Tom McLeish (1962-2023): natural philosopher

I was very sad to hear last month that Tom McLeish died of cancer. He was an extraordinary person and scientist. Tom can been characterised as a polymath or a "renaissance man".

Tom's career is briefly sketched in an obituary from the University of York, where for the last few years he held a position, created for him, Professor of Natural Philosophy in the physics department.

A small measure of Tom's influence on me is that there are eight posts on this blog about his work and another seven posts on my soli deo gloria blog.

Tom was best known in the scientific community for his work on the theory of soft matter, for which he was elected a Fellow of the Royal Society. I highly recommend his Very Short Introduction on the subject. But the influence and recognition of his intellectual contributions go far beyond his work on soft matter. For example, after the publication of The Poetry and Music of Science: Comparing Creativity in Science and Art by Oxford University Press in 2019, the following year the journal Interdisciplinary Science Reviews devoted a whole issue to seven different reviews of the book, with a response from Tom. 

In 2015, Tom visited the University of Queensland for two days. During this time he gave three different seminars, including in the School of Chemical Engineering, and the Centre for the Study of Science, Religion and Society in Emmanuel College. I wasn't game to also ask him to give a seminar in the physics department, although now I wish I had.

One of my fond memories of Tom was being with him in Cyprus at a small interdisciplinary meeting on the science of human flourishing, sponsored by CERN (Rolf Heuer) and the Templeton World Charity Foundation (Andrew Briggs). Tom was so excited that he was able to race off and go scuba diving during an afternoon break to a particularly choice spot. To me, Tom lived with the passion, excitement, and wonder of a little kid, as he encountered the world of nature and ideas. There was no jadedness, no cynicism, BS, no self-promotion, no exclusivity, just excitement about life in all its richness.

I love the moments in this video, during his recent Boyle lecture, where he talks about the physics of rubber, entropy, emergence, and the importance of choosing appropriate scales to investigate phenomena.

My condolences to Tom's family, friends, and colleagues. He died much too young and will be sorely missed.

Einstein on big questions

The mere formulation of a problem is far more essential than its solution, which may be merely a matter of mathematical or experimental skills.

To raise new questions, new possibilities, to regard old problems from a new angle, requires creative imagination and marks real advance in science.

I am enough of an artist to draw freely upon my imagination. Imagination is more important than knowledge. Knowledge is limited. Imagination encircles the world.

Albert Einstein and Leopold Infeld (1938), The Evolution of Physics

I recently encountered this quotation in The Poetry and Music of Science: Comparing Creativity in Science and Art by Tom McLeish. I have heard many times the "Imagination is more important than knowledge" quote, sometimes as a dubious justification for dubious ideas. However, I did not know the context. 

My postdoctoral advisor, John Wilkins tried to drill into me, the idea in the first paragraph, that just coming up with a well-defined formulation of a problem could be a significant advance. This idea certainly had some impact on me, since I sometimes hear my non-scientist wife quote it!

On reflection, I am afraid that I too easily lose sight of this priority of defining problems, just like the method of multiple alternative hypotheses. Good science is hard.

Why am I reading this article? What question am I trying to answer?

Why am I writing this paper? What question am I trying to answer?

What is the problem I assigning a student to work on? Is it well-formulated?

Defining good research questions is hard work and requires discipline.

A Myth about Condensed Matter Physics?

What is condensed matter physics about? 

In his beautiful book, The Problems of Physics (originally published in 1987), Leggett has a nice chapter about condensed matter physics, Physics on a human scale. The abstract begins:

This chapter argues that the widespread notion that the discipline of condensed matter physics is devoted to deriving the properties of complex many-body systems from that of their atomic-level components is a myth, and that the analogy of map-making is much more appropriate.

Here are some quotes that clarify Leggett's argument.

a number of cases, particularly in the traditional areas of the physics of gases and crystalline solids, in which a model which treats the behaviour of the whole as essentially just the sum of that of its parts (atoms or electrons) has been quite successful; and a few more in which, even if a ‘one- particle’ picture fails, a description in terms of pairs of particles interacting in a way which is not particularly sensitive to the environment gives good results. But these cases, despite the fact that they totally dominate the presentation of the subject in most elementary textbooks, are actually the exception rather than the rule. 

In virtually all the frontier areas of modern condensed-matter physics, the relationship between our understanding of the behaviour of matter at the microscopic level of single atoms and electrons, and at the macroscopic level of (say) liquids and solids, is actually a good deal more complicated than this.

