Molecular theory of the living cell: concepts, molecular mechanisms, and biomedical applications
Gespeichert in:
| 1. Verfasser: | |
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| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
New York [u.a.]
Springer
2012
|
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | XXI, 748 S. Ill., graph. Darst. |
| ISBN: | 1461421519 9781461421511 |
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Datensatz im Suchindex
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|---|---|
| adam_text | Sungchul Ji
Molecular Theory
of the Living Cell
Concepts, Molecular Mechanisms,
and Biomedical Applications
^J Springer
Contents
1 Introduction 1
Part I Principles, Laws, and Concepts
2 Physics 7
2 1 Thermodynamics of Living Systems 7
211 Three Thermodynamic Systems: Isolated,
Closed, and Open 7
212 Free Energy vs Thermal Energy
in Enzymic Catalysis 9
213 The First Law of Thermodynamics 10
214 The Second Law of Thermodynamics 11
215 The Third Law of Thermodynamics
and Schrodinger s Paradox 12
216 Are There More Laws of Thermodynamics? 15
2 2 The Franck-Condon Principle (FCP) 18
221 FCP and Born-Oppenheimer Approximation 18
222 Franck-Condon Principle in Chemistry 20
223 The Generalized Franck-Condon Principle (GFCP)
or the Principle of Slow and Fast Processes (PSFP) 21
2 3 Complementarity 24
231 Complementarity vs Supplementarity 24
232 Information-Energy Complementarity and Gnergy 27
233 Complementarian Logic 29
234 The Principle of Generalized Complementarity
and Complementarism 31
235 Two Kinds of Complementarities:
Kinematics vs Dynamics and Wave vs Particle 33
Contents
236 Three Types of Complementary Pairs
(or Complementarities) 40
237 The Wave-Particle Complementarity in Physics,
Biology, and Philosophy 43
238 The Conic Theory of Everything (CTE) 50
239 The Cookie-Cutter Paradigm and Complementarity 51
2 4 Renormalizable Networks and SOW AWN Machines 52
241 Definition of Bionetworks 52
242 Chunk-and-Control (C amp; C) Principle 54
243 Living Systems as Renormalizable Networks
of SOWAWN Machines 58
244 Hyperstructures and SOWAWN Machines 60
245 Micro-Macro Correlations in Bionetworks 61
2 5 The Theory of Finite Classes 64
2 6 Synchronic vs Diachronic Causes 66
Chemistry 69
3 1 Principle of Self-Organization and Dissipative Structures 69
311 Belousov-Zhabotinsky Reaction-Diffusion System 73
312 Intracellular Dissipative Structures (IDSs) 73
313 Pericellular Ion Gradients and Action Potentials 74
314 Three Classes of Dissipative Structures in Nature 75
315 The Triadic Relation Between Dissipative Structures
(Dissipatons) and Equilibrium
Structures (Equilibrons) 76
316 Four Classes of Structures in Nature 78
317 Activities versus Levels (or Concentrations)
of Bioploymers and Biochemicals in the Cell 79
3 2 Configurations versus Conformations; Covalent
versus Noncovalent Interactions (or Bonds) 81
3 3 The Principle of Microscopic Reversibility 82
Biology 85
4 1 The Simpson Thesis 85
4 2 Molecular Machines, Motors, and Rotors 86
4 3 What Is Information? 87
4 4 The Chemistry and Thermodynamics of Information 91
4 5 Synchronic Versus Diachronic Information 92
4 6 The Quantum Information and Enzymic Catalysis 96
4 7 The Information-Entropy Relations 97
4 8 The Minimum Energy Requirement
for Information Transmission 101
4 9 Info-Statistical Mechanics and the Gnergy Space 102
Contents
4 10 The Free Energy-Information Orthogonality
as the Bohr-Delbruck Paradox 106
4 11 What Is Gnergy? 107
4 12 Two Categories of Information in Quantum Mechanics 109
4 13 Information-Energy Complementarity as the Principle
of Organization 110
4 14 The Quantization as a Prelude to Organization I l l
4 15 Simple Enzymes Are to Enzyme Complexes What Atoms
Are to Quantum Dots 114
4 16 It From Bit and the Triadic Theory of Reality 116
Engineering 119
5 1 Microelectronics 119
511 Enzymes as Soft-State Nanotransistors 119
5 2 Computer Science 121
521 The Principle of Computational Equivalence
and a New Kind of Science (NKS) 121
522 Complexity, Emergence, and Information 123
523 Two Kinds of Complexities in Nature: Passive
and Active 127
524 The Principle of Recursivity 129
