Freiburg University 2006

Welcome! We are Alife Mutants.

This term was invented by Martin Schneider on the Rule 110 Winter Workshop in 2004 [http://www.rule110.org/amhso/index.html]. We play without rules. We discover the rules that govern life, the universe and everything to exploit these rules and to create Artificial Life. Our short-time aim was the trip to Boston in November 2006 to take a prize in the iGEM. The long term goal now is to REALLY do it in 2007!

The poster presentation at Jamboree iGEM2006 - "Barbie Nanoatelier: Open Source DNA-nanotechnology" [ppt,pdf]

Summary

• we started a new branch of Biobricks depository for DNA-origami parts, devices, and systems;
• following Paul Rothemund [http://www.dna.caltech.edu/~pwkr/] we created an universal DNA-platform for a patterning on the nanometer scale that will allow to organize chemical reactions, assembling and qubits;
• we proposed a correlation spectroscopy/microscopy for the investigation of DNA folding;
• we designed the tetrahedral nanobot NAUTILUS, which is a 3D-DNA building block for a hierarchical assembly, nanoswarm, and amorphous computing;
• we suggested DNA-origami cryptography;
• we emphasized aesthetic principles of AL-design; and
• we founded "Barbie Nanoatelier: Open Source DNA-nanotechnology" that’s the way to AL and AI!

The hive #101

The Freiburg Team (well, at least half of it...) from left to right: Irina Petrova, Andrei Kouznetsov, Daniel Hautzinger.

• Origami Man
• Daniel Hautzinger
• Olga Soboleva
• Irina Petrova
• Yutthaphong Phongbunchoo
• Mona Klein

• Andrei Kouznetsov
• Tamara Ulrich (ambassador, ETH Zurich)

• Svetlana Santer
• Jan Korvink

Projects

No.1 - The Pipe

PipeLife

The idea is to design a strand of DNA such that it wraps into a specific shape.

There are three different stages for this project: First, the DNA should fold into a two-dimensional rectangular sheet. Secondly, this sheet should wrap itself up into the shape of a short pipe. And last, these little pipes should hook themselves up to each other such that they form one single long pipe (more details).
The DNA sequence for the Pipes design can be found [http://omnibus.uni-freiburg.de/~kouznet/pipe/Tube-M13mp18-NEB-d.txt here], design picture is [http://omnibus.uni-freiburg.de/~kouznet/pipe/pip6.jpg here], the set of staples is [http://omnibus.uni-freiburg.de/~kouznet/pipe/StapleTube.txt here]. We’ll put the AFM pictures on the wiki as soon as we receive the DNA from the company...

No.2 - Haute Couture: Barbie Nanoatelier

Barbie Nanoatelier: Open Source DNA-nanotechnology

Once the process of DNA folding into 3D structures is understood, shapes can be chosen arbitrarily. The idea of the Barbie Nanoatelier is that the DNA should wrap into a 3D T-Shirt, 3D Pants, etc.

"sea of parts"

We need a library of molecular primitives that could be interchanged in the desirable way for a bottom-up design on the nanometer scale. Registry of DNA molecular parts and standardization is an actual question of bionanotechnology. We just put first examples of a new class of BioBricks - ORIGAMI BioBriks into [http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2006partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2006&group=Freiburg depository] and publish basic ideas [http://omnibus.uni-freiburg.de/~kouznet/DNA-plug.txt], [http://omnibus.uni-freiburg.de/~kouznet/T-shirt.txt], [http://omnibus.uni-freiburg.de/~kouznet/DNA-NanoSwarm.txt]. We try to merge a ‘dead DNA’ with an ‘alive DNA’.

Surrealistic Science

We also try to pump some aesthetic principles and rules (symmetry, periodic patterns, recursion, and plasticity) into our creatures. We like it because it needs a huge of imagination and really very difficult. Nobody can build a bra! - von Neumann's self-reproducing ... bra :))

Sketches - T-Shirt from DNA

Step 1

Step 2

Step 3

Step 4

Olga Soboleva, the presentation in Bremen sponsored by Volkswagen Stiftung

The DNA sequence for the T-Shirt design can be found [http://omnibus.uni-freiburg.de/~kouznet/t-shirt/T-shirt_M13mp18_NEB_d.txt here], the picture is [http://omnibus.uni-freiburg.de/~kouznet/t-shirt/T-shirt.jpg here], and the staples are [http://omnibus.uni-freiburg.de/~kouznet/t-shirt/T-shirt_staples.txt here] there.

Hey, venture capitalists, where are you? The price of all of 50 billion T-Shirts would be only 7200bases x €0.17/base = €1224. Don’t miss the chance. It could be a great business tomorrow!

Ladies and Gentlemen, please, visit the demonstration of last Nike nano collection. (Enter) Oh, aroma of the podium [http://omnibus.uni-freiburg.de/~kouznet/LoveParade2005.mp3 music]

Jobs: Still looking for catwalk models!!

No.3 - Individual projects

Other projects and prices could be found on individual Mutant's pages (Real iPod nano, Captain Nemo). In addition, you can find some hot information on ‘GEM Freiburg Fellow 2006’ page. The other toys will be unconventional computing, cryptography, nanoelectronics, nanooptics, drug delivery systems, smart nanomaterials, nanoswarm, eventually an artificial life and Origami Man. Time is money!

