Ben McFarland
 on March 09, 2020

Living with Contagious Uncertainty

In the midst of Seattle's CoV-19 outbreak, biochemist Ben McFarland provides a daily log of feelings, adaptations, and discovery.

Seattle skyline in a pink sunset

I have lived in Seattle for almost 24 years. I’ve experienced earthquakes, blizzards, a partial eclipse, wildfire smoke that turned the sun red, and multiple 40-day stretches of rain. Each is uncertain in a different way. What I hadn’t experienced until this week was being at the epicenter of a scary, new viral infection. That was a new kind of uncertainty that affected my family’s life, my work as a biochemistry professor at Seattle Pacific University, and our service at Bethany Community Church.

I’m one of those people who still gets a paper newspaper each morning. Over seven days, and through seven headlines, it became clear that the first U.S. community to be hit hard by the viral infection was my own. As the uncertainty continues, I’m looking back through those headlines, and I see that God was near in each uncertain minute.

Friday, February 28, Seattle Times headline: “Virus fear pummels Alaska, Boeing stock.”

At first the virus seemed far away. I know students from Europe who were worried about returning home to a quarantined family over spring break in a few weeks, but no one knew about the news we would receive that night.

As the weekend began, we learned that a student from a high school north of Seattle had tested positive for this coronavirus. The red flag with this case is that he had not travelled internationally, so he did not catch the virus from somewhere else but from someone else. This case was the first known local coronavirus infection in the U.S.

We didn’t know whether there was one “someone else” with the virus or one thousand. So we carried on with our plans and checked the news every five minutes. I received an email from my university that it had convened a committee to keep an eye out and offer advice. Something was starting to happen. I tried to push my mind toward prayer as it anxiously wandered.

Saturday, February 29: “Two new coronavirus cases seen locally.”

The high school student was one of these cases, and the second was a person who had traveled from Asia. This was enough to convince everyone to move—out to the stores. By mid-day, Costco’s parking lots were full and checkout lines were long. I’m not sure why you’d shop at the place with open-air samples when you’re worried about viral spread, but I guess it’s where you go when you want to stock up.

My family was in Eastern Washington at a Bible Quiz meet, while I had stayed home to work on a book proposal. I texted my wife, reasoning that lines might be shorter hundreds of miles away, and asked if we needed milk or anything perishable.

grocery carts in a row

We had enough milk already, so they didn’t go shopping, but the contingency plans had begun. The uncertainty was catching, and it had spread to the supermarket: Would it take an hour to pick up milk? Would they even have milk? What should we buy more of today in case it would be sold out tomorrow?

Sunday, March 1: “King County patient is first in U.S. to die of COVID-19”

Three new cases were confirmed, all people who had caught it from the community. One had died. Two were from a long-term care facility, and many more from there had symptoms. This contagion was picking up speed.

We didn’t have time to read the paper. We were at church to sing a choral setting of Psalm 27. My wife and I met in that church choir 23 years ago, and now we have four boys, two of whom are now tenors singing one row in front of me.

One of the biggest benefits of being in a choir is that, after practicing a song, the text saturates your thoughts and becomes a part of you, replaying throughout the day. It had become natural to sing, “The Lord is the strength of my life, of whom then shall I be afraid?” It was also natural to apply the “whom” to the coronavirus.

The sermon text was Psalm 73. I must have been thinking about the physical body: as I took notes in my Bible, I drew a box around every time a body part was mentioned. “Heart,” “feet,” “eyes,” “mouth,” “tongue,” “hand,” and “flesh” are all in the Psalm, even though the main topic was about a spiritual crisis. Body, soul, and spirit blur together in ancient Hebrew song, harmonizing like notes in a chord.

In Psalm 73, the crisis reaches a turning point when the psalmist assembles with God’s people in God’s holy place. Mine did, too. The last verse of the psalm spoke to me: “But it is good for me to draw near to God: I have put my trust in the Lord God.” (Psalm 73:28) Thousands of years ago, this song blazed a trail that I followed in 2020. The virus was near, but God was nearer still, for those who draw near to Him. I didn’t just think that—I knew it—through word and music.

Monday, March 2: “2nd U.S. coronavirus death in King county; more cases likely”

The next morning, the paper told us that the virus had claimed another life, and there were at least a half-dozen more cases confirmed from the same long-term care facility. Despair whispered that this was only the beginning. Maybe despair told part of the truth, I still don’t know. But then something caught my eye that I had not seen before in the newspaper: biochemical data.

That’s not a normal reaction, I know. But as a biochemist, it drew me like a magnet.

Two viral genomes from Washington state had been sequenced and posted online, at, a site built to post and compare viral genomes. Trevor Bedford, researcher from the Fred Hutchinson Cancer Research Center, had compared them and said he thought that the virus had been passing from human to human for about six weeks.

I opened the site and found the first Washington coronavirus (CoV) genome, from mid-January, opened it on my computer, and there it was: 29,884 letters, A’s, C’s, G’s, and T’s representing the four different nucleotides in the virus’s genetic code. Only three of those letters distinguished this virus from the dozens of others posted at the site.

When I compared it to the second Washington CoV genome, I saw that the same three letters were different. For the same three places to be different in exactly the same way, out of tens of thousands of possibilities, is unlikely to be a coincidence. The two viruses must be related.

