The Story of Science is a nice video series

 I am on the lookout for good video resources about science that I can recommend to others, particularly non-scientists. By chance, I recently came across the BBC production, The Story of Science: Power, Proof, and Passion, hosted by Michael Mosley.

There is also a beautiful book that goes with the series, containing more detail, including colour illustrations. I was able to get the DVDs and the book from my local public library.

I particularly appreciate that science is presented as a human endeavour and progress is influenced by local contexts (economic, political, religious, ...). That can be acknowledged and enjoyed without descending into a social constructivist view of scientific knowledge. In a similar vein, the series does not have an ideological edge, or embrace some common tropes that too often popular video treatments may promote such as science the saviour, science the moneymaker, science the spoiler, science the monster-maker, ... or that science is uncontrollable, is inscrutable, or is the domain of evil/eccentric geniuses,....

The series introduced me to several colourful characters who played key roles in the history of science, including Hennig Brand, Hans Sloan, Georges Cuvier, Horace-Benedict de Saussure, Simon Sevin, Richard Trevithick, ...

Elite imitation and flailing universities

The mission of universities is thinking: teaching students to think and enabling scholars to think about the world we live in. Yet, it is debatable whether most universities in the world achieve these goals. Arguably, things are getting worse. Universities are flailing. Why?

Most universities desperately want to be elite. They want to be like Harvard, Caltech, Oxford, Princeton, Berkeley, Stanford, ...

But non-elite universities do not have the necessary resources to be elite. Yet they are controlled by elites (management on high salaries, faculty educated at elite universities) who want to be elite and so settle for elite imitation.

"A flailing university is what happens when the principal cannot control its agents. The flailing university cannot implement its own plans and may have its plans actively subverted when its agents work at cross-purposes. The non-elite university flails because it is simultaneously too large and too small: too large because the non-elite university attempts to legislate and regulate every aspect of the work of faculty and students and too small because it lacks the resources and personnel to achieve its ambitions. 

To explain the mismatch between the non-elite universities' ambitions and their abilities, consider the premature demands by elites in non-elite universities for goals, policies, curricula, infrastructure, and outcomes more appropriate to an elite university. 

In order to satisfy external actors (government, business, parents, ...) non-elite universities often take on tasks that overwhelm institutional capacity, leading to premature load bearing. As these authors put it, “By starting off with unrealistic expectations of the range, complexity, scale, and speed with which organizational capability can be built, external actors set both themselves and (more importantly) the students and researchers that they are attempting to assist to fail”. 

The expectations of external actors are only one source of imitation, however. Who people read, listen to, admire, learn from, and wish to emulate is also key. Another factor driving inappropriate imitation is that the elites in non-elite universities—senior management and high-profile faculty—are closely connected with business elites and elite universities, usually more closely than they are to the students and faculty at their own university. As a result, this elite initiates and supports policies that appear to it to be normal even though such policies may have little relevance to the student and faculty as a whole and may be wildly at odds with the university capacity. This kind of mimicry of what appear to be the best elite university policies and practices is not necessarily ill intentioned. It is simply one by-product of the background within which the elites operates. University managers engage with business elites and managers at other non-elite universities."

I actually did not write most of the text above, I just took the text from the first two pages of the article below and replaced some words (e.g. Indian state with non-elite university, Indian citizens with students and faculty). 

Premature Imitation and India’s Flailing State 

Shruti Rajagopalan, Alexander T. Tabarrok

I came across the article after listening to a podcast episode that interviews the two authors, recommended by my son.

I also recommend Shutri's own podcast, Ideas of India, including a recent episode, Where did development economics go wrong?

Previously, I have discussed similar issues from the angle of the strategic importance for nation building of non-elite institutions within a country, and how science curricula should focus more on basic skills.

What do you think? Are universities like a flailing state? Is the problem elite imitation?

Why is there so much symmetry in biological systems?

 One of the biggest questions in biology is, What is the relationship between genotypes and phenotypes? In different words, how does a specific gene (DNA sequence) encode information that allows a very specific biological structure with a unique function to emerge?

