Saturday, October 17, 2015

SBOL 2.0, governance, and Jake's self-perception

This past summer, one of the most significant scientific milestones I've been involved with is the publication of the SBOL 2.0 standard for representation of biological designs.  What it's all about is being able to better describe and exchange information about the genetic constructs and similar such systems that people are trying to build.  Perhaps the best way to describe it is with this diagram I prepared for a talk, comparing SBOL 2.0 to previous standards:


FASTA is about as bare-bones as it comes: pretty much just listing out the DNA sequence that you want.  GenBank lets you annotate that sequence with descriptive information about what the different parts mean, and SBOL 1.0 lets you describe the structure of a design hierarchically in terms of annotated sequences that get combined together as "parts" to make bigger designs.  SBOL 2.0 lets you talk about function as well, describing the way that these parts interact with one another to create the overall behavior of a design.

Conceptually, it's fairly simple, but in practice it took several years to work out and the arguments are not yet over.  The document that we produced is more than 80 pages long, and we're still tinkering with bits and pieces as we try to understand all of the consequences of what we've built.

SBOL is heavy on my brain right now because for the past week, I've been at the COMBINE meeting, where the communities for SBOL and a number of other biological standards meet up to try to improve their systems, work on interoperability, etc.

This is still not something I ever thought I would be doing with my life.  Even now, in my prejudicial mind, standards design is still something done by grey little people who care passionately about trivial and boring things.  I struggle with this, because I look at my work in this area and simultaneously feel that it is highly important and mind-numbingly stultifying to anybody who isn't actually in the room arguing passionately about the potential long-term consequences of adding a single arrow to a diagram.

A case in point: one of the things that I'm most proud of this week was the updated governance document I drafted, and my mediation of discussion on this document, which helped tune it to become widely accepted; the updated version now appears well on its way to official approval by a formal community vote.  So, apparently I am proud of work I've done on adjusting the methods for making decisions regarding an experimental standard for interchange of information about biological designs that will allow faster prototyping of improved systems for biomedicine, biomanufacturing, etc.  That's at least five levels of separation from anything that really affects the larger world. Looked at in that light, this is clearly the very definition of obscurity.  And yet, let me spell it out in another way...
  • Good governance, which gets openness, power, and decision-making right, is critically important for the health of a community, and a number of little warning signs have indicated that the SBOL community needed to adjust its governance to match the way the group has developed and grown.
  • If the SBOL community governs itself effectively, then it will make better decisions that are more likely to lead to a useful and effective standard.
  • If the SBOL standard works well, it will make it a lot easier for people to develop good biological engineering tools.
  • Those biological engineering tools will make it a lot easier to safely and predictably engineer with and for living organisms.
  • Used responsibly, those capabilities can help make all of humanity healthier and safer, as well as improving our ability to manage our environmental impact on a global scale.


This nail I've driven in is very small and unimportant, almost certainly, and yet it matters.  It matters a lot, and not at all, all at the same time.  And I suppose that's just the way the world works, on a planet with seven billion interconnected and increasingly technologically powerful individuals.  Our civilization is remarkably strange and obscure in its operation, and I'm glad when I find satisfaction in the parts I play.
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