About a month ago two unrelated events happened:
- I presented our work on gene knockout libraries across four yeast strains at a systems biology conference1
- The screen of my Fairphone stopped working properly
Luckily, the Fairphone 2 is designed to be easy to repair; I ordered a new screen for about 100 Euros2 and once received I could change it in under 5 minutes without having to unscrew a single bolt. While I was waiting for the new screen I tried to see whether I could still use the phone without its screen on. Given that non-phone devices running Android are available, I wasn’t too surprised to see that the phone was booting up fine and even allow me to send whatsapp messages using the web interface, meaning that it was connecting to wifi/cellular.
At the beginning of the presentation I poked fun at our own experiment by referencing a seminal opinion piece called “Can a biologist fix a radio?”. In it the author challenges the way much of molecular biology is conducted; that is, by taking each gene out and looking for the ones that make the biological system “stop working”. The analogy with the radio shows how this approach wouldn’t necessary lead to a proper understanding on the way a radio works by taking each resistor out sequentially without a more formal electrical engineering approach (or using systems biology at the other end of the analogy).
Even though I did mange to fix my smartphone without having to fully understand how it works, the fact that it was still “working” without its screen indicates another potential pitfall in biological studies: are we able to tell when a system is broken (or “fit” in biological jargon)? If I had chosen to use the ability to connect to a wifi or cellular network and exchange data as a (fair enough!) measure for the fitness of my phone in the “laboratory setting” of my desk I would have not realized that it wouldn’t be of much use to browse the web or send a message when away from my computer. The situation would be even worse if I used the green LED that turns on while charging, which could miss problems with the antenna, the camera, and many other components, including software. We can intuitively tell what the “fitness function” of man-made artifacts is, while for biological systems we can only take educated guesses and hope that our measurements are of relevance outside the lab.
Anyway, we have used colony size on solid agar for each gene knockout in our study, which is now available as a preprint.