20.20/Biocomputing

Vision

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

Action Items

• Hit up Sussman and Knight again -- in particular, clarify exactly why Sussman thought the ribozyme idea was such a useful important thing to do.
• Research RNA folding / 2,3-ary structure
• Research tRNAs (see links below for starters)
• The Tech Spec Review is on Wednesday, 9 April (4 weeks after 3 Ideas).

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.

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

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.