Now I need to do something practically!

[Ujjwal Thaakar]

I got interested in Synthetic Biology about a month back since then have been trying to relearn the biology I forgot. Now I can say I have a basic idea about genetics and I'd quickly like to do something practical. What are the options that I have. What all do I need to set up my own little biospace and ensure safety

Please be as detailed as possible about the various techniques and procedures.

[Nathan McCorkle]

Are you near the sea where you can get fresh seafood? If so you can
try to isolate a glowing culture.

Do you know any professors who do molecular biology work? Talking to
them would be a good way to find people with extra resources and lab
space maybe! It's common to trade organisms and plasmids (DNA) in the
field... you just gotta ask and hope that the other person is kind
enough!

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--
-Nathan

[Nathan McCorkle]

also there's the simple DNA extraction from fruits

On Sun, Mar 3, 2013 at 1:26 AM, Ujjwal Thaakar <ujjwal...@gmail.com> wrote:

[Dakota Hamill]

Assess the situation.

Figure out what you want to do. 

Ask yourself, what do I want to accomplish?

 Do you want to do this as a hobby on the side maybe once a weekend?  Do you want to make this your lifelong obsession and start a company someday based around your research?  Do you want a job in a lab? What is your end goal?

Plenty of people have hobbies, and plenty of people have obsessions, sometimes the two go hand in hand.

My friend who flies model airplanes does it as a hobby, it is not his career.

I do science every waking hour of my day, it is both a hobby and an obsession and a way of life.

The answers to those questions will help decide what you actually need.  If you want to do a strawberry DNA extraction you need soap, table salt, and rubbing alcohol amounting to maybe $1.00.  If you want to do a bacterial transformation, perhaps $50.  If you want to change the world...however much stuff costs on ebay!

There are thousands of .pdfs and youtube videos a google away relating to all sorts of basic lab techniques and experiments, so I don't know how many people will hold your hand here for something that has been asked 1000 times and write out a step by step.  If, on the other hand, you want to do extreme cutting edge science, well then, get to the drawing board and start dreaming up fantastical ideas, then get to the lab bench and put them into practice!

If you ask specific questions you will probably get specific answers, and lots of people on here are very excited to help and share knowledge.  

The best advice I can give you is to just do it.  Just get in the lab, even if it is your kitchen, and do real hands on experiments.  After years in school and in the lab, I think I might draw the conversion rate at about:

 1,000 lecture/reading hours = 1 hour in the lab

Hands on experience will trump only reading every single time, in the sciences and in every other trade, but combine the two and you can be a great force of change!

Would you hire someone who read about putting nails into wood  for 10 years in books, or someone who was a carpenter's apprentice for one summer?  

So, perhaps elaborate on what it is you want to do and maybe we can offer more specific advice.

 

[Nathan McCorkle]

On Sun, Mar 3, 2013 at 6:42 PM, Dakota Hamill <dko...@gmail.com> wrote:
> 1,000 lecture/reading hours = 1 hour in the lab
>

I've heard the opposite too though, 1 hour in the journal section is
worth 10 in the lab, etc... I think it depends on the scale and scope
of a project/goal, actually.

> Hands on experience will trump only reading every single time, in the
> sciences and in every other trade, but combine the two and you can be a
> great force of change!
>
> Would you hire someone who read about putting nails into wood for 10 years
> in books, or someone who was a carpenter's apprentice for one summer?

For instance, I might be more inclined to ask the bookworm for advice
on building a sky scraper from the ground up over a 1 summer
contractor's intern.


--
-Nathan

[Dakota Hamill]

I'm not saying planning doesn't help.  I'm saying at some point you just have to try shit out yourself and not rely on what someone else said to do.  Even if you fail a hundred times, you learn a lot from the experience, whereas if you just read of others success's and failures, you don't live them yourself and don't learn what caused them to begin with.  Also, I'd still hire the kid who poured concrete, layed steel, and welded rebar over the person who just read about how to do it.  There are a lot of tricks of the trade in every profession that you can't learn from a book.

[Mega]

I know I post this everytime :D 

But it shows well how easy genetic engineering can be, and that you can set up a lab in your basement (if legal) 

[Ujjwal Thaakar]

Eventually yes I'd like to do cutting edge stuff and start a company but right now I'm only a month old in this field and kinda clueless. I truly believe in that practical work is more important than reading - more important but you need both. I just need some guidelines about where to start practically. Working on fruits sounds safe. I have access to a pharmacy lab in my university at what level do I start? Any good references?

[Ujjwal Thaakar]

I don't think there is anyone doing much serious work here but I'll search more. I just have to itch to do something with my own hands so what's the most basic and easy thing I can start with. Right now am aiming amateur stuff and then slowly go on to serious cutting edge stuff.

[Eugen Leitl]

On Mon, Mar 04, 2013 at 04:21:15AM -0800, Ujjwal Thaakar wrote:

> I don't think there is anyone doing much serious work here but I'll search

How would you define serious work?

[Ujjwal Thaakar]

As in as far as I know no there is no one involved in synthetic biology. I'm not too sure so I'll find out.

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Thanks
Ujjwal

[Eugen Leitl]

On Tue, Mar 05, 2013 at 01:22:40AM +0530, Ujjwal Thaakar wrote:
> As in as far as I know no there is no one involved in synthetic biology.
> I'm not too sure so I'll find out.

Oh, you're just looking into synthbio way of doing things.
That is admittedly Big Science, and out of budget even
for most advanced amateur, or small-pocket professional.

