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.

Response

I’m really interested in the development of a new method that decreases the rate of DNA mutations in humans, using one of the genes found in the DNA of whales, the CIRBP (cold inducible RNA building protein) gene provides a significant performance at non homologous end joining, which is a mechanism that cells use to repair damaged DNA, especially when DSB (DNA double strand break) occurs. Although this gene is also found in humans, it doesn’t express the same sufficient amount of the protein as the amount expressed in whales, that explains why whales survive and live longer than humans, although they are bigger in size, which means they have more genes and more divisions that should increase their error prone and susceptibility to cancer. Applying procedures to human cells, where they receive the CIRBP gene from whale cells, could lead to significant development in the field of age-related medical conditions and in cancer resistance, since both are induced by DNA mutations.

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.

Response

a. Any case of DNA being modified should be handled cautiously and it should be applied with the intent to benefit humans and never to harm. Such a policy can be applied by: i. Ensuring that such procedures are only carried out by professionals who receive special training, have experience in such fields, and have a degree related to the field. ii. Verifying the approval of the patient to undergo such a procedure through obtaining their informed consent.

b. Such procedures must be offered to all patients regardless of their ethnicity, race, or religion, to exploit this policy: i.Making advertisements and posters that show how such procedures are inclusive to all, they can include ads on TV or through social media. ii.Providing each hospital in the country with the financials and equipment necessary, no matter where they are located to ensure that this procedure reaches as many neighborhoods as possible.

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.). Purpose: What is done now and what changes are you proposing? Design: What is needed to make it “work”? (including the actor(s) involved - who must opt-in, fund, approve, or implement, etc) Assumptions: What could you have wrong (incorrect assumptions, uncertainties)? Risks of Failure & “Success”: How might this fail, including any unintended consequences of the “success” of your proposed actions?

Response

a. Research institutions should collaborate with university students through an annual competition, to attempt to solve some of the health care issues that the country has suffered from throughout the year:

i. Purpose: some countries have applied such projects before, but they usually face issues due to the knowledge imbalance between researchers at institutions and students, such difference in knowledge levels can potentially delay the process. I propose that a short training program offered by research institutions becomes mandatory for participating students, the aim of this program is to teach students basic research skills and methodologies. In addition to that, students should be chosen to participate based on their academic standing and a test provided by the university to challenge their creativity.

ii. Design: the concerned governmental establishments like the Ministry of Health should provide their approval and allocate the appropriate funds necessary for the project’s success. Universities and research organizations should provide space for such projects to take place by providing labs and lecture classes.

iii. Assumptions: the criteria for choosing the participating students might be unfair, because not all students have both the ability to obtain a good academic standing and being able to provide creative ideas and solutions. Also funding such projects can be very costly and require a huge budget.

iv. Risks of failure and success: the winning research ideas don’t get funded or adapted by any institution, and the project succeeds but won’t be held again due to the high cost it requires in order for it to be done efficiently.

b. Biotech and pharmaceutical companies should offer only a specific amount of the proposed therapy at every specific period:

i. Purpose: this policy is already applied to some gene therapies, however the problem is that they use a waitlist system, where patients, with varying degrees of severity, must wait for long periods of time, uncertain of whether they’re going to receive the therapy after waiting or not, due to the shortage in production. Another problem is the shortage in centers that offer such therapies, especially that they’re provided by specific places and hospitals that contain the right conditions to offer the treatment. I propose that there should be studies done on the level of the nation to estimate the number of patients suffering from this specific medical issue, and based on the number received, the government should fund more biotech companies to increase the overall production of materials necessary for that therapy. Additionally, the government should focus more on building other centers for therapy, building more hospitals that have the capacity to offer such treatments, or at least check which hospitals that already exist, can provide them with treatment, and support them with the equipment they need to do so.

ii. Design: universities and research institutions can participate by attempting to find alternative materials that would provide the same result but require less cost, these research studies can be funded by the government or using tax money, or thorough donation organizations like the Bill and Melinda gates foundation.

iii. Assumptions: the studies that show the percentage of the population suffering from this specific medical condition could be inaccurate, due to problems with the basis chosen to determine whether a person has the condition or not, also nonresponse bias can occur, where the participants who respond do not represent all of the population because they differ from the participants that do not respond.

iv. Risks of failure and success: if this policy fails, and the shortage in production remains, the rate of mortality for patients suffering from this specific condition is going to increase, and the rate of patients who will develop drug resistance, due to constant changes between different medications with different doses to compensate for the shortage of the treatment, will also increase. The failure can also include corruption in the waitlist system, where the priority for receiving patients might be altered based on deals done with whoever is responsible for organizing the waitlist. There could also be a biosecurity threat, where the genetic information of the patients might be unprotected and used without the consent of the patient.

