Difference between revisions of "Hackteria Lab Commons"
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== First Ideas ==
== First Ideas ==
Latest revision as of 19:16, 10 December 2010
- 1 First Ideas
- 2 mouse and blocks
- 3 Spectroscopy
- 4 Tardigrade Farm
- 5 Some general electronics
- 6 Colonized Colonizer
- 7 ++ Linux Drivers for webcams
- 8 Microscope-incubator-device
- 9 Ideas about Hackteria Workshops
- 10 Questions
- 11 Experimental Cuisine
- 12 Magnetotactic bacteria
- 13 Some Links
- 14 For Reference: The Biopunk Manifesto
- 15 Backalley DNA Sequencer
After observing the micro world I would like to interact. To do so we could build a mircomanipulator using intelligent materials: <gallery> File:Manip.jpg File:manip2.jpg File:rigidgrab.jpg|http://www.me.unm.edu/~lumia/Microgripperwebsite/main.htm File:stacked-parts.jpg|http://robotics.eecs.berkeley.edu/~ronf/milli-robot.html </gallery>
Check out the movies:
Update, Thursday April 8th, 0:46, Urs<br> Some first results with most simple micromanipulator done. Building it was a matter of some 30 minutes (felt time). Hot glue, acrylic and coil wire. The results are ok. Difficult to adjust on the microscope lucifer due to the big magnification. Had some first interaction with a tardigrada. Not sure weather she/he/it liked it. At one point the tardigrada rose on the manipulator. From an engineering perspective the Micrometer scale is already quite challenging. The human hand is (when helped by a good visual feedback through the microscop) capable of executing quite sensitive movement. The manipulator (as for now) helps a litte. Think the lever construction is a good starting point for automated / remote interaction. <br> File:Manip1.jpg File:Manip3.jpg
Instead of using a webcam I would like to experiment with an array of phototransitors. In combination with the laser projection microscope (by Marc) this could give a low res picture of the microcosmos. <br>
Could look something like this:<br> 240px
I will bring some of these and some analog multiplexers... <br> 240px
Update, Thursday April 8th, 0:46, Urs<br> The phototransistor array is soldered together. While commercial digital cameras are in the mega (1'000'000) pixel range I thought that 20 pixels soldered and hard-wired by hand is already a lot. The ambient light photo transistor sensors work like a charm. Interfacing using 4 multiplexers (4061) was busy work. There is still a little glitch some where in the wiring. Still I am happy with the result and Marc is having fun while poking around with the laser on the DIY camera (which is always a good sign for me). The software was a little bit a pain (needs some (abstract) concentration which is some how difficult in creative sessions). Concatenating the pixel camera with the (identicaly looking) LED Display was no big deal. <br> <br>
mouse and blocks
I am interested in possible approaches for the visualization of nano effects in micro-scale.<br> first basic idea: <br> mouse and blocks - tardigrades which will be led by controlled obstacle patterns, made of magnetic nanoparticles. <br> first approach would be, trying to realize a controlled "moses effekt"(Dusseiller 2010), dividing water with the <br> help of magnetic nanoparticles.<br> <br>
I've got 4 of the photometer boards made up from this tutorial here -> http://www.rsc.org/Education/EiC/issues/2007Sept/BuildYourOwnSpectrophotometer.asp and i have some extra 3140 opamps for making some more. I'd like to develop a couple of these into 'proper' spectrometers, develop a suitable (maybe PDMS based) organism container and see if there is a way to get spectroscopic data out of organic change.
I've been culturing tardigrades for a while now with moderate success, but I'd like to develop a proper 'tardigrade farm' for future hackteria use. These entails the making up of proper media such as Chalkey's and Soil extract, and it would be good if we can do this without needing a proper lab. It might also be necessary to develop a bespoke container and parallel chlorococcum (tardi food algae) culture. If the whole thing could be partially or completely automated it would be fun.
Some general electronics
I'm also hoping that someone can give me a hand for a couple of hours to get over my brain block in controlling some 12v solenoid valves from arduino. I'll bring the solenoid valves and the arduino if someone else brings the brain...
