A Typed Programming Language for Biological Systems
DNA contains seven functional data types that compose into a complete programming model. We formalize each as a typed construct, implement them in Haskell, and synthesize a unified orchestration language for biological intent, AI prediction, genome editing, and regulatory traceability.
Seven biological data types compose into a complete programming model
data Genome = Genome { code :: [ProteinCode] -- Paper I: Executable Functions , regulators :: [Regulator] -- Paper II: Control Flow , ncRNAs :: [RNAControl] -- Paper III: Signals , structure :: [Structure] -- Paper IV: Memory Layout , repeats :: [Repeat] -- Paper V: Self-Modifying , epigenetics :: [State] -- Paper VI: Runtime State , programs :: [Program] -- Paper VII: Orchestration }
Matthew Long · The YonedaAI Collaboration · Chicago, IL · March 2026
A Type-Theoretic Framework for the Central Dogma
Formalizes the central dogma (DNA→mRNA→Protein) as a typed compilation pipeline. Codons as opcodes, alternative splicing as dependent types, mutations as type errors.
A Type-Theoretic Framework for Gene Expression
Promoters as function entry points, enhancers as environment variables, silencers as access control. Gene regulatory networks as typed dataflow graphs.
A Type-Theoretic Framework for Post-Transcriptional Control
miRNA as guard clauses, siRNA as exception handlers, lncRNA as middleware scaffolds, tRNA as natural transformations between codon and amino acid functors.
A Type-Theoretic Framework for Genome Organization
Telomeres as linear resources, centromeres as synchronization primitives, TADs as memory segments, chromatin loops as pointers.
A Type-Theoretic Framework for Genome Plasticity
Transposons as endofunctors on the genome category. Cut-and-paste as move semantics, copy-and-paste as template instantiation, domestication as naturalization.
A Type-Theoretic Framework for Chromatin Accessibility
DNA methylation as monadic configuration, histone modifications as access permissions, chromatin remodeling as garbage collection, bivalent chromatin as type superposition.
A Type-Theoretic Framework for Morphogenesis
Hox genes as the main module, morphogen gradients as distributed config, cell fate as refinement type narrowing, Waddington landscape as type lattice.
For Biological Programming
Synthesizes all 7 types into a unified language specification with parser, type checker, compiler (4 targets), and runtime. Includes PCSK9 knockout worked example.
Typed intermediate representation for targets, sequences, edits, assays, evidence
Declarative language for programs: design, edit, screen, validate
Targets: SBOL, Benchling, AlphaFold, LIMS/ELN, assay planning
Off-target, payload, manufacturability, provenance constraints
PCSK9 Knockout Therapy in DNA-Lang
program PCSK9_KO {
target t = gene("PCSK9")
edit e = knockout(target=t)
guides g = design_guides(
target=t,
method=CRISPR_Cas9,
require PAM="NGG"
)
guides safe_g = filter(g, off_target_score < 0.05)
require v.payload_size <= delivery_capacity(LNP)
assay a = plan_assay(
system = hepatocyte_organoid,
readouts = [editing_rate, LDL_reduction]
)
run a
collect evidence
}