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Mock Experiments

My first instinct when faced with a new experiment is to imagine the result. I predict what the graph will look like: the red ‘test’ sample having a beautifully curve diverging from the black ‘control’ line. Three tidy asterisks will denote the significance of the result on the page of a prestigious journal.

But hoping for a good result is never productive. Even getting a result is not guaranteed. A new experiment poses many new challenges not all of which can be foreseen. And so, after a brief moment dreaming of results, I rapidly progress to a planning phase.

I ask a colleague if they have done a similar experiment and I attempt to follow their protocol. If no one has done the experiment before I turn to the literature to find the published methods of other labs. Occasionally, no report can be found and I need to design the protocol myself.

This necessity is among my favourite aspects of science. I get to find a new way to answer a question. This takes planning and patience and test runs. I’ve learned the hard way that untested methods used in a big experiment lead to frustration. And so I do mock experiments with many replicates that each have a small, well-controlled variable.

An example: I need to permeabilize a cell without destroying an intracellular marker. Think: poking holes in a water balloon but not having the water leak out. I’d done it before, and I was sorely tempted to skip my test. After all: the imagined result looked so good: the three asterisks were scornful of my uncertainty. But I was working with a new cell type and a new intracellular marker. I wasn’t going to take anything for granted. I designed a mock experiment.

A mock experiment is not to be treated lightly. It is tempting to take shortcuts but if you are sloppy and get ambivalent results what was the point of trying it in the first place? You’ll simply need to do it again.

I planned to test 4 different permeabilization methods. #3 was my favourite: it had worked well for me before. But the others were thrown in for good measure on the suggestion of other protocols and my mentors. The result:

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All four methods failed: none showed the intracellular signal. But the outcome was definitive My non-permeabilized control has a signal. What a relief! I could have confidence in my negative data. Of course I was frustrated. But my test had not failed. It confirmed my methods were inadequate. Those four well-documented conditions could not work. I would not need to try them again. Next week, I could go on and try different conditions without questioning my earlier result.

This approach to science extends beyond the lab. On Monday Mercury will be aligned directly between the Sun and the Earth. I’m very looking forward to this transit for many weeks. I bought solar film that reduces light’s intensity by 100 000x making it safe to look at the Sun through my binoculars. But the film must be cut and taped around the lenses. It is delicate and any tear or blemish will compromise its safety, rendering it useless. And I only had enough film for one attempt. How to assure my success?

A mock experiment! Using wax paper the size of the film I cut out circles and tried to tape them over my lenses. There was a problem: the film crinkled and would not lay flat. I tried again with square-cut wax paper. Now I had leverage to smooth the paper over the lens. I reran the test: success again! By the time I did it with the real solar film the task was routine: my hands worked intuitively.

Have you seen the Sun directly? An unblemished against a midnight background. I was thrilled. I had planned my experiment, tested my method, and carried out my plan as desired. That’s a reward in and of itself. And if it’s sunny on Monday and I see a tiny dot outlined on a brilliant glowing background, I won’t need any asterisks to know this result’s significance.

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The views expressed in this content represent the perspective and opinions of the author and may or may not represent the position of Indiana University School of Medicine.
Author

Stefan Tarnawsky

MS4 MD/PhD Student. Going into Internal Medicine; interested in Heme/Onc. Bread baker, bonsai artist, aspiring astronomer.