By Eoin Murphy

30 October 2018 - 10:15

Scientist holding a glowing stick
'If I have designed my experiment correctly, I should be able to collect valid and reliable data.' Photo ©

doctor-a licensed under CC0 1.0 and adapted from the original

On #ChecklistDay, biochemistry PhD researcher Eoin Murphy shares the checklist he uses to design research proposals.

This is one of many checklists I will use today:

  • written protocol
  • all chemicals and materials
  • protective clothing

They are simple reminders, but they help reduce the potential for mistakes. They also help me carry out my experiments with confidence.

I make checklists before breakfast 

Every evening before I leave the lab, I write a digital checklist of the next day's tasks. It helps me begin the next day in a structured and organised way.

As I go through my morning routine the next day, my mind runs through the digital checklist from the previous evening, and I make mental additions.

My checklist for a research project

Scientists design research projects, and those have to be awarded funding or granted permission by a research institution.

To convince people that the research is important, scientists create a detailed project proposal.

This is the checklist I use to create that proposal:

1. What question do I want to answer?

Before I begin a research project, I must identify a question that I believe should be answered. It has to be an original question. I do research to be sure it is original, then I decide if I can answer the question in an objective manner that will advance the field.

Here is an example. In my area of research I am looking at the role of a group of proteins in increasing a persons risk to Huntington’s disease. The question I have asked is:

Which of two of these proteins plays a bigger role in development of the disease?

2. Can I design appropriate experiments to answer the question?

Before I create experiments, I investigate existing knowledge about the question I want to answer. I do that with a detailed search of scientific literature. I assemble all the information I can find from books, journals and any other sources where information has been published.

Then, I begin to form hypotheses. These hypotheses will guide me as I design experiments, and help to create measurable data.

One hypothesis I might put forward is:

Protein A plays a bigger role than Protein B in the development of the disease.

However, depending on what I find in the literature, I could develop the hypothesis that both proteins work together in combination.

3. Is my data measurable?

If I have designed my experiment correctly, I should be able to collect valid and reliable data. That data will allow me to test my hypotheses and begin to answer my research question.

Scientific controls are used as a comparison against the test measurements. One example of a scientific control from my work is the presence or lack of my protein of interest.

My positive control would be cells which show the protein I am interested in, and my negative control would be cells which do not show the presence of this protein. Using these controls demonstrates that my experimental procedure has been successful.

For my experiments, the test measurement would be a group of other protein samples prepared under different conditions. I would test these samples against the controls to see if my protein of interest is present.

For data to be valid, I must include all necessary controls in my experiments. This is crucial.

If I have designed an experiment well, the controls minimise the potential affect of all other variables. That creates more reliable data. But for the data to be truly reliable, I have to repeat experiments several times. Then, I can examine the data to confirm its statistical significance.

4. Can I analyse the data?

The data I collect from my experiments must be analysed. When I design my project, it's essential to identify validated methods of analysis that will allow me to understand my findings and come to a conclusion.

In the case of my research, I am interested in what is happening to DNA as well as the proteins being expressed by the cells.

To investigate the DNA, I extract it from the cells, make multiple copies of it using PCR (Polymerase Chain Reaction). Then I can visualise the DNA by running on a special gel.

To investigate the protein, I break open the cell, release all its contents and create what is known as a whole cell extract. The proteins released can then be examined using a technique called Western blot. This technique uses electricity to separate the cells' proteins by size on a gel. Then, I can search to see if my protein of interest is present.

Eoin is the 2018 FameLab Ireland runner-up and Government of Ireland Postgraduate Scholar at the Department of Biochemistry at the National University of Ireland Galway. He is researching potential use of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeatsgene) editing to create therapeutic targets for Huntington's disease. 

Calls for the FameLab Ireland 2019 competition are now open. Calls for the FameLab UK 2019 competition will open in November. 

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