Week 1 HW: Principles and Practices

1. First, describe a biological engineering application or tool you want to develop and why. This could be inspired by an idea for your HTGAA class project and/or something for which you are already doing in your research, or something you are just curious about.

    I have been exploring the feasibility of this idea of blood degrading/cleaning fabric which could be developed through biological engineering. The engineering of the fabric will be such that it will react only when in contact with blood to release substances which will degrade the blood. If achieved, this fabric will find application in various places where blood cleanup is a challenge. For example hospitals and operation procedures where blood spills into table, floor, instruments etc and contaminate the area. It could also be used in sanitary pads so that blood is degraded and prevents leaks rather than the current approaches of soaking and absorbing.
   

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. Below is one example framework (developed in the context of synthetic genomics) you can choose to use or adapt, or you can develop your own. The example was developed to consider policy goals of ensuring safety and security, alongside other goals, like promoting constructive uses, but you could propose other goals for example, those relating to equity or autonomy.

    To ensure that a bio-functional fabric designed for blood degradation contributes to an ethical future, governance must address two primary things 
    a)biological risks of the material 
    b)accessibility.
          A. Biological risks of the material
                 sub goal 1 - The desigh of the fabric should be such that it does not function outside its intended environment. A good
                              approach is to integrate kill switches or a kind of auxotrophy.
                 sub goal 2 - The enzymes/substances released to degrade blood should not cause direct or indirect harm to human skin, like
                              irritation or allergies. Hence rigorous clinical trials must be conducted to ensure this.
          B. Accessibility
                 sub goal 1 - Menstrual blood stains has been a huge problem for women across the world and across generations. There is still
                              no 100% reliable product which for tackling this problem and giving women a sense of mental peace. This fabric 
                              can be a breakthrough innovation for adressing this challenge hence the manufacturing of it should be as cheap as 
                              possible without compromising its quality and functionality. So that it is affordable and accessible to every
                              menstruating woman.
                sub goal 2 - There could be potential misuse of this technology like destroying forensic evidence or damaging biological
                             infrastructure. Governance should be applied to ensure its misuse.

3.Next, describe at least three different potential governance “actions” by considering the four aspects below (Purpose, Design, Assumptions, Risks of Failure & “Success”). Try to outline a mix of actions (e.g. a new requirement/rule, incentive, or technical strategy) pursued by different “actors” (e.g. academic researchers, companies, federal regulators, law enforcement, etc). Draw upon your existing knowledge and a little additional digging, and feel free to use analogies to other domains (e.g. 3D printing, drones, financial systems, etc.). 1.Purpose: What is done now and what changes are you proposing? 2.Design: What is needed to make it “work”? (including the actor(s) involved - who must opt-in, fund, approve, or implement, etc) 3.Assumptions: What could you have wrong (incorrect assumptions, uncertainties)? 4.Risks of Failure & “Success”: How might this fail, including any unintended consequences of the “success” of your proposed actions?

     To address the safety of users, the environmental impact of disposal, and the market adoption of bio-functionalized fabrics, we can structure three distinct governance actions. These involve a mix of legal liability, technical standardization, and financial nudging.
     1.Mandating of safety trials and certifications for the fabric
     Purpose: Currently, safety responsibility for new materials is often diffused between the manufacturer and the end-user (e.g., a
     hospital). This proposal mandates that for any "active" bio-functional material, a Designated Safety Officer (DSO) at the manufacturing
     company must hold personal legal liability for the product’s safety profile.
         Design - 
           Actors: Federal Regulators (like the FDA or BIS in India) and Corporate Boards.
           Mechanism: To receive a commercial license, the company must submit a "Safety Ownership Charter." If the fabric causes unexpected
           skin degradation or allergic reactions due to poor enzyme stabilization, the DSO is the primary point of contact for legal inquiry,
           similar to how a "Chief Information Security Officer" handles data breaches.
     2. Incentives for users to have market adoption
     Purpose: New technology is expensive. Currently, hospitals stick to cheap, traditional chemical cleaners (like bleach) because they are
     cost effective. This proposal provides a Green-Tech Subsidy for institutions that replace harsh chemical cleaners with bio-functional
     fabrics
         Design - 
           Actors: Department of Finance/Treasury and Health Ministries.
           Mechanism: Hospitals that can prove a %age reduction in "Harmful Chemical Purchase" (by using these fabrics instead) receive a tax
           rebate or increased government funding. This is modeled after "Carbon Credits" in the energy sector.
     3.Developing disposal standards
       Purpose: Currently, medical waste is incinerated or landfilled. This proposal introduces a mandatory Enzymatic Deactivation Protocol—a
       specific chemical or thermal step that must be performed before the fabric can leave a facility.
         Design-
         Actors: Environmental Protection Agencies (EPA) and Waste Management Firms.
         Mechanism: The fabric must be designed to change color (e.g., from blue to white) when exposed to a specific "deactivating agent"
         (like high-pH soap or UV light). Disposal companies will be legally barred from picking up "active" (blue) fabric. This creates a
         visual, low-tech verification system for safety.