Traffick or un/aware handling of organisms has been an underlaying reason for that what social sciences call as -colonialism- (we live in the realm of fungi!). I will like propose shared observations to compare _realtime_ (via video streaming) with some of our collegues in Colombia different micro-organisms, minerals, strains.. that could lead us to share thoughts on the many bio tactics introduced by colonialist strategies. There are many conceptual layers to it, from how much observation affects the experiments to micro biological "peace&love war" on drugs. The fact that we open a parallel view across continents will lead our experimental approach. (still to much to elaborate on this.. but at least it express one possible vector i will like to put effort to implement for the sake of the continuity of our networked collaborative practices). --Alejo 10:45, 3 April 2010 (UTC)
++ Linux Drivers for webcams
In case one has the need to reinstall gspca video based drivers, there is this guide that helped me out reconfigure a meesed up system:
Karmic: get the latest drivers for gspca, uvc, usbvideo and other 
For a list of supported webcams under linux see here -> 
I would be interested in starting to work on a DIY-microscope-incubator-glovebox-device to be able to work with mammalian cells and to find out if it´s possible to do some basic live cell imaging. So generally, I would like to learn more about the culturing and incubation of cells over a longer period of time and to find out how if it´s possible in a DIY way at home/in the atelier.
I´m very interested in visiting the light microscopy center of ETH Zurich.
Update, Thursday April 8th, 0:46, Urs<br> Felt some consensus seems to be there on the incubator. I am really happy about our progress on the rough concept of the incubator. Pieces are coming together and some really interesting synergies (like growing chamber = droplet = lens = biosphere) are there. Interconnections between functional units can be established. While technical aspects are ostensible thinking about the incubator concept as a representation of the ongoings in the HackteriaLab might be interesting (Ma be this is particularly true for verena looking into the Lab from outside).
Ideas about Hackteria Workshops
One of the central idea of the hackteria project is the development and conduction of introductory workshops into the world of biological arts. while some artist have developed a strong relation to the biological science, introducing living media into their work and processes, the field is not very easy to enter for emerging artists. By the breaking down of biological techniques, simple instruction to set up a functional lab in an artists atelier and critical and theoretical reflection about these processes a hackteria workshop should help artists to start working independantly with biological media.
here are some ideas and topics that might be interesting to condense into a introductory workshop format.
- On the origin of species
Evolution, variability, species, chimera, what is out there
Hybrid system, cybernetics, measurement and control, symbiosis
How to start a lab, tools, diy,
- diy microscopy
History of scientific instrumentation, microcosmos, visual experience
- on instrumentation
Spectroscopes, microscopes, absorbtion/emission, pumps, incubators
- Genetic media
Genetic code vs digital code, extraction, synthesis, sequencing, visualization of genetic information, privacy
- Flesh! Animal tissue
Life outside of the organism, cell culture, artificial organs, xenografting
- on plants
- Synthetic biology
Genetic manipulation, bacteria, viral transfection, biobricks, artificial life
Analysis, interaction and manipulation of biological phenomena on the nanoscale, motorproteins, nanoparticles, lipids, new instruments
- living colors
Life as paint, patternig, growth patterns, time based, fluorescence
I have some questions. I will ask questions. (I'll collect some of these <s>here</s> over the next days and hope others will join as well. <s>We might also open up a separate Q&A page ...?</s>)
The Topics & Questions Section can be found on the BookOfHackteria subpage!
A hackteria tardigrade recipe book...
the following from - http://heywoodgould.com/pages/?p=180
“Tardigrades produce a sugar called trehalose just before they go into a state of suspended animation,” Durg says. “Trehalose protects them against conditions of heat and dehydration, plus invasion by foreign bacteria and viruses. They also generate a large protein which rebuilds their cell structures.” He stops with an astonished look. “On the molecular level they are invulnerable!”
What if the tardigrade’s protective powers could be transferred to human beings? Durg thought.
“What if tardiigrades were the greatest health food ever invented?”
He began experimenting. “I got a few wet branches in Prospect Park and made my first harvest,” he says. “Imagine my delight when, the tardigrades turned out to be pleasantly chewy like calamari.”
Moistened with egg yolk and sprinkled with panko the tardigrades made a light, pleasant cutlet. Durg adapted other recipes, producing Tardigrada Parmigiana, Spicy Tarigrada Roll, Spaghetii and Tarigrada Balls…
He reopened with a hard sell slogan: “Eat at Durg’s, Live Forever…”
Response was immediate. Diners came away reporting new vigor.
“I feel so good I might start bothering Barb again,” George H.W. Bush said.
With a six month waiting list, Durg has to be brutal. The other night John McCain exploded when told he couldn’t have a table.
“It’s your duty as an American to seat me,” he screamed at Durg. “Do you want Sarah Palin to be president?”
At that, the entire restaurant arose in unison.
William Shatner, 78, was the first to the door. “Come back, Senator,” he pleaded. “You can have my table.”
