Synthetic Biology:Abstraction hierarchy

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After lab meeting, a few of us were having a discussion on what the schema for the Registry should look like. (The notes from that discussion will be posted elsewhere.) During the discussion, we started talking about the abstraction hierarchy that is on the Registry page and originally from one of Drew's slides.

Image:AbstractionHierarchy.jpg

Current abstraction layers definitions

The question that arose is, what is the distinction between a device and system? Generally, to date we haven't had a crisp distinction between parts, devices and systems. The working definitions to date are something like

  • DNA = low level DNA sequence ... a string of A,T,G,C's
  • Part = RBS, CDS, promoter, terminator; a piece of DNA in BioBricks format that has a specific function.
  • Device = inverter; something else with a higher level function; composed of multiple parts
  • System = ring oscillator; composed of many devices

Proposed abstraction layers definitions

Obviously, the distinctions are somewhat vague. The idea that dawned on me during the course of the discussion with Jason and Ilya is to use the following (slightly more crisp?) distinctions

  • DNA = low level DNA sequence ... a string of A,T,G,C's
  • Part = a piece of DNA in BioBricks format which usually has a specific function.
    • a terminator stop transcription
    • a promoter initiates transcription
  • Device = a basic or composite part whose input OR output has units of PoPS (or whatever units the general information signal in the devices have).
    Another way of thinking of this definition is that a device is any part for which a transfer curve can be drawn in which one of the axes is in PoPS.
    The key thing to note in this description is that certain BioBricks in the database might be considered a part in one context and a device in another context.
    Jason has been using an operational distinction between devices and systems saying that a device is something whose behavior you can screen for whereas a system's behavior cannot be screened. Thus, what is a system today might be a device tomorrow if a clever screen is devised. We should think about whether that definition is more useful than this one or if the two could be merged.
    • an inverter is a device. Its input and output are PoPS
    • an RBS.GFP.Term is a device. Its input is PoPS and its output is fluorescence.
    • a constitutive promoter is a device. It has no input and its output is PoPS. (Note: a promoter is a part in other contexts).
    • UT-Austin's photons to PoPS converter is a device.
  • System = Any device which has neither an input nor an output in PoPS.
    Some systems can easily be transformed to devices.
    • a promoter.GFP.Term is a system. It has no input and its output is fluorescence.
    • The UT-Austin's project is a system. Its input is photons and its output is blue/white color.
    • the repressilator is a system. It has no input (or its input could be IPTG/aTc) and its output is fluorescence. The repressilator could easily become a device however. If a duplicate copy of one of the promoters is present. Then that promoter has an output of PoPS which could be hooked up to some device. Thus in this case, the repressilator becomes a device.

Thus, the exact classification of a particular BioBrick is not fixed. In some situations, you might think of promoter as a part because you are referring to a promoter than can be regulated by a certain repressor. In another situation, you think of a promoter as a device because you need a constant PoPS source in your device/system. In other words, parts, devices and systems are not disjoint.

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