[BBF Standards] systemic limitation of biobricks for combinatorial logic?

Drew Endy endy at MIT.EDU
Thu May 29 08:03:01 EDT 2008 

Regarding defined cellular volumes, I would encourage you (again) to  
read Barry Canton's dissertation (MIT Class of 2008, bcanton at mit.edu)  
and also to study the 2007 UCSF iGEM project (see earlier comments in  
thread below).

Also, for folks who are thinking about computation inside cells,  
there's an interesting dissertation by George Homsy ("Performance  
limits on chemical computation") that is available via: http://dspace.mit.edu/handle/1721.1/30085

Finally, let's try to keep the standards at biobricks.org mailing list  
focused on technical standards for synthetic biology.  We have our  
hands full keeping track of both experimental and computational  
standards on this list.

For example, if you wanted to more strongly frame the conversation  
below about defining standard biological chassis in which to operate  
BioBrick standard biological parts, that would be well-suited to this  
technical standards mailing list.  If a conversation is more  
exploratory and information, please consider starting/moving it to the discuss at syntheticbiology.org 
  mailing list.

Finally, I'll point out two other interesting mailing lists:  announce at syntheticbiology.org 
  for announcements of general interest, and legal at biobricks.org for  
discussion of legal issues having to do with BioBrick standard  
biological parts, specifically, and synthetic biology more broadly.

Cheers,
Drew



On May 29, 2008, at 4:15 AM, Dr. Markus Schmidt wrote:

