Week 1 HW: Principles and Practices

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1. Describe a biological engineering application or tool you want to develop and why

One biological engineering application I would like to develop at HTGAA is an active dressing or biomaterial for treating superficial wounds that incorporates bromelain, a proteolytic enzyme derived from pineapple.

This biomaterial would primarily promote gentle enzymatic debridement, reduce local inflammation, and support the healing process, using a naturally occurring and potentially accessible compound. The interest in this application stems from the fact that bromelain has demonstrated anti-inflammatory and proteolytic properties, but its direct, uncontrolled use can cause irritation or tissue damage. Therefore, integrating this compound into a controlled biomaterial would maximize therapeutic benefits and minimize potential risks, especially in primary healthcare settings or areas with limited access to healthcare facilities.

Main Objective

To ensure that the development and use of a bromelain-containing biomaterial is safe, ethical, and does not cause harm to patients.

Sub-objectives

a. To ensure the safety and biocompatibility of the biomaterial before its clinical or educational use.

b. To prevent misuse or unregulated use, such as unsupervised home application, inappropriate concentrations, or self-medication.

c. To promote responsible and evidence-based use, especially in low-resource or educational settings.

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

Action 1: Establishment of Minimum Formulation and Use Protocols

Purpose

Currently, bromelain can be acquired and used in biomedical applications without clear regulatory oversight. This action proposes the development of minimum standardized protocols for bromelain concentration, encapsulation, and safe use in biomaterials, in order to reduce potential risks and misuse.

Design

This action requires the participation of universities, biomaterials faculty, and ethics committees. Technical guidelines for academic and experimental use would be developed and subsequently reviewed and validated by institutional regulatory bodies or internal review committees.

Assumptions

It is assumed that safe concentration ranges for bromelain can be clearly defined. However, variability in enzymatic activity may occur depending on the source and processing of bromelain, which introduces uncertainty.

Risks of Failure and “Success”

  • Failure: Protocols are not consistently followed or are perceived as unnecessary by users.
  • Unintended success: The existence of protocols is used to justify premature or unauthorized clinical applications without sufficient preclinical or clinical trials.

Action 2: Mandatory Biocompatibility and Degradation Assessment

Purpose

The purpose of this action is to ensure that bromelain-containing biomaterials do not cause tissue damage, adverse biological reactions, or uncontrolled degradation when applied to biological environments.

Design

This action involves conducting basic in vitro evaluations, such as cytotoxicity and degradation tests. Additionally, these assessments would be incorporated as a standard requirement in biomedical engineering curricula and supervised by faculty members and academic committees.

Assumptions

It is assumed that in vitro assays provide an adequate approximation of in vivo behavior and that participating institutions possess the minimum technical and financial resources required to perform these tests.

Risks of Failure and “Success”

  • Failure: Experimental results are misinterpreted or oversimplified by students or developers.
  • Unintended success: Positive in vitro results generate a false sense of safety, leading to unauthorized testing in human subjects.

Action 3: Regulation of Discourse and Dissemination of the Product

Purpose

This action aims to prevent bromelain-based biomaterials from being promoted as inherently “natural” or “safe” without sufficient scientific evidence supporting such claims.

Design

Ethical communication guidelines would be established for academic and preclinical projects. This includes reviewing the language used in presentations, posters, publications, and online materials, with oversight from faculty members and evaluators.

Assumptions

It is assumed that non-expert audiences may misinterpret terms such as “natural” or “enzymatic,” and that developers are aware of and willing to uphold their responsibility for accurate and ethical communication.

Risks of Failure and “Success”

  • Failure: Continued dissemination of exaggerated or misleading claims regarding safety or efficacy.
  • Unintended success: Increased popularity and informal adoption of the product without adequate regulatory supervision.

