[BBF Standards] Two separate standards

[Josh Perfetto]

I think you are making some very insightful remarks without realizing it :)
The only way to engineer large-scale systems is by breaking the system down
into modular units with well-defined interfaces, otherwise it just gets too
complex.  The circuit diagram analogy is perfect: inputs, black boxes, and
outputs, and I think it is a reasonable representation at this level.  If we
are defining things at this level, and have well-defined interfaces like
PoPs for inputs and outputs, then I agree with you that it is not necessary
to specify the DNA sequence of the entire circuit, but rather just define
the order of the black boxes, which can define their own DNA sequences.  You
can replace one black box of the circuit diagram with another and predict
what will happen.  Once we standardize how to specify devices at this level,
including devices with multiple inputs, it will be very powerful.

When we drill down into other levels, like the upstream and core portions of
a promoter, obviously PoPs is a totally useless interface for defining how
these parts fit together, and so a circuit diagram is not appropriate for
specifying the workings of a promoter as you said.  We need to decide at
which levels standardization would be useful and how to define interfaces
between parts at these useful levels.  However I don't think it's essential,
at this stage, to model the world.  For example, if we want to standardize
how to define promoter behavior, we can leave the internals of promoter
working as a black art, or at least out of the scope of standardized parts,
and only define the characteristics of the promoter at that level, at least
for now.

I have not been in this community very long and am unsure about the exact
definition that others are attributing to the term "devices" (and I think
this does vary a bit, perhaps because it is not yet standardized :) ).  But
I don't see any problem with defining devices formally in terms of A) PoPS
in/out, and B) other modifiers like UV/LuxR.  I think a key question is how
much these other modifiers from B are standardized in their definition vs.
how much this is an ad-hoc definition.  I think it's probably best to follow
the 80/20 rule and standardize the 20% of properties that have are used 80%
of the time, like chemical concentration, where the chemical in question is
defined by something like CAS registry number, while leaving the other
specialized properties that some devices might measure, like magnetic field
orientation, unstandardized.

-Josh

 

-----Original Message-----
From: Deepak Chandran [mailto:deepakc at u.washington.edu] 
Sent: Friday, March 14, 2008 7:24 PM
To: Josh Perfetto
Cc: 'Drew Endy'; standards at biobricks.org
Subject: Re: [BBF Standards] Two separate standards

Hello Josh and Drew and rest,

The Polkadots system is a great example. Basically what I am saying is 
that the sequence doesn't need to be specified in order to define the 
polkadots system. As long as I know the parts and the order in which 
they are placed on the plasmid(s), I can reconstruct the system. By 
"interaction between parts", what I mean is that in order to understand 
how polkadots is working, I need to see the circuit that is presented on 
the polkadots website. It would be nice if the circuit diagram was our 
standard representation, but that is not reasonable.

I think an operon is a similar case -- it is a very simple circuit. One 
can draw a diagram that explains how an operon functions. So, I am 
looking at operons as engineered objects (though humans didn't engineer 
them first).

What I am proposing is that circuits such as polkadots or even operons 
should be defined in such a way that a synthetic biologist can cut out 
one of the components of the circuit and replace it with another 
device/part. If we cannot do that, then these biological circuits are 
not engineerable.

On the contrary, a promoter is different. I don't know how one can 
explain the inside of a promoter using a circuit diagram. The fact that 
promoters can be broken down into smaller components is true. But can 
you take the first half of one promoter and stick it to the second half 
of another promoter (I don't know)? Would the resulting promoter have 
predictable behavior? Similarly, can I take pieces of two RBS and piece 
them together and be able to predict the function of the resulting RBS? 
In constast, replacing the promoter or RBS inside an operon has 
predictable behavior, and the affect of replacing parts inside the 
polkadots can also be predicted (just like I can predict the result of 
changing my computer's CPU). I suppose one could say replacing protein 
domains has predicable behavior.

By "interaction between parts", I did not mean any particular type of 
interaction. But I was not clear on this: is PoPS the standard 
input/output for BioBrick parts? Does this mean that I cannot have a 
device that uses UV as an input and/or produces LuxR as an output?

--Deepak

Drew Endy wrote:

> Not true.  A promoter can be disassembled, for example in bacteria, 
> into -10 and -35 regions.
>
> You may find it helpful to stop thinking about natural objects such as 
> operons and start thinking about devices as *engineered* objects.
>
> For example, consider the material produced in 2004 by the Polkadorks:
>
> http://parts.mit.edu/wiki/index.php/IAP2004:Polkadorks
>
> In the Polkadorks work you can see that they clearly defined device 
> boundaries based on PoPS, including PoPS pass-through boundaries 
> leading to multi-device mRNA. 
Josh Perfetto wrote:
> 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
>>>
>>> _______________________________________________
>>> Standards mailing list
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>>>       
>
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