General Law of Growth and Replication and the Unity of Biochemical and Physical Mechanisms

Second Revised Edition

  

by Yuri K. Shestopaloff

 

Table of Contents


Acknowledgements 11
About the author 12
Prehistory of the research 13
Introduction 14
Chapter 1. Growth as a complex multifactor phenomenon governed by laws of Nature 21
1.1. How we cognize Nature. General methodological concepts 21
1.2. Some ancient perceptions of growth 24
1.3. Modern views on growth 26
1.4. Growth is a multifactor and general phenomenon that requires a multidisciplinary approach 28
Chapter 2. Growth of living organisms from the evolutionary perspective 30
2.1. Growth and replication as evolutionary components 30
2.2. How numbers and Nature’s laws create order from chaos 31
2.3. Competition for resources as an evolutionary driving force 35
Chapter 3. Biochemical growth mechanisms 37
3.1. Examples and common features of biochemical growth mechanisms 37
3.1.1. Mammalian cells 39
3.1.2. Polar gradients of kinase Pom1 40
Chapter 4. Physical and biochemical growth mechanisms and their mathematical representations 42
4.1. Mathematical formulation of the general growth mechanism 43
4.1.1. Specific influx and its dependence on the growth phase 43
4.1.2. Introducing growth ratio and growth equation 45
4.1.3. Generalized growth law and some thoughts about fundamental laws of Nature 53
4.2. How much to grow? Some inferences from the growth equation 58
4.3. Growth rates of different cell’s constituents 60

4.3.1. Mathematical relationship between growth rate and mass increase 60
4.3.2. Ribosome rate of synthesis 61
4.3.3. Relationship of rate of synthesis and influx 64
4.3.4. Biochemistry of growing Amoeba 70
4.3.5. Finding specific influx through the rates of synthesis of biochemical components 72
4.3.6. Additional nutrient requirements to support the growing cell’s “infrastructure” 73
4.4. Full cycle growth. Amoeba’s example 77
4.4.1. Review of experimental data on Amoeba growth 77
4.4.2. Finding the asymptotic value of the maximum possible volume 79
4.4.3. Finding growth ratio and computing growth curves 83
4.4.4. Accounting for the additional nutrient influx required for DNA synthesis 90
4.4.5. Amoeba’s division mechanism 91
4.4.6. Inherent unity of growth ratio, biochemical machinery and biomass synthesis 98
4.4.7. Application of growth equation. Why is the growth rate highest at the beginning? 99
4.4.8. Application of the growth equation. Why can the same cells grow small and large? 100
4.4.9. Inflection points of growth curves as potential growth stoppers 105
4.4.10. Validity of growth equation’s in light of results on modeling growth of Amoeba 106
4.4.11. A side note about one old but well forgotten validation criterion 108
4.5. The fastest growth scenario 110
4.5.1. Inflection point of the growth curve as a trigger of division 110
4.5.2. Modeling the growth of fission yeast using the growth equation 113
4.5.3. Change of influx during growth 118
4.5.4. Modeling the growth of wild type fission yeast. Additional influx for DNA synthesis 120
4.5.5. Modeling the growth of mutant 128
4.5.6. The growth scaling mechanism revisited 132
4.5.7. Summary of growth modeling results 133
4.5.8. Generality of the physical growth mechanism 135
4.6. Application of the general growth mechanism to problems of metabolic flux analysis 136
4.6.1. Growth of Saccharomyces cerevisiae 136
4.6.2. Biomass synthesis 146
4.6.3. Sensitivity of methods for estimation of biomass production 149
4.6.4. Growth of E. coli and biomass production 149
4.6.5. S. cerevisiae as an example of how organisms provide fast growth 150
4.7. Application of the general growth mechanism in biotechnology and bioengineering 153
4.7.1. Balanced growth 153
4.7.2. Dynamic growth 155
4.7.3. Other flux analysis and bioengineering applications 155
4.7.4. Secretion of industrial substances 156
4.8. Growth and reproduction of multicellular organisms 157
4.9. Growth and reproduction as inherently multifactor phenomena 161

4.9.1. Fragments and the Whole 161
4.9.2. An integral view of the growth phenomenon. Distribution of resources 162
4.9.3. The relationship between biomass production and the growth ratio 163
4.9.4. Growth cycle progression as a consequence of changes of growth ratio and biomass production 165
Chapter 5. Growth mechanisms that are based on geometrical form of organisms 170
5.1. Cells’ shape as a growth suppression factor 170
5.2. A cylinder as one of the fastest growing geometrical forms 174
5.3. Growth of embryonic cells in Drosophila. Geometrical growth suppression mechanism 175
5.4. Growth suppression by cells’ elongation in the growth of blastocysts in pigs 179

Chapter 6. Properties of growth ratio. Organisms’ overgrowth through the form change 181
6.1. Changing the growth ratio 181
6.2. Correlation between the elongated shape and the growth rate 186
6.3. Growth ratio conjecture 188
6.4. Overgrowth and natural selection 190
6.5. Principle of compartmentalization. Further generalization of the growth mechanism 194

6.5.1. Compartmentalization as an evolutionarily developed mechanism 194
6.5.2. Using growth equation for reducing organisms and systems 195
6.5.3. Generalization of growth law 196
6.6. General growth law and evolutionary development 197
Chapter 7. Bioelectromagnetism as a driving force of growth and other biological processes 200
7.1. General nature of electromagnetic mechanisms 200
7.2. Electromagnetism as the driving force in energy generation and other biochemical processes 201
7.3. Integrity of electrical properties of biological substances 202

Chapter 8. Systemic view of growth 204
8.1. The subject of systems biology 204
8.2. Major areas of systems biology 206

Chapter 9. Growth and organization of populations of biological species 208
9.1. Logistic growth curve. Classical approach

9.2. Population growth equation9.2.1. Deriving general population growth formula

9.2.2. Defining parameters of the population growth formula    

9.3. Computing growth curves

9.3.1. Population growth of organisms whose mass remains constant   

9.3.2. Population growth of organisms whose grown mass can substantially decrease  

9.3.3. Population growth with periodic nutrients influx. Maximum mass does not change  

9.3.4. Population growth with periodic nutrients influx when maximum mass changes  

9.4. Generalizing population growth formula for two and more offsprings and different life span 

9.5. Some thoughts about other possible applications of the population growth equation 

9.5.1. Generalization of introduced population growth formulas for other problems   

9.6. Summing up results for the population growth study

Conclusion 232
References 234
Index Table 239
Recent books by Yuri K. Shestopaloff 243
Recent articles by Yuri K. Shestopaloff 245



 

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Last modified: 04/25/15