Week 2 Problem Set

PSET #2

ASSIGNED: Friday 17 April 2020

DUE: 5:00p Pacific Friday 24 April 2020

NOTES:

• Given the unique circumstances of Spring 2020 we ask you to do your best to maximize your learning. Each problem set is an opportunity to assess your learning, identify gaps, reflect on what you have learned, and determine what you wish to learn next.
• Problem sets must be completed individually unless stated otherwise.
• Please turn in your completed problem sets as an electronic copy via Gradescope. Please make sure to clearly indicate the starting and ending boundaries of your answers to each question on Gradescope.
• Please do not go over any word limits and where appropriate show your work (e.g., calculations with appropriate units).

(Q1) Malaria and Artemisinin (20 points)

Think back to the case study: Production of artemisinin via yeast

Q.1.a. List three major lessons from the pre-class reading? (bullet points)

Q.1.b. List two to three questions that can help you frame a solution for addressing malaria? (bullet points)

Note: For the following estimation questions please show your step-by-step calculations, keep track of units, and clearly state your assumptions.

Q.1.c. The World Health Organization (WHO) estimated that in 2017 there were 219 million cases of malaria. If 3 grams (3 g) of artemisinin are required per treatment of 1 individual, how many total grams of artemisinin are needed per year?

Q.1.d. Sweet wormwood plants can produce 70 kg of artemisinin/ha land, where ha is a hectare of land. Using your answer from Q.1.b., estimate how many total hectares of land would be needed to produce enough artemisinin to treat all individuals suffering from malaria each year?

Q.1.e. Producing artemisinin via yeast-based fermentation can yield 25 g of artemisinin/liter. What volume of a reactor do you need to produce enough supply of artemisinin to treat all individuals suffering from malaria each year? Use your answer from Q.1.c.

Q.1.f. Imagine that in the near future you are the head of the WHO’s Malaria Project. In this future, land usage has become a challenge for the production of artemisinin given the need to grow food. You are presented with the following data: in order to “feed” the yeast-based brewing process you need to supply 1.6 kg sugar/liter (which yields 25 g artemisinin/liter). If you can produce 7500 kg sugar from 1 hectare, how many hectares of land would you need to produce enough artemisinin?

Q.1.g. As the head of the WHO’s Malaria Project, would you switch artemisinin production from wormwood to production via yeast? If yes, please explain why. If not, what would you want to see before considering a switch?

(Q2) Fantastic Voyage (20 Points)

In the near future, you and your team are planning to remove an inoperable tumor from the brain of an important scientist. You conclude that the only way that the tumor can be destroyed is to remove it from the inside of the patient’s own body. You imagine a submarine that can be shrunk and will carry the team of experts and doctors.
Sadly, however, a shrink ray does not exist in this future Fantastic Voyage

Instead, you can begin to engineer living matter, microbes or patient’s cells that are already small. Briefly read the abstract of the paper titled Acoustic reporter genes for noninvasive imaging of microorganisms in mammalian hosts, which enables imaging and control of living matter in mammalian hosts.

Q.2.a. In your own words, summarize the abstract in 2-3 sentences. What is the main claim of this paper?

Q.2.b. According to the paper, what is the origin and purpose of the gas-filled protein nanostructures in nature?
What is the typical size of the gas-filled proteins? How are the gas-filled proteins visualized in the paper (what technique)? Can the gas-filled proteins be visualized directly via a light microscope (yes/no)? Why?

Q.2.c. Can you think about and describe another application (medical or other) for these engineered microbes (bullet points).

Q.2.d. In your opinion, what are the paper’s strengths and significance? What are the paper’s shortcomings and deficiencies? How can the paper improve?

(Q3) Rousseau and Hobbes (30 Points)

Q.3.a. How do Rousseau’s assumptions about human nature differ from Hobbes’? (2 bullet points)

Q.3.b. Do you think those practicing bioengineering should be licensed? If yes or no, who gets to decide?

(As you think about the above question, also consider: What are the advantages or disadvantages of a license? Who gets to be licensed? Who decides the rules for the license? Is there an exam? Where do practitioners go to receive a permit? How the assumptions from Hobbes and Rousseau could lead to differences regarding how people are organized, or organize themselves.)

Craft an answer in response to some or all of the above questions.
Do your best to summarize your thoughts in one paragraph.

Note: In Q.3.b., we are looking for a clearly stated and logical argument that uses the stated assumptions from Q.3.a. Use these assumptions, combine them with examples, and describe your position.

(Q4) Leadership and Bioengineering (30 Points)

Consider the following scenario; many people around the world do not have access to safe, essential pain medication. On the other hand, opioid abuse and addiction to painkillers is a crisis in the United States. Today it is technically feasible to produce opioids in yeast via a fermentation process link But a more difficult question remains. What should bioengineers do so that by 2030 all people (8 billion) have responsible access to pain medications?

Q.4.a. Practice a Framestorm, what questions you should ask to best frame your desired future? (5 questions)

Q.4.b. Practice a Futures wheel, What would be the direct and indirect future consequences of your wish (draw a map similar to here)

Next, revisit Dr. Palmer’s testimony from the reading (Transcript from here. Dr. Palmer offers five recommendations for the Senators to secure future U.S. leadership in the bioeconomy.

Q.4.C. Which recommendation(s) might help you in realizing a responsible access to pain medications? Which recommendation(s) might prevent you from realizing it? Why? Would you have offered a different recommendation? What and why? (Do your best to summarize your thoughts in one paragraph.)

Note: In Q.4 we don’t have a “correct answer” in mind. Instead, we wish for you to think deeply. We want to enable you to practice your written communication skills. Finally, we wish for you to take steps towards becoming a leader (similar to Dr. Palmer) to be able to direct discussions around bioengineering.

Additional Learning Resource

Biology refresher-2: If you would like to review or learn more about the structure of DNA, use the following resource link-1. If you would like to watch brief videos describing transcription (going from DNA to RNA) use: video-1 and video-2 Next, if you need a refresher on amino acids and proteins, use the following resources: Video: What is a Protein? And Slides from PDB101. A review of the above topics will be helpful in understanding the material in the subsequent weeks.
In general, explore biology is a useful resource.

Extra learning-1: Entirely optional videos for all learners that explore useful topics related to this week’s learning. You are not expected to watch all of these videos. We simply want to enable you and give you the option of learning more as you wish.

1. Coronaviruses 101: Focus on Molecular Virology by Britt Glaunsinger

2. Engineering Microbes to Solve Global Challenges by Jay Keasling

3. Realizing Synthetic Carbon Dioxide Fixation by Tobias Erb

4. Synthetic Biology in a Societal Context by Emma Frow

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