CREDIT: P. HORÁLEK / ESO

How researchers are making do in the time of Covid

The coronavirus pandemic has shuttered labs and sidelined scientists all over the world. Here’s a look at how some of them have coped.

Anil Ananthaswamy • knowable
Dec. 2, 2020 21 minSource

How researchers are making do in the time of Covid

The coronavirus pandemic has shuttered labs and sidelined scientists all over the world. Here’s a look at how some of them have coped.

12.2.2020

One of the astonishing aspects of the human response to the Covid-19 pandemic has been how quickly scientists pivoted to studying every facet of the virus in order to mitigate the loss of life and plan for a return to normalcy. At the same time, a lot of non-coronavirus research ground to a near halt. 

With research labs and offices shuttered for all but essential workers, many scientists were stuck at home, their fieldwork and meetings canceled and planned experiments kicked down the road as they struggled to figure out how to keep their research programs going. Many took the opportunity to catch up on writing grants and papers; some — in between caring for kids — came up with strategic workarounds to keep the scientific juices flowing.

To gauge how researchers in different fields are managing, Knowable Magazine spoke with an array of scientists and technical staff — among them  a specialist keeping alive genetically important strains of fruit flies, the maintenance chief of an astronomical observatory working to keep telescopes safe and on standby during the lockdown, and a pediatrician struggling to manage clinical trials for a rare genetic disease. Here are a few slices of scientific life during the pandemic.  

Agnieszka Czechowicz, Stanford University School of Medicine

Czechowicz is a pediatrician in Stanford’s division of stem cell transplantation and regenerative medicine, where she manages a research group that develops new therapies and conducts clinical trials on rare genetic diseases.

Agnieszka Czechowicz’s father suffers from severe Parkinson’s disease. The coronavirus pandemic forced him to remain indoors and away from people, robbing him of the physical conditioning and social interactions he needs to cope with his disease. A recent fall left him in the hospital, bringing the additional worry that he might contract Covid-19 there and isolating him further.

For Czechowicz, his situation brought into sharp relief the challenges the coronavirus has forced upon those carrying out clinical trials, including those she is running, which involve patients traveling to hospitals around the country. “Would I have him travel to any clinical site right now for a new Parkinson’s treatment?” she says. “Absolutely not.”

The pandemic forced Czechowicz to halt clinical trials she oversees for a rare genetic disease of children called Fanconi anemia, a condition that impairs the body’s ability to repair damaged DNA and often leads to bone marrow failure and cancer. The treatment Czechowicz and colleagues are testing involves extracting blood-forming stem cells from the patient’s bone marrow, inserting a healthy copy of a missing or malfunctioning gene and then reinfusing those cells back into the patient.

“Every aspect of what I do is massively impacted by the pandemic,” Czechowicz says. One of her early-stage clinical trials involves testing the safety of the therapy. But during the initial shutdown — which started in mid-March and lasted for two months — her patients could not readily travel to Stanford for the necessary follow-up visits, and remote monitoring was difficult.

“There’s special blood testing and bone marrow testing that we need to do. In particular, it’s critical to get the samples to make sure the patients, for example, aren’t developing leukemia,” she says. “There’s no way to know that without really checking the bone marrow.” She had to clear large hurdles to get her patients evaluated.

Another early-stage trial, designed to determine the effectiveness of the therapy, also had to stop enrolling new patients. Because speed is important when it comes to treating Fanconi anemia — the children are likely losing stem cells all the time — any delay in treatment can be a source of great anxiety for their parents. Czechowicz had to explain to them why the trials were temporarily halted. “It was really challenging to have these discussions with the families,” she says.

With the easing of travel and workplace restrictions, the families began traveling to Stanford in June — but with infections back on the rise, many families are becoming hesitant again, says Czechowicz. Fortunately, her trials are small, so she can guide each family through the process of safely resuming the trials and continuing with follow-up. Her own team also has to follow strict safety protocols. For example, even though her lab has 10 members, only two can be in the lab at any one time, and only one parent is allowed into the clinic with the child.

Not all clinical trials can pay such close attention to individual patients. Large trials with hundreds of patients can involve multiple sites and require much more monitoring, so resuming those remains difficult. Also, restrictions on working full bore are slowing the pipeline for new therapies. “The impact of that, we’re not going to see for many years to come,” Czechowicz says. 

Abolhassan Jawahery, University of Maryland, College Park

Jawahery is a particle physicist and a member of LHCb, one of the main experiments at the Large Hadron Collider (LHC) at CERN, the particle physics laboratory near Geneva.  

In December 2018, well before the coronavirus pandemic began, the LHC shut down for upgrades. Housed in a 27-kilometer-long tunnel about 100 meters underground, the LHC accelerates two beams of protons, one clockwise and one counterclockwise, and makes them collide head-on at four locations. There, four gigantic subterranean detectors — ATLAS, CMS, LHCb and ALICE — sift through the debris of particles created by the collisions, looking for evidence of new physics. (For example, ATLAS and CMS found the Higgs boson, the fundamental particle of the Higgs field, which gives all elementary particles their mass.)

