Friday, October 30, 2020

Classic fails about predicting the scientific future

There are many statements that are attributed to famous scientists that turn out to be widely wrong. A decade ago I wrote about one from Brian Pippard predicting the end of condensed matter physics in the 1960s.

However, just like Einstein quotes, it turns out that many of these statements in the popular folklore are often wrongly attributed. For example, according to the Wikipedia entry on Lord Kelvin,
The statement "There is nothing new to be discovered in physics now. All that remains is more and more precise measurement" has been widely misattributed to Kelvin since the 1980s, either without citation or stating that it was made in an address to the British Association for the Advancement of Science (1900).[86] There is no evidence that Kelvin said this,[87][88] and the quote is instead a paraphrase of Albert A. Michelson, who in 1894 stated: "… it seems probable that most of the grand underlying principles have been firmly established … An eminent physicist remarked that the future truths of physical science are to be looked for in the sixth place of decimals."[88]
I love Bill Bryson's book A Brief History of Nearly Everything.  I recently read in it that the Surgeon General of the United States of America, William Stewart, said in 1967:
“The time has come to close the book on infectious diseases. We have basically wiped out infection in the United States.”
Wow, that sure was wrong. There are now 9 million covid-19 cases and more than 200,000 deaths in the USA. I was going to write a blog post about this. But, then I discovered these two nice articles.

In 2015 an article in the New Yorker
One of Science’s Most Famous Quotes Is False By Michael Specter

A 2013 article in the journal Infectious Diseases of Poverty
On the exoneration of Dr. William H. Stewart: debunking an urban legend 
Brad Spellberg and Bonnie Taylor-Blake

Basically, Stewart never said this, nor held this view. In contrast, many of his contemporaries did.

And then there is all the hype about current materials research leading to revolutions in computing, medicine, transportation, commerce, ...

Thursday, October 22, 2020

What is condensed matter physics? (revised)

I have just rewritten chapter 1 of Condensed Matter Physics: A Very Short Introduction.  I obtained very helpful feedback on my first version from a freelance editor. This has given me fresh eyes for the whole manuscript, which I am now rewriting. She suggested moving some strong material from later chapters into the first chapter, particularly the fact that CMP is all about emergence. I have also benefited from other readers and blog commenters. For example, David Sholl's asked about how CMP is different from other approaches to materials science.

Here is the new version. 

I welcome comments. But, again you are probably not my intended audience. Rather, it is your family, undergraduates, or colleagues in biology or social sciences.

Tuesday, October 20, 2020

The physics of the SARS-CoV-2 virion

 Some progress is being made in understanding the structure and dynamics of the SARS-CoV-2 virions (virus particles) that are responsible for the pandemic. A nice starting point for the non-expert is a recent article in The New York Times.

A fundamental question is what is the structure and symmetry of the virion? In particular, does it have the icosahedral symmetry possessed by many virions, as discussed in a talk I gave earlier this year and in a recent review (with lots of nice pictures). As far as I am aware, there are still no definitive results on the overall structure and symmetry. 

This preprint has some really nice images and videos such as the video below. 

SARS-CoV-2 structure and replication characterized by in situ cryo-electron tomography

Steffen KleinMirko CorteseSophie L. WinterMoritz Wachsmuth-MelmChristopher J. NeufeldtBerati CerikanMegan L. StaniferSteeve BoulantRalf Bartenschlager

Mathematical aside: the authors note that the geometric problem of how to place the spike protein (S) trimers on the surface of the virion is related to the "Tammes Problem" or the seventh unsolved mathematical problem listed by Steve Smale: how do you arrange a specific number of points on a sphere with the largest possible minimum distance between the points.

The paper below shows that the nucleocapsid protein (N) is similar to that for SARS-CoV and MERS. The protein can form dimers and tetramers, steps in the self-assembly of the whole virion.

Specific viral RNA drives the SARS CoV-2 nucleocapsid to phase separate

Christiane IsermanChristine RodenMark BoernekeRachel SealfonGrace McLaughlinIrwin JungreisChris ParkAvinash BoppanaEthan FritchYixuan J. HouChandra TheesfeldOlga G TroyanskayaRalph S. BaricTimothy P. SheahanKevin WeeksAmy S. Gladfelter

Some nice soft matter physics is in the preprint below. It argues that the N protein can undergo liquid-liquid phase separation with the viral genome. Aside: even before covid, liquid-liquid phase separation was quite a hot topic in cell biology, as recently discussed by Tom McLeish. 

Architecture and self‐assembly of the SARS‐CoV‐2 nucleocapsid protein 

Qiaozhen Ye, Alan M. V. West, Steve Silletti, Kevin D. Corbett

Finally, the paper below combines molecular dynamics simulations with experiments to argue that the stalk of the spike protein has three hinges giving the head of the spike unexpected orientational freedom so it can scan the host cell surface.