Like big questions in many fields, this is a question about emergence.

In biology, this mapping from genotype to phenotype occurs at many levels from protein structure to human personality. An example is how the RNA encodes the structure of a SARS-CoV2 virion.

A fascinating thing about biological structures is that many have a certain amount of symmetry. The human body has reflection symmetry and many virions have icosahedral symmetry. What is the origin of this tendency to symmetry? Could evolution produce it?

Scientists will sometimes make statements such as the following about evolution.

Symmetric structures preferentially arise not just due to natural selection but also because they require less specific information to encode and are therefore much more likely to appear as phenotypic variation through random mutations.

How do we know this is true? Can such a statement be falsified? Or at least, can we produce concrete models or biological systems that are consistent with this statement?

There is a fascinating paper in PNAS that addresses the questions above.

Symmetry and simplicity spontaneously emerge from the algorithmic nature of evolution 

Iain G. Johnston, Kamaludin Dingle, Sam F. Greenbury, Chico Q. Camargo, Jonathan P. K. Doye, Sebastian E. Ahnert, and Ard A. Louis 

Here are a few highlights from the article. First, how one gets specific about information content and algorithms.

Genetic mutations are random in the sense that they occur independently of the phenotypic variation they produce. This does not, however, mean that the probability P(p) that a Genotype-Phenotype [GP] map produces a phenotype p upon random sampling of genotypes will be anything like a uniformly random distribution. 

Instead, ... arguments based on the coding theorem of algorithmic information theory (AIT) (7) predict that the P(p) of many GP maps should be highly biased toward phenotypes with low Kolmogorov complexity K(p) (8). 

High symmetry can, in turn, be linked to low K(p) (6, 9–11). An intuitive explanation for this algorithmic bias toward symmetry proceeds in two steps: 

1) Symmetric phenotypes typically need less information to encode algorithmically, due to repetition of subunits. This higher compressibility reduces constraints on genotypes, implying that more genotypes will map to simpler, more symmetric phenotypes than to more complex asymmetric ones (2, 3). 

2) Upon random mutations these symmetric phenotypes are much more likely to arise as potential variation (12, 13), so that a strong bias toward symmetry may emerge even without natural selection for symmetry.

The authors consider several concrete models and biological systems that illustrate this bias toward symmetry. The first involves the structure of protein complexes, as given in the Protein Data Base (PDB).

A) Protein complexes self-assemble from individual units. 

(B) Frequency of 6-mer protein complex topologies found in the PDB versus the number of interface types, a measure of complexity 

𝐾˜
$$K˜(p). 

Symmetry groups are in standard Schoenflies notation: C6, D3, C3, C2, and C1. There is a strong preference for low-complexity/high-symmetry structures. 

(C) Histograms of scaled frequencies of symmetries for 6-mer topologies found in the PDB (dark red) versus the frequencies by symmetry of the morphospace of all possible 6-mers illustrate that symmetric structures are hugely overrepresented in the PDB database. 

Note the logarithmic scales for the probabilities (frequencies), meaning that the probabilities span four orders of magnitude. The authors claim that "many genotype–phenotype maps are exponentially biased toward phenotypes with low descriptional complexity. "

This intuition that simpler outputs are more likely to appear upon random inputs into a computer programming language can be precisely quantified in the field of AIT (7), where the Kolmogorov complexity K(p) of a string p is formally defined as a shortest program that generates p on a suitably chosen universal Turing machine (UTM). 

From AIT the authors produce a bound (equation 1, and below), that exhibits the exponential decay of probability with complexity, similar to that seen in their graphs, such as the one shown below, for a model gene regulatory network that is modeled by 60 ordinary differential equations (ODEs). The red dashed line is the bound below.

𝑃(𝑝)≤2−𝑎𝐾˜(𝑝)−𝑏,  [1

Scaled frequency vs. complexity 𝐾˜(𝑝)for the budding yeast ODE cell cycle model (30). Phenotypes are grouped by complexity of the time output of the key CLB2/SIC1 complex concentration. Higher frequency means a larger fraction of parameters generate this time curve. The red circle denotes the wild-type phenotype, which is one of the simplest and most likely phenotypes to appear. The dashed line shows a possible upper bound from Eq. 1. There is a clear bias toward low-complexity outputs.

