The Road to Research #2: So you want to design an experiment?

You’ve been working in a lab now for a couple months, go you! You’ve cleaned glassware, helped with various projects, and now it’s time for you to move on to the next step: creating your own experiment. In my first year at CU Boulder, after a couple months of volunteering in the Johnson lab, I decided to apply for my first research grant and start my own project. CU Boulder has a specific program called the Biological Undergraduate Research Skills and Training (BURST) research grant which is specifically designed for first year research students. It requires a very simple application, provides students with a $2,500 stipend, and the Biological Sciences Initiative hosts workshops in grant writing, research ethics, and professional development. However, before you can apply for grants, you have to plan your research project.

#1: What is your research question?

You know the scene in Monty Python and the HiELwqcnoly Grail when the Bridgekeeper asks the knights: ‘what is your quest?’ well scientific research is similar. A research question is always the first step to starting an experiment, and even though it seems simple, it can sometimes be the most time consuming part of experimental design. A tendency most young scientists have (including myself) is to ask questions that are extremely broad and have the potential to change an entire scientific field. These types of questions are what most researchers spend their entire careers investigating, and it’s not only infeasible, it shows immaturity. That’s why it’s necessary to think deeply about your question and refine your goals constantly.

Okay, so I probably completely freaked you out, but don’t change majors just yet, I have some tips that will help you.

  • When in class, lab meetings, or while listening to StarTalk constantly write down things that interest you. It helps to have a notebook set aside solely for the purpose of thinking about science, looking through some of my past notes I see: ‘cell differentiation in embryonic development…’ from a particularly rad lecture in MCDB 2150, ‘snail sexual vs. asexual reproduction… evo advantage for infection recovery?’ from my brief career as a gastropod matchmaker in the Johnson lab, and ‘what mutations caused SIV to evolve into HIV?’ from my weekly Radiolab story. As you can tell, these aren’t close to being research questions, but it helps you understand what excites you in science.
  • For me, it became apparent from these musings that I was very interested in infectious diseases, immunology, and microbiology. I knew that I was interested in the process of parasitic infection, specifically the mechanisms of cercarial release. Now that I knew what excited me, I had to think about the resources I had in the laboratory and at the university. I personally knew I was uncomfortable with the idea of purposefully infecting, euthanizing, and dissecting amphibians so I opted to work primarily with invertebrates, specifically gastropods. This might be applicable to you as well when choosing research subjects: do you prefer working with cell cultures, or are you okay with handling pissed off lab rats on a daily basis?
  • Now that you have an idea of the subjects that excite you and the types of organisms you want to work with you have to identify gaps in knowledge. No one wants to work hard on a research project and then discover that it has been done before, so before you begin anything you have to investigate the current state of research in your field. My favorite way to do this is to begin with a simple Google Scholar or Web of Science search, I will usually start the search with: subject of interest + model organism. For example, I began with: cercarial release + gastropods, I usually try to find the most recent articles I can (you can do this by changing the search filters) as they give you the best idea of what questions still remain. By skimming through the discussion parts of papers you can often find the authors discussing gaps in knowledge which still exist despite their discoveries. For example my research partner and I found this: ‘because microphallid trematodes of H. ulvae retain the potential of killing their amphipod second intermediate host, the production and release of exudates by C. volutator that depress cercarial emergence might be an anti-parasitic adaptation. No comparable observation exists in other systems.’ (Mouritsen 2002) which inspired us to make a comparable experiment to his in a different parasite-host system.
  • Okay, so now you have a: biological system of interest (parasitology), accessible research subjects (infected gastropods), and background knowledge (your literature searches). Now you can begin to formulate your question, ours was: Does exposing helisoma snails to different host chemical cues influence cercarial emergence? Once you have a preliminary question, be prepared to scrutinize it and constantly edit, I often go through a checklist to test if my research question is ready.


#2: How will you approach your research question?

Now that you know what you want to answer, you must begin to think about how you will approach your question. When establishing your methods break it up into four different sections: materials/subjects, experimental design, experimental set up, and procedure development. I like to think of it like baking brownies. You have the idea, ‘I want brownies’, but before you can pop a pan in the oven you have to make the brownie mixture. You need to collect your ingredients and baking tools, you have to determine how many batches and servings of brownies you will make, you must to determine what bowls and pans you will use, and you need to find or determine a recipe to follow. It seems overwhelming, but if you treat your experiment like brownie making, it makes it easier.

  • Materials and Subjects: Though it may seem silly at first, you must collect every tool you will need throughout your entire experiment before you even begin. I like to make a list similar to the one I bring to the grocery store. Consider every little thing from different colored sharpies to containers of agar to ensure they are ordered and organized before your trials begin. The last thing you want is your experiment to come to a grinding halt due to a back order of pipette tips (darn Alkali Scientific). Also consider your research subjects, how many will you need? Do you have to breed or order them? What will their housing needs entail?
  • Experimental Design: There are three different types of designs: single factor, multi-factor, and a time series, you must determine which type will be best for your experiment. If you are only studying one independent variable then a single factor design is suitable, if multiple variables are being studied than a multi-factor design must be used (2×3 or 3×3), and a time series experiment is necessary when examining an independent variable that changes markedly over time. Without going into too much detail about the statistics behind these designs (if you’re interested this is a great resource). Don’t worry about this too much, your PI will be able to help you a lot with this part.
  • Experimental Setup: The importance of this step may vary depending on what materials you are working with, but for my BURST experiment figuring out where the research subjects would be located was essential. The following picture shows a perfect example of a good experimental set up. Notice that we put the uninfected subjects that were producing our chemical cues on the top shelf. We also labeled the containers clearly, assured that the water quality and amount were constant, and placed our project in a low traffic area where we could control temperature and light. Putting the infected snails on the bottom shelf ensured that no parasites could accidentally spill out and infect the uninfected populations. It may seem nit-picky now, but planning ahead and scrutinizing small details is what makes good experiments great ones.


  • Procedure: Though the procedure changes throughout your trials as unforeseen issues arise, it is essential to plan a detailed procedure ahead of time. I am a visual learner, so I often like to draw my procedures out, the picture below is an example of the procedure used in my BURST experiment. Notice that I have labeled which treatments each research subject will undergo, despite the fact that some snails died throughout the experiment and adjustments needed to be made. Whether you prefer writing or drawing your procedure make sure you share it with your colleagues and friends who can help you troubleshoot potential problems before you even begin.


Check out my next blog entry where I’ll be discussing my experience getting the CURE research grant and how to use laboratory technology!


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