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Introduction to Synthetic Biology

Overview of course structure and topics

CH391L Spring 2014 Course Syllabus

Introduce the Format of course, grading, and policies.

Grading Rubrics

Final project description

Synthetic biology concept map

E. chromi video

Transgenic Spidergoats

Drew Endy on Synthetic Biology

Endy interview #2

Revisit the concept map.

Recombinant DNA and the Asilomar Conference | Cartagena Protocol on Biosafety

What is Synthetic Biology

Types of studies referred to as synthetic biology (and other fields that might also claim them).

  • "The goal of synthetic biology is to extend or modify the behavior of organisms and engineer them to perform new tasks."[1]
  • "Synthetic biologists come in two broad classes. One uses unnatural molecules to reproduce emergent behaviours from natural biology, with the goal of creating artificial life. The other seeks interchangeable parts from natural biology to assemble into systems that function unnaturally." [2]
  • Bottom-up assembly of genes, organelles and organisms.
    • In contrast to traditional "top-down" genetic approaches that look for mutated versions of existing organisms.
    • Ex:Re-factoring and re-writing genomes from scratch.
    • Create chemical systems with biological behaviors (e.g., self-replication).
  • Application of engineering principles to biology.
    • Standardized parts that give predictable outcomes when put together in different combinations.
    • Instantiating algorithms and problems from physics and math into biology. (e.g., oscillators)
    • Ex: circuits, DNA computing, metabolic engineering
    • Rewriting biological sequences in ways that could not be achieved (quickly) by natural evolution

Challenges in Synthetic Biology

  • Lack of predictability of complex biological systems
  • Evolutionary breakdown of engineered systems (i.e. The organism decides it doesn't like its engineering).
  • Escape of recombinant organisms and synthetic genes from the laboratory.
  • Engagement with and educating the general public (e.g. genetically modified foods).
  • Dual Use research

Timeline of Synthetic Biology

Year Event
1970 Discovery of first site-specific restriction enzyme [3]
1972 First publication on recombinant DNA [4]
1976 First genome sequenced- Bacteriophage MS2 [5]
1981 Introduction of phosphoramidite method of DNA oligonucleotide synthesis. [6]
1983 First genetically modified plant is produced [7]
2000 The "Repressilator" [8]
2002 Creation of the first synthetic virus [9]
2003 First use of the term "BioBrick" [10] First chemically synthesized bacteriophage genome assembled [11]
2004 First iGEM Jamboree
2005 "Adventures in Synthetic Biology" Nature Cover
2006 Human Genome Project completed [12]
2007 First application of context-free grammars in CAD software for Synthetic Biology (GenoCAD) [13]
2008 First synthetic genome assembled [14]
2010 Creation of Mycoplasma mycoides JCVI-syn1.0, the first microbe with a self-replicating synthetic genome. [15]
2012 Storage of digital information using DNA popularized in the media, Economist (Archives Could Last Thousands of Years when Stored on DNA)

Wiki editing

Examples from Spring 2013:

Ancestral Sequence Reconstruction

DNA Computing

Computer-Aided Design

How to edit a wiki: Instructions for Wiki Editing

First Assignment: using, editing, and critiquing a wiki page

Ethics and standards

  • Do NOT delete other people's work or comments.
  • Always preview your changes before saving them.
  • DO NOT use copyrighted material unless you have permission.
  • ALWAYS CITE material or concepts used from sources;DO NOT PLAGIARIZE