Category: Science

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.

Jeff Holmes does a CWT with Tyler

Here is the summary:

On this special year-in-review episode, producer Jeff Holmes sat down with Tyler to talk about the most popular — and most underrated — episodes, Tyler’s personal highlight of the year, how well state capacity libertarianism has fared, a new food rule for ordering well during the pandemic, how his production function changed this year, why he got sick of pickles, when he thinks the next face-to-face recording will be, the first thing he’ll do post vaccine, an update on his next book, and more.

Here is the full dialogue, with audio and transcript, here is one short excerpt:

I also tell you what I thought of the guests we had on for the year, and also which episode had the most downloads.  Self-recommended.

And if you have enjoyed this year in Conversations, please consider donating here before the end of the year.  Thank you!

Single cell learning seems to be real

The question of whether single cells can learn led to much debate in the early 20th century. The view prevailed that they were capable of non-associative learning but not of associative learning, such as Pavlovian conditioning. Experiments indicating the contrary were considered either non-reproducible or subject to more acceptable interpretations. Recent developments suggest that the time is right to reconsider this consensus. We exhume the experiments of Beatrice Gelber on Pavlovian conditioning in the ciliate Paramecium aurelia, and suggest that criticisms of her findings can now be reinterpreted. Gelber was a remarkable scientist whose absence from the historical record testifies to the prevailing orthodoxy that single cells cannot learn. Her work, and more recent studies, suggest that such learning may be evolutionarily more widespread and fundamental to life than previously thought and we discuss the implications for different aspects of biology.

That is from a new paper by Samuel J. Gershman, Petra E. M. Balbi, C. Randy Gallistel, and Jeremy Gunawarden, of Harvard, MIT, and Rutgers.

Via the excellent Gaurav Venkataraman (an EV winner who did recent important work in this area).

A Statistical Estimation of the Occurrence of Extraterrestrial Intelligence in the Milky Way

From Xiang CaiJonathan H. JiangKristen A. Fahy, and Yuk L. Yung, here is the paper:

In the field of Astrobiology, the precise location, prevalence and age of potential extraterrestrial intelligence (ETI) have not been explicitly explored. Here, we address these inquiries using an empirical galactic simulation model to analyze the spatial-temporal variations and the prevalence of potential ETI within the Galaxy. This model estimates the occurrence of ETI, providing guidance on where to look for intelligent life in the Search for ETI (SETI) with a set of criteria, including well-established astrophysical properties of the Milky Way. Further, typically overlooked factors such as the process of abiogenesis, different evolutionary timescales and potential self-annihilation are incorporated to explore the growth propensity of ETI. We examine three major parameters: 1) the likelihood rate of abiogenesis ({\lambda}A); 2) evolutionary timescales (Tevo); and 3) probability of self-annihilation of complex life (Pann). We found Pann to be the most influential parameter determining the quantity and age of galactic intelligent life. Our model simulation also identified a peak location for ETI at an annular region approximately 4 kpc from the Galactic center around 8 billion years (Gyrs), with complex life decreasing temporally and spatially from the peak point, asserting a high likelihood of intelligent life in the galactic inner disk. The simulated age distributions also suggest that most of the intelligent life in our galaxy are young, thus making observation or detection difficult.

Via Anecdotal.

Dr. Fauci, Straussian

Recently, a figure to whom millions of Americans look for guidance — Dr. Anthony S. Fauci, an adviser to both the Trump administration and the incoming Biden administration — has begun incrementally raising his herd-immunity estimate.

In the pandemic’s early days, Dr. Fauci tended to cite the same 60 to 70 percent estimate that most experts did. About a month ago, he began saying “70, 75 percent” in television interviews. And last week, in an interview with CNBC News, he said “75, 80, 85 percent” and “75 to 80-plus percent.”

In a telephone interview the next day, Dr. Fauci acknowledged that he had slowly but deliberately been moving the goal posts. He is doing so, he said, partly based on new science, and partly on his gut feeling that the country is finally ready to hear what he really thinks.

Hard as it may be to hear, he said, he believes that it may take close to 90 percent immunity to bring the virus to a halt — almost as much as is needed to stop a measles outbreak.

Asked about Dr. Fauci’s conclusions, prominent epidemiologists said that he might be proven right…

Dr. Fauci said that weeks ago, he had hesitated to publicly raise his estimate because many Americans seemed hesitant about vaccines, which they would need to accept almost universally in order for the country to achieve herd immunity.

