Programming the Way Biology Programs David Evans University

Programming the Way Biology Programs David Evans University of Virginia, Department of Computer Science NSF Advanced Computation Inspired by Biological Processes NSF Biologically Inspired swarm. cs. virginia. edu Conference, Arlington, VA 7 -8 April 2003 Computation

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 NSF Biologically Inspired Computation swarm. cs. virginia. edu 2

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 – 3 B base pairs (~250 MB) • Two human programs differ by about 500 KB NSF Biologically Inspired Computation swarm. cs. virginia. edu 3

Research Goal • Build robust, survivable systems from unreliable components – Learn from biological systems that do this • Learn about biology by building biological programs (speculative) NSF Biologically Inspired Computation swarm. cs. virginia. edu 4

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) NSF Biologically Inspired Computation swarm. cs. virginia. edu 5

Building a Sphere state center emits (radius, 6), (alive, 1) transitions (alive < 1) from d (center, fill) d Selvin George http: //swarm. cs. virginia. edu/cellsim NSF Biologically Inspired Computation state fill emits (alive, 1) diffuses radius transitions (alive < 1) from d and (radius > 1) (fill, fill) d swarm. cs. virginia. edu 6

Radius 7 “sphere” (1200 cells) NSF Biologically Inspired Computation swarm. cs. virginia. edu 7

Distributed Wireless File Service File Distribution and Update Server inhibit replicate NSF Biologically Inspired Computation swarm. cs. virginia. edu 8

Distributed Wireless File Service File Distribution and Update NSF Biologically Inspired Computation swarm. cs. virginia. edu 9

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) NSF Biologically Inspired Computation swarm. cs. virginia. edu 10

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 NSF Biologically Inspired Computation swarm. cs. virginia. edu 11

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 NSF Biologically Inspired Computation swarm. cs. virginia. edu 12