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

[James Lawson]

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!
>>
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>>     
>
>
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