Tooling in the regulatory space of biology allows one to subtlety alter the mass transfer within existing networks - which can be harder to figure out, but often allows a delicate touch to cause a strong effect. And, especially, if you want to work in non-mammalian systems, I suspect you can actually start to build otherwise orthogonal networks.
At Serotiny we are playing with designing proteins and synthetic receptors whole cloth - which, though it can generate entirely new functionality, also brings with it all the challenges of dropping an invented capability into an existing system. You can be very creative, but integrating that creativity can itself become a challenge downstream.
Honestly, I think they are complementary approaches, and in the end, I suspect many of these approaches will ultimately converge (again, see 'life'). But we require expertise in each area first.
http://www.wired.co.uk/article/at-home-with-the-dna-hackers
As a cell biologist turned programmer, i am certainly interested to see if anyone can make something really work in this domain.
But also a bit frustrated that people are focusing on genetic circuits, which are slow and boring compared to protein-based signalling networks!