Explained | Why has Marc Tessier-Lavigne, the President of Stanford University, resigned?

Marc Tessier-Lavigne speaks to the media at Stanford University in Stanford, February 4, 2016.
| Photo Credit: AP

The president of Stanford University, Marc Tessier-Lavigne, resigned from his post and will be stepping down on August 31 after an investigation found evidence of “manipulation of research data” in widely-cited papers in which he was the principal author. 

According to The Stanford Daily, the university’s news outlet, the investigation found that Dr. Tessier-Lavigne failed to correct mistakes in several scientific papers published over the years. The investigation also found that his lab fostered an unhealthy lab dynamic where Dr. Tessier-Lavigne would reward ‘winners’ while marginalising or shunning ‘losers’. 

Dr. Tessier-Lavigne who is a neuroscientist has been the president of Stanford University for the last seven years.

Why the investigation?

The investigation was launched by the Stanford Board of Trustees after an article by the same news outlet reported in November that Dr. Tessier-Lavigne’s research was under investigation for misconduct. 

After eight months of inquiries, the Scientific Panel constituted by the university’s Board of Trustees special committee released a 95-page report on July 17. The investigation was conducted by Mark Filip, a former deputy attorney general and other well-known scientists such as the Nobel laureate Randy Schekman, former Princeton president Shirley Tilghman, former Harvard provost Steve Hyman and two other members of the National Academies. 

The investigation specifically looked at twelve papers where Dr. Tessier-Lavigne is a co-author which was part of the allegation that emerged for the first time on a website called PubPeer — a crowd-sourced platform where the scientific fraternity discusses issues regarding scientific publications.

The Panel was also charged with looking into any other issues and leads pertaining to the integrity of the scientific process in Dr. Tessier-Lavigne’s work. Under this, certain allegations came up against Dr. Tessier-Lavigne’s work when he was working as an executive and scientist at Genentech, a San Francisco-based biotechnology company. 

What did the report find?

The report specifically pointed out five papers published over the last two decades where Dr. Tessier-Lavigne was the principal author yet “failed to decisively and forthrightly correct mistakes in the scientific record.”

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The report concluded that while the results of the research conducted under Dr. Tessier-Lavigne were hedged, the investigators found no evidence that he manipulated the data himself or was aware of manipulation during the review process. 

The fudging of results has not been a lone incident at Stanford University but has “spanned labs at three separate institutions” where Dr. Tessier-Lavigne has worked. 

The report also said that Dr. Tessier-Lavigne “has not been able to provide an adequate explanation” for why he did not correct the mistakes in the papers even when he had multiple opportunities to do so. 

In 2001, a fellow scientist in the field pointed out a possible doctored image in a paper by Dr. Tessier-Lavigne published in the journal Science. According to the report, Dr. Tessier-Lavigne wrote to the colleague that he would contact the journal and issue a correction, however, he did neither.

To date, at least two of Dr. Tessier-Lavigne’s papers published in Science still contain errors. The report noted that Dr. Tessier-Lavigne has not followed up for seven years on unpublished corrections. “Dr. Tessier-Lavigne did not have an explanation for deciding to not follow up on the corrections beyond that he has a practice of drafting many emails to see how they read but only sends a portion of them and that he concluded the communication was unnecessary,” the report said.

A similar incident happened in 2004 when editors of the journal Nature found evidence of manipulated data in a research paper. However, the explanation provided by Dr. Tessier-Lavigne was “ not fully responsive to the range of publicly expressed concerns”, the report said. 

Now what?

As a result of the investigation, Dr. Tessier-Lavigne will have to retract three out of five of his research papers and make extensive corrections in the other two. 

One of these papers was a widely-publicised study on Alzheimer’s which claimed to have turned the understanding of the neurodegenerative disease on its head. The report found the central conclusions of the paper to be incorrect and said that the quality of research in Dr. Tessier-Lavigne’s lab “fell below accepted scientific practices, let alone Dr. Tessier-Lavigne’s self-described standard of scientific excellence.”

The report also said that the panel “believes that mistaken narrative of fraud in certain reporting may stem from a conflation of various events.”

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What did Marc Tessier-Lavigne say?

Dr. Tessier-Lavigne in a statement issued on July 19 against the findings of the report where he said, “I am gratified that the Panel concluded I did not engage in any fraud or falsification of scientific data.”

He also said that he has “never submitted a scientific paper without firmly believing that the data were correct and accurately represented.”

Responding to the allegation of not doing enough to correct the mistakes in the research paper, Dr. Tessier-Lavigne said that while he took steps in the past to address the issues, in certain cases they have been insufficient.

Dr. Tessier-Lavigne also said that he will be tightening the protocols in place such as systematically matching processed images to the original ones. He will remain at Stanford University as a faculty and keep running his lab.

In the meanwhile, the Board has named Dr Richard Saller, a professor of European Studies and former Dean of Humanities, will serve as interim president starting from September 1.