Fascinating critters. The first idea for now is to try and see whether we can find any in Lake Zurich. Here's a short and simple set of instructions on where to go looking for such bacteria, how to catch them and how to look for them in samples under a microscope:
These instructions say to look for magnetotactic bacteria in salt water, but we know that they can be found in freshwater, too, such as Magnetobacterium bavaricum (Chiemsee).
Magnetotaxis, as imagined by miss.gunst
For Reference: The Biopunk Manifesto
by Meredith Patterson, copied from Meredith Patterson's LiveJournal
Scientific literacy is necessary for a functioning society in the modern age. Scientific literacy is not science education. A person educated in science can understand science; a scientifically literate person can *do* science. Scientific literacy empowers everyone who possesses it to be active contributors to their own health care, the quality of their food, water, and air, their very interactions with their own bodies and the complex world around them.
Society has made dramatic progress in the last hundred years toward the promotion of education, but at the same time, the prevalence of citizen science has fallen. Who are the twentieth-century equivalents of Benjamin Franklin, Edward Jenner, Marie Curie or Thomas Edison? Perhaps Steve Wozniak, Bill Hewlett, Dave Packard or Linus Torvalds -- but the scope of their work is far narrower than that of the natural philosophers who preceded them. Citizen science has suffered from a troubling decline in diversity, and it is this diversity that biohackers seek to reclaim. We reject the popular perception that science is only done in million-dollar university, government, or corporate labs; we assert that the right of freedom of inquiry, to do research and pursue understanding under one's own direction, is as fundamental a right as that of free speech or freedom of religion. We have no quarrel with Big Science; we merely recall that Small Science has always been just as critical to the development of the body of human knowledge, and we refuse to see it extinguished.
Research requires tools, and free inquiry requires that access to tools be unfettered. As engineers, we are developing low-cost laboratory equipment and off-the-shelf protocols that are accessible to the average citizen. As political actors, we support open journals, open collaboration, and free access to publicly-funded research, and we oppose laws that would criminalize the possession of research equipment or the private pursuit of inquiry.
Perhaps it seems strange that scientists and engineers would seek to involve themselves in the political world -- but biohackers have, by necessity, committed themselves to doing so. The lawmakers who wish to curtail individual freedom of inquiry do so out of ignorance and its evil twin, fear -- the natural prey and the natural predator of scientific investigation, respectively. If we can prevail against the former, we will dispel the latter. As biohackers it is our responsibility to act as emissaries of science, creating new scientists out of everyone we meet. We must communicate not only the value of our research, but the value of our methodology and motivation, if we are to drive ignorance and fear back into the darkness once and for all.
We the biopunks are dedicated to putting the tools of scientific investigation into the hands of anyone who wants them. We are building an infrastructure of methodology, of communication, of automation, and of publicly available knowledge.
Biopunks experiment. We have questions, and we don't see the point in waiting around for someone else to answer them. Armed with curiosity and the scientific method, we formulate and test hypotheses in order to find answers to the questions that keep us awake at night. We publish our protocols and equipment designs, and share our bench experience, so that our fellow biopunks may learn from and expand on our methods, as well as reproducing one another's experiments to confirm validity. To paraphrase Eric Hughes, "Our work is free for all to use, worldwide. We don't much care if you don't approve of our research topics." We are building on the work of the Cypherpunks who came before us to ensure that a widely dispersed research community cannot be shut down.
Biopunks deplore restrictions on independent research, for the right to arrive independently at an understanding of the world around oneself is a fundamental human right. Curiosity knows no ethnic, gender, age, or socioeconomic boundaries, but the opportunity to satisfy that curiosity all too often turns on economic opportunity, and we aim to break down that barrier. A thirteen-year-old kid in South Central Los Angeles has just as much of a right to investigate the world as does a university professor. If thermocyclers are too expensive to give one to every interested person, then we'll design cheaper ones and teach people how to build them.
Biopunks take responsibility for their research. We keep in mind that our subjects of interest are living organisms worthy of respect and good treatment, and we are acutely aware that our research has the potential to affect those around us. But we reject outright the admonishments of the precautionary principle, which is nothing more than a paternalistic attempt to silence researchers by inspiring fear of the unknown. When we work, it is with the betterment of the community in mind -- and that includes our community, your community, and the communities of people that we may never meet. We welcome your questions, and we desire nothing more than to empower you to discover the answers to them yourselves.
The biopunks are actively engaged in making the world a place that everyone can understand. Come, let us research together.
