What Star Trek Taught Me About Flow Cytometry
It is no secret that I am a very big fan of the Star Trek franchise. There are many good episodes and lessons explored in the 813+ episodes, 12 movies (and counting). Don’t worry, this blog is not going to review all 813, or even 5 of them. Instead, some of the lessons I have taken away from the show that have applicability to science and flow cytometry.
“Darmok and Jalad at Tanagra.” (ST:TNG season 5, episode 2)
This is probably one of my favorite episodes, which involves Picard and an alien trying to establish a common ground and learn to communicate with each other. This is such an important concept not just flow cytometry but in science in general. Each field, each discipline has its words and acronyms. These can make people entering the field uncomfortable. Therefore, it is critical for us to ensure while discussing flow cytometry, that our concepts are properly communicated.
Another important area is in our publications. How many times have you read a paper only to walk away and not fully understand how the experiments were performed or what the data meant?
This brings us to the issues with reproducibility.
As has been reported, about 50 to 90% of published data in pre-clinical research is not reproducible. In this article by Freedman and colleagues (2015), they identify four areas that contribute to irreproducibility (Figure 1)
A full quarter of irreproducibility is data analysis and reporting. Thus it is important for us as flow cytometrists to ensure we communicate our experimental protocols and data analysis efficiently to the reader. The solution to this is to adopt the MiFlowCyt standard.
This standard, developed by the ISAC data standards task force guides you as to what information should be included in a paper in supplemental material. Adopted by Cytomer A and some other journals. I encourage you to submit this information to any journal you are publishing in, and help reduce that 25%.
“It is possible to commit no mistakes and still lose. That is not a weakness. That is life” (ST:TNG season 2, episode 21)
In an episode where Data learns a life-lesson. Picard says this to help him understand a fundamental truth. This is equally true in science and flow cytometry.
The best experimental design can fail.
The important thing is to figure out how to move on. Troubleshooting is a critical part of this process.
When an experiment fails, the first thing I do is to start to retrace back my steps. Things that can help with this process are the reference control. This is useful to determine if there were issues in the staining and processing of the sample. Instrument quality control provides another important piece of information. This ensures that the machine is behaving. However, since most QC is performed at the start of the day, integrating a QC tube into the experiment will give you a peace of mind. And if you run this tube before the experiment you can know if there is an issue at the time you begin. For this to be successful, make sure to keep a record and track the results. Interested in learning more about this process, read this blog.
Infinite Diversity in Infinite Combination (IDIC) (ST:TOS season 3, episode 7)
I love this concept. It first made its appearance in the Original Series. As a concept from the Vulcans, and has shown up from time to time in other episodes and series. At one level, this sounds like a way to design a polychromatic panel. That there are many ways to put together a combination of antibodies and fluorochromes to answer an experimental question.
That is not quite true however, because panel design is more than just throwing the reagents from the refrigerator into a tube and seeing what comes out on the instrument. There are many different considerations that play into designing a good panel. If you’re working on designing your own panel, you can find some advice here.
Since panels are so critical to experimental design, Cytometry A started publishing a unique article type called the Optimized Multicolor Immunophenotyping (OMIP).
Right now, there are 70 published OMIPS in the 10+ years time since the idea was first revealed. The beauty of the OMIP is it provides the reader with a wealth of information, from what combinations of fluorochromes and antibodies were used to how to analyze the data. An example, from the first OMIP by Mahnke and Roederer (2010).
In addition to this example of data analysis and the table of reagents used in the OMIP, including clone, fluorochrome and the purpose for the given antibody. The third component of an OMIP is a summary table that describes the conditions that the OMIP is applicable to.
“I canna’ change the laws of physics.” (ST:TOS season 1, episode 4)
One of the most classic lines that is quoted from Star Trek, said by Montgomery ‘Scotty’ Scott to Kirk. I bring this up as a cautionary tale while reading marketing material from vendors as they tout the abilities of their instrument.
Fundamentally, all flow cytometers have a fluidics system. This a way to bring the cells to the interrogation point and to waste (or to be sorted). An optics system – that is used to excite the fluorochromes and measure the emitted photons. They also have an electronics system that transforms the measured photons into a digital, electronic signal that can be sorted for analysis later.
Take, for example, electrostatic cell sorters. There is a distinct relationship between the nozzle size, sheath pressure and frequency of droplet formation.
The laws of physics apply to all of our instruments so it’s good to know what they are.
Of course, there are some cases where we can push the laws of physics, such as in Super Resolution microscopy, but that is a topic for another blog.
“Things are only impossible until they’re not.” (ST:TNG season 1, episode 17)
In science, one of our jobs is to make the impossible: possible.
Look at how we continue to push our understanding of cells. When I first started working on B-cell development, it was possible to identify the major developmental stages using four antigens. Over time, and with more powerful instruments, we found more subsets, understanding the developmental process and what happens when it goes wrong.
Coupled with the ongoing development in automated analytical techniques, we can start to identify populations we didn’t even know to look for. Jonathan Irish termed these populations as ‘Cyto Incognito’. These techniques remove the inherent bias that we bring to our analysis.
We often rely on mnemonics to help us remember things (like ROY-G-BIV). I find myself looking for memorable quotes that trigger me to remember some important point or other. Here you have 5 quotes from my favorite show. I hope this journey through important aspects of flow cytometry as seen through this lens inspires you to look around for ways to remember these and other crucial concepts in flow.
If you are a Star Trek fan, drop me an email with your favorite quote, and how it applies to flow cytometry. Until the next blog, Live Long and Prosper.
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ABOUT TIM BUSHNELL, PHD
Tim Bushnell holds a PhD in Biology from the Rensselaer Polytechnic Institute. He is a co-founder of—and didactic mind behind—ExCyte, the world’s leading flow cytometry training company, which organization boasts a veritable library of in-the-lab resources on sequencing, microscopy, and related topics in the life sciences.More Written by Tim Bushnell, PhD