20.20/Biocomputing
Vision
To develop novel models of computation appropriate to the biological world.
Project Idea
- Current: Invertase chain as cell-cycle counter
Here is where final technical information goes!
- Write to DNA: transmit bits of information from outside cell to inside cell & have cell rewrite DNA as appropriate
- RNA aptamer that recognizes an arbitrary RNA sequence & lights up GFP, or triggers kinase cascade, or alters expression of some related gene, or...
- DNA Turing machine (poorly specified)
- Implement Game of Life using actual cells; design bacterium that can obey an arbitrary version of Life rules
Action Items
- Figure out invertase inhibition!
- Address other actionable questions on the specs page and the brainstorms page.
- Our final presentation is Weds 7 May -- next week!
- Technical documentation is due Weds 14 May, which is in two weeks.
Team Members
20.20 Students
- Kelly Drinkwater (Foo)
- Raphael Rush (Bar)
- Star Simpson (Baz)
20.902 Students
- Kay Aull
- Stephanie Nix
Brainstorming
- Biological neural nets
- DNA-encoded Turing machine
- Adder circuit
- PCR readout for genetic switches
- Addressable DNA modification based on RNA input
- Fix scaling issues
- RNA binding screens
- Circuit elements of protein cascades
- Ontology for standard biological parts
3 Ideas Presentation
...was a great success. See contents on the brainstorming page.
- Idea 1: Intercellular communication (Game of Life)
- Idea 2: DNA Turing Machine
- Idea 3: Signaling (Ribozymes)
Here is the feedback we received from the class poll at the end:
- Which idea addresses the most important challenge or opportunity? #3 52%, #2 33%, #1 15%
- Which idea would have the greatest impact if fully successful? #3 61%, #2 29%, #1 11%
- Which idea is most competitive with alternative technologies? #3 59%, #2 30%, #1 11%
- Which idea has the greatest certainty and fewest unknowables? #3 48%, #1 28%, #2 24%
The class seems to agree with us that the ribozyme idea is pretty cool and actually viable as a project.
Directory of Interesting Things
Literature and Similar
tRNA on the RCSB Protein Data Bank.
Aminoacyl-tRNA Synthetases on the RCSB Protein Data Bank.
tRNA, the Adaptor Hypothesis and the Wobble Hypothesis: lots of good information about tRNA. Nonstandard bases / base pairings; lack of neurotic specificity in the last base of the anticodon; genes coding for tRNAs in E. coli; the works. As well as some good textbook references.
A DNA and Restriction Enzyme Implementation of Turing Machines
The Neurally Controlled Animat: Biological Brains Acting with Simulated Bodies
Computing with DNA. Shortish review in Nature by Jack Parker, describing Adleman's traveling-salesman solver and Shapiro's Turing-machine-oid.
People
Ron Weiss's web page. He also wrote a really interesting review paper a few years back on the subject. I can't remember where it is...
Christina Smolke's web page. Seems to be doing interesting RNA things potentially related to our ribozyme idea.
Amorphous Computing Home Page.
Ehud Shapiro @ the Weizmann Institute in Israel, working on DNA Turing machines using restriction enzymes (among other things).
Tom Knight's lab; see also here.
