[BBF Standards] data exchange issue 1: Abstraction

[Raik Gruenberg]

Drew Endy wrote:
 > A BioBrick part is any basic biological function that can be encoded
 > as DNA.
 >

> 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?

Ralph Santos wrote:
> (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.

It may not be a counterexample. Parts/Biobricks are continuous stretches of DNA. 
They abstract some, often very basic, functionality (like, Ribosome-binding). 
They have defined points of attachment -- Biobrick prefix and suffix -- which 
are used to hook them into larger composite parts. These composite parts then 
work together to form devices. Sometimes a single part can already be a device 
in it's own right but this is rare. Some devices can be encoded in a single 
stretch of DNA as a composite part, others can't.

With this rigid definition (one Biobrick = one DNA), we stay close to the 
experimental application / assembly, and we remain consistent. Lumping different 
sequences into one part creates problems. A tiny codon optimization by one 
engineer may be considered a major change by another (because it affects folding 
kinetics or disrupts his favorite restriction site).

That's why, I like Jacks TTL proposal:

 > (1) Associate the ID numbers with the precise sequences
...
 >
 > TTL Databook approach to classifying digital circuits packages.  The IDs
 > of TTL devices encode their function, format, tolerance, and package
 > in different portions of the ID.

This boils down to a Biobrick / Biobrick-family distinction where one can browse 
the catalog at different levels of the family hierarchy. For the task ahead, I 
would prefer, if this familiy tree would be flexible (multiple inheritance) 
rather than strictly hierarchical. The last two tiers of families could be:

- variants of the same (reference) Biobrick
- versions of each variant
- format versions of each version

In this case the actual Biobrick would also include the format definition and a 
change of format would create a new Biobrick. This looks now preferable to me.

BTW, devices can be classified into families, too. The actual (exact version of 
a) device would then be again defined by its actual Biobricks in their actual 
version and format.

Ah well, here comes Reshma's mail... he gives propably a better summary.

/Raik

-- 
________________________________

Dr. Raik Gruenberg
http://www.raiks.de/contact.html
________________________________