DNA sequence in letters

The second genome also has three new differences, or mutations, in three more places. Thanks to the data posted openly online, I could see them with my own eyes. Coronaviruses mutate about every two weeks on average, so three mutations times two weeks per mutation equals six weeks of time between the first “grandparent” sequence and the second “grandchild” sequence. That amount of time fits with the time between samples, and implies that a “couple hundred” people were infected without knowing it.

It was one thing to read it in the paper, and quite another to reconstruct it on my own. In the midst of uncertainty, the letters on the screen defined a logical set of conclusions that said that the virus has been infecting people and mutating for at least a few weeks.

The bad news was that it was spreading without us knowing it. But the good news was that we were starting to decode how fast and how much it had spread. We had a set of footprints we could follow to catch this killer.

In an uncertain world that didn’t make sense, this path of reasoning was a lifeline. So I did what any teacher would do: I passed it on by incorporating it into my class that afternoon (recorded on YouTube).

I changed my lesson because the anxiety on campus was palpable. The students heard about each of these events before I did, and I had even seen some wearing masks. When I showed the students this chain of reasoning, I don’t know if you can hear it in the video, but I felt this in the room: every eye was on me (for once), shoulders visibly relaxed, and hands shot up for questions.

This knowledge doesn’t eradicate a single virus or cure a single physical symptom. But it dispels the mental fog of misinformation and worry, so that we see this virus for what it is: a nasty, horrible virus, possibly ten times worse than the seasonal flu, but one with atoms and lipids and protein and RNA that can be read like a book so that we can see where it has been. We are decoding its secret history.

Students today grow up in a confusing, uncertain, at times vicious world. I had worried that my scientific explanation might give them more worries, because it reveals that this virus is indeed contagious and deadly. But every small bit of it that we understand, like the RNA sequence, the mutation rate, and the population size, that gives hope. This is science as therapy, and science as grace.

Tuesday, March 3: “State coronavirus death toll up to 6”

More people died on Monday, possibly even as I was teaching. On Tuesday, I checked the news every hour. It seems like every time I checked there was another case, or worse, another fatality.

All day Tuesday I graded papers and advised students, as the virus continued to spread. Every doorknob hid a potential contagion. My wife texted me and my first thought was that one of the kids was sick. But the news was good: she had found a promising recipe for homemade hand sanitizer. I intermittently waited, worked, and sometimes trusted.

Even though it was a slow day, I was tired at the end of it. I realized I had been making two sets of plans: one for if school continued and one for if it closed. Planning everything twice takes twice as much work. It’s a kind of double life that everyone has to live when you don’t know if you’ll be sick tomorrow, but it’s similar to if you don’t know if it will snow tomorrow, or if there will be an earthquake or a financial disaster. Each of us could be gone tomorrow. You have to prepare, but also trust.

Wednesday, March 4: “ ‘We’ve been missing a lot of cases’: Faulty tests, red tape allowed coronavirus to spread undetected in state”

The next day, the drumbeat of cases continued. I told my first-year science writing class about the genome data and answered questions. I heard good news directly from students with family in Asia: cases were finally falling. I heard stories of quarantined family members with cabin fever, and advised caution and a little more patience until this all played out. I felt hope, although tempered with the realization that if it took a month in China, it could take a month in Washington—and then the infection could recur later. How long?

Thursday, March 5: “China tried a lockdown; should Seattle? Experts caution that Beijing’s extreme quarantine measures could cause more harm than good here”

Today, as I write this, it is the seventh day after the coronavirus appeared in my county. Today was my last lab period of the quarter, so we have done the experimental work we need to do, and I’ve made contingency plans for my students to turn in their reports online. We are ready for either possibility now.

In my science writing class, the students are working on an art chemistry project that I accelerated so they could complete it this week. My two sets of plans are in place and each day I’ll decide which one I should use.

We just got the email that all activities at church have been cancelled for at least a week. Hopefully these measures will slow the spread of the disease enough that our overtaxed medical system can respond to the sick.

The church has an ancient calling to tend the sick. It seems odd that right now that care is being exercised by opting not to meet in large groups so as not to spread it to the most vulnerable (those 60 years and older). I can’t change this, so I watch and wait.

Where two or three are gathered, Jesus said he’d be among them, and in my house we have six, so that’ll work. We’ll consider this a little outpost of the Kingdom of God until we can meet again and sing together.

Right now I don’t know if we have a week or a month of isolation ahead, and I don’t know if someone I love will get sick. That’s a real and scary possibility. The first Washington case was just published in the New England Journal of Medicine, and that patient had two weeks of intense illness, and he’s ten years younger than me.

I don’t know if that man’s case is typical or not. All I know is that God made a world with rules. The contagion follows rules and hides where we can’t see it. But by following these rules, we can take the virus apart, isolate its genes, find out where it’s been, and eventually predict where it’s going. Wherever that is, we know that God stands with us, today, to the end of the world, and beyond. So be it.

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About the author

Ben McFarland

Ben McFarland teaches biochemistry and chemistry at Seattle Pacific University in Seattle, Washington. He grew up near Kennedy Space Center and wanted to be a paleontologist in the second grade. He received a dual B.S. in Chemistry and Technical Writing from the University of Florida and a Ph.D. in Biomolecular Structure and Design from the University of Washington. His research uses the rules of chemistry to redesign immune system proteins. In 2013 he received an Evolution and Christian Faith (ECF) grant from BioLogos to write A World From Dust: How the Periodic Table Shaped Life (Oxford University Press, 2016). He lives near Seattle with his wife Laurie and his children Sam, Aidan, Brendan, and Benjamin.