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Why Two Parents Are the Ultimate Privilege | The Free Press

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One of the words that’s become utterly void of meaning in the last few years because of its overuse and misuse is privilege. White privilege, male privilege, able-bodied privilege, gender privilege, heterosexual privilege, even hot privilege. In these contexts, privilege is a stain, an original sin meant to guilt the offending party into repentance. 

“Check your privilege” became a common refrain of the past decade. What all of this has done is confuse and undermine the idea of real privilege, which, of course, really exists in this country. 

The ultimate privilege in America is not being born white or straight or male. The ultimate privilege, as Melissa Kearney argues, is being born into a household with two parents.

Melissa Kearney is an economist at the University of Maryland and her new book, The Two-Parent Privilege: How Americans Stopped Getting Married and Started Falling Behind, argues that declining marriage rates in America—and the corresponding rise in children being raised in single parent households—are driving many of the country’s biggest economic problems. In the 1950s, fewer than 5 percent of babies in this country were born to unmarried mothers. Today, nearly half of all babies in America are born to unmarried mothers. Most surprising—and worrisome—is how this trend is divided along class lines, with children whose mothers don’t have a college degree being more than twice as likely—compared to the children of college-educated mothers—to live in a single parent home. 

Many of the arguments Kearney makes in her book are what you might call common sense. And yet the book has received criticism. But as celebrated economist and our friend Tyler Cowen said of Melissa’s book, “it’s remarkable that such a book is so needed, but it is.”

The word privilege, as Melissa Kearney uses it, is not a dirty word. Quite the opposite. It’s aspirational. It’s meant to inspire policies, programs, and changes in our social norms to even the playing field so that we can do better for all of our children. So that every child in America has the best possible chance for flourishing. That is what every child in this country deserves. 

Click here to listen to my full conversation with Melissa or read an edited excerpt below. —BW

Why people aren’t getting married anymore:

BW: Over the past 40 years, there has been a dramatic decline in the share of children living with married parents. In the 1950s, less than 5 percent of babies in America were born out of wedlock. Today, half of all babies in this country are born to unmarried mothers. How did we get from there to here? 

MK: It’s a misconception that couples are becoming less wed to the institution of marriage, so they’re just cohabiting. That’s not the case. Roughly 30 percent of kids in the U.S. live outside a two-parent home. More kids in the U.S. than in any other country in the world are now living with just one parent. And it’s not about an increase in divorce. Divorce in the U.S. is down from the mid-eighties. This decline in marriage, this rise in the share of kids living with just one parent, and this rise in nonmarital childbearing, has happened predominantly outside the college-educated class. That’s why this topic is so instrumental to conversations and concerns about inequality and threats to social mobility. It’s really among more economically vulnerable parents that there’s been this rise in kids living outside of a two-parent or married parent setting. 

BW: This wasn’t always the case. From the 1960s through the 1990s, women with college degrees were actually less likely to be married than women without college degrees. What happened in those intervening decades?

MK: In the ’60s and ’70s, there was a sociocultural revolution in the U.S., which included changing expectations about marriage, a greater acceptance of having a child outside of a marriage, and changing expectations about gender norms. We saw decreases in marriage across the education distribution in roughly equal proportion. In the ’80s, ’90s, and early 2000s, marriage rates among college-educated adults stabilized. Economics is a big part of the story. College-educated adults did really well in those decades, and they continued to see increases in their earnings. But outside the college-educated class, men saw their employment rates decline and their earnings decline.

We saw a loss in a number of jobs that in previous generations provided family-sustaining, well-paying jobs for men without college degrees: manufacturing jobs, industrial production jobs, etc. Those jobs were eliminated, and we saw a corresponding decrease in marriage and an increase in the share of kids living in single-mother homes among affected communities such that economists have drawn a causal connection. That’s the sort of unromantic model that strips out love and compatibility and just looks at the economic incentives to marry or not. It turns out to be pretty predictive. 

BW: The one big exception to the rule here is Asian American families, who across all education groups and all classes have really high rates of marriage and two-parent households. Why do you think that is, and what can we learn from their success? 

MK: That was the finding that surprised me the most when writing this book. Among whites, among blacks, among Hispanics, there’s this huge college gradient. But among Asian Americans, regardless of maternal education, there are really high rates of two-parent homes. So the least-educated moms who identify in the census as Asian American are more likely to live in married parent situations than the most educated Hispanic and black moms. It’s not explained by different economic situations. Non-college-educated Asian men saw the same economic trends over the past 40 years as white men, black men, and Hispanic men, but without the subsequent reduction in marriage. That makes me think that there is a strong role here for social convention.

Why the decline in marriage is bad for children and bad for the economy: 

BW: You say that the decline in the two-parent household has economic consequences that we cannot afford to ignore. Why is a two-parent household, from the perspective of an economist—not a social conservative or a pastor—better than one parent in the household? 

MK: Two parents combined have more resources than one. Two parents in a home bring in the earnings—or at least the earnings capacity—of two adults. And so, in a very straightforward way, we see that kids growing up in single-mother homes are five times more likely to live in poverty than kids growing up in married parent homes. (Kids in single-father homes are three times as likely to live in poverty.) Some of that reflects the fact that people with lower levels of education or income are more likely to become single parents. But even if you compare across moms of the same education group, you see that kids who grow up in a household with two parents have household incomes that are about twice as high. That means that those parents are paying for things like a nicer house in a safe neighborhood with good school districts. But they also spend more time with their kids. We see that kids who grow up with married parents have more parental time invested in them: reading to your kid, talking to your kid, driving your kids to activities. If there are two parents in the household, there’s just more time capacity.

None of this is to denigrate single moms or single dads. It’s just a reflection of the reality that two adults in the household have more combined time than one alone. Another set of resources that we have a lot of evidence on is there’s more “emotional bandwidth” (and less stress) in households that have two parents as compared to one. We see in the data that married parents are less likely to resort to spanking and harsher parenting. They’re more likely to report having strong, nurturing bonds with their kids. We also see that kids from two-parent households are less likely to have behavioral issues. They’re more likely to reach educational milestones. They’re less likely to get in trouble with the law. All things that set them up to be in a better position to thrive in life. 

It’s certainly not the case that all of these single-parent households would be better off if the second parent were in the house. We have evidence that when the second parent might be a negative influence, the child is better off with just one parent. If the second parent would bring instability and chaos, that’s not good for the kid. 

BW: Some people might hear all of these dire statistics and think, “We were better off in the world before the 1960s, where men had a very clear socially prescribed role as the breadwinners and women had a very clearly socially prescribed role, which is they took care of the home, and maybe we should return back to that.” How would you respond? 

MK: I do not in any sense bemoan women’s economic independence. Unequivocally, I think it’s a good thing that women are more able to provide financially for themselves and their children and not have to be married. Having said that, to the extent that these trends are being driven by men’s economic opportunity and position being eroded, that’s a bad thing. And we should be able to hold both of those thoughts in our mind at the same time, that women having economic opportunities is a good thing and men losing earnings potential and employment is a bad thing.

Another important thing to note is in survey evidence, you don’t see widespread rejection of marriage as an institution. You don’t see in the U.S. that there’s been a widespread move away from the desire to get married. Rather, it feels like achieving a stable, married home is a bit of a luxury good. It’s something that’s harder for people without higher levels of education and income to achieve. So for that reason, we should not be okay with that advantageous institution being something that’s increasingly out of reach for those who aren’t in the highest education income classes in our society. 

On solutions to the single-parent problem:

BW: What are some of the policies and programs that you think the local and federal government should adopt to help strengthen families? 

MK: If you look at the Administration for Children and Families budget, only 1 percent of their budget goes to community programs that have an explicit goal of strengthening families. I would put a lot more money and research emphasis on building up an evidence base in the kinds of community programs that work and then scale them. We also need to double down on all of the things that we talk about to improve the economic position of adults in this country without college degrees. If the adult can’t bring in money and doesn’t have stable employment, that brings so many struggles. Bolstering the economic position of vulnerable adults and parents is really critical and we just haven’t done enough there. 

I also think we need to promote a social convention of two-parent homes for kids. We do have social science evidence suggesting that role models matter, that celebrity messaging matters, that local leader messaging matters. This is why I think it’s important we’re honest about the benefits of two-parent households and fatherhood engagement for kids. I think many people are rightly hesitant to promote two-parent households because in the past, single mothers and their children were so stigmatized that they were essentially outcasts from communities. We should never go back to that, but there’s got to be a way for us to promote two-parent involvement in their kids’ lives. 

BW: One of the things that is surprising about our current moment is that some of the programs, including subsidies and tax credits, that used to be thought of as the precinct of the political left, have now been embraced by surprising people on the right. Talk to us about the changing politics of this issue that makes you think bipartisanship might be possible on this.

MK: People on the left have traditionally been more willing or eager to spend money to help low-income families. Now, people on the right are very explicit about the need for pro-family policy agenda. We all want to build a healthier society for families, and we should be supporting vulnerable families regardless of parental marriage structure. In the past, cash welfare was only available to single moms, and if you had a man living in the house, you would lose your check. Obviously, that’s a bad idea.

Even though we don’t explicitly disincentivize marriage now, our tax and transfer system does implicitly disincentivize marriage. For example, if you’re married and you’re both working, you’re much less likely to qualify for the earned income tax credit because our tax code works where you pool the income across two people. So a woman who might be on the margin of making $30,000 gets the earned income tax credit. If she marries that guy making $50,000, her and her child lose the earned income tax credit and lose Medicaid. This gives her the incentive to cohabit instead of getting married. And so our tax and transfer system unintentionally does discourage marriage—at least between two people who work. We should be getting rid of all of those legacy effects.

Why this is “forbidden” research:

BW: This book and your findings have been received like it’s been a nuclear bomb, at least in certain contexts. Why is that? How did this topic become so out of bounds? 

MK: This issue was first raised very prominently by Daniel Patrick Moynihan in the ’60s when he was an analyst at the Department of Labor, and he wrote a memo calling attention to the large share of unmarried moms in that black American community at the time. A big part of his memo was saying there’s high unemployment rates among black men that’s contributing to this. But in the ’60s, it got shut down with accusations of him being a racist. And there was some really unfortunate language that would strike us now as unproductive, as cultural shaming. So it got shut down as a racist topic for years.

In the ’80s and ’90s, the welfare reform debate had explicit language in the final federal law calling attention to the rise in nonmarital childbearing as a social problem. So it very much took this position that marriage was beneficial for kids. But during that debate, there were some really ugly, racialized stereotypes of the welfare queen. So I do think the racial element has made it particularly challenging to talk about. 

BW: You write that you would speak to your fellow scholars about your plans for writing this book, and they would say things along the lines of, “I tend to agree about all of this, but are you sure you want to be out there saying this publicly?” How many areas of research, inquiry, and basic curiosity about the most important things in our lives and culture are third rail now? If it’s taboo to write a book saying two parents in a house are better materially than one, what else is off-limits, and what can we do to combat that? 

MK: The University of Chicago Press published my book. It wasn’t an easy process. I got four reviews, and one of the reviewers basically told the Press, “You should not be publishing a book in 2023 that calls for a return to marriage.” So even at the Chicago Press, which you might think is the most committed to just telling the hard truths, it wasn’t a walk in the park to get this book past the reviewers. This worries me deeply as a scholar, as a teacher, as a researcher. It worries me deeply that there are right answers and there are wrong answers among academics.

There are clear pressures of what topics are valued, what topics people should pursue, what topics are going to get published in the best journals. I think that is really antithetical to what we should be doing as scholars. When my friends outside the academy ask, “Is it really as bad as people say?” I’m like, “Oh, it’s something that worries me deeply.”

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Liked on YouTube: Lighting the Beacons and Other Perfect Movie Metaphors

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Lighting the Beacons, and Other Perfect Movie Metaphors
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Liked on YouTube: I Was SCARED To Say This To NASA... (But I said it anyway) - Smarter Every Day 293

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I Was SCARED To Say This To NASA... (But I said it anyway) - Smarter Every Day 293
If you'd like to consider joining the Patreon Sticker Team, Click Here! 👉 <a href="https://ift.tt/LIhPKmA" rel="nofollow">https://ift.tt/LIhPKmA</a> 👈 A big thanks to the Jim Way, Executive Director of the American Astronautical Society for Inviting me to Speak: <a href="https://ift.tt/IkHdtYo" rel="nofollow">https://ift.tt/IkHdtYo</a> A big thanks to The University of Alabama in Huntsville for Hosting: <a href="https://www.uah.edu/" rel="nofollow">https://www.uah.edu/</a> Dr. Jason Cassibry is my PhD Advisor: <a href="https://ift.tt/tS0IT4M" rel="nofollow">https://ift.tt/tS0IT4M</a> Talk Filmed by: <a href="https://ift.tt/RJmzEMc" rel="nofollow">https://ift.tt/RJmzEMc</a> Click here if you're interested in subscribing: <a href="http://bit.ly/Subscribe2SED" rel="nofollow">http://bit.ly/Subscribe2SED</a> ⇊ Click below for more links! ⇊ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ GET SMARTER SECTION This talk was given at the von Braun Space Exploration Symposium: <a href="https://ift.tt/Ox0fdzE" rel="nofollow">https://ift.tt/Ox0fdzE</a> What Made Apollo a Sucess? NASA SP 287 <a href="https://ift.tt/C9wuvRq" rel="nofollow">https://ift.tt/C9wuvRq</a> Saturn V Quarterly Reports: <a href="https://www.youtube.com/watch?v=_Hm4taLUCmw&list=PLbEPfQne9a3zPJRdBb-HAqhdCHcAADeYq" rel="nofollow">https://www.youtube.com/watch?v=_Hm4taLUCmw&list=PLbEPfQne9a3zPJRdBb-HAqhdCHcAADeYq</a> Artemis III <a href="https://ift.tt/UgGX7Fo" rel="nofollow">https://ift.tt/UgGX7Fo</a> NRHO Orbit: <a href="https://ift.tt/hnxkRKF" rel="nofollow">https://ift.tt/hnxkRKF</a> <a href="https://ift.tt/7Qs8xMR" rel="nofollow">https://ift.tt/7Qs8xMR</a> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Tweet Ideas to me at: <a href="http://twitter.com/smartereveryday" rel="nofollow">http://twitter.com/smartereveryday</a> Smarter Every Day on Facebook <a href="https://ift.tt/OsyuSta" rel="nofollow">https://ift.tt/OsyuSta</a> Smarter Every Day on Patreon <a href="https://ift.tt/h30YAQr" rel="nofollow">https://ift.tt/h30YAQr</a> Smarter Every Day On Instagram <a href="https://ift.tt/bzNxRfq" rel="nofollow">https://ift.tt/bzNxRfq</a> Smarter Every Day SubReddit <a href="https://ift.tt/uy2j4gK" rel="nofollow">https://ift.tt/uy2j4gK</a> Ambiance, audio and musicy things by: Gordon McGladdery <a href="https://ift.tt/lX05PJR" rel="nofollow">https://ift.tt/lX05PJR</a> <a href="https://ift.tt/5xoAU49" rel="nofollow">https://ift.tt/5xoAU49</a> If you feel like this video was worth your time and added value to your life, please SHARE THE VIDEO! If you REALLY liked it, feel free to pitch a few dollars Smarter Every Day by becoming a Patron. <a href="https://ift.tt/h30YAQr" rel="nofollow">https://ift.tt/h30YAQr</a> Warm Regards, Destin
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The road ahead for EV adoption is made of gravel - The Verge

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Every day, Mitch Stults commutes about 60 miles each way from his home in Muscle Shoals, Alabama, a town of 17,000 people, to his job as a sales manager for a manufactured homebuilder in Cullman.

