[100ideas]

75% success rate for systems with this complexity (>10 elements) is probably just as good if not better than what would be expected by designing “by hand,” and the latter approach does not scale past the current order of magnitude (to 100+ component designs). I think that’s their main argument.

[jamessb]

A major problem with further scale-up is the availability of parts. In an electrical circuit the signals voltages that are constrained to wires; in a a genetic circuit the signals are concentrations of proteins/compounds that are diffusing around the cell. This gives a problem: to have independent logic gates you need transcription factors that will bind to distinct promoter sequences, without crosstalk. If you're doing this in a cell rather than cell-free system you also need to avoid crosstalk with the host cell.

The problem isn't so much in designing the circuit abstractly as finding specific parts with which to construct it. One approach is to partition the circuit across multiple cells [0, 1].

[0]: http://www.nature.com/nature/journal/v469/n7329/full/nature0...

[1]: http://journals.plos.org/ploscompbiol/article?id=10.1371/jou...

[100ideas]

Eukaryotic cells solve the "crosstalk problem" by building the control regions that regulate gene expression out of modular, hierarchically-organized binding sites for multiple transcription factors (TFs).

In prokaryotic systems there is (in a very approximate, generic sense) a one-to-one correspondence between the concentration of a particular transcription factor and the expression (or repression) of the genes downstream of the binding site for that transcription factor.

The control regions in eukaryotic genomes have binding sites for multiple transcription factors, combinations of which may become binding sites for other transcription factors (larger TFs which bind to certain combinations of smaller TFs), etc.

In this way, the specific sequence of TF binding domains in the regulatory region of a eukaryotic gene provides a particular and potentially unique "address" in "Transcription Factor State Space" by which the gene can be controlled.

For more information on this amazing topic, check out "The Regulatory Genome" by Eric H. Davidson. Here is an excerpt from the first page of chapter 4:

"Whatever their extent, however, development gene regulatory networks have an internal structure, in that they are composed of diverse kinds of modular parts and connections among these parts. Here 'modular' takes on a simple functional meaning: it is used to denote small subsets of genes within the overall network that together execute given 'jobs,' e.g., to operate a certain differentiation gene battery, or to transduce an extracellular signal into a certain regulatory state.

In what follows, sets of regulatory genes that execute modular functions are usually referred to as constituting 'subcircuits' of the network, because as we shall shortly see they are 'wired together' within the subcircuit by their gene regulatory interactions. Just as the target site inputs of an individual cis-regulatory [note: cis- prefix in this context indicates gene regulation via non-expressed sequences of DNA proximal to a gene in the genome] module are integrated to generate novel outputs according to its genomic design, so the outputs of these subcircuits are integrated to generate logic outputs which depend on their organization, that is, their wiring architecture."

- https://books.google.com/books?id=F2ibJj1LHGEC&pg=PA126

[edit 1: added link to google books & excerpt]