Help needed: BBC Documentary in need of guidance

[Sam Francis]

Hi all,

The other night I attended the biohacking lab at the London hackspace and a few of you recommended I put my requests to the collective hivemind on here.

I'm a producer for a BBC Radio 4 Specials in the UK and we're doing a documentary on synthetic biology for our Futureproofing series (http://www.bbc.co.uk/programmes/b04hyy1p). To help give a good idea the ease and the limitations of doing synthetic biology with DIY lab equipment we want to get our two reporters to begin the show with an experiment, which we will then use as a strand to tie the whole story together.

As such could any of you suggest an experiment that shows off the potential of the technology that two journalists un-trained in biology and largely ignorant could do with minimum supervision?

We have a few requirements:

1. the ideal would be something that works on radio - perhaps bacteria that produces a gas/bubbles that we could then record popping, or produces radiation that can then be picked up on a Geiger counter, which we can in turn record beeping and whatnot - though this is not vital
2. we must be able to start and complete the experiment in two weeks
3. the experiment can be carried out using only basic kit or the equipment at the London hackspace (https://wiki.london.hackspace.org.uk/view/Group:Biohacking )
4. it must be interesting enough to capture the imagination of the outside world

Any ideas, musings or suggestions would be greatly appreciated.

Best wishes,

Sam

[Ilya Levantis]

I came across this post on the biofaction website: http://www.biofaction.com/synth-ethic/?p=44

Might be worth getting in touch with Joe Davis - does anyone here have his details?

[Jonathan Cline]

Do Genomikon kit for sure.  Synbio engineer new bacteria in a short afternoon.  Make them glow.    The best journalism mentions references explicitly so please make sure to do that. 

Also read the diybio faq, http://openwetware.org/wiki/DIYbio/FAQ
 


"Produces radiation" um, what.  FFS..   Note you will never get bubbling because the yields on anything a bacteria makes will be so low, that if one tiny visible bubble forms per hour, you'd be lucky.

Curiously.. the most publicly fascinating and most photographed and most filmed "experiment" of a local & highly celebrated diybio lab here in the biotech center of the world (right down the street from Life Technologies) was made when I brought in an aquarium pump bubbler and stuck the air-producing end into a big beaker of water.  Then I added food coloring to make the water green and put it near a tube rack.  The journalists loved it.  WOW!   A bubbling experiment in a biotech lab!   Filmed for the evening news!   (I'm not kidding.)  I didn't have the heart to tell them it was just water with a cheap $12 Walmart aquarium pump --- then likely they would not have cared because they just wanted sexy, emotionally-jarring images for the masses.  They had little interest in the real bacto-culture experiment growing just a table away, or the custom electronics with column filtration setup next to that.  Not photogenic enough for them I suppose.    I believe one of the biggest limitations of DIY biology is primarily the lack of education of... certain people.. people like..  hmm... let's see.. who might I be thinking of..  guess..


So regarding the radio listening audience.  Any audio will only come from the equipment you use.  Probably motor sounds from the vortexer and centrifuge and microwave oven.   Maybe the fluorescent tubes in the UV illuminator will buzz softly.   If they have a fridge, then of course that fan will make a nice hum.   Now you could make a custom electronics hack, like connect a light-sensitive resistor or photodiode to an opamp and get it to produce a sine wave depending on how bright the bacteria is glowing *but no one does that in science, that is just a gimmick for impressing poseurs* --- however you could build the circuit in an afternoon using my data acquisition article in BioCoder Issue #6 (I mention this not as a plug, only what comes to mind as a basic reference circuit which a biohacker group should be able to build up in a few hours).

You could also try using a spikerbox, with one of the spikerbox example experiments.  That makes a loud click or squeal from it's speaker when the neuron fires in a poor little insect which you've penetrated by a needle probe.  You might like that part (journalists love to vivisect don't they?).  The spikerbox is actually used in science.   A group can build the spikerbox from a simple kit in an afternoon.   Supply your own crickets.  https://backyardbrains.com/products/spikerbox


## Jonathan Cline
## jcl...@ieee.org
## Mobile: +1-805-617-0223
########################

On Wednesday, April 29, 2015 at 5:16:57 AM UTC-7, Sam Francis wrote:

Hi all,

The other night I attended the biohacking lab at the London hackspace and a few of you recommended I put my requests to the collective hivemind on here.

