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To Test and Approve

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To Test and Approve

The necessity of waiting in research teaches a synthetic biologist about her field and her faith.

By Heidi Klumpe

Illustrations by Katie Howerton

Every so often, in a burst of creative and carbohydrate-loving energy, I set out to make a loaf of bread. I find a link titled something like “The Easiest Loaf of Bread You’ll Ever Make” or “Basically Bakes Itself!” or “No Knead to Fear!” But below the title, the recipe is not a straightforward roadmap to culinary success. While the dough starts as a ball and ends as a loaf, it must also pass through unexpected intermediate shapes. For undisclosed reasons, it must rest multiple times, dividing my time into impossible-to-recover twenty-minute shards. And at the end, I still might end up with a sourdough frisbee indistinguishable from hardtack.

Breadmaking frustrates me because of its ambiguous place between a slam dunk and a long shot. It is challenging enough to provide a sense of accomplishment, but it is so commonly done and so simple in its requirements (flour! time!) that expecting success seems reasonable. I cannot begrudge breadmaking its complexity, since that is what draws me to it. But in a world where so many other people are making and selling bread, why would I do something that someone else can do better, and will my half-baked outcome even be worth all the trouble?

It was during one of these exasperating proofing steps that I realized something: the feelings I have about making bread match all my feelings about doing experiments.

This parallel should have been obvious. Yeast, by which bread rises to something heavenly, is also the model organism I work with for my postdoctoral research. However, while many things we produce in lab are technically edible, we strive not to make bread, but to generate data. Yeasts are particularly attractive to scientists because they are relatively simple single-celled organisms but have many of the biological innovations that appear in more “exciting” forms of life (read: humans), such as a nucleus and chromatin. Yeasts also repair their genomes in a particular way that makes their DNA very easy to edit. Which means that if on a Monday you have an idea for a new way a cell could function (without a particular gene, eating another sugar, making a protein it has never made before), by Friday you could have built that cell, and on the following Monday have a culture flask full of them.

Despite having the conveniences of decades of advances at my fingertips, this wait still seems too long. A good chunk of the time, successfully engineering a strain will take longer than a week. If you’re a beginner, like I was at the start of my postdoc, you’ll forget a step, misunderstand how to handle some of the reagents, or have accidentally designed something that’s impossible to make. Even my more experienced colleagues can be surprised by the nuances of yeast biology, often a direct consequence of trying out ambitious and unexplored ideas. 

In this way, experiments represent the same kind of paradox as bread. Trying to understand how to build with biology should be a meaningful challenge. But should it be quite so challenging as going two or three months without having a new answer to the question, “So what are you working on for your project these days?” Surely “science,” often used synonymously with unquestionable and predictable truth, should work most of the time. In my hands, it rarely does.

For both bread and experiments, I find myself pushing up against two kinds of frustration: waiting for things to finish and waiting for something to happen.

For both bread and experiments, I find myself pushing up against two kinds of frustration: waiting for things to finish and waiting for something to happen. When baking, I must follow directions that explicitly ask me to sit on my hands, but I’m also waiting to see whether there will even be bread at the end. For my experiments, I cannot shorten a ten-minute spin in the centrifuge, since even a deep knowledge of biochemistry does not change how long it takes to separate DNA from the other components in a cell. And at the same time, you’re still waiting to see if your DNA extraction is successful. “Finishing” does not mean your wait is over.

Both forms of waiting permeate all kinds of scientific research. Chemical synthesis, microkelvin fridge cooling, astrophysics simulations, and neural network training all take time. As an astronomer, you might even have to wait for the stars (or other celestial objects) to literally align before you can begin observing. But layered on top of all of this is a hazier kind of waiting, where you wait for an experiment to work, for a paper to be completed, or simply for a big, career-defining idea to come. 

In all these cases, the usual problems of waiting apply. Working toward an unknown outcome is a gamble because your hard work and sacrifice may all be wasted. And such waits are unavoidable because it always takes longer to test an idea than to come up with one. But in science, many of the roadblocks are set up by the laws of nature themselves. (Though whether struggling against impersonal forces is better than facing a human enemy is probably up to your temperament.) Another challenge in research is that you don’t always get to learn from failure. Experiments may fail for reasons that are too niche for you to bother figuring out or too random for you to understand. Then there’s the problem of feeling that you should be able to think yourself out of your problem. This prolonged waiting feels like a painful referendum on your intelligence, while the perceived importance of a scientific finding can justify the endless prolonging of a project. 

Much of the work I do now benefits from even longer, historical waits in science.

Photo by National Cancer Institute on Unsplash 2

And yet, waiting in research is perversely productive at times. In measuring my cells’ responses to particular signaling proteins, waiting a longer time before collecting data produces cleaner results. In fitting our data to mathematical models, waiting for the computer to sample larger regions of parameter space yielded a better theoretical understanding of our system. In the year it took to perfect a robotic protocol for preparing hundreds of protein mixtures, I learned how to program and fix nearly every part of our liquid-handling robot, because I had, over the course of many weeks, seen every one of them malfunction. Much of the work I do now benefits from even longer, historical waits in science. A decades-long effort to lower the cost of sequencing DNA means I can understand the evolutionary history of the proteins I study simply by going online. Many of the Bayesian methods we use for analyzing our data are only possible because of a centuries-long wait for computers to catch up with mathematical theory.

