Matthew Loper: Mod1 Day 5

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1. Ligation Results

Transformations Colonies Expected
5 ug M13K07 plasmid ~800 lots

It seems as though none of the bacteria transformed. Only the positive control grew any colonies. This could be a result of many factors but I hypothesis that it has to do with either bad reagents or imprecision in following the protocol. Specifically, the water bath was not at precisely 42 degrees when we performed heat shock.

Response to Article
Professor Arnold’s statement, "(Synthetic Biology) has a catchy new name, but anybody over 40 will recognize it as good old genetic engineering applied to more complex problems" suggested a curmudgeon old male professor who is set in his ways and clings to the status quo to avoid becoming an obselete member of his field. Upon further investigation, it was revealed that Frances Arnold is a relatively young woman professor who is conducting cutting edge research at Caltech. These findings lead me to believe that Professor Arnold’s quotation is somewhat out of context in this article. The article makes it seem as though Professor Arnold is downplaying the groundbreaking advances in the field of Synthetic Biology over the last several years and that she is saying that these advances are nothing new to get excited about. However, Professor Arnold’s work includes “protein engineering, metabolic engineering, biological circuit design, and directed evolution,” which all depend on the tremendous recent advances in Synthetic Biology. I believe that Professor Arnold’s contention is not with the significance of the new field of Synthetic Biology but rather its definition. She does not feel that Synthetic Biology is an entirely new field, she thinks it is simply the next logical step in the advancement of genetic engineering. This view is flawed in several ways.
Genetic engineering is the practice at approaching biological problems in the context of nature’s design tactics. It involves understanding and manipulating natural systems in order to improve on them. Synthetic Biology takes components from nature and manipulates them so that they are understandable and functional in a human context. Examples of this include the bacterium mentioned in the article (Craig Ventor’s alternative energy production, blinking, and photo replication). Professor Endy’s work on redesigning the T7 genome is an example of taking a natural system and redesigning it so that it is more easily understood and manipulated by humans. In a field so young as Synthetic Biology, the potential for future applications is truly exhilirating. With increased understanding of how the components of cells behave, engineered organisms will become less and less like their wild type ancestors. The unnecessary components will be stripped down to the essential parts and combined standard parts will interact in a way that is predictable and controlled. The boundaries of Computational and Synthetic Biology are already blurring and it is not farfetched to imagine a day when an engineer will be given a problem, model the solution organism in silico, then produce the organism from scratch. At this point it will be entirely clear that Synthetic Biology has far surpassed the simple insertion of a gene into an organism that is genetic engineering.