[BBF Standards] Two separate standards

[Deepak Chandran]

Drew,

Agreed: we do not care about non-functional composite parts.
But is the solution to throw them into the pile of "parts"? You had 
mentioned some weeks ago that the fimH transcription unit (can't seem to 
find that link) is a part, not a device; if I remember correctly, it has 
two promoters/operators that are regulated separately. Such a construct 
seems to match the descriptions of a device, not a part. Is this correct?

--Deepak

Drew Endy wrote:
> Deepak,
>
> One of the great strengths underlying synthetic biology is that we get 
> to invent what we hope to construct (and depict).
>
> We don't have to describe everything that already exists.  We also 
> don't have to describe everything that could be [trying to describe 
> everything is one of the great costs, challenges, and at times, 
> failures of systems biology.
>
> So, in this context, let me ask you a question...
>
> Do we really care about composite parts that are not properly defined 
> devices?
>
> Wouldn't this be like Texas Instruments worrying about every possible 
> combination of transistors, resistors, and capacitors.  Instead TI 
> only considered combinations of parts that resulted in useful devices, 
> and they described only these objects in their Transistor Transistor 
> Logic Data Book.
>
> The only time I've ever seen combinations of parts that are not 
> themselves well defined devices being tracked electronically is during 
> a semi-automated BioBrick standard assembly process.  In this case, 
> the build intermediates need to be tracked during a ligation-based DNA 
> assembly process.  Randy Rettberg developed a software tool to handle 
> this [http://parts.mit.edu/r/parts/assembly/index.cgi]
>
> In any case, remember that we don't have to describe *every* thing, 
> only those things that we care enough to try to make and use.  
> Standards restrict and delimit some possibilities in order that work 
> goes forward and more exciting possibilities can come true.
>
> Cheers!
> D.
>
> On Mar 17, 2008, at 12:38 PM, Deepak Chandran wrote:
>
>> Drew,
>>
>>  This description is clear. The confusion comes when you allow parts 
>> made from other parts to be categorized as "parts" as well -- how can 
>> this be? At the same time, they may not be devices either because 
>> they do not have proper interfaces.
>>
>> --Deepak
>>
>> Drew Endy wrote:
>>> Exactly correct.
>>>
>>> DNA engineers will be concerned with how to construct DNA.
>>>
>>> Parts engineers will be concerned with how to build parts at the  
>>> primary nucleic and amino acid sequence level (and whatever else  
>>> synthetic biological parts get made from).
>>>
>>> Device engineers will be concerned with how parts are best 
>>> organized  to make devices.
>>>
>>> System engineers will be concerned with how devices are best 
>>> organized  to make systems.
>>>
>>> Each type of engineer needs to be able to communicate at least one  
>>> level "down" and "up" in this abstraction hierarchy.  Such  
>>> communication should be limited and well structured.
>>>
>>> Meanwhile, I don't mean to add fuel to any "larger than life T7  
>>> autogene fires," but check out the last 6 pages from the synthetic  
>>> biology comic book, if you've not seen it before.
>>>
>>> http://www.nature.com/nature/comics/syntheticbiologycomic/index.html
>>>
>>> Pages 7-8 detail making a device from parts.
>>>
>>> Pages 9-12 detail some issues of common signal carriers for  
>>> transcription based devices.
>>>
>>> Cheers!
>>> D.
>>>
>>>
>>>
>>>
>>> On Mar 15, 2008, at 2:11 PM, Herbert Sauro wrote:
>>>
>>>
>>>> I think Deepak has made a useful observation. At one level an engineer
>>>> won't care about the DNA sequence, of more interest is the functional
>>>> properties of the boxes he/she is putting together. On the other hand,
>>>> the designer of functional boxes will be concerned with the DNA  
>>>> sequence
>>>> since in designing for example a promoter or gene with a specific
>>>> property the DNA sequence is clearly paramount. It looks like 
>>>> there  may
>>>> be a natural separation here.
>>>>
>>>> Herbert Sauro
>>>>
>>>>
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>>>>
>>>
>>>
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>