For its next set of experiments, which aim to probe the properties of subatomic particles with greater precision, the LHC needed to increase the intensity of its proton beams. Consequently, the four detectors needed to be upgraded too, to handle the resultant higher temperatures and increased radiation at the sites of the particle collisions. The work was on track for a restart around May 2021 until the pandemic swept all the scientists’ careful plans away.

The LHC and its four detectors are each run by a separate collaboration. CERN, which manages the LHC, is hopeful it can restart the collider by February 2022. “They think that they can get the accelerator going if there are no more major catastrophic events,” says physicist Abolhassan Jawahery. But the impact on the four detectors is less clear.

For the LHCb upgrade, Jawahery’s team at the University of Maryland had been working on building about 4,000 extremely sensitive electronic circuit boards. These boards have to be “burned in” before they can be sent to CERN. “We put them in an oven, literally cooking the boards and then running extensive tests in order to get them ready so that we can put them in the accelerator and run them for 10 to 20 years,” says Jawahery. “And none of that could be done during the pandemic shutdown.”

The team resumed its work in June, but with restrictions put in place by the state of Maryland. Jawahery runs two labs, and for months was allowed only two people at a time in one lab and three in the other, making progress extremely slow. Still, his team is fortunate that it does not depend on supplies from countries hit hard by the coronavirus. Other labs weren’t so lucky. Scientists in Milan, for example, built some electronics and detector components for the LHCb, and a lab at Syracuse University in New York built sensors that relied on shipments from Milan. When Milan was completely closed down at the height of the pandemic, Syracuse, too, stopped working on Milan-dependent components.

For Jawahery the lockdown had a silver lining. The LHC’s most recent run had produced about 25 gigabytes of data per second — but his team had found little time to analyze any of it before the pandemic. “We were complaining that we were spending all our time building the new instrument and the data keeps on coming,” he says. When he and his team were locked out of their labs, they turned to their data backlog. “We could do actual physics,” he says. “We are already getting ready to publish some papers.” 

Gordon Gray, Princeton University

Gray is a professional Drosophila  specialist in the department of molecular biology. 

Gordon Gray has been called the chef de cuisine of Princeton’s fly kitchen, where he has been feeding flies for 46 years. He concocts meals for millions of fruit flies, at least 150 liters each week. When the pandemic hit in March and universities around the world shut down, Princeton deemed Gray’s work an essential service: The Drosophila fruit flies could not be allowed to die off.

Princeton’s flies include mutant and transgenic strains — everything from ones that allow researchers to study the genes that influence normal development of a fly embryo’s organs, to those that have cancer-causing mutations. If the flies starved, researchers would need months or years to recreate these strains, says Princeton molecular biologist Elizabeth Gavis. And often, as techniques in molecular biology improve, the biologists reexamine flies they had studied earlier to get a more fine-grained understanding, making it worthwhile to preserve the strains.

Normally, if a lab had to shut down, researchers would send their flies to stock centers, such as one at Bowling Green State University in Ohio, that preserve the flies as part of their genetic library. But the stock centers couldn’t handle Princeton’s flies, so Gray found himself on his own. “It’s basically catch as catch can with regards to the various labs here, just to keep things operational,” he says.

For months, university pandemic restrictions have allowed only one person to be in Gray’s kitchen at a time. This has caused problems. Before the pandemic began, Gray, who is in his late 60s, had started training someone as a backup. But because of the one-person restriction, Gray and his trainee haven’t been able to work together. Gray envisions doing so soon, while wearing masks, keeping nearly 12 feet apart and communicating using hand signals.

To whip up a batch of fly food, or media, Gray uses a 50-liter steel cauldron, to which is attached a mixer that looks like an outboard motor. Gray fills the cauldron with water and adds agar, sugars, yeasts, salts and cornmeal, then brings it to a boil, all the while stirring watchfully. “You don’t want it to boil over, because when it does you wind up with a gigantic pancake on the floor, which you have to scoop up immediately because it gels,” he says. Once the suspension cools to the right temperature, Gray adds an acid to inhibit mold, then dispenses precise amounts of the media into bottles and vials.

Even before the pandemic, Gray’s kitchen was isolated, to keep errant fruit flies from contaminating the pristine media. But at least he could work regular hours, because he knew the rhythms of the 10 or so fly labs he cooked for. That has changed. Labs, restricted to two occupants at a time, are now working seven days a week on rotating shifts. Gray comes in to work at all hours, because he cannot predict when each batch of fly food will run out and he’ll need to cook more.

He tries to work mostly at night to avoid coming into contact with others. But he still worries for his health, given his asthma and age-related risk. The relentless pandemic is taking a toll. “It’s exhausting,” he says. “It doesn’t help not knowing when we will return to a sense of normalcy.” 

Celeste Kidd, University of California, Berkeley

Kidd is a child developmental psychologist who uses behavioral tests and computational methods to understand how children acquire knowledge. 

When UC Berkeley locked down in March, Celeste Kidd found herself closeted at home, dealing simultaneously with virtual meetings and her three-year-old son. During the early days of the pandemic, Kidd kept a supply of treats handy, and when her toddler came up to her during a meeting she’d sneak him some under the desk. But she hadn’t accounted for how long the pandemic would last. “It turns out that’s not a good strategy, long term,” she says. “I was very literally rewarding him for bad behavior.”

