[BBF Standards] Two separate standards

[Deepak Chandran]

Hello Raik,

Thank you for the elaborate reply. I am afraid I am still not clear on a 
few things. I am sorry for continue this discussion for so long, but I 
am hoping it will be fruitful in the end. I think the following two 
questions should resolve my confusions:

1) Can you give an example of a composite part (single DNA strand with 
multiple parts) that can be fully described without any kind of 
descriptions on how the individual parts influence one another (i.e. 
"circuit diagram")? Additionally, can you give an example where the 
sequence is necessary to describe the composite part (assuming that the 
individual parts have not been altered in any way), except for spacers?

2) Suppose I make an oscillator using available parts. The oscillator is 
contained on a single plasmid. It does not really have any defined 
input/output -- it just expresses three repressors that oscillate.
Small question: is this a still device, even though it cannot be 
connected to anything else?
Bigger question: suppose I want to replace one of the repressors inside 
the part. Would I need to get the sequence of the part, identify the 
original repressor sequence, and then cut/paste the new repressor 
sequence? This would be "hacking" and not quite "engineering".

--Deepak

Raik Gruenberg wrote:
> Hi Deepak,
>
> Deepak Chandran wrote:
>> Hello Raik and rest,
>>
>> Reshma's description on devices is very clear (on the link you had 
>> provided). My discussions were targeting basic biological parts vs 
>> composite parts (instead of basic parts vs devices). Turning a part 
>> into a device is a matter of adding the correct interface and 
>> identifying the function (correct?).
>
> Half-correct. The difference is also that a device can (and often 
> will) bundle disconnected parts into a single functional unit. With 
> disconnected I mean parts that are *not* linked up into a single 
> composite Biobrick but are, for example, co-transfected on different 
> plasmids but need to *work* together (rather than being coded 
> together). The classic example are the quorum sensing devices. There 
> is a receiver and a sender but the receiver is in one strain and the 
> sender in another. It's sensible to unite them into one device because 
> they operate together and the PoPS interface is defined like cell1 -> 
> sender [black box] receiver -> cell2. But no single (composite or not) 
> part can implement this device. Many other devices *can* be 
> implemented in a single composite part, as a matter of convenience, 
> don't have to. I think that devices that are distributed within or 
> across cells may actually become the normal case in the future.
>
>>
>> Nonetheless, any composite part is a circuit made from basic parts. This 
>
> Here I disagree. A composite part is simply a part that happens to be 
> composed of other parts. Full stop. No interfaces or circuit implied. 
> Just a technical feature of the assembly process. A matter of 
> technical convenience and choice.
>
>> circuit wiring diagram is very important to include in our standard 
>> representation of any composite part, whether it is an complex 
>> oscillator or a protein generator. Such a circuit wiring diagram does 
>
> An oscillator is a device. In many (not all) cases, this device *can* 
> be implemented in a single composite biobrick but doesn't need to. If 
> the implementing engineer decides to bundle all parts of the 
> oscillator into a single composite part, then the resulting device 
> "coincides" with this single composite part. But that's a technical 
> choice.
>
>> not exist for basic biological parts (correct?).
>>
>> This does not have anything to do with the Registry's hierarchy or 
>> what family a part belongs under. I am just saying that in order to 
>> fully describe a composite part, I would need different descriptors 
>> than when describing a basic part.
>
> So I would then argue that you are still talking about the description 
> of devices. You would create a composite Biobrick and then you wrap 
> this composite Biobrick into a device to describe its interfaces and 
> operation characteristics. Even better, you as designer describe the 
> device in detail including the full parts-list and all connections, 
> and the implementing engineer can from this blueprint decide whether 
> all parts need to be next to each other on a single piece of DNA or 
> whether he prefers to break the device into several co-expressed 
> parts. This also means that a given device will, in contrast to a 
> Biobrick part, not any longer correspond to an exact DNA sequence, at 
> least not a single consecutive DNA sequence.
>
>>
>> Additionally, I do not understand why the sequence information is 
>> needed for composite parts -- isn't this redundant information which 
>> makes room for errors in a database?
>
> Sorry, I put that wrong. The definition on the standards wiki is 
> clearer. Composite Biobricks are defined as a "sequence" of basic 
> biobricks plus the intervening scar. So there is no redundancy. This 
> is also how I implemented it in the Brickit data scheme. The point was 
> that a composite Biobrick still has a unique DNA sequence (which can 
> be calculated from the sub-part sequences).
>
>>
>> If there are two representations (for basic and composite parts), the 
>> I agree with Ralf that they should not be allowed to wander 
>> completely independent of one another.
>
> There should be a clear distinction between devices and parts 
> (=Biobricks for our task) but composite and basic parts are just two 
> variants of the same thing. This also allows us to first nail down the 
> "minimal" data exchange standard for Biobricks (composite and basic) 
> which will foremost cater to the search, assembly and exchange of 
> Biobrick DNA fragments. In parallel we (or you and Ralfph :-) can 
> start working on the description of devices. The minimal Biobrick 
> standard may already include the concept of a "Biobrick Device" as a 
> bag of Biobricks working together but without much further details.
>
> Well, there remain interesting questions how to distribute functional 
> descriptions between devices and parts. Should a Ribosomal Binding 
> Site part be also wrapped into a device (Input interface: 
> Ribosome-affinity, output interface: PoPS)? I was hoping to solve this 
> with the Biobrick family concept.
>
> Greetings,
> Raik
>
>>
>> --Deepak
>>
>> 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
>>>
>>> Deepak Chandran wrote:
>>>> Hello Josh, Drew, and rest,
>>>>
>>>>    While it seems logical to first have standard definitions for 
>>>> promoter, rbs, coding regions, terminators, etc. before working on 
>>>> standards for devices and systems, I think the two are somewhat 
>>>> independent. People have been building biological circuits 
>>>> successfully (iGEM students for example). What I am proposing is 
>>>> for some of us (myself included) to write out a format that can 
>>>> represent all of the iGEM projects. This format can allow others to 
>>>> take iGEM projects (and any other such projects) and connect them 
>>>> together to form larger circuits without having to understand the 
>>>> details of the project itself. All these circuits will be 
>>>> represented in the standard language so that one does not need to 
>>>> reconstruct an entire device to reuse it. I think this is very much 
>>>> possible while the standards on promoters/rbs/etc are still 
>>>> pending. It is also a bit easier maybe, because many concepts can 
>>>> be borrowed from engineering disciplines.
>>>>
>>>> --Deepak
>>>>
>>>> Josh Perfetto wrote:
>>>>> 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
>>>>>>>>
>>>>>>>> _______________________________________________
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>>>>>>       
>>>>>   
>>>>
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>>>
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