System-Level Design Group

KU Institute for Information Sciences


This year’s New Directions In Software Technology (NDIST) workshop is focusing on computating and biology. In particular, synthetic biology. Lots of interesting things going on.1

first day. So, forgive lack of detail.

Opening talk gave some great examples of using biological systems to model Boolean algebra. I asked the question of why we use biology to mimic abstractions derived from circuits. The great answer I got was that we’re not. Boole did his work as a mathematical abstraction and not tied directly to circuits. What we’re doing is implementing a useful abstraction, not mimicing digital circuits. I wonder why when not start with a Turing Machine rather than Boolean algebra, but I think one can argue one is certainly prerequisite for the other.

Jay Sussman (MIT) gave a talk entitled “We Don’t Understand Computing” that was pretty interesting.

Interesting small group discussion. One thing that came out is that circuits have two concepts of time while biology adds a third that it replicates.

Thoughts from the day:

  1. Turnaround time for synthetic biology builds is horrifically long in comparison to other technologies. This is not fatal, but suggests there is a long way to go.
  2. We do not have our abstractions set yet. We don’t have Kirchoff or Ohm for biological systems. We’re trying to hide that with Boole, but that’s fine.
  3. I still think we’re trying to jam biology in to digital computing rather than bringing computing to biology. The A-Machine was not binary. The first computers were not binary. We discovered binary’s utility later. Maybe that will happen here as well.

Quotes from the day:

Don’t shoot yourself in the foot with that sliver bullet - Jay Sussman

When new complexities are discovered in systems, scientists publish papers abou them, characterize and study them. Engineers try to figure out the hell to get rid of them. - John Knight (paraphrased)

  1. I didn’t decide to blog on this until after about half of the