Category: Science

What are the most important statistical ideas of the past 50 years?

We argue that the most important statistical ideas of the past half century are: counterfactual causal inference, bootstrapping and simulation-based inference, overparameterized models and regularization, multilevel models, generic computation algorithms, adaptive decision analysis, robust inference, and exploratory data analysis. We discuss common features of these ideas, how they relate to modern computing and big data, and how they might be developed and extended in future decades. The goal of this article is to provoke thought and discussion regarding the larger themes of research in statistics and data science.

By Andrew Gelman and Aki Vehtari, via Lampros Tzontsos.

Who first noticed the tech was ready for human genome sequencing? (that was then, this is now)

Perkin Elmer’s last purchase had been a Cambridge, Massachusetts, company called PerSeptive Biosystems, a protein-analysis enterprise started by Lebanese-born wunderkind Noubar Afeyan seven years earlier, when the ink was still wet on his Ph.D. from MIT. Afeyan had sold his company to Perkin Elmer for almost $400 million. The deal had yet to be finalized, and formally speaking Afeyan wasn’t yet a Perkin Elmer employee. But he was at the meeting in Foster City, too. Like Lipe and Barrett, he shared White’s vision of “moving up the food chain” and getting into the genetic information business. But like them, he didn’t really have a clear idea how that was to be done.

It was Afeyan, the newcomer, who first said the words. The head of the multicapillary-machine production team was winding up a presentation on the instrument’s design and capacity. There were twenty-odd people around the table, discussing such matters as pricing, costs, and marketing strategy. This was the first time Afeyan had heard that the project even existed. He was taking some notes and idly doing some calculations. “You know, with enough of these machines, we could sequence the whole human genome,” he remarked. A few people chuckled at the notion, and the discussion returned to serious topics. But now Hunkapiller was hunched over his yellow pad, scribbling. After a minute he looked up. “He’s right,” he said. “Who’s right?” asked White. “Noubar. With two hundred machines, we could sequence the human genome in three years.” Most people in the room hardly knew Noubar Afeyan, but they knew Michael Hunkapiller. He would not interrupt a serious discussion except for something even more serious.

That is from James Shreeve’s The Genome War, here is more detail from the NYT in 1999, and for the pointer I thank Patrick Collison.  Of course that is the same Afeyan Noubar who co-founded Moderna and now chairs it, here is my earlier CWT with him.

Had Covid? You May Need Only One Dose

The barriers are breaking. Step by step we move closer to First Doses First. New results from a small-scale study suggest that people who have had COVID have strong reactions to the first dose and may not need the second dose.

NYTimes: Based on these results, the researchers say, people who have had Covid-19 may need only one shot.

“I think one vaccination should be sufficient,” said Florian Krammer, a virologist at the Icahn School of Medicine at Mount Sinai and an author on the study. “This would also spare individuals from unnecessary pain when getting the second dose and it would free up additional vaccine doses.”

…People who have had Covid seem to be “reacting to the first dose as if it was a second dose,” said Akiko Iwasaki, an immunologist at the Yale School of Medicine. So one dose is probably “more than enough,” she said.

A study published earlier this month reported that surviving a natural infection provided 83 percent protection from getting infected again over the course of five months. “Giving two doses on top of that appears to be maybe overkill,” she added.

So for the 25 million to 100 million Americans who have already been infected by COVID it may be better for them personally to delay the second dose. In short, a significant fraction of second doses have little to no value. This (unsurprising) finding means that First Doses First is an even better strategy even if we can’t condition doses on previous infection.

Most important, First Doses First gets more people significant immunity faster which is good for the vaccinated and also drives down R which is good for society as a whole, even the unvaccinated.

The Biden administration has been more pro-active than the Trump administration on tests and vaccination and has already made some goods calls on getting more doses out faster. I hope they continue to be bold. We need quick, bold, and decisive action.

Sci-founder fellowship

Sci-Founder Fellowship is a program to help early career scientists start companies of their own. We believe that companies can often be the best way to pursue translational research, and not enough scientists consider this as serious option.

The Fellowship program provides an investment up to $400,000 to each founding team to get started, along with mentorship and a peer-network of other scientists starting companies to help support you.

