Fwd: query from PBS NewsHour

[Bryan Bishop]

From: Lee Koromvokis <lkoro...@newshour.org>

Date: Fri, Mar 30, 2012 at 3:44 PM
Subject: [diybio-boston] query from PBS NewsHour
To: "diybio...@googlegroups.com" <diybio...@googlegroups.com>

Hello,

I am a producer for the PBS NewsHour.  Correspondent Paul Solman and I are looking to interview a group of bio hackers--and also hopefully see some bio hacking!--for a story we are doing about the potential benefits and risks of synthetic biology. (Actually, it is part of a larger story about all the scientific and technological breakthroughs that could happen sooner than most people realize because of Moore's Law and DIY innovators). Anyone interested?

Lee Koromvokis | Producer, PBS NewsHour 

T 914.241.6220 | M 914.282.1498

LKoro...@newshour.org

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[Jason Bobe]

Mac and I did a PBS Newshour interview back in 2008:

http://www.pbs.org/newshour/bb/science/july-dec08/diybio_12-30.html

It was an odd interview that went something like this:

Interviewer: What is DIYbio?

Mac and Jason: We are people who want to roll-up our sleeves and do biology as a hobby, etc...

Interviewer: How is it regulated?

...Then 45 minute Q&A on safety.

The interview was over and I was like, "hey, you never asked us what we are working on?"  At the time, Mac was running sessions building DIY set-ups for DNA extraction from strawberries and running gels w/ 9V batteries.  I was working on swabbing crosswalk buttons to see what microbes lived there...

--

I'm afraid of feeding the hype machine that has been bult up around this, which seems like how this is being positioned.

I'd be curious to hear from the mailing list:

(1) Is anyone actually doing DIY work on synthetic biology?  What makes it DIY (e.g. taking place in a community lab)?  What makes it synbio (and not just biology or molecular biology)?

(2) So far, I think the community has shown tremendous innovative capacity around low-cost tools/devices like dremelfuge, gogo-fuge, open pcr.  It is unclear to me whether the community (or which parts of it) will be a fountain of innovation in synbio anytime soon.  

Thanks,

Jason

On Friday, March 30, 2012 2:09:05 PM UTC-7, Bryan Bishop wrote:

From: Lee Koromvokis <lkoro...@newshour.org>

Date: Fri, Mar 30, 2012 at 3:44 PM
Subject: [diybio-boston] query from PBS NewsHour
To: "diybio-boston@googlegroups.com" <diybio-boston@googlegroups.com>

Hello,

I am a producer for the PBS NewsHour.  Correspondent Paul Solman and I are looking to interview a group of bio hackers--and also hopefully see some bio hacking!--for a story we are doing about the potential benefits and risks of synthetic biology. (Actually, it is part of a larger story about all the scientific and technological breakthroughs that could happen sooner than most people realize because of Moore's Law and DIY innovators). Anyone interested?

Lee Koromvokis | Producer, PBS NewsHour 

T 914.241.6220 | M 914.282.1498

LKoro...@newshour.org

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[Nathan McCorkle]

On Fri, Mar 30, 2012 at 5:33 PM, Jason Bobe <jaso...@gmail.com> wrote:
> I'd be curious to hear from the mailing list:
>
> (1) Is anyone actually doing DIY work on synthetic biology?  What makes it
> DIY (e.g. taking place in a community lab)?  What makes it synbio (and not
> just biology or molecular biology)?
>
> (2) So far, I think the community has shown tremendous innovative capacity
> around low-cost tools/devices like dremelfuge, gogo-fuge, open pcr.  It is
> unclear to me whether the community (or which parts of it) will be a
> fountain of innovation in synbio anytime soon.

I'm concentrating on equipment for now, but I foresee within 2-5 years
having a proper system to whip out synBio organisms pretty fast...

--
Nathan McCorkle
Rochester Institute of Technology
College of Science, Biotechnology/Bioinformatics

[Avery louie]

I am working on synthetic bio at school, and I most of the molecular bio I have been doing DIY with others could (or will) soon be shifted in that direction.

--Avery

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[Joseph Jackson]

If the story is about DIY innovation in the context of the larger shifts happening in many fields including Open Hardware (Maker Bot, Arduino ecosystem, DIY Drones), then it could be worthwhile.  Yet another Synthetic Biology Hype or Hysteria piece....coming on top of Zimmer's NY Times thing and the Friends of The Earth petition to halt all "extreme genetic engineering" is not the framing that anybody needs.   

I was at SYNBERC this week and even the world's leading PI's are not churning out breakthroughs at a breakneck pace....it ain't gonna be happening in DIY groups anytime soon.  The mood was a bit somber actually...very concerned about what happens NSF funding runs out in 2016 and finding follow on $$ to continue building infrastructure for the emerging field.  Really, we are just barely seeing the fruits of next generation sequencing start to come on line.  12 years after the human genome project and the technology will probably hit the clinic/consumer in a big (economically/medically significant) way only in 2015....about a 15 year time lag.  A lot more citizen science and DIY projects could layer on top of the infrastructure that is coming online in this space.  