> Here is a comment to JCs request from today.
> The smallest bioprocessing unit (BPU) would be the cell, at least in
> conventional thinking, so creating a structure that could harbour
> those BPU in a controlled way would be agood starting point.
>
> Probably there is more out there, anyway, here is an article about
> such a structure
>
> Methods Mol Biol. 2007;352:237-48.Links
> Compartmentalized self-replication: a novel method for the directed
> evolution of polymerases and other enzymes.
> Ghadessy FJ, Holliger P.
> MRC Laboratory of Molecular Biology, Cambridge, UK.
>
> Compartmentalized self-replication (CSR) is a novel method for the
> directed evolution of enzymes and, in particular, polymerases. In its
> simplest form, CSR consists of a simple feedback loop involving a
> polymerase that replicates only its own encoding gene (self-
> replication). Self-replication occurs in discrete, spatially separate,
> noncommunicating compartments formed by a heat-stable water-in-oil
> emulsion. Compartmentalization ensures the linkage of phenotype and
> genotype (i.e., it ensures that each polymerase replicates only its
> own encoding gene to the exclusion of those in the other
> compartments). As a result, adaptive gains by the polymerase directly
> (and proportionally) translate into genetic amplification of the
> encoding polymerase gene. CSR has proven to be a useful strategy for
> the directed evolution of polymerases directly from diverse
> repertoires of polymerase genes. In this chapter, we describe some of
> the CSR protocols used successfully to evolve variants of T. aquaticus
> Pol I (Taq) polymerase with novel and useful properties, such as
> increased thermostability or resistance to the potent inhibitor,
> heparin, from a repertoire of randomly mutated Taq polymerase genes.
>
> Although the compartimentalization was used for different reasons it
> could be a useful starting point .What do you think?
> Markus
>
> Am 29.05.2008 um 08:46 schrieb J C:
>
>> Previously I was thinking at the micro level regarding cell-cell
>> communication
>> or spatial separation of signals.  Is a more macro separation
>> possible, i.e.
>> colony-colony communication?  If each colony represents minimal logic
>> elements, and signals a neighboring colony, then the communication  
>> and
>> signal compatibility/separation occurs at the junction only.
>> Uniqueness of
>> the signals is only a design criteria within the colony.
>>
>> Again, I'm a computer engineer so I don't know specifics of how
>> colonies could
>> neighbor to create signaling pathways while ensuring the colony
>> remains
>> in tact.
>>
>> The resulting circuits would be physically large (I'm not sure what
>> the minimum
>> size of a stable biobrick is, on the order of 1 cm^2 or needs to be
>> larger?)
>> because each colony would effectively represent the "maximum micro-
>> processing
>> unit".  Chaining these together yields combinatorial circuits.  Like
>> laying out
>> discrete transistors on a printed circuit board.  where the  
>> underlying
>> circuit board substrate is agar (?).  What kind of signaling would
>> this be,
>> and how would the signal be drawn to the colony boundary?
>>
>> To build on this, note that most printed circuit boards are multiple
>> layer,
>> i.e. the signaling pathways between logic components exist both on
>> the surface and within the board itself.  So if some material for
>> physical separation
>> of the colonies exists (some membrane?) then the colonies can stack
>> vertically.  (Similar to layering P-N regions on silicon chips with
>> vias to
>> connect 3-dimentional layers to each other)
>>
>> Anyway it's an idea to add to the list, I'm sure someone has
>> discussed it
>> before? Where?
>>
>> Cheers
>> JC
>>
>>
>> On Tue, May 20, 2008 at 4:46 AM, Dr. Markus Schmidt
>> <markus.schmidt at idialog.eu> wrote:
>>> Thanks JC for bringing the issues back into the disussion. The
>>> system-wide
>>> visibility of all gate outputs is a serious obstacle to the
>>> development of
>>> the standardized biopart concept. When I posted the message on
>>> lacking
>>> specifity in February there was hardly any reaction, which really
>>> surprised
>>> me. Sure as long as the experimental phase of biobricks now runs
>>> systems
>>> that contain only few parts, all these problems do not arise, but
>>> thinking
>>> about the future and about the prospect of this approach we should
>>> dedicate
>>> a susbstantial amount of time and energy to come up with solutions.
>>>
>>> If we take electronic integrated circuits as an example (and not  
>>> as a
>>> metapher), than producing compartiments is the goal.
>>>
>>> Which ways are there to produce compartiments?
>>>
>>> To begin with I would say there are spacial, chemical, sematic or
>>> time-based
>>> compartiments.
>>>
>>> 1. Spacial:
>>> 1.1. new organelles. This is a nice idea but how many organelles
>>> can you
>>> engineer into a cell? Tens, hundreds, but certainly not millions.
