The Organic Codes: An Introduction to Semantic Biology Book

	Foreword
	Dedication
	Acknowledgements
	Introduction	1
Ch. 1	The microscope and the cell	9
	The cell theory	10
	The problem of generation	12
	The problem of embryonic development	15
	The two versions of the cell theory	17
	Mechanism	19
	The chemical machine	21
	The computer model	24
	The autopoietic cell	27
	The epigenetic cell	29
Ch. 2	Theories of evolution	33
	Traditional biology	34
	Lamarck's contribution	36
	Darwin's bet	38
	Natural selection	40
	Organs of extreme perfection	41
	Common descent	44
	The second mechanism of evolution	49
	The Modern Synthesis	51
	Molecular evolution	54
	The third mechanism of evolution	57
	Macroevolution	60
	Where is biology going to?	63
Ch. 3	A new model for biology	67
	The logic of embryonic development	67
	Reconstructions from incomplete projections	69
	A memory-building approach	71
	The algebraic method	75
	The theoretical limit	79
	ART: an iterative algebraic method	80
	The memory matrix	82
	Density modulation	84
	MRM: the family of memory algorithms	86
	The two general principles of MRM	89
Ch. 4	Organic codes and organic memories	93
	The characteristics of codes	93
	The organic codes' fingerprints	96
	The bridge between genes and organism	99
	The splicing codes	101
	The signal transduction codes	105
	Contextual information	111
	Determination and cell memory	112
	The other face of pattern	114
	Hints from developing neurons	117
	The key structures of embryonic development	119
Ch. 5	The origin of life	121
	The primitive Earth	122
	Chemical evolution	127
	Postchemical evolution	129
	The metabolism paradigm	131
	The replication paradigm	134
	The RNA world	138
	Replication catastrophes	140
	Eigen's paradox	142
	The ribotype theory	145
	The genetic code	148
	Evolution of the code	155
	The ribotype metaphor	157
	Copymakers and codemakers	159
	The handicapped replicator	161
Ch. 6	Prokaryotes and eukaryotes	163
	The potassium world	164
	Two forms of life	166
	Three primary kingdoms	168
	The last common ancestor	173
	The origins of bacteria	175
	The cytoskeleton	178
	The compartments	180
	Chromosomes	182
	The seven kingdoms	185
	Three thousand million years	187
Ch. 7	The Cambrian explosion	191
	The fossil record	192
	The experimental data	193
	Body plans and phylotypic stages	196
	The traditional explanations	201
	The Cambrian singularity	202
	The stumbling-block	203
	The reconstruction model	204
	Multicellular structures	206
	Biological memories	209
	A new model of the Cambrian explosion	210
	The conservation of the phylotypic stage	213
Ch. 8	Semantic biology	217
	The semantic theory of the cell	219
	The semantic theory of embryonic development	221
	The mind problem	224
	The semantic theory of mental development	226
	Artifacts and natural selection	228
	The semantic theory of evolution	229
	About organic codes	234
	The language model	236
	The Individuality Thesis	237
	The development of semantic biology	240
Ch. 9	A brief summary	243
	The first principle	244
	The second principle	245
	The third principle	246
	The fourth principle	247
	The first model	248
	The second model	249
	The third model	250
	The fourth model	251
	Conclusion	253
App	Definitions of life	255
	Afterword	265
	References	279
	Index	295