Synthetic Biology, if you date the "official" birth of the field to the creation of SYNBERC in 2006, is only 6 years into its existence.  Keasling is doing his best to lobby NSF for another 5 yrs post 2016....taking this out to 2021 when SYNBERC may have accomplished its mission to build a mature infrastructure to support the formation of industry around this.  DARPA is talking in terms of 2030s for their horizons....so about an 18 year time frame for the fruits of "Living Foundries."

With all the hype fest about SynBio, it is in danger of going the route of "Nanotech."  Remember at the turn of the century...1999-2000 when nanotech was going to change the whole economy and everyone was worried about grey goo.  We ended up with nano particle sunscreen....a mundane consumer product that is a fry cry from the idea of molecular manufacturing.  Science/Tech seems to go through these hype cycles (everyone familiar with the Gartner Hype Cycle  http://en.wikipedia.org/wiki/Hype_cycle)

We will eventually get to the promised land of synthetic biology, nanotech, etc etc but in the mean time, a lot of people need to take a damn chill pill.  Silicon Valley in particular, tends to get swept away and I see a certain amount of this in my neck of the woods *cough cough LOL.  Too bad we can't brew up said Chill Pill using synthetic biology.      

On Friday, 30 March 2012 14:09:05 UTC-7, Bryan Bishop wrote:

From: Lee Koromvokis <lkoro...@newshour.org>

Date: Fri, Mar 30, 2012 at 3:44 PM
Subject: [diybio-boston] query from PBS NewsHour
To: "diybio-boston@googlegroups.com" <diybio-boston@googlegroups.com>

Hello,

I am a producer for the PBS NewsHour.  Correspondent Paul Solman and I are looking to interview a group of bio hackers--and also hopefully see some bio hacking!--for a story we are doing about the potential benefits and risks of synthetic biology. (Actually, it is part of a larger story about all the scientific and technological breakthroughs that could happen sooner than most people realize because of Moore's Law and DIY innovators). Anyone interested?

Lee Koromvokis | Producer, PBS NewsHour 

T 914.241.6220 | M 914.282.1498

LKoro...@newshour.org

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[Nathan McCorkle]

On Sat, Mar 31, 2012 at 3:11 AM, Joseph Jackson <joseph....@gmail.com> wrote:
> We will eventually get to the promised land of synthetic biology, nanotech,
> etc etc but in the mean time, a lot of people need to take a damn chill
> pill.  

Thumbs Up to that.

[Jason Bobe]

On Mar 31, 2012 5:01 AM, "Nathan McCorkle" <nmz...@gmail.com> wrote:
>
> On Sat, Mar 31, 2012 at 3:11 AM, Joseph Jackson <joseph....@gmail.com> wrote:
> > We will eventually get to the promised land of synthetic biology, nanotech,
> > etc etc but in the mean time, a lot of people need to take a damn chill
> > pill.  
>
> Thumbs Up to that.

yes, well said.

Jason

>
> --
> Nathan McCorkle
> Rochester Institute of Technology
> College of Science, Biotechnology/Bioinformatics
>

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[Tom Randall]

(1) Is anyone actually doing DIY work on synthetic biology?  What makes it DIY (e.g. taking place in a community lab)?  What makes it synbio (and not just biology or molecular biology)?

Thanks,

Jason

I have a lab at home and will likely soon be doing something that loosely might be considered synbio, but only because I intend on ordering a sequence from one of the companies like Blue Heron.
Specifically the project is that I have a morphological mutant in my organism of interest, an ascomycete fungus Neurospora crassa. I am interested in determining the gene responsible for the phenotype of this mutation. It has been genetically mapped so I know within 20-40 kb where it is. I have in the past done Sanger sequencing on a candidate gene, which found no mutation in or around that particular gene so decided to simply get the whole genome sequenced. Hopefully then I can compare that sequence to reference and find a SNP/indel responsible. If that is possible, I intend to order a sequence of ~ 1 kb around this mutation, including the candidate mutant allele, and transform this into a strain with the wild type allele of this candidate gene in order to generate a replacement of the wt allele with the mutant allele by homologous recombination in order to re-create the original phenotype and thus confirm (or not) the genetic lesion that resulted in the original mutant allele. I have sent the DNA from this mutant strain to Operon, but only last week so the sequencing is still is in progress. I would say this is only loosely synbio because I am simply going to be using a synthetic construct as a convenient  tool in the context of what is really a molecular genetics/bioinformatics project.

