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Bruce Damer's talk at EE380, the Stanford University Computer Systems Colloquium (Jan 13, 2010)

Bruce Damer's talk at EE380, the Stanford University Computer Systems Colloquium (Jan 13, 2010)



Bruce Damer's talk at EE380, the Stanford University Computer Systems Colloquium (Jan 13, 2010)

Bruce Damer's talk at EE380, the Stanford University Computer Systems Colloquium (Jan 13, 2010)



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    Bruce Damer's talk at EE380, the Stanford University Computer Systems Colloquium (Jan 13, 2010) Bruce Damer's talk at EE380, the Stanford University Computer Systems Colloquium (Jan 13, 2010) Presentation Transcript

    • Big Science…
    • … aims to cast light on the darkest places in our knowledge
    • Chemically Recreating the Origins of Life: Miller-Urey, 1953
    • But how easy is this going to be?
    • Model for a minimal cell
    • How do we get… From here… to here?
    • Protocells must form on their own through successive “ratchets” of complexity Ref Pierre-Alain Monnard, FLinT
    • Fundamental Living Technologies Laboratory Odense, Denmark University of Southern Denmark, Odense
    • Protocells from Chemical Soups
    • Origins of Life the “hard way” ”
    • Your chemical origins of life computing equipment
    • Radically new chemical life cycles
    • feeding light (hv) heating container division information replication metabolic conversion addition of resources
    • Enter… The EvoGrid Simulating an Origin of Life
    • EvoGrid inspirer Richard Gordon: “The Artificial Life community should get down to the basics and simulate an Origin of Life.” -Professor, University of Manitoba, Canada
    • Step #1: Engage in a Thought Experiment… Make a Movie!
    • But is this realistic? Freeman Dyson: “the simulation should be truly ‘messy’, ie: nature is not clean and neat as you are showing in the movie, cells are more like dirty water surrounded by garbage bags” -Professor, Institute for Advanced Study Princeton, NJ NJ
    • Penny Boston: “The simulation must model abstract universes and not attempt a high fidelity chemistry model, all that counts is if you can demonstrate a method for supporting ever increasing levels of emergent complexity” -Associate Professor of Cave and Karst Science Director, Cave and Karst Studies Dept of Earth & Environmental Science New Mexico Tech, Socorro, NM
    • Boston: “You need this…. to originate and evolve complex life (and civilization)”
    • So how does “this computer” compute? How does life compute?
    • Water Freezing
    • What makes up a cell?
    • Vesicles Forming
    • Vesicle Growth
    • Vesicle Entry
    • Proto-genes forming on their own
    • “ proto genes” forming on clays
    • Proto-genes forming with help from our friends the ribosomes
    • Bringing it all together: Protocell Division
    • The Inner Life of the Cell (Harvard)
    • So how to map this computer onto this one?
    • The EvoGrid is a worldwide, cross-disciplinary effort to create an abstract, yet plausible simulation of the chemical origins of life on Earth. One could think of this as an artificial origin of life experiment. Our strategy is to employ a large number of computers in a grid to simulate a digital primordial soup along with a distributed set of computers acting as observers looking into that grid. These observers, modeled after the very successful @Home scientific computation projects, will be looking for signs of emergent complexity and reporting back to the central grid. Our starting point is very early along the path of emergence in a phase one might call "prevolution" in that the fundamental mechanisms supporting symbolic codings for replication (and evolution through Darwinian Natural Selection) must in fact emerge from a tabula rasa (ie: no engineer coded in a genetic system). This is where the EvoGrid differs from earlier “Artificial Life” efforts.
    • Our goal is to set up conditions and operation to enable us to witness the emergence of structures in space (rings, catalysts, containers/vesicles, simple repeating strings) or reaction sequences in time (autocatalytic sets for example) within the EvoGrid simulation. With this as a foundation a ratcheting up of complexity may then occur, hopefully through several plateaus. Years in the future, the observing of entities which code their own constructions and reproduction using an artificial genome would be a major scientific breakthrough for emergence science and hopefully shed light on the possible chemical origins of life on Earth. The intellectual and computational breakthroughs will come through optimizing the pathway for vectors of ever higher self organization across the valleys of events of extremely low probability.
    • The EvoGrid: conceptually a large central artificial chemistry simulation operated upon by analysis clients
    • What is the ‘Secret Sauce’ of the EvoGrid? Answer: Stochastic hill-climbing algorithm utilizing analysis, feedback and temporal backtracking
    • How might this work for a molecule?
    • EvoGrid Architecture (for nerds)
    • Simulation Manager Database Schema
    • Data Formats Movement
    • The simulation so far… First runs with GROMACS, May 2009 (thermodynamic runaway)
    • Test Simulations: Dec 2009-Jan 2010
      • Objective: search for complex “big” molecules forming
      • Run cycles: 1000 iterations of 1000 randomly distributed atoms in heat bath within GROMACS for 1 second
      • Data produced one day’s runs:
      • 251 simulations producing 5,480MB of history data with 40MB of statistics
      • From 251 simulations we have 196,421 pending branches, so each simulation produces 782 possible branches
      • 792MB of metadata produced (input parameters for GROMACS)
    • Simulation #144,204: Highest Score 2.2303 avg-avg-molecule-size 9.355 avg-max-molecule-size 17 max-max-molecule-size 4.47307 max-avg-molecule-size 33.0584 search-evogrid-complexity-1 Based on these numbers, it looks like one large molecule, of 17 atoms "wide", is forming. The term “molecule size” means the maximum link count between any two atoms in the molecule. But nothing has been visualized yet!
    • Limitations & Next Steps
      • Atom types are not real and interaction forces are randomly generated
      • Must move beyond simple random generation and testing one generation to storing and reloading states through time
      • Must move to covalent bonding supported by GROMACS 4.0 (QM)
      • Must develop more analysis (beyond just “size of molecule”)
      • Need input from “real chemists”
      • Distribution of EvoGrid onto real Grid (beyond just two computers) @ CALIT2-UC San Diego
      • Development of EvoGrid@Home running via the BOINC network
      Future home of the EvoGrid?
    • … Stand by for more! (we need help, coding jobs available: bruce@damer.com )
    • And Finally… Why is a simulation of the origin of life important to Humanity?
    • One reason among many: How do Earth Life (and we) get out into the Universe? Freeman Dyson’s Trees
    • Visit us at: www.evogrid.org Thank You!