Thomas Pollom: Module 1 Day 4

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1. Prepare a table with the results of your ligations and transformations. Calculate your transformation efficiency (# colonies/μg plasmid DNA) based on the transformation you performed with M13K07. In three or four sentences, interpret the ligation results.

Plate Transformation Expected Results Colonies Transformation Efficiency
1 regular M13K07 plasmid many colonies ~ 200 colonies 40,000 colonies /ug DNA
2 backbone (no ligase) no colonies 0 colonies 0 colonies / ug DNA
3 backbone + ligase no colonies 0 colonies 0 colonies / ug DNA
4 backbone + insert + ligase some colonies 0 colonies 0 colonies / ug DNA
5 backbone + insert + ligase some colonies 0 colonies 0 colonies / ug DNA

The fact that no colonies formed on any of the four experimental plates for any of the eleven groups in this class seems to indicate that either something was wrong with one of the reagents or with a part of the protocol during the process of preparing the backbone and plasmid. It seems unlikely that all of our different sequences somehow killed the E. Coli; eleven different sequences all having this effect is too much of a coincidence. The most obvious possibility is that the DNA ligase was no good (had been denatured perhaps) because plates 3, 4, and 5 all depend on working DNA ligase for the successful culture of bacteria (otherwise the linear DNA never forms a plasmid and is metabolized upon entering the bacteria cell). This seems like the most likely explanation to me, but I'm sure other possibilities also exist.

2. Choose one of the following two essays to write a thoughtful response to their "fighting words." Rebut the quoted statements by first explaining what the quote refers to, explaining why the author or quoted individual might have said it, and then provide at least five counter points or examples to support the opposite point of view. Draw your arguments from your experiments with M13 whenever possible. Print out two copies of this portion of the assignment. Next time you and your lab partner will exchange responses and provide feedback to each other on the writing and ideas within.

Essay 1: Choose ONE of the following quotes to address. Both come from Andrew Pollack in the New York Times, Tuesday, Jan 17, 2006, Custom-Made Microbes, at Your Service which quotes Professor Arnold of Caltech as saying:

  • "(Synthetic Biology) has a catchy new name, but anybody over 40 will recognize it as good old genetic engineering applied to more complex problems."


  • "There is no such thing as a standard component, because even a standard component works differently depending on the environment. The expectation that you can type in a sequence and can predict what a circuit will do is far from reality and always will be."

Essay 2: Editorial: Meaning of Life in Nature (2007) 447: 1031 - 1032:

  • "it would be a dismiss the idea that life is a precise scientific concept"