Kidd’s son soon learned that acting up during her meetings meant more candy. “I knew that would happen. I did it anyway because I didn’t have the bandwidth to come up with a better solution,” she says. But Kidd knew from her own research that children are also extremely flexible and can unlearn behaviors. Eventually, she had a chat with her son. First, she admitted to him that she had made a mistake by giving him candy when he disrupted her meetings, and that was “bad” of her. Then she brought in new rules: no candy for misbehaving — and misbehavior could even mean no treats for the rest of day. “We had some meltdown moments,” says Kidd. “But he gets it now and he doesn’t do those things.”

Her son may be the only child Kidd gets to interact with during the pandemic. That’s a huge loss for her research, because the bulk of her work focuses on young children. In normal times, families would bring their children to her lab, where her research team would track their gaze as they watched videos. In one study, for example, infants about seven to nine months old would look away (demonstrating lack of interest) when the events in the video were either too complex or too simple, suggesting that infants use their cognitive resources for stimuli that have just the right amount of information.

Such work, of course, requires the presence of parent, child and researchers, all in the same room. “None of that is going to happen anytime soon,” she says. “Those families are not going to feel comfortable coming in for a while.”

Kidd is also concerned about the impact of the pandemic on younger scientists. One of her undergraduate students had spent six months working on a study aimed at exploring the complexity of kids’ play patterns using physical objects and their relation to working memory and other cognitive resources.  The university had approved the protocol, but shelter-in-place orders went into effect the week the first child was to come for the experiment. “I feel so bad for her as a young scientist, to have done all this hard work and then right when you get to the fun part, which is collecting the data and finding out if her ideas have lasting merit, she doesn’t get to do that part,” Kidd says.

The situation might be even worse for grad students and postdocs. “All of them are experiencing a big blow to morale in general, because there is so much uncertainty about what the future holds,” she says. University budget cuts mean fewer slots for graduate students and fewer jobs for postdocs. “It’s very hard to stay motivated and get things done when you’re not sure if there will be a payoff in the future,” says Kidd. “That’s literally a study that we ran in the lab so we’re all acutely aware of it.” 

Maxime Boccas, ESO Paranal Observatory

Boccas is the head of maintenance, support and engineering at the European Southern Observatory’s Paranal Observatory in Chile. 

When the massive domes of the Very Large Telescope, a constellation of four 8-meter-class telescopes atop Mount Paranal in Chile’s Atacama Desert, open to the night sky each evening and the telescopes get ready for observations, it’s like a dragon waking up.

When the pandemic hit in March, the dragon on Mount Paranal closed its eyes to the cosmos and slept — the first shutdown in its 20-year history, which included a major earthquake in 2010 that paralyzed much of the rest of Chile. For those who had to leave Paranal, it was like being sent away from home. “We spend 40 percent of our life here,” says Maxime Boccas, who oversaw the process of ensuring an orderly shutdown of the site’s scientific and technical facilities. “We work and sleep here, and we stay here eight days in a row.” Some of Boccas’s colleagues have been doing that for 20 to 25 years. Leaving Paranal was like leaving their second home. “That was a weird feeling.”

The skeleton staff — just 20 of the normal 150 or so people remained on site — kept the observatory safe, ensuring that essential systems continued working: computers that astronomers were accessing remotely, the fire detection system and the earthquake protection system essential for protecting the 8-meter-wide primary mirrors from Chile’s frequent quakes. The mirrors will likely never be made again, says Boccas. “All the factories that cast and polished them are dismantled. If we lost a mirror, it would take between 5 and 10 years to build up the factory again and fabricate it.” So each mirror has an airbag — a tube that inflates around it when the system detects tremors — and other protections.

During the shutdown, astronomers kept their fingers crossed. “They were anxious that no big thing, like a supernova in our galaxy, would explode,” Boccas says. The heavens have been quiet, but the six-month shutdown harmed research that involves continuously monitoring the same patch of the sky for transient phenomena such as gamma ray bursts. “It creates a hole in their science program,” says Boccas.

The observatory began a slow return to normalcy on September 9. Boccas is overseeing the reawakening of each telescope, one at a time. The staff — still less than full strength — is now working in shifts that have doubled from 8 to 15 days to limit the amount of travel to and from the site. The four large telescopes are now up and running again, and Boccas hopes they will be back to working together as one by the end of January.

Boccas, his crew and a few lucky astronomers are glad to be back at Paranal. “It really feels like a family and I think everyone has noticed that,” he says. “Even in the kitchen, they have to cook for 30 people instead of 150, so the quality of the food is different, it’s slightly better.”  

But even as people return to the observatory, Boccas worries about long-term effects of the shutdown. Given the reduced staff, he has had to cut down on the frequency of preventive maintenance tasks, such as changing belts and lubricating motors, potentially shortening the lifetime of some components. “We will not know until six months, a year or three years from now,” he says. 

This article originally appeared in Knowable Magazine, an independent journalistic endeavor from Annual Reviews. Sign up for the newsletter.

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