planet.donarmstrong.com

“It is not easy when people start listening to all the nonsense you talk. Suddenly, there are many more opportunities and enticements than one can ever manage.”

– Michael Levitt, Nobel Prize in Chemistry, 2013

In 1990 Glendon MacGregor, a restaurant waiter in Pretoria, South Africa, set up an elaborate hoax in which he posed as the crown prince of Liechtenstein to organize for himself a state visit to his own country. Amazingly, the ruse lasted for two weeks, and during that time MacGregor was wined and dined by numerous South African dignitaries. He had a blast in his home town, living it up in a posh hotel, and enjoying a trip to see the Blue Bulls in Loftus Versfeld stadium. The story is the subject of  the 1993 Afrikaans film “Die Prins van Pretoria” (The Prince of Pretoria). Now, another Pretorian is at it, except this time not for two weeks but for several months. And, unlike MacGregor’s hoax, this one does not just embarrass a government and leave it with a handful of hotel and restaurant bills. This hoax risks lives.

Michael Levitt, a Stanford University Professor of structural biology and winner of  the Nobel Prize in Chemistry in 2013, wants you to believe the COVID-19 pandemic is over in the US. He claimed it ended on August 22nd, with a total of 170,000 deaths (there are now over 200,000 with hundreds of deaths per day). He claims those 170,000 deaths weren’t even COVID-19 deaths, and since the virus is not very dangerous, he suggests you infect yourself. How? He proposes you set sail on a COVID-19 cruise.

Levitt’s lunacy began with an attempt to save the world from epidemiologists. Levitt presumably figured this would not be a difficult undertaking, because, he has noted, “epidemiologists see their job not as getting things correct“. I guess he figured that he could do better than that. On February 25th of this year, at a time when there had already been 2,663 deaths due to the SARS-CoV-2 virus in China but before the World Health Organization had declared the COVID-19 outbreak a pandemic, he delivered what sounded like good news. He predicted that the virus had almost run its course, and that the final death toll in China would be 3,250. This turned out to be a somewhat optimistic prediction. As of the writing of this post (September 21, 2020), there have been 4,634 reported COVID-19 deaths in China, and there is reason to believe that the actual number of deaths has been far higher (see, e.g. He et al., 2020, Tsang et al., 2020, Wadham and Jacobs, 2020).

Instead of publishing his methods or waiting to evaluate the veracity of his claims, Levitt signed up for multiple media interviews. Emboldened by “interest in his work” (who doesn’t want to interview a Nobel laureate?), he started making more predictions of the form “COVID-19 is not a threat and the pandemic is over”. On March 20th he said that “he will be surprised if the number of deaths in Israel surpasses 10“. Unfortunately, there have been 1,256 COVID-19 deaths in Israel so far with a massive increase in cases over the past few weeks and no end to the pandemic in sight. On March 28th, when Switzerland had 197 deaths, he predicted the pandemic was almost over and would end with 250. Switzerland are now seen 1,762 deaths and a recent dramatic increase in cases has overwhelmed hospitals in some regions leading to new lockdown measures. Levitt’s predictions have come loose and fast. On June 28th he predicted deaths in Brazil would plateau at 98,000. There have been over 137,000 deaths in Brazil with hundreds of people dying every day now. In Italy he predicted on March 28th that the pandemic was past its midpoint and deaths would end at 17,000 – 20,000. There have now been 35,707 deaths in Italy. The way he described the situation in the country at the time, when crematoria were overwhelmed, was “normal”.

I became aware of Levitt’s predictions via an email list of the Fellows of the International Society of Computational Biology on March 14th. I’ve been a Fellow for 3 years, and during this time I’ve received hardly any mail, except during Fellow nomination season. It was therefore somewhat of a surprise to start receiving emails from Michael Levitt regarding COVID-19, but it was a time when scientists were scrambling to figure out how they could help with the pandemic and I was excited at the prospect of all of us learning from each other and possibly helping out. Levitt began by sending around a PDF via a Dropbox link and asked for feedback. I wrote back right away suggesting he distribute the code used to make the figures, make clear the exact versions of data he was scraping to get the results (with dates and copies so the work could be replicated), suggested he add references and noted there were several typos (e.g. the formula clearly had wrong indices). I asked that he post it on the bioRxiv so it could receive community feedback, and suggested he fill in some details so I and others could better evaluate the methods (e.g. I pointed out that I thought the use of a Gaussian for was problematic).