We will mentor you — our team includes the former director of Y Combinator’s research non-profit, a co-founder of Color Genomics, and a co-founder of Mammoth Biosciences.

If you think you could be a good fit, please apply here.

Have more questions? Take a look at our FAQ.

Here is the link.

Gender and the dynamics of economics seminars

This paper reports the results of the first systematic attempt at quantitatively measuring the seminar culture within economics and testing whether it is gender neutral. We collected data on every interaction between presenters and their audience in hundreds of research seminars and job market talks across most leading economics departments, as well as during summer conferences. We find that women presenters are treated differently than their male counterparts. Women are asked more questions during a seminar and the questions asked of women presenters are more likely to be patronizing or hostile. These effects are not due to women presenting in different fields, different seminar series, or different topics, as our analysis controls for the institution, seminar series, and JEL codes associated with each presentation. Moreover, it appears that there are important differences by field and that these differences are not uniformly mitigated by more rigid seminar formats. Our findings add to an emerging literature documenting ways in which women economists are treated differently than men, and suggest yet another potential explanation for their under-representation at senior levels within the economics profession.

That is from a new paper by Pascaline Dupas, Alicia Sasser Modestino, Muriel Niederle, Justin Wolfers,
and the Seminar Dynamics Collective.  Via Kris Gulati.

Why U.S. Immigration Barriers Matter for the Global Advancement of Science

From Ruchir Agarwal, Ina Ganguli, Patrick Gaule, and Geoff Smith:

This paper studies the impact of U.S. immigration barriers on global knowledge production. We present four key findings. First, among Nobel Prize winners and Fields Medalists, migrants to the U.S. play a central role in the global knowledge network— representing 20-33% of the frontier knowledge producers. Second, using novel survey data and hand-curated life-histories of International Math Olympiad (IMO) medalists, we show that migrants to the U.S. are up to six times more productive than migrants to other countries—even after accounting for talent during one’s teenage years. Third, financing costs are a key factor preventing foreign talent from migrating abroad to pursue their dream careers, particularly talent from developing countries. Fourth, certain ‘push’ incentives that reduce immigration barriers – by addressing financing constraints for top foreign talent – could increase the global scientific output of future cohorts by 42% percent. We conclude by discussing policy options for the U.S. and the global scientific community.

Via the excellent Kevin Lewis.

How Rapidly ‘First Doses First’ Came to Britain

Tim Harford writes about the whiplash he experienced from the debate over delaying second doses in Britain.

What a difference a couple of weeks makes. In mid-December, I asked a collection of wise guests on my BBC radio programme How to Vaccinate the World about the importance of second doses. At that stage, Scott Gottlieb, former head of the US Food and Drug Administration, had warned against stockpiling doses just to be sure that second doses were certain to be available, Economists such as Alex Tabarrok of George Mason University had gone further: what if we gave people single doses of a vaccine instead of the recommended pair of doses, and thus reached twice as many people in the short term? This radical concept was roundly rejected by my panel

…. “This is an easy one, Tim, because we’ve got to go with the scientific evidence,” said Nick Jackson of the Coalition for Epidemic Preparedness Innovations. “And the scientific evidence is that two doses is going to provide the best protection.”

My other guests agreed, and no wonder: Jackson’s view was firmly in the scientific mainstream three weeks ago. But in the face of a shortage of doses and a rapidly spreading strain of “Super-Covid”, the scientific mainstream appears to have drifted. The UK’s new policy is to prioritise the first dose and to deliver the second one within three months rather than three weeks…..the recommendation comes not from ministers but from the Joint Committee on Vaccination and Immunisation (JCVI).

Strikingly, many scientists have given the move their approval.

See also Tyler’s previous post on this theme.

By the way, if the J&J single-dose vaccine comes in at say 80% effective it is going to be interesting to see how people go from ‘a single-dose at 80% effective is too dangerous to allow for 8-12 weeks’ to ‘isn’t it great we have a single-dose 80% effective vaccine!’.

