I’ve been reading about iGEM and the Registry of Standard Biological Parts. It’s a component view of biology – that there are parts in biology that can be used much like electronic parts.
Eh, I know they don’t think it’s that simple, but it sure can be misleading what they are trying to do.
These folks are characterizing biological parts and creating a catalogue from which to plug and play and mix and match to create circuits that do something. They are looking to establish standards, construction tools, and some abstraction to make it easier to build synthetic systems. And that’s all fine and good. It’s like the early days of electronics. And they have done some amazing things, light replicating photography with bacteria, some cool circuits, and more.
But, in my biomedical-scientist eyes, I just wished they would think more than just creating digital circuits on analogue systems. Also, I feel that biology doesn’t gate well, I mean, it’s very non-linear and hard to do on-off ‘mathematics’ with biological components. And by trying to build digital stuff, they lose the value of analogue.
In short, I think the questions they are asking are not the right ones for the system.
And thinking back to Craig Venter, moving forward, synthetic biologists are going to have to think of analogue, of biological answers to questions. We are so accustomed to neat and clean binary fixes to things, but seem to forget that in biology, so much is probability, fuzziness, and selection, and failure is so much more nuanced.
I’ve designed many macromolecules and expression systems, grew all sorts of micro and macro organisms, and dealt with all sorts of biological systems. In so many ways, we were not far from the brewers of Mesopotamia, coaxing and praying for a healthy growth and production of the right enzymes.
Yet, we have had in the past 30 years, and even more so in the past 5, a deeper understanding of the mechanisms. But, we mustn’t just translate that all into our digital minds, we need to think of these organisms and molecules on their terms.
When I was a grad student, my advisor was a physical chemist doing biochemistry. To him, DNA wasn’t just A T C and G, but a chemical entity. I came out of there seeing proteins and DNA in a way that my molecular biologist colleagues did not, and a deeper understanding of the complex interactions in biological systems.
In the same way, synthetic biology is going to have to go beyond linear circuit building, but take advantage of the strength of these marvelous billion-year evolved systems.
Here’s a video of Drew Endy, a leader in this field, putting synthetic biology in perspective:
BONUS: If you really get a kick out of visualizations, the Machinery of Life, by David Goodsell, is a really neat peek into the molecular world at the scale of proteins and bacteria.