One minor comment is that I was surprised that the authors did not reference the classic 1956 paper by Crick and Watson. They introduced the concept of "genetic economy". Prior to any knowledge of the actual structure of virions, they predicted that virions would have icosahedral symmetry because that reduced the cost of the genome coding for the structure of the virion.

Hence, it would be interesting to explore the relationship between the PNAS paper and this one.

Structural puzzles in virology solved with an overarching icosahedral design principle

Reidun Twarock & Antoni Luque

There is a nice New York Times article about the PNAS paper. I thank Sophie van Houtryve for bringing that to my attention leading me to the PNAS paper.

Anthony Jacko (1985-2022): condensed matter theorist

I was very sad when last week I learned of the death of Anthony Jacko, a former member of the Condensed Matter Theory group at UQ. He was only 36 years old, having been diagnosed with stage 4 cancer at the end of last year.

Jacko's funeral was this week. Family and friends spoke warmly of his intelligence, humour, faithfulness, passion for life, and endearing quirkiness. There were both tears and laughs.

I will say something here about his scientific contributions, though at times like this what we achieve professionally does not really seem that important.

I first met Jacko as an undergraduate at UQ when he took an advanced undergraduate condensed physics course with me in 2006. That year he did an undergraduate honours (fourth year) project with Ben Powell and John Fjaerestad, on the Kadowaki-Woods ratio. This work eventually led to a Nature Physics paper, that I discussed in this blog post.

In 2007 I was quite happy when Jacko decided to do a Ph.D. with me and Ben Powell. We tried to come up with simple effective Hamiltonians for organometallic complexes that are used in organic LEDs and solar cells. Although we made some progress, I think the questions we tried to address have still not been answered definitively. The most progress has subsequently been made by Ben Powell.

For a postdoc, Jacko moved to Frankfurt to work with Roser Valenti and Harald Jeschke (now at Okayama University). I was really impressed how Jacko learned how to do reliable DFT-based electronic structure calculations and to use Wannier orbitals to extract tight-binding model parameters. Jacko brought this expertise back to Ben Powell's group at UQ, where he worked from 2013 to 2018.

During that time Jacko co-authored a string of really nice papers that inspired me to write multiple blog posts, such as those below. Looking back over that work I see how careful, solid, and systematic it is. Basically, good science, that we do not see enough of these days.

The broad issue is as follows. Understanding strong electron correlations in complex molecular materials requires effective Hamiltonians that are a realistic representation of the essential physics and chemistry. Sometimes next-nearest-neighbour interactions and subtleties in crystal structure really do matter. Other times they do not. The methods used by Jacko provided a robust way of doing this.

How robust are your tight-binding model parameters?

Common challenges with constructing diabatic states and tight-binding models

Quantum spin liquid on the hyper-honeycomb lattice

Springy stringy molecular crystals

Faculty hope that former students will come to their funeral. We also hope that we won't have to attend the funeral of any of our students. It is very sad.

An endowment is being created at The University of Queensland, to fund an undergraduate physics prize that will be awarded each year in honour of Jacko.

My condolences to Jacko's partner, Alana, and to family and friends.

Predicting new states of quantum matter is highly unlikely

Last year New Scientist published a nice article by Jon Cartwright

States of matter: The unthinkable forms beyond solid, liquid and gas

From time crystals to supersolids, we keep discovering extraordinary new kinds of matter – now the true challenge is being able to predict what we'll find next

Unlike the typical New Scientist article, this one is a measured and reasonable discussion about reality, rather than the latest wild and breathless speculations that the magazine is rife with. Unfortunately, it is behind a paywall.

I was interviewed for the article, which ends (see below) by contrasting my pessimism with the optimism of Andrei Bernevig. His optimism is based on this recent paper that reports a systematic identification of stoichiometric compounds that have topological bands and so can support topological states of matter. That is important and wonderful work. But, it is looking at what can be considered a "one-electron" problem, and so does not shake my pessimism. I do hope I am wrong.

