[BBF Standards] data exchange issue 1: Abstraction

[Ralph Santos]

Herbert Sauro wrote:
> Drew, I'm not try to be difficult here, but can you also indicate what 
> you mean by a basic biological function. The other thing that confuses 
> me is what is the difference between a device and a part because if a 
> part can also be a composite then what is a device?
>
> Herbert
>
>   

Herbert, I think you raise several good points here.  Although it's good 
to have a "big tent" definition of a part to encourage inclusion, I 
think much of the potential of parts won't be realized until there's 
also a more rigorous definition of a part which allows one to compose 
systems of biobricks in a manner that not only defines some constraints 
and rules of composition but allows one to reliably predict what the 
resulting behavior of the composed system will be.  Right now, my 
concerns with the current hierarchy are:

(1) Right now, parts include so many different kinds of entities 
(snippets of DNA including biobrick ends, full plasmids, small RNA's, 
etc.) that one cannot sensically abstract a part in any uniform fashion.

(2) There are currently no boundaries on part behavior, so there's no 
starting point to define any generalizable rules on how to compose parts 
or define the behavior of part assemblies.

A counterexample to illustrate what I'm talking about are electronic 
components: resistors, capacitors, IC's, etc.

They all observe the "lumped circuit abstraction".  They operate as tiny 
discrete units and there are defined points of attachment to hook them 
into a larger system.  In schematics they're often illustrated as 
circles or dots, and on the physical component they are wires or pins or 
tabs.  While there is a wide variety of components, there is the 
constraint of defined points for attachment/composition/interaction.

As for boundary conditions, there are many.  First is the simplification 
that they communicate only through wires or other conductors (i.e. 
circuit board traces).  While many components can radiate EM fields 
directly, this falls outside the abstraction and this is controlled in 
physical systems with shielding and other measures.

Furthermore, the constraints support some sort of logic or discipline 
for understanding the behavior of composed systems.  For analog circuits 
there's Ohm's law, Kirchoff's laws, and differential equations.  For 
digital circuits it's even simpler.  Signals are reduced to saturation 
levels, we abstract those as binary signals, and we use Boolean logic to 
understand the behavior of composed systems.

I realize that the whole point of the standardization effort is to work 
toward achieving this goal.  However, it seems useful as part of this 
process to try and identify or understand what the characteristics the 
standard towards which we're working should include.

What are your thoughts on the matter?

---ralf