Week 1 HW: Principles and Practices

𓃠 Week 1 Homework 𓃠

1. First, describe a biological engineering application or tool you want to develop and why.

I want to build a Biological 3D Printer :D It is a quite crazy idea, basically a biological 3D printer takes in a DNA file and prints it and expresses it right away and delivers the target product in vial.

How it works: You download a DNA file (a plasmid sequence) for a specific function, like a molecule that smells like chocolate, or a protein that glows red, or a specific medication. You send the file to the printer, which synthesizes or assembles the genetic instruction, expresses it using a cell-free system or bacterial chassis, and delivers the purified product in a vial.

I want to build this because I want to democratize manufacturing. Right now, biology is locked in big labs. I want to bring ‘Bio-Production’ to the home, the remote clinic, or even a spaceship. If you can email a file, you should be able to print a cure (or a scent).

2. Next, describe one or more governance/policy goals related to ensuring that this application or tool contributes to an “ethical” future, like ensuring non-malfeasance (preventing harm). Break big goals down into two or more specific sub-goals.

Main Goals include:

A. Preventing Malicious Use (Biosecurity): to make sure such printers will not be used to create harmful, toxic or dangerous products or molecules, maybe this can achieved through:

1. DNA Screening: We can screen the DNA sequence that is requested for printing, to check and prevent the process if it encodes for a dangerous molecule or a viral toxin

2. Reagent Lock-in: To make sure the reagents, proteins and raw materials in the printer are only viable inside the printer environment and cannot be extracted and used else where

B. End User Safety & Reliability (Biosafety): we need to make sure the printed molecule is exactly what it claims to be, and to make sure no mutation or contamination has occured

1. Proofreading Mechanism: we can apply a proofreading startegy during and after printing and synthesis to confirm similarity between the printed the DNA and the uploaded DNA file

2. Proper Elimination of undesired or faulty molecules: we need to be able to safely and properly discard or eliminate mutated or contaminated sequences once identified

3. Next, describe at least three different potential governance “actions” by considering the four aspects below (Purpose, Design, Assumptions, Risks of Failure & “Success”).

A. Action 1: International Regulation & Monitoring: This action can be pursued & applied through international health organizations like WHO and local alikes

1. Purpose: We can regulate what DNA sequences get printed through a digital signature that has to be approved by such organiztions, and the printer can only print these approved sequences

2. Design: We can have a main website similiar to the iGEM registry where users can submit new DNA sequences that they want to print and Organizations like the WHO can have a team of scientists + AI that periodically screen new DNA sequences that get submitted and either give it a signature for public use or flag it as Dangerous/Toxic and prevents its printing

3. Assumptions: We assume that bad people cannot manipulate the signature or bypass its checking before printing

4. Risks of Failure & Success:

   4a. Failure: Risks include Hackers being able to bypass certain signatures and produce dangerous and harmful products through the printers or even hijacking the printers themselves to allow it to print without checking anything

   4b. Success: If these regulations get applied so strictly, it could possibly lead to a lack of innovation and creativity and less DNA sequences the end users are able to print, Also local regulations would also mean some molecules might be allowed to be printed in one country and not allowed in another

B. Action 2: Companies Regulation: This Regulation is applied through the parent company that sells the printers

1. Purpose: We can regulate the usage printers reagents and chemicals and make sure it only uses certified or accepted reagents, more like printers cartridge system or coffee pods, mainly to make sure users can’t take the reagents and use it elsewhere

2. Design: The company can design the printer and cartridge so that they become dependant on each other, maybe the reagents need an activation factor that is only in the printer system or hardware so that without it, the reagents are dormant and cant be used

3. Assumptions: We assume the chemical “lock” is not breakable by other chemistry sets, we also assume users can afford the prices of the printer reagent cartridges

4. Risks of Failure & Success:

   4a. Failure: Risks include bad people managaing to break the chemical formula and use the reagents in other probably malicious work

   4b. Success: Monopoly, if one company produces those reagents and it can increase prices or stop selling to specifc countries or competitors for company gains

C. Action 3: Community Integration & Bio Bug Bounty Programs: This action involves both the companies and the community for a shared safe future

1. Purpose: Integrate the Community into the process through lectures and workshops about proper usage of the printers, how to deal with malfunctions, how to submit DNA designs and the application of Bug Bounty incentive programs to quickly and effictevly patch errors, faults or flaws in the printer’s software and hardware

2. Design: Incentives can be offered to people who can bypass certain security checks in the printer or print a certain toxic molecule that the print is not supposed to print, this helps turn possible hackers into quality assurance testers.

3. Assumptions: We assume the bounty hunters will report all findings and that the incentive given is enough to make sure they report to us.

4. Risks of Failure & Success:

   4a. Failure: A bounty hunter discovers a major defect in the printer but recieves a bigger incentive from another competitor or bad groups and delivers the information to them instead

   4b. Success: It is actually hard to think of one. maybe all these trials and errors and bug hunting will make the printer model known and allow for competitors to start companies and compete with us

4. Next, score (from 1-3 with, 1 as the best, or n/a) each of your governance actions against your rubric of policy goals. The following is one framework but feel free to make your own:

5. Last, drawing upon this scoring, describe which governance option, or combination of options, you would prioritize, and why. Outline any trade-offs you considered as well as assumptions and uncertainties

Based on the scoring matrix, I recommend a Hardware-First, Software-Verified Hybrid Strategy, prioritizing Action 1 (Digital Screening) as the immediate standard, supported by Action 2 (Reagent Lock).