Stults was driving a King Ranch pickup 110 miles per day, spending an estimated $1,000 on gas per week, and getting just 13 miles to the gallon. “That was when I decided to give a Tesla a try,” he said.

Stults, 29, began hunting for a Tesla Model Y and found one at a dealership in Tupelo, Mississippi, 87 miles away. He traded in his King Ranch a few days later.

But the thrill of an electrified ride didn’t last long. Three months later, Stults returned the Tesla and traded it in for a GMC half-ton Duramax diesel pickup. 

“That was when I decided to give a Tesla a try.”

“I ended up getting over it because of the job that I do,” Stults said, noting that there are times when he has to go off-road to get to a wooded property. “The tipping point was a customer needed a set of stairs, and I had no way to get them out to them,” More importantly, however, he said that even with a range of 315 miles, he had moments of anxiety. “There were a few times where it was just hopes and prayers that you find a Supercharger,” he said. 

Stult’s attempt to go all-electric and his very real struggles with electric range are not uncommon in rural America. Rural populations make up about 20 percent of the current population in the US, according to the most recent numbers from the Census Bureau, and 68 percent of all the lane miles in the US are in rural America, according to the Bureau of Transportation Statistics. On average, Americans drive about 15,000 miles per year, and those in rural areas drive roughly 10 more miles per day than urban dwellers, which amounts to nearly 4,000 additional miles per year. Everything in rural America is just further apart. 

That distance has been an issue for everything from the current EV infrastructure and broadband rollout for rural America to the basic electricity installation in decades past, according to Nicholas Jacobs, an assistant professor of government at Colby College in Maine and the author of The Rural Voter: The Politics of Place and the Disuniting of America, released in November this year.

“You’re talking about big swaths of space that are just more expensive to cover when you’re dealing with infrastructure projects,” he said. “We learned that with electrification during the New Deal. There’s a reason why electricity didn’t get to rural America until the 1950s,” Jacobs said.

Everything in rural America is just further apart

These challenges have spurred the federal government to make huge promises to help electrify the country, including huge investments to the tune of $7.5 billion to help America make the electric transition.  

Yet, there are some questions about how rural America will get to the electric future alongside the country’s more populous cities, which already boast more income, higher EV adoption rates, and more public EV charging infrastructure. Between a current lack of robust public charging infrastructure, divisive politics, and class warfare surrounding everything from technological hurdles and climate change to the practicality of EVs, the rural EV transition is facing a very bumpy road ahead. 

Electrification in rural America: where are we now?

It’s difficult to get clear numbers on the EV transition in rural America. For one, public charging infrastructure is a bit of a moving target, with everyone from utilities, auto manufacturers, and private companies to governments and universities racing to install new chargers. Richard Mohr, senior VP of Americas at ChargePoint, points out just how fast the build-out is happening in rural areas. 

“When you look at EV charging deployments outside of large metropolitan areas, there are multiple charging companies deploying AC charging across segments of where people work, play, and sleep,” Mohr said. “It’s getting harder to not find some kind of charger.” 

“It’s getting harder to not find some kind of charger.”

He also shared his own anecdote involving his son, who attends school in northern Alabama and drives a Ford Mustang Mach-E. From one summer to the next, Mohr and his son went from being unable to find any chargers that were on their route to finding numerous ones. 

Like Tesla, some automakers are paying for their own charging installations. Volvo recently completed its charger installation in partnership with Starbucks, installing 60 chargers at 15 stops between Seattle and Denver, through some rural areas. Alex Tripi, head of electrification at Volvo, said that the company specifically chose that route because it had been underserved with charging. 

Electric co-ops like the National Rural Electric Cooperative Association, or NRECA, say that they are approaching electrification in whatever way makes the most sense for each individual community. “That might mean becoming directly involved in the deployment of charging infrastructure, but it could also mean helping or partnering with other providers interested in meeting that need. Just as long as the job gets done,” according to Jennah Denney, the electric vehicle strategy and solutions manager at NRECA.

EV registrations in rural areas in the US are still relatively low compared to those in cities, according to the Environmental and Energy Study Institute. Most rural areas register new electric vehicle rates of between 0 and 0.5 percent, which translates to fewer than five (and, in many cases, zero) registered EVs per 10,000 people in the majority of nonmetro counties​​​​, according to the 2021 report. 

EV registrations in rural areas in the US are still relatively low compared to those in cities

A recent study looked at data across eight years for the adoption of electric cars and SUVs. It concluded that advancing technology will continue to drive EV adoption in all communities, including rural ones. “If electric vehicles are offered as ubiquitously as gasoline vehicles, and if their technology goes where we think it’s going to go, then we would expect roughly half of people to prefer an electric over a gasoline for both cars and SUVs,” said Jeremy Michalek, a professor of mechanical engineering and engineering and public policy at Carnegie Mellon University and a co-author of the study. 

Another study shows that demand for electric pickup trucks is also up but notes that particular market is a bit more complicated due to everything from vehicle availability (there are a smaller number of all-electric pickups on the market today) to politics. As Michalek points out, there are some pickup truck buyers who simply won’t make the electric shift, no matter how much EV technology improves.

He refers to them as “holdouts” and said that, according to his study, there are about 22 percent of pickup truck buyers who simply won’t go all-electric. Holdouts take issue with everything from claims that climate change is a human-caused phenomenon to the idea that buying an EV sends jobs overseas, a frequent Donald Trump-repeated falsehood

Politics and rural electrification

To be sure, we can’t talk about EVs without talking about politics and class division. According to Michalek at Carnegie Mellon and Jacobs at Colby, the divides are particularly acute in rural America. 

Jacobs said that when electrification is framed around a transition to renewable energy or climate goals, it’s frequently met with the resistance of tribal politics. 

“These are not usually discussed by mainstream political figures as policies that benefit rural Americans,” he said. “These are usually draped in the imagery and the culture or cultural signals that this is something that progressives, read urban people, mostly care about. That’s not to say it’s true. But there’s certainly a perception out there that things like electrification are not from rural America, maybe not for rural America.” 

There are some pickup truck buyers who simply won’t make the electric shift, no matter how much EV technology improves

That sentiment has frequently manifested itself in behavior like vandalism and “ICE-ing,” a practice that occurs when internal combustion engine vehicles park in spots reserved for charging electric vehicles. Republican candidates for president on the stump have been trying to turn EVs into a wedge issue throughout the primary campaign.

Then there’s the sheer expense of EVs, which automatically excludes those with fewer financial resources. According to Kelley Blue Book, the average new EV price for the month of October this year was $51,762, nearly $4,000 more than the average price of an internal combustion engine vehicle. Rural per capita income as of the most recent USDA Economic Research Service report from 2021 was just shy of $50,000 per year at $49,895. Urban per capita income, in contrast, was $66,440 per year. EV ownership also generally requires the installation of a home charger and an upgrade to electrical panels, which can cost thousands, all of which means that EVs are still well out of reach for lower-income buyers, a phenomenon that is particularly acute in rural areas.

Stults had his own experience underlining what the experts say about both politics and income disparities in rural areas. Stults said that a motorcycle rider rode up next to him at a stop light while he was driving his Tesla, flipped him the bird, and sped off. He said it didn’t really bother him but that it did embody some of the sentiment that arises around the electric transition. 

“I think it’s going to take some time to grow in rural parts of the country,” Stults said. “They think it’s stupid because you can’t always charge it.” He continued, “The other thing around here is, it can be the middle of Kentucky or Tennessee — when you have something that automatically categorizes you to, ‘Oh he thinks he’s better than me because he has a Tesla,’ that just goes on a lot. Not just with cars, but with anything.”

Grid and technology challenges

Changing hearts and minds isn’t the only challenge to electrifying transportation in rural areas. Everything from grid updates to changes in how power is generated at peak usage times needs to be improved in order to make the transition smoother and more equitable. 

“Your utility has many constraints and needs across their whole distribution system,” Casey Donahue, the founder of Optiwatt, an app that helps EV owners optimize their home electricity usage for EV charging, said. “If everyone plugs in their electric vehicle at the same time and all charge at the same time, it’s going to put a lot of undue stress on the system. That causes utilities to fire up some peaker plants that are pretty much the dirtiest electricity we can generate.” 

“I think it’s going to take some time to grow in rural parts of the country.”

Transformers, which distribute power to individual locations, will need to be updated. “Local infrastructure does often have to be upgraded when there’s a large adoption of electric vehicles,” Michalek said. “A lot of those transformers are designed to cool down at night when nobody’s using them. So that’s when they go through their cycle. So if you charge at night, and then you’re just constantly using the transformer, they actually break down faster.” That’s problematic since the US is facing an ongoing transformer shortage for grid upgrades, with backorders taking more than a year to clear.

The EV transition could also affect the way that pollution impacts rural America. As cities get more electric vehicles, local emissions drop because fewer idling internal combustion vehicles are stuck in traffic. At the same time, the demand on power companies, which are generally located in more rural areas, increases, causing a potential increase in pollution around those plants.

“Some of the emissions go out of the urban areas where lots of cars are driving around and might move to become more distributed in the rural areas because there’s a smokestack from a power plant and those emissions get distributed over a really wide, wide area,” Michalek said. “I don’t think we’re talking about peak concentration of pollutants in rural areas. There’s just a little bit of a redistribution of where the pollution is happening.”

Finally, there is the question of managing high-demand periods for public charging infrastructure and its impact on rural areas. While most charging is done at home, there are times like the holidays when Michalek notes that demand may well outstrip public charger supply, which could put considerable stress on rural charging infrastructure. “On peak travel days, suddenly everybody needs a public charger,” Michalek said. “I do worry about the effect of this on rural  areas. Because some of that local infrastructure, if it’s mostly used by locals, there may be plenty of it, but then on peak travel days when lots of people are rolling through, suddenly there’s no charger available for the people who live there.”

A bumpy road ahead?

All of this points to a potentially bumpy road ahead for the electrification of rural America. Yet, as EV sales flatten in urban areas thanks to a saturation of early adopters, there’s still opportunity in rural communities. 

In spite of his experience with his Tesla, Stults said he does miss the crossover. He still said that he’d go all-electric all over again and that he hasn’t soured on the electric transition at all, and he thinks that more people like him will make the shift, even if there is some resistance.

“You know, maybe it’s going to be like guns,” Stults said. “People will hide their motorized vehicles, so they have a gas vehicle,” he said, “But I think people are interested enough in it. If they’re saving money, and they can fill up the same way they fill up with gas, the way the world’s going, I promise you, they’ll go electric.” 

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Visual timeline: 'Proximal Origin'

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Published early in the pandemic, an article in Nature Medicine titled “The proximal origin of SARS-CoV-2” — known to many simply as “Proximal Origin” — helped push the lab leak theory of the origins of COVID-19 to the outer fringes by March 2020.

“We do not believe that any type of laboratory-based scenario is plausible,” the analysis stated, which had been read about three million times within weeks of publication. “Our analyses clearly show that SARS-CoV-2 is not a laboratory construct or a purposefully manipulated virus.”

For years, the infectious diseases community had debated whether cutting-edge virology — gain-of-function research that generates more dangerous viruses — could cause a pandemic. Once a pandemic arrived, that debate abruptly ended.  

The virologists had sold the public on an irrefutably natural origin. 

But emails and Slack chat messages acquired through the Freedom of Information Act and subpoenaed by the House Select Subcommittee on the Coronavirus Crisis show that the virologists who wrote the analysis privately expressed concerns that the virus could have emerged from a lab. They also reveal the depth of involvement of some of the most powerful men in science, including former pandemic response leader and National Institute of Allergy and Infectious Diseases Director Anthony Fauci, in shaping the article. Fauci’s institute had funded the Wuhan Institute of Virology through an American research organization called EcoHealth Alliance.

The controversy over “Proximal Origin” represents years of unanswered questions about how a scientific hypothesis that some scientists and intelligence agencies now consider likely was cast as a conspiracy theory — culminating in a committee hearing this summer.  

Four of the five virologists behind “Proximal Origin” — Scripps Institute virologist Kristian Andersen, University of Sydney virologist Eddie Holmes, University of Edinburgh virologist Andrew Rambaut and Tulane School of Medicine virologist Robert Garry — have subsequently coauthored other high impact articles in favor of the theory that the pandemic emerged from the Huanan Wholesale Seafood Market in Wuhan. (A fifth coauthor of “Proximal Origin,” Columbia University virologist Ian Lipkin, has since distanced himself from the group.) In the world’s most prestigious journals and newspapers, these four virologists have cast the evidence for a natural origin as so compelling — so “dispositive” — as to render evidence pointing to the Wuhan Institute of Virology immaterial or the makings of a conspiracy theory.

The virologists’ Slack messages, emails, early drafts, and interview transcripts span 1,096 pages, while emails released through FOIA include hundreds more — yet the controversy over “Proximal Origin” remains unsettled.

Five thousand people have signed a petition accusing the virologists of fraud and calling for the retraction of “Proximal Origin,” including dozens of professionals in science and technology. Yet the virologists and their defenders say their private messages expressing concern about genetic engineering and the Wuhan Institute of Virology simply show a change of their perspective over time — a “textbook example of the scientific method at work.”

“It is easy to sow doubt – to take sentences from here and there in email streams and compare early thinking with later conclusions and presume any change is due to some unspecified pressure rather than a change in the weight or direction of evidence,” the Australian Academy of Science said in an August statement

Yet a new timeline by U.S. Right to Know shows that some of the contradictory private and public statements were written on the very same day. The timeline shows that, even as the virologists incorporated core concepts into their paper that were in favor of a natural origin, they simultaneously bemoaned to their coauthors that they were incomplete — even “crap.”

A few examples:

First, the day after the virologists shared an analysis with their funders arguing that engineering SARS-CoV-2 would require “significant amounts of molecular work,” Garry said privately that a graduate student could do it. “Proximal Origin” argues that any genetic engineer would follow computer modeling from the lab of Ralph Baric, a University of North Carolina virologist and frequent collaborator of the Wuhan Institute of Virology, who had mapped out the mutations optimal for binding to human receptors called ACE2. “Proximal Origin” argues that although the virus binds to human receptors optimally, it does not have these predicted mutations, thus is natural. The same day this argument was first incorporated into their analysis, Garry said that lab escape would not be “crackpot…given the [gain-of-function] research we know is happening.” Other Slack messages demonstrate an awareness of other approaches to researching viruses utilized by the Wuhan Institute of Virology and its collaborators.

Second, the virologists wrote in “Proximal Origin” that scientists would have never experimented with a novel virus that had not been published in the scientific literature. Privately the virologists acknowledged that the Wuhan Institute of Virology had “loads [of novel viruses] in their freezers” and that they could conduct engineering experiments on novel viruses “on a whim.” This concept at the core of their paper — that a novel virus would never be subject to gain-of-function experiments — was described by the virologists themselves as partially “foolhardy” and “crap.” They cribbed the idea from one of the world’s most controversial gain-of-function virologists, who was concerned about new biosafety regulations. They described him internally as “unbelievably conflicted.” He was not credited.

