Synthetic Biology: Parts Registry
MIT hosts a database of “Standard Biological Parts.” The idea is that a Synthetic Biologist can pick and choose these “biobricks,” and assemble a biological machine in the black box style of engineering. Now normally I just complain about the science or new technology featured. This is clearly a work in progress and I will do my best to suspend judgement. They readily admit that this system will be replaced with better paradigms. Here are my thoughts.
I’m doing my best to decipher this biobricks parts registry. I recognize a lot of the names, but their descriptions are are incomplete or less than accurate. Also, with extensive research done on every gene in here and a century of foundation science, why would they make up a whole new lexicon of descriptive terms? Perhaps they want to break from the old, but at the same time they separate the designer from the complexity of the components. An unfortunate side effect is that this obscures the nature of the components. Somtimes it is hard to figure out whether the componet is functioning on the DNA, RNA or protein level. They need to go a lttle deeper before I would use it.
In my own work I keep all of my components such as tags and reporters in a databse that includes their sequences and restriction sites. When I need something I have the all of the data right there. Yes it does get confusing sometimes. I have repeatedly introduced frame shifts or cut out an IRES between bicistronic genes. But the reason for that is my components are not refined yet either. (And I am dyslexic)
Granted, there are some interesting creations made using biobricks, I respect their efforts and hope to contribute to the Synthetic Bio community. However, biobricks seem on par with a scripting language. This is great for doing basic things and maybe that is all we can do with our current understanding. A more fundamental method of design will come however and with it we will accomplish so much more.