FoS II · Midterm 2

Explain it to someone

The last midterm was a role-play: you were the doctor, explaining things to patients. This one may not be, but the practice is worth it either way. Each person below asks the question they would actually ask.

Answer out loud or type in the box, then open the model answer and check it against the list of what a good answer covers. Anything you type is kept on this device only.

How to answer as the doctor or scientist

  1. Name it plainly. Say what it is in everyday words. Define any term the first time you use it.
  2. How it works. Walk the mechanism step by step: DNA to mRNA to protein to trait, record to decode to device, and so on.
  3. Why it might help them. Connect it to the person's own situation and what they care about.
  4. The honest limit. Say what it cannot do, or what has not been shown yet. Name the specific gap.
  5. What would tell us more. Name the evidence that would close the gap: a control group, a larger trial, longer follow-up, a test in another environment.

Don't promise: cures, restores, will, proves, necessarily. A patient hears those as guarantees.

Lecture 7 — GMOs

A shopper at the grocery store

"I saw apples that don't turn brown. Did they mess with the apple's DNA? Is it a different apple now?"
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Those apples use a technique called RNA interference, or RNAi. The apple's own browning gene is left exactly as it was. What's added is a sequence that makes the apple produce a small piece of RNA matching that gene's message.

Normally the browning gene's message, the mRNA, gets turned into an enzyme that makes the cut apple go brown. The cell uses the matching RNA to find and destroy that message, so less enzyme is made, and the apple browns less.

So the browning gene isn't edited; it's silenced. That's different from CRISPR, which cuts and changes the DNA itself. RNAi usually turns the enzyme down rather than removing it completely.

A good answer covers

  • Names RNAi and says it acts on mRNA, not the gene's DNA
  • Walks the chain: less mRNA, less enzyme, less browning
  • Contrasts with CRISPR, which edits the DNA
  • Says knockdown (reduced), not knockout (gone)

Lecture 8 — Stem cells

A patient with Parkinson's disease

"I read that scientists cured Parkinson's in a dish using stem cells made from a patient. When can I get that?"
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What the lab did is real, but "cured" goes too far. They took a patient's skin cells, reset them into stem cells called iPSCs by adding four gene-switching proteins, and then guided those into the kind of nerve cell Parkinson's affects, dopamine neurons. Because they came from the patient, they're a genetic match.

Making the right cells in a dish is the first step. Before this could treat you, we'd need to know the cells mature fully, survive being transplanted, don't form tumors, aren't rejected by the immune system, connect into the right brain circuits, and release dopamine in a controlled way that actually improves movement.

Cells in a dish also don't experience the brain's environment or how the disease progresses. Answering those questions takes transplant studies and trials with long follow-up, so I can't give you a date.

A good answer covers

  • Explains iPSCs: adult cells reset by four transcription factors
  • Says why a patient's own cells matter (genetic match)
  • Separates making the cell type from restoring function
  • Lists specific gaps: maturity, survival, tumors, rejection, integration, function
  • Avoids promising a cure or a timeline

Lecture 9 — Cultivated meat

A restaurant owner

"Is lab-grown chicken real chicken? And if it works, why can't I buy it cheaply?"
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Yes, it's real chicken cells. A small sample of muscle is taken from a living bird, and its muscle stem cells, called satellite cells, are grown in a nutrient liquid. They multiply from a few cells to billions, then get signals to stop dividing and fuse into muscle fibers. Plant-based meat is different: it contains no animal cells at all.

It's expensive because the cells need everything a chicken's body gave them. The growth factors that tell cells to grow are costly; oxygen has to be pumped in; waste has to be removed; and everything must stay sterile, because there's no immune system and germs grow much faster than chicken cells.

Small batches work. Bigger tanks make oxygen delivery, mixing and sterility harder, and thick cuts need blood vessels the culture doesn't have. So: it's real and possible, but cheap large-scale production hasn't been shown yet.

