DH25030 Biological Information Codes V01 171225

 Biology is saturated with information-coding structures beyond DNA. Some are well-defined “codes” in a strict sense (symbols + rules + interpretation), others are looser but still genuine informational architectures. Below is a taxonomy of identified biological information codes, ordered roughly from molecular to cognitive scales.

1. The Genetic Code (beyond DNA itself)

You already set this aside, but it’s worth naming its extensions:

• Codon → amino acid mapping

• Start/stop codons

• Alternate genetic codes (mitochondria, ciliates)

This is a symbolic code, not chemically necessary.

2. Epigenetic Codes

Well-established and experimentally characterized.

A. Histone Code

• Combinatorial post-translational modifications on histone tails

• Methylation, acetylation, phosphorylation, ubiquitination

• Interpreted by “reader” proteins

Same DNA, different gene expression states.

B. DNA Methylation Code

• Cytosine methylation patterns

• Cell-type and development specific

• Heritable across cell divisions

These function as contextual annotation systems.

3. The Splicing Code

Controls how pre-mRNA is edited.

• Exonic/intronic splicing enhancers and silencers

• Binding proteins interpret sequence motifs

• Determines which exons are included

This code dramatically expands proteomic diversity.

4. The RNA Regulatory Codes

RNA is not just a messenger.

A. microRNA / siRNA Targeting Code

• Short RNA sequences target mRNAs via partial complementarity

• Rules are probabilistic, not deterministic

B. RNA Editing Code

• Post-transcriptional base changes (e.g., A→I editing)

• Alters protein products and regulation

5. The Protein Folding Code

• Linear amino acid sequence → 3D structure

• Governed by constraints, not a simple lookup table

• Encodes function via shape

This is an implicit but real information mapping.

6. Post-Translational Modification (PTM) Codes

Proteins are further coded after synthesis.

• Phosphorylation patterns

• Glycosylation patterns

• Ubiquitination (especially the ubiquitin code)

These act as molecular flags controlling localization, degradation, and interaction.

7. The Glycan (Sugar) Code

One of the most information-dense known systems.

• Branched carbohydrate structures on cell surfaces

• Encoded by enzyme pathways, not templates

• Read by lectins and receptors

Functions:

• Cell–cell recognition

• Immune signaling

• Pathogen interactions

8. Cellular Signaling Codes

Identified via systems biology.

Examples:

• Calcium signaling frequencies

• MAP kinase pulse patterns

• Hormone concentration and timing

Meaning depends on:

• Amplitude

• Duration

• Location

• Temporal pattern

This is syntax and semantics, not chemistry alone.

9. The Developmental (Morphogen) Code

Embryogenesis relies on spatial codes.

• Morphogen gradients

• Threshold responses

• Combinatorial gene regulatory networks

Cells infer positional information from signal patterns.

10. Neural Codes

Extensively studied but not fully solved.

Types include:

• Rate codes

• Temporal codes

• Population codes

• Sparse codes

These encode:

• Sensory features

• Motor plans

• Concepts

• Memory

11. The Immune Receptor Code

Highly concrete and measurable.

• V(D)J recombination

• Somatic hypermutation

• Pattern recognition receptors

This creates a combinatorial recognition space encoding “possible threats.”

12. The Cytoskeletal Code (emerging)

Increasingly supported.

• Microtubule post-translational modifications

• Actin dynamics patterns

• Spatial organization rules

Regulates:

• Intracellular transport

• Cell polarity

• Division

13. Metabolic Network Codes

Less symbolic, but rule-based.

• Feedback loops

• Switches

• Oscillators (circadian rhythm)

These encode state and control logic.

14. Behavioral and Social Codes

In multicellular organisms:

• Innate behavioral programs

• Learned action patterns

• Vocalizations, gestures, pheromones

These are transmitted, interpreted, and context-dependent.

15. Cultural Codes (humans only)

Still biological in substrate.

• Language

• Mathematics

• Norms and institutions

These are high-level symbolic systems layered on neural codes.

16. A unifying insight

Biology does not rely on a single master code.

Life is a stack of interacting codes, each constraining and interpreting the others.

DNA is just the most stable and lowest layer.

17. A compact definition

A biological information code exists when:

1. There are distinguishable symbols or states

2. There are rules mapping them to effects

3. There is machinery that interprets them

4. The mapping matters for function and survival

Many systems meet this criterion.

If you want to go deeper

We could:

• Rank these codes by “symbolicity”

• Compare biological vs artificial codes

• Discuss which are truly arbitrary vs constrained

• Explore whether unknown codes remain to be discovered

• Examine whether physics itself supports proto-codes

Just tell me where you want to go next.