Last week was the most recent SBOL workshop (actually, just part of the larger COMBINE workshop on biological standards). I attended remotely, so I was only there for a portion of the event, but I was still able to participate in many of the key discussions on the issues that we are trying to resolve with SBOL. Modern video conferencing is amazing, and we also just adopted new moderation rules (aimed at making discussions more inclusive and constructive) that also have the side effect of making it much easier for remote participants to get a word in edgewise.
Sitting in these discussions, the main emotions that I felt were frustration and despair, driven by my perceptions that nobody seemed to be able to agree on anything, that things I'd thought were settled were all coming apart again, and that we were just not making progress. Often, in meetings such as these, I am put in mind of the famous quote often attributed to Oscar Wilde: "The problem with Socialism is that it takes up too many evenings." Open standards development has much the same failure mode of seemingly never-ending meetings in which everybody needs to have their say and the pettiest disagreements can seem the most impossible to overcome.
Today, however, at our SBOL editors meeting, as were were going over the state of work in progress, I was pleasantly surprised to discover just how nearsighted those perceptions were. In fact, coming out of those apparently frustrating discussions, we have:
- A tidy solution to a nasty technical problem (colons vs. underscores in URIs) that had threatened half the software tools that make use of SBOL.
- Agreement with the curators of the Systems Biology Ontology that they will add a collection of terms that we need for representing genetic interactions.
- A pretty good draft for how to represent combinatorial designs in SBOL, which lots of people want because they are using them to do "mix and match" tests of lots of different variants of their genetic designs.
- An elegant means of representing topological information about genetic designs (e.g., is this a linear fragment of DNA or a circular plasmid?).
- A solid draft for how to include information on the provenance and derivation of genetic designs, which will be critical for tracking how systems are built and exchanged, particularly once they are deployed outside of the lab.
- Agreement on a simplification of how we link information about genetic components with information about how they are combined to build a larger system---an improvement so clear that it feels incredibly obvious in retrospect.
- Rough consensus on most of a major new version of SBOL visual, for diagrams that mix genetic information with information about chemical and genetic interactions.
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| Example genetic system diagram from current draft of SBOL Visual 2.0 |
That's actually quite a lot of progress! So, why the disconnect between my perception in the meeting and the reality discovered afterward? I think that much of it is due to the fact that discussions spend very little time on the things that people do agree about. Instead, we naturally focus on the points of disagreement. There is also often a process of "chewing over" an idea, even if one ultimately agrees with it, in order to really understand it and to understand its implications. With good moderation that keeps things civil, inclusive, and impersonal, you may actually hear a lot more potential disagreements (since people aren't feeling silenced), but if the fundaments are good, you can make a lot of progress even through the billowing conversational smoke of apparent disagreement.
I don't enjoy the process, but I think I may be good at it, I do like what we can achieve, and I believe that those results will be very important for a lot of people, including me, and so I stay involved. Just sometimes, the grinding sound you hear may be both the progress of the standard and also my own teeth.
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