Re: [DIYbio] Where do i start? (learning about synbio)

Hi Axel,

The core of synthetic biology at its highest level are bio bricks: http://biobricks.org/

The greatest amount of innovation in the history of mankind is happening at igem: http://igem.org/Main_Page

Beg, borrow, steal to be involved in these competitions!  You will get a 200,000 biology education for free.  You will not be able to fathom how backward/simple non-syn bio actually is in your wildest imagination.  My advice to you is not to interact with these people as they hate syn bio as it is about 1000% more complex then anything they could possibly begin to understand and they hate it!!!!!!!!  Everything in biology is political at this moment.  Its all about patents, tenure, and amazing amounts of non-tenure enslavement.  When you speak to a phd in biology etc... they are going to try to turn you into their little slave.  

Understand that the major issue with syn bio at the moment is stability.  The bio bricks are just not stable as of yet.  Drew Endy claims to have refined the usage of bio bricks to get 90% stability.  My hunch is he is using a compartment in a cell to isolate the bio brick expression which was discovered at an igem competition.  

My advice to you is to do the following:

1.  Repeat every igem experiment that has ever been done (if not in the lab, via software using bio python and a simulator like clotho)

2.  Realize that understanding the lab stuff isn't really that important.  What is important is understanding that your dealing with proteins.  Most everything in a cell is about handling, generating, and communicating via proteins.  If you find that a particular protein is novel, create a gene for it then have an external lab like http://www.blueheronbio.com/About/HowToOrder.aspx create an ecoli cell of it and mail it to you

3.  Learn and play the protein folding game: http://fold.it/portal/

Understand the real problems of synthetic biology:

1.  There is no easy, quick, cheap way to determine a proteins shape (the only way is xray crystal lithography, its like rubbing two rocks together to get a radio signal)  Don't let anyone tell you that protein shape doesn't matter, they are lying or stupid!!!!!!!!!!!

2.  There are no high quality standardized software simulator/development tools for doing synbio (for example in electrical engineering there is spice etc...)  There are snippets of code and a mismash of tools etc...  Its all little tricks that nobody wants to share, you can find them if you look though :>

3.  There are no formal courses on syn bio that are very good, its just too new and so radically advanced most biology professors just mess up the whole presentation of its cutting edge science

If you want my humble advice, get computer science engineers to help you understand synthetic biology.  They cut through the garbage and get right to the important stuff.  In my non-humble opinion synthetic biology is just a new way of computation and we are recreating computers via cells.  Computer engineers already know how to do this with silicon, just need to redo it via cells.  It is my belief that synthetic biology is a sub domain of computer science.  Don't ever tell a biologist this, they are terrified that this could be and is true and will hurt you and your family.

-Tim

P.S.

If you want to help me I have created a backward chaining rules engine to assist in creating expert systems here:

https://github.com/wheath/jsrule-engine

I want to make expert systems that help non-synbio people to learn and use synthetic biology concepts/tools.

On Tue, Jul 9, 2013 at 1:38 AM, Axel Krantz <axel....@gmail.com> wrote:

I'm interested in learning to work with synthethic biology as it seems to be a thing of the future. But i am uncertain of what i should start studying to get going. Any ideas of websites, university courses, litterature etc?

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