CHE.496/2008/Schedule/Engineering principles

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CHE.496: Biological Systems Design Seminar

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Engineering principles

  • Discussion leader: Kevin

  • Synthetic biology - putting engineering into biology link
    • Purpose: This article articulates the technical aspect of synthetic biology (i.e., scientific principles that enable the engineering of biological systems). In addition, examples of artifical genetic networks are described. These systems are just the beginning of synthetic biology. As the enabling technologies are perfected (in particular DNA synthesis, standardized cloning, genome engineering of a suitable cellular chassis, and increased modeling capabilities), synthetic biology will move from foundational work to applications (e.g., novel proteins, more complex artificial gene networks).
    • Review standardization, abstraction, heirarchy (see Assignment 2 notes)
    • Use of standards already in place
      • Standardization
      • Abstraction
      • Modularity
      • Predictability
      • Reliability
      • Uniformity
    • Important tools
      • Standardized cloning
      • De novo DNA synthesis
      • Providing chassis
    • Use of Devices
      • Oscillators
      • Switches
      • Logic gates
    • Problems of joining two modules together

  • Synthetic biology: new engineering rules for an emerging discipline link
    • Purpose: This article sheds light on the fact that the traditional engineering principles of standardization, abstraction, and decoupling will have to be modified to take into account the nature of biological systems. How can engineering biology be made a reality? How can predicability and reliability be achieved? The only way to do this is to take into account the cellular context of the modules (parts, devices, and systems) that make up the entire biological system or network. In this way, synthetic biology shares the holistic perspective of systems biology.
    • A good analogy for synthetic biology is computer engineering. The cell can be thought of as a computer, the genomes as the operating systems, and BioBricks as software applications (maybe even plug-and-play components). Cell cultures or tissues can be likened to computer networks. This is the basis for a lot of synthetic biology research that focuses on cell-cell communication and cooperation to solve problems.
    • Assembly of modules occurs in an existing cellular context. Although organisms have been broken down into composable parts, we are not able to assemble these parts ex nihilo.
    • Reiteration of biological devices
    • Assessment of overall system
      • Must consider that all things are happening in the cell
    • Types of Modules:
      • Cascades
      • Cell to cell signaling
    • Important notes
      • Natural evolution works!
      • Must examine overall population

  • Brain-storming exercise
    • Last time, we touched on the logistical significance of starting a team. We came up with some good ideas on team management, but we didn't touch on the actual project very much. To get the gears rolling a bit, discuss possible pathways to create hydrogen in a cell. What types of organisms should we start looking? What kind of environment will we need to grow the cells in? How are we going to measure hydrogen production? This isn't meant to be a final plan, so you don't need to do any background research. The goal is just to brainstorm some ideas to 'plant the seeds' for the project.