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Understanding Abstraction in Engineering Complex Biological Systems

This lesson, presented by Dr. Natalie Kuldell, explores the concept of abstraction in engineering, particularly as it relates to synthetic biology. Abstraction serves as a hierarchical tool that facilitates the design and assembly of complex biological systems using DNA sequences as defined "parts." This lesson highlights the importance of interfaces and standardization in synthetic biology, illustrating how collective expertise is essential for developing functional devices from biological components. Learn how abstraction streamlines the engineering of biotechnologies.

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Understanding Abstraction in Engineering Complex Biological Systems

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  1. Abstraction • Lesson 2 presented by Dr.Natalie Kuldell

  2. Abstraction Hierarchy a human invention designed to assist people in engineering complex systems Sequences of DNA encode “parts”

  3. “Part” – sequence of DNA with human defined function AAAATGCACCCGCTGTCGATCAAACGCGCGGTGGCGAATATGGTGGTCAACGCCGCCCGTTATGGCAATGGCTGGGTCAAAGTCAGCAGCGGAACGGAGCCGAATCGCGCCTGGTTCCAGGTGGAAGATGACGGTCCGGGAATTGCGCCGGAACAACGTAAGCACCTGTTCCAGCCGTTTGTCCGCGGCGACAGTGCGCGCACCATTAGCGGCACGGGATTAGGGCTGGCAATTGTGCAGCGTATCGTGGATAACCATAACGGGATGCTGGAGCTTGGCACCAGCGAGCGGGGCGGGCTTTCCATTCGCGCCTGGCTGCCAGTGCCGGTAACGCGGGCGCAGGGCATGACAAAAGAAGGGTAATCTAGAGGCATCAAATAAAACGAAAGGCTCAGTCGAAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCCTGAGTAGGACAAATCCGCCGCC

  4. “Part” – sequence of DNA with human defined function AAAATGCACCCGCTGTCGATCAAACGCGCGGTGGCGAATATGGTGGTCAACGCCGCCCGTTATGGCAATGGCTGGGTCAAAGTCAGCAGCGGAACGGAGCCGAATCGCGCCTGGTTCCAGGTGGAAGATGACGGTCCGGGAATTGCGCCGGAACAACGTAAGCACCTGTTCCAGCCGTTTGTCCGCGGCGACAGTGCGCGCACCATTAGCGGCACGGGATTAGGGCTGGCAATTGTGCAGCGTATCGTGGATAACCATAACGGGATGCTGGAGCTTGGCACCAGCGAGCGGGGCGGGCTTTCCATTCGCGCCTGGCTGCCAGTGCCGGTAACGCGGGCGCAGGGCATGACAAAAGAAGGGTAATCTAGAGGCATCAAATAAAACGAAAGGCTCAGTCGAAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCCTGAGTAGGACAAATCCGCCGCC

  5. “Part” – sequence of DNA with human defined function AAAATGCACCCGCTGTCGATCAAACGCGCGGTGGCGAATATGGTGGTCAACGCCGCCCGTTATGGCAATGGCTGGGTCAAAGTCAGCAGCGGAACGGAGCCGAATCGCGCCTGGTTCCAGGTGGAAGATGACGGTCCGGGAATTGCGCCGGAACAACGTAAGCACCTGTTCCAGCCGTTTGTCCGCGGCGACAGTGCGCGCACCATTAGCGGCACGGGATTAGGGCTGGCAATTGTGCAGCGTATCGTGGATAACCATAACGGGATGCTGGAGCTTGGCACCAGCGAGCGGGGCGGGCTTTCCATTCGCGCCTGGCTGCCAGTGCCGGTAACGCGGGCGCAGGGCATGACAAAAGAAGGGTAATCTAGAGGCATCAAATAAAACGAAAGGCTCAGTCGAAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCCTGAGTAGGACAAATCCGCCGCC

  6. Parts

  7. Abstraction Hierarchy a human invention designed to assist people in engineering complex systems Assemblies of devices make a system Assemblies of parts make up devices Sequences of DNA encode “parts”

  8. Abstraction Hierarchy a human invention designed to assist people in engineering complex systems

  9. Parts make devices

  10. Abstraction: 4-Parts to make “NOT” gate

  11. Building biology from parts is a new way to engineer biotechnologies Slide from Nathan Hilson, JBEI

  12. Abstraction Hierarchy a human invention designed to assist people in engineering complex systems • Everyone has to do their job right for the final product to work • No single person understands everything about the final product • Interfaces between layers are critically important

  13. Synthetic Biology Standardization Abstraction Synthesis A+A+C+T+T… Genetic Engineering rDNA Sequencing PCR Tools that make biology easier to engineer

  14. Putting Abstraction to Work: Choose your System

  15. Abstraction • Lesson 2 presented by Dr.Natalie Kuldell

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