I'm a producer for a BBC Radio 4 Specials in the UK and we're doing a documentary on synthetic biology for our Futureproofing series (http://www.bbc.co.uk/programmes/b04hyy1p). To help give a good idea the ease and the limitations of doing synthetic biology with DIY lab equipment we want to get our two reporters to begin the show with an experiment, which we will then use as a strand to tie the whole story together.

As such could any of you suggest an experiment that shows off the potential of the technology that two journalists un-trained in biology and largely ignorant could do with minimum supervision?

We have a few requirements:

1. the ideal would be something that works on radio
   

1. we must be able to start and complete the experiment in two weeks
2. the experiment can be carried out using only basic kit or the equipment at the London hackspace (https://wiki.london.hackspace.org.uk/view/Group:Biohacking )
3. it must be interesting enough to capture the imagination of the outside world

[Cathal Garvey]

Hi Sam,

Bubbly-audibles are doable, but not without some slight of hand. For
example, yeast will carbonate the water where you grow it if you keep it
under pressure, that's how you get a head on beer or bubbles in
traditional ginger ales. If you get the formulation right (ask a
chemist, not I!) you can probably select for larger bubbles, and I
imagine surface tension plays a role in the noise of the emerging
bubbles (but you'll still need a good mic!).

Radiation is *easy*, but only in the visual spectrum. You're not going
to get any radiation of high enough energy to make a geiger counter
click! Although I can imagine a few far-future possibilities, it doesn't
look physically possible with what we now know/have to make
higher-than-'indigo' light with Synbio. However, (again with the slight
of hand), a geiger counter is really just a luminometer for
high-frequency light (X-Rays/Gamma-Rays), right? So make a low-frequency
one; use a photodiode and a dark-box, and you could probably tune things
to give you a click-click-click style output like a geiger counter.

You'll note that, for flashy mediagenic stuff, both of my above
solutions are inorganic! Sorry. Synbio is better at producing cheap
medicines for global disease, for feeding us, for clothing us, for
changing the world in ways obvious or subtle, but it's not great at
producing audibly flashy stuff for radio. :)

On 29/04/15 13:01, Sam Francis wrote:
> Hi all,
>
> The other night I attended the biohacking lab at the London hackspace
> and a few of you recommended I put my requests to the collective
> hivemind on here.
>
> I'm a producer for a BBC Radio 4 Specials in the UK and we're doing a
> documentary on synthetic biology for our Futureproofing series
> (http://www.bbc.co.uk/programmes/b04hyy1p

> <http://www.bbc.co.uk/programmes/b04hyy1p>). To help give a good idea

> the ease and the limitations of doing synthetic biology with DIY lab
> equipment we want to get our two reporters to begin the show with an
> experiment, which we will then use as a strand to tie the whole story
> together.
>
> As such could any of you suggest an experiment that shows off the
> potential of the technology that two journalists un-trained in biology
> and largely ignorant could do with minimum supervision?
>
> We have a few requirements:
>

> 1. the ideal would be something that works on radio - perhaps bacteria

> that produces a gas/bubbles that we could then record popping,
> or produces radiation that can then be picked up on a Geiger
> counter, which we can in turn record beeping and whatnot - though
> this is not vital

> 2. we must be able to start and complete the experiment in two weeks
> 3. the experiment can be carried out using only basic kit or

> the equipment at the London hackspace
> (https://wiki.london.hackspace.org.uk/view/Group:Biohacking )

> 4. it must be interesting enough to capture the imagination of the

> outside world
>
> Any ideas, musings or suggestions would be greatly appreciated.
>
> Best wishes,
>
> Sam
>

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--
Scientific Director, IndieBio Irish Programme
Now running in Cork, Ireland May->July
Learn more at http://eu.indie.bio and follow along!
Twitter: @onetruecathal
Phone: +353876363185
miniLock: JjmYYngs7akLZUjkvFkuYdsZ3PyPHSZRBKNm6qTYKZfAM
peerio.com: cathalgarvey

[Nathan McCorkle]

On Wed, Apr 29, 2015 at 11:34 PM, Jonathan Cline <jnc...@gmail.com> wrote:
> So regarding the radio listening audience. Any audio will only come from
> the equipment you use.

Well you could poke a stick at a goat, or a puppy... they are biology
that would make audible gas and other noises. There was that blue/GFP
rabbit... though I don't think rabbits make much noise, and while the
bulk of the work could be done in 2 weeks... you'd need a while for it
to gestate.