Third, the virologists publicly have attributed their rapid shift from favoring a lab origin to favoring a zoonotic origin largely to the news that a coronavirus up to 99 percent similar to SARS-CoV-2 had been discovered in pangolins, scaly anteaters used in traditional Chinese medicine. But the newly released messages show that within minutes of receiving the sequence of this virus, the “Proximal Origin” virologists noticed it was approximately 90 percent similar to SARS-CoV-2, far too dissimilar to serve as a precursor virus. “The more pango sequences I see the less likely I find that they are intermediate – I think they’re just one of many animals with SARS-like CoVs,” Andersen said. Rambaut told the New York Times that a virus identified at the Wuhan Institute of Virology called RaTG13 that is 96% similar to the novel coronavirus was not a close relative. Two days later, Rambaut grumbled to his coauthors that coronaviruses allegedly found in pangolins were not close enough to SARS-CoV-2 to dispel concerns about the Wuhan lab’s cousin virus. “Up to 99% [similar] is no good. There is a 342 [base pair] stretch of RaTG13 that is identical to [SARS-CoV-2]. Sigh,” Rambaut wrote. Two days after the pangolin coronavirus sequence was made available, Andersen and Rambaut said privately that they remained undecided between a natural or lab origin.

Fourth, the virologists made jokes about the possibility that the Wuhan Institute of Virology and its American partner EcoHealth Alliance ignited the pandemic, even as they drafted an analysis that helped shield these institutions from greater scrutiny. An early draft of “Proximal Origin” dismissed as “conspiracy theories” concerns about an American collaboration with the Wuhan Institute of Virology to conduct gain-of-function research on coronaviruses. The same day this idea was incorporated into the draft, Rambaut joked that perhaps EcoHealth Alliance “had planned a press conference predicting which virus would cause the next pandemic but then it escaped from the lab early.” The same day a preprint of “Proximal Origin” published largely dismissing any lab scenario, Andersen shared privately that the suspicions of Sen. Tom Cotton, R-Ark., about the Wuhan Institute of Virology were on target. “Tom Cotton is trending with COVID-19 on the Twitters at the moment. I gotta say – the guy isn’t totally wrong,” he said.

In addition, the newly revealed messages raise questions about the integrity not only of “Proximal Origin” but other high impact papers the virologists would go on to coauthor in favor of the zoonotic hypothesis. 

The virologists would privately justify asserting a natural origin with limited genomic evidence because of the epidemiological evidence that the virus had emerged from live animal stalls at a wet market. But the new private messages show that they were not confident in that evidence either, expressing skepticism about the quality of data out of Wuhan, data they would go on to employ to assert a wet market origin with near certainty in other prestigious outlets like Science and The Atlantic

・Read our past investigations on the origins of Covid-19 here.
・Access the original Slack messages and emails we reference in this timeline.
・A few additional emails released by Select Subcommittee Democrats in their staff report are here.
・Drafts of ‘Proximal Origin’ can be found here.

The ‘bizarre backstory’ of ‘Proximal Origin’

The genesis of “Proximal Origin” is by now well known: The virologists expressed alarm about a section of the SARS-CoV-2 genome that was “inconsistent with expectations from evolutionary theory.”  After a teleconference on February 1, 2020, with some of the world’s most influential funders of scientific research — Wellcome Trust Director Jeremy Farrar in the U.K., and National Institutes of Health Director Francis Collins and Fauci in the U.S. — they began accumulating evidence against that theory that the virus could have originated in a lab. 

The purpose of the call was described by one of the virologists as “challenging a certain theory and if we could, drop it.

The virologists’ messages show that their article was written under the direction of Farrar, who served as unofficial liaison between the virologists and Fauci and Collins. 

The incentive to produce something these “higher ups” would like appears to have been  immense. Altogether Collins, Fauci and Farrar oversaw about $72 billion in scientific funding that year.

Despite the difficulties posed by Beijing’s censorship and the novel coronavirus’ unexplained properties, the virologists wrote a paper within the span of a month that could serve as a “conclusive statement which will then be the go to scientific statement to refer to,” according to Farrar.

Farrar, who had acquired a burner phone for the purpose of discussing the possibility the virus had originated from a lab, also simultaneously shepherded drafts to the World Health Organization, emails show. Today Farrar serves as chief scientist at the WHO.

The “Proximal Origin” analysis was also shaped by controversial gain-of-function virologists concerned about restrictions on future research, and watered down in response to editors at the prestigious scientific journal Nature Medicine who sought a conclusive statement against any lab origin.

Soon after the call Farrar, Fauci, and Collins, the virologists began aligning their analysis to the conclusion predetermined by many within the scientific community.

“I personally think we should get away from all the strange coincidence stuff. I agree it smells really fishy but without a smoking gun it will not do us any good. The truth is never going to come out (if escape is the truth),” Rambaut said the day after the teleconference. “Given the shit show that would happen if anyone serious accused the Chinese of even accidental release, my feeling is we should say that given there is no evidence of a specifically engineered virus, we cannot possibly distinguish between natural evolution and escape so we are content with ascribing it to natural processes.”

“I totally agree that that’s a very reasonable conclusion. Although I hate when politics is injected into science – but it’s impossible not to, especially given the circumstances,” Andersen replied.

Three days after the teleconference, Andersen advised the National Academies of Sciences, Engineering and Medicine that it should come out more forcefully against the “crackpot” and “fringe” theory that SARS-CoV-2 had been engineered as a bioweapon or for basic research, and that the virus is “consistent with natural evolution,” precisely reversing what he said privately a couple of days earlier. (“We all find the genome inconsistent with expectations from evolutionary theory. … I’m pretty sure by now they think I’m a complete crackpot. … It’s [lab emergence] not some fringe theory.”) 

The scientists behind “Proximal Origin” expressed a sense of collaboration with these powerful scientific funders to dampen the global debate.

“Pressure from on high … all came together very quickly in the end. Jeremy Farrar and Francis Collins are very happy. Works for me,” University of Sydney virologist Eddie Holmes said.

The virologists searched for natural explanations for the furin cleavage site — a feature on the spike protein that supercharged the novel coronavirus into the most widespread pandemic pathogen in a century. They grasped for a natural explanation for the immediate transmissibility of SARS-CoV-2 as compared to other coronaviruses like SARS or MERS.

But it wasn’t easy. 

Their private messages describe pangolin coronavirus data as “sketchy” and too dissimilar to SARS-CoV-2 to be meaningful, acknowledged that a natural origin would require a “convoluted” series of events, noted the “weird” suppression of key data by Beijing authorities, and grappled with an “iffy” and “majorly confusing” viral family tree. 

After weeks of digging for evidence, the virologists concluded that the unusual features of the novel coronavirus could occur in nature.  A draft of their paper stated that a lab origin was “not necessary,” but the published version went further, asserting that a lab origin was not “plausible.” 

Many messages suggest the purpose of the article was to steer the media, the public, and policymakers away from speculation about lab-related scenarios.

While the group expressed some concerns about rumors on the fringes — about deliberately released bioweapons and a withdrawn paper about SARS-CoV-2 containing bits of HIV — the recently revealed messages also show the virologists helped to quash credible concerns emanating from the scientific community and U.S. government. 

Marc Lipsitch, a Harvard University epidemiologist, had circulated concerning comments raised about the lab in Wuhan by Richard Ebright, a molecular biologist at Rutgers University — both longtime critics of the riskiest gain-of-function research. The “Proximal Origin” virologists were fielding questions from reporters at Science and the New York Times.  

The influence of ‘Proximal Origin’

The article was endorsed by Fauci in front of reporters and cameras at the White House, cited by the Defense Intelligence Agency, and briefed to analysts at the State Department. According to recent reporting, Fauci cited the “Andersen paper” to persuade the Central Intelligence Agency to alter its assessment of the origin of the pandemic from lab to nature.

Since its publication, the virologists behind “Proximal Origin” have received awards, appeared in newspapers around the world, and have continued to highlight their authorship of one of the most widely cited and read scientific papers in history. “Proximal Origin” was published in the spring of 2020 and by that summer, Fauci’s NIAID had awarded $82 million to a network of scientists that included Andersen, Garry and EcoHealth Alliance. Yet despite all of their professional success, the virologists have yet to quiet all of the questions about their integrity. 

Pressed by members of Congress at a hearing this summer, Andersen, flanked by a team of attorneys, backed off prior claims that anyone who disagreed with “Proximal Origin” was a conspiracy theorist.

But in the months since, Andersen has deflected criticism about “Proximal Origin” by returning to a familiar refrain.

“Accusing domain experts of fraud is a commonly used tactic by conspiracy theorists,” he said in a tweet.

A faulty premise

On January 21, 2020, Chinese scientists highlighted a feature of SARS-CoV-2 called a furin cleavage site situated in an ideal place in the spike protein of the novel coronavirus — a feature never seen before in a coronavirus of its kind. 

Furin cleavage sites had been shown to make flu viruses more dangerous, and would have been easy to add “without a trace.”

The “Proximal Origin” virologists predicted it would endow the new virus with significantly stronger transmissibility than SARS. The discovery put them on edge

Days later, the Wuhan Institute of Virology released a preprint announcing the lab had identified a close cousin to the novel coronavirus in its freezers — a 96 percent match. 

These two revelations were largely responsible for igniting the chain of events that led to “Proximal Origin.” 

On a February 1 conference call, Andersen and Holmes presented their concerns about the furin cleavage site and the Wuhan Institute of Virology. Present on the call were Farrar, Fauci, Collins, all of the “Proximal Origin” authors except for Lipkin, and three virologists looped in by Farrar — Erasmus Medical Centre virologists Ron Fouchier and Marion Koopmans, and Charité virologist Christian Drosten. 

Fouchier and Drosten — who have both conducted gain-of-function experiments and were considered “conflicted” — pushed back forcefully on the hypothesis that SARS-CoV-2 was engineered.

They argued that labs would never pick a completely novel coronavirus as a “backbone” for gain-of-function experiments. 

Their colleagues delivered their rebuke in the presence of the virologists’ funders, Farrar, Fauci and Collins. The presence of Fauci and Collins may have been particularly sensitive given their history of support for the riskiest gain-of-function research. Fauci’s institute at the NIH had funded coronavirus discovery and gain-of-function experiments at the Wuhan Institute of Virology, records would later show, something he had been made aware of a few days earlier.

But notes written by Andersen on the same day as the call show that Fouchier’s and Drosten’s opinions didn’t dampen the authors’ concerns about engineering. 

“The only thing that remains perplexing … is the fact that it has a furin site with O-linked glycans in the spike protein between S1 and S2,” the notes read.

Soon after the call, four of the five authors of “Proximal Origin” — everyone but Lipkin — began exchanging notes on Slack. Andersen named the chat “Project Wuhan Engineering.”

“Nice channel title,” Rambaut said.

“Super secret too,” Andersen replied. “I think the main thing still in my mind is that the lab escape version of this is so friggin’ likely to have happened because they were already doing this type of work and the molecular data is fully consistent with that scenario.”

In the more private forum, Andersen commented on the pushback from Fouchier and Drosten. A cursory review of work in Wuhan showed the lab’s interest in discovering novel bat coronaviruses that had not yet emerged in human populations and testing which genetic mutations could transform them into dangerous viruses. 

“Both Ron and Christian are much too conflicted to think about this issue straight – to them, the hypothesis of accidental lab escape is so unlikely and not something they want to consider. The main issue is that accidental escape is in fact highly likely – it’s not some fringe theory,” Andersen wrote the next day, on February 2. “I absolutely agree that we can’t prove one way or the other, but we never will be able to.”

“That doesn’t mean that by default the data is currently much more suggestive of a natural origin,” he continued. “It’s not – the furin cleavage site is very hard to explain.”

“My fear is that the likes of [Drosten] and [Fouchier] put the question that’s being asked here into the same category [as conspiracy theories] … I’m pretty sure by now they think I’m a complete crackpot,” Andersen said.

Andersen said that engineering would be “impossible to prove” except for “the most simple scenario.” Yet this “simple scenario” would be described as emblematic of nearly all plausible virology work involving engineering in “Proximal Origin.”

“He is looking for very specific evidence proving this is unnatural (which is understandable), but except for the most simple scenario where somebody plugged a gene into a preexisting backbone, [engineering] would simply be impossible to prove,” Andersen said. “The presence of furin a priori moves me slightly more towards accidental release, but it’s well above my paygrade to call the shots on a final conclusion.”

Garry also appeared to challenge the notion that a lab would never work with a novel virus in an email to his coauthors on February 2. Biological engineers would in fact be likely to study a bat virus that had not yet spilled over into humans, he said.

“If you were doing gain of function research you would NOT use…SARS or MERS…These viruses are already human pathogens,” he said. “What you would do is choose a bat virus that had not yet emerged [in humans].” 

Garry continues by describing “simple” hypothetical experiments involving engineering and serial passage of coronaviruses that could have resulted in SARS-CoV-2. This sort of experimentation would eventually be dismissed as implausibly complicated in the published version of “Proximal Origin.” 

“I aligned [the novel coronavirus] with the 96% bat CoV sequenced at the [Wuhan Institute of Virology]. Except for the RBD the S proteins are essentially identical at the amino acid level – well all but the perfect insertion of 12 nucleotides that adds the furin site. S2 is over its whole length essentially identical. Do the alignment of the spikes at the amino acid level – its stunning. Of course, in the lab it would be easy to generate the perfect 12 base insert that you wanted,” he said.

“A likely explanation could be something as simple as passage SARS-live CoVs in tissue culture on human cell lines (under BSL-2) for an extended period of time, accidentally creating a virus that would be primed for rapid transmission between humans via gain of furin site (from tissue culture) and adaption to human ACE2 receptor via repeated passage,” Garry said. “I really can’t think of a plausible natural scenario where you get from the bat virus or one very similar to it to nCoV where you insert exactly 4 amino acids, 12 nucleotides, that all have to be added at the exact same time to gain this function – that and you don’t change any other amino acid in S2? I just can’t figure out how this gets accomplished in nature. In this scenario RaTG13 the WIV virus was generated by a perfect deletion of 12 nucleotides while essentially not changing any other S2 amino acid. Even more implausible IMO.”

“Maybe then pass [the novel bat coronavirus] in human cells for a while to lock in the [receptor binding domain], then you reclone and put in the mutations you are interested in — one of the first a polybasic cleavage site,” he continued, using another term for the furin cleavage site. 

“The furin site would be the first thing to add for sure,” Andersen said. 

Fouchier and Drosten also underestimated the lab’s capabilities, Andersen said.

“For the SARS [gain-of-function] studies they created a reverse genetics system for their bat virus on a whim,” Andersen said. “So Ron and Christian’s argument (which I found to be the strongest) about that not being feasible is not true – they were already creating those.”

The virologists further questioned Fouchier’s impartiality.

“Ron … is not going to want it to be a GOF [gain-of-function] escape,” Rambaut said.

Fouchier’s name in the scientific community has become synonymous with controversial research on highly pathogenic avian flu — which is estimated to have a 50 percent fatality rate — generating a new airborne virus. The New York Times described it as the “doomsday virus.” Fouchier’s experiment spurred a debate in the scientific community about whether scientific experiments with the potential to cause pandemics should be permitted.

Despite their private skepticism and concerns about Fouchier’s conflicts of interest, his ideas were immediately incorporated into the earliest drafts of “Proximal Origin.”

