[BBF Standards] Two separate standards

[Drew Endy]

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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