CH391L/S14/Introduction

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." Andrianantoandro2006
 * "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." Benner2005
 * 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

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