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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 Li...
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...
Penny Boston: “The simulation must model abstract universes and not attempt a high fidelity chemistry model, all that coun...
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 orig...
Our goal is to set up conditions and operation to enable us to witness the emergence of structures in space (rings, cataly...
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 tem...
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 <ul><li>Objective: search for complex “big” molecules forming </li></ul><ul><li>Run cy...
 
 
 
 
 
 
Simulation #144,204: Highest Score 2.2303  avg-avg-molecule-size 9.355  avg-max-molecule-size 17  max-max-molecule-size 4....
Limitations & Next Steps <ul><li>Atom types are not real and interaction forces are randomly generated </li></ul><ul><li>M...
…  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!
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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)

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

  1. 1. Big Science…
  2. 2. … aims to cast light on the darkest places in our knowledge
  3. 12. Chemically Recreating the Origins of Life: Miller-Urey, 1953
  4. 13. But how easy is this going to be?
  5. 14. Model for a minimal cell
  6. 15. How do we get… From here… to here?
  7. 16. Protocells must form on their own through successive “ratchets” of complexity Ref Pierre-Alain Monnard, FLinT
  8. 17. Fundamental Living Technologies Laboratory Odense, Denmark University of Southern Denmark, Odense
  9. 18. Protocells from Chemical Soups
  10. 19. Origins of Life the “hard way” ”
  11. 20. Your chemical origins of life computing equipment
  12. 21. Radically new chemical life cycles
  13. 22. feeding light (hv) heating container division information replication metabolic conversion addition of resources
  14. 23. Enter… The EvoGrid Simulating an Origin of Life
  15. 24. 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
  16. 25. Step #1: Engage in a Thought Experiment… Make a Movie!
  17. 27. 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
  18. 28. 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
  19. 29. Boston: “You need this…. to originate and evolve complex life (and civilization)”
  20. 30. So how does “this computer” compute? How does life compute?
  21. 31. Water Freezing
  22. 32. What makes up a cell?
  23. 33. Vesicles Forming
  24. 34. Vesicle Growth
  25. 35. Vesicle Entry
  26. 36. Proto-genes forming on their own
  27. 37. “ proto genes” forming on clays
  28. 38. Proto-genes forming with help from our friends the ribosomes
  29. 39. Bringing it all together: Protocell Division
  30. 40. The Inner Life of the Cell (Harvard)
  31. 41. So how to map this computer onto this one?
  32. 42. 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 &quot;prevolution&quot; 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.
  33. 43. 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.
  34. 44. The EvoGrid: conceptually a large central artificial chemistry simulation operated upon by analysis clients
  35. 45. What is the ‘Secret Sauce’ of the EvoGrid? Answer: Stochastic hill-climbing algorithm utilizing analysis, feedback and temporal backtracking
  36. 46. How might this work for a molecule?
  37. 50. EvoGrid Architecture (for nerds)
  38. 51. Simulation Manager Database Schema
  39. 52. Data Formats Movement
  40. 53. The simulation so far… First runs with GROMACS, May 2009 (thermodynamic runaway)
  41. 55. Test Simulations: Dec 2009-Jan 2010 <ul><li>Objective: search for complex “big” molecules forming </li></ul><ul><li>Run cycles: 1000 iterations of 1000 randomly distributed atoms in heat bath within GROMACS for 1 second </li></ul><ul><li>Data produced one day’s runs: </li></ul><ul><li>251 simulations producing 5,480MB of history data with 40MB of statistics </li></ul><ul><li>From 251 simulations we have 196,421 pending branches, so each simulation produces 782 possible branches </li></ul><ul><li>792MB of metadata produced (input parameters for GROMACS) </li></ul>
  42. 62. 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 &quot;wide&quot;, is forming. The term “molecule size” means the maximum link count between any two atoms in the molecule. But nothing has been visualized yet!
  43. 63. Limitations & Next Steps <ul><li>Atom types are not real and interaction forces are randomly generated </li></ul><ul><li>Must move beyond simple random generation and testing one generation to storing and reloading states through time </li></ul><ul><li>Must move to covalent bonding supported by GROMACS 4.0 (QM) </li></ul><ul><li>Must develop more analysis (beyond just “size of molecule”) </li></ul><ul><li>Need input from “real chemists” </li></ul><ul><li>Distribution of EvoGrid onto real Grid (beyond just two computers) @ CALIT2-UC San Diego </li></ul><ul><li>Development of EvoGrid@Home running via the BOINC network </li></ul>Future home of the EvoGrid?
  44. 64. … Stand by for more! (we need help, coding jobs available: bruce@damer.com )
  45. 65. And Finally… Why is a simulation of the origin of life important to Humanity?
  46. 66. One reason among many: How do Earth Life (and we) get out into the Universe? Freeman Dyson’s Trees
  47. 68. Visit us at: www.evogrid.org Thank You!

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