Programming the Way Biology Programs

David EvansUniversity of Virginia, Department of Computer Science

NSF Advanced Computation Inspired by Biological Processes Conference, Arlington, VA 7-8 April 2003

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Copying How Nature Programs

• Mimic the Process– Evolutionary programming, genetic

algorithms, genetic programming

• Mimic the Results (this talk)– Take advantage of the trillions of

organisms that have died already to lead nature towards good programs

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Observations About Nature’s Programs

• Responsive– Aware of state of self and surroundings

• Localized– Communication through chemical diffusion

• Redundant– Millions of cells die every second, but humans

keep working• Remarkably Expressive

• Human genome – 3B base pairs (~250MB)• Two human programs differ by about 500KB

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Research Goal

• Build robust, survivable systems from unreliable components– Learn from biological systems that do this

• Learn about biology by building biological programs (speculative)

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Cell-Based Programming Model

• Correspondence to biological cells– Genes turn on and off state changes– Emit different chemicals depending on state,

sense chemicals in surroundings– Cells can divide asymmetrically

• Lots of simplifications: not simulating reality– Mass conservation optional– No chemical interactions– No physical forces (except collisions)

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state center emits (radius, 6), (alive, 1) transitions (alive < 1) from d (center, fill) d

state fill emits (alive, 1) diffuses radius transitions (alive < 1) from d and (radius > 1) (fill, fill) d

Building a Sphere

Selvin Georgehttp://swarm.cs.virginia.edu/cellsim

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Radius 7 “sphere” (1200 cells)

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Distributed Wireless File ServiceFile Distribution and Update

Server

replicate

inhibit

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Distributed Wireless File Service

File Distribution and Update

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Amorphous Computing• MIT AI/LCS Research Project

• Growing Point Language (Daniel Coore)– Botanical model of programming– Able to make complex topologies using

gradients

• Origami Shape Language (Radhika Nagpal)

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Education• “Education across the Biological,

Mathematical, and Computer Sciences” (last month)

• Work toward curricula that require all CS students to learn biology, and all biology majors to learn computer science– Requires CS courses that teach computer

science to non-majors– Requires Biology courses that don’t require 4

semesters of Chemistry

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Summary• Biology has killed trillions of organisms

to solve complex engineering problems– We should be able to learn from both the process and the solutions nature found

• Fifty years ago, biology and computer science became deeply intertwined– Academia still hasn’t caught up