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Reader’s Roadmap

Roadmap1 min261 words

Suggested one-semester course: Chapters 1, 2, 4, 5, 7, 8, 12, 14, 16, 18. Full two-semester sequence: All chapters in order, with Appendix A as prerequisite reading.

Molecular Flow

Information becomes function through controlled transformations

Follow one signal from durable sequence to a context-dependent biological action.

DNA

Store

A four-symbol sequence preserves heritable constraints.

ATG CCG TAA


Ch.	Title	Key Topics


Part I: The Biological Computer
1	The Code of Life	DNA structure, Central Dogma, information density
2	DNA Computing	Adleman, strand displacement, CRNs, molecular logic
3	Gene Regulation as Computation	Regulatory circuits, epigenetics, biological logic gates

Part II: The Intelligence Stack
4	Machine Learning Foundations	Neural networks, optimization, representation learning
5	Transformers and Large Language Models	Attention, GPT, scaling laws, emergent abilities
6	Biological Foundation Models	AlphaFold, ESM-2, Evo, Enformer, genomic LMs

Part III: The DOGMA Architecture
7	DOGMA: The Six-Stage Pipeline	Genomic bases, regulation, synthesis, transcription, expression, realization
8	HelixHash	Double-helix representation, motifs, bond matrices, novelty
9	Tera: The Hidden Regime State	Multi-objective pressure, mutation families, meta-policy
10	TetraData Structure & TetraMemory	3D computation, tetrahedral meshes, structured memory
11	CodonForge: The DNA Compiler	Codon opcodes, gene programs, SDANS compilation

Part IV: Building the Evolutor
12	The Evolutionary Training Loop	Prompt genomes, mutation, selection, distillation
13	Foundation Models on Genomic Data	FASTA corpora, curriculum learning, helix-aware training
14	The Measured DOGMA Baseline	Checkpoints, perplexity, generation failures, next experiments

Part V: Toward AGI
15	Scaling and Post-Transformer Architectures	Scaling laws, SSMs, hybrid architectures, DOGMA scaling
16	What Is AGI? Foundations and Paths	Definitions, biological arguments, DOGMA v3 roadmap
17	Ethics, Safety, and Responsibility	Dual-use, alignment, verifiability, governance

Part VI: Practicum
18	Hands-On: Building Your First DOGMA System	6 labs, capstone project
19	The Future We Are Building	Vision, open problems, research community

Suggested one-semester course: Chapters 1, 2, 4, 5, 7, 8, 12, 14, 16, 18.
Full two-semester sequence: All chapters in order, with Appendix A as prerequisite reading.