“The virus backbone (beyond spike) is not an indicator of a human source of 2019-nCoV emergence,” Fouchier wrote in a Feb. 2 email to the group. “The virus itself has not been described or characterized previously and no reverse genetics system has been described for this virus.”

It became the paper’s keystone argument against the hypothesis that SARS-CoV-2 was engineered. 

“If genetic manipulation had been performed, one of the several reverse-genetic systems available for betacoronaviruses would probably have been used,” the article echoed. “However, the genetic data irrefutably show that SARS-CoV-2 is not derived from any previously used virus backbone.”

Just three days after voicing his concerns, Andersen adopted Fouchier’s argument in a conversation with a group of scientists tapped by the National Academies of Sciences, Engineering, and Medicine to examine COVID-19’s origins for the White House Office of Science and Technology Policy — a group that Andersen said he believed was organized by Fauci. The Office of the Director of National Intelligence and the Federal Bureau of Investigation were also involved.

“I do wonder if we need to be more firm on the question of engineering. The main crackpot theories going around at the moment relate to this virus being somehow engineered with intent and that is demonstrably not the case,” Andersen said.

“Engineering can mean many things and could be done for either basic research or nefarious reasons, but the data conclusively show that neither was done (in the nefarious scenario somebody would have used a SARS/MERS backbone and optimal ACE2 binding as previously described, and for the basic research scenario would have used one of the many already available reverse genetic systems),” he said. “If one of the main purposes of this document is to counter those fringe theories, I think it’s very important that we do so strongly and in plain language (‘consistent with’ [natural evolution] is a favorite of mine when talking to scientists, but not when talking to the public – especially conspiracy theorists).”

By this date, the draft dismissed the virus “being engineered or otherwise created with intent” as “largely incompatible with the data.”

The day after his email to the National Academies stating the virus is “consistent with natural evolution,” and two days after drafts of “Proximal Origin” began dismissing the idea of a virus “created with intent,” Andersen told his coauthors he leaned toward the virus having been developed in cell culture in the lab. 

“Definite lean for me too,” Garry replied.

Serial passage 

After discounting engineering, Andersen and Garry said he leaned toward a lab origin through a technique known as serial passage. This technique can generate more dangerous viruses in the lab through serial infections in cells or lab animals.  Andersen and Garry appeared to think it could be the most likely explanation for the unusual features of SARS-CoV-2.

On February 8, an early draft of “Proximal Origin” circulated to the scientific funders — Farrar, Fauci, Collins — and the gain-of-function virologists — Fouchier, Koopmans and Drosten — firmly ruled out the possibility that SARS-CoV-2 had been engineered, but still considered a lab origin via serial passage a viable scenario. The group also considered spillover through an intermediate host and undetected circulation in humans.

The changes did not go far enough for Fouchier. In response to the new draft, he once again pushed back on any lab origin by arguing no close relative to SARS-CoV-2 had been described in published scientific literature.

“I am not in favor of publishing as is. I fail to see how the last of the three discussed scenarios (passaging) does not fall under the category of ‘laboratory manipulation.’ There is no evidence that might hint to this scenario and hence it should be put aside just like the engineering option,” he said. “As far as I am aware, no laboratory has worked on passaging the pangolin-origin virus, the bat-CoV RaTG13, or another closely related virus or had access to it prior to the outbreak. That nCoV-2019 could originate from a SARS-like virus in Chinese labs can also be excluded.”

The authors did not buy that argument either.

“Crap comments … basically just saying it can’t be true,” Holmes said.

“Not only has this been done, it’s specifically being done in Wuhan. In BSL 2,” Andersen wrote. “That in itself means that we can’t just dismiss a lab theory off hand by saying ‘not possible.’ That would be very foolhardy.”

“The furin link keeps bugging me too,” Andersen continued. “I can’t find any good references on it in the published literature for [coronaviruses].”

“Conflating the absence of evidence with actual evidence against,” Rambaut said.

Fouchier also said that he opposed a draft of the article that considered the lab leak theory because it could lead to “harm to science”through renewed debates about biosafety.

“This manuscript would be much stronger if it focused on the likelihood of the first two scenarios as compared to intentional or accidental release,” Fouchier said. “That would also limit the chance of new biosafety discussions that would unnecessarily obstruct future attempts of virus culturing for research and diagnostic purposes for any (emerging/zoonotic) virus.”

Koopmans, the director of Fouchier’s department at Erasmus Medical Center, opposed calling attention to the furin cleavage site at all.

“By zooming in on a specific finding that is NOT in the public domain as far as I know, I think this will generate its own conspiracy theories,” Koopmans said.

“Call me conspiratorial (OK that horse left the barn), but I think there may be some hallway talk going on at Erasmus,” Garry said.

“Unbelievable how conflicted Ron is,” Andersen grumbled on Slack. “Much too conflicted to think about this issue straight,” he said in a separate message.

The “Proximal Origin” virologists did not immediately discount serial passage in response to this feedback, but did seek other evidence they could use to rule it out. They expressed optimism that a coronavirus found in pangolins would provide the missing pieces.

Andersen reassured Fouchier and Koopmans that he did not support publishing the “open-ended” version of the article they had written without additional evidence for a natural origin. He shared their concern that it could “backfire.”

“As to publishing this document in a journal, I am currently not in favor of doing so,” he said. “I believe that publishing something that is open-ended could backfire at this stage. I think it’s important that we try to gather additional evidence – including waiting on the pangolin virus sequences and further scrutinizing the furin cleavage site and O-linked glycans – before publishing. That way we can (hopefully) come out with some strong conclusive statements that are based on the best data we have access to. I don’t think we are there yet.”

“Let’s hope more [pangolin] sequences come out … Would be critical evidence against cell culture hypothesis (which I’m still leaning towards),” Andersen said on Slack a few days later.

The virologists speculated that prematurely dismissing serial passage in the lab could invite backlash.

“I think we need a stronger argument than an assertion that no lab has done those experiments,” Rambaut said. “The pangolin virus that was announced in the press conference might solve this issue if it has the furin cleavage site insertion which would be all but conclusive for the natural scenario.”

Rambaut expressed hope that the pangolin coronaviruses would fill in the missing pieces.

However, when the sequences of the pangolin coronaviruses were published, the virologists’ hopes were dashed — the pangolin coronaviruses lacked a furin cleavage site. 

The “Proximal Origin” virologists reached back to Fouchier’s argument – the one they had dismissed as “crap.” 

“A hypothetical generation of SARS-CoV-2 by cell culture or animal passage would have required prior isolation of a progenitor virus with very high genetic similarity, which has not been described,” the article states. “We do not believe that selection during passage, or any other type of laboratory-based scenario, is plausible.”

No smoking gun

An overarching premise of “Proximal Origin” is that the genome of SARS-CoV-2 alone can disprove the theory the virus is man-made, but many of the virologists involved in “Proximal Origin” made private statements acknowledging lab viruses can be indistinguishable from natural ones.

Garry noted the furin cleavage site appeared inserted “like a scalpel” and that it would be “relatively easy” to insert. 

“Even though there’s some strange research going on here, there’s no smoking gun. Not quite sure what such a gun would look like though,” Andersen said on February 2. “I’m not quite sure what a virus from culture vs. an intermediate host would look like – I think they’d probably be indistinguishable.” 

“You can synthesize bits of the genes de novo with perfect precision and then add them in without a trace,” Garry wrote in a February 6, 2020, message. 

Even after “Proximal Origin” was published, Andersen expressed doubts to his coauthors that they could truly rule out engineering since a lab technique called Gibson assembly does not leave signs of genomic manipulation . 

“No obvious signs of engineering anywhere, but that furin site could still have been inserted via Gibson Assembly … and clearly creating the reverse genetic system isn’t hard,” he said.

But he found little support among his coauthors, whose position against the lab leak theory had solidified.

The ‘half furin cleavage site’

The virologists hoped for more evidence of a natural origin so that they could produce the “conclusive” statement sought by Farrar, Fauci and Collins, Fouchier, Koopmans and the journal Nature.

On February 24, Holmes relayed some promising news. His lab had discovered RmYN02, a bat coronavirus in Yunnan Province that was 93 percent similar to SARS-CoV-2. 

Holmes shared unpublished data from his lab showing that RmYN02 had an apparent insertion in the same place in the genome where the SARS-CoV-2 furin cleavage site was located. 

The furin cleavage site in SARS-CoV-2 is made up of twelve nucleotides that encode four amino acids, PRRA. The bat coronavirus has two amino acids in common with the SARS-CoV-2 furin site – PAA.

The new data suggested that it was theoretically possible for a furin site to develop naturally. The virologists called it a “half furin cleavage site.”

They hypothesized that recombination — the exchange of genetic material between at least two separate viral genomes — could explain the furin cleavage site in SARS-CoV-2.

“I’m now very strongly in favour of a natural origin,” Holmes said. “The component bits of the virus are more or less there in a tiny sample of wildlife.”

“I was always in favour of the pre-adapted jump from animals hypothesis but now it is plausible that that was directly from bats,” Rambaut said.

Both Garry and Andersen remained more cautious.

“No polybasic site, HOWEVER, this provides a mechanism,” Andersen wrote.

“I don’t see how it gets us any closer to discriminating between any of the models. There still needed to be recombination and evolution in either an animal, animals, humans or all of the above. It does not rule out or in lab passage,” Garry said, adding that it is “no smoking gun.”

“I think this lends pretty strong support for an animal origin of the ‘confusing’ features of the virus, so I think it’s important to include. None of this disproves accidental lab infection,” said Andersen. “However, it shows that all the steps can occur in nature.”

“Makes it much more likely the full furin site could have been acquired very early in humans or potentially in an intermediate host,” Andersen said.

“It was necessary to examine the lab hypothesis, but we did and it’s not necessary to invoke lab escape and the events leading to nCov-19 all could have and in all likelihood did occur in nature,” said Garry.

But after examining the nucleotides that made up the amino acids, enthusiasm faded.

“You need 2 transitions and three deletions (or insertions) to go between [the furin cleavage sites],” Rambaut said. “l am not convinced these are related inserts. … I still think that all it tells you is there are some bat viruses with an insertion at this site.”

“Yes, but I think that is an enormous given that 99% of the lab escape idea from genomics was the [furin] cleavage site insertion and we’ve not seen this in any other bat virus… I also think it may be a different insertion, but it means these insertions are happening in nature,” Holmes replied.

“I don’t think this data necessarily argues against accidental release, it shows insertions at this site can happen in nature, making the need to reach for a non-natural explanation much diminished,” Andersen said.

“Proximal Origin” would go further than Garry and Andersen’s statements that a lab origin was “not necessary,” asserting a lab origin was not “plausible.”

While some virologists agree a recombination event involving a virus like RmYN02 could explain the furin cleavage site in SARS-CoV-2, other scientists have raised doubts

When first asked about his 180 degree turn on the possibility of a lab origin, Andersen said in an email to the New York Times that “features in SARS-CoV-2 that initially suggested possible engineering were identified in related coronaviruses.” 

The virologists’ private messages show that with regard to the furin cleavage site, that’s only “half” true.

‘The paradox’: Holes in the natural origin story

Even after the virologists set aside the mysterious furin cleavage site, holes in the natural origin story remained.

The virus emerged with an infectiousness not seen in any coronavirus in natural history. The receptor binding domain — the segment on the spike protein that binds to host cells — appeared to be highly fit.

“Let’s not forget that what we’ve observed is completely unprecedented as far as I know. Never before has a zoonotic virus jumped into humans and spread through the population like wildfire with this kind of speed,” Andersen said on February 10. “This in itself would require further inquiry.”

The virologists flagged the immediate facility with which the virus infected human cells as among the unusual features of the virus that were “already noticed or easy to discover.” 

Researchers would by February 18 estimate that SARS-CoV-2 bound to human cell receptors called ACE2 between 10 and 20 times better than SARS.

The virologists at once acknowledged that the novel virus appeared “optimized” to bind to ACE2, yet argued that “importantly, the interaction is not predicted to be optimal” by previous computer modeling.

The virologists argued that any genetic engineer would use a model of optimal receptor binding discovered in 2008 by a frequent collaborator with the Wuhan Institute of Virology — University of North Carolina coronavirus engineering expert Ralph Baric. 

They described this observation as “strong evidence” the virus is not lab-made. 

By February 3, the earliest drafts of “Proximal Origin” included the argument that a scientist interested in working with coronaviruses would exclusively rely on such modeling for his experiments.

“While these analyses suggest that 2019-nCoV may be capable of binding the human ACE2 receptor with high affinity, importantly, the interaction is not predicted to be optimal,” a February 3 draft reads. “Additionally, several of the key residues in the RBD of 2019-nCoV are different from those previously described to be optimal for human ACE2 receptor binding. This latter point is strong evidence against 2019-nCoV being specifically engineered as, presumably, in such a scenario the most optimal residues would have been introduced, which is not what we observe.”

The same day, Garry sent a Slack that appears to contradict the idea that a genetic engineer would only follow the path determined by this computer modeling.

“It’s not crackpot to suggest [lab escape] could have happened given the GoF research we know is happening,” Garry said on February 3.

The argument in “Proximal Origin” also clashes with statements the virologists made suggesting that the literature published by the Wuhan Institute of Virology and the Baric lab appeared to be almost a “how-to manual” for constructing SARS-CoV-2 in the lab.

The argument in “Proximal Origin” only considers one narrowly defined lab-based scenario. Yet the virologists privately discussed other approaches that could have led to the generation of a virus like SARS-CoV-2 in a lab — through reverse genetics, or a combination of engineering and serial passage —  approaches that the authors privately acknowledged the Wuhan lab to have the capacity and expertise to undertake.

Other messages make clear that even after incorporating this argument into their analysis, the virologists remained puzzled by how the virus had emerged preadapted for human spread.

Privately Andersen on February 11 described the “optimal human ACE2 [receptor binding domain]” as “not so consistent” with a natural spillover of the virus from an animal to a human. 

The spike protein’s evolution as measured by a ratio called dN/dS also posed a problem. Andersen found early SARS-CoV-2 spike sequences had a low dN/dS, showing it wasn’t changing much. This calculation suggested the spike had emerged highly evolved to infect human cells. This contrasted with SARS, whose dN/dS was initially high, and then decreased as it circulated and adapted to humans.

“It is indeed striking that this virus is so closely related to SARS yet is behaving so differently. It seems to have been preadapted for human spread since the get go. It’s the epidemiology I find most worrying,” Holmes said in a message on February 10. 

“This whole thing is doing my brain in. I literally swivel day by day thinking it is a lab escape or natural,” Rambaut said on February 20, several days after supposed new evidence led the group to do a 180-degree turn on their initial concerns about a possible lab origin. 

“My brain is a badly calibrated [Markov chain Monte Carlo],” Andersen agreed.

The evidence that SARS-CoV-2 emerged instantaneously pandemic-ready also posed a “paradox.” 

In drafts of the paper dated February 14 and February 15, the virologists note “a paradox,” but note they are “not sure whether to include” it. 

“We still have the paradox,” Rambaut said on February 24 as they prepared their manuscript for publication. “If the virus is human adapted, it should have started circulating as soon as it arose. But we don’t see any genetic variants that are likely older than Autumn 2019.”

“Yes – paradox still in full force,” Garry replied.