Somehow all this history was not enough to teach grad-school me that waiting is not the emptiness before a sudden result, but a mysteriously useful period. I learned this decisively while writing the manuscript containing all the data and insights collected during my PhD. Shaping and distilling many years of work was exhausting. I had created every part of the paper at least five times and kept getting feedback like “I’m just not sure it’s clear,” or “Doesn’t this sentence seem a bit heavy to you?” or worse, “I’ve had a new idea for how to represent the data,” or worst, “Let’s have another look at the abstract.” Entire figures disappeared while new ones emerged, like continents in a sped-up version of plate tectonics. I felt like Atlas trying to hold up the world before it fell apart, or an endurance athlete completing a marathon to nowhere. I joked that the manuscript was “diffusing,” a gradual spreading that paradoxically emerges from the random walk of particles with no net movement. 

But after weeks of styling myself as a martyr to someone else’s perfectionism, I looked back at my early, beloved drafts. I was shocked to see that they were confusing and heavy; I couldn’t imagine explaining the data any other way than the one we had arrived at through the revision process. When I considered all the steps that were necessary to educate myself about the real meaning of the results, to shape the narrative, and to improve the figures, I realized it could only happen with a prolonged wait. I’ve relearned this lesson every time I make something new, whether it’s a manuscript or a hypothesis or a protocol. Anything good takes a long time to come together, and the duration of that wait isn’t measured in something like minutes or days, but something unrelated to time all together, like micro-epiphanies or the number of touches. So much of what I perceive to be true about waiting is false. What feels like emptiness contains imperceptible rotations and shifts that together produce movement. While I feel like I actively engage in this process, large parts of it are outside my control.

The lack of control is hard to accept. My first instinct for filling the emptiness is to reach for relief, like Twitter (people talk about science there!) or organizing my to-do list (meta-work with no stakes!). My second is to work longer hours, based on a bad assumption about how close the finish line is or that waiting is only about time. Neither of these tactics helps much. 

There are some more practical approaches to waiting that can be helpful, like presenting your work to clarify the story and get feedback or breaking the problem into smaller and more informative sub-problems. But lately, I have tried to “nourish” the wait. Leaving the lab to run or read fiction freshens my mind. (Though hobbies don’t exist to support work, nor are they guilty pleasures.) I think the main thing is that it should bring pleasure. I remember a friend saying he traded morning swims for reading his favorite textbook, since learning something new brought more delight than laps did. I also try to find fuel for the small and passive changes that occur while I wait, seeking out random interactions with people or ideas, or welcoming the pivots that come when someone asks, “So what are we really trying to do?” I’ve even found that being open about what I’m struggling with, even with all the social and professional costs of confessing my neediness, has often been the only way out of the forest. I used to think I should only talk to someone about my project once it started working when, in reality, those conversations are most useful during or even before the problems “start.” 

While the challenges of research have definitely played a part in my sanctification, they also provide a symbol of sanctification, particularly what all this waiting is for.

Photo by Theme Photos on Unsplash

The view of waiting as nonlinear, imperceptible change brings further questions, though. For example, where does the change occur? When I waited for my manuscript to improve, was the key step a change in my understanding or a change in the paper itself? And where do these changes come from? Is everything somehow initiated by me, or am I acted upon by an external force? The answer seems to be a little bit of both.

This tying together of the internal and the external always reminds me of the discussion of faith and deeds in James 2, where the author lays out the ridiculousness of faith without deeds, as well as deeds without faith. If I truly believe in the gospel, I should expect to see it in my actions, even though good “deeds” by no means indicate the right condition of my heart. Intriguingly, I think this passage emerges as part of a discussion about whether or not someone has really changed. From this perspective, questions about my own sanctification sound strangely like my questions about waiting in science. How should faith change me, internally or externally? And can I participate in my own sanctification, or does it happen to me? 

While the challenges of research have definitely played a part in my sanctification, they also provide a symbol of sanctification, particularly what all this waiting is for. Perfecting the practice of the scientific method does not guarantee your success; rather, it means you have a process for reliably finding the truth. This is often the opposite of success, since finding out what is true generally means explaining why I was wrong. Similarly, sanctification does not bring blessings, those things I superficially presume to be religious success. Romans 12:2 (NIV) says, “[B]e transformed by the renewing of your mind. Then you will be able to test and approve what God’s will is—his good, pleasing, and perfect will.” In my reading, sanctification (“mind renewal”) also produces an empirical process (“test and approve”) for finding valuable information (“his good, pleasing, and perfect will”). 

Nonetheless, while this highlights what we wait for in a general sense, it still does not illuminate the specifics. What am I supposed to be learning? Which parts of my understanding of the world are good and true, and which await replacement? A dear friend pointed out that perhaps her most frustrating wait in science was for the “eureka” moment that scientists who write memoirs or get interviewed often talk about. The survivorship bias of considering only the lives of the most successful scientists ill prepares us for waiting because it may not give us the right things to wait for. Similarly, the sanctification of those we consider to be “saints” will not necessarily illuminate our own path.

These days, I feel very much in the grip of waiting, in both my research and my faith. My project is in a “muddy middle” that one mentor assured me was part of all projects. And I still have a lot of questions about who God is and how he interacts with the world. But I have hope that waiting is a way to get to the answers.

Heidi Klumpe is a postdoc in biomedical engineering working at Boston University.