On most class days, I have one group of my Microbiology students do a presentation on an influential microbiologist. Today, they talked about Jo Handelsman, who is of course famous for all sorts of things, not the least of which is the fact that she currently works in the White House. I was flattered that my students noticed that I’ve been using techniques straight out of Handelsman’s Scientific Teaching textbook — must mean I’m doing them right!
Today I prattled on way too long — we talked about metagenomics, and I felt like it was necessary to cover lots of molecular biology topics that will form the basis for many of our future discussions. PCR, cloning, Sanger vs. Illumina sequencing — hard to turn those into interactive experiences. Except….
The last 15 minutes of class were devoted to an exercise designed to illustrate the pros and cons of Sanger and Illumina sequencing. I copied the chorus from the Beatles’ “I am the Walrus” over and over on sheets of paper and then cut the paper up into different size pieces. Big pieces went into envelopes labeled “Sanger” and small pieces (about 1/3 as big) went into envelopes labeled “Illumina”. Students were allowed to draw 4 Sanger pieces OR as many Illumina pieces as they wanted. Then they had to “assemble” them and try to figure out what they said.
Sanger won this round — probably because the Beatles were better known to these 20-somethings than I suspected, but still for the usual reasons of longer fragments being easier to figure out. Still, the students appeared to intuit some of the problems faced by assembly programs:
1) Repetition: “the eggm” and “I am the” appear in multiple places in the chorus and make assembly complicated if you don’t know the song
2) It’s exhausting: assembly takes a ton of work — if 40 fragments wear out a human, 40,000,000 might wear out even a powerful computer
3) Somebody said my instructions were unclear — haha, maybe — I used this as an in to talk about the travails of working with open-source software written by scientists who don’t comment their code…
4) The words are nonsense: I picked “I am the Walrus” because the words are meaningless and if you don’t know the song you’re not going to be able to use your expectations about English to put them together. I used this to explain the difference between re-sequencing (easy) and de novo sequence assembly (super hard).
All in all I think it was a useful lesson. I apologize to the building custodians (and my wife) who are going to be picking up tiny strips of paper with meaningless letters on them for the next few days…