The initial correspondence rapidly turned into a flurry of email on the ISCB Fellows list. Levitt was full of advice. He suggested everyone wear a mask and I and others pushed back noting, as Dr. Anthony Fauci did at the time, that there was a severe shortage of masks and they should go to doctors first. Several exchanges centered on who to blame for the pandemic (one Fellow suggested immigrants in Italy). Among all of this, there was one constant: Levitt’s COVID-19 advice and predictions kept on coming, and without reflection or response to the well-meaning critiques. After Levitt said he’d be surprised if there were more than 10 deaths in Israel, and after he refused to send code reproducing his analyses, or post a preprint, I urged my fellow Fellows in ISCB to release a statement distancing our organization from his opinions, and emphasizing the need for rigorous, reproducible work. I was admonished by two colleagues and told, in so many words, to shut up. 

Meanwhile, Levitt did not shut up. In March, after talking to Israeli newspapers about how he would be surprised if there were more than 10 deaths, he spoke directly to Israeli Prime Minister Benjamin Netanyahu to deliver his message that Israel was overreacting to the virus (he tried to speak to US president Donald Trump as well). Israel is now in a very dangerous situation with COVID-19 out of control. It has the highest number of cases per capita in the world. Did Levitt play a role in this by helping to convince Netanyahu to ease restrictions in the country in May? We may never know. There were likely many factors contributing to Israel’s current tragedy but Levitt, by virtue of speaking directly to Netanyahu, should be scrutinized for his actions. What we do know is that at the time, he was making predictions about the nature and expected course of the virus with unpublished methods (i.e. not even preprinted), poorly documented data, and without any possibility for anyone to reproduce any of his work. His disgraceful scholarship has not improved in the subsequent months. He did, eventually post a preprint, but the data tab states “all data to be made available” and there is the following paragraph relating to availability of code: 

We would like to make the computer codes we use available to all but these are currently written in a variety of languages that few would want to use. While Dr. Scaiewicz uses clean self-documenting Jupyter Python notebook code, Dr. Levitt still develops in a FORTRAN dialect call Mortran (Mortran 1975) that he has used since 1980. The Mortran preprocessor produces Fortran that is then converted to C-code using f2c. This code is at least a hundred-fold faster than Python code. His other favorite language is more modern, but involves the use of the now deprecated language Perl and Unix shell scripts.

Nevertheless, the methods proposed here are simple; they are easily and quickly implemented by a skilled programmer. Should there be interest, we would be happy to help others develop the code and test them against ours. We also realize that there is ample room for code optimization. Some of the things that we have considered are pre-calculating sums of terms to convert computation of the correlation coefficient from a sum over N terms to the difference of two sums. Another way to speed the code would be to use hierarchical step sizes in a binary search to find the value of lnN that gives the best straight line.

Our study involving as it did a small group working in different time zones and under extreme time pressure revealed that scientific computation nowadays faces a Babel of computer languages. In some ways this is good as we generally re-coded things rather than struggle with the favorite language of others. Still, we worry about the future of science when so many different tools are used. In this work we used Python for data wrangling and some plotting, Perl and Unix shell tools for data manipulation, Mortran (effectively C++) for the main calculations, xmgrace and gnuplot for other plotting, Excel (and Openoffice) for playing with data. And this diversity is for a group of three!

tl;dr, there is no code. I’ve asked Michael Levitt repeatedly for the code to reproduce the figures in his paper and have not received it. I can’t reproduce his plots.

Levitt now lies when confronted about his misguided and wrong prediction about COVID-19 in Israel. He claims it is a “red herring”, and that he was talking about “excess deaths”. I guess he figures he can hide behind Hebrew. There is a recording where anyone can hear him being asked directly if he is saying he will be surprised with more than 10 COVID-19 deaths in Israel, and his answers is very clear: “I will be very surprised”. It is profoundly demoralizing to discover that a person you respected is a liar, a demagogue or worse. Sadly, this has happened to me before.

Levitt continues to put people’s lives at risk by spewing lethal nonsense. He is suggesting that we should let COVID-19 spread in the population so it will mutate to be less harmful. This is nonsense. He is promoting anti-vax conspiracy theories that are nonsense. He is promoting nonsense conspiracy theories about scientists. And yet, he continues to have a prominent voice. It’s not hard to see why. The article, similar to all the others where he is interviewed, begins with “Nobel Prize winner…”

In the Talmud, in Mishnah Sanhedrin 4:9, it is written “Whoever destroys a soul, it is considered as if he destroyed an entire world”. I thought of this when listening to an interview with Michael Levitt that took place in May, where he said:

I am a real baby-boomer, I was born in 1947, and I think we’ve really screwed up. We cause pollution, we allowed the world’s population to increase three-fold, we’ve caused the problems of global warming, we’ve left your generation with a real mess in order to save a really small number of very old people. If I was a young person now, I would say, “now you guys are gonna pay for this.”