That was then, this is now, now it’s now again

To see how much the sanitary and medical revolutions have changed the risks of global interaction, examine what kills Americans abroad these days: cardiovascular events including heart attacks account for 49 percent of all deaths, injuries for a further 25 percent, and infectious diseases other than pneumonia for just 1 percent…even travel to pathogen-rich environments has become far, far safer than it used to be: a study of 185 deaths of US Peace Corps volunteers,  placed in some of the world’s least healthy countries, found that unintentional injuries and suicides were far more deadly than infection, accounting for more than 80 percent of deaths between them.

That is from Charles Kenny’s new and excellent The Plague Cycle: The Unending War Between Humanity and Infectious Disease, which was started well before Covid.

Protection against dengue?

The dengue virus uses a particular protein, called Non-Structural Protein 1 (NS1), to latch onto the protective cells around organs. It weakens the protective barrier, allowing the virus to infect the cell, and may cause the rupture of blood vessels. The research team’s antibody, called 2B7, physically blocks the NS1 protein, preventing it from attaching itself to cells and slowing the virus’s spread. Moreover, because it attacks the protein directly and not the virus particle itself, 2B7 is effective against all four dengue virus strains.

That is cited by the excellent Jodi Ettenberg, from new January 2021 research.  If I  hear more I will let you know.

What should I ask Sarah Parcak?

Yes I will be doing a Conversation with her.  Here is part of her Wikipedia entry:

Sarah Helen Parcak is an American archaeologist, Egyptologist, and remote sensing expert, who has used satellite imaging to identify potential archaeological sites in Egypt, Rome, and elsewhere in the former Roman Empire. She is a professor of Anthropology and director of the Laboratory for Global Observation at the University of Alabama at Birmingham. In partnership with her husband, Greg Mumford, she directs survey and excavation projects in the Faiyum, Sinai, and Egypt’s East Delta.

And here is Sarah on Twitter.  Here is her very useful bio page.  Here is her book Archaeology from Space: How the Future Shapes the Past.  So what should I ask her?

My Conversation with the excellent Noubar Afeyan

Among his other achievements, he is the Chairman and co-founder of Moderna.  Here is the audio and video and transcript.  Here is part of the summary:

He joined Tyler to discuss which aspect of entrepreneurship is hardest to teach, his predictions on the future of gene editing and CRISPR technology, why the pharmaceutical field can’t be winner takes all, why “basic research” is a poor term, the secret to Boston’s culture of innovation, the potential of plant biotech, why Montreal is (still) a special place to him, how his classical pianist mother influenced his musical tastes, his discussion-based approach to ethical dilemmas, how thinking future-backward shapes his approach to business and philanthropy, the blessing and curse of Lebanese optimism, the importance of creating a culture where people can say things that are wrong, what we can all learn by being an American by choice, and more.

Here is one excerpt:

AFEYAN:

I should point out, Tyler, what these people don’t yet realize is that mRNA, in addition to being unique in that it’s really the first broadly applied code molecule, information molecule that is used as a medicine and with all the advantages that come with information — digital versus analog — or where you actually have to do everything bespoke, the way drugs usually work.

The other major advantage that it has is that it is something that is actually taking advantage of nature. There was a lot of know-how we had going into this around how the process could be done. In fact, let me tell you the parallel that we used.

We have a program in cancer vaccines. You might say, “What does a cancer vaccine have to do with coronavirus?” The answer is the way we work with cancer vaccines is that we take a patient’s tumor, sequence it, obtain the information around all the different mutations in that tumor, then design de novo — completely nonexistent before — a set of peptides that contain those mutations, make the mRNA for them, and stick them into a lipid nanoparticle, and give it back to that patient in a matter of weeks.

That has been an ongoing — for a couple of years — clinical trial that we’re doing. Well, guess what? For every one of those patients, we’re doing what we did for the virus, over and over and over again. We get DNA sequence. We convert it into the antigenic part. We make it into an RNA. We put it in a particle. In an interesting way, we had interesting precedents that allowed us to move pretty quickly.

And at the close:

Imagine if all of us were also born imagining a better future for ourselves. Well, we should be, but we’ve got to work to get that. An immigrant who comes here understands that they’ve got to work to get that. They have to adapt. The problem is, if you’re born here, you may not actually think that you’ve got to work to get that. You might think you’re born into it.

This will be a funny thing to say, and I apologize to anybody that I offend. If we were all Americans by choice, we’d have a better America because Americans by choice, of which I’m one, actually have a stronger commitment to whatever it takes to make America be the place I chose to be, versus not thinking about that as a core responsibility.

