Code Biology

PART I - The Paradigms of Biology 1. Chemistry versus Information 1.1 The Chemical Paradigm 1.2 The Information Paradigm 1.3 Shannon's Information Theory 1.4 Sequences and specificity 1.5 The ontological claim of the Information paradigm 1.6 The ontological claim of the Chemical paradigm 1.7 The idea that 'Life is artifact-making 1.8 The origin of linear and digital sequences 1.9 A useful metaphor 1.10 The issue of meaning 1.11 What is mechanism? 2. The Code Paradigm 2.1 Schrodinger's prophecy 2.2 The 'special constraints' solution 2.3 The new observables 2.4 Names and 'nominable' entities 2.5 Organic information 2.6 Organic meaning 2.7 The discovery of new worlds 2.8 Life and semiosis 2.9 The Code model of semiosis 2.10 The defining features of signs and meanings 2.11 The sequences of genes and proteins 2.12 Two types of organic signs 2.13 A new beginning 3. A Gallery of Organic Codes 3.1 The Apparatus of protein synthesis 3.2 The Genetic code 3.3 Stereochemistry and arbitrariness 3.4 The Splicing codes 3.5 The Metabolic code 3.6 The Signal Transduction codes 3.7 The Signal Integration codes 3.8 The Histone code 3.9 Is the 'Histone Code' an organic code? 3.10 The Tubulin code 3.11 The Sugar code 3.12 The Glycomic code 3.13 The Sequence codes 3.14 Organic codes and biology PART II - Major Steps in Macroevolution 4. Life before the Cell 4.1 The twin problems of the beginning 4.2 The replication paradigm 4.3 Ribosoids 4.4 Nucleosoids 4.5 Nucleosoid evolution 4.6 Heterosoids 4.7 A primitive apparatus 4.8 Statistical proteins 4.9 First and last common ancestor 4.10 The ancient genetic code 4.11 The modern genetic code 4 12 Steps towards the cell 4.13 The ribotype theory of the cell 5. The First Three Billion Years 5.1 The 'Stony Carpets' 5.2 The Iron Bands 5.3 The Age of the Protista 5.4 Three primary kingdoms 5.5 The first cells 5.6 Two evolutionary strategies 5.7 The RNA codes 5.8 The fluid genome 5 9 Evolving the cytoplasm 5.10 The cytoskeleton codes 5.11 The compartment codes 5.12 The Tree and the Web 5.13 What happened in the Precambrian? 6. Evolving the Embryos 6.1 The rediscovery of epigenesist 6.2 Body plans and animal phyla 6.3 A cascade of inductions 6.4 Determination and cell memory 6.5 Self-regulating embryonic fields 6.6 Arranging cells in space 6.7 The unexpected from molecular embryology 6.8 The classification of animals 6.9 The Cambrian explosion 6.10 The origin of animals 6.11 The Hox codes 6.12 The codes of the body plans 6.13 The logic of the embryos 7. Brain and Mind 7.1 Evolving the neuron 7.2 The intermediate brain 7.3 The instinctive brain 7.4 Making mental images 7.5 Sensations and perceptions 7.6 A universal neural code 7.7 Mechanisms of brain development 7.8 Codes in brain development 7.9 Theories on the brain-mind relationship 7.10 The 'first-person' experiences 7.11 The code theory of mind 7 12 The interpretive brain 7.13 Three brain macroevolutions 8. Origins of Language 8.1 Chomsky's definitions of language 8.2 Sebeok's definitions of language 8.3 The bone of contention 8.4 A third foundation of language 8.5 A juvenile ape 8.6 Fetalization and brain wiring8.7 Brain size and language genes 8.8 The cerebra bifida model 8.9 Mind and reality 8.10 Steps in the ontogeny of mind 8.11 Interacting brains 8.12 A hidden asymmetry 8.13 Rules of neural development 8.14 Specifically human 8.15 The third modelling system 8 16 Our rational faculties 8 17 The codes of language PART III - A New Science of Life 9. Biosemiotics 9.1 Matter controlled by symbols 9.2 Physical biosemiotics 9.3 Darwinian biosemiotics 9.4 The Peirce framework 9.5 Zoosemiotics 9.6 Peircean biosemiotics 9.7 Hermeneutic biosemiotics 9.8 A book review for Sebeok 9.9 A pluralistic enterprise 9.10 Organic semiosis 9.11 Animal semiosis 9.12 Sense and reference 9.13 The worlds of semiosis 9.14 Two types of Biosemiotics 9.15 A new beginning 10. Code Biology 10.1 What is the cell? 10.2 The von Neumann machine 10.3 A machine capable of self-assembly 10.4 The concept of Codepoiesis 10.5 Extensions of the Modern Synthesis 10.6 Mechanisms of evolution 10.7 Copying and coding 10.8 Organic codes as constraints 10.9 The Major Steps in Macroevolution 10.10 The characteristics of the codes 10.11 Different types of codes 10.12 Unpredictable features 10.13 The Three Worlds of life 10.14 Code biology 10.15 There was a time References Author Index Subject Index