4. Score (from 1-3 with, 1 as the best, or n/a) each of your governance actions against your rubric of policy goals

Does the option:Option 1Option 2Option 3
Enhance Biosecurity
• By preventing incidents213
• By helping respond213
Foster Lab Safety
• By preventing incident123
• By helping respond213
Protect the environment
• By preventing incidents132
• By helping respond132
Other considerations
• Minimizing costs and burdens to stakeholders321
• Feasibility231
• Not impede research123
• Promote constructive applications213

5. 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, Action 2 (Mandatory Biocompatibility and Degradation Assessment) should be prioritized, as it most directly supports non-malfeasance by reducing the risk of biological harm through early safety evaluation.

Action 1 (Minimum Formulation and Use Protocols) should be implemented alongside it, as standardized guidelines help prevent misuse and ensure consistency across academic and experimental settings.

Action 3 (Regulation of Discourse and Dissemination) serves as a complementary measure, addressing risks related to misinformation and informal adoption.

The main trade-off is the increased cost and effort associated with testing and protocol enforcement; however, this is justified by the ethical need to prioritize safety. This approach assumes institutional capacity for basic testing and acknowledges uncertainty in translating in vitro results to real-world use.

Bibliography

  • Ahmad, T., Ismail, A., Ahmad, S.A. et al. Extraction, characterization and molecular structure of bovine skin gelatin extracted with plant enzymes bromelain and zingibain. J Food Sci Technol 57, 3772–3781 (2020). https://doi.org/10.1007/s13197-020-04409-2
  • Kansakar, U., Trimarco, V., Manzi, M. V., Cervi, E., Mone, P., & Santulli, G. (2024). Exploring the Therapeutic Potential of Bromelain: Applications, Benefits, and Mechanisms. Nutrients, 16(13), 2060. https://doi.org/10.3390/nu16132060

Subsections of Week 1 HW: Principles and Practices

Assignment – Week 2 Lecture Prep

Assignment – Week 2 Lecture Prep

Homework Questions from Professor Jacobson:

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?

  1. The biological machinery for copying DNA, known as polymerase, has an error rate of approximately 1:10⁶. This error rate is significant when compared to the length of the human genome, which is approximately 3.2 Gbp (3.2 billion base pairs). Without additional correction, copying the entire human genome just once would result in thousands of errors. Biology deals with that discrepancy with MutH, MutL, and MutS enzyme system, which recognizes and repairs mismatched base pairs to ensure higher fidelity

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?

  1. An average human protein is approximately 1036 base pairs (bp) long. Because the genetic code is redundant (multiple different three-nucleotide codons can code for the same single amino acid) there are astronomically many different DNA sequences that can theoretically code for the same protein.
  2. In practice, many of these alternative codes do not work for several reasons:
  • Secondary Structure Interference: Different DNA or RNA sequences result in different Minimum Free Energy (MFE) secondary structures.
  • Base Pairing Energetics: The stability of the genetic material is affected by its GC content.
  • RNA Cleavage: Specific sequences may inadvertently trigger RNA cleavage rules

Homework Questions from Dr. LeProust:

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

  1. The most commonly used method for oligonucleotide synthesis currently is the phosphoramidite method, originally developed by Caruthers in 1981. This process typically occurs via solid-phase chemical synthesis

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

  1. Direct synthesis of oligos longer than 200 nucleotides (nt) is difficult primarily due to the cumulative error rate and chemical efficiency of the synthesis cycle

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

  1. Direct base-by-base chemical synthesis is not used to create a 2000bp (2kb) gene because the physical and chemical limitations of the phosphoramidite process make it impossible to produce a sequence of that length with any meaningful accuracy or yield.

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”?

  1. The ten essential amino acids in animals are histidine, arginine, valine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, and tryptophan. This directly relates to the concept of the “Lysine Contingency”, which emphasizes the critical role of lysine as a limiting essential amino acid for growth and survival. From my point of view, attempting to genetically modify organisms to alter these fundamental nutritional requirements is ethically questionable.