Emergence of complex patterns

I think it is amazing how in the universe we see diverse and beautiful patterns and structures. Even relatively simple systems can self-organise to produce things one would not expect or predict. Consider clouds, turbulent flows, leopard spots, a tree leaf, spiral galaxies, biological cells...

It is also amazing and beautiful that we can develop relatively simple mathematical models that can produce similar patterns.

This is emergence!

Here is a beautiful example that recently came to my attention.

The associated PRL is

Faraday-Wave Contact-Line Shear Gradient Induces Streaming and Tracer Self-Organization: From Vortical to Hedgehoglike Patterns

Héctor Alarcón, Matías Herrera-Muñoz, Nicolas Périnet, Nicolás Mujica, Pablo Gutiérrez, and Leonardo Gordillo

There is also a Physics story too.

Chemical fingerprints on blood diamonds

“Fortunately, the majority of gentlemen who are persuaded to steal things don’t really know a huge amount about science”

This is a choice quote in a fascinating article, New Australian technology tracks down gold thieves and blood diamonds ["New tech to trace dodgy diamonds" in the print edition] in the Australian Financial Review (AFR) Weekend.

It describes the work of John Watling, Chief Scientist at the company Source Certain. Basically by measuring the relative amounts of different trace elements [chemical impurities] in a sample of gold or diamond one can determine what mine that it has come from.

Sage wisdom on computational materials science

Roald Hoffmann and Jean-Paul Malrieu are two of my favourite living theoretical chemists. Both greatly value the role of concepts and intellectual clarity in theory. Hoffmann has featured in 22 posts on this blog.

They recently published a wonderful trilogy in  Angewandte Chemie.

Simulation vs. Understanding: A Tension, in Quantum Chemistry and Beyond. 

Part A. Stage Setting

Part B. The March of Simulation, for Better or Worse

Part C. Toward Consilience

I add this trilogy to my list of 5 papers every computational chemistry student should read, suggested by me a decade ago. [Malrieu is author of one of those and Hoffmann co-author of another.]

Although the trilogy addresses and uses specific examples from computational quantum chemistry it is just as relevant to anyone interested in computational materials science. Actually, I hope that anyone interested in materials science would read and digest it as it gives a sober and balanced perspective about the relationship between theory, simulation, and understanding.

Articles are timely as they address hype about how AI techniques will "revolutionise" materials theory. 

The articles are beautifully written and engage with broader themes such as philosophy of science, culture, art, and politics.

Finally, I just love this photo of the two authors, both in their eighties. the photo reflects some of the joy they find in science, so beautifully expressed in these articles.

I thank Ben Powell for bringing the papers to my attention.

Covid-19 in a different world

 

Covid-19 has turned the world upside down. Different people and communities have had very different experiences. In my state of Queensland, it is almost a different world. To illustrate I share the data above, which prompted a three-day lockdown in Brisbane. For reference, Queensland has a population of 5.2 million.

A number of factors have contributed to the relatively positive situation. Australia is an island. Our borders were closed early. There was unity between state and federal governments. Generally, lockdowns have been pronounced promptly. Although Australians do not like authority and are a rebellious bunch, lockdowns and mask mandates have generally been observed. We are not immune from conspiracy theories and vaccine hesitancy. But, overall we have not been plagued by the same level of "politicisation" that has hobbled other countries. 

In some ways, I feel I am living in a different world.

Yet, some of this good fortune should not lead to pride and complacency. Things may still come unstuck. The Delta variant is spreading in Sydney and half the country is in lockdown. The government vaccine rollout has been dubbed a "stroll out".  Only 12 percent of the population has been fully vaccinated. Australia is currently ranked last among the OECD countries. 

The associated "blame game" has even been featured in The New York Times.

Is condensed matter physics too abstract?

