Week 1 HW: Principles and Practices & Lecture 2 Prep

1. Can flashes of light be used to grow a computer? The idea is to shine light at cells to get them to produce proteins that reconfigure the structure that surrounds the cell. I’m curious if cells can produce proteins that cause interactions in their surrounding environment.

2. #Goal: Maintain Biodiversity.

   • Reduce Proliferation
   • Inhibit self-replication ability

3. Action 1: Create Biological Testing Grounds. Researchers across academia and private sectors partner with municipal governments to set aside land via legislation that can be used for testing how cell-computers interact with their environment.

   Action 2: Create an organization that maintains a digital database of synthetic genomes. The government funds the database maintenance and internet infrastructure to ensure it remains accessible to future generations.

   Action 3: Create legislation that limits the molecules that researchers can surround cell-computers with.

4. Approach	Maintaining Biodiversity	Fostering Lab Safety	Increasing Bioliteracy
   Biological Testing Grounds	2	1	2
   Synthetic Genome Database	3	3	1
   Legislating Molecules	1	2	3

5. I would prioritize the creation of biological testing grounds because it scores evenly for maintaining biodiversity and increasing bioliteracy. I think increasing bioliteracy by itself furthers the mission of maintaining biodiversity. In order for biological testing grounds to help with bioliteracy, they need to be labelled on maps and include explanatory signage at the specific sites.

The assumption behind biological testing grounds is that there exists a technology that can prevent the spread of synthetic DNA beyond its borders (the assumption behind this assumption is that this technology would be calibrated to the DNA that’s being tested, so it doesn’t affect all DNA).

One uncertainty is that the findings from observing how a cell-computer interacts with the molecules in the biological training grounds might not translate to the rest of the world. However, the sub-goal of reducing proliferation should minimize harm to biodiversity. The assumption behind reducing proliferation being helpful is that quantity is a danger instead of the ability of cell-computers to change their surroundings.

Ethical concerns from this week: I read the report titled, “Charting the Future of Biotechnology” by the National Security Commission on Emerging Biotechnology and saw mentions of biotechnology being used for defense and warfare. I am concerned about if trying to create messaging about the peaceful uses of biotechnology will take away attention from the warfare uses of biotechnology.

Week 2 Lecture Prep Professor Jacobson:

1. Error rate of polymerase is 10^{6. The human genome is 3.2x10}9. DNA polymerase does proof-reading to correct for the error.
2. I’m not sure. I see that the average human protein is 1036 base pairs. I don’t know how to do the permutation math for how many different combinations there could be.

Dr. Leproust:

1. Oligo pools?
2. GC bias? I’m not sure.
3. I don’t know.

George Church:

Histidine Isoleucine Leucine Lysine Methionine Phenylalanine Threonine Tryptophan Valine Arginine

Well Lysine is an essential amino acid so it does not seem right to remove something that’s essential from creatures.

Week 2 HW

Part 1

Hi. I used the KPNI enzyme repeatedly in the virtual digest. Is it possible to re-use enzymes? I think not. The DNA will have already been cut up.

Part 3

I chose the protein phytochrome, which is found in plants and which detects red light. I chose phytochrome because I wanted to use a protein that’s found in plants. Initially I thought about choosing a protein that’s in asparagus. I learned that asparagus is green because of chlorophyll not because of a protein.

Codon optimization might be useful for speeding up protein production. I chose to optimize codon usage for spreading earthmoss because I like moss.

A cell-dependent way to produce phytochrome is:

• put the DNA into a plasmid
• put the plasmid into spreading earthmoss (how???? I wonder if putting the plasmid into water and putting the water onto the earthmoss would work)

5.1 DNA Read

i) The DWORF gene because it’s short. I am imagining that a shorter gene will be easier for me to read. AI prompts: “what’s the shortest dna sequence found in nature?” and “can you name me the functional genes that encode for short peptides” ii)Next generation sequencing by synthesis because I want to see the colors light up one by one as the DNA is synthesized.

1. I don’t know.
2. Input: Human DNA. Preparation: I don’t know.
3. Add adaptors to end of DNA sequence. Denature DNA to get one strand. Make nucleotides have fluorescent tags. Polymerase will make the complementary strand. A camera takes images of what’s happening.
4. Short single-stranded nucleotide sequences.

5.2 DNA Write

i) A genetic circuit so I can learn what it is. When light is detected, light up. ii) Chip based DNA synthesis. involving….a silicon wafer….optical addressing…. I don’t yet understand how manipulating protons related to synthesizing DNA..~~– I don’t know what the limitations of this technology are.

5.3 DNA Edit

i) Edit the DNA of the green algae that sits on lakes to see if it can send light into the water below it. Why? To see if something that grows with light can also emit light.