525 Fuzzy Logic 132
526 Fuzzy Logic and Bohr s Complementarity 132
527 The Knowledge Uncertainty Principle (KUP) 134
528 The Universal Uncertainty Principle 142
5 3 Cybernetics 151
531 Control Theory 151
532 The Law of Requisite Variety 154
533 Principles of After-Demand Supply (ADS)
and Before-Demand Supply (BDS) 156
Linguistics, Semiotics, and Philosophy 159
6 1 Linguistics 159
611 The Biology-Linguistics Connection 159
612 The Isomorphism Between Cell and Human
Languages: The Cell Language Theory 164
613 The Complexities of the Cellese and the Humanese 168
614 Double Articulation Arbitrariness of Signs,
and Rule-Governed Creativity 169
6 2 Semiotics 173
621 The Peircean Theory of Signs 173
622 The Principle of Irreducible Triadicity:
The Metaphysics of Peirce 175
623 Peircean Signs as Gnergons 176
624 Macrosemiotics versus Microsemiotics:
The Sebeok Doctrine of Signs 180
xvi Contents
625 Three Aspects of Molecular Signs: Iconic, Indexical,
and Symbolic 181
626 Human and Cell Languages as Manifestations
of Cosmolanguage 182
627 Semiotics and Life Sciences 183
628 Semiotics and Information Theory 184
629 The Cell as the Atom of Semiosis 185
6 2 10 The Origin of Information Suggested
by Peircean Metaphysics 186
6 2 11 The Triadic Model of Function 188
6 2 12 The Principle of Prescinding 189
6 3 Philosophy 191
631 The Five Causes Doctrine 191
632 The Principle of Closure 192
633 The Anthropic Principle 193
634 The Table Theory 193
635 The Principle of Mobius Relations 195
636 The Pragmatic Maxim of Peirce 195
637A New Architectonics Based on the Principle
of Information-Energy Complementarity 196
638 The Triadic Theory of Reality 197
639 The Type-Token Distinction 199
Part II Theories, Molecular Mechanisms, and Models
7 Molecular Mechanisms: From Enzymes to Evolution 203
7 1 Molecular Mechanisms of Ligand-Protein Interactions 203
711 Thermodynamics and Kinetics of Ligand-Protein
Interactions 203
712 Active versus Passive Bindings 208
713 The Kinetics of Ligand-Protein Interactions:
The Pre-fit Mechanism Based on the Generalized
Franck-Condon Principle 209
714 The Franck-Condon Mechanism
of Ligand-Membrane Channel Interactions 213
715 Scalar and Vectorial Catalyses: A Classification
of Enzymes 214
7 2 Enzymic Catalysis 217
721 Enzymes as Molecular Machines 217
722 Enzymes as Coincidence Detectors 220
723 Enzymes as Building Blocks of the Temporal
Structures of the Cell 222
724 Enzymic Catalysis as an Active Phase Transition 227
725 Enzymes as Fuzzy Molecular Machines 228
Contents xvii
8 The Conformon 231
8 1 The Definition and Historical Background 234
8 2 The Generalized Franck—Condon-Principle-Based
Mechanism of Conformon Generation 238
8 3 Experimental Evidence for Conformons 240
8 4 Conformons as Force Generators of Molecular Machines 243
85A Bionetwork Representation of the Mechanisms
of the Ca++ Ion Pump 246
8 6 Ion Pumps as Coincidence Detectors 248
8 7 The Conformon Hypothesis of Energy-Coupled
Processes in the Cell 249
8 8 The von Neumann Questions and the Conformon Theory 251
9 Intracellular Dissipative Structures (IDSs) 255
9 1 Experimental Evidence for IDSs 255
9 2 The p53 Network as a Multidimensional Hypernetwork 259
9 3 Interactomes, Bionetworks and IDSs 265
10 The Living Cell 269
10 1 The Bhopalator: A Molecular Model of the Living Cell 269
10 2 The IDS-Cell Function Identity Hypothesis 273
10 3 The Triadic Structure of the Living Cell 274
10 4 ATopological Model of the Living Cell 275
10 5 The Atom-Cell Isomorphism Postulate 277
10 6 A Historical Analogy Between Atomic Physics
and Cell Biology 282
10 7 Evolving Models of the Living Cell 287
Part III Applications: From Molecules to Mind and Evolution
11 Subcellular Systems 297
11 1 Protein Folding and Info-statistical Mechanics 297
11 2 What Is a Gene? 301
11 2 1 Historical Background 301
11 2 2 The Watson-Crick (Sheet Music)
and Prigoginian Forms {Audio Music) of Genetic
Information 307
11 2 3 The Iconic, Indexieal, and Symbolic Aspects
of the Gene 310
11 2 4 Three Kinds of Genes: drp-, dr-, and d-Genes 314
11 2 5 Two-Dimensional Genes: The Quality-Quantity
Complementarity of Genes 321