[Patrik D'haeseleer]

On Monday, March 4, 2013 1:41:14 PM UTC-8, eleitl wrote:

Oh, you're just looking into synthbio way of doing things.
That is admittedly Big Science, and out of budget even
for most advanced amateur, or small-pocket professional.

Note true. Basic genetic engineering experiments like inserting green fluorescent protein are fairly easy for a careful amateur, and can be done using cheap educational kits. And every year, hundreds of undergraduates and high schoolers are doing very creative synthetic biology projects as part of the  IGEM competition.

Where it gets more expensive is when you start synthesizing your own genes from scratch. But there's an awful lot you can do with preexisting genetic parts.

[Mega]

Well, saynthetic biology is still a quite expensive buisness...

Unfortunately.

 

You'll need at very least 2000-3000 Dollars to print out something useful.... Which then has the possibility of not working at all...

[Eugen Leitl]

On Tue, Mar 05, 2013 at 12:53:57AM -0800, Patrik D'haeseleer wrote:
> On Monday, March 4, 2013 1:41:14 PM UTC-8, eleitl wrote:
> >
> > Oh, you're just looking into synthbio way of doing things.
> > That is admittedly Big Science, and out of budget even
> > for most advanced amateur, or small-pocket professional.
> >
>
> Note true. Basic genetic engineering experiments like inserting green
> fluorescent protein are fairly easy for a careful amateur, and can be done
> using cheap educational kits. And every year, hundreds of undergraduates
> and high schoolers are doing very creative synthetic biology projects as
> part of the IGEM competition.

GM is not synbio.

> Where it gets more expensive is when you start synthesizing your own genes
> from scratch. But there's an awful lot you can do with preexisting genetic

Which is precisely what synthetic biology is.

> parts.

[Nathan McCorkle]

On Tue, Mar 5, 2013 at 12:53 AM, Patrik D'haeseleer <pat...@gmail.com> wrote:
> On Monday, March 4, 2013 1:41:14 PM UTC-8, eleitl wrote:
>>
>> Oh, you're just looking into synthbio way of doing things.
>> That is admittedly Big Science, and out of budget even
>> for most advanced amateur, or small-pocket professional.
>
>
> Note true. Basic genetic engineering experiments like inserting green
> fluorescent protein are fairly easy for a careful amateur, and can be done
> using cheap educational kits.

Wouldn't you just call that cloning, rather than synBio?

And every year, hundreds of undergraduates and
> high schoolers are doing very creative synthetic biology projects as part of
> the IGEM competition.

iGem is almost 'amateur' except that the school or some company forks
over a few thousand $ for student stipends and reagent cost.
Technically hasn't iGem barred non-academic amateurs?

> Where it gets more expensive is when you start synthesizing your own genes
> from scratch. But there's an awful lot you can do with preexisting genetic
> parts.

If the parts already exist, again, wouldn't this technically be
cloning, not synBio?

--
-Nathan

[Patrik D'haeseleer]

On Tuesday, March 5, 2013 9:26:21 AM UTC-8, Nathan McCorkle wrote:

> Note true. Basic genetic engineering experiments like inserting green
> fluorescent protein are fairly easy for a careful amateur, and can be done
> using cheap educational kits.

Wouldn't you just call that cloning, rather than synBio?

Just like writing a "Hello World" program could be called "editing" rather than "software engineering"? I'd say cloning is one of the tools to learn to do synthetic biology. Now, put a different promoter in front of that GFP gene, few people will complain about calling that synthetic biology...

And every year, hundreds of undergraduates and
> high schoolers are doing very creative synthetic biology projects as part of
> the  IGEM competition.

iGem is almost 'amateur' except that the school or some company forks
over a few thousand $ for student stipends and reagent cost.
Technically hasn't iGem barred non-academic amateurs?

Most of the cost of running an IGEM team typically goes towards student stipends. See this calculation from 2008, for example. IGEM teams also receive hundreds of parts from previous year's competitions on a couple of 384 well plates, and there's enough parts there that teams can do incredibly interesting projects without doing any additional gene synthesis.

Getting access to those IGEM biobrick distribution plates as an unaffiliated amateur may be tricky, but you may be able to get some parts from a friend at a university. After all, IGEM has been sending out hundreds of these kits all over the world now. You can also get some reasonably priced plasmids from Addgene or other sources (again - may need to order through a friend at a university) and reengineer those to do something different. You can also clone genes directly out of the original organisms (e.g. Lux operon out of Vibrio), and do interesting things with those. All those options can be significantly cheaper than synthesizing genes from scratch.

Of course, there are definitely some synthetic biology projects that fall into the Big Science category, like re-engineering entire genomes like Craig Venter is doing. But there's plenty of smaller scale synthetic biology projects that are most definitely within range of "advanced amateur, or small-pocket professional".
 

> Where it gets more expensive is when you start synthesizing your own genes
> from scratch. But there's an awful lot you can do with preexisting genetic
> parts.

If the parts already exist, again, wouldn't this technically be
cloning, not synBio?

Not when you're designing and implementing a novel genetic circuit from existing parts. Or doing combinatorial assembly of pathways from libraries of existing parts, like Amyris and JBEI are doing. Of course, "synthetic biology" is still a fairly new field, and some people will disagree on where the boundaries of the definition lie (or how to distinguish it from genetic engineering, which is another can of worms). For example, the whole purpose of the BioBricks foundation is to come up with a collection of well characterized, low side-effect parts that then can be reused in arbitrarily new combinations. If BioBricks are the equivalent of lego blocks then, to me, synthetic biology is much more about how to build something cool with legos, rather than how to make your own lego blocks from scratch.
 
Patrik