Yesterday I’ve been to the Waag FabLab, where we discussed using a fab@home fabber to create the installation for this project. It seems that a generic fabber would do fine for the most part. The main issue is to replace the syringe in the fabber with a magnetic valve that can be opened and closed with precision.
A manufacturer called Eriks makes such valves here in the Netherlands, but I usually get lost among the gazillion items in hardware catalogues…
The bio.display project is oriented around communicating the results of contemporary biology and making this all accessible to the everyday person. So that he can touch it, feel it, try it out - which makes him familiar with this era of technological development, and thus reduces the fear, uncertainty and doubt usually associated with DNA-related biotech.
But it seems that actually one of the obstacles on this road is raised jointly by both parties involved. Both society and the scientific community seem to have a consensus on raising a thick brick wall between them. On one side this seems like deliberate ignorance on people’s part: they just don’t want to know the gory details of life. On the other hand, this is also convenient for scientists, as random people don’t question what’s going on in the lab.
Unfortunately for me, this wall raised here is really a problem. One can’t just get the parts as a layperson to do DNA transformation at outside of a lab, and this seems to be ‘the right thing’ according to both scientists and lawyers. Even initiatives like OpenWetware, which really claim to be open to the public won’t respond to you if you’re not part of an established institution. Institutions like ATCC, which aim to provide proven material for experimentation on a non-profit basis will send stuff to you if you have a company letterhead, certified lab protocols, etc.
And even the most basic part of this, knowledge itself is guarded heavily, as one can’t access the scientific publications that provide all the background information. It’s not that you can’t actually buy it, but subscription prices are excessive for a single person, and thus the barrier of entry is quite high - it takes a well-funded organization to be part of this league.
Of course, the Science Commons initiative tries to solve this last issue, but its still in its infancy.
But I don’t really see how a better communication and mutual trust can be established between science and society without both parties opening up to each other.
As it is clear now that the original concept for this project can not be realized in the given timeframe, a different concept has to be implemented for the installation that is going to be shown at the Naturalis. One that is still interesting and de-mystifies genetic manipulation, but that is also feasible to do.
The new concept revolves around creating an installation, that produces drawings based on user input. Imagine your visit to the installation: go there, draw your icon, have the machine do the work, and then you get a plate to take home with you. Wait overnight or two days, and you have your DNA-transformed own picture yourself!
Of course, I will still be working on the original dynamic display concept, at least to the extent that we know what would it take to actually reach that goal.
Imagine a simple 16×16 or 32×32 pixel icon drawing interface, where you can create your simple sketch. This input the drives a mechanism, that works on a plate of bacteria. The mechanism will make parts of the bacteria express GFP and thus glow, while other parts remain without having GFP expressed, and thus dark. After the machine is done doing its manipulations, it takes some time (a day, maybe two) for the work to be expressed.
Pretty much like making a photograph: you take a picture, develop it in a lab, and wait for some time until the picture develops. Remember: in early photography, these timescales were on the order of hours as well.
Technically speaking, the machinations done by the installation would either be the DNA transformation itself on a some parts of the plate, while not on the others. This is quite difficult to do, as DNA transformation is a complicated process, you have to heat shock the bacteria, etc.
A simpler solution is to have bacteria all over that has the GFP-producing DNA in it, but this DNA needs arabinose to actually express the fluorescent protein. So the machine would just selectively put arabinose unto parts of the plate that need to glow.
Mechanically all this will be done by modifying a fab@home 3D fabber, and creating a syrenge in it that is capable of the above feats.
by bus, because of the train strike...
On the quest to try to replicate the DNA transformation process in a kitchen-like environment, one of the obstacles is to create competent cells. These cells are degraded in a way that the alien DNA plasmid can flow into them, thus allowing the DNA transformation itself.
Maarten de Smit just wrote me that there’s a way this can happen in a natural setting, by using water that is high on Calcium, according to [Baur]. Imagine - DNA transformation in a bottle of still mineral water 
Or would you prefer sparkling?
On April 25th, on Jennifer Willet’s BioArt course I’ll be holding one of the classes, where we’ll perform the pGLO experiment based on the corresponding BIO-RAD kit. We also came up with the idea of trying to perform the same DNA transformation but instead of using lab-grade materials, we’d only utilize commercially available off-the-shelf tools.
Looking at the pGLO transformation manual (download the complete manual and the quick-guide from here, need to register first, which is free), we need to find kitchen-grade equivalents for the following tools, that are not included in the BIO-RAD kit:
The following are included in the kit, but it would be nice if we could come up with a protocol that do not need these materials, but can be replaced with commercially available stuff:
My gut feeling is that the above list is available in a regular pharmacy, one way or another. What seems to be really hard to get are:
I’ve started to register the domain name corpora.hu so that we’ll have a URL that is easier to remember. It will be regsitered in 17 days, then we’ll migrate to it…