11 2 6 DNA and RNA as Secondary and Primary
Memories of the Cell 322
11 2 7 Cell Architectonics 325
xviii Contents
11 3 Single-Molecule Enzymology 327
11 3 1 Waiting Time Distribution of Cholesterol Oxidase 329
11 3 2 Molecules, Conformers, and Conformons 336
11 3 3 Isomorphism Between Blackbody Radiation
and Enzymic Catalysis 343
11 4 The Conformon Model of Molecular Machines 368
11 4 1 The Conformon Model of Biomotrons 369
11 4 2 Static/Stationary versus Dynamic/Mobile
Conformons 377
11 4 3 Stochastic Mechanics of Molecular Machines 378
11 4 4 Biopolymers as Molecular Machines:
Three Classes of Molecular Machines
and Three Classes of Their Mechanisms of Action 380
11 5 The Conformon Theory of Oxidative Phosphorylation 382
11 6 Deconstructing the Chemiosmotic Hypothesis 383
11 7 Molecular Machines as Maxwell s Angels 388
12 Whole Cells 391
12 1 DNA Microarrays: A Revolution in Cell Biology 391
12 2 The DNA Microarray Technique 392
12 3 Simultaneous Measurements of Transcript Levels (TL)
and Transcription Rates (TR) in Budding Yeast 395
12 4 RNA Trajectories as Intracellular Dissipative
Structures (IDSs) or RNA Dissipatons 395
12 5 The IDS-Cell Function Identity Hypothesis:
Experimental Evidence 398
12 6 The Transcription-Transcript Conflation 400
12 7 The Mechanistic Modules of RNA Metabolism 405
12 8 Visualizing and Analyzing RNA-Dissipatons 409
12 8 1 ViDaExpert 409
12 8 2 Ribonoscopy: Looking at RNA 411
12 8 3 Ribonics: The Study of Ribons with Ribonoscopy 419
12 9 Structural Genes as Regulators of Their Own Transcripts 420
12 10 Rule-Governed Creativity (RGC) in Transcriptomics:
Microarray Evidence 426
12 11 Genes as Molecular Machines 428
12 12 The Isomorphism Between Blackbody Radiation
and Whole-Cell Metabolism: The Universal Law
of Thermal Excitations (ULTE) 433
12 13 The Cell Force: Microarray Evidence 444
12 14 The Quantization of the Gibbs Free Energy Levels
of Enzymes and the Living Cell 448
Contents xix
12 15 Time-Dependent Gibbs Free Energy Landscape (TGFEL):
A Model of Whole-Cell Metabolism 459
12 16 The Common Regularities (Isomorphisms)
Found in Physics, Biology, and Linguistics:
The Role of Gnergy 462
12 17 Signal Transduction 466
12 18 Computing with Numbers Words, and Molecules 474
13 Mechanisms of the Origin of Life 479
13 1 The Anderson Model of the Origin
of Biological Information 479
13 2 The Conformon Model of the Origin of Life 481
14 Principles and Mechanisms of Biological Evolution 487
14 1 Darwin s Theory of Evolution 492
14 2 The Cell Theory of Evolution 494
14 3 The Principle of Maximum Complexity 497
14 4 Evolution as a Triadic Relation 498
14 5 The Gnergy Principle and Biological Evolution 506
14 6 The Thermodynamics and Informatics
of the Control Underlying Evolution and Development 506
14 7 The Zeldovich-Shakhnovich and the MTLC
(Molecular Theory of the Living Cell or the Bhopalator)
Models of Evolution: From Sequences to Species 509
15 Multicellular Systems 521
15 1 The Morphogenesis of Drosophila melanogaster 521
15 2 The Role of DNA, RNA, and Protein Gradients
in Drosophila Embryogenesis 526
15 3 The Triadic Control Principle (TCP) 526
15 4 The Synchronic vs Diachronic System-Environment
Interactions 530
15 5 The Dissipative Structure Theory of Morphogenesis 532
15 6 The Tree-Ring-and-Landscape (TRAL) Model
of Evolutionary and Developmental (EvoDevo) Biology 534
15 7 Quorum Sensing in Bacteria and Cell-Cell
Communication Networks 539
15 8 Morphogenesis as a Form of Quorum Sensing 542
15 9 Carcinogenesis as Quorum Sensing Gone Awry 543
15 10 Symmetry Breakings in Morphogenesis
and Cosmogenesis 544
15 11 Allometry 547
15 12 Micro-Macro Coupling in the Human Body 554
16 What Is Life? 573
16 1 The Definition of Life 573
16 2 Life According to Schrodinger 574
xx Contents
16 3 Life According to Bohr 574
16 4 Life According to Prigogine 577
16 5 Life According to Pattee 578
16 6 Life Based on the Information-Energy
Complementarity 579
16 7 Active versus Passive Phase Transitions:
Is Life a Critical Phenomenon? 580
17 Why Is the Cell So Complex? 585
17 1 The Structural Complexity of the Living Cell 587
17 2 The Dynamic Complexity of the Living Cell 590