Definitely recommended, he is working to save many many lives, and with great success.

Can open access scientific publishing work?

That is the top of my latest Bloomberg column, another link here, here is one excerpt:

The Indian government has a proposal, called the “One Nation, One Subscription” plan, to buy bulk subscriptions of the world’s most important scientific journals and provide them free to everyone in India. Given the porousness of the internet, and the widespread availability of VPN services, general worldwide access is likely to result. Sci-Hub, based in Russia, already offers open access to many scientific publications.

But why stop there? Rather than just reproducing published articles, the publication process could be opened up altogether.

And the key part:

The biggest problem for an open-access regime is how to ensure good refereeing, which if done correctly raises the quality of academic papers. Under the current system, editors decide which papers get refereed, and they choose the identities of the referees. Those same referees are underpaid and underincentivized, and often do a poor or indifferent job.

Many of the original papers on mRNA vaccines, for example, were rejected numerous times by academic journals, hardly a ringing endorsement of the status quo. More generally, since publication is currently a yes/no decision, the refereeing system creates incentives to avoid criticism and play it safe, rather than to strike out with bold new ideas and risk rejection.

Under my alternative vision, research scientists would be told to publish one-third less and devote the extra time to volunteer refereeing of what they consider to be the most important online postings. That refereeing, which would not be anonymous, would be considered as a significant part of their research contribution for tenure and promotion. Professional associations, foundations and universities could set up prizes for the top referees, who might be able to get tenure just by being great at adding value to other people’s work. If the lack of anonymity bothers you, keep in mind that book reviews are already a key determinant for tenure in many fields, such as the humanities, and they are not typically anonymous.

Freer entry yes, open access yes, but also more refereeing.

“Second Doses” post-mortem

The most striking thing about the Biden administration shift to a version of “First Doses First” is how little protest there has been.  Given how many public health experts were upset about the idea only a few days ago, you might expect them to organize a Wall Street Journal petition from hundreds of their colleagues: “Biden administration proposal endangers the lives of millions of Americans.”

But of course they won’t do that.  Some of that is pro-Democrat partisanship, but that is not even the main factor.  One reason is that public health experts, with their medical and quasi-medical backgrounds, typically have very little sense of how to respond in the public arena if challenged.  For instance, not a single one stepped forward with a calculation to defend “Second Doses.”  They are not especially good at “the internet rules of the game,” which of course are now supreme (not always for the best, to be clear).

The second and probably most important reason is that, as I had explained, sins of omission are treated as far less significant than sins of commission.  Now that a version of “First Doses First” is on the verge of becoming policy, to do nothing about that is only a sin of omission, and thus not so bad.  Remarkable!  Status quo bias really matters here.

I haven’t seen a single peep on Twitter opposing the new policy.

Just keep all this in mind the next time you see a debate over public health policy.  There is often less behind the curtain than you might think.

Quantum Technology for Economists

That is the title of a new paper by Isaiah Hull, Or Sattath, Eleni Diamanti, and Goran Wendin.  Much of it I did not understand, but maybe you will.  Here is one excerpt:

Our overview of quantum money starts with a full description of the original scheme, which was introduced circa 1969, but only published later in Wiesner (1983). We will see that it achieves what is called “information-theoretic security,” which means that an attacker with unbounded classical and quantum resources will not be able to counterfeit a unit of the money. Since this original scheme was proposed, the term “quantum money” has come to refer to a broad variety of different payment instruments, including credit cards, bills, and coins, all of which use of quantum physical phenomena to achieve security.The real promise of quantum money is that it offers the possibility of combining the beneficial features of both physical cash and digital payments, which is not possible without the use of the higher standard of security quantum money offers.In particular, a form of currency called “public-key” quantum money would allow individuals to verify the authenticity of bills and coins publicly and without the need to communicate with a trusted third party. This is not possible with any classical form of digital of money, including cryptocurrencies, which at least require communication with a distributed ledger. Thus, quantum money could restore the privacy and anonymity associated with physical money transactions, while maintaining the convenience of digital payment instruments.

Makes those crypto people look like David Laidler!  See also this Behera and Sattath paper.