How the coronavirus is changing the culture of science and publication

A torrent of data is being released daily by preprint servers that didn’t even exist a decade ago, then dissected on platforms such as Slack and Twitter, and in the media, before formal peer review begins. Journal staffers are working overtime to get manuscripts reviewed, edited, and published at record speeds. The venerable New England Journal of Medicine (NEJM) posted one COVID-19 paper within 48 hours of submission. Viral genomes posted on a platform named GISAID, more than 200 so far, are analyzed instantaneously by a phalanx of evolutionary biologists who share their phylogenetic trees in preprints and on social media.

“This is a very different experience from any outbreak that I’ve been a part of,” says epidemiologist Marc Lipsitch of the Harvard T.H. Chan School of Public Health. The intense communication has catalyzed an unusual level of collaboration among scientists that, combined with scientific advances, has enabled research to move faster than during any previous outbreak. “An unprecedented amount of knowledge has been generated in 6 weeks,” says Jeremy Farrar, head of the Wellcome Trust…

The COVID-19 outbreak has broken that mold. Early this week, more than 283 papers had already appeared on preprint repositories (see graphic, below), compared with 261 published in journals. Two of the largest biomedical preprint servers, bioRxiv and medRxiv, “are currently getting around 10 papers each day on some aspect of the novel coronavirus,” says John Inglis, head of Cold Spring Harbor Laboratory Press, which runs both servers. The deluge “has been a challenge for our small teams … [they] are working evenings and weekends.”

Here is the full story, via Michael Nielsen.

Comments

Amazing - almost as if an entire industry devoted to monetizing the process of publishing research results is unnecessary.

I suspect the incentives on this topic are slightly different than most topics

Absolutely - but don't imagine that a company like Elsevier is not working hard to ensure its profits remain secure.

Incentives matter.

.....in so far as this topic is actually working towards scientific results?

Publishers add the least value to the whole chain. The researchers and reviewers do the work. The webhost serves up content for cheap. Publishers do what exactly? Stand back and collect checks?

The modern world is working

Kaggle is one of the places where this is happening online, it's designed for this sort of lean iterable (data) science. In the last 90 days alone there have been ~800 notebooks/datasets/comments published: https://www.kaggle.com/search?q=coronavirus

As an anti-stagnationist I am pleased to read this confirmation.

However,all the efforts to bypass the FDA, etc, has failed to produce a test for the virus that works.

The CDC, and other institutions that have released test kits have not produced a test to detect COVID-19 reproducibly.

Only lots of workers toiling away following costly rules of science and technology will provide a test that has an estimated level of trust.

Tanstaafl.

Note, what is notable is how socialist the global community is acting in response to COVID-19 risks.

Anyone want to argue capitalism a la Milton Friedman would produce a faster solution to the actual or feared threats? Ie, the number one priority is profit which requires scarcity of knowledge, products, and services in the market.

"Note, what is notable is how socialist the global community is acting in response to COVID-19 risks."

You don't understand socialism (or theory), I guess. This is the opposite of 20th cen. socialism, where a small cadre of functionaries would serve as gatekeepers and arbiters of "pravda" (truth), on the basis of ideology.

The FDA and CDC acting as Top Men and gatekeepers is how socialism works.

Yeah, I know, it's mulp and he doesn't really congrue with our reality....

I really thought it was a joke, parody, when someone said that Larry Kudlow had been added to the pandemic task force.

Don't you know how such teams are assembled? You need a few troubleshooters, who don't have much experience in the field, but will ask -- and don't jump on me for this -- "dumb", non-expert questions, that can be helpful.

And given that the Trumpeter trusts him, it's an indication that he is taking the virus seriously.

^ that was a response to anonymous

Trump has had numerous problems attracting and keeping talent. The fact that his team is full of anti-vaxxers, anti-science baboons and his consistent downplaying of the global pandemic shows he's a bit of a nincompoop when it comes to anything science.

Right, he was added for an audience of one.

Trump knows that the virus is going away. Kudlow is on board for the really important thing to Trump - the Dow Jones electability index.

Or maybe, they all know the coronavirus may well cause a serious downturn and they need an economist watching everything very closely. The fact that Pence is heading it and Kudlow is in the group indicates that Trump is far more concerned than he's willing to say out loud. As Tyler would say, there's a Straussian reading of this situation.

Ultimately there isn't much anyone can do about this except not make it worse. Whether anonymous is humored or not is immaterial.

Right now the most important thing to do is to get ahold of all the hospitals and verify their infection disease protocols, make sure everyone is going to deal with infections in a way that doesn't spread it. The US system did well with SARS, Ontario did extremely poorly vs Vancouver which probably saw more numbers but managed to not make it worse. The other is to get the testing stuff out in a timely way, which means hollering at bureaucrats. Another is to talk to retailers to get early indications of runs on various things where action can be taken to allay the panic.

https://thediplomat.com/2020/02/the-coronavirus-outbreak-how-democratic-taiwan-outperformed-authoritarian-china/
taken with a grain of salt, but interesting how they are approaching this, even all the politicians looking after the interests of the citizenry instead of angling for political advantage.

The Democrats are in the unenviable position of cheering for 100,000 deaths and serious disruption. That would put a smile on Pelosi's face.

"which means hollering at bureaucrats."