c. Hospitals should provide transportation services for disabled patients, allowing them to arrive to the hospital to receive their treatment:

i. Purpose: this service is already available at some hospitals, but it has some issues including the long distance that patients must travel to receive the treatment, sometimes it can be across governorates or states, this is due to the lack of centers that provide such services. In addition to that the lack of vehicles that are equipped to handle wheelchairs makes it difficult for these services to be applied efficiently. I propose that the government should build new centers or equipped hospitals at multiple cities, to decrease the pressure that is put on the few existing ones, solving this problem would be a huge step in enhancing not only this service but also other projects related to gene therapies. The government should also allocate some of the funds to collaborate and work with vehicle manufacturing companies to produce more cars that are specially designed to handle wheelchairs, also to train the drivers of these vehicles so they learn how to handle emergencies and how to treat patients in the appropriate way.

ii. Design: governmental institutions should fund and sponsor these services to ensure they reach the entirety of the population, vehicle manufacturing companies and importing companies can both play a crucial role in providing and maintaining this service, also transportation offices are needed to be in contact with the concerned hospitals or centers, in order to build functional and organized schedules.

iii. Assumptions: if the built schedules are not followed or if they are insufficient, this could cause a huge delay in the service and patients could potentially lose their appointments or be behind on their treatment schedule.

iv. Risks of failure and success: if the service succeeds, it could cause a huge problem regarding the environment, which includes high rates of pollution and waste products obtained from both vehicle manufacturing companies and hospitals.

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. 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.

Response

The governance of research organizations collaborating with university students, to solve national problems in healthcare fields should be prioritized since it has a lot of potential to benefit societies whether minimizing the risk of people developing specific diseases, or inventing new therapies, it also provides chances for students to work with professionals, it would also be a great addition to their resumes. the institutions that would make great audience for such policy would be local universities, as such projects can spotlight great minds found in such institutions and provide support to them and their ideas, it can also represent the level of education offered by such universities, and help them build a good reputation that attracts more students over coming years.

• 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.

Response

Ethical concerns that arose during the lecture came from discussing the difficulties in making new governances for the new challenges emerging quickly, one of these challenges is “brewing drugs”, and its ethical concerns include risks on the life of the individual making these drugs, and risks of such activities becoming normalized in societies. The governance that should be applied to minimize this phenomenon is by forcing mandatory participation for students at high schools and universities, in lectures offered to them by anti-drug use organizations. Another governance includes consequences for any person who’s under legal age including mandatory therapy sessions.

Week 2 HW: dna-read-write-and-edit

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 of polymerase is 1:10^{6 nucleotides, and the length of the human genome is 3.2 gbp or Gega base pair (=3.2* 10}9), this means that if we divide the length of the genome by one million, we would get 3 thousand, which represents the number of errors per genome of a single person. Our bodies use polymerase proof reading which is a process done by DNA polymerases, where they have the ability to detect mistakes done in the newly synthesized DNA strand, while simultaneously building it, when such mistakes are detected, they stop their function, send the new strand to a different site, where they preform exonucleases activity on it by cutting out the wrong base that was added, from the 3’ to 5’ side, then the DNA polymerases enzymes return to their original site and continue their function. These modifications are done within the replication process, there are other modifications that are done after the replication process (post-replication modifications) including mismatch repairs where some proteins are able to detect base pair mismatches on the new DNA strand and they cut them out and build the correct matches using the template strand.

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?

The average human protein has 1036 amino acids, so there would be 10^623 different sequences that code for such a protein, although this number is huge, most of it doesn’t actually end up producing the protein, one of the reasons include codon bias in cells, where cells have some codons that they prefer more than the rest even if all of these codons code for the same amino acid, so these cells have the matching tRNAs for these favorable codons in a higher concentration than the rest, so if a mRNA strand has a lot of rare codons, it will translated slowly, which could influence the functionality of the produced protein. Another problem that can happen is if the mRNA has too many common codons, where the translation will be too fast, and the resulting amino acids won’t have enough time to fold efficiently, since amino acids start folding which ribosomes are doing the translation. Also, these codon sequences can contain pre-mature stop codons that bring the translation process to an end, and no proper protein will be formed.

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

solid-phase phosphoramidite oligonucleotide synthesis is the most common used method to produce oligonucleotides, the solid phase is used because it makes it easy to purify the product from unwanted components.

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

Making oligos that are longer than 200nt is considered difficult because of the high chance that yield is poor, this is because the attachment of nucleotides is uncertain within a single cycle, so as the number of cycles increases, the less the attachment will be.

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

It would be difficult to make because it requires a lot of cycles, which means a high possibility of unattached nucleotides, and it would be extremely difficult to separate or remove the uncoupled pieces.

6. Given slides #2 & 4 (AA:NA and NA:NA codes)] What code would you suggest for AA:AA interactions?

Glutamate and Lysine for an electrostatic interaction