[BBF Standards] Two separate standards

[Josh Perfetto]

Hi Deepak,

I think that the view that a promoter cannot be sub-divided reflects a
particular level of interest.  From another point of interest, it would be
very interesting to break promoters down into UPE, spacers, core promoters,
boxes, etc., and look at the "interactions within the part" with factors
like UBF1.

You are bringing up an interesting point with your operon.  There are a
couple ways you could define an operon.  For example, you could create an
operon sensitive to a specific repressor, and define it in part by a
function that relates the concentration of that repressor to the level of
polymerase that will flow out.  Or, you could define it in such a way as it
has an interchangeable repressor sub-part, and define the operon in part by
a function which is dependent on another function defined by the sub-part
part definition.

If we were to take the first approach, it doesn't mean that the operon can't
be decomposed which obviously it can, it just means that such decomposition
is not an interface of the part, but an internal detail of the part.  The
second approach doesn't represent the ability to arbitrary combine parts and
be able to predict what will happen, but rather a part which is specifically
designed to take another part of a specific type and as a parameter and
predict what will happen.

But stepping back for a moment, aren't we now really discussing devices?
I.e. the first approach is a single device with a PoPs out that's dependent
on a specific repressor, while the second approach is two devices, the first
with a PoPs out, and the second that relates its PoPs in and the level of a
specific repressor to produce a PoPs out value?  When you say "the 
interaction between the parts is the crucial information", it seems that
you're really either talking about an interface in terms of PoPs (in which
case these parts could be called devices at least in my understanding of how
the term is being used), or are proposing that another interface besides
PoPs be standardized in the definition of parts.

-Josh

-----Original Message-----
From: standards-bounces at biobricks.org
[mailto:standards-bounces at biobricks.org] On Behalf Of Deepak Chandran
Sent: Friday, March 14, 2008 2:31 PM
To: Drew Endy
Cc: standards at biobricks.org
Subject: Re: [BBF Standards] Two separate standards

Drew,

The parts,devices,systems hierarchy is fine. What is confusing to call 
an entire operon (possibly more than one promoter, rbs, gene) a "part" 
and a simple promoter a "part" as well. I can take an operon apart and 
replace one of the rbs, whereas the promoter cannot be taken apart. 
There is a difference between these two from an engineering perspective.

I think that the operon should be defined in terms of the parts that it 
is made from and how they are interacting. Each individual part would 
then contain the sequence information and other characteristics. For 
anything made from multiple parts (say a bistable switch), the 
interaction between the parts is the crucial information. But if you 
take a basic part like a promoter, there is no interaction within the 
part. This is why I think that the standard definitions for basic parts 
and parts made from more than one part should be different.

Again, I am completely open to disagreement here. It would be sufficient 
to explain how you can apply the same standards to describe a bistable 
switch and a promoter.

--Deepak

Drew Endy wrote:
> Parts are parts.  I'd use the language basic parts if you need a 
> modifier.
>
> Devices are composite parts.  But, not all combinations of parts are 
> devices.  Devices are limited by the requirements bounding device 
> specification.  For example, polymerase per second (PoPS) serves to 
> define a common signal carrier for inputs and outputs when dealing 
> with gene expression devices.
>
> Note that there is no absolute physical definition of a part.  You can 
> keep drilling down into particles and sub-atomics.  So, I believe that 
> the standards should be linked to the human-invented abstraction 
> hierarchy (i.e., parts, devices, systems), which was invented for 
> practical reasons (i.e., it is good for something).  Support for 
> reliable physical and functional composition is definitely one of the 
> first and best goods that we can have.
>
> For the small amount of protein engineering work going on.  Docking 
> and phosphorylation motifs are typically though of as parts.  For the 
> small amount of RNA engineering work going on, aptamers and ribozyme 
> active sites are also thought of as parts.
>
>
>
> On Mar 14, 2008, at 12:14 PM, Deepak Chandran wrote:
>
>> Hello standards group,
>>
>> From all the standards discussion, I think that there are two separate
>> standards for parts. If this is the case, then it should be made 
>> explicit.
>>
>> The first type of standard is for atomic parts (better word needed?)
>> such as promoters, rbs, etc. (that cannot be broken down further). The
>> "standards" for these parts is simply a list of characteristics. For
>> example, a promoter would have its sequence and Jason-units as its
>> characteristic feature. RBS would have sequence and some other units.
>> The list of characteristic features are probably best if developed by
>> experimentalists -- the question to ask is: what is it that makes this
>> promoter unique?
>> Sequence information is definitely needed for atomic parts.
>>
>> The second type of standard is for composite parts (better word?) such
>> as iGEM projects. I do not think that the sequence for composite parts
>> is needed -- if we know the atomic parts that make up this composite
>> part, then we can easily determine the sequence. What is needed is the
>> order in which the atomic parts are arranged on the plasmid and the
>> circuit-diagram that explains the mechanism of the part. Someone should
>> be able to take a composite parts and replace some of the atomic parts
>> just like upgrading a computer by replacing the RAM.
>>
>> One can wonder whether things like protein domains or fusion proteins
>> are atomic or composites. I think the question is whether the part is
>> modular (i.e. whether it can be taken apart and reconstructed using
>> slightly different components).
>>
>> In summary:
>> A language is needed for composite parts.  (sequence not needed)
>> A list of characteristics is needed for atomic parts. (sequence needed)
>>
>> If there is disagreement on this, please let me know why, so that I can
>> eliminate my confusion. If there is agreement, then perhaps we should
>> make this fact explicit and categorize our proposals to one of the two.
>> We can make more directed progress that way.
>>
>> By the way, this categorization is not meant to disturb the
>> part/device/system hierarchy.
>>
>> Ralf, I think that you language makes more sense if it is for composite
>> parts, because you would need more descriptions for an atomic part. I
>> will comment on that later.
>>
>> --Deepak
>>
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