SEED Reflections

Wow.  SEED came and went in the blink of an eye -- what a whirl-wind!  The following are some only lightly organized reflections on what went well, what didn't, and what might change next year.

Goals

For me, the core of synthetic biology is the ability to solve real-world problems by creating new organisms.  So that's what I wanted the students to do:

  • Choose a real-world problem they were interested in that could be addressed with a new organism
  • Describe that organism's new behavior and how it would address the problem
  • Plan a plasmid or two that implements the new behavior
  • Build those plasmids out of reusable genetic parts (BioBricks)
  • Test their plasmids
  • Communicate their results

....over the course of 8 Saturdays together.  The difficulty, as I outlined in the previous post, is that there's an enormous amount of domain knowledge and operational skill involved in this.  Did it work? Read on!

Project Selection

I left the choice of an interesting problem up to the students.  They each came up with a problem, then wrote it on the whiteboards around the classroom so they could think about their classmates' proposed problems.  Then, they self-assorted into 5 groups around five different problems.

What worked: The students were all really stoked to be working on projects of their own choosing. This was reflected again and again in the feedback we got from the students.

What didn't work: While I had asked the students to develop their own ideas based on a list of parts from the Parts Registry that could be useful in solving them, I'm not sure they understood quite what I was asking for.  Thus, we ended up with 5 cool problems to work on -- only one of which had the pieces we'd need available to us.  Due to an incomplete understanding of the relevant biology, we also ended up with several projects that were biologically impossible.

What could change: I am still thinking about how to balance the authenticity and engagement that you get from allowing the students to choose their own project, with the predictability and improved success rate you get from constraining their choices. I think one way to go about it would be to choose a project area for them to work on, one that had good parts support and a number of "obvious" good projects, then allow the students some choice within the project space.

Circuit Design

I did some reading and came up with a set of related questions that the students could feasibly build plasmids to answer.  But how to give them experience actually doing the plasmid design? I ended up hacking together some "datasheets" for the parts and backbones that would actually be useful, then putting them in folders for each of the projects.  This gave the students a chance to practice thinking about what each part did, how it related to the other parts, and how they would be assembled into transcriptional units.

What worked: There was a lot of engagement with this activity -- by far the best non-lab activity we did.  I think we lost some of the students; but there was also a lot of them that really got it by the end, which was really rewarding.

What didn't work: This was also a significant amount of work on my end -- there was a lot of content to create for what was essentlly a one-off lesson.

What could change: I think that constraining the projects (as above) could ameliorate this substantially.  You could give each group the same set of parts and have them come up with different designs.

Plasmid Constuction

We completed a single BioBricks build cycle:

  • Digest the parts
  • Ligate the digested parts
  • Transform the ligations
  • Miniprep

All this was pretty straightforward on their end.

What worked: They loved (loved!) the lab work.  The more pipetting, the better -- miniprep day was the best, followed by the day they did transformations.

What didn't work: On my end, it required preparing a pretty massive number of parts from the Registry distribution plates.  I also designed and synthesized a number of parts (usually promoters for which repressors were available in the Registry but for which there were no promoters on the plates) -- with all of the attendant issues for a cloning cycle.  In the end, each group tried to build 2 or 3 plasmids -- but I think each group only managed to get one to go together.

Finally, there was at least one group that was quite large, and I was really sad to read in the feedback that at least one student felt like they were stuck watching everyone else pipette but didn't have a chance to themselves.  No bueno.

What could change: More constrained projects mean fewer parts to synthesize (or none at all??), higher success rates, and the possibility for the instructors to build things behind-the-scenes.  Also, I'd love to think about ways to spend more time in the lab.  We were about 50-50 this year, and even though I think the classroom stuff was important, it was clearly less engaging. (One alternative: make the classroom stuff more engaging?)

Experimental Design and Characterization

I asked the students to design their own experiments to test the plasmids.  This worked out okay -- but again, we ran into the trouble of not enough biology background.  We also ran into issues with plasmids they had designed but hadn't managed to build (and that I couldn't get to go together in the intervening week.)  At the end of the day, I pretty much had to propose experiments that were related to the problems they wanted to solve.

The actual experiments were pretty straightforward -- most were growth-rate measurements under different conditions.  (For example: some of the students wanted to work on lead bioremediation for drinking water.  They had a plasmid that constitutively expressed a lead-binding protein.  The experiment: do the engineered coli grow in media containing heavy metals better than an un-engineered strain?)

What worked: For the most part, the students had experiments that could directly test the functionality of at least one of the plasmids they had built. And connecting that experiment back to their system and their problem was good practice.

What didn't work: Sometimes that connection wasn't super-solid. A lot of the disconnect came from not having managed to build all the plasmids that they proposed to make. Changes to improve the success rate would make this more straightforward.

What could change: One of the hardest connections to make in the plasmid design phase is with the experiments you want to do to test them. I'd like to think of some way to de-couple these a little bit, which could make both the design and the subsequent experiments more straightforward.

Science Communication

The last day, the students are expected to give presentations, posters or demonstrations to their parents. This year I asked each group to give a 10-minute talk. I demonstrated what I wanted using an example project we had been discussing all semester. We spent most of the last session together (before the wrap-up session) doing talk planning, then actually working on the slides.

What worked: They all gave talks. They all spoke pretty fluently about the projects they were working on and why they were interesting and what their approach was. The best talks took a deep dive into the human practice implications of their project and did a solid job with data interpretation.

What didn't work: We spent a long time talking about science communication, and even so I thought the structure of the talks was pretty universally shaky.

What could change: I'd love an opportunity for them to communicate more about their science -- learning happens via practice and feedback, and I'd love them to have more opportunities for both.  The question is ... when?

Takeaways

There are clearly things that could change next year. I think it's also really clear that the students got a lot out of SEED this last semester.  There were at least two students who told me they wanted to continue to study bioengineering in college, which I count as a success.  (-:  And maybe some of them will get involved in iGEM, which seems like an obvious extension of this....

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