Progress in Theoretical Biology

Contributors

Preface

Contents of Previous Volumes

The Dynamics of Feedback Control Circuits in Biochemical Pathways

I. Introduction

II. Kinetic Equations

III. Inducible Systems

IV. Repressible Systems

V. Discussion

References

Stable Dynamics of Genetic Networks

I. Introduction

II. Connectance and Forcing Connectance

III. Connection between Forcible Functions and Internal Homogeneity

IV. Distribution of Number of Forcible Inputs among Boolean Functions

V. Density of Noncontractible Functions

VI. Metrics for Natural Boolean Order

VII. Upper Bound on Forcing Connectance

VIII. Large, Growing, Sparsely Connected Genetic Networks Condense and Have Largest Forcing Components

IX. Joint Distribution of Cycle and Disclosure Length

X. Distribution of Cycle and Disclosure Length: Predicted and Observed Effect of Forcibility

XI. Genetic and Metabolic Implications

References

Simplest Genetic Systems Controlling Ontogenesis: Organization Principles and Models of Their Function

I. Simulation of the System Controlling λ Phage Development

II. Some General Principles of the Organization of Bacteriophage Ontogenetic Systems

II. Kinetic Equations

III. Epigenes

References

Conceptual Framework Shifts in Immunogenetics: The Anatomy of the Ag System

I. Introduction

II. Materials and Methods

III. Complex-Simple Labeling of Sample Categories

IV. Labeling of Group II Sample Categories

V. Complex-Simple Restrictions

VI. Some Simple-Complex Pseudo-Mysteries

VII. Predictive Power of the New Framework

VIII. The Structure of Serology

IX. Summary and Conclusions

References

Communication, Memory, and Development

I. Introduction

II. Between the Devil and the Deep Blue Sea: Noise versus Saturation

III. The Statistics of Switches: Gain Control and Adaptation in On-Center Off-Surround Networks

IV. Contrast Enhancement and Short-Term Memory

V. The Statistics of Messages: Randomness Prevents Randomness

VI. Competitive Group Interactions

VII. Hysteresis, Peak Shifts, and Slow Drifts

VIII. Ratio Processing by Antagonistic Cells

IX. Slow Waves and Pacemakers

X. Long-Term Memory

XI. Reaction-Diffusion Models in Development

XII. Regeneration of Hydra's Heads

XIII. The Analogy between Regulation and Adaptation

XIV. Blastula to Gastrula in the Sea Urchin

XV. Pseudopodal Signaling and Self-Corrective Feedback

XVI. Some Experimental Tests

XVII. Production versus Directed Growth

XVIII. Biochemical Memory and the Folds of Rhodnius

XIX. Slime Mold Aggregation and Slug Motion

XX. Adhesiveness, Growth, Cell Streaming, and Division

XXI. Chemical Substrates of STM and LTM: Cyclic Nucleotides, Ions, Transmitters, and Protein Synthesis

References

A Theory of Human Memory: Self-Organization and Performance of Sensory-Motor Codes, Maps, and Plans

1. Introduction

2. Stimulus Sampling of Spatial Patterns

3. Sensory Codes and Motor Synergies

4. Ritualistic Learning of Arbitrary Acts

5. Nonspecific Arousal as a Command

6. Self-Organization of Codes and Order Information

7. Instrumental Conditioning

8. STM Reverberation until Reward Influences LTM

9. Rehearsal Resets STM Order Information Using Feedback Inhibition and Decouples Order and Velocity Information

10. An Emergent Neocortical Analog

11. Control of Performance Duration by STM and Arousal

12. Serial Learning and STM → LTM Order Reversal

13. Storing Spatial Patterns in STM

14. Gain Control and Adaptation in On-Center Off-Surround Networks

15. Contrast Enhancement in STM

16. Tuning of STM and Releasing Subliminal Maps by Arousal

17. Adaptive Coding and the Emergence of Command Chunks

18. Feature Detectors

19. Development of an STM Code

20. Stabilizing the STM Code: Expectation, Resonance, Rebound, and Search

21. Pattern Completion, Hysteresis, and Gestalt Switching

22. Context-Dependent Coding and Restricted Conditions for Receding

23. Reset, Reaction Time, and P300

24. Hierarchical Critical Periods and Retrograde Amnesia

25. Invariance of the Past Code under Future Sequential Inputs

26. Bowing of the STM Pattern

27. Regulation of STM Primacy, Recency, and Bowing by Lateral Inhibition

28. Feedback Inhibition by Rehearsal in an Opaque STM Field

29. Transient Memory Span and Free Recall

30. Parallel versus Serial Search in STM

31. The Influence of Rehearsal on Chunking

32. Immediate Memory Span, and Readout of LTM Order Information by Feedback Signals from Commands

33. A Minimal Model of Structural versus Transient Components of Memory

34. Prediction

35. Sensory Feedback and Interference by Its Delay

36. Greater Weight and Longer Duration of Higher-Order Chunks

37. Spatio-temporal Self-Similarity and the Resolution of Uncertainty

38. Order-Preservation in the Future Field of Motor Commands

39. Masking of STM by More Cell Sites or Amplified Signals

40. STM Drift toward a Norm: Primary Gradient Induces Secondary Gradient

41. Masking of Lower-Order Codes

42. Clustering, Compression, Spacing, and Completion

43. The Magic Number Seven and Self-Similar Coding

44. Suppression of Uniform Patterns and Edge Detection

45. The Growth of On-Center Off-Surround Connections

46. Goal Gradient and Plans

47. STM Order Reversal: Item Learning versus Order Learning

48. Circular Reaction and Map Formation

49. Quenching of Irrelevant Cues

50. Feedforward Reset of Sequential Terminal Maps

51. Posture, Isometrics, Saccades, and Feedforward Motor Control

52. Feedforward versus Feedback Control of Sequential Map Performance

53. Sequential Switching between Sensory and Motor Maps

54. Map Reversal by Antagonistic Rebound

55. Imprinting, Imitation, and Sensory–Motor Algebra

56. Self-Tuning and Multidimensional Inference in a Parallel Processor

57. No Sensory Feedback Implies No Map Formation

58. Does the Psychophysical Power Law Influence Imitation Errors?

59. Rhythm and Phrasing

60. Reciprocal Intermodality Feedback, Internal Hearing, and Naming

61. Automatic versus Controlled Information Processing

62. Visual versus Auditory Processing and Cerebral Dominance

63. Concluding Remarks: Universal Adaptive Measurement

Subject Index