Unusual metal-insulator transitions arising from interplay of frustration, flat bands, and strong correlations

My colleagues and I recently posted a preprint

C3 symmetry breaking metal-insulator transitions near a flat band in the half-filled Hubbard model on the decorated honeycomb lattice

H. L. Nourse, Ross H. McKenzie, B. J. Powell

We study the single-orbital Hubbard model on the half-filled decorated honeycomb lattice. In the non-interacting theory at half-filling, the Fermi energy lies within a flat band where strong correlations are enhanced and the lattice exhibits frustration. We find a correlation driven first-order metal-insulator transition to two different insulating ground states - a dimer valence bond solid Mott insulator when inter-triangle correlations dominate, and a broken C3 symmetry antiferromagnet that arises from frustration when intra-triangle correlations dominate.

The metal-insulator transitions into these two phases have very different characters. 

The metal-broken C3 antiferromagnetic transition is driven by spontaneous C3 symmetry breaking that lifts the topologically required degeneracy at the Fermi energy and opens an energy gap in the quasiparticle spectrum. 

The metal-dimer valence bond solid transition breaks no symmetries of the Hamiltonian. It is caused by strong correlations renormalizing the electronic structure into a phase that is adiabatically connected to both the trivial band insulator and the ground state of the spin-1/2 Heisenberg model in the relevant parameter regime. 

Therefore, neither of these metal-insulator transitions can be understood in either the Brinkmann-Rice or Slater paradigms.

We welcome comments.

Quotes to entice and entertain the reader

Some authors make use of epigraphs in their books. An epigraph is a short quotation at the beginning of a chapter that aims to set the stage for what follows. My general observation is that many of the epigraphs are rather obscure and the connection to the content of the chapter is not clear. Perhaps, I am just too ignorant about classical literature, or perhaps some authors are just trying to be too clever. But, sometimes I think they are creative, enticing, and even humorous.

I tried having a go at using epigraphs for Condensed Matter Physics: A Very Short Introduction. Unfortunately, after doing this I discovered that epigraphs are no longer allowed in the VSI series.

Anyway, I had fun doing it and so here I present the epigraphs I came up with.

1 What is condensed matter physics?

… thin flakes like frost on the ground appeared on the desert floor. When the Israelites saw it, they said to each other, “What is it?” … [they] called the bread manna. [Manna sounds like the Hebrew for What is it?]  It was white like coriander seed and tasted like wafers made with honey.

Exodus 16 

2 A multitude of states of matter

“There are more things in heaven and earth, Horatio, than are dreamt of in your philosophy.” 

Hamlet

3 Symmetry matters

The chief forms of beauty are order and symmetry and definiteness, which the mathematical sciences demonstrate in a special degree...

Aristotle, Metaphysics

4 The order of things

John Milton, Paradise Lost

5 Adventures in Flatland

Points, Lines, Squares, Cubes, Extra-Cubes — we are all liable to the same errors, all alike the Slaves of our respective Dimensional prejudices

Edwin Abbott, Flatland

6 The critical point

Aristotle answers: "Because only particulars can be perceived, and science is of  universals." ...out of numerous particulars the universal becomes evident.

George Henry Lewes 

7 Quantum matter

"I think I can safely say that nobody understands quantum mechanics." 

Richard Feynman

8 Topology matters

A mathematician who does not know the difference between a doughnut and a coffee mug is a topologist.

9 Emergence

F. Scott Fitzgerald: “The rich are different from you and me.” 

Ernest Hemingway: “Yes, they have more money.” 

10 The endless frontier

"New frontiers of the mind are before us, and if they are pioneered with the same vision, boldness, and drive with which we have waged this war we can create a fuller and more fruitful employment and a fuller and more fruitful life."

Franklin D. Roosevelt

I believe the times demand new invention, innovation, imagination, decision. I am asking each of you to be pioneers on that New Frontier.

John F. Kennedy

What do you think about epigraphs? 

Can you give a book in which you thought they were particularly good?

What do you think of those above?

I welcome alternative suggestions.