Part III: Epigenetic Mechanisms
"Beyond the sequence lies another layer of meaning—ψ writing upon ψ, memory beyond memory, inheritance beyond DNA."
Overview
Part III explores the epigenetic landscape where ψ = ψ(ψ) manifests as heritable information beyond DNA sequence. Through methylation, histone modifications, and regulatory RNAs, we discover how cells remember their identity and pass this memory to their descendants.
Chapters
Chapter 33: ψ-Propagation via Chromatin Remodellers
ATP-dependent machines that restructure nucleosomes
Chapter 34: Phase Separation and Collapse Compartmentalization
Liquid-liquid phase transitions organizing nuclear domains
Chapter 35: Collapse Memory via Nucleosome Positioning
The grammar of DNA wrapping around histones
Chapter 36: Non-Coding RNA in ψ-History Embedding
Regulatory RNAs that shape gene expression
Chapter 37: Imprinting and Parental ψ-Bias
Parent-of-origin specific gene expression
Chapter 38: ψ-Interference via RNA Silencing
Small RNAs that regulate gene expression
Chapter 39: Antisense Collapse Dynamics
Regulatory interactions between complementary RNAs
Chapter 40: Genomic Folding as Structural Collapse
Three-dimensional organization of chromosomes
Chapter 41: ψ-Collapse Logic in X-Inactivation
Silencing an entire chromosome
Chapter 42: Pseudogenes and Functional Echo
Evolutionary remnants with regulatory functions
Chapter 43: Somatic vs Germline Collapse Tracks
Different epigenetic strategies for different cell lineages
Chapter 44: Genetic Redundancy as ψ-Forking
Backup systems in the genome
Chapter 45: ψ-Recombination during Meiosis
Shuffling genetic information
Chapter 46: ψ-Fixation in Genetic Drift
Random changes in allele frequencies
Chapter 47: Collapse in Allelic Exclusion
Choosing one allele over another
Chapter 48: ψ-Noise and Genetic Stochasticity
Stochastic fluctuations in gene expression
Key Concepts
- Epigenetic Memory: Information inherited without DNA changes
- Chromatin States: Dynamic configurations encoding cell identity
- Enzymatic Writers: Molecular machines that create marks
- Regulatory Networks: Interconnected systems maintaining states
- Transgenerational Effects: Memory beyond individual lifetimes
The Memory Principle
Throughout Part III, we witness ψ = ψ(ψ) creating layers of memory beyond genetic sequence. Epigenetics reveals how the same genome can generate different stable states—how ψ remembers not just what it is, but what it has been and what it might become.
Next: Part IV examines how these multilayered information systems drive evolutionary change and conservation across deep time.