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. For this, you can choose one or more relevant audiences for your recommendation, which could range from the very local (e.g. to MIT leadership or Cambridge Mayoral Office) to the national (e.g. to President Biden or the head of a Federal Agency) to the international (e.g. to the United Nations Office of the Secretary-General, or the leadership of a multinational firm or industry consortia). These could also be one of the “actor” groups in your matrix.

  Specifically, I recommend a combination of Action 1 (Certified Safety) and Action 2 (Disposal Standards), integrated into the existing BioE3 Policy (Biotechnology for Economy, Environment, and Employment).
  Accountability (Action 1): In a rapidly growing startup ecosystem, clear responsibility prevents "innovation at any cost." By mandating a
  Safety Lprocedure, we ensure that biological risks are managed efficiently.
  Environmental Integrity (Action 2): India's waste management infrastructure is currently being modernized. Standardizing Enzymatic
  Deactivation at the fabric level ensures that these "smart" textiles don't become a new category of persistent bio-pollution in local
  ecosystems.

Homework Questions from Professor Jacobson

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? Error rate of polymerase - 1:10^{6 length of human genome = 3.2 * 10}9 error rate of polymerase = 10^{6 this implies (3.2*10}9)/10^6 = 3200 roughly hence, 3200 errors will occour everytime human genome is copied. The MutS Repair system involving proeins MutS, MutL, MutH is employed to improve rate of error. MutS identifies mismatches. A small cut is made in the erroneous strand and DNA pol III holoenzyme and ligase resynthesizes the correct sequense.

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? average human protein has 1036 bp and since there are 4 nucleotides 4^1036 combinations are possible. Reasons why many codes do not work in practise is - 1. GC content - Higher GC content may lead to structural instability or synthesis faliure 2. DNA and RNA sequences naturally fold into secondary structures based on minimum free energy. If a sequence forms tight “hairpins” or complex folds it can prevent the cellular machinery from properly transcribing or translating the gene. 3. There is a necessary balance between codon redundancy and diversity. Biology has optimized for a specific set of 20 amino acids to maximize the complexity of possible constructs while maintaining stability.

Homework Questions from Dr. LeProust

1. What’s the most commonly used method for oligo synthesis currently? The most commonly used method currently is phosphoramidite DNA synthesis. This is a cyclic chemical process that typically takes about 5 minutes per cycle. The cycle consists of four main steps: Deprotection, Base Coupling, Capping and Oxidation

2. Why is it difficult to make oligos longer than 200nt via direct synthesis? Yield decay is one of the major reason. The total yield follows the formula $(1 - 1/N)^{N \approx 37%$ for an oligo of length N. As the number of couplings increases, the percentage of perfect full-length products drops exponentially. Chemical synthesis has a significantly higher error rate compared to biological systems, roughly 1 mistake per 100 bases ($1:10}2$). By contrast, biological polymerase with proofreading is far more accurate at $1:10^6$

3. Why can’t you make a 2000bp gene via direct oligo synthesis? Direct synthesis of a 2000bp sequence is not currently feasible because the probability of a perfect sequence would be near zero. As stated above, the error rate for chemical synthesis is 10^-2 this would result in dozens of errors per molecule.

Homework Question from George Church

What are the 10 essential amino acids in all animals and how does this affect your view of the “Lysine Contingency”?

The 10 essential amino acids are : Arginine, Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Threonine, Tryptophan, Valine

The “Lysine Contingency” suggests that an organism dependent on an external source of an amino acid (like Lysine) can be easily “turned off” if that source is removed. However, modern synthetic biology, particularly the work on Genomically Recoded Organisms (GROs), significantly shifts this perspective. In GROs, scientists have successfully recoded all instances of a specific codon (such as the UAG stop codon) and reassigned it to mean something else entirely. Instead of relying on a standard essential amino acid like Lysine, researchers can reassign a codon to a Non-Standard Amino Acid (NSAA) like p-acetylphenylalanine (pAcF) or phosphoserine (Sep).