What are standards and why should we bother developing them? I suspect to many people including my fellow scientists and perhaps even some engineers, that standards are nether a rewarding nor worthwhile endeavor. Standards however are the invisible hand that increases our industrial and scientific productivity and helps reduce costs. Can you imagine a world where every workshop produced its own design of thread on a nut and bolt, or every power company generated electricity at a different voltage, or every internet provider used a different protocol for sending email, or every part of the world used a different way to represent time… the list goes on. The world would be an intolerable place without standards. Ultimately standards improve efficiency, productivity and above all reduce costs.
Developing standards however is never easy. The main issue is usually not the technical details but the social issues that have to be addressed. Developing a standard is usually slow and costly. Setting standards is often accompanied by political, commercial and personal struggles. The different stake holders in the enterprise will have opposing requirements and there will be professional maneuvering to win favor or career advancement. Many outside the standardization process will not be able to understand why the process takes so long.
I have been involved in developing two standards and have observed the development of a number of others. The two standards I am referring to are SBML (Systems Biology Markup Language) and SBOL (Synthetic Biology Open Language). SBML was started in 2000 in order to help users exchange computational models of biochemical networks between different software tools. Ten years later SBML has proved to be a very popular standard in the systems biology community with over 200 tools supporting SBML. The second standard, SBOL, was started in 2008 with a workshop I instigated in Seattle and sponsored by Microsoft. Here I want to briefly discuss SBOL and it potential role in synthetic biology.
I am assuming that most readers know what synthetic biology is, if not here is a brief definition from the Royal Society in the UK:
“Synthetic biology is an emerging area of research that can broadly be described as the design and construction of novel artificial biological pathways, organisms or devices, or the redesign of existing natural biological systems.”
The FAQ at syntheticbiology.org is also a useful resource.
What would a standard in synthetic biology be for? The area SBOL is currently focusing on is developing a standard way to represent synthetic biology designs. An immediate application would be the ability to easily extract a design from a publication. At the present time if you try to extract a design from a published paper it is unlikely, without much effort, that you’ll be able to reproduce the design. The original repressilator is a good example; try to reproduce the repessilator from the published description and you will fail. The reasons for this are simple – describing the design of a synthetic circuit using English prose means you’re very likely to miss something critical from the description. Imagine trying to describe an electronic circuit or even a computer algorithm using just plain English, it is very likely it will not work plus it would be very tedious to use because each author is likely to have their own way of describing the circuit including how they built and tested the circuit or algorithm. The way engineers get around this is to develop standards. In electronic design we have a standard way to visually depict a circuit or special languages such as Verilog or VHDL. What we need then is something similar to either a standard visual presentation (such as SBOLv) or a special language that describes an engineered cell. This is the purpose of SBOL.
In a later blog I’ll describe SBOL itself in more detail, its philosophy and future direction.