This inconvenient complexity was ultimately omitted from the analysis.

While a “half furin cleavage site” had been identified, the bat coronavirus with the “half furin cleavage site” had a very different receptor binding domain than the virus’ closest relative, RaTG13, as well as the pangolin coronaviruses. How these viruses or related viruses could have recombined into SARS-CoV-2 remained perplexing. 

“Some convoluted shit going on here,” Rambaut said.

On February 26, as the manuscript was finalized, the virologists decided to avoid “proposing anything too specific.”

“I think we should stick to the original plan for this article as much as possible and not try to be too detailed about what we think happened (e.g. which bits in which hosts),” Holmes said. “I say this because I am certain that the picture is going to change rapidly as new data come out and I am loathe to make any strong conclusions when the sample is so small.  … I just don’t think we need to propose anything too specific.”

Even in skirting these complex questions, the virologists were confronted with a lab scenario that was impossible to rule out.

Genomic analysis couldn’t rule out the scenario of a researcher becoming accidentally infected by a natural virus  — such as the dozens of SARS-like coronaviruses the Wuhan Institute of Virology had collected over the years.

“At this stage we unfortunately just can’t rule out a potential accidental infection from the lab,” Andersen said.

“No, we can’t and should not because that would have precipitated the cries COVER-UP. No doubt Tulane would have been implicated,” Garry replied.

But ultimately the virologists decided they “shouldn’t even mention it.”  

“The only thing that is left in the ‘conspiracy’ side of things is that a researcher became infected through handling, sampling or culturing bat viruses (i.e. the exact one that became nCoV),” Rambaut said on February 25. “But we don’t (and cannot) address the actual nature of the zoonotic event from an evolutionary/genomic event so we shouldn’t even mention it.”

The ‘spurious’ connection to the wet market

The virologists acknowledged amongst themselves that the data pointing to a wet market may be shaky or the output of a censorious regime.

These statements contrast starkly with the public stances they would become famous for in scientific papers and the press in the following years. The coauthors of the “Proximal Origin” analysis would go on to lead the world’s most headline-grabbing scientific analyses in favor of the wet market theory of the pandemic’s origins.

The virologists speculated whether the wet market outbreak was a “red herring” due to “detection bias,” which would artificially make it seem like Covid came from the market simply because authorities mainly looked for cases connected to the market at the beginning of the pandemic instead of looking at other areas in the city.

“Someone should tell Nature that the fish market probably did not start the outbreak,” Garry said, as the virologists weighed the possibility of undetected circulation in humans prior to that outbreak.

On January 24, 2020, a paper in The Lancet found 13 of the 41 first official cases had no connection to the market. The “Proximal Origin” authors said in their earliest notes that the wet market connection may be “spurious” and that there was “some doubt on that already.”

While furin cleavage sites had been studied in highly pathogenic avian flu, it generally required very crowded and poorly ventilated conditions to arise. The wildlife sold at the Huanan Wholesale Seafood Market were not packed densely enough to facilitate the evolution of a furin cleavage site.

“The hypothetical [progenitor] virus with the optimal furin like site also had to evolve a near perfect RDB that was as [Andersen] put it ‘lock and loaded’ to bind to human ACE2,” Garry said on February 3. “The major hangup I have is the polybasic cleavage site. Clearly it can arise in highly pathogenic avian flu, but it’s not really a ‘natural’ process.”

“No way the selection could occur in the market. Too low a density of mammals: really just small groups of 3-4 in cases,” Holmes said.

“That is what I thought as well, which begs the question where would you get intense enough transmission (like the poultry farms for [H5N1]) to generate and pass on the furin site insertion?” Garry replied.

“That’s the million dollar question,” Rambaut said.

The virologists expressed concern about the clampdown on genomic data and other epidemiological evidence from the wet market. 

Yet the same virologists would set aside these concerns in subsequent years to assert the certainty of a wet market origin.

In a 2022 paper in Science whose coauthors included Holmes, Andersen, Garry and Rambaut, the virologists concluded that the official case numbers pinpointed the wet market as the pandemic’s epicenter and rejected concerns that biased data collection by the China Centers for Disease Control skewed this picture.

Like “Proximal Origin,” the Science paper gave the impression that its conclusions were airtight and that the origins debate had concluded. Like “Proximal Origin,” it received global media coverage.

But privately, Holmes said that official case numbers from China may not be accurate.

On March 29, 2020, about two weeks after “Proximal Origin” was published, Holmes said that according to his sources in the country, COVID-19 cases in China outstripped officially reported cases several times over, and that some hospitals in Wuhan had been discouraged from reporting cases.

“There is so much repression and deceit it is ridiculous,” Holmes said. “The true number of cases is probably a log more than reporting (I was consistently hearing 5% prevalence in Wuhan). I’ve also heard some of the hospitals in Wuhan are declining to test because they want to report low/no numbers.”

The 2022 Science paper further reported that positive samples swabbed around the wet market clustered where live animals were sold, showing that the pandemic emerged from a zoonotic jump. 

But private messages show the virologists expressed immediate skepticism about the quality of this data.

“They release these vague ‘environmental sampling’ results. What does that mean?” Holmes said on February 3.

Holmes, a visiting professor at the China CDC, had a contact there who had shared the unpublished environmental samples by February 9, 2020. The virus detected around the wet market was identical to the virus detected in patients, suggesting that humans and not an intermediate host had spread the virus around the wet market.

“I have seen the ‘environmental’ sequences (I hope this is OK to mention it Eddie?) – they are identical to the Wuhan backbone. But who knows what they are,” Rambaut said.

“If by identical you mean 100% like a lot of the SARS-CoV-2 sequences, my first guess would be it probably means they did not come directly from any animal,” Garry replied

“The environmental [sequences] are spectacularly uninformative,” Holmes said. “Pretty shocking if this is the best they have.”

“Yup. The environmental samples were entirely uninformative – I’m not actually convinced they’re environmental,” Andersen said.

“Kinda bummed that the ‘environmental’ samples didn’t show anything at all,” Andersen said in another message.

A 2023 analysis cowritten by Holmes, Andersen, Garry and Rambaut that examined the DNA of possible intermediate hosts in these very swabs, highlighting raccoon dog DNA in particular. Once again, their analysis received global press attention. The media likened raccoon dog DNA in these samples to fingerprints found at the scene of a crime. However, a more in-depth analysis of these samples has undermined this claim, showing no correlation between viral RNA and the DNA of a plausible intermediate host. One sample containing raccoon dog DNA highlighted by the virologists in particular was found to only contain a single read of the virus.

The “Proximal Origin” virologists’ private messages align more closely to the China CDC’s own interpretation of the samples it swabbed around the wet market. The Chinese scientists have argued the virus detected in the swabs was nearly identical to that found in humans, and emphasized that they took samples in the areas of the market where animals were sold. As a result, any clustering of positive samples with animal stalls was not meaningful.

After “Proximal Origin” was published, the virologists privately expressed other justifications for ruling out a lab origin — ones too shallow to be featured publicly in Nature Medicine.

“I’ve not heard of any cover-ups etc. [China CDC Director] George Gao has led most of the sampling and genomic work and he’s too dumb to set up a sophisticated theory,” Holmes said. “Why would the [Wuhan Institute of Virology] group then publish RaTG13 that would only help point the finger at them? Makes no sense.”

Lingering doubts

Two of the five “Proximal Origin” authors, Andersen and Lipkin, privately expressed that “Proximal Origin” had not truly ruled out all laboratory-based scenarios after their letter was published in Nature Medicine.

By April 3, 17 days after “Proximal Origin” first appeared in Nature Medicine, Andersen began “second guessing” in light of other scholarship. A 2013 paper posted to the virology blog Virological showed that serial passage experiments on coronaviruses tended to amplify a 12 nucleotide insert in the spike protein — like the furin cleavage site. These inserts were “arginine rich,” just like the furin cleavage site in SARS-CoV-2, Andersen said.

“The whole furin site being messed with in [tissue culture] has me second-guessing myself,” Andersen said on Slack. “When we went through this whole process, remember we talked about ‘passage might make viruses acquire these sites’? We couldn’t find a reference, but somebody just posted on Virological, which led me to this [paper].”

Garry described the pattern as “freaky.”

“I don’t think any of this new knowledge goes against what we said in the paper, but it does make our ‘definitely not passage’ argument weaker,” Andersen said.

Soon after, the Washington Post reported on State Department cables detailing a shortage of trained professionals at the Wuhan Institute of Virology. 

The news spooked Andersen. 

On April 17, just as Fauci cited “Proximal Origin” as evidence the virus was consistent with natural evolution from the White House press briefing room, Andersen fretted privately to his coauthors on Slack. 

“I’m a little worried about these ‘cables,’” Andersen said. “Because is it possible that they might have something? I’m putting all this to typical Trump BS smoke and mirrors (and just plain idiocy), but I’m not quite willing to die on this hill.”

More digging into the scientific literature showed the virologists had likely misinterpreted the meaning of the virus’ O-linked glycans, carbohydrate chains that are usually attached on proteins close to prolines, and were predicted to exist in SARS-CoV-2 because of the proline (P) in the furin cleavage site (PRRA). Because these carbohydrate chains can help shield viruses from a host’s immune system, the virologists reasoned that SARS-CoV-2 must have evolved naturally in the presence of an immune system. 

“The generation of the predicted O-linked glycans is also unlikely to have occurred due to cell-culture passage, as such features suggest the involvement of an immune system,” Proximal Origin reads.

But by a month after its publication, Andersen privately conceded that a 2017 paper showed this was likely wrong, and that this error toppled a key argument against the possibility of the virus arising out of certain lab experiments. 

“I really really want to go out there guns swinging saying ‘don’t be such an idiot believing these dumb theories – the president is deflecting from the real problems’ but I’m worried that we can’t fully disprove [cell] culture,” Andersen said. “Our argument was mostly based on the presence of the O-linked glycans – but they could likely play a different role. 

Andersen also reiterated a sticking point that each of the virologists had acknowledged in the weeks prior but which was neglected in “Proximal Origin” — that methods in modern virology allow viruses to be easily engineered without leaving a trace.

“We also can’t fully rule out engineering (for basic research) – yes, no obvious signs of engineering anywhere, but that furin site could still have been inserted via Gibson Assembly (and clearly creating the reverse genetic system isn’t hard – the Germans managed to do exactly that for SARS-CoV-2 in less than a month),” Andersen said in the same message. 

Even the “half furin cleavage site” in the bat coronavirus RmYN02 did not explain how a furin cleavage site appeared in SARS-CoV-2, Andersen said. 

“RmYN02 has an arrangement around that site, but it’s not this type of insertion,” he wrote. “I agree with you that it’s evidence for ‘this all occurs naturally,’ but it still doesn’t put a nail in the coffin of [the lab] theory.”

The other virologists brushed off Andersen’s concerns.

“Point taken that there truly could be intercepted ‘cables,’ but of what? We already know that the Chinese went into deep cover-up mode for example by shutting down the market and destroying the ‘evidence.’” Garry said. “It’s possible WIV characterized a NCoV-19 isolate earlier than the first noted cases in Dec I suppose, but that doesn’t make WIV the proximal origin of the virus. It’s also possible that the Chinese knew about a new respiratory virus spreading before the fish market cases.”

Andersen backed off on the question of engineering the next day, but again pressed his coauthors on the possibility of other lab experiments.

“While our evidence against engineering is very (very!) strong, our evidence against culturing isn’t (the presence of O-linked glycans probably controls activity of the [furin cleavage site] and isn’t a mucin like domain like we describe),” Andersen continued. “Again, I’m pretty sure this is all smoke and mirrors, but I’d need to see those actual cables before I put my head on the chopping block.” 

Andersen found little support among his coauthors, whose positions against the lab leak theory had hardened since the publication of “Proximal Origin.”

“Let’s face it, unless there is a whistleblower from the WIV who is going to defect and live in the west under a new identity we are NEVER going to know happened in that lab. Never,” Holmes said.

“The market is just too coincidental to ignore,” Holmes replied. “I see no reason to invoke lab escape whatsoever.”

The virologists received global media attention for “Proximal Origin.” 

The article reached millions within days, becoming the most high impact paper across any scientific discipline, according to Altmetric

“That’s tenure secured right there,” Andersen said in March shortly after publication.

At the same time, the virologists began to field angry emails from people who believed the pandemic leaked from a lab.

As the lab leak and zoonotic tribes began to solidify, Andersen appears to have pushed any lingering doubts to the side.

“I have decided that I am going to die on this hill, so I’ll talk to a few reporters and try to beat some sense into them,” Andersen said, linking to an article about the Trump administration tasking intelligence agencies to look into the Wuhan Institute of Virology. 

Andersen was not the only coauthor of “Proximal Origin” who doubted the soundness of the paper after its publication. 

Lipkin — who was privately mocked by some of the other virologists on the paper — later criticized his coauthors for overstating the case for a wet market origin, the committee discovered.

While the other “Proximal Origin” virologists claimed near definitive evidence for a wet market outbreak in a February 2022 preprint, Lipkin critiqued the analysis as “unverifiable” in an email to a reporter.

“Our colleagues fueled this with armchair epidemiology based on unverifiable data sets and terms like ‘dispositive evidence,’” he said

 “The Wuhan Institute of Virology has worked with bat samples and cultured bat viruses at BSL-2. This is a matter of published record – materials and methods in two papers.  This is unacceptable,” Lipkin said in a separate October 2022 email. 

‘Pango madness’

The virologists have pointed to the discovery of pangolin coronavirus sequences that resembled SARS-CoV-2 as critical to their 180 degree turn on the question of a lab origin.

“The features in SARS-CoV-2 initially suggested possible engineering were identified in related coronaviruses, meaning that features that initially looked unusual to us weren’t,” Andersen told the New York Times in June 2021. “For example, we looked at data from coronaviruses found in other species, such as bats and pangolins, which demonstrated that the features that first appeared unique to SARS-CoV-2 were in fact found in other, related viruses.”

But the new messages demonstrate these pangolin sequences were not in fact persuasive, especially as the virologists examined them more closely.

Holmes’ accounts differ, but either on January 30, two days before the teleconference, or February 2, one day after, University of Hong Kong virologist Tommy Lam contacted him about pangolin coronaviruses of interest.

By February 5, the virologists discussed the pangolin genomic data sampled from Guangdong and shared with Holmes by Lam. 

Though the pangolin coronavirus lacked a furin site and was too dissimilar from SARS-CoV-2 to be a progenitor, the receptor binding domain was a close match, containing six key residues that matched those of the novel coronavirus.

“Pango madness,” Holmes wrote. “Very similar to [the novel coronavirus] in [the receptor binding domain], sharing most of the key residues. Closer than RaTG13.”

Andersen expressed concerns about the “sketchy” quality of the data. Nonetheless, he renamed the Slack channel from “Project Wuhan Engineering” to “Project Wuhan Pangolin.” 

“With the pangolin virus possessing 6/6 key sites in the receptor binding domain, I am in favour of the natural evolution theory,” Holmes said in an email that included Farrar, Fauci and Collins on February 8.

South China Agricultural University announced on February 7 in a press release that it had isolated its own pangolin coronavirus from Guangdong reported to be 99 percent similar to the new coronavirus.

The virologists waited for the sequence to be released, hoping it would resolve their questions about the furin cleavage site and more closely align with the novel coronavirus than its closest known relative, the Wuhan Institute of Virology virus RaTG13.

