format fix

Author: ChainlessCoder

content/posts/codon_ECC_Idea.md

@@ -48,20 +48,20 @@ Codons may not function in isolation — rather, they behave more like context-s
 
 Let’s imagine a hypothetical error-correcting scheme embedded in codon usage:
 
-### 1. Encoding Phase (Evolution)
+### Encoding Phase (Evolution)
 - The genome chooses synonymous codons based not only on efficiency but:
   - The **preceding codons** (context)
   - Pattern logic (GC content, rhythm)
   - Inserted "check codons" at intervals
 
-### 2. Error Detection Phase (Cellular Machinery)
+### Error Detection Phase (Cellular Machinery)
 - If a ribosome or repair enzyme encounters a codon that:
   - Violates expected codon pair rules
   - Is too rare
   - Disrupts a codon pattern
 - The region is flagged for **surveillance or decay** (e.g., NMD)
 
-### 3. Repair/Correction Phase
+### Repair/Correction Phase
 - RNA or DNA repair pathways compare the suspect codon to a statistically likely version
 - The system either degrades the transcript or attempts **localized correction**
 
@@ -73,18 +73,18 @@ This could even work across **codon groups**, maintaining consistency over small
 
 This is speculative, yes — but also testable:
 
-### a. Simulate ECC in Silico
+### Simulate ECC in Silico
 - Model codon usage with and without embedded rules
 - Introduce mutations, and measure if rule-breaking codons correlate with translation failure
 
-### b. Codon Swap Mutagenesis
+### Codon Swap Mutagenesis
 - Create synthetic genes:
   - One with natural codon use
   - One randomized
   - One with intentional ECC-style codon logic
 - Measure robustness to UV, transcriptional error, etc.
 
-### c. RNA Feedback & Decay
+### RNA Feedback & Decay
 - Use nonsense mutations in ECC vs. non-ECC designs
 - See which trigger decay or repair responses more strongly
 

docs/posts/do-codons-carry-hidden-instructions-a-case-for-built-in-error-correction-in-the-genetic-code/index.html

