As health authorities isolate the sick, set up quarantines
and close borders, early efforts to stop a coronavirus pandemic are also trying
something completely different: “open science.”
The COVID-19 outbreak that began in Wuhan, China, has
become an important test case for the risks and benefits of open science — a
movement long-simmering within the global research community. By calling for
rapid, free and public posting of scientific findings, it amounts to a
rebellion against the old ways of conducting and reporting research.
Scientists throughout the world are publicly sharing
brief clinical reports and gene sequences of the novel coronavirus, bypassing
the careful curation and peer review that still dominates the distribution of
most scientific information.
The benefits? Lightning-fast collaborations that might help
forestall a pandemic.
The risks? Bad science can share that spotlight and, when something as scary as this coronavirus comes along, contribute to the cacophony of conspiracy theorists on the internet.
In this case, because of the seriousness of the epidemic,
virus genomes are being released three to six days after sample collection.
“We haven’t seen this before,” said Dr.
Trevor Bedford, a computational biologist at Fred Hutchinson Cancer
Research Center in Seattle.
He is tracking the virus on Nextstrain, a public website
he developed for scientists that provides informative and animated maps of
viral evolution. These phylogenetic charts — family trees for viruses — can
help guide the public health response as an epidemic unfolds, whether it be
avian influenza, Ebola, coronavirus or Zika.
“I’ve been talking about ‘real-time’ phylogenetics for a
long time, and now we are there,” he said.
In a blog
post from his Fred Hutch lab, Bedford explained how the analysis of
genomic data led him to conclude that a lack of genetic diversity in strains as
the outbreak grew pointed to “sustained human-to-human” transmission, springing
from a recent jump from animals to people just a month or two earlier.
“As this became clear to me, I spent the week of Jan. 20
alerting every public health official I know,” he wrote.
A kind of crowd-sourced peer-review
Bedford is an early user of bioRxiv (pronounced
Bio-Archive), an online server where scientists post the first drafts of papers
they may or may not submit later to academic journals. Online, these
“preprints” are subject to a kind of crowd-sourced peer review. The work is
disseminated to colleagues around the world, who provide valuable public
critiques. By their nature, however, they are works in progress, and should not
be confused with established fact.
The downside became apparent on Jan. 31, after a group of
researchers at the Indian Institutes of Technology posted on bioRxiv an analysis that purported to find an “uncanny
similarity” between tiny segments of the virus’ genes to sequences found in HIV
— implying that new virus could be a laboratory-generated mutant. The authors
posted a link to their paper on Twitter, and their claim gained attention
Within hours, Bedford and other genomics experts posted
fierce criticism of the bioRxiv paper. They pointed out that these same short
sequences can be matched in coronaviruses previously found in wild bats and are
commonplace in nature. If you searched for these short sequences in gene
libraries, you’ll spot them “throughout the tree of life,” Bedford said later
in an interview.
The chastened authors marked their paper “withdrawn” two
days later, but a contagion of weak science and outright falsehoods had been
unleashed. Freely available to anyone, the story morphed and blossomed on the
websites of conspiracy theorists who headlined that “Scientists Confirm” the
virus was “Man-Made.”
“In the scientific realm, things corrected themselves very
quickly. That’s exactly how you want science to happen,” Bedford said. “But the
post was picked up by various websites that are outside of the scientific
dialog, and it doesn’t seem to be easily squashed.”
Circulating faster and more freely
Dr. John Inglis, executive director of Cold Spring Harbor
Laboratory Press, co-founded bioRxiv in 2013 and manages it today. Although the
site uses a screening process for bogus claims before putting up papers, he
said it was “unfortunate” that this paper got through. “We have since had a
great deal of discussion on how to ensure that a similar incident does not
happen,” Inglis said.
BioRxiv has since added a bright yellow band across all its
postings to stress that these papers are “preliminary reports that have not
been peer-reviewed … and should not be reported in news media as established
Aided by social media, data and scientific chatter are
circulating faster and more freely, for better or for worse. In the worst
cases, unproven claims can be hijacked by traffickers in fear, sensation and
Inglis said responsible journalists rely on a network of
trusted, expert sources — just as scientists do among their own colleagues — to
assess the veracity and importance of preprint research.
Karl Bates, director of research communications for Duke
University, notes that preprints and crowd-sourced peer review got a foothold
decades ago in physics and astronomy. BioRxiv is modeled after arXiv, an open-access server
founded for physicists in 1991, with more than 1.6 million postings.
“I think open science is healthy,” he said. “It would be
even better if the science news media did a better job of explaining that this
is part of a process, that science is a sort of ongoing argument.”