Condensed matter physics is about the properties of real materials. Real stuff that you can see and touch and that you can use to make very practical things like TV screens and mobile phones. Yet, I find it fascinating and somewhat ironic that in condensed matter theory very abstract ideas and mathematical techniques keep cropping up (and being extremely useful): variable spatial dimensions, imaginary frequencies, topology, Chern numbers, conformal invariance, ...

Yet, there is a danger with abstraction. Theoretical condensed matter is not pure mathematics. Perhaps, too often fancy and beautiful mathematics is prized over physical intuition and insight. Theory may take precedence over experiment. How does one find the appropriate balance?

This is part of broader issues about the role of abstraction and formality in education.

Pierre de Gennes (1932-2007) was arguably the founder of soft matter as a research field, as recognized by the Nobel Prize in Physics in 1991. He began his career working on superconductivity and went on to develop a unified framework to understand soft matter (liquid crystals, polymers, foams, colloids...), introducing ideas such as order parameters, scaling, renormalisation, and universality.

After his Nobel, de Gennes gave many lectures in French high schools, which were then published as a book, Fragile Objects: Soft Matter, Hard Science, and the Thrill of Discovery. I highly recommend it, both as a popular introduction to soft matter, but also to hear the perspective of a great scientist on education and research.

de Gennes spent almost his whole life living and working in France. In the book he rants about the French system, particularly its obsession with entrance exams, mathematics, formality, and the abstract.

“Manual skills, visual acumen, the sense of observation, an interest for the physical world which surrounds us, are all qualities that are neglected or downgraded.”

“To work in a garage seems to me the best initiation to a professional life.”

“Ignorance of the real world causes grave distortions.”

“the positivist prejudice”

I found this fascinating because one thing de Gennes is famous for is showing how some properties of a polymer can be understood by considering a theory involving a vector of dimension n, where n was a continuous variable, in the limit where n approaches zero! That is pretty abstract! But, I guess the point is that he is not against abstraction, exams, and mathematics, per se. Rather, he is against them taking on a life of their own.

de Gennes concerns are also shared by Henri Alloul (well known for beautiful NMR experiments on strongly correlated electron materials) author of Introduction to the Physics of Electrons in Solids. In the Preface, he writes, 

In many countries, teaching traditions have always given pride of place to a formal, and essentially deductive, presentation of the physics, i.e., starting from formal hypotheses and leading up to observable consequences. This deductive approach leaves a purely a posteriori verificational role to observation, and hides the thinking that has gone into building up the models in the first place. Here we shall adopt the opposite approach, which begins with the fact that in science in general, and in solid state physics in particular, the qualitative understanding of a phenomenon is an important step which precedes the formulation of any theoretical development. We thus urge the reader to carry out a careful examination of the deeper significance of experimental observations, in order to understand the need for specific models and carry out realistic approximations.

The debate about abstract mathematics is also central to contrasting views about the Institute for Advanced Study at Princeton.

de Gennes's views would have also resonated with Harry Kroto who shared The Nobel Prize in Chemistry for the discovery of buckyballs. He credited playing with Meccano as a child as very important in his scientific development.

Sweet demonstrations of phase transitions

This week my wife and I did some science experiments with kids, aged about 8-12, at a holiday kids club organised by our church. The first day we did rockets, using the old standbys of baking soda rockets and mentos and coke.

On the second day, we did the science of chocolate. Ten years ago (!) we had done this based on some demonstrations developed at Harvard, described in this paper The Science of Chocolate: Interactive Activities on Phase Transitions, Emulsification, and Nucleation. 

Teaching kids about phase transitions with ice and steam is not quite as exciting or memorable as them melting chocolate in their mouths. An important scientific idea is:

Physical properties of matter (such as melting temperature) change with differences in chemical composition.

This is illustrated by the different melting temperatures of white, milk, and dark chocolate.

We also tried to mix water and oil, with and without the presence of detergent. This illustrates ideas about emulsification, including hydrophobic interactions. This is relevant to the production of nice smooth and uniform chocolate because the cocoa powder can only dissolve in the cocoa butter when an emulsifier is present.

