Synthetic Biology for Programmers

Joshua D. BruningSynthetic Biology for ProgrammersExamplesPhotographic filmWater that changes pH when exposed to arsenicSalmonella that secretes spider silk proteins instead of toxinsToggle switch

Sensitive to light, living photographic film.2Science + EngineeringConvergence of biology and engineering

Apply principles of software engineering to biology.How we build biological systems.Were computer scientists. What do we care about biology?Were interested in writing programsin the computer world, we write programs. Its also true in biology. We can design organisms.Living world provided by nature to the physical world of engineers.30 years ago, enzymes that allowed us to cut and paste DNA. Recombinant DNA technology. Cut and splice together. Concerns about destructive use, but excitement about constructive use.Very limited technology access to physical material.4 new inventions:*Standardization1864 William Sellers werent standards for screw threads; had to go to the same buyer when a screw brokeNo standards for measuring in a cell; no standard*AbstractionUseful to hide information and hide complexity so when we build bigger objects How do we do this in biology? Never refined and processed. Can we design synthetic proteins?Stone age. Collect, refine, repackage*DecouplingGenetic engineering right now you have to understand everything. How to measure, design, etc.3RepresentationBase = bit

WetwareSoftware that Builds Hardware

Reading (Sequencing)Partial analysis (~1 million bp)2008: ~$1,0002009: ~$300-$500Full human genome (~3 billion bp)2008: ~$350,0002009: ~$99,000

6Writing (Synthesizing)$1/bpphiX-174: $5,386Smallpox: $186,102Human: ~$3,000,000,000

DNA Synthesis chemical process in which you start with ATCG derived from sugarcane (think ethanol food problem)Chemistry for this in 1982 (40, 60, 100 units (nucleotides) long gene is 1,000)6 years ago engineers started working hard on this EX. Photocopiers - Synthesizers had dropped by a factor of 2 in the past 4 years$16 to $8 to $4 to $2 to $1 (should continue that trend for the next 3 years)Designers and builders now separation of dutiesDont care about access to the material we need access to informationEX. Music analog to digital; how they are shared and usedEbola and smallpox are not physically accessible; Center for Disease Control or over in Russia; genomes are onlineInformation to material rather than material to information; material = information7AbstractionSystemsDevicesPartsDNABioBricksOpen-source genetic partshttp://partsregistry.orgLong-term goal: to build a synthetic living organism that is completely understood

9RefactoringGenetic programming vs. Structural programmingBacteriophage T7Evolution does not select for design that man will easily understandGods spaghetti codeNot documented! Where are the manuals?10EmulationGraph theoryBoolean networksOrdinary differential equationsStochastic differential equationsMaster equationsSocial IssuesRisk/SecurityWhats wrong with the DNA God gave us?Economics/PatentsOrganizationCan we accept risk; who can do it?; who can we trust?Remilitarization of biological weapons12Genetically encoded logic; counters made out of proteins and DNA.Every time a cell divides, then increment; study agingWith yeast, you count the number of scars under a microscopeHuge return

Materials fabrication, information processing, chemical processing, energy processing, health

Biology as a technology

How long to change someones biology? (e.g. diabetic producing insulin)

Misuse overtake positive use? Could misuse of hammers overtake positive use?

Wouldnt start computer virus from the premise of there will be no computer viruses Irresponsible

Bait-and-switch pathogen Russia continued program after Nixon abandoned

24 hours detection 24 hours therapy

$800 30 copies of every genome

Licensing of synthesizers? (most in Asia)13