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

[Reshma Shetty]

Hey all,

A few (hopefully) clarifying comments ...

On Tue, May 20, 2008 at 11:24 AM, Deepak Chandran
<deepakc at u.washington.edu> wrote:
> A question concerning PoPS devices: do they truly resolve the cross-talk
> problem?

No.

Three inverters of the same kind would interfere with one
> another, so what aspect of this particular issue does it solve? My
> understanding was that PoPS is a way of establishing compatible
> input/output relationships.

Using PoPS as a common signal carrier resolves (in part) the issue of
designing and building *composable* transcription-based devices.  The
PoPS signal stanadard allows devices that either produce or receive a
PoPS signal to be combined with other devices that produce or receive
a PoPS signal.  (If devices are defined to produce or receive proteins
instead, then most devices will not be composable.  See the comic for
details.) By establishing a common signal carrier for
transcription-based devices, we can move on to the next problem of
ensuring that signal levels between devices are actually matched ...
which is a whole topic in itself.  :)

If there was a PoPS device that does not use
> any protein to achieve its function, then it would evade the crosstalk
> problem; but is it possible to build a genetic network that has no
> proteins (setting aside RNA-based transcription factors)?

The crosstalk problem exists whenever you rely on molecular
specificity in your device or system.  DNA, RNA, and protein-based
devices could all have potential crosstalk issues.  Though, DNA- and
RNA-only based devices are generally more amenable to rational design
to avoid crosstalk.

Just my two cents.

Thanks,

Reshma