological
description of the evolution of chemical species
2. Solution of the system of
equations
3. Explicit solutions
4. Consequence: selection in
molecular systems
II.
Evolution with complementary instruction. The case
of DNA or RNA replication
III. Protein biosynthesis: selforganising enzymic
cycles
1. Catalytic
protein cycles
2. Selfreproducing hypercycle
Chapter VII : Evolution and Physiology
I.
Evolution and selforganisation of molecular systems
1. Introduction
2. The three phases of evolution
3. Darwinian systems
II.
A coherent interpretation of evolution
1. Creation
of thermodynamically stable spatiotemporal structures
2. Selforganisation and the
evolution of molecular bioystems
3. Evolution of the species in
terms of information theory
4. Recapitulation: the scenario
of evolution
III.
Functional biology and evolutionary biology
1. Darwinism
and physiology: the principle of vital coherence
2. An elementary model of evolution

a. Formalisation
of the principle of vital coherence in term
of the level of organisation

b. Description
of an elementary model of evolution

c. Discussion
and results: can this model be generalised ?
Summary of Part II
* * * * *
PART III : CELLULAR ORGANISATION OF LIVING MATTER
Introduction to Part II
Chapter
VIII : Cellular Organisation
I.
Cell description
II. Cell organisation and regulation
1. Formation
of structures at the cellular level
2. Regulation and metabolic
pathways

a. The
glucose6phosphate pathway

b. The
Krebs cycle (the citric acid cycle)

c. Interpretation
of regulatory phenomena

d. The
phenomenon of inverse regulation
III.
Cell growth: an introduction
1. Growth
2. Development
3. Differentiation
4. Morphogenesis
Chapter
IX : Regulation of Cell Function through Enzvme
Activity
I.
Introduction to the regulation of enzyme synthesis
II. Theoretical model of regulation
III. Regulation of protein biosynthesis in higher
organisms
Chapter
X : Cell Growth and Morphogenesis
I.
General aspects
II. Unicellular organisms
1. Differentiation
in the Acrasiales
2. Human red blood cells
3. Some examples of cell differentiation
at the molecular level
2. Positional
information and cell differentiation
3. Control
and cell differentiation

a. Transcriptional
control

b. Posttranscriptional
control

c. Posttranslational
control

d. Mathematical
models of control in cell differentiation
IV.
Morphogenesis: Turing's theory
1. General
aspects
2. Theoretical models
of morphogenesis
3. Morphogenesis:
local theory and global theory
V.
A description of growth for functional organisation
1. A break
in the functional interaction: consequences on
the stability of biological systems
2. Evidence
for the existence of selfassociation: An increase
in stability
Chapter
XI : Cell Division
I.
The cell cycle
1. Description
2. Models of the cell cycle
3. The limit cycle model of biochemical
oscillations
II.
Development of a cell population
1. Kinetics
with variables (t, a)
2. Kinetics with variables (t,m)
III.
Analysis of the cell cycle: population theory
1. Leslie
matrices applied to population studies
2. Interpretation of the FLM
curve by population theory
Chapter
XII : Cell Growth, Division and Differentiation
I.
Asymmetrical cell division
II. Cell growth
1. Analytical
description: mass and volume
2. Global description of the
behaviour of a cell
III.
Mechanochemical approach to morphogenesis: Murray's
mechanical model for mesenchymal morphogenesis
IV.
Topological description of developmental dynamics:
potential of functional organisation
1. Introduction:
Variational principles in biology
2. The potential of functional
organisation
3. Criterion
of maximality for the potential of organisation:
a class of biological systems

a.
State of maximum of organisation

b.
The extremum hypothesis: a class of biological
systems

a
. The organisational state is an attractor

b
. Consequence: the extremum hypothesis for
the time variation of the number of
sinks
4. Criterion
of evolution for the functional organization: orgatropy
5. Criterion
of specialisation and reorganization of the (OFBS)
during development

a.
Criterion of specialisation

a
. The concept of specialisation

b
. The relation between specialisation and
hierarchisation

b.
Consequence: mathematical expressions of specialisation
and emergence of a level of organisation

c.
Functional order

d.
Timevariation of an (OFBS) during development
V.
A comparison between biological and physical systems
1. Structural
entropy and functional orgatropy
2. The consequence of the optimum
principle
3. On the meaning of the optimum
principle
Summary of Part
III
Conclusion
to Volume I : Unity at the Gene Level
* * * * *
Mathematical
Appendices
Appendix
A : Vector analysis
1. Gradient
of a function U(x,y,z)
2. Divergence of a vector
3. Green's theorem
4. The Laplace function: the
second order scalar operator
5. Summary
Appendix
B : Dynamic systems
1. Notion
of a dynamic system
2. The Hamiltonian form. Conservative
systems
3. Stability: Lyapunov functions
4. Limit cycles, critical points,
Jacobian, Hessian
5. Partial differential equations
6. Some notes on the terrninology
of ordinary differential equations.
Compact differential manifolds
Appendix
C : Notations in matrix algebra
Appendix
D : Probability and information theory
1. Probability
2. The Shannon function of information
Symbols and
constants (mainly in CGS units)
* * * * *
General
reading
Bibliography
Index
* * * * *