[BBF Standards] Two separate standards

[Ralph Santos]

Hi Raik, Deepak, and all,

Actually I like the idea behind what Deepak's going after in this 
discussion of two standards, but instead of thinking in terms of "parts" 
versus "devices" I think it's more useful to think in terms of "inside" 
versus "outside looking in".  Also, I agree completely with Raik in that 
there must be two separate independent standards.  However, I think 
Deepak is onto a basic, fundamental point of there being two 
perspectives which a standard must accept and encompass, and each 
perspective has a distinct logical construction and set of terms.  In 
fact, I prefer Raik's notion of incorporating them into one logical 
framework because considering them as two separate indpendent standards 
suggests they can develop and evolve independently and oblivious to one 
another, which is not the case.  For a standard to be coherent, the 
functional interfaces Reshma articulated that Raik cites must ultimately 
be traceable to their origin in the part's construction, and developing 
them as two separate standards would make it easy to lose that connection.

That said, I think there is still an important point in Deepak's 
suggestion in that the language for describing the functional behavior 
of a part must be separable from its construction.  This is essential 
for the scenario Deepak cited in an earlier message about the problem of 
removing one part from a system and replacing it with a similar part.  
By definition, this task says nothing whatsoever about the DNA sequence 
of the new replacement part.  The essential parameters defining the task 
are the behavior of the device at its interface.

While it is the case that causally the behavior of the part flows from 
its DNA composition, as far as the task as finding a replacement part is 
concerned this logical arc is turned around:  one starts with a 
description of behavior, one ends up with sequence.  Logically, since 
interface behavior can be described in terms that leave sequence 
composition entirely unstated or unspecified, some part of the 
functional behavior language must be anchored in basic terms that have 
nothing to do with part composition.  Bear in mind that I'm not saying 
that one can't ever include DNA sequence composition in a part.  In the 
cases of BBa_G00100 and BBa_G00101, where the parts consist of priming 
sites, its function and its DNA composition are inseparable.  So a 
functional interface language must have an option to talk about sequence 
composition, but it must also have an option to leave it out of a 
description entirely.  However this should be done without losing the 
connection between the fundamental issues anchored in part composition, 
which I think is better handled if one follows Raik's suggestion and 
handle it within the context of a larger standard.

---ralf


Raik Gruenberg wrote:
> Hi Deepak,
>
> the starting point of your interesting discussion may be a mix-up of the terms 
> 'device' and 'part'. Which is kind of not surprising because our use of the 
> terms is often fuzzy. Please have a look at our current Biobrick, Part, Device 
> definition (and comment if there is anything unclear or inconsistent):
>
> http://openwetware.org/wiki/The_BioBricks_Foundation:Standards/Technical/Exchange#What_is_a_Biobrick.3F
>
> So parts/Biobricks are the physical pieces of DNA that are passed around -- 
> something you can put into a plasmid, run on a gel, sequence, etc. Composite 
> Biobricks are still the very same, their sequence (which is still unique) just 
> happens to be a concatenation of other Biobricks.
>
> As Drew and Josh pointed out, there is no single 'atomic' detail level in 
> biology but modularity is emerging in hierarchical layers. So what you would 
> consider a basic part may be constructed as composite part by somebody else.
>
> By contrast, our definition of a device better approaches what you were talking 
> about:
>
> *  Devices are combinations of one or more parts that have a human-defined function.
> * Some devices can be encoded in a single stretch of DNA (a basic or composite 
> part), others encompass disconnected parts (e.g. encoded in two different 
> locations, possibly even cells).
> * (suggestion Reshma) Devices expose specified interfaces for their functional 
> connection with other devices (example: PoPS)
> * (suggestion Raik) A Biobrick device is defined by a unique combination of 
> unique Biobricks
>
> So this is the level where we can start to create 'black boxes' with 
> standardized interfaces.
>
> Following this definition I would re-formulate your question ;-) Do we need two 
> different standards -- one for parts, and one for devices?
>
> IMO, since we already have two different names for it, we can keep them in the 
> same standard. We just have to keep the standard *open* for the definition of 
> interfaces and functions at different levels (of modularity).
>
> Greetings,
> Raik
>
>