17 3 The Fourfold Complexities in Physics and Biology 594
17 4 The Law of Requisite Variety and Biocomplexity 595
17 5 Cybernetics-Thermodynamics Complementarity 595
17 6 The Universal Law of Thermal Excitations
and Biocomplexity 596
17 7 The Quality-Quantity Duality and Biocomplexity 597
18 Ribonoscopy and Personalized Medicine 599
19 Ribonoscopy and Theragnostics 607
20 The Knowledge Uncertainty Principle in Biomedical Sciences 621
20 1 The Toxicological Uncertainty Principle (TUP) 621
20 2 The Pharmacological Uncertainty Principle (PUP) 630
20 3 The Medical Uncertainty Principle (MUP) 630
20 4 The U-Category: The Universal Uncertainty
Principle as a Category 631
21 Towards a Category Theory of Everything (cTOE) 633
Appendix A 643
Appendix B 647
Appendix C 651
Appendix D 653
Appendix E 655
Appendix F 657
Appendix G 659
Appendix H 665
Appendix 1 669
Contents xxi
Appendix J 673
Appendix K 677
Appendix L 679
Appendix M 691
Appendix N 695
Appendix O 697
Glossary 699
References 705
Index 731
|
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| id | DE-604.BV039973659 |
| illustrated | Illustrated |
| indexdate | 2024-07-10T00:15:19Z |
| institution | BVB |
| isbn | 1461421519 9781461421511 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-024831146 |
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| physical | XXI, 748 S. Ill., graph. Darst. |
| publishDate | 2012 |
| publishDateSearch | 2012 |
| publishDateSort | 2012 |
| publisher | Springer |
| record_format | marc |
| spelling | Ji, Sungchul Verfasser aut Molecular theory of the living cell concepts, molecular mechanisms, and biomedical applications Sungchul Ji New York [u.a.] Springer 2012 XXI, 748 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Molekularbiologe (DE-588)1023071983 gnd rswk-swf Cytologie (DE-588)4070177-3 gnd rswk-swf Zelle (DE-588)4067537-3 gnd rswk-swf Physikalische Chemie (DE-588)4045959-7 gnd rswk-swf Biologie (DE-588)4006851-1 gnd rswk-swf Cytologie (DE-588)4070177-3 s DE-604 Physikalische Chemie (DE-588)4045959-7 s Biologie (DE-588)4006851-1 s Zelle (DE-588)4067537-3 s Molekularbiologe (DE-588)1023071983 s Erscheint auch als Online-Ausgabe 978-1-4614-2152-8 HEBIS Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=024831146&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Ji, Sungchul Molecular theory of the living cell concepts, molecular mechanisms, and biomedical applications Molekularbiologe (DE-588)1023071983 gnd Cytologie (DE-588)4070177-3 gnd Zelle (DE-588)4067537-3 gnd Physikalische Chemie (DE-588)4045959-7 gnd Biologie (DE-588)4006851-1 gnd |
| subject_GND | (DE-588)1023071983 (DE-588)4070177-3 (DE-588)4067537-3 (DE-588)4045959-7 (DE-588)4006851-1 |
| title | Molecular theory of the living cell concepts, molecular mechanisms, and biomedical applications |
| title_auth | Molecular theory of the living cell concepts, molecular mechanisms, and biomedical applications |
| title_exact_search | Molecular theory of the living cell concepts, molecular mechanisms, and biomedical applications |
| title_full | Molecular theory of the living cell concepts, molecular mechanisms, and biomedical applications Sungchul Ji |
| title_fullStr | Molecular theory of the living cell concepts, molecular mechanisms, and biomedical applications Sungchul Ji |
| title_full_unstemmed | Molecular theory of the living cell concepts, molecular mechanisms, and biomedical applications Sungchul Ji |
| title_short | Molecular theory of the living cell |
| title_sort | molecular theory of the living cell concepts molecular mechanisms and biomedical applications |
| title_sub | concepts, molecular mechanisms, and biomedical applications |
| topic | Molekularbiologe (DE-588)1023071983 gnd Cytologie (DE-588)4070177-3 gnd Zelle (DE-588)4067537-3 gnd Physikalische Chemie (DE-588)4045959-7 gnd Biologie (DE-588)4006851-1 gnd |
| topic_facet | Molekularbiologe Cytologie Zelle Physikalische Chemie Biologie |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=024831146&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT jisungchul moleculartheoryofthelivingcellconceptsmolecularmechanismsandbiomedicalapplications |