Club

• [http://omnibus.uni-freiburg.de/~kouznet/iGEM.htm Manifesto, Self-education program]
• [http://omnibus.uni-freiburg.de/~kouznet/Fellow06.htm GEM Freiburg Fellow 2006]
• [http://omnibus.uni-freiburg.de/~kouznet/GEMnews.htm News]

SB Preliminary

• [http://sommercampus2006.informatik.uni-freiburg.de/iGemAbend?action=AttachFile&do=get&target=iGemAbend.pdf iGemAbend]
• DNA plug-and-play platform [http://omnibus.uni-freiburg.de/~kouznet/DNAplatform6.pdf 24.05.06] [http://omnibus.uni-freiburg.de/~kouznet/DNAplatform6-1.pdf 27.06.06]
• [http://omnibus.uni-freiburg.de/~kouznet/BioVLSI.pdf Very Large-Scale Integration design in Biology]
• [http://omnibus.uni-freiburg.de/~kouznet/GS-design.pdf Genetic systems design from the DNA modules]

• Argo-machine, especially for hackers (presentation in Jena)

• [http://omnibus.uni-freiburg.de/~kouznet/life6000.pdf Life with a price of 6000 €]

Now we see it could be cheaper, but it will need a great intellectual impact. So, we’re opened for sponsors and relationships.

Comments

As I understand it, the idea is to create a "life automaton" consisting of 6 proteins? That is what I took out of your proposal. That seems quite ambitioned, but I can't really judge it, and even if it is quite ambitioned, that does not mean that it is bad, of course.

My understanding says that you are using 6000 € for denovo synthesis of 6 genes required for making minimal life. Right?

So, what if after all the simulations and tests on the computer, you order the DNA for minimal life and it turns out that it doesn't work... What will you do then?

This is because biology is unpredictable and you must not assume that the DNA which you order will work in the first time itself... You must keep some backup money or plans...

You have to separate specifically the general and specific objectives to long and short time; implications, obstacles and limitations.

OK, fine.. So you want to go in a completely different direction by creating alternative life.. Good.. All the best for this project.

Well, if you want to go to the extremes then are you limiting yourself to already established phenomena such as DNA, membranes, etc. You may want to adopt a completely new and novel ideas which might be simpler than DNA and other stuff of the normal cell.

So, keep all the options open. Research the literature well and create Artificial Life...

The easy and serious way

• [http://www.edge.org/documents/archive/edge187.html#church George Church CONSTRUCTIVE BIOLOGY] - a nice paper about the challenges of modern biology
• [http://webcast.berkeley.edu/events/details.php?webcastid=15766 The webcasts from SB2.0] [http://openwetware.org/wiki/Synthetic_Biology:Synthetic_Biology_1.0/Videos and SB1.0]
• [http://video.google.com/videosearch?q=iGEM iGEM related videos on Google Video]

These people do great things

Albert Libchaber [http://www.rockefeller.edu/research/abstract.php?id=93] Carlos Bustamante's lab [http://alice.berkeley.edu/] Darko Stefanovic [http://www.cs.unm.edu/~darko/] David Deamer [http://www.chemistry.ucsc.edu/deamer_d.html] David Liu [http://www.fas.harvard.edu/~biophys/David_R_Liu.htm] Eric Kool’s group [http://www.stanford.edu/group/kool/] Erik Winfree [http://www.dna.caltech.edu/~winfree/] Fred Menger’s group [http://www.chemistry.emory.edu/faculty/menger/index.html] Friedrich Simmel [http://www.nano.physik.uni-muenchen.de/nanobio/group/fritz.html] Gerald Joyce [http://exobio.ucsd.edu/joyce.htm] Hao Yan [http://www.biodesign.asu.edu/labs/yan/index.php] Jack Szostak’s lab [http://genetics.mgh.harvard.edu/szostakweb/] Luc Jaeger [http://www.cnsi.ucsb.edu/directory/faculty/jaeger/jaeger.html] Molecular Computing Group [1] Ned Seeman [http://seemanlab4.chem.nyu.edu/nanotech.html] Peixuan Guo [http://www.vet.purdue.edu/PeixuanGuo/index.html] Pier Luigi Luisi’s group [http://www.plluisi.org/index.html] 'Protolife' by Norman Packard & Mark Bedau [http://www.protolife.net/] Radhika Nagpal [http://www.eecs.harvard.edu/~rad/] Richard Kiehl [http://www.ece.umn.edu/users/kiehl/index.html] Seung-Wuk Lee [http://leelab.berkeley.edu/index_files/Page542.htm] Steen Rasmussen [http://www.ees.lanl.gov/staff/steen/] Steven Benner [http://www.chem.ufl.edu/benner.html] Thomas LaBean [http://www.fitzpatrick.duke.edu/AboutCenter/faculty/about_labean.html] William Shih [http://research2.dfci.harvard.edu/shih/] Sorry whom aren’t on the list!

Local

An Analysis of Synthetic Biology Research in Europe and North America [http://www2.spi.pt/synbiology/] SB database [http://www.synthetic-biology.info/] DNA synthesis: ATG-Biosynthetics [http://www.atg-biosynthetics.com/] febit [http://febit.de/europe/en/] 'Spiegel' about iGEM competition on August 14, 2006 [http://www.spiegel.de/spiegel/0,1518,431399,00.html] 'Neue Zürcher Zeitung' about SB on August 23, 2006 [http://www.nzz.ch/2006/08/23/ft/articleEEA5E.html] New GEM on the simiki wiki page [http://ernie.imtek.uni-freiburg.de/simiki/GeneticallyEngineeredMachines]