>>> 1.2. cell-cell communications. of course this is an option but it is
>>> basically the same situation as in the organelles, although with
>>> the option
>>> to increase the number of differnet cells without the packing
>>> problems of
>>> organelles. Basically the way by wich the cells communicate is the
>>> bottleneck.
>>> 2. Chemical:
>>> 2.1. Number of molecules to be used as an information carrier is
>>> extremely
>>> large but at the cost of reduced specifity and increasing cross  
>>> talk.
>>> 2.2. Quorum sensing. This is done by molecules and only because it
>>> involves
>>> the extracellular environment it doesn't mean it solves the problem
>>> of open
>>> logic gates.
>>> 3. Semantic:
>>> 3.1. I guess the zinc finger story comes in here, an approach that
>>> target
>>> the genetic code. The information you can store on a lets say x  bp
>>> long DNA
>>> is 4^x (may be reduced for some mutation-robustness meassures) and
>>> could
>>> provide enough specifity to deal with ultra large scale circuits.
>>> This is
>>> actually a promising approach, programming an RNA computer
>>> 4. Time-based
>>> 4.1. PoPS, for Polymerase Per Second. This is a nice idea (and the
>>> comic is
>>> fun) and transcends/converts the problem of chemical specifity to a
>>> unambigous signal unit. OK, lets say you found a way to meassure
>>> the PoPS
>>> rigt on the DNA. Say you meassuered x PoPS. Then you have a
>>> subsequent PoPS
>>> analyzer that makes e.g. the following decision: if x<y output=0;
>>> if y<x<z
>>> output undefined; if z<x output=1. Problem solved, isn't it? Well
>>> it is but
>>> only in the case if the PoPS analyzer (counter) sits right after
>>> the PoPS
>>> relevant piece of DNA, otherwise you would have to transfer the
>>> result x
>>> into a chemical signal to transport it to another part of DNA or
>>> elsewhere
>>> and then you run into the same problem of open logic gates. So if
>>> you avoid
>>> that and realize a linear logic line (a Ford like assembly line)
>>> you are
>>> quite limited in running your software.
>>>
>>> However, what I think can be done is to combine all these
>>> approaches in
>>> order to push the limit of the maximum number (Nmax) of realizable
>>> "logic
>>> gates" or operations a little bit. Maybe each approach can help us
>>> to push
>>> the Nmax by a factor of 100 or 1000 (or maybe more).
>>> However, this is way a different story than with Moore's law, where
>>> basically the reduction of size ( and packaging) of logic gates was
>>> and is
>>> the main driving force to improve the number of transistor per chip.
>>>
>>> Cheers, Markus
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> Am 20.05.2008 um 05:35 schrieb Drew Endy:
>>>
>>>> As background information relevant to your discussion:
>>>>
>>>> 1. there is a common signal carrier for gene expression devices.   
>>>> it
>>>> is called PoPS, for Polymerase Per Second.  read about it here:
>>>> http://openwetware.org/wiki/Adventures
>>>>
>>>> 2. biochemical cross talk within a self mixing volume can be  
>>>> handled
>>>> via the specificity of molecular interactions.  look up zinc finger
>>>> DNA binding proteins.  read Reshma Shetty's dissertation from MIT
>>>> (this year).  Also read Zarrinpar A, Park SH, Lim WA., PMID:
>>>> 14668868
>>>>
>>>> 3. new organelles could be created thereby providing engineered
>>>> additional spatial insulation.  see the 2007 UCSF iGEM team's  
>>>> second
>>>> project (here: http://parts.mit.edu/igem07/index.php/UCSF/Organelle_Intro)
>>>> .  Also read Barry Canton's dissertation from MIT (this year).
>>>>
>>>> 4. cell-cell signaling can be used to communicate across bacteria.
>>>> read Weiss and Knight
>>>> (http://www.princeton.edu/~rweiss/papers/rweiss-dna6.pdf
>>>> ) and more recent papers from Ron's lab at Princeton (see
>>>> http://weisswebserver.ee.princeton.edu/pubs.html)
>>>> .
>>>>
>>>> Drew
>>>>
>>>>
>>>>
>>>> On May 19, 2008, at 10:42 PM, James Lawson wrote:
>>>>
>>>>> Hi folks,
>>>>>
>>>>> This might be a little from left field, and I don't have the
>>>>> solution, but I have had this idea since I became familiar with  
>>>>> the
>>>>> gene-centric abstraction level that the entire Biobricks /  
>>>>> standard
>>>>> parts systems is based on. I don't think the level that we're
>>>>> designing these systems at is helping us here, particularly with
>>>>> respect to this system-wide visibility of gate outputs. We have no
>>>>> 'encapsulation' mechanism. The non-nucleated cells we're using as
>>>>> chassis for these systems don't have any mechanism for membrane-
>>>>> based compartmentalisation, so any all the 'computation' is done  
>>>>> in
>>>>> pretty much the same compartment. Nucleated, compartmentalised
>>>>> cells
>>>>> are able to get a step further by creating an encapsulation
>>>>> mechanism, where some kind of reaction or transformation of  
>>>>> species
>>>>> may be contained within a delineated zone.
>>>>>