In a February 8 email that included all of the virologists, Fauci, Farrar and Collins, Andersen said that he believed “everybody on this email” hoped the pangolins would alleviate concerns about a lab leak.

“The pangolin virus that was announced in the press conference might solve this issue if it has the furin cleavage site insertion which would be all but conclusive for the natural scenario,” Rambaut said.

If the genomes lived up to their hype and had the unique furin cleavage site, they would provide strong evidence that COVID-19 emerged from nature. Emails sent by Collins and Farrar suggest they were eager to see the sequences.

“Has the actual sequence of the pangolin coronavirus been released? That will be VERY interesting. Does it have the furin cleavage site?” Collins asked.

“I do not think so yet but…chasing!” Farrar replied.

However the virologists soon realized pangolins lacked the characteristics of an intermediate host.

Drafts of “Proximal Origin” acknowledged that “for the virus to acquire the furin cleavage site … this [intermediate] animal host would have to have a high population density – to allow the necessary natural selection to proceed efficiently – and an ACE2 gene that is similar to the human orthologue.”

Pangolin receptors appeared too dissimilar from human ones to facilitate the evolution of a virus so “preadapted” to spread in humans.

“I was trying to get a sense of how similar pangolin ACE2s were to human and whether replication in that host could lead to a receptor that’s quite finely tuned to the human receptor. Not very clear that that’s the case,” Andersen said on February 7.

In addition, closer inspection of the press release from the scientists in Guangdong showed the pangolin coronavirus was “up to 99 percent similar” to the novel coronavirus. The virologists acknowledged that it was unlikely to be a close enough relative to settle the virus’s origin.

“We really need to see if the pangolin data is as good as they claim,” Holmes said. “Indeed, it’s actually ‘up to 99%’ rather than ‘99%.’ That fooled me.”

Just days after telling the New York Times that the Wuhan Institute of Virology’s RatG13 was not a close relative of SARS-CoV-2, he appeared to privately grumble that the pangolin sequences were not close enough to dispel concerns about RatG13.

“Up to 99% is no good. There is a 342 bp stretch of RatG13 that is identical to CoV. Sigh,” Rambaut replied.

“The implications of a 99% similarity and a 99.8% similarity are pretty profound and at least would dramatically alter the discussion,” Garry said.

On February 18, Rambaut shared the sequence of what he believed was the “pango99” virus.

The virologists soon noticed that the pangolin coronaviruses did not hold the key to the pandemic’s origin.

“Pango99 (if that is what it is) doesn’t have the furin site,” Rambaut said.

“When they say ‘up to 99%” they mean an average of 90%,” Rambaut said on February 18.

“I think they have got over-excited with their results and claimed too much,” Holmes said

Garry said the pangolin receptor binding domain was unlikely to have contributed to a recombinant that led to the novel coronavirus. 

“No more of a smoking gun than RaTG13 as far as nCoV goes – not close enough to be the progenitor nor locally close enough to make a strong case that it might serve as a substrate for a recombinant that lead to nCoV,” he said.

The virologists updated their draft of “Proximal Origin” with the claim that finding a pangolin coronavirus with a similar receptor binding domain to the human optimized one in SARS-CoV-2 proved it was the result of natural selection. But privately the virologists were stuck on the lack of a furin cleavage site.

Far from dispelling their concerns about lab accidents, Andersen and Garry speculated about whether the pangolin coronavirus had been studied in a lab in serial passage and acquired the furin cleavage site that way.

“Without an insert, the closer it is the more likely the [serial] passaging theory becomes,” Rambaut said.

“Question is – did they recently realize that pangolins carry CoVs and then grew them in the lab to see if they could infect human cells? This is quite a high probability event,” Andersen said in a separate message. “Clearly none of these pangolin sequences were the source though.”

“The more pango sequences I see the less likely I find that they are intermediate – I think they’re just one of many animals with SARS-like CoVs,” he also said.

The virologists resolved to stay vague on the question of which animal could have served as the intermediate host.

“I don’t think we want to come down too heavily on the side of pangolins for now. I would just putting a bloody great question mark there. Or use a generic rodent sort of thing,” Holmes said on February 12.

Andersen may have remained concerned about the data quality, too.

“Four pangolin sequences just dropped as well – unfortunately these are similar to the previous and not similar in the [receptor binding domain],” Andersen said on February 17. “I’m starting to think that one pango that stands out might not actually be correct.”

A few days later, after the article’s submission to Nature Medicine, a peer reviewer opposed its publication because they believed the pangolin sequences were likely to resolve the origin mystery. The virologists pushed back, saying they were not a close enough match to have a direct relationship to the pandemic.

“The more sequences we see from pangolins (and we have been analyzing/discussing these very carefully) the more unlikely it seems that they’re intermediate hosts,” Andersen said. “They definitely harbor SARS-CoV-like viruses, no doubt, but it’s unlikely they have a direct connection to the COVID-19 epidemic.”

“Unfortunately none of this helps refute a lab origin and the possibility must be considered as a serious scientific theory (which is what we do) and not dismissed out of hand as another ‘conspiracy’ theory. We all really, really wish that we could do that (that’s how this got started), but unfortunately it’s just not possible given the data,” Andersen continued.

The pangolin data would not be published for weeks due to censorship in China.

“Unfortunately, they may not publish this any time soon because they have faced huge criticism in China, I think mainly from admitting that pangolin are illegally trafficked into China which apparently you are not meant to say. Very Chernobyl,” Holmes said.

When the pangolin sequences were finally published, only 1 gene was 99 percent similar to SARS-CoV-2.  The spike gene was only 84.5 percent similar, and had no furin site.

The pangolin coronaviruses were sourced from a single dataset first described in an October 2019 paper, outside inquiries later revealed. The data, renamed without attribution to the earlier paper, came from a handful of pangolins seized by Guangdong Customs in March 2019. 

The virologists’ private messages contrast sharply with their public depiction of the pangolin coronaviruses as a major revelation and turning point. 

Concerns about the Wuhan lab and EcoHealth Alliance

Though “Proximal Origin” only makes a passing reference to biosafety, the virologists expressed serious concerns about risky research and biosafety at the Wuhan Institute of Virology, the new messages show. 

The “Proximal Origin” paper does state that basic research involving the passage of coronaviruses has been done at biosafety level two “across the world.” 

Biosafety levels range from one to four (BSL-1 to BSL-4), with one being the most lax. 

But the virologists’ private messages show their concerns about the biosafety levels being hazardously low, specifically at the Wuhan Institute of Virology where scientists had a strong interest in conducting gain-of-function research that could make coronaviruses more dangerous. 

Andersen observed that potentially risky experimentation with coronaviruses in Wuhan was conducted at a “completely nuts” level of BSL-2, which is much less safe than the BSL-3 required for typical experiments with SARS and MERS and the BSL-4 level required for the most dangerous viruses. Biosafety level two would be insufficient for a virus as infectious as SARS-CoV-2.

“Performing these in BSL-3 (or less) is just completely nuts! IMO it has to be performed at BSL-4 with extra precautions,” Andersen said

Andersen also expressed concerns about gain-of-function research more generally.

“Honestly I’m not sure that type of knowledge is at all actionable, while, of course, being exceptionally dangerous. It only takes one mistake,” he said in the same message.

The virologists also recognized the lab’s “very strong focus” on spike proteins in coronaviruses — where the worrying furin cleavage site mutation resides.

“The main concern … is the kind of stuff that is being done – getting MERS-like viruses to infect humans, getting SARS-like viruses to cause disease in mice and infect humans, etc.” Andersen said. “There’s a very strong focus on the spike protein for all of that work.”

“Good idea to lay these arguments out for a limited discussion. And quite frankly so we can learn from it even if it wasn’t an escape – it easily could’ve been,” Rambaut replied. “If nothing else – the fact that we are discussing this shows how plausible it is.”

Because SARS-like viruses circulate in South China, the virologists also asked how a SARS-like coronavirus could have arrived hundreds of miles away in the metropolis of Wuhan without sparking other outbreaks along the way. 

Holmes remarked that all SARS-like coronaviruses had been found hundreds of miles from Wuhan in southern China. Holmes also noted that the Wuhan Institute of Viroogy found most of their coronaviruses in Yunnan Province.

“Interestingly, all the SARSr-CoVs that are capable of using human ACE2 were found in R. sinicus in Yunnan Province,” Andersen quoted from Shi Zhengli’s paper

“There are bat betaCoVs from Hubei [Wuhan’s province] but they fall into different clades and are not from R. affinis. The Wuhan group seem to sample almost exclusively in Yunnan. Must have loads in their freezers. So, [IN] that sense it’s no surprise that their virus is from Yunnan. BUT, if natural, what must mean is that there is a betaCoV from a bat from Hubei that is >96.5% similar to 2019-nCoV AND that there must be an intermediate host that is even closer still. Again, may all be natural. But I am struck by how differently this virus is behaving from SARS,” Holmes said.

Garry notes that the city of Wuhan was treated as an unlikely site of exposure to bat coronaviruses in an EcoHealth Alliance study.

“Sera from Wuhan – I kid you not – was used a control group,” Garry said

Andersen made a similar observation about RaTG13, the cousin virus identified at the Wuhan Institute of Virology.

“I believe RaTG13 is from Yunnan, which is about as far away from Wuhan as you can be and still be in China. What are the chances of finding a viruses that are 96% identical given that distance?” he said.

“Ebola got from Middle Africa to West Africa in 10-20 years,” Rambaut replied, another allusion to the controversial origins of the 2014 West African Ebola outbreak.

It’s clear others in the virology community were talking about the Wuhan Institute of Virology too. Holmes relayed a rumor from a professional conference that the lab had a novel SARS-like virus in the fall of 2019.

“I met this guy who said his mate at the Wuhan Institute of Virology had a human ‘SARS-like CoV’ sample from August 2019,” Holmes said.

More generally, the virologists demonstrated they were aware of the years-long debate within the scientific community in the years before COVID-19 emerged over whether new techniques in virology research could spark a pandemic. 

“The mind can play tricks and one of those tricks is denial,” Garry said. “SARS-CoV-1 escaped from Chinese labs 2, 3 or 6 times (depending on your source) AFTER the outbreak that killed 10% of people infected was over. Yes, Wuhan maybe getting too much of the attention – could be anywhere. We know two groups in Guangdong were doing metagenomics and growing CoV from pangolins perhaps for years. Escape via a custodian or researchers could happen from a lab and you would PROBABLY never know it.”

The virologists privately ridiculed the Wuhan Institute of Virology’s chief American partners — the nonprofit EcoHealth Alliance and Baric’s lab at the University of North Carolina — joking they had possibly released the novel coronavirus, even as they publicly supported these scientists. 

Andersen, Garry, Rambaut and Holmes had previously been critical of EcoHealth Alliance’s plans to expand its approach to pandemic prevention by seeking to collect every virus circulating in nature and predict which could spill over into the human species. 

But after the pandemic emerged from Wuhan, the virologists pivoted to defending EcoHealth’s research as essential to stopping the next pandemic.

Yet the virologists continued to make private gibes about EcoHealth, its virus collection program with the U.S. Agency for International Development called PREDICT, and Baric’s lab.

They mocked EcoHealth Alliance President Peter Daszak, as “Dastwat” and the “Grand Wizard of EgoHealth.” 

Garry proposed creating a diagram to outline the origin possibilities in play — which at that point included the virus escaping from the Wuhan lab after passage in cell culture.

“A diagram outlining the three scenarios with cartoons … Don’t make the cell culture passage scientist look asian (but maybe resemble an Ego guy),” Garry joked

“We need a cartoon picture of Peter Daszak to use in all the figures,” Rambaut agreed.

Garry followed up first with a cartoon of a mad scientist, then a sketch resembling Daszak.

The virologists noted that PREDICT underwrote EcoHealth’s work to uncover novel bat coronaviruses in Southern China, where COVID-19’s closest cousin viruses circulate. 

“One thing I find kinda funny here – all of this work getting bat samples was supported by PREDICT. So if they’re not able to predict the pandemics they themselves cause, then I’d say their program is in pretty bad shape,” Andersen said on February 3.

“Perhaps they had planned a press conference predicting which virus would cause the next pandemic but then it escaped from the lab early?” Rambaut said.

“Any [intermediate] animal being identified would be beneficial to them – otherwise we’re all going to point fingers at them telling people that they’re so shit that they can’t even predict the outbreaks of their own making…Too harsh?” Andersen said on February 7.

The virologists also expressed concerns about the work of Baric.

Drafts of “Proximal Origin” as early as February 3 state that “genetic data clearly shows that 2019-nCoV is not derived from any previously used virus backbone, including those recently posited by various conspiracy theories based on a 2015 paper in Nature Medicine,” with a reference to a coronavirus gain-of-function collaboration between UNC and the Wuhan lab that privately concerned the virologists.

“Proximal Origin” had ruled out a gain-of-function experiment gone awry, but privately the jokes continued.

In a February 10 message, Garry joked about the “next [novel coronavirus] diseases that escapes from anywhere – say a lab in North Carolina.”

Mere days after joking about PREDICT, Daszak and Baric as potentially culpable for the pandemic, the virologists received their first citation: A letter published in The Lancet circulated by Daszak condemned any questions about the Wuhan Institute of Virology as stoking prejudice and distrust, and cited an early version of “Proximal Origin” published on a virology blog.

By the time “Proximal Origin” published in the spring, the virologists appeared comfortable with their analysis supporting the continuation of the virus hunting and gain-of-function research they had privately expressed concerns about, even in light of concerns raised by other credible scientists like Ebright, Lipsitch, and University of Washington Professor Carl Bergstrom.

“Ebright/Lipsitch/Bergstrom are going to try to use this to end GOF research when I think this is going to be time we need it most,” Holmes said on April 17.

The ‘big ask’: The influence of powerful scientific institutions

The virologists glossed over many of the unresolved scientific complexities about the virus and the circumstantial evidence pointing to the lab in order to write “Proximal Origin” within a matter of weeks. 

The recently released messages depict a motive behind their rush to firmly conclude a zoonotic origin: Fauci and Collins, whose institution funded the research of Andersen, Garry and Lipkin, and Farrar, whose institution funded Holmes and Rambaut, appeared to push the virologists to publish something that would “dampen down” the lab leak theory.

As some of the most influential funders of scientific research in the world, Fauci, Farrar and Collins had their own motives for downplaying the possibility that gain-of-function research had ignited the emergent pandemic. Farrar said that a credible group of scientists should rein in the discussion about Wuhan’s labs “before that debate gets out of hand.”

Farrar passed along drafts and updates to Fauci and Collins. Farrar also sought their input as to whether it should be published at all. The virologists nicknamed Fauci and Collins the “Bethesda boys” after NIH’s headquarters of Bethesda, Maryland. 

Fauci and Collins simultaneously exchanged emails about whether the NIH could be linked to the Wuhan Institute of Virology’s research on RaTG13, the novel coronavirus’ close cousin virus. Fauci had been alerted by late January that his institute had funded coronavirus discovery and research in Wuhan through the EcoHealth Alliance. Collins also expressed concerns the theory could damage “international harmony.”

As the February 1 teleconference got underway — with Fauci, Farrar, Collins, the “Proximal Origin” authors, and the gain-of-function virologists including Fouchier and Koopmans on the line — the “Proximal Origin” authors exchanged thoughts on Slack. 

