easydriver – Samposium https://samnicholls.net The Exciting Adventures of Sam Mon, 20 Mar 2017 22:47:48 +0000 en-GB hourly 1 https://wordpress.org/?v=5.7.5 101350222 We made a Lego DNA Sequencer to teach kids about DNA, Sequencing and Phenotypes https://samnicholls.net/2017/03/15/lego-sequencer/ https://samnicholls.net/2017/03/15/lego-sequencer/#respond Wed, 15 Mar 2017 23:24:23 +0000 https://samnicholls.net/?p=2217 Every year the university is host to over a thousand primary school pupils as part of British Science Week. Last year you may remember I ran an activity that taught you how to be a sequence aligner through the medium of Lego. Describing what I’d like to do differently in future, I included the following:

To improve, my idea would be to get participants to construct a short genome out of Lego pieces that can be truly “sequenced” by pushing it through some sort of colour sensor or camera apparatus attached to an Arduino inside a future iteration of the trusty SAMTECH Sequencer range.

So I’d like to introduce the Sam and Tom Industrys Legogen Sequenceer(TM) 9001:

The Sequencer

The Lego “Sequenceer” has a tray that holds a small stack of Lego bricks (up to 12). Once loaded, a toothed side to the tray is pulled along a track with a gear attached to a stepper motor that was commandeered from an old Epson printer. An RGB colour sensor sits just over the track on a small acrylic bridge, in very close proximity to the passing bricks. The stepper is programmed to actuate a calibrated number of steps per brick, stopping to allow the RGB sensor to take a reading of a brick’s colour before moving to the next.

Our software then translates these readings to one of the four DNA bases and prints the result on the serial port for the user to see. Once complete, the stepper mode is reversed and the tray is “ejected” such that it protrudes once more out the front of the machine to allow for unloading and loading of the next Lego brick DNA sequence.

The Activity

My previous activity tasked pupils to align pre-constructed Lego DNA sequences to each-other. The goal was to introduce the idea of short read sequencing and how alignment of a short sequence is hard, let alone that of an unexpectedly-long human genome (highest guesses for base pair length were in the thousands). In general, the students enjoyed, but I felt I could massively improve the task if we used Lego for its intended purpose: construction.

This year, after quizzing pupils on what they know about DNA, I once again introduce the concept of using 2×2 blocks of Lego as DNA bases. We have four colours, matching the four bases of DNA we see in our own genomes. I explain that today we will be construct a 10 base DNA sequence, representing the entire genome of a monster, and that we can find out what that genome is with our sequencer.

I designed some official looking forms onto which the pupils could copy out the base calls for each of the ten bases on their monster’s genome, which all happen to be a gene that controls an interesting phenotype:

Our young scientists then look at our “monster datasheet”, that decodes each of the genes and what the phenotype for each of the alleles will be:

Now given their sequenced monster genome, and the datasheet, we ask the pupils to make their monster’s phenotype a reality – draw their monster to add to our records! The hardest part? Naming their newly discovered monster. Finally they add their name and school, to credit them with their discovery. Here was our first of the day. I stole our department’s stamp for an additional feeling of official-ness:

Conclusion

I’m so pleased with how this project has turned out. Not only is the sequencer itself the coolest electronics project I’ve had a hand in, but the reaction to the stand on the day from children and adults alike was so positive. The pupils loved the concept: getting to build something with Lego, and then drawing a cool monster that has special powers is clearly a recipe for success. It is rewarding to see that they’ve enjoyed the activity, as well as to know they can now tell you something about DNA and phenotypes too.

This is a significant improvement on my stand from last year. We get to look at bases and DNA, sequencing and importantly, how changes in bases correspond to changes in a phenotype: which makes us who we are. The activity tells much more of a story, rather than just aligning Lego bricks to explain that a hard problem is indeed hard. Here, we get to physically construct a tangible proxy to a genome and find out something about it through an experiment. Finally we add the result to the sum of knowledge of the subject of monsters discovered so far. My wall is now full of unique and interesting monster records, each drawn with some artistic license from the scientist in charge. Though, despite the large sequence space, I was amused to note the bias for 8 legged and 8 eyed monsters due to an environmental pressure for the selection of the T nucleotide: the colour blue.

Once again, I’ve had much more fun than my regular grumpy-self was expecting. I’ve been reminded that public engagement can be very rewarding.

Engage engagement

Some pictures of the stand from the day:

Finally, here are the images from our inaugural Monster Lab:

Monster Lab: Aber Uni Science Week 2017

tl;dr

  • Tom and I upgraded the old SAMTECH 9000 to create the Arduino-powered self-scanning Legogen Sequenceer 9001
  • Spending the entire day with children continues to be absolutely exhausting
  • Public engagement continues to be rewarded
  • Lego is an excellent way to introduce the concept of DNA, and genomes
  • Blue is a particularly popular favourite colour
  • Primary school children aren’t as dumb as everyone says they are
  • Packs of genuine 2×2 Lego bricks are really bloody expensive
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