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