‘A world where journals might just go away’
As the coronavirus outbreak puts open science under the
microscope, the sharp divisions over how research is conducted and distributed
are coming into focus.
Sue Biggins, senior vice president and director of the Basic Sciences
Division at Fred Hutch, sees a certain inevitability in the rise of open
science. “We have to think about a world where journals might just go away,”
“Everything’s going to be on the internet. I want to see us
focus on how to make things work for the next generation, and not just where we
are now,” said Biggins.
Driving the movement for open science is a mounting
resentment against the power of scientific publishing houses that charge high
fees for access to the works they publish, and the lengthy and opaque
peer-review processes they employ. With trained scientific editors and networks
of academic volunteers who analyze submissions, the premier houses produce
elite journals such as Cell, Science and Nature, whose selections for print can
make or break academic careers.
“If you want to fly high with the so-called ‘high-impact’
journals, the review process can drag along for a year,” said Dr. Randy
Schekman, a University of California, Berkeley cell biologist who won the Nobel
Prize in Physiology or Medicine in 2013.
In 2011, he was named the founding editor-in-chief of eLife, which provides
free access to papers that are published after a streamlined peer-review
process, and he served there for seven years. Coincidentally, eLife recently
launched a pilot project, Transparent Review in Preprints, by which its peer-review
services will be offered to authors of bioRxiv papers.
Schekman also is a leading advocate for the University of
California library system’s decision last year to break with Elsevier, publisher of Cell and nearly 3,000
other journals, over open access and subscription fees. More than 30 prominent
UC faculty members have resigned from Cell Press editorial boards.
Negotiations between the publisher and the 10-campus system are expected to
“Being a public institution, they wanted more for their
money. They want all the work published by UC scholars to be open access, and
Elsevier balked at that. It would put a huge dent in their excessive profit
margins,” Schekman said.
Trump administration floats proposed executive order
As that battle carries on, the Trump administration has
floated a proposed executive order that all federally funded research be made
immediately available to the pubic upon publication — directly challenging
paywalls by some publishers that restrict such access, for up to a year, to
those who pay. Schekman and 20 other Nobel laureates signed a letter to Trump in
support of it. “The old model of subscription publication is not a good fit for
the modern electronic era,” they wrote.
The White House proposal has further alarmed publishers,
particularly those run by scientific societies, which rely on revenues from
subscribers to validate the science through peer review and distribute their
Fred Hutch transplant physician Dr.
Stephanie Lee, who holds the David and Patricia Giuliani/Oliver Press
Endowed Chair in Cancer Research and is president of the American Society of
Hematology, responded for the society in a letter to President Trump. She wrote
that the proposal could significantly harm “scientific rigor, discovery and
innovation” by threatening the resources needed to staff a high-quality peer
review, curation and dissemination system. (At this time, Fred Hutch
has not taken a position on the proposed executive order.)
The push for open access, however, has strong support from
powerful players. bioRxiv has received funding from the Chan Zuckerberg Initiative,
a limited liability company founded by Facebook founder Mark Zuckerberg and his
wife, Dr. Pricilla Chan. The Bill & Melinda Gates Foundation since 2017
requires all peer-reviewed research funded by the organization to be
immediately and freely available through open access publication. eLife was
launched with support from the Howard Hughes Medical Institute, the Max Planck
Society and the Wellcome Trust.
Stakeholders in the debate over open science have set aside
some their differences in response to the coronavirus crisis. Nearly 100
publishers, research foundations and drug makers have pledged to provide open access to new research
regarding the disease and share laboratory findings with the World Health
Organization, “at least for the duration of the outbreak.”
Top-tier medical journals have been establishing
open-access, peer-reviewed sister publications, such as the American Medical
Association’s JAMA Network Open, launched in 2018. Researchers pay a fee
to post peer-reviewed articles on the online site, in a process designed to be
quicker than other JAMA journals’.
Dr. Frederick Rivara, a professor of pediatrics at Seattle
Children’s, is editor-in-chief. “I think we in the health sciences have been a
little late in adopting open science,” he said. “The principle is that, by
design, research conducted openly and transparently leads to better science,
and it is what we are all trying to do.”
ABOUT THE AUTHOR
Sabin Russell is a staff writer at Fred Hutchinson Cancer Research Center. For two decades he covered medical science, global health and health care economics for the San Francisco Chronicle, and wrote extensively about infectious diseases, including HIV/AIDS. He was a Knight Science Journalism Fellow at MIT, and a freelance writer for the New York Times and Health Affairs. Reach him at firstname.lastname@example.org.
This article is courtesy of Fred Hutchinson Cancer Research Center. View the original here.