Scientific Anthology: Failure as a Stepping Stone

Introduction

Failure is often seen as a negative part of scientific discovery. Failure is inherently bad. But failure is not completely bad. When it is not a completely indomitable failure, it provides an opportunity for growth, and quite often is a stepping stone towards success, or brings you one step closer from achieving your goal.

This anthology is a collection of 15 carefully curated pieces which reflect the importance and the nuances around failure and its role in the scientific world. As you will find, failure is not only an irremovable component of science and progress, but a driving force into scientific discovery and advancement.
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Scientific Anthology: Failure as a Stepping Stone

Shotgun Sequencing

Helena’s research on DNA probes reminded me of a technique I learned about in synthetic biology that is widely used today in science. Since these DNA probes were synthetic short single-stranded chains of DNA, they were able to adhesively attached to its complementary strand in a mixture of media. To bring it to the next step, is finding out the sequence needed in order to make that synthetic strand of DNA. Helena’s group may have had one specific sequence of interest but what if a research wanted to know the sequence of an entire genome?

Honestly, how this process works doesn’t make much sense but for researchers, it has been an amazing tool. One technique is called Shotgun Sequencing. Basically, in short terms, you “blow up” the genome into smaller fragments and a computer system puts it back together by looking for overlapping sequences. This technique was proven to be more efficient with both time and cost of the process. The previous type of sequencing took a very long time and cost a large amount of resources. However, if I remember correctly, whole genome shotgunning sequencing is not as accurate. Since you are breaking up the whole genome and putting it back together in one piece rather than piece by piece, if there is a problem with one section, theres no way of telling what section went wrong.

Shotgun Sequencing

Discovering DNA Sequence

After reading Chapter 3 of Pointing From The Grave, I thought it was very interested that Weinberg devoted this chapter to focusing on the development of DNA, its base pairing, and eventual uses. One part that really stuck out to me was the discussion of running DNA on an agarose gel. Specifically, Weinberg stated that,

“Using a restriction enzyme – a protein that cleaves the DNA strands at designated positions. These lengths would be immobilized by dropping them on one end of the dish of agarose gel to which an electric current would be applied” (p 41).

This discussion of using DNA on a gel in order to discover the sequence stood out to me because it related back to my time in Synthetic Biology. Today, we use gel electrophoresis, similar to the one described in the novel as a southern blot, to detect the sequences of DNA in our whole fragment. In Synthetic biology specifically we used restriction enzymes to cut as specific points in order to understand banding pattern and sequences present in yeast. In addition, this correlates to what I learned in Cancer Biology and what I am doing in my independent research of breast cancer cells. Essentially, we used Western blot to understand protein expression to characterize cancer cells and their aggression. Overall, it is very interesting to see the development of DNA and the technologies associated with it in different types of labs, whether it was synthetic or cancer related.

Discovering DNA Sequence

Synthetic Biology

(YEAST)

In the lecture portion of the Synthetic Biology course I took, you learn about different genome sizes, techniques for sequencing, how to build a genome from scratch etc. One of the cool things about this class is that the lab portion of this course offers you very real research experience that international. The yeast genome has recently been fully sequenced to where every nucleic acid has been identified within it. Knowing the sequences of all sections of the genome, the yeast genome project has now become the challenge of building it from raw materials, dNTPS. Every week in lab you build upon your synthetic DNA sequence making it longer and longer to eventually have a successful synthetic sequence of the genome. As awesome as this sounds, doing this is actually very difficult. When I took this course none of the material worked and I always had blank bands on my electrophoresis gel. There were also a ton of steps involved with making synthetic DNA that many errors could occur with simple techniques. Science is always tricky and takes effort to accomplish something.

“Individuals get smarter because they’re connected to the network” (pg. 60).

Being that this is an international program, multiple minds are working on this same experiment of building a synthetic genome. People can learn from other’s failures in building the genome. Learn what techniques work and which ones didn’t.

Synthetic Biology