About 40 minutes into the call, the virologists exchanged enigmatic messages. 

“Big ask!” Holmes wrote

“Destroy the world based on sequence data. Yay or nay?” Andersen replied.

A few minutes later, Andersen makes another reference to an apparent request.

“Makes sense what he’s saying – but man, that’s hard to pull off,” he said.

The precise nature of the “big ask” remains unclear.

But it is clear that after the call, the group of virologists began accumulating evidence to suggest the virus was not engineered and shelving the evidence pointing to a lab.

“I think someone needs to lay out the science of this before it gets out of hand (and causes more formal investigations),” Rambaut said on February 8 on an email chain that included Farrar, Fauci and Collins.

Rambaut brainstormed about how to dig for stronger evidence to discredit the lab origin hypothesis than the idea that a scientist would only experiment on a known virus.

“I think we need stronger arguments than an assertion that no lab has done those experiments,” Rambaut said on February 8. “Is it possible to argue that A) a passaging experiment wouldn’t create the features we see? Or B) that there are logical reasons why someone wouldn’t do such an experiment?”

The virologists have insisted that they approached the problem as agnostic scientists, and intermittent Slacks do indicate some desire to weigh the lab origin possibility with fairness.

“I just think we need to lay out the features in the data and leave it open as to the cause,” Holmes said on February 3. “Just outline what needs to be explained and leave it like that. Irrespective of what the answer is, and will likely never know, these are really important bits of biology.”

“I think we should stick to our guns about the message and not tone it down just to get it published,” Holmes said on February 20.

But the new messages also show how that impartiality receded amid pressure from their powerful funders, their virologist peers, and editors from the journal Nature

The virologists had not even been grappling with the evidence for a week when Farrar asked if they could provide information to three of the most prestigious journals in the world.

Messages indicate that Farrar offered to use his position of power overseeing billions in scientific funding at the Wellcome Trust to place the piece in a high profile scientific journal.

“When can you update? Lancet, Nature, [New England Journal of Medicine] will all review immediately,” Farrar said on February 7. “Can I help with any of the editors?”

Farrar also said he would share a copy of their analysis with the WHO.

“Jeremy is pushing us to get a paper ready to go (prob. Nature),” Rambaut said on February 8.

“At this stage, it feels more like a school project than a full-on scientific paper to me, but we can definitely get it into shape,” Andersen replied.

Farrar made his aim clear in an email the same day.

“The theory of the origin of the has gathered considerable momentum not in social media, but increasingly among some scientists, in main stream media, and among politicians,” Farrar said. “The aim of this was to bring a neutral, respected, scientific group together to look at the data and in a neutral, considered way provide an opinion and we hoped to focus the discussion on the science, not on any conspiracy or other theory and to lay down a respected statement to frame whatever debate goes on — before that debate gets out of hand with potentially hugely damaging ramifications.”

“My preference is that a carefully considered piece of science, early in the public domain, will help mitigate more polarised debate,” Farrar continued. “If not, that debate will increasingly happen and science will be reacting to it. Not a good position to be in.”

Any ambiguity as to Farrar’s aim was dispelled in another email also dated February 6 in which he relayed a request from Koopmans — who the “Proximal Origin” virologists knew opposed addressing the lab leak theory at all — to “dampen down further the ‘conspiracy’ idea” as soon as possible.

“Possible to dampen down further the ‘conspiracy’ idea and make totally neutral? Talking with [Koopmans] last night and with the WHO meeting next week…both wondering whether actually publishing this sooner, but ruthlessly on the science….is worthwhile to put that flag down.” 

The virologists sought Farrar’s permission for every incremental question: whether to publish the paper, what preprint service to use, whether to add another author to the byline, even whether to circulate it to a wider email chain.

“Had a chat with Jeremy this morning,” Rambaut reported on February 12. “Really not much more to say. … Just that he still thinks it is important to get a matter-of-fact paper out there.”

“Yes, let’s just finish it,” Holmes replied.

Andersen would later tell a colleague that the process had been “a little rushed,” especially since he had been offline for several days, but cited “pressure from the higher ups to get it out.”

“Sorry the last bit had to be done without you … pressure from on high,” Holmes told Andersen. “All came together very quickly in the end. Jeremy Farrar and Francis Collins are very happy. Works for me,”

Both Farrar and Collins urged the group to publish the analysis as soon as possible, with particular attention on how it would be covered in the press.

“Keen to get out ASAP,” Farrar said.

“This is really well done, and I would argue ought to be made public ASAP,” Collins said.

On February 17, Farrar requested the draft be edited to tweak the sentence, “it is unlikely that SARS-CoV-2 emerged through laboratory manipulation of an existing SARS-related coronavirus,” to “it is improbable that SARS-CoV-2 emerged through laboratory.”

Farrar proposed holding a press conference. Discussions about whether to hold a press conference may have included Daszak, one email suggests

“It’s going to blow,” Holmes said on February 6. “Hence why Jeremy wants is thinking about putting something out. Hence the toned down version I just sent him.”

The group hoped the pangolin coronaviruses would prove a natural origin.

“Our main work over the last couple of weeks has been focused on trying to disprove any type of lab theory, but we are at a crossroad where the scientific evidence isn’t conclusive enough to say that we have high confidence in any of the three main theories considered,” Andersen said on February 8. “Like Eddie – and I believe Bob, Andrew, and everybody on this email as well – I am very hopeful that the viruses from pangolins will help provide the missing pieces. For now, giving the lab theory serious consideration has been highly effective at countering many of the circulating conspiracy theories.”

“We now have (and we will get more) pangolin data … We think we can tie this up even tighter with the next iteration and make a conclusive statement which will be the go to scientific statement to refer to,” Farrar echoed on February 8 — just a week after their analysis had begun.

Yet as the pangolin coronaviruses proved disappointing, Garry expressed concerns their data was insufficient.

“I have to admit likewise that I don’t really know the answers — maybe someone else does,” Garry said on February 10. “The data we have is just insufficient. … Even [the pangolin coronavirus] prob not helping (unless it magically has a furin cleavage site, which seems very doubtful).”

But under pressure to produce a published report in favor of a non-lab origin for the powerful funders, the group pressed forward with arguments and data they privately lacked confidence in.

When Andersen pitched the piece to the journal Nature, he said that it had been “prompted” by the higher ups.

“There has been a lot of speculation, fear mongering, and conspiracies put forward … Prompted by Jeremy Farrah, Tony Fauci, and Francis Collins … [we] have been working through much of the (primarily) genetic data,” he said.

Pressure from their peers, Nature

The virologists received pressure to distance themselves from the “conspiracy” position from colleagues in the field of virology who conduct gain-of-function research, namely Koopmans, Fouchier and Drosten. Their colleagues opposed giving oxygen to the lab leak theory at all, or even calling the public’s attention to the unusual furin cleavage site.

A dispute occurred between the “Proximal Origin” virologists and the gain-of-function virologists over whether ignoring the possibility of a lab leak or credibly considering and dismissing it would be more effective at quashing ideas they considered conspiratorial.

Specifically, acknowledging the possibility the virus emerged from serial passage could lead to headlines saying “top scientists consider this could have come from the lab,’” Andersen said.

But the virologists also knew a rejection of the lab leak theory without the appearance of having seriously considered it could lead to accusations of a “coverup.”

“This is already out there in full force so it’d be very important to discuss. Can’t just sweep that under the rug,” Andersen said on February 9.

While it ruled out lab origin scenarios, the preprint on the virology blog Virological released on February 17 included some the ambiguity the virologists were privately grappling with. Conclusively proving any origin theory would be difficult — perhaps impossible. 

“Although genomic evidence does not support the idea that SARS-CoV-2 is a laboratory construct, it is currently impossible to prove or disprove the other theories of its origin described here, and it is unclear whether future data will help resolve this issue,” the preprint read.

However, any discussion of a lab origin was scrubbed from the final draft of “Proximal Origin” after editors with the journal Nature questioned whether the piece would “feed or quash the conspiracy theories.”

The virologists apparently considered wielding Farrar’s influence to get around the rejection from the journal Nature.

“I get a sense that Nature might be a little gun shy … hence, we’d need to go all the way to the top,” Andersen said.

“Good idea – let Jeremy know and give him the rationale why Reviewer 2 was full of it,” Garry replied.

“The possibility [of a lab leak] must be considered as a serious scientific theory (which is what we do) and not dismissed out of hand as another ‘conspiracy’ theory,” Andersen told the journal. “We all really, really wish that we could do that (that’s how this got started), but unfortunately it’s just not possible given the data.”

In response to the journal’s pushback, the virologists made a tweak that would dramatically alter the meaning of “Proximal Origin,” changing their conclusion from saying that a lab origin was not “necessary” to stating that a lab origin was not “plausible.”

Andersen set to work on a press release titled: “The COVID-19 coronavirus epidemic has a natural origin, scientists say.”

The pressure to reject the lab leak theory within the scientific community was so immense that an anonymous whistleblower submitted a tip to a journalist in July 2020 that sought to expose the “Proximal Origin” virologists for having briefly entertained the lab leak theory. 

Holmes found himself defending the group for having ever considered the possibility. 

“I … strongly reject the idea that we should not have raised nor discussed the possibility of lab escape: as scientists we have to present all the data and discuss it openly. That’s all we did. To have not mentioned the possibility of lab escape would have been negligent,” Holmes said.

Media manipulation

The recent messages released by the committee show in new detail how the authors of “Proximal Origin” collaborated with Farrar, Fauci and Collins to curtail discussion of the Wuhan Institute of Virology in the media.

“The idea of engineering and bioweapon is definitely not going away and I’m still getting pinged by journalists. I have noticed some of them starting to ask more broadly about ‘lab escape’ and for now I have just ignored them – there might be a time where we need to tackle that more directly head on, but I’l let the likes of Jeremy and Tony figure out how to do that,” Andersen said on February 4.

“We’ll all likely be facing the lab escape or natural question head-on and should have a consistent response,” Garry said as they prepared for their manuscript to publish.

Several messages demonstrate the virologists’ desire to find evidence of the furin cleavage site and other aspects of the genome in nature in order to aid their “messaging.”

“Every little [bit] helps,” Andersen said on February 7.

“I’m actually rooting for some animal virus (bat, pangolin, something else hopefully not one of Kristian’s cats) to have a [furin cleavage] site,” Garry said.

“I think we’re ALL rooting for some animal virus here -would make the messaging so much easier!” Andersen said.

Across several messages, the virologists strategize like public relations professionals.

The earliest drafts of “Proximal Origin” begin with notes on features of the virus “already noticed or easy to discover.”

The group also expresses some anxiety about the press, and specifically the New York Times, finding out they are examining the origins of the pandemic at the request of Farrar, Fauci, and Collins.

Don McNeil, then a veteran science reporter at the New York Times, asked well-informed questions of Rambaut and Andersen after being tipped off by a source that the U.S. government was investigating whether the virus had any connection to the Wuhan Institute of Virology.

“Ignoring could further escalate, which I have to be very careful about. … one main problem I have too is that my name is on … ‘official’ things looking at this – so I need to be able to deflect potential future enquiries that could directly involve/name me,” Andersen said.

The virologists immediately began deflecting his questions.

For example, McNeil asked whether genetic manipulation could be detected in a virus.

“I gotta say, he pretty much nailed it. Let’s not tell him,” Andersen said

“Genetic manipulation leave signatures in a virus…No,” Garry said to the other virologists. “You could put the furin site in very cleanly.”

“Yes. But I didn’t say that,” Rambaut replied.

“I am thinking of just replying and saying that ‘I see nothing in the genome that would make me believe it has been genetically manipulated in the lab,’” Rambaut wrote

“Andrew’s response is credible and correct, but is not going to satisfy all the reporters,” Garry pointed out. “McNeil very credible [but] like every reporter can be mislead [sic].

Andersen also told McNeil that there was no way the virus could be a lab construct, repeating the false rationale at the center of “Proximal Origin” — that engineering is easily detected.

“A lot of conspiracy theories are talking about this being either a lab strain that had previously been produced or some new recombinant,” Andersen wrote to the reporter. “These rumors are demonstrably false – we would have been able to easily pick that up if that were the case, however it is not.”

Beyond ‘Proximal Origin’

While the messages clearly show the distortion of the issue in the media, the degree to which the authors of “Proximal Origin” influenced the U.S. government remains ambiguous. 

It’s not precisely clear to what degree the U.S. government was informed about concerns that SARS-CoV-2 was engineered and about “Proximal Origin” before its publication — even after the release of hundreds of pages of communications.

It is clear that Andersen briefed an interagency meeting organized by the State Department’s intelligence analysts soon after the paper published, an email obtained by U.S. Right to Know shows. Documents obtained by U.S. Right to Know shows that the article was incorporated by the Defense Intelligence Agency into its early COVID-19 origins report.

The Office of the Director of National Intelligence released a statement in April 2020 claiming that the intelligence community agreed with the “wide scientific consensus” that the virus had not been engineered, an apparent reference to “Proximal Origin,” but the genesis of this statement remains unclear. 

But there are conflicting accounts as to whether the U.S. intelligence community was alerted to the virologists’ concerns about a lab leak.

According to Holmes, Andersen informed the U.S. intelligence officials soon after flagging potential signs of engineering to Farrar and Holmes.

When Fauci first learned about the furin cleavage site, he said that if the virologists agreed there was cause for concern, that MI5 and the Federal Bureau of Investigation should be notified. Fauci, who was meeting with the White House and National Security Council regularly by that time, said that he would alert unnamed officials.

But Farrar’s memoir makes no mention of U.S. intelligence services. The memoir only states that Fauci alerted Collins, and that both were concerned about “anti-China rhetoric” from Trump.

“Patrick Vallance informed the intelligence agencies of the suspicions; Eddie did the same in Australia,” Farrar wrote. “Tony Fauci copied in Francis Collins, who heads the US National Institutes of Health (the National Institute of Allergy and Infectious Disease, which Tony heads, is part of the NIH). Tony and Francis understood the extreme sensitivity of what was being suggested, given the anti-China rhetoric coming from both President Trump and US Secretary of State Mike Pompeo.”

References to global intelligence agencies in the newly revealed messages provide little clarity. 

Lipkin — who said in a transcribed interview with the congressional committee that he gathered intelligence about outbreaks for the CIA — apparently told Holmes that “higher ups, including intel” were concerned about the furin cleavage site.

“If Lipkin says higher ups are concerned and intel involved it’s consistent with all we know too,” Garry replied.

In deflecting questions from the New York Times reporter McNeil, Andersen wrote to him: “National security? White House? Spooks? I wish my life was that exciting.”

But Andersen indicated in a sidebar to the other virologists that he was being dishonest: “I really … wished my life wasn’t this exciting…”

Twice — when contacted by the New York Times and by Lipkin — the virologists expressed little surprise at the news that the U.S. government and intelligence services were investigating the possibility of a lab origin.

Recent reporting states that Fauci cited “Proximal Origin” to persuade a CIA team to alter its assessment of the pandemic’s origin away from theories related to Wuhan’s coronavirus labs.

Despite all of the intrigue around “Proximal Origin” and the ongoing congressional investigation, the text of the article itself remains unchanged. 