Chicken embryos are pretty cool, you could easily isolate the heart
and get chunks/cells growing in culture within a day or two... but
you'd need quite the microphone to hear the beating (maybe a piezo
microphone would work if taped directly to the culture dish?)... or
some software to convert a video of the beating heart cells into audio
(I bet this actually wouldn't be too hard with some openCV in Python
or something). But I guess simply dissecting something isn't really
bioengineering.

Chicken embryo heart cells beating in culture
https://www.youtube.com/watch?v=M30-oInTKs4

Beating chick (chicken) embryo heart explant
https://www.youtube.com/watch?v=sJduWqtq-Ts


You could grow some yeast, trap the gas, then emit the gas through a
horn or harmonica... but again, simply growing something isn't really
bioengineering (at least in the media-popular mind).

[Pieter Waag]

Perhaps you could approach it the other way around, use sound to manipulate growth.

At last year's graduation show of the Royal Art Academy in The Hague Sebastian Frisch presented his Biophonic installation, containing roots of corn that grew towards a speaker.

http://www.codedmatters.nl/artist/sebastian-frisch/

Or take Matthijs Munnik's microscopic opera based on transgenic C. elegans made in collaboration with the Netherlands Consortium for Systems Biology: https://www.youtube.com/watch?v=TgumhLhfI6g

http://we-make-money-not-art.com/archives/2011/01/microscopic-opera.php

Also one of the participants in our biohack academy, Giacomo experimented with sound patterns.

[Jonathan Cline]

Dear World,

I am truly sorry that you find math and science so incredibly boring.   (Try evolving.)

## Jonathan Cline
## jcl...@ieee.org
## Mobile: +1-805-617-0223
########################

On 4/30/15 12:47 AM, Cathal Garvey wrote:

[Jeswin]

On Thu, Apr 30, 2015 at 4:02 PM, Jonathan Cline <jcl...@ieee.org> wrote:
> Dear World,
>
> I am truly sorry that you find math and science so incredibly boring. (Try
> evolving.)
>

I think they are looking for "sounds in biology" because it is a radio
production. I would think it is a show similar to NPR's Radio Lab, who
do pretty neat stuff with sound to get across their story.

[Sam Francis]

Hi Cathal,

Thanks for the suggestions. I'll look into these, but judging by the Luddites I work with I doubt we'll be able to fashion a luminometer as you've suggested. I appreciate the help though.

Thanks,

Sam

[Sam Francis]

HI Nathan,

Thanks for the advice. While poking a puppy with a stick might prove a point about biology I doubt we could get that past our health and safety compliance officer (what if the puppy attacked, what if the puppy looked sad and broke all our hearts etc etc).

I'll look into your chicken embryo idea. Have you worked on these kind of projects yourself? Is getting chicken embryo cells as simple as getting a fertilised egg or am I being too simplistic here?

Best Wishes,

Sam

[Sam Francis]

You are forgiven.

[Sam Francis]

Hi Pieter,

Thanks for these, although we could do this I fear it might detract from the focus of the documentary - which is all about the practical applications of synthetic biology and the ease with which people can now begin bio-engineering.

[Sam Francis]

HI Jonathan,

Thanks for this. I'll look into trying to put together some sort of light sensitive apparatus but doubt we'd have much of the equipment you suggested - a "photodiode" or an "opamp" - lying around the office. This may prove technically and financially unworkable.

I'm not sure where the "journalists love to vivisect" stereotype from but I'll suggest it to the reporters. I'm sure it's what we're really looking for.

I appreciate the suggestions though.

[Nathan McCorkle]

On Tue, May 5, 2015 at 10:44 AM, Sam Francis <sam.fra...@gmail.com> wrote:
> HI Nathan,
>
> Thanks for the advice. While poking a puppy with a stick might prove a point
> about biology I doubt we could get that past our health and safety
> compliance officer (what if the puppy attacked, what if the puppy looked sad
> and broke all our hearts etc etc).

Just throwing out ideas... wouldn't actually want a puppy to be poked
unless absolutely necessary :)

>
> I'll look into your chicken embryo idea. Have you worked on these kind of
> projects yourself?

Yep, first time was during a laboratory class, then I grabbed an extra
egg and did it again for a maker-club we had at school.

> Is getting chicken embryo cells as simple as getting a
> fertilised egg or am I being too simplistic here?

You're exactly right! My school bought them from a local farm that
sold them to people looking to hatch them.

>
> Best Wishes,
> Sam

Let us know how it goes!