Discussing chocolate is also an opportunity to discuss Milton Hershey (USA) and the Cadbury family (UK). They were not only philanthropists but were proactive in taking care of employees and their families, e.g. constructing schools, parks, and affordable housing. Richard and George Cadbury developed the garden village of Bournville; now a major suburb of Birmingham. I particularly like this sentence in the Wikipedia entry on George Cadbury, showing how he was far ahead of his time.

In 1901, disgusted by the imperialistic policy of the Balfour government and opposed to the Boer War, Cadbury bought the Daily News and used the paper to campaign for old age pensions and against the war and sweatshop labour.^[4]

Other scientific articles of interest include the following. The first two discuss how there are six different polymorphs (crystal structures) of chocolate. The competition between these states comes into play with tempering, snapping, shine, and smoothness. [Aside: In general, calculating the relative energies of different polymorphs of molecular materials is a major scientific challenge.]

Chocolate: A Marvelous Natural Product of Chemistry, Ginger Tannenbaum

Using Differential Scanning Calorimetry To Explore the Phase Behavior of Chocolate Michael J. Smith

The kitchen as a physics classroom Amy C Rowat, Naveen N Sinha, Pia M Sörensen, Otger Campàs, Pere Castells, Daniel Rosenberg, Michael P Brenner and David A Weitz

The science and politics of the origins of covid-19

I want to begin by stating some hypotheses. Some may be obvious. Others may be contentious. I will number them so that people can easily make comments about specific ones. The underlying issues are illustrated in recent debates about the possible origins of covid-19.

1. Systematic critical thinking is essential to scientific progress and public policy. Healthy doses of skepticism can be valuable.

2. Science progresses well by making multiple hypotheses and examining carefully what evidence is consistent with each of the hypotheses. This is something that Murray Gell-Mann wished someone had told him when he was twenty years old.

3. Transparency is essential to science. People need to share data, including primary data. The more that such data is publicly available the better. This is what open science advocates. 

4. Science is built on ethical conduct, both implicit and explicit. It is important that declarations of conflicts of interest are not just a box-ticking exercise.

5. Scientists cannot have allegiance to some greater authority than truth and integrity. Problematic allegiances include to a company, a family, an institution, a political party, or to a nation. An example is the case of the recent change to the charter of Fudan University, indicative of the stranglehold that the Chinese Communist Party has over Chinese universities.

6. Given these issues about integrity and conflicts of interest luxury journals are problematic because there is a conflict of interest between the commercial success of the publisher in the short term (achieved by promoting hype, i.e. newsworthy sexy scientific breakthroughs, even if they are wrong) and the boring work of doing careful painstaking science.

7. One approach to solving some of these problems is self-regulation of scientific communities. However, when sub-communities (e.g. virologists, string theorists) self-regulate this may be impeded by conflicts of interest.

8. Given the issues above, science journalists need to be more critical and skeptical. Too often they seem in awe of scientists and want to promote hype as it sells. Journalists need to ask more hard questions about conflicts of interest, weak reasoning, claimed "breakthroughs", hype, proposed great technological applications, and the "science as saviour" narrative.

9. There is a fear among scientists about publically speaking about scientific uncertainty and ambiguity. This fear is understandably driven by the experience of "skeptics" latching onto uncertain statements to promote climate change denialism, young-earth creationism, and anti-vaccines. Thus, a great challenge in public engagement is to educate about the role of uncertainty in science.

10. Science always occurs in a political context whether it is in Australia, Romania, or China. The context will always have some influence, but it should not be determinative.

11. The greater the stakes (whether potential Nobel Prizes, company profits, government scandal, a disaster) in play, the greater the likelihood will be for mistakes, corruption, deception, and cover-up. Consequently, the level of scientific diligence and regulation needs to be proportionate to the possible benefits and risks. Extraordinary claims require extraordinary evidence.