In 2022, two of the coauthors were revealed to have undisclosed ties to the Wuhan Institute of Virology. Lipkin worked with the lab through a partnership between Columbia University and EcoHealth Alliance, an email obtained by U.S. Right to Know shows. And Holmes coauthored a paper about RaTG13, the cousin virus to SARS-CoV-2 identified at the Wuhan lab, the year before the pandemic emerged, an accidental release of sequences on an NIH database revealed. These connections remain undisclosed in the paper.

Springer Nature, the parent company of Nature Medicine, has yet to respond to calls to retract the paper, and the editor of the journal has blocked many of the article’s critics on social media.

While more than 5,000 people have signed a petition describing “Proximal Origin” as fraud, these signatures are equivalent to a small fraction of the more than 5 million people who have read “Proximal Origin,” and an even smaller fraction of the millions influenced by the accompanying media coverage that cast the lab leak theory as a far-fetched conspiracy theory.

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Is AI leading to a reproducibility crisis in science?

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During the COVID-19 pandemic in late 2020, testing kits for the viral infection were scant in some countries. So the idea of diagnosing infection with a medical technique that was already widespread — chest X-rays — sounded appealing. Although the human eye can’t reliably discern differences between infected and non-infected individuals, a team in India reported that artificial intelligence (AI) could do it, using machine learning to analyse a set of X-ray images1.

The paper — one of dozens of studies on the idea — has been cited more than 900 times. But the following September, computer scientists Sanchari Dhar and Lior Shamir at Kansas State University in Manhattan took a closer look2. They trained a machine-learning algorithm on the same images, but used only blank background sections that showed no body parts at all. Yet their AI could still pick out COVID-19 cases at well above chance level.

The problem seemed to be that there were consistent differences in the backgrounds of the medical images in the data set. An AI system could pick up on those artefacts to succeed in the diagnostic task, without learning any clinically relevant features — making it medically useless.

Shamir and Dhar found several other cases in which a reportedly successful image classification by AI — from cell types to face recognition — returned similar results from blank or meaningless parts of the images. The algorithms performed better than chance at recognizing faces without faces, and cells without cells. Some of these papers have been cited hundreds of times.

“These examples might be amusing”, Shamir says — but in biomedicine, misclassification could be a matter of life and death. “The problem is extremely common — a lot more common than most of my colleagues would want to believe.” A separate review in 2021 examined 62 studies using machine learning to diagnose COVID-19 from chest X-rays or computed tomography scans; it concluded that none of the AI models was clinically useful, because of methodological flaws or biases in image data sets3.

The errors that Shamir and Dhar found are just some of the ways in which machine learning can give rise to misleading claims in research. Computer scientists Sayash Kapoor and Arvind Narayanan at Princeton University in New Jersey reported earlier this year that the problem of data leakage (when there is insufficient separation between the data used to train an AI system and those used to test it) has caused reproducibility issues in 17 fields that they examined, affecting hundreds of papers4. They argue that naive use of AI is leading to a reproducibility crisis.

Machine learning (ML) and other types of AI are powerful statistical tools that have advanced almost every area of science by picking out patterns in data that are often invisible to human researchers. At the same time, some researchers worry that ill-informed use of AI software is driving a deluge of papers with claims that cannot be replicated, or that are wrong or useless in practical terms.

There has been no systematic estimate of the extent of the problem, but researchers say that, anecdotally, error-strewn AI papers are everywhere. “This is a widespread issue impacting many communities beginning to adopt machine-learning methods,” Kapoor says.

Aeronautical engineer Lorena Barba at George Washington University in Washington DC agrees that few, if any, fields are exempt from the issue. “I’m confident stating that scientific machine learning in the physical sciences is presenting widespread problems,” she says. “And this is not about lots of poor-quality or low-impact papers,” she adds. “I have read many articles in prestigious journals and conferences that compare with weak baselines, exaggerate claims, fail to report full computational costs, completely ignore limitations of the work, or otherwise fail to provide sufficient information, data or code to reproduce the results.”

“There is a proper way to apply ML to test a scientific hypothesis, and many scientists were never really trained properly to do that because the field is still relatively new,” says Casey Bennett at DePaul University in Chicago, Illinois, a specialist in the use of computer methods in health. “I see a lot of common mistakes repeated over and over,” he says. For ML tools used in health research, he adds, “it’s like the Wild West right now.”

How AI goes astray

As with any powerful new statistical technique, AI systems can make it easy for researchers looking for a particular result to fool themselves. “AI provides a tool that allows researchers to ‘play’ with the data and parameters until the results are aligned with the expectations,” says Shamir.

“The incredible flexibility and tunability of AI, and the lack of rigour in developing these models, provide way too much latitude,” says computer scientist Benjamin Haibe-Kains at the University of Toronto, Canada, whose lab applies computational methods to cancer research.

Data leakage seems to be particularly common, according to Kapoor and Narayanan, who have laid out a taxonomy of such problems4. ML algorithms are trained on data until they can reliably produce the right outputs for each input — to correctly classify an image, say. Their performance is then evaluated on an unseen (test) data set. As ML experts know, it is essential to keep the training set separate from the test set. But some researchers apparently don’t know how to ensure this.

The issue can be subtle: if a random subset of test data is taken from the same pool as the training data, that could lead to leakage. And if medical data from the same individual (or same scientific instrument) are split between training and test sets, the AI might learn to identify features associated with that individual or that instrument, rather than a specific medical ailment — a problem identified, for example, in one use of AI to analyse histopathology images5. That’s why it is essential to run ‘control’ trials on blank backgrounds of images, Shamir says, to see if what the algorithm is generating makes logical sense.

Kapoor and Narayanan also raise the problem of when the test set doesn’t reflect real-world data. In this case, a method might give reliable and valid results on its test data, but that can’t be reproduced in the real world.

“There is way more variation in the real world than in the lab, and the AI models are often not tested for it until we deploy them,” Haibe-Kains says.

In one example, an AI developed by researchers at Google Health in Palo Alto, California, was used to analyse retinal images for signs of diabetic retinopathy, which can cause blindness. When others in the Google Health team trialled it in clinics in Thailand, it rejected many images taken under suboptimal conditions, because the system had been trained on high-quality scans. The high rejection rate created a need for more follow-up appointments with patients — an unnecessary workload6.

Efforts to correct training or test data sets can lead to their own problems. If the data are imbalanced — that is, they don’t sample the real-world distribution evenly — researchers might apply rebalancing algorithms, such as the Synthetic Minority Oversampling Technique (SMOTE)7, which generates synthetic data for under-sampled regions.

However, Bennett says, “in situations when the data is heavily imbalanced, SMOTE will lead to overly optimistic estimates of performance, because you are essentially creating lots of ‘fake data’ based on an untestable assumption about the underlying data distribution”. In other words, SMOTE ends up not so much balancing as manufacturing the data set, which is then pervaded with the same biases that are inherent in the original data.

Even experts can find it hard to escape these problems. In 2022, for instance, data scientist Gaël Varoquaux at the French National Institute for Research in Digital Science and Technology (INRIA) in Paris and his colleagues ran an international challenge for teams to develop algorithms that could make accurate diagnoses of autism spectrum disorder from brain-structure data obtained by magnetic resonance imaging (MRI)8.

The challenge garnered 589 submissions from 61 teams, and the 10 best algorithms (mostly using ML) seemed to perform better using MRI data compared with the existing method of diagnosis, which uses genotypes. But those algorithms did not generalize well to another data set that had been kept private from the public data given to teams to train and test their models. “The best predictions on the public dataset were too good to be true, and did not carry over to the unseen, private dataset,” the researchers wrote8. In essence, this is because developing and testing a method on a small data set, even when trying to avoid data leakage, will always end up overfitting to those data, Varoquaux says — that is, being too closely focused on aligning to the particular patterns in the data so that the method loses generality.

Overcoming the problem

This August, Kapoor, Narayanan and their co-workers proposed a way to tackle the issue with a checklist of standards for reporting AI-based science9, which runs to 32 questions on factors such as data quality, details of modelling and risks of data leakage. They say their list “provides a cross-disciplinary bar for reporting standards in ML-based science”. Other checklists have been created for specific fields, such as for the life sciences10 and chemistry11.

Many argue that research papers using AI should make their methods and data fully open. A 2019 study by data scientist Edward Raff at the Virginia-based analytics firm Booz Allen Hamilton found that only 63.5% of 255 papers using AI methods could be reproduced as reported12, but computer scientist Joelle Pineau at McGill University in Montreal, Canada (who is also vice-president of AI research at Meta) and others later stated that reproducibility rises to 85% if the original authors help with those efforts by actively supplying data and code13. With that in mind, Pineau and her colleagues proposed a protocol for papers that use AI methods, which specifies that the source code be included with the submission and that — as with Kapoor and Narayan’s recommendations — it be assessed against a standardized ML reproducibility checklist13.

But researchers note that providing enough details for full reproducibility is hard in any computational science, let alone in AI.

And checklists can only achieve so much. Reproducibility doesn’t guarantee that the model is giving correct results, but only self-consistent ones, warns computer scientist Joaquin Vanschoren at the Eindhoven University of Technology in the Netherlands. He also points out that “a lot of the really high-impact AI models are created by big companies, who seldom make their codes available, at least immediately.” And, he says, sometimes people are reluctant to release their own code because they don’t think it is ready for public scrutiny.

Although some computer-science conferences require that code be made available to have a peer-reviewed proceedings paper published, this is not yet universal. “The most important conferences are more serious about it, but it’s a mixed bag,” says Vanschoren.

Part of the problem could be that there simply are not enough data available to properly test the models. “If there aren’t enough public data sets, then researchers can’t evaluate their models correctly and end up publishing low-quality results that show great performance,” says Joseph Cohen, a scientist at Amazon AWS Health AI, who also directs the US-based non-profit Institute for Reproducible Research. “This issue is very bad in medical research.”

The pitfalls might be all the more hazardous for generative AI systems such as large language models (LLMs), which can create new data, including text and images, using models derived from their training data. Researchers can use such algorithms to enhance the resolution of images, for instance. But unless they take great care, they could end up introducing artefacts, says Viren Jain, a research scientist at Google in Mountain View, California, who works on developing AI for visualizing and manipulating large data sets.

“There has been a lot of interest in the microscopy world to improve the quality of images, like removing noise,” he says. “But I wouldn’t say these things are foolproof, and they could be introducing artefacts.” He has seen such dangers in his own work on images of brain tissue. “If we weren’t careful to take the proper steps to validate things, we could have easily done something that ended up inadvertently prompting an incorrect scientific conclusion.”

Jain is also concerned about the possibility of deliberate misuse of generative AI as an easy way to create genuine-seeming scientific images. “It’s hard to avoid the concern that we could see a greater amount of integrity issues in science,” he says.

Culture shift

Some researchers think that the problems will only be truly addressed by changing cultural norms about how data are presented and reported. Haibe-Kains is not very optimistic that such a change will be easy to engineer. In 2020, he and his colleagues criticized a prominent study on the potential of ML for detecting breast cancer in mammograms, authored by a team that included researchers at Google Health14. Haibe-Kains and his co-authors wrote that “the absence of sufficiently documented methods and computer code underlying the study effectively undermines its scientific value”15 — in other words, the work could not be examined because there wasn’t enough information to reproduce it.

The authors of that study said in a published response, however, that they were not at liberty to share all the information, because some of it came from a US hospital that had privacy concerns with making it available. They added that they “strove to document all relevant machine learning methods while keeping the paper accessible to a clinical and general scientific audience”16.

More widely, Varoquaux and computer scientist Veronika Cheplygina at the IT University of Copenhagen have argued that current publishing incentives, especially the pressure to generate attention-grabbing headlines, act against the reliability of AI-based findings17. Haibe-Kains adds that authors do not always “play the game in good faith” by complying with data-transparency guidelines, and that journal editors often don’t push back enough against this.

The problem is not so much that editors waive rules about transparency, Haibe-Kains argues, but that editors and reviewers might be “poorly educated on the real versus fictitious obstacles for sharing data, code and so on, so they tend to be content with very shallow, unreasonable justifications [for not sharing such information]”. Indeed, authors might simply not understand what is required of them to ensure the reliability and reproducibility of their work. “It’s hard to be completely transparent if you don’t fully understand what you are doing,” says Bennett.

In a Nature survey this year that asked more than 1,600 researchers about AI, views on the adequacy of peer review for AI-related journal articles were split. Among the scientists who used AI for their work, one-quarter thought reviews were adequate, one-quarter felt they were not and around half said they didn’t know (see ‘Quality of AI review in research papers’ and Nature 621, 672–675; 2023).

Although plenty of potential problems have been raised about individual papers, they rarely seem to get resolved. Individual cases tend to get bogged down in counterclaims and disputes about fine details. For example, in some of the case studies investigated by Kapoor and Narayanan, involving uses of ML to predict outbreaks of civil war, some of their claims that the results were distorted by data leakage were met with public rebuttals by the authors (see Nature 608, 250–251; 2022). And the authors of the study on COVID-19 identification from chest X-rays1 critiqued by Dhar and Shamir told Nature that they do not accept the criticisms.

Learning to fly

Not everyone thinks there is an AI crisis looming. “In my experience, I have not seen the application of AI resulting in an increase in irreproducible results,” says neuroscientist Lucas Stetzik at Aiforia Technologies, a Helsinki-based consultancy for AI-based medical imaging. Indeed, he thinks that, carefully applied, AI techniques can help to eliminate the cognitive biases that often leak into researchers’ work. “I was drawn to AI specifically because I was frustrated by the irreproducibility of many methods and the ease with which some irresponsible researchers can bias or cherry-pick results.”

Although concerns about the validity or reliability of many published findings on the uses of AI are widespread, it is not clear that faulty or unreliable findings based on AI in the scientific literature are yet creating real dangers of, say, misdiagnosis in clinical practice. “I think that has the potential to happen, and I would not be shocked to find out it is already happening, but I haven’t seen any such reports yet,” says Bennett.

Cohen also feels that the issues might resolve themselves, just as teething problems with other new scientific methods have. “I think that things will just naturally work out in the end,” he says. “Authors who publish poor-quality papers will be regarded poorly by the research community and not get future jobs. Journals that publish these papers will be regarded as untrustworthy and good authors won’t want to publish in them.”

Bioengineer Alex Trevino at the bioinformatics company Enable Medicine in Menlo Park, California, says that one key aspect of making AI-based research more reliable is to ensure that it is done in interdisciplinary teams. For example, computer scientists who understand how to curate and handle data sets should work with biologists who understand the experimental complexities of how the data were obtained.

Bennett thinks that, in a decade or two, researchers will have a more sophisticated understanding of what AI can offer and how to use it, much as it took biologists that long to better understand how to relate genetic analyses to complex diseases. And Jain says that, at least for generative AI, reproducibility might improve when there is greater consistency in the models being used. “People are increasingly converging around foundation models: very general models that do lots of things, like OpenAI’s GPT-3 and GPT-4,” he says. That is much more likely to give rise to reproducible results than some bespoke model trained in-house. “So you could imagine reproducibility getting a bit better if everyone is using the same systems.”

Vanschoren draws a hopeful analogy with the aerospace industry. “In the early days it was very dangerous, and it took decades of engineering to make airplanes trustworthy.” He thinks that AI will develop in a similar way: “The field will become more mature and, over time, we will learn which systems we can trust.” The question is whether the research community can contain the problems in the meantime.

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