>>>>> Leveraging any of these membrane compartmentalisation (or membrane
>>>>> mircodomain) based systems of encapsulation would require some
>>>>> pretty extensive engineering and standardisation of the transport
>>>>> and cytoskeletal systems within a cell, so I guess it isn't really
>>>>> tractable for a while.
>>>>>
>>>>> To add to Herbert's comments:
>>>>> In unicellular organisms, one could say that quorum sensing  
>>>>> systems
>>>>> are analogous to neural networks in multicellular organisms as a
>>>>> solution to this problem of encapsulation and input/output
>>>>> visibility management we're talking about. I have heard quite a  
>>>>> lot
>>>>> about people doing engineering with quorum sensing systems and I
>>>>> think this is probably where the synthetic biology community will
>>>>> continue to look to. I don't really know how much we know about
>>>>> heterogeneous bacterial colonies - perhaps someone could enlighten
>>>>> me on the state of the field?
>>>>>
>>>>> Kind regards,
>>>>> James Lawson
>>>>>
>>>>> Herbert Sauro wrote:
>>>>>>
>>>>>> Funny you should mention this solution:
>>>>>>
>>>>>>> Can this be solved by using single cells for each circuit, then
>>>>>>> somehow providing inter-cell communication?
>>>>>>> (Also seems quite difficult, correct?)
>>>>>>
>>>>>> Because this is how evolution got round the problem by inventing
>>>>>> neural circuits.
>>>>>>
>>>>>> Herbert Sauro
>>>>>>
>>>>>> J C wrote:
>>>>>>
>>>>>>> Hi all,
>>>>>>> I have been reading about biobricks for some time,
>>>>>>> I am a computer engineer.
>>>>>>>
>>>>>>> For combinatorial logic, it seems the limitation of biobricks
>>>>>>> is the system-wide visibility of all gate outputs, is this
>>>>>>> correct?
>>>>>>> In circuits with multiple gates, each gate must employ a unique
>>>>>>> input signal and output signal, otherwise the multiple outputs
>>>>>>> will conflict with the inputs.
>>>>>>>
>>>>>>> How is this being addressed other than by finding unique
>>>>>>> signals to feed to each gate?
>>>>>>>
>>>>>>> This is not a scalable solution for larger circuits, i.e. adders
>>>>>>> or latches (RAM storage for more than 1 bit).
>>>>>>>
>>>>>>> Can this be solved by using single cells for each circuit, then
>>>>>>> somehow providing inter-cell communication?
>>>>>>> (Also seems quite difficult, correct?)
>>>>>>>
>>>>>>> There was a similar comment on this recently, though I didn't
>>>>>>> see any solution discussion?
>>>>>>>
>>>>>>> http://biobricks.org/pipermail/standards_biobricks.org/2008-February/000034.html
>>>>>>> "The lack of physical separation of signals, as is the case in
>>>>>>> microelectronics, could be one of the biggest limitations to the
>>>>>>> standardized bioparts concept. "
>>>>>>>
>>>>>>>
>>>>>>> The idea offered in that thread,
>>>>>>> "Actually this could lead to a design process where you operate
>>>>>>> e.g. on a
>>>>>>> system level and design your nice circuit, but depending on the
>>>>>>> circuit the
>>>>>>> design computer programme chooses one of different devices (and
>>>>>>> finally
>>>>>>> parts) that interact in the way you like."
>>>>>>>
>>>>>>> This is actually quite impossible for multi-gate designs.  A
>>>>>>> multi-
>>>>>>> bit adder
>>>>>>> or memory storage would require far too much complexity.  The
>>>>>>> components
>>>>>>> (i.e. "transistors") need to have completely compatible outputs
>>>>>>> so
>>>>>>> that
>>>>>>> any output can connect to any input.  Otherwise they are not
>>>>>>> "generic parts".
>>>>>>> Similar issues led to much complexity in the early days of
>>>>>>> semiconductor
>>>>>>> fab.
>>>>>>>
>>>>>>> --
>>>>>>> Cheers!
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Standards mailing list
>>>>>>> Standards at biobricks.org
>>>>>>> http://biobricks.org/mailman/listinfo/standards_biobricks.org
>>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
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>>>>>>
>>>>>
>>>>> <j_lawson.vcf>_______________________________________________
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>>>>
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>>>
>>>
>>> *----------------------------------------------------------*
>>> Dr. Markus Schmidt
>>> International Dialogue and Conflict Management
>>> Abt-Karlg. 19/21, 1180 Vienna, Austria
>>> phone: +43(0)19900811
>>> mobile: +43 660 6856623
>>> www.idialog.eu
>>> email: markus.schmidt at idialog.eu
>>> *-----------------------------------------------------------*
>>>
>>>
>>>
>>>
>>>
>>
>>
>>
>> -- 
>> [ Copyright 2006 jncline at gmail.com All Right s Reserved ]
>
>
>
> *----------------------------------------------------------*
> Dr. Markus Schmidt
> International Dialogue and Conflict Management
> Abt-Karlg. 19/21, 1180 Vienna, Austria
> phone: +43(0)19900811
> mobile: +43 660 6856623
> www.idialog.eu
> email: markus.schmidt at idialog.eu
> *-----------------------------------------------------------*
>
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