Hardware is the Hardest Barrier, Software can be hacked, and Bounties are reactive and takes a while to build community knowledge. Physical reagent cartridges is a very robust fail-safe for preventing accidental contamination or malicious misuse by non-experts, however reagents can be found elsewhere and maybe chemically designed to imitate the proposed solutions, so having signatured DNA sequences remain the most reliable approach.

These actions however carry tradeoffs that include lack of creative space for other users to design DNA sequences they like and have to go through a rigrous application process to get approved and signatured, and the Reagent Lock risks Company Monopoly if it is allowed to be the sole producer of these types of reagents.

6. Reflecting on what you learned and did in class this week, outline any ethical concerns that arose, especially any that were new to you. Then propose any governance actions you think might be appropriate to address those issues. This should be included on your class page for this week.

One of the ethical concerns that arose to me is how “Open Source” in this setting can actually do more harm than good, if a lab builds a toxic molecule or a virus using the printer in a closed setting, we can basically lock up and quarantine the lab, but with open source, if the process goes online on the internet, there is no going back, and now anyone can have it. this ties back to the importance of the proposed Signature only printing action, as it can help mitigate the effects of distributed dangerous DNA sequences and trying to print it, maybe also we will need to make these printers Online only, so proper monitoring of what is being printed and by whom, of course users must be informed of this and be allowed to either accept such terms to buy the printer and use our products or refuse, and in the case of refusal, and taking biosecurity into consideration, the products should not be sold to the user nor permitted for use in this case

𓃠 Week 2 Lecture Prep 𓃠

1. Nature’s machinery for copying DNA is called polymerase. What is the error rate of polymerase? How does this compare to the length of the human genome. How does biology deal with that discrepancy?

The error rate for polymerase is 1:10⁶. The Human Genome is ~ 3.2 Gbp, doing the math means that it makes 3200 errors each time which is alot. Biology deals with these errors through proofreading and corrections, one example is the MutS Repair System where it fixes the mismatches and repairs them using DNA polymerase and Ligase

2. How many different ways are there to code (DNA nucleotide code) for an average human protein? In practice what are some of the reasons that all of these different codes don’t work to code for the protein of interest?

An Average human protein can be up to 1036 bp, each 3 (called a codon) codes for an amino acid, but amino acids can be coded by many combinations in those codons, making the different ways to code for the average human protein way too much and increases exponentially. In practice, the many of these theoretical coding sequences do not work well since the nucleotide sequence determines the physical behavior of the mRNA molecule. One of the reasons is formation of mRNA secondary structures, such as hairpins and loops, which are governed by the “Minimum Free Energy” of the sequence. Other reasons include that specific nucleotide patterns can create recognition sites for cellular enzymes like RNase, leading to in vivo cleavage and the destruction of the mRNA before it can be translated

3. What’s the most commonly used method for oligo synthesis currently?

The phosphoramidite method performed via Solid-Phase Synthesis of Oligos is the current most common method. It starts with phosphoramidite Coupling then Capping of unreacted sites followed by Oxidation and then Deblocking. These steps are then repeated for as much times needed for the synthesis

4. Why is it difficult to make oligos longer than 200nt via direct synthesis?

(Had to look up more info about this topic using AI) It mainly returns to difficulties regarding Yield, Truncation Products and Depurination. The longer the synthesized chain gets, the lower the yield gets, and it is not uniform but exponential. Additionally Long Chains accumalate Truncation Products which may happen because of errors or depurination from acids added during the synthesis stage. On the bright side, Twist Bioscience has came up with an Enhanced Process & Chemistry allowing PCR yield to go up to >10 fold increase, 1:2000 error rate and acheiving a 500bp Oligos

5. Why can’t you make a 2000bp gene via direct oligo synthesis?

This touches back to the previous question, with exponential Yield Decay, a 2000bp gene would have a very tiny yield, making most of the produced bases possibly junk, also the depurination issue arises, because the base pairs at the very beginning of the chain will need to resist and endure the acids added in the Deblocking phase up to 2000 times which is difficult. The current process of creating the 2000bp gene would creating multiple oligos (200bp - 500bp) and stitching them together using DNA ligase.

6. [(Advanced students)] Given the one paragraph abstracts for these real 2026 grant programs sketch a response to one of them or devise one of your own:

I chose the Smart-RBC: Smart Red Blood Cells Grant

My Proposal: The “Oxygen Turbo Cell”

The Idea: I propose creating a “High-Performance” Red Blood Cell that acts like a backup oxygen tank for hikers, firefighters or Rescue teams in extreme conditions. We can engineer the RBCs’ Heamoglobin to be much more sensetive to markers that arise in low oxygen or hypoxic settings.

To work it should have a biosensor that can detect Lactic Acid, which is the acid that gets produced in low oxygen settings and causes the burning sensation in your muscles when you run and once the cell senses high acid levels, the engineered haemoglobin gets activated and lets go of even more oxygen that it normally would creating a higher oxygen surge instantly into the muscles or brain to properly and rapidly accomodate to the new environment. Since these cells have no nucleus or DNA (Enuculated), they are just temporary “smart delivery bags”, They circulate for a few weeks to keep the hiker safe, then naturally die off without changing the hiker’s permanent genetics.

This also solves the “Natural Acclimation Time” problem mentioned in the abstract. Instead of waiting weeks for the body to get used to high altitude, or low oxygen environments, a person can receive a transfusion of these “Oxygen Turbo Cells” and be ready immediately to tackle these extreme environments and this applies to what the abstract mentioned as “enhance physiological resilience”.

AI citation: i used Gemini to help with idea validation and properly tying it back to match the requirements of the Grant Program