Well I hope someone is blistering the ass of whomever at the CDC is in charge of coronavirus testing. That's currently a national disgrace. The CDC has managed to run less than 500 tests in the last 6 weeks. They've botched the chemical reagents on the large volume kit they tried to roll out. And the FDA/CDC has, for the most part, refused to allow hospitals to run their own tests.

I'm shocked that reporters at the press conference weren't all over that issue.

The narrative is that the CDC is the competent and serious voice of reason, so it's bad form to ask hard questions about their performance.

A good friend is a Canadian hospital doc. He tells me “5 cases will bring down the healthcare system in the province.” I gather they generally run closer to the edge than the US in terms of capacity and in normal times just perform less care for complex cases. He said that patients in the hallways is normal operation for them, so it wouldn’t take much to overwhelm it.

Interesting, which province? (Healthcare is administered at the provincial level)

I'd prefer not to say. It matched my experiences with a western and an eastern province's healthcare systems, though, so I'm willing to credit it as being reasonably representative.

If it helps, he's at a major hospital in an urban center affiliated with a medical school. This isn't a case of rural neglect.

"The Democrats are in the unenviable position of cheering for 100,000 deaths": by the time this is over that might seem a modest total. Nobody knows yet. Nobody can know yet.

Still, "cause of death" is a somewhat malleable concept.

What non-scientists generally don't understand is that formal peer review is, by and large, meaningless in the long run. It keeps the worst publications out (in terms of quality), but science operates best by pushing past the boundaries of what's currently understood. Errors are GOING to occur, and every scientist knows this. Being wrong is not a crime in science; it's an inevitable part of doing science.

The actually important review is the informal peer review--in other words, looking at what fellow scientists say about your paper, whether they use the information or not. Some publications that pass formal peer review are found to be incorrect or irrelevant and never get used. Some that never passed peer review get cited routinely (this can happen due to age, publication style, and a few other mechanisms).

Sounds like when lives are on the line, people remember this. They convert to actual review of data by one's peers, rather than a formal, bureaucratic review process. And that's a good thing. The question now is, can this be scaled to standard publications without a worldwide crisis to drive it?

Just read this:

"“Travel restrictions don’t work: people find another way around it, it might only slow the virus down,” said Dr. Clare Wenham, of the London School of Economics Global Health Initiative."

https://www.nytimes.com/2020/02/26/world/europe/coronavirus-european-union.html?action=click&module=Top%20Stories&pgtype=Homepage

That's a baffling comment. Slowing down a virus, such as this, means that the patient inflow into hospitals is slower. Which means the critical patients get better care. Which means that less people die.

In the present case you don't have to look any further than the difference in mortality rates between Hubei China and the rest of the country. Locking down Hubei clearly helped contain the virus and allowed the rest of China time to cope.

How can experts keep repeating such obviously idiotic comments?

Stats from China:

Mortality Rate (2.1% Nationwide, 4.9% Wuhan, 3.1% Hubei, and 0.16% other provinces) reported by the NHC of China

FYI, Wuhan is located in Hubei.

The most surprising thing about the statistics coming from Hubei is the near absence of confirmed infections in those under the age of 20. Only 2% of all the cases were in that age cohort. It may be that young people don't present with serious symptoms and are not seen by healthcare workers. Major morbidity and mortality are in the >70 years bracket. this all comes from an epidemiological look at the data published on line by JAMA.

+1, Yes, since I have 4 grade school kids, I was concerned about that very issue. Fortunately, they should remain healthly regardless of how this develops.

In start contrast to the "all hands on deck" approach reported at Tyler's link, we learn:

"Top expert on viral infections must get Pence’s approval before issuing statements"

I'm afraid this actually is pretty transparent. Trump took the goodfellas he already had in the room, and assigned to them the job of managing expectations more than mobilization.

I guess we'll see if a pandemic can be jaw-boned into compliance.

"Mike Pence Orders All Women To Wear New Coronavirus-Resistant Uniforms"

https://babylonbee.com/news/mike-pence-orders-all-women-to-wear-new-coronavirus-resistant-uniforms

I don't really know much about Pence, and want to leave him room to succeed.

But to do that I think he's going to have to listen to scientists more than manage their messages.

the corona beer virus, neat oral sex game, did anyone tell you herpes is spread to keep people from engaging in oral sex? yes, dementia is a oral sex punishment? yes, and most diseases are spread intentionally including the corona beer virus as punishment for sins

these diseases are mostly nuclear weapons diseases everyone being burned in the manhattan project yellow bric road to revelations

I had thought the CDC was more competent than they are looking like. There's this story:

"CDC declined to test new coronavirus patient for days, California hospital says"

"Officials said the case could mark a turning point as the first case of the virus spreading among the general public in the United States, because there is no known origin for it."

"“With testing so limited right now, we're flying somewhat blind, while being reassured that we're not flying toward a mountain,” tweeted Jeremy Konyndyk, a senior fellow at the Center for Global Development who directed the U.S. Agency for International Development's Office of Foreign Disaster Assistance during the Ebola outbreak. "

https://thehill.com/policy/healthcare/484903-cdc-declined-to-test-new-coronavirus-patient-for-days-california-hospital

I really do hope these are abberations and not a sign that the CDC is highly overrated.

You don't understand. Under Obummer, the CDC was a national disgrace. Clearly, anyone suggesting the CDC is not better than in the past is suffering from extreme TDS.

Frankly, this is a serious national health issue, and all those attempting to turn it into a game of politics are idiots.

Ray Lopez doesn't have any to say about how awesome PATENTS are?

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