[Dakota Hamill]

Entire genome sequenced?  That's pretty hardcore.

http://www.broadinstitute.org/annotation/genome/neurospora/MultiHome.html  says it's 41Mb.  

Wouldn't that cost tens of thousands of dollars to sequence?

[Cathal Garvey]

Synthetic forward genetics? Awesome! I heartily endorse such excellent and ambitious science! :)

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[Tom Randall]

$2500 for 1 lane of Illumina HiSeq which should provide the necessary coverage for a small genome like this; other companies I got quotes from were around $3500. It is a little over the top, but my day job is in bioinformatics analyzing other peoples data, so I also want my own data to play with since I know how to run the necessary programs and thus do not have to also pay for the analysis.

[Dakota Hamill]

That's really cool Tom, some serious dedication there!  

I found a website last week that seemed to be pretty big on neurospora, so you might find it useful if you havn't already seen it.

www.fgsc.net  the fungal genetics stock center

in particular they have a list of Neurospora deposits if you check over on the left hand side 

http://www.fgsc.net/scripts/catalogDetails.asp?CatNum=1001

and then again, some gene libraries of N. crassa

http://www.fgsc.net/craslib.html

Good luck on your project keep us filled in

[Tom Randall]

Yes, that is where I get most of my strains from.
Thanks

[Jason Bobe]

On Sunday, April 1, 2012 3:36:42 PM UTC-7, Tom Randall wrote:

$2500 for 1 lane of Illumina HiSeq which should provide the necessary coverage for a small genome like this; other companies I got quotes from were around $3500. It is a little over the top, but my day job is in bioinformatics analyzing other peoples data, so I also want my own data to play with since I know how to run the necessary programs and thus do not have to also pay for the analysis.

The term "synthetic biology" gets thrown around a lot and it is not always clear what people mean when they use it.  As you say, many common molecular biology projects involve DNA synthesis.  Some of the DNA sequencing projects I've worked on require custom barcoded primer sets, which must be synthesized (i.e., typically ordered from a vendor).  Although I would not say that multiplex DNA sequencing using barcoded primers = synbio!

Your project sounds cool.  Sounds like you may just push it ahead by paying out-of-pocket, but two ideas....I have heard of one person working w/ LA biohackers applying to BGI and receiving free DNA sequencing for an extremophile genome, but I think this was a circumstance where it was a previously unsequenced organism.  Have you thought about putting your project up on PetriDish.org?  $2500 seems like an achievable #, especially if there is a compelling story behind this mutant fungus.  What is the backstory?  Why is this fungus variant interesting?

Jason

   

[helicase]

Plus another $400 or so for library synthesis, right?

[Tom Randall]

That is included.

[Tom Randall]

Your project sounds cool.  Sounds like you may just push it ahead by paying out-of-pocket, but two ideas....I have heard of one person working w/ LA biohackers applying to BGI and receiving free DNA sequencing for an extremophile genome, but I think this was a circumstance where it was a previously unsequenced organism.  Have you thought about putting your project up on PetriDish.org?  $2500 seems like an achievable #, especially if there is a compelling story behind this mutant fungus.  What is the backstory?  Why is this fungus variant interesting?

Jason

   

Thanks for the ideas. Unfortunately there is really no compelling story aside from old fashioned biocuriosity. I had used this strain (name of the gene is col-4) in some genetics projects years ago and had the hypothesis that it might be an allele of a sequenced gene called pph-1 that mapped to this spot. Likely not the case based on sequencing I have already done, but now I want to know what it is. It is also a good shakedown for my lab. All the equipment/techniques work and I want to put them together into a project that might be publishable before I go onto more potentially interesting projects I am thinking of.

[Tom Randall]

An update on my sequencing project, has turned out nicely so far.

http://www.roningenetics.org/Sequencing.html

 

[Jason Bobe]

Kudos to the online lab notebook and protocols.  Really great to see your home lab via the video on the homepage!  It sounds like you've been piecing it together since 2005.  What is your most coveted piece of equipment? 

It would be great to see pics/videos of other home labs that exist out there. 

Jason

[Tom Randall]

 

Kudos to the online lab notebook and protocols.  Really great to see your home lab via the video on the homepage!  It sounds like you've been piecing it together since 2005.  What is your most coveted piece of equipment? 

It would be great to see pics/videos of other home labs that exist out there. 

Jason

Sorry for the late reply. I think the most valuable piece of equipment is the G76 New Brunswick Shaker (I have three). Not only are they necessary for growing E .coli/S. cerevesiae for transformation and plasmid preps but as I also brew beer, I use if for growing up the yeast stocks I have for that. Also, there are other non-science uses, a shaker is perfect for making butter (see the last protocol here: http://www.roningenetics.org/Protocols.html) and for making cheese where you basically need a big water bath and a G76 offers good temperature control in the range of 30-40C.
Tom