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Deep ocean currents in Antarctica are slowing earlier than predicted

Antarctica sets the stage for the world’s greatest waterfall. The action takes place beneath the surface of the ocean. Here, trillions of tonnes of cold, dense, oxygen-rich water cascade off the continental shelf and sink to great depths. This Antarctic “bottom water” then spreads north along the sea floor in deep ocean currents, before slowly rising, thousands of kilometres away.

In this way, Antarctica drives a global network of ocean currents called the “overturning circulation” that redistributes heat, carbon and nutrients around the globe. The overturning is crucial to keeping the earth’s climate stable. It’s also the main way oxygen reaches the deep ocean.

But there are signs this circulation is slowing down and it’s happening decades earlier than predicted. This slowdown has the potential to disrupt the connection between the Antarctic coasts and the deep ocean, with profound consequences for the earth’s climate, sea level and marine life.

Our new research, published in the journal Nature Climate Change, uses real-world observations to decipher how and why the deep ocean around Antarctica has changed over the past three decades. Our measurements show the overturning circulation has slowed by almost a third (30%) and deep ocean oxygen levels are declining. This is happening even earlier than climate models predicted.

We found melting of Antarctic ice is disrupting the formation of Antarctic bottom water. The meltwater makes Antarctic surface waters fresher, less dense, and therefore less likely to sink. This puts the brakes on the overturning circulation.

Why does this matter?

As the flow of bottom water slows, the supply of oxygen to the deep ocean declines. The shrinking oxygen-rich bottom water layer is then replaced by warmer waters that are lower in oxygen, further reducing oxygen levels.

Ocean animals, large and small, respond to even small changes in oxygen. Deep-ocean animals are adapted to low oxygen conditions but still have to breathe. Losses of oxygen may cause them to seek refuge in other regions or adapt their behaviour. Models suggest we are locked in to a contraction of the “viable” environment available to these animals with an expected decline of up to 25%.

Slowdown of the overturning may also intensify global warming. The overturning circulation carries carbon dioxide and heat to the deep ocean, where it is stored and hidden from the atmosphere. As the ocean storage capacity is reduced, more carbon dioxide and heat are left in the atmosphere. This feedback accelerates global warming.

Reductions in the amount of Antarctic bottom water reaching the ocean floor also increases sea levels because the warmer water that replaces it takes up more space (thermal expansion).

Freshening of shelf waters reduces the flow of dense water and slows the deepest parts of the overturning circulation while also reducing deep oxygenation.
| Photo Credit:
Kathy Gunn, author provided

Signs of a worrying change

Making observations of bottom water is challenging. The Southern Ocean is remote and home to the strongest winds and biggest waves on the planet. Access is also restricted by sea ice during winter, when bottom water forms.

This means observations of the deep Southern Ocean are sparse. Nevertheless, repeated full-depth measurements taken from ship voyages have provided glimpses into the changes underway in the deep ocean. The bottom water layer is getting warmer, less dense and thinner.

Satellite data shows the Antarctic ice sheet is shrinking. Ocean measurements taken downstream of regions of rapid melt show the meltwater is reducing the salinity (and density) of coastal waters.

These signs point to a worrying change, but there are still no direct observations of the deep overturning circulation.

What did the scientists do?

We combined different types of observations in a new way, taking advantage of each of their strengths.

The full-depth measurements collected by ships provide snapshots of ocean density, but are usually repeated about once a decade. Moored instruments, on the other hand, provide continuous measurements of density and speed, but only for a limited time at a particular location.

We developed a new approach that combines ship data, mooring records, and a high resolution numerical simulation to calculate the strength of Antarctic bottom water flow and how much oxygen it transports to the deep ocean.

Our study focused on a deep basin south of Australia that receives bottom water from several sources. These sources lie downstream of large meltwater inputs, so this region is likely to provide an early warning of climate-induced deep ocean changes.

The findings are striking. Over three decades, between 1992 and 2017, the overturning circulation of this region slowed by almost a third (30%) causing less oxygen to reach the deep. This slowing was caused by freshening close to Antarctica.

We found this freshening reduces the density and volume of Antarctic bottom water formed, as well as the speed at which it flows.

The observed slowdown would have been even greater if not for a short-lived climate event that drove a partial and temporary recovery of bottom water formation. The recovery, driven by increased salinity, further illustrates the sensitivity of bottom water formation to salinity changes on the Antarctic continental shelf.

Worryingly, these observations show that changes predicted to occur by 2050 are already underway.

What next?

Ice loss from Antarctica is expected to continue, even accelerate, as the world warms. We are almost certain to cross the 1.5℃ global warming threshold by 2027.

More ice loss will mean more freshening, so we can anticipate the slowdown in circulation and deep oxygen losses will continue.

The consequences of a slowdown will not be limited to Antarctica. The overturning circulation extends throughout the global ocean and influences the pace of climate change and sea level rise. It will also be disruptive and damaging for marine life.

Our research provides yet another reason to work harder – and faster – to reduce greenhouse gas emissions.

Kathy Gunn, CSIRO; Matthew England is Scientia Professor and deputy director of the ARC Australian Centre for Excellence in Antarctic Science, UNSW Sydney; and Steve Rintoul is CSIRO Fellow, CSIRO.

