20.20/Biocomputing

Vision

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

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

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

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...

Computing with DNA. Shortish review in Nature by Jack Parker, describing Adleman's traveling-salesman solver and Shapiro's Turing-machine-oid.