Darwin on steroids: Bio design, diversity & selection
From goals to practical choices. Design tools. Classes of genetic/protein modules. Assignment: Build a library from DNA chips.
Wang HH, Kim H, Cong L, Jeong J, Bang D, Church GM (2012) Genome-scale Promoter Engineering by Coselection MAGE. Nature Methods.
Goodman DB, Church GM, Kosuri S (2013) Causes and effects of N-terminal codon bias in bacterial genes. Science 342:475-9. PMID: 24072823
Shapiro Beth, Mammoth 2.0: will genome engineering resurrect extinct species?. Genome Biology 16, 68–3 (2015).
1. Design a selection experiment to evolve an organism to acquire a specific property, i.e. temperature resistance, UV radiation resistance etc.
2. Answer the questions from one (1) of the following topics.
Topic A - Human Genome Project Write
In class we discussed the idea of a “Human Genome Project 2.0”, but instead of reading DNA, writing DNA.
(1) If humanity were to undertake such a project, what would be the benefits? What types of new science and engineering would be enabled if we had such a synthetic human genome? Please provide specific examples.
(2) Conversely, why might we not want to proceed with such an endeavor? What are the risks?
(3) Map out a technical strategy for synthesizing a human genome. What technologies would be required? What are existing tools we could leverage? For certain tools that do not exist, what should their capabilities be?
Topic B - De-extinction
Having the technology to do genome-scale DNA synthesis, we are given the ability to bring extinct species back to life. In fact, there is already a list of candidate species, with high profile publications concerning their de-extinction projects. You can see a detailed list of those projects, along with a set of selection criteria and many discussions about the ethical considerations for such an undertaking, in the Revive & Restore website.
If you were to select one extinct species to revive,
(i) which species would you chose and why?
(ii) investigate what were the conditions that drove the selected species to extinction in the first place and
(iii) taking into account your findings, propose a plan for the survival of the species after de-extinction.
Extra credit: Answer questions of both topics.