This is seventh in a series of posts about UC Berkeley's 2013 International Genetically Engineered Machine (iGEM) team. If you'd like to catch up: part 1, part 2, part 3, part 4, part 5, and part 6.

As we head into the final stretch, we're focusing on the indigo dyeing process over biosensors this year. Our initial results indicate that the biosensor would require a lot of "tuning" to be functional. Every sensor has the following requirements:

(1) It must be off in the absence of the thing it is supposed to sense.

(2) It must be "on" in the presence of the thing that is is supposed to sense.

A perfect sensor acts like a switch - but practically everything in biology is a dial. There is no "off" and "on", only "less on" and "more on". It takes a lot of tweaking, for example, simply to guarantee that the sensor will have low enough activity in the "off" state to avoid it looking like the "on" state. Imagine if your phone was always ringing, but rings slightly louder when you have a call. Technically, it's a sensor - but not a very useful one.

There's oodles to tweak, too. You can adjust how much of a protein that you're make, the proportions of proteins in the cell, and their structures. So biosensors have been placed firmly on the backburner.

This is hardest on the students who've been putting the most time into biosensors over the summer. It's invariably disappointing to be headlining a part of the project that gets dropped, but this is how research works. Scientists and engineers who never fail are insufficiently ambitious. A good engineer identifies less promising projects quickly and dispatches them ruthlessly, then moves on to the next opportunity.

So, we're taking on indigo production and dyeing. We've been able to make indigo in bacteria since the beginning of the summer. At the moment we're more interested in the dyeing process itself, and how we might scale up production.


The team tours the Advanced Biofuels Process Demonstration Unit (ABPDU) at the Joint BioEnergy Institute (JBEI).

Next up: can our syn bio approach compete with industrial indigo production? Can we replace the current dyeing method with something more environmentally friendly?


Terry D. Johnson is a Berkeley bioengineering lecturer and author. He has been co-advising Berkeley's iGEM team since 2008, and will be one of the lead judges for the North America region this year. His writings here do not necessarily reflect the views of iGEM HQ, Berkeley, or possibly himself, after further contemplation.