What do new synthetic biologists need to know?

I am super-excited to be teaching SEED this semester! The SEED Academy is a program run out of MIT's Office for Engineering Outreach Programs whose goal is to give under-represented and under-resourced students exposure to various engineering disciplines. The spring semester of senior year, the topic is Synthetic Biology.

The rest of the SEED experiences are very project-focused; for example, in the Aero/Astro semester, they build (and then shoot off) model rockets. I've spoken to previous SEED synbio instructors, and while the students did lab work, they didn't really have a project focus in the way that other SEED modules do.

I think this semester it's time to change that. Between BioBuilder and iGEM, it's pretty clear that highschoolers can do "real" synthetic biology. More on how I'd like to structure the course later, but I've been giving some thought to "content" -- ie, "what do new practitioners of synthetic biology need to know to get started?"

I've done a bit of mind-mapping and have come up with four broad categories of "content" knowledge.  If the goal of a synthetic biologist is to "program cells with DNA", then we can attack that goal with four questions:

  1. What does a cellular program look like? This is a set of knowledge and skills based around the idea of a specification.  In terms of learning goals, I want my students to be able to take a problem (like "is this water safe to drink?") and turn it into a specific cellular behavior that they want ("detect arsenic in the water and turn red if it's found.") Being able to do that successfully depends on knowning ...
  2. What are the pieces of a cellular program?  Promoters and RBSes and genes oh my!  I want my students to be able to choose pieces to put together that implement the specification.  This depends on knowing what the pieces are, and what they do.  The "what they do" part, in turn, depends on knowning...
  3. How does a cell "run" a program? Here is where the cellular and molecular biology comes in.  The most important parts are basically the central dogma, but with an engineering twist.  For example, DNA is transcribed to RNA.  What controls whether, and how much, RNA is made from a gene? The RNA is transcribed to protein; how can we moderate or control this process? What effect does the protein have on the cell? What effect does the protein have on the circuit? I want students to be able to predict how a circuit will behave based on some relatively basic cellular and molecular biological knowledge.
  4. How do we build a gene circuit? This is the "biotechnology" part -- manipulating DNA.  I want students to be able to build a gene circuit based on a particular assembly technology (in this case, biobricks.) This means learning about, and using, restriction enzymes and ligases and chemically competent cells and sequencing.  (Oh yes, and using pipettors and thermocyclers and other things.) Interestingly enough, this is where many peoples' minds go when they think about "learning synthetic biology."  And sure, it's important -- but only one of the building blocks.

The difficulty here, I think, is the interrelatedness of the four areas. How to sequence learning opportunities so that they all build on eachother? Stay tuned...

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