Backalley DNA Sequencer
I've been thinking about how to build a primitive but usable DNA sequencer for a while now. During the Hackteria Lab Days, I settled for an approach of how to do this and compiled a short text to introduce the project and outline the steps necessary to develop it. If anyone decides to try and build one too, I'd be thrilled to hear from them and exchange experience on the progress. Shoot me an email: thalheim at informatik dot hu dash berlin dot de
The goal is to build a lowcost semi-automated DNA sequencer. We don't expect to get anywhere near the performance of a bleeding-edge device, but we do hope that the sequencer will permit to undertake small sequencing endeavours, such as sequencing of single human genes or exploratory metagenome sequencing.
The motivation behind this project is to help enable enthuasiastic amateurs and citizen scientists. It's about the equivalent of going down to your local lake, taking a water sample and looking at the sample under the microscope. Just that now, you read the DNA sequences contained in the sample. This genomic information can then be analyzed further, for example by cross-checking against the wealth of publicly available sequence databases.
The idea is to build the system around the method of Sanger sequencing. Sanger sequencing has gone out of fashion; the newer sequencers use a different approach that is better suited to parallelization and automation. However, Sanger sequencing is a relatively simple, low-tech method. The fabrication and chemicals involved are still very much accessible to a DIY approach today. Hence, this first attempt at building a low-cost DIY sequencer focuses on the Sanger method.
The Sanger method works by selectively synthesizing DNA fragments that terminate on a given nucleotide. The result is a pool of DNA molecules of different lengths. The molecules of different lengths are then separated using gel electrophoresis. Knowing the lengths of the DNA molecules and the nucleotides they terminate on then permits a reconstruction of the original sequence.
The system can be built incrementally, adding a little automation at each step. Here's a short description of the final system, its components and what they do:
* Gel slides - Instead of using the slab gel usually employed, the gels will be embedded in a custom-made plastic carrier. One option here is to laser-cut carriers that feature channels and wells into which the gel is poured. The alternative is to just cast a gel on a flat plastic carrier. The advantage of a channeled carrier is that it would require less gel, possibly decreasing the cost of a gel run. * Gel cast - Mold to cast the gels including a comb to create wells in the gel * Gel electrophoresis (GE) chamber * Power supply for gel electrophoresis * Transilluminator * Camera - monitors the gel in realtime to permit a shutdown the power supply before the samples run beyond the gel boundaries; takes images of a gel once it's done * Sensors for buffer fill levels and temperature * Buffer pump - can release fresh buffering solution into the GE chamber if the fill level drops below a certain threshold * Processing unit (desktop computer and/or arduino/similar) - receives input from the sensors and the camera, controls the power supply, buffer pump and transilluminator. When the buffering solution or gel overheat, it can regulate or shut down the power supply. The finished gel images are analysed to automatically reconstruct the sequence. This processing should also involve some kind of measurement for the quality of a run. * Contraption for automatically changing gel slides (probably involving some kind of stack for new gel slides and one for finished gel slides, and a mechanism to transfer a gel slide from the "new" stack into the GE chamber and then to the "finished" stack)
The idea is for the user to pre-load a range of samples into the system (either directly onto the slides or via some kind of intermediate storage), turn on the system and then come back the next morning to find a file with the sequence information.
The main improvement over manual Sanger sequencing is a) that gels can run on their own, without constant attention from the user and b) that the time-consuming and error-prone task of reconstructing the sequence from a gel is automated.
Incremental project stages
1. Gel slides, gel mold, agarose - evaluate whether it's possible to pour agarose gel into a channeled design with good results 2. GE chamber, gel slides, gel mold, power supply, transilluminator - pretty much everything is done manually at this stage. Evaluate possible designs for the gel slides, GE chamber, and whether gels can be dry-loaded. 3. Add camera and processing unit that can determine when a gel is finished and automatically shut down the power supply. 4. Add software that can evaluate the quality of a gel and assemble the sequence from the gel image. 5. Add temperature and fill-level sensors that are monitored by the processing unit, and software to regulate the power supply based on the temperature readings. 6. Add buffer pump and software, such that the fill level of the GE chamber will be regulated automatically. 7. Add contraption that can load and unload gels into and out of the GE chamber, plus software that controls the loading and unloading.
All evaluation should initially be done with a DNA ladder and then with custom samples.
* Suitable material (thinking polycarbonate at the moment) * Access to laser cutter * Agarose
* GE chamber * Gel slides * Power supply * Transilluminator * Gel mold * Agarose * DNA ladder * Buffer
The objectives of this stage are:
* Get a basic setup running * Determine designs and dimensions for the GE chamber, transilluminator, gel mold and gel slides
* Can a gel be "dry-loaded"? * Does the buffer solution have to be changed after every run because of contaminations? Or can it be reused for several runs? * What are suitable dimensions for the GE chamber and the gel slides? * What is a good and cost-effective design for the gel slides?