A good answer covers

  • Real animal cells, unlike plant-based meat
  • The stages: biopsy, grow, expand, differentiate, harvest
  • Cost drivers: growth factors, media, sterility
  • Scale-up and thickness limits (oxygen, mixing, no blood vessels)

Lecture 10 — Organoids

A parent whose child has a genetic neurodevelopmental condition

"The lab made a "mini brain" from my son's cells. Does that mean they can see what's wrong with his brain?"
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It's called a brain organoid. The lab reset your son's cells into stem cells, then gave them signals that make them grow into a small piece of tissue resembling part of a developing brain. Because it carries his genes, they can compare how his cells develop and how active his neurons are against cells from someone without the condition, and they can test drugs on it.

But it isn't his brain, and it isn't thinking or feeling. It has no blood supply, it stays immature, more like early developing tissue than an adult brain, it's missing some cell types, and it isn't connected to a body. Organoids also vary from one to the next.

So a difference they find tells us how his cells behave in a dish. It doesn't show what he experiences or how he'd respond to a treatment. That would take many organoids, matched controls, and then studies in people.

A good answer covers

  • Explains what an organoid is and that it self-organizes from stem cells
  • Why patient-derived cells are useful
  • Specific limits: no blood supply, immature, missing cell types, no body, variable
  • Says it shows nothing about consciousness or his symptoms

Lecture 11 — BCIs

A person with a cervical spinal cord injury

"If I join the brain-implant trial, will I be able to walk again?"
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I want to be straight with you: no, that isn't what this device does. Your brain still plans movements and your muscles can still work; the injury cut the connection between them.

The implant has electrodes that record the movement signals in your motor cortex, and software learns to translate them into commands for a computer cursor or another device. It goes around the injury rather than repairing it, so your spinal cord stays as it is.

What it has given people so far is control of a computer, and with that some independence with everyday digital tasks. This is an early safety trial with very few people and no control group. In the first participant some of the electrode threads pulled back from the brain, and performance dropped until software changes recovered it, so long-term stability isn't known yet.

A good answer covers

  • Answers the question honestly, first
  • Motor pathway: intact cortex, intact muscle, broken link
  • Record, decode, act: bypass, not repair
  • Separates device control and independence from restored function
  • Trial limits: few participants, no control group, thread retraction

Lecture 12 — Recombinant DNA

A patient with diabetes

"My insulin says it's made by bacteria. How can bacteria make a human hormone?"
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Every living thing reads DNA using the same genetic code, so bacteria can follow the instructions in a human gene.

Scientists cut the human insulin gene out with a restriction enzyme, which cuts DNA at one specific sequence. They cut open a small loop of DNA called a plasmid with the same enzyme, so the ends match. Another enzyme, DNA ligase, seals the gene into the loop.

The plasmid goes into bacteria, which copy it as they multiply and make human insulin from the gene. The insulin is then purified for you to use.

A good answer covers

  • The shared genetic code is why it works
  • Restriction enzyme cuts, ligase joins
  • Plasmid carries the gene; host cell copies it and makes the protein
  • Not every question needs all five template steps; this one is mostly mechanism

Lecture 12 — Gain of function

A worried neighbor

"There's a lab near my house doing "gain-of-function" research on bacteria. Should I be scared?"
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"Gain of function" just means an organism gained or increased some ability, like glowing, digesting a new sugar or growing at a different temperature. On its own, that doesn't mean more dangerous.

The worrying kind is a disease-causing germ that becomes easier to spread or more harmful. You'd only know that from experiments that compare the changed germ with the original, measure the change directly, use controls and repeat the result. Knowing a gene was inserted isn't enough.

Labs are also matched to the risk: biosafety level 1 for harmless lab strains, up to level 3 for serious airborne diseases, with controlled access and inward airflow, and level 4 with full-body suits for the most dangerous agents. I'd ask what organism they work with, what was changed, and what level they operate at.

A good answer covers

  • Gain of function is an outcome, not a synonym for danger
  • Danger means transmissibility or virulence in a pathogen
  • What evidence a claim needs: comparison, measurement, controls, repetition
  • BSL levels matched to hazard and exposure route

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