Game of life in E coli Conway's Game of Life in E coli Principles - - PowerPoint PPT Presentation

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Game of life in E coli Conway's Game of Life in E coli Principles - - PowerPoint PPT Presentation

Jul 13, 2023 334 likes •609 views

Game of life in E coli Conway's Game of Life in E coli Principles of Synthetic Biology David Joy December 7 th 2015 Game of life in E coli What is Conway's Game of Life? "Gospers glider gun" by Kieff - Own work. Licensed under CC

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Game of life in E coli

Conway's Game of Life in E coli Principles of Synthetic Biology David Joy December 7th 2015

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Game of life in E coli

  • What is Conway's Game of Life?

"Gospers glider gun" by Kieff - Own work. Licensed under CC BY-SA 3.0 via Commons - https://commons.wikimedia.org/wiki/File:Gospers_glider_gun.gif#/media/File:Gospers_glider_gun.gi f

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Game of Life in E coli

  • Simple Rules:

– Count the number of neighbors that are ON

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Game of Life in E coli

  • Simple Rules:

– If there are exactly two neighbors, stay the same

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Game of Life in E coli

  • Simple Rules:

– If there are exactly three neighbors, turn ON

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Game of Life in E coli

  • Simple Rules:

– If there are exactly three neighbors, turn ON

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Game of Life in E coli

  • Simple Rules:

– Otherwise, turn OFF

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Game of Life in E coli

  • Simple Rules:

– Otherwise, turn OFF

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Game of life in E coli

  • Why implement the Game of Life in E coli?

"EscherichiaColi NIAID" by Credit: Rocky Mountain Laboratories, NIAID, NIH - NIAID: These high- resolution (300 dpi) images may be downloaded directly from this site. All the images, except

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Game of Life in E coli

  • Simple example of Cell-to-Cell Communication
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Game of Life in E coli

  • That can lead to complex behaviors
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Game of Life in E coli

  • How would we implement it in E coli?
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Game of Life in E coli

  • Level sensor to count our neighbors
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Game of Life in E coli

  • Logic Gates to apply the rules of the game
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Game of Life in E coli

  • Memory to remember our current state
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Game of Life in E coli

  • And an output system to signal other cells
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Game of Life in E coli

  • Converting logic gates to biological circuits

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  • ut
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Game of Life in E coli

  • Converting logic gates to biological circuits
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Game of Life in E coli

  • Converting logic gates to biological circuits
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Game of Life in E coli

  • Converting logic gates to biological circuits
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Game of Life in E coli

  • Spatial Arrangement
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Game of Life in E coli

  • Simulation:

Blinker

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Game of Life in E coli

  • Simulation:

Beacon

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Game of Life in E coli

  • Simulation:

Spaceship

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Game of Life in E coli

  • Discussion

– The logic gate network works

  • Most of the constants are biologically reasonable
  • It's a big circuit, but not the biggest

– The level sensors are finicky

  • Need really precisely tuned constants
  • Need really high cooperativity
  • Probably need to implement this as multiple components
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Game of Life in E coli

  • Conclusions:

– Cell-to-cell communication is a powerful tool for

creating programmable biological systems

– Modeling can show the strengths, and weaknesses

  • f trying to program biology as a logic system