@@ -76,7 +76,7 @@ <h1 class="title">Do Codons Carry Hidden Instructions? A Case for Built-in Error
           ·
         </span>
         <span>
-          637 words
+          631 words
         </span>
         <span class="split">
           ·
@@ -101,16 +101,16 @@ <h1 class="title">Do Codons Carry Hidden Instructions? A Case for Built-in Error
     <li><a href="#-the-idea-codons-as-biological-error-correcting-codes">💡 The Idea: Codons as Biological Error-Correcting Codes</a></li>
     <li><a href="#-a-theoretical-framework-codonframeecc-v1">🛠️ A Theoretical Framework: CodonFrameECC v1</a>
       <ul>
-        <li><a href="#1-encoding-phase-evolution">1. Encoding Phase (Evolution)</a></li>
-        <li><a href="#2-error-detection-phase-cellular-machinery">2. Error Detection Phase (Cellular Machinery)</a></li>
-        <li><a href="#3-repaircorrection-phase">3. Repair/Correction Phase</a></li>
+        <li><a href="#encoding-phase-evolution">Encoding Phase (Evolution)</a></li>
+        <li><a href="#error-detection-phase-cellular-machinery">Error Detection Phase (Cellular Machinery)</a></li>
+        <li><a href="#repaircorrection-phase">Repair/Correction Phase</a></li>
       </ul>
     </li>
     <li><a href="#-could-this-be-real-how-to-test-it">🔬 Could This Be Real? How to Test It</a>
       <ul>
-        <li><a href="#a-simulate-ecc-in-silico">a. Simulate ECC in Silico</a></li>
-        <li><a href="#b-codon-swap-mutagenesis">b. Codon Swap Mutagenesis</a></li>
-        <li><a href="#c-rna-feedback--decay">c. RNA Feedback &amp; Decay</a></li>
+        <li><a href="#simulate-ecc-in-silico">Simulate ECC in Silico</a></li>
+        <li><a href="#codon-swap-mutagenesis">Codon Swap Mutagenesis</a></li>
+        <li><a href="#rna-feedback--decay">RNA Feedback &amp; Decay</a></li>
       </ul>
     </li>
     <li><a href="#-why-it-matters">🌍 Why It Matters</a></li>
@@ -146,7 +146,7 @@ <h2 id="-the-idea-codons-as-biological-error-correcting-codes">💡 The Idea: Co
 <p>Codons may not function in isolation — rather, they behave more like context-sensitive tokens, similar to how words in a sentence derive meaning from their neighbors. Just as language follows syntactic rules and grammar, codon sequences might follow subtle, evolutionarily-tuned patterns that help maintain the integrity of the message being translated.</p>
 <hr>
 <h2 id="-a-theoretical-framework-codonframeecc-v1">🛠️ A Theoretical Framework: CodonFrameECC v1 <a href="#-a-theoretical-framework-codonframeecc-v1" class="anchor">🔗</a></h2><p>Let’s imagine a hypothetical error-correcting scheme embedded in codon usage:</p>
-<h3 id="1-encoding-phase-evolution">1. Encoding Phase (Evolution) <a href="#1-encoding-phase-evolution" class="anchor">🔗</a></h3><ul>
+<h3 id="encoding-phase-evolution">Encoding Phase (Evolution) <a href="#encoding-phase-evolution" class="anchor">🔗</a></h3><ul>
 <li>The genome chooses synonymous codons based not only on efficiency but:
 <ul>
 <li>The <strong>preceding codons</strong> (context)</li>
@@ -155,7 +155,7 @@ <h3 id="1-encoding-phase-evolution">1. Encoding Phase (Evolution) <a href="#1-en
 </ul>
 </li>
 </ul>
-<h3 id="2-error-detection-phase-cellular-machinery">2. Error Detection Phase (Cellular Machinery) <a href="#2-error-detection-phase-cellular-machinery" class="anchor">🔗</a></h3><ul>
+<h3 id="error-detection-phase-cellular-machinery">Error Detection Phase (Cellular Machinery) <a href="#error-detection-phase-cellular-machinery" class="anchor">🔗</a></h3><ul>
 <li>If a ribosome or repair enzyme encounters a codon that:
 <ul>
 <li>Violates expected codon pair rules</li>
@@ -165,18 +165,18 @@ <h3 id="2-error-detection-phase-cellular-machinery">2. Error Detection Phase (Ce
 </li>
 <li>The region is flagged for <strong>surveillance or decay</strong> (e.g., NMD)</li>
 </ul>
-<h3 id="3-repaircorrection-phase">3. Repair/Correction Phase <a href="#3-repaircorrection-phase" class="anchor">🔗</a></h3><ul>
+<h3 id="repaircorrection-phase">Repair/Correction Phase <a href="#repaircorrection-phase" class="anchor">🔗</a></h3><ul>
 <li>RNA or DNA repair pathways compare the suspect codon to a statistically likely version</li>
 <li>The system either degrades the transcript or attempts <strong>localized correction</strong></li>
 </ul>
 <p>This could even work across <strong>codon groups</strong>, maintaining consistency over small windows — like how RAID systems use parity blocks.</p>
 <hr>
 <h2 id="-could-this-be-real-how-to-test-it">🔬 Could This Be Real? How to Test It <a href="#-could-this-be-real-how-to-test-it" class="anchor">🔗</a></h2><p>This is speculative, yes — but also testable:</p>
-<h3 id="a-simulate-ecc-in-silico">a. Simulate ECC in Silico <a href="#a-simulate-ecc-in-silico" class="anchor">🔗</a></h3><ul>
+<h3 id="simulate-ecc-in-silico">Simulate ECC in Silico <a href="#simulate-ecc-in-silico" class="anchor">🔗</a></h3><ul>
 <li>Model codon usage with and without embedded rules</li>
 <li>Introduce mutations, and measure if rule-breaking codons correlate with translation failure</li>
 </ul>
-<h3 id="b-codon-swap-mutagenesis">b. Codon Swap Mutagenesis <a href="#b-codon-swap-mutagenesis" class="anchor">🔗</a></h3><ul>
+<h3 id="codon-swap-mutagenesis">Codon Swap Mutagenesis <a href="#codon-swap-mutagenesis" class="anchor">🔗</a></h3><ul>
 <li>Create synthetic genes:
 <ul>
 <li>One with natural codon use</li>
@@ -186,7 +186,7 @@ <h3 id="b-codon-swap-mutagenesis">b. Codon Swap Mutagenesis <a href="#b-codon-sw
 </li>
 <li>Measure robustness to UV, transcriptional error, etc.</li>
 </ul>
-<h3 id="c-rna-feedback--decay">c. RNA Feedback &amp; Decay <a href="#c-rna-feedback--decay" class="anchor">🔗</a></h3><ul>
+<h3 id="rna-feedback--decay">RNA Feedback &amp; Decay <a href="#rna-feedback--decay" class="anchor">🔗</a></h3><ul>
 <li>Use nonsense mutations in ECC vs. non-ECC designs</li>
 <li>See which trigger decay or repair responses more strongly</li>
 </ul>