If the activity just described is not what condensed-matter physics is all about, then what is it about? I would claim that the most important advances in this area come about by the emergence of qualitatively new concepts at the intermediate or macroscopic levels—concepts which, one hopes, will be compatible with one's information about the microscopic constituents, but which are in no sense logically dependent on it. 

... [these new concepts] provide a new way of classifying a seemingly intractable mass of information, of selecting the important variables from the innumerable possible variables which one can identify in a macroscopic system;

All this is not to deny that an important role is played in condensed-matter physics by attempts to relate the macroscopic behaviour of bulk matter to our knowledge concerning its constituent atoms and electrons. Indeed, the theoretical literature on the subject is full of papers which at first sight seem to be claiming to ‘derive’ the former from the latter—that is, to do exactly what I have just said condensed-matter physicists do not do. 

It is precisely this compelling need to isolate, from a vast and initially undifferentiated mass of information, the features which are relevant to the questions one wishes to ask, which distinguishes condensed-matter physics qualitatively from areas such as atomic or particle physics...

In this situation I believe that it is sensible to reorient our view of the kinds of questions that we are really asking in condensed-matter physics. Rather than chasing after the almost certainly chimerical goal of deducing the behaviour of macroscopic bodies rigorously from postulates regarding the microscopic level, it may be better to view the main point of the discipline as, first, the building of autonomous concepts or models at various levels, ranging all the way from the level of atomic and subatomic physics to that of thermodynamics; and, second, the demonstration that the relation between these models at various levels is one not of deducibility but of consistency—that is, that there are indeed ‘physical approximations’ we can make which make the models at various levels mutually compatible.

In different words, condensed matter physics is all about emergence! [Although, I know Leggett does not like the way the word is used]. 

The centrality of intermediate scales was also emphasised by Tom McLeish in Soft Matter: A Very Short Introduction.

When I recently read Leggett's chapter I was concerned that this might be in conflict with my draft manuscript of Condensed Matter Physics: A Very Short Introduction.  In the first chapter, I wrote the following.

The central question of Condensed Matter Physics

Generally, condensed matter physicists grapple with one question. Because it is so important I state the question in three different ways.

• How do macroscopic properties emerge from microscopic properties? 

• How do the properties of a state of matter emerge from the properties of the atoms in the material and the interactions between the atoms?

• How do the many atoms in a material interact with one another to collectively produce a particular property of the material? 

I think this is consistent with Leggett's perspective, particularly because I do later emphasise emergence and intermediate scales. On the other hand, I may not have the same emphasis (or strong language) that Leggett does. 

Leggett's view is particularly pertinent today because a quarter of a century later there are probably a lot more people who would say that they are condensed matter physicists but would subscribe to the "myth". This is because of the rise of computational materials science due to massive increases in computational power and better computational methods such as those based on Density Functional Theory (DFT), using "better" functionals and DMFT (Dynamical Mean-Field Theory).

What do you think?

Lessons from the discovery of liquid crystals

I recently learned a little about the history of the discovery of liquid crystals, stimulated by Soft Matter: A Very Short Introduction by Tom McLeish. Besides being a fascinating story there are lessons about the importance of curiosity-driven research, interdisciplinarity, serendipity, and the long road to technology.

Friedrich Reinitzer (1857 - 1927) was a botanist and chemist who worked at the Institute of Plant Physiology in Prague. He was studying cholesterol with the aim of determining its molecular weight. He produced crystals of cholesteryl benzoate and measured their heat capacity as a function of temperature. Aside: For chemists today this measurement is known as differential scanning calorimetry (a constant source of heat is added and the temperature measured as a function of time). 

In 1888, Reinitzer observed that the crystal melted at 145.5 degrees Celsius (signified by absorption of heat), forming a milky liquid. However, at 178.5 degrees Celsius, there was a second absorption of heat, and the liquid became transparent. This suggested that there were two melting transitions. Puzzled by this Reinitzer consulted the physicist and crystallographer, Otto Lehmann, who promoted the idea that this was a new state of matter, which he dubbed a "liquid crystal" (or flowing crystal).

Today, cholesteryl benzoate is classified as a chiral nematic liquid crystal, which is also sometimes known as a cholesteric liquid crystal, in honour of the first one. A schematic of the ordering is shown below.

