On the arXiv, I have posted a new version of my review article, Emergence: from physics to biology, sociology, and computer science.
I have added expanded sections on molecular structure, quantitative measures of causal emergence, and biological evolution.
There are also many minor additions and corrections. I hope the hyperlinked Table of Contents is helpful.
I welcome feedback and suggestions. I am sure there is much more to do.
An example of emergent entities in condensed matter physics are quasiparticles. The concept can be described with the following analogue. When a horse gallops through the desert it stirs up a dust cloud that travels with it. The motion of the horse cannot be separated from the accompanying dust cloud. They act as one entity. Similarly, in a system consisting of many interacting particles, when one particle moves it carries with it a “cloud” of other particles. This composite entity is referred to as a quasiparticle. It turns out to be easiest to understand the whole system of particles in terms of the quasiparticles rather than in terms of the individual particles.
Quasiparticles are composite objects. Like the constituent particles in the system, quasiparticles each have properties such as charge, mass, and spin. However, these properties of a single quasiparticle may be different from those of the individual particles of which it is constituted. An example is holes in semiconductors; the many electrons in a crystal act collectively to produce a hole (the absence of a single electron), a quasiparticle with the opposite charge to that of a single electron. A more striking example is for the fractional quantum Hall states; the charge of the quasiparticles can be a fraction of the charge on a single electron.
Different musical instruments produce distinct sounds because they are made of different materials, and they vibrate in different ways in response to different stimuli. In general, the vibrations of a medium reflect something about the medium itself. Chapter 3 discussed how in a crystal the number of distinct ways that sound can travel through a crystal reflects the symmetry and ordering of the atoms in the crystal.
When the skin on a drum is hit by a drumstick the skin vibrates at particular frequencies. Similarly, a state of matter responds to external stimuli such as light, sound or heat, by oscillating at particular frequencies. These vibrations travel through the matter as waves. The properties of these waves reflect the particular order present in the state of matter. Here is a specific example. When a neutron with a particular energy and momentum is absorbed by a ferromagnetic crystal the interaction of the magnetism of the neutron with that of the atoms in the crystal produces a collective oscillation of the magnetic state of the crystal in time and space. Known as a spin wave, this oscillation has a particular frequency and wavelength. In quantum theory, waves and particles are equivalent to one another. The energy and momentum of a particle are related to the waves’ frequency and wavelength, respectively. Particles equivalent to light waves are known as photons; particulate equivalents of sound waves are known as phonons. And similarly, the particle equivalent of a spin wave is known as a magnon. These collective excitations are quasiparticles. Whereas the particles in a system may interact strongly with one another, the quasiparticles may interact weakly with one another. This makes analysis and understanding of the relevant theories more tractable.
The quasiparticle concept is a powerful theoretical tool in condensed matter physics. It is the basis for the construction of models that enable emergent phenomena to be understood in terms of the effective interactions between components such as quasiparticles, rather than in terms of the actual constituent particles and their interactions. This approach requires profound physical insight in order to discern what the truly essential components of a system are. Lev Landau was one of the first theoretical physicists to take this approach, introducing the idea of quasiparticles in his theories of superfluidity in 4He and of liquid 3He. This approach was also central to the BCS theory of superconductivity. Phil Anderson was also a master of the approach, using intuition to propose models that were simple enough for analysis and yet complex enough to capture the essential physics associated with a particular state of matter. In 1977 he was awarded the Nobel Prize for work using this approach to understand two specific systems: magnetic atoms in metals and the motion of electrons in materials that are not crystals and are dirty in the sense of containing many impurities.
The theory of evolution explains the origin of biological diversity and levels of similarity between species. A characteristic of emergence is that many iterations of a simple law (natural selection of the fittest to reproduce) can produce novel, diverse and rich structures. In biological evolution many generations in a population can produce new traits and species.
Many of the most debated issues about evolution relate to the different characteristics of emergence and are briefly discussed below.
Scales
Central to emergence are the ideas of “many” and of scales. The former can take two forms: a system composed of many interacting components, or a system that undergoes many iterations according to a rule that is repeated many times. For evolution, both forms of “many” are relevant and have several dimensions. Evolution occurs in a population, i.e., a community of many members of a species living in a specific environment. Each member of the population has a specific genotype (many genes), which largely determines biological characteristics, from proteins to organs, defined as the phenotype. The environment also consists of many interacting species. Natural selection can act at multiple levels: on genes, cells, organisms, species, and groups of species.
