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)TRANSCRIPT
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Big Science…
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… aims to cast light on the darkest placesin our knowledge
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Chemically Recreating the Origins of Life: Miller-Urey, 1953
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But how easy is this going to be?
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Model for a minimal cell
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How do we get…
From here… to here?
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Protocells must form on their own through successive “ratchets” of complexity
Ref Pierre-Alain Monnard, FLinT
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Fundamental Living Technologies LaboratoryOdense, Denmark
University of Southern Denmark, Odense
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Protocells from Chemical Soups
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Origins of Life the “hard way””
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Your chemical origins of life computing equipment
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Radically new chemical life cycles
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feeding
light (hv)
heating
containerdivision
informationreplication
metabolicconversion
addition of resources
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Enter… The EvoGrid
Simulating an Origin of Life
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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
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Step #1: Engage in a Thought Experiment…
Make a Movie!
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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, NJNJ
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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 ScienceDirector, Cave and Karst StudiesDept of Earth & Environmental ScienceNew Mexico Tech, Socorro, NM
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Boston: “You need this…. to originate and evolve complex life (and civilization)”
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So how does “this computer” compute? How does life compute?
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Water Freezing
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What makes up a cell?
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Vesicles Forming
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Vesicle Growth
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Vesicle Entry
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Proto-genes forming on their own
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“proto genes” forming on clays
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Proto-genes forming with help from our friends the ribosomes
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Bringing it all together: Protocell Division
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The Inner Life of the Cell (Harvard)
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So how to map this computer onto this one?
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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.
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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.
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The EvoGrid: conceptually a large central artificial chemistry simulation operated upon by analysis clients
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What is the ‘Secret Sauce’
of the EvoGrid?
Answer: Stochastic hill-climbing
algorithm utilizing analysis, feedback
and temporal backtracking
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How might this work for a molecule?
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EvoGrid Architecture (for nerds)
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Simulation Manager Database Schema
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Data Formats Movement
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The simulation so far…
First runs with GROMACS, May 2009(thermodynamic runaway)
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Test Simulations: Dec 2009-Jan 2010Objective: search for complex “big” molecules formingRun 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 statisticsFrom 251 simulations we have 196,421 pending branches, so each simulation produces 782 possible branches792MB of metadata produced (input parameters for GROMACS)
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Simulation #144,204: Highest Score
2.2303 avg-avg-molecule-size9.355 avg-max-molecule-size17 max-max-molecule-size4.47307 max-avg-molecule-size33.0584 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!
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Limitations & Next Steps
Atom types are not real and interaction forces are randomly generatedMust move beyond simple random generation and testing one generation to storing and reloading states through timeMust 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 DiegoDevelopment of EvoGrid@Home running via the BOINC network
Future home of the EvoGrid?
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And Finally…Why is a simulation of the origin of life important to Humanity?
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One reason among many: How do Earth Life (and we) get out into the Universe?
Freeman Dyson’s Trees
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Thank You!
Visit us at: www.evogrid.org