This article is republished from The Conversation.

The Conversation

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COVID-19 origins | GISAID U-turn adds to confusion over ‘new’ Chinese data

The Wuhan Huanan Wholesale Seafood Market, where a number of people related to the market fell ill with the novel coronavirus, sits closed in Wuhan, January 21, 2020.
| Photo Credit: Dake Kang/AP

In an unusual turn of events, the scientists who recently announced what they said was “compelling” evidence that the COVID-19 pandemic had a ‘natural’ origin rather than being the product of a lab experiment gone awry were banned by GISAID from using the database that contained the genomic information they used for their study – only for the latter to make a U-turn shortly after.

Many scientists have expressed surprise about the ban and the volte face, which appears to have further vitiated public conversations as well as intensified the spotlight on China’s recalcitrance against international investigations on the virus’s origins.

Where did the virus originate?

GISAID is an open-access database that was launched in 2008. It hit international headlines when, in January 2020, just before the pandemic began, researchers in China uploaded the first genetic sequence of the novel coronavirus to its server, giving the international community of virus and vaccine researchers quick and valuable insight into the virus that would change the world.

Soon, however, many scientists turned their attention to how or where the virus originated. Its first cases had been reported from the city of Wuhan, in China’s Hubei province, where there was also a wet market where there was both legal and illegal animal trade. Chinese authorities quickly shut the market, against the backdrop of multiple countries – China included – entering punishing lockdowns.

To this day, however, dispositive proof of the virus’s origins remains lacking. Conspiracy theories swirl on the internet and social media platforms, even as there are at least two groups of scientists divided on the issue. Part of the problem is that China has restricted access to genetic and biological data from the pandemic’s early days, related to the virus’s spread – even to a World Health Organization team that visited the country as part of a probe into the origins in 2021.

On March 16, American magazine The Atlantic reported that an international group of researchers had obtained data from the GISAID database uploaded by individuals affiliated with the Chinese Center for Disease Control (CCDC), but which was soon taken down. In this window, they had downloaded the data.

When they analysed it, they reportedly found genetic material belonging to raccoon dogs and to the novel coronavirus but not to humans in one part of the market. This conclusion appeared to favour the zoonotic theory of the virus’s origins over the lab-leak theory. It also contravened a claim by the Chinese team. The latter had collected the data in January 2020 and previously analysed it in a non-peer-reviewed paper in February 2022. That paper had said only infected humans had brought the virus into the market.

How did GISAID react?

But on March 21, GISAID published a statement citing two issues it had with the group’s conduct. The statement said this group had published their “analysis report in direct contravention of the terms they agreed to as a condition to accessing the data, and despite having knowledge that the data generators are undergoing peer-review assessment of their own publication” – i.e. the Chinese group’s paper was undergoing peer-review, a precursor to the paper being published by the journal Nature. Shortly afterwards, some of the researchers who were part of the group reported on Twitter that they could no longer access GISAID, indicating they had been banned.

GISAID’s terms of use require those who download the data to “make best efforts to collaborate with the data generators and involve them in such analyses and further research using such data.”

The database operators also took a bleak view of the international group announcing their findings via a media report and accused it of wanting to scoop the publication of the Chinese team’s paper.

How did scientists react?

The statement has raised a few concerns in the scientific community.

First, members of the international group had told The Atlantic that they had made efforts to collaborate with the Chinese team, whereas the statement indicates that they didn’t. But at 1:58 pm on March 22, one of the members of the international group tweeted that they had shared proof of their attempts to collaborate with the Chinese team and that GISAID had restored their access to the database.


Second, some scientists have opined that GISAID’s action, to ban members of the group from accessing SARS-CoV-2 genome data, amounts to gatekeeping, contradictory to its purpose to facilitate data-sharing. Francois Balloux, director of the University College London Genetics Institute, tweeted one potential explanation: that GISAID had “worked very hard” to gain the trust of CCDC, so having CCDC members continue using GISAID could be more valuable than scientific analyses being reported sooner.

This possibility is reminiscent of a New York Times investigation in 2021 that found the WHO had made secret concessions in an effort to negotiate China’s cooperation. It also leads into the third concern. GISAID’s statement had interpreted the international group’s decision to publicise their findings via the media rather than a scientific paper to be an attempt to scoop the Chinese team’s results.

But one member, Angela Rasmussen, tweeted early on March 22 that the group didn’t intend to have their findings written up as a paper in the interest of “transparency and the ethical imperative to openly share critical findings about pandemic’s origin that has been withheld from public view for at least a year and likely longer.”

Fourth, according to GISAID, the Chinese team uploaded the genomic data to the database and then removed it because they were revising it to share with the peer-reviewers looking over their paper, and after being entreated to collaborate. However, an explanation remains forthcoming as to why the data was uploaded after three years, not sooner.

On March 17, the World Health Organization asked China to answer this question – after both the international group and the Chinese team had made presentations on their findings to the health body.

For now, the debate over the virus’s origins remains open.

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