tsbatth

I think what he meant was that current field of synthetic biology (not all) is focused around putting in synthetic pathways in Yeast, E coli or other organisms which have been studied intensely for the purpose of producing commodity chemicals and other novel functions; which is true.. E coli and yeast are really popular because of their fast growth rate, their ability to switch to fermentation, and the availability of standardized parts. The problems occur when you introduce hetrologous proteins and enzymes in these bugs so you have to do a lot of trouble shooting and tweaking to overcome toxic effects of intermediates, low production of a certain intermediate, protein production or transcription problems blah blah it goes on and on. And the longer and more complex the pathway the longer it takes, you also need to have a high enough titers of the product to be feasible so you have to study the organism a lot before you can really get something going.

Discovering useful enzymes is also a highly complex task as you're taking organisms from a microbial community which first needs to have its metagenome sequenced before you can even begin to find what you're looking for, and after you have that its not easy as it sounds. You need to develop some sort of high throughput assay targeting the compound and protein you're looking for, which can vary depending on what it is.

The natural selection procedure wont work in the real world because there are wayyyyyyy too many unaccounted variables for which you have to select before you can even begin to think of something that will translate in a vast ocean filled with diverse life, microbes, chemicals, solvent conditions etc... etc... Another factor is that you cant select few bugs that will metabolize the infinitely (exaggeration) complex and diverse set of different chemicals in a typical oil spill, I guess you could somehow select for a microbial community that might do this but also highly unlikely. You need the microbial diversity of the vast ocean floor to begin to degrade down those chemicals, and that also takes some years. That solution can't be recreated in a minimal media agar plate. You could however select for bugs which can break down specific chemicals or survive under very specific conditions.

I haven't read the paper yet, but did you use a MAGE like platform to insert in DNA at bit by bit into a BAC?

It works if you're selecting for a specific variable, or even a set of variables and environmental conditions. But for something such as cleaning up an oil spill in the ocean, well lets just say that most lab strains of E coli are a bunch of pussies in a world of big mean creatures which have adapted to their environment since forever.