The milkiness was not explained until the 1960s by Pierre-Gilles de Gennes, who exploited an analogue with a superconductor in a magnetic field.

More detail is in the paper

Liquid‐Crystal Science from 1888 to 1922: Building a Revolution 

Michel Mitov 

This discovery of liquid crystals was the first of many cases where a new state of matter was discovered by a thermodynamic measurement. Others include superfluid 4He (the lambda transition) and superfluid 3He, as I have recently highlighted.

Signatures of soft matter

What is soft matter? 

Soft Matter: A Very Short Introduction by Tom McLeish has just been published.

McLeish identifies six characteristics of soft matter.

1. Thermal motion 

They exhibit large local spatial rearrangements of their microscopic constituents under thermal agitation. In contrast,  "hard" materials experience only small distortions due to thermal motion.

2. Structure on intermediate length scales

There are basic units ("fundamental" structures), typically involving a very large number (hundreds to thousands) of atoms, that are key to understand soft matter behaviour. These basic units are neither macroscopic nor microscopic (in the atomic sense), but rather mesoscopic (meso from the Greek word for middle). The relevant scales range from several nanometres up to a micrometer. An example of these length scales is those associated with (topological) defects in liquid crystals, such as those shown below.

Image is from here.

3. Slow dynamics

The mesoscopic length scales and complex structures lead to phenomena occurring on time scales of the order of seconds or minutes.

4. Universality

The same physical properties can arise from materials with quite different underlying chemistries.
This characteristic is of significant practical relevance. Solving a problem for one specific material can also solve it for whole families of materials. This universality is also of deep conceptual significance as understanding a general phenomenon is usually more powerful than just a specific example. 

5. Common experimental techniques

The dominant tools are microscopy, scattering (light, x-rays, neutrons), and rheometers which measure mechanical properties such as viscosity (rheology).

6. Multi-disciplinarity

Soft matter is studied by physicists, chemists, engineers, and biologists. 

The chapter titles in the book are 

Milkiness, muddiness, and inkiness [Colloids]

Sliminess and stickiness [Polymers]

Gelification and soapiness [Foams and Self-assembly]

Pearliness [Liquid crystals]

Liveliness [Active matter]

I highly recommend the book. Hopefully, later I will write a review.

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

 View ORCID ProfileSteffen Klein,  View ORCID ProfileMirko Cortese,  View ORCID ProfileSophie L. Winter,  View ORCID ProfileMoritz Wachsmuth-Melm,  View ORCID ProfileChristopher J. Neufeldt, Berati Cerikan,  View ORCID ProfileMegan L. Stanifer,  View ORCID ProfileSteeve Boulant,  View ORCID ProfileRalf Bartenschlager,  Petr Chlanda

View ORCID Profile

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 Iserman, Christine Roden, Mark Boerneke, Rachel Sealfon, Grace McLaughlin, Irwin Jungreis,  View ORCID ProfileChris Park, Avinash Boppana, Ethan Fritch, Yixuan J. Hou, Chandra Theesfeld, Olga G Troyanskaya, Ralph S. Baric,  View ORCID ProfileTimothy P. Sheahan, Kevin Weeks, Amy 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.

In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges

1. View ORCID ProfileBeata Turoňová1,2,*, 
2. View ORCID ProfileMateusz Sikora3,*, 
3. View ORCID ProfileChristoph Schürmann4,*, 
4. View ORCID ProfileWim J. H. Hagen1, 
5. View ORCID ProfileSonja Welsch5, 
6. View ORCID ProfileFlorian E. C. Blanc3, 
7. View ORCID ProfileSören von Bülow3, 
8. View ORCID ProfileMichael Gecht3, 
9. View ORCID ProfileKatrin Bagola6, 
10. View ORCID ProfileCindy Hörner4,7, 
11. View ORCID ProfileGer van Zandbergen6,8,9, 
12. View ORCID ProfileJonathan Landry10, 
13. View ORCID ProfileNayara Trevisan Doimo de Azevedo10, 
14. View ORCID ProfileShyamal Mosalaganti1,2, 
15. View ORCID ProfileAndre Schwarz1, 
16. View ORCID ProfileRoberto Covino3,11, 
17. View ORCID ProfileMichael D. Mühlebach4,7, 
18. View ORCID ProfileGerhard Hummer3,12,†, 
19. View ORCID ProfileJacomine Krijnse Locker13,†, 
20. View ORCID ProfileMartin Beck1,2,†
21.