12. Beware of the argument from authority. A hypothesis should be accepted or rejected based on the quality of the reasoning and evidence provided, not on the scientific prestige (or lack thereof) of the proponent.

All of the claims above I see played out recently in debates about the origins of covid-19. Two distinct hypotheses are dissected in a helpful and long article recently published in the Bulletin of Atomic Scientists.

The origin of COVID: Did people or nature open Pandora’s box at Wuhan?  Nicholas Wade 

Hypothesis 1. The virus spread from a wet market in Wuhan. The virus was zoonotic, i.e. as a result of evolution it crossed the species barrier from bats to humans.

Hypothesis 2. The virus spread from the Wuhan Institute of Virology where a research group was investigating bat viruses and doing "gain of function" research to see how the bat viruses might be modified genetically into a form that could infect humans. 

The article is worth reading because it carefully lays out the science while also raised many of the issues I mention above. A few things that I learned follow.

There is significant evidence that the MERS, SARS1, Ebola viruses are zoonotic. The evidence consists of finding intermediate genetic forms in intermediate species. Often this evidence was found within months of the disease outbreak. In contrast, after 18 months there is still no evidence of intermediate forms for SARS2.

The "gain of function" research in Wuhan was being funded by the USA National Institutes of Health, via a grant to the EcoHealth Alliance of New York, led by Peter Daszak. Wade writes

"We stand together to strongly condemn conspiracy theories suggesting that COVID-19 does not have a natural origin,” a group of virologists and others wrote in the Lancet on February 19, 2020, when it was really far too soon for anyone to be sure what had happened. Scientists “overwhelmingly conclude that this coronavirus originated in wildlife,” they said, with a stirring rallying call for readers to stand with Chinese colleagues on the frontline of fighting the disease.

Contrary to the letter writers’ assertion, the idea that the virus might have escaped from a lab invoked accident, not conspiracy. It surely needed to be explored, not rejected out of hand. A defining mark of good scientists is that they go to great pains to distinguish between what they know and what they don’t know. 

It later turned out that the Lancet letter had been organized and drafted by Peter Daszak, ... This acute conflict of interest was not declared to the Lancet’s readers. To the contrary, the letter concluded, “We declare no competing interests.”

Wade points out that there is no direct evidence for either of the two hypotheses (which he calls theories).

He also talks quite a bit about "who is to blame" and claims that we need to know the answer as to which hypothesis is correct in order to know how to prevent the next pandemic. However, I disagree. Based on the evidence we already have we can conclude the following.

A. New deadly viruses can be zoonotic. The best way to reduce their likelihood is to close wet markets and reduce environmental destruction.

B. Even if SARS2 did not spread from the "gain of function" research in Wuhan it is completely plausible that it could have. Thus, given such risks that research should be stopped until a case is made that the possible benefits outweigh the risks and that it is done with much greater transparency and regulation than currently.

For balance I include an extract from Wikipedia

In May 2021, Wade published an article which advanced the claim that COVID-19 likely originated from a leak at the Wuhan Institute of Virology.^[12][13] Wade's article generated significant controversy,^[14] and has become one of the most-cited pieces in support of the lab leak hypothesis.^[15] This claim is at odds with the prevailing view among scientists that the virus most likely has a zoonotic origin.^{[16][17][18][19]} Some experts have supported taking the lab leak possibility seriously, while the majority consider it very unlikely, calling it "speculative and unsupported".^[20][21] Others noted the explosive and implausible nature of Wade's allegations about virologists conspiring to avoid blame for causing the pandemic,^[22] with Science-Based Medicine among those calling Wade's argument a conspiracy theory.^[23]

Another article worth reading (recommended by a commenter on this blog) is

Beijing’s useful idiots: Science journals have encouraged and enforced a false Covid narrative by Ian Birrell.