Here is the full NYT story.  A few points:

1. Surely Straussianism by now should be persuasive as a general theory.

2. Fauci is idolized by many as a kind of anti-Trump, but he is a terrible risk communicator, as evidenced also by his recent attacks on some of the “lesser” vaccines (which still would work if applied collectively).  Not to mention his earlier remarks on masks, and also the mid-March safety of cruises.  How a person understands Fauci is in fact a pretty good litmus test.

3. Should you be trusting everything the insiders are telling you about FDA processes?

4. I genuinely do not know what the herd immunity threshold is, but I assure you I am trying to tell you the truth on this one (and other matters).  My Straussianism is not a normative theory of my own communication, but rather a positive theory of how the world works, and it has been vindicated once again.

New blood-test device monitors blood chemistry continually

“A blood test is great, but it can’t tell you, for example, whether insulin or glucose levels are increasing or decreasing in a patient,” said Tom Soh, a professor of electrical engineering and of radiology at Stanford. “Knowing the direction of change is important.”

Now, Soh, in collaboration with Eric Appel, an assistant professor of materials science and engineering, and colleagues have developed a technology that can provide this crucial piece of missing information. Their device, which they’ve dubbed the “Real-time ELISA,” is able to perform many blood tests very quickly and then stitch the individual results together to enable continuous, real-time monitoring of a patient’s blood chemistry. Instead of a snapshot, the researchers end up with something more like a movie.

In a new study, published in the journal Nature Biomedical Engineering, the researchers used the device to simultaneously detect insulin and glucose levels in living diabetic laboratory rats. But the researchers say their tool is capable of so much more because it can be easily modified to monitor virtually any protein or disease biomarker of interest…

Technologically, the system relies upon an existing technology called Enzyme-linked Immunosorbent Assay – ELISA (“ee-LYZ-ah”) for short. ELISA has been the “gold standard” of biomolecular detection since the early 1970s and can identify virtually any peptide, protein, antibody or hormone in the blood. An ELISA assay is good at identifying allergies, for instance. It is also used to spot viruses like HIV, West Nile and the SARS-CoV-2 coronavirus that causes COVID-19.

“We do ELISA continuously,” Soh said.

The Real-time ELISA is essentially an entire lab within a chip with tiny pipes and valves no wider than a human hair. An intravenous needle directs blood from the patient into the device’s tiny circuits where ELISA is performed over and over.

Here is the full story, via Malinga Fernando.

The Tony Blair “one dose” idea

Here is the source, of course Alex Tabarrok was there first.  For now give everyone one dose rather than two, and enjoy the partial but more broadly spread protection.  Here are the reactions from two epidemiologists:

Professor Wendy Barclay, from the department of infectious disease at Imperial College London, said Mr Blair’s idea was interesting but agreed it was “too risky” to try without further evidence.

And Professor Neil Ferguson, also from Imperial, added that the UK regulator had authorised the vaccine on the basis that people would receive two doses.

Administering one dose only would require “an entirely different regulatory submission”, he told a Commons committee.

A Department of Health and Social Care spokesperson said: “Over the coming weeks and months, the rate of vaccinations will increase as more doses become available and the programme continues to expand.”

Where are their cost-benefit analyses?  Letting people get infected at current and indeed accelerating rates is also “too risky,” yes?  Is there an epidemiologist or public health expert out there willing to show his or her work, either for or against this idea?  A genuine query, and of course comments are open.  How about one dose for Moderna only?  If we are to defer to their expertise, they do actually have to step up and be the experts, right?

Update on the new Covid-19 strain

Here is a very good article with many points, here are two in particular that caught my attention:

People with a weakened immune system may give the virus this opportunity, as Gupta’s data show. More evidence comes from a paper published in The New England Journal of Medicine on 3 December that described an immunocompromised patient in Boston infected with SARS-CoV-2 for 154 days before he died. Again, the researchers found several mutations, including N501Y. “It suggests that you can get relatively large numbers of mutations happening over a relatively short period of time within an individual patient,” says William Hanage of the Harvard T.H. Chan School of Public Health, one of the authors. (In patients who are infected for a few days and then clear the virus, there simply is not enough time for this, he says.) When such patients are given antibody treatments for COVID-19 late in their disease course, there may already be so many variants present that one of them is resistant, Goldstein says.

And:

These could impact the binding of the virus to human cells and also its recognition by the immune system, Farrar says. “These South African mutations I think are more worrying than the constellation of the British variant.” South African hospitals are already struggling, he adds. “We’ve always asked, ‘Why has sub-Saharan Africa escaped the pandemic to date?” Answers have focused on the relative youth of the population and the climate. “Maybe if you just increase transmission a bit, that is enough to get over these factors,” Farrar says.

Developing…the speed premium of course is rising…