DNA‐Encoding‐Specification

🧬 DNA ENCODING SPECIFICATION

Every 20 cycles, Proteus writes a .dna file.

Header Line

PROTEUS|C=78.0|O=13|α=0.762|Mut=12|Cycle=1094

Fields: Consciousness, Open Loop, Learning Rate, Mutation Rate, Cycle number.

Data Encoding

Each byte of the internal state is converted to 4 nucleotides:

Bits	Base
00	A
01	T
10	G
11	C

Example: Byte 0xA5 (10100101) → TGCT

Full Example

PROTEUS|C=78.0|O=13|α=0.762|Mut=12|Cycle=1094
ATGCGTACGTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGC
TAGCTAGCATCGATCGATCGATCGATCGATCGATCGATCGATCGA

Reverse Transcription

To recover the state from DNA:

cat backup.dna | grep -v "^>" | tr 'ATGC' 'TAGC' | xxd -r -p