20.20/Biocomputing

Vision
To develop novel models of computation appropriate to the biological world.

Project Idea
Here is where final technical information goes!
 * Current: Invertase chain as cell-cycle counter
 * 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
Main brainstorms page
 * 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.

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

A Dicer-like protein in Tetrahymena has distinct functions in genome rearrangement, chromosome segregation, and meiotic prophase

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.

Jake Beal's web 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.

Miscellaneous
Registry of Standard Biological Parts

BioBricks Foundation