Project Menhed: The In-Silico Biological Color Factory.

In Ancient Egypt, color was not just decoration; it was essence. The scribes used a palette (called a Menhed) to mix pigments that defined their reality. They used ochre for red and malachite for green. They were brilliant, but they were limited by what they could dig out of the ground.

Today, we are not limited by geography. We are limited only by our genetic code.

The Problem with Color

Look around you. The dye in your shirt, the ink in your pen, the coloring in your food. Most of it comes from petrochemicals. It is an industry built on extraction, toxicity, and waste.

There is a better way. Bacteria have been turning sugar into vibrant pigments for billions of years. The problem? Biology is messy, hard to engineer, and really expensive to test.

The Constraint (And The Opportunity)

I do not have a million dollar wet lab. I do not have industrial fermenters. I do not have a venture capital fund backing me.

But I have a laptop. I have Python. And I have the biological databases of the world at my fingertips.

Convention says I should wait until I have a lab to start building. I disagree. “Creativity loves constraints”.

Because I cannot physically test my designs, my code must be flawless. My metabolic models must be robust. My simulations must be reality proof. This constraint forces me to be a better engineer.

Introducing: Project Menhed

Today, I am officially launching Project Menhed under Djoser Genomics.

The name comes from the Scribe’s Palette. But instead of mixing ink, we are mixing genes. The goal is to design, model, and validate a commercial grade bacterial dye factory entirely In Silico (computationally).

Phase 1: The Red Ink (Lycopene)

We are starting with Lycopene, a vibrant red pigment. My mission is not just to make a bacteria “turn red”. Any biology student can do that. My mission is to engineer a strain so efficient that the theoretical Cost of Goods Sold (COGS) beats synthetic chemical dyes.

I will be using the modern Synthetic Biology stack:

• Bioprospecting: Mining gene clusters.
• AlphaFold: Validating enzyme structures in 3D.
• COBRApy: Modeling Metabolic Flux to ensure the bacteria doesn’t starve.
• Python/React: Building interactive tools to visualize the output.

And Others.

The “Black Box” Protocol

This project aims to be a learning resource, but also a potential business. To balance these goals, I will operate under a “Black Box” Protocol:

• I WILL share the process, the math, the struggles, and the yield data publicly.

• I WILL NOT share the specific proprietary genetic sequences or the final plasmid architecture.

This ensures I can share my journey with you while protecting the intellectual property for future commercialization.

The Risk

I might fail.

The models might show that the biology is too toxic. The economics might not work out. I might spend three months coding only to find out the yield is too low.

But that is the point. I am simulating the risk now, so that when we eventually build the lab, we build it right.

Project Menhed is online.
The factory is open.
Follow the build log here at Djoser Genomics.