Microscopic and macroscopic scales can also manifest in different ways. In terms of length, the micro- and macro- scales can be defined in terms of genotypes and phenotypes, respectively. In terms of time, microevolution and macroevolution roughly correspond to directly observable timescales and geological timescales, respectively. They are associated with the emergence of new traits within a species and new species, respectively.
Novelty
Development of new traits and species occurs over many generations, due to the repetition of the rule of natural selection.
Evolution theory uses concepts such as natural selection, survival of the fittest, niches, and hierarchical trees, that are not present in chemistry and physics.
Connecting micro- and macro- properties
As for other systems, this is one of the great challenges of emergence. Genotypes and phenotypes are extremely well characterised. Genotype-phenotype maps seek to connect these micro- and macro- levels. A detailed understanding of how microevolution leads to macroevolution is a challenge.
Discontinuities
In microevolution, new traits occur within a species due to (continuous) adaptation to the environment. In contrast, in macroevolution, new organs and species can occur suddenly (at least on geological timescales). An example is the Cambrian explosion of new life forms. Extinctions can also represent discontinuities.
Evolution of a population occurs in response to changes in an environment. New traits, new species, and extinctions can be viewed as qualitative changes due to quantitative changes. For example, small changes in the oxygen concentration in the atmosphere is one (among many) hypotheses for the cause of the Cambrian explosion.
Using techniques from statistical physics, the transition of a species from survival to extinction can be viewed as a non-equilibrium phase transition to an absorbing state. The order parameter is the population and a toy model is directed population.1
Diversity with limitations
All species are based on the same biochemistry of DNA and proteins. Yet from these same building blocks there is an incredible diversity: more than 8 million distinct species, including more than 10,000 species of birds and more than 15,000 species of ants. Darwin said nature produces “endless forms most beautiful.”
But there are limitations. For example, the number of species with more than one head, brain, heart, or liver is limited. There are many more genotypes than phenotypes.
The dominant view is that evolution is driven by random genetic mutations. Debates have arisen about how much evolution is limited (constrained) by morphology and environment.
Ball stated: (p. 332)
“convergent evolution is often regarded as a sign that certain shapes or structures are ideal adaptations to particular environments for physical reasons: wings consisting of flat, thin membranes are best for flying, torpedo-shaped bodies a streamlined for efficient swimming, and so on… There is a tendency in evolutionary biology to regard natural selection as a process with an infinite palette: anything is possible so long as it doesn't break the laws of physics. But the laws of physics might impose more constraint than that, precisely because biology uses rather than merely suffers them.”
Universality
Not all mutations produce a change in phenotype. There are neutral mutations. There are many more genotypes than phenotypes. In other words, genotype-phenotype maps are many-to-one.
Species that are unrelated or distantly related (in the tree of life) sometimes have traits or behaviours that are similar. Convergent evolution is the hypothesis that natural selection produced the same outcome in a different context.
Modularity at the mesoscale
The economist Simon pointed out that evolution can occur on much faster time scales than might be expected because of modularity. According to Clune et al.
“A long-standing, open question in biology is how populations are capable of rapidly adapting to novel environments, a trait called evolvability [1]. A major contributor to evolvability is the fact that many biological entities are modular, especially the many biological processes and structures that can be modelled as networks, such as metabolic pathways, gene regulation, protein interactions and animal brains [1–7].”
Ball highlighted how domains in proteins provide functional modules that evolution uses: (pp. 174-5)
“the evolution of metazoan proteins is not so much a slow affair of letting random genetic mutations change one amino acid for another and seeing what effect it produces. Rather, it constitutes a reshuffling of already functional modules to produce multidomain molecules with new potential - a strategy much more likely to yield successful results… the “unit” of molecular evolution here is not really the base pair of DNA or the amino acid or protein, or the gene itself, by the peers at a scale intermediate between the two: the module of a domain. It seems that this shuffling, rather than the slow mutation of primary base sequences, is what has driven the evolution of animals.”
Johnston et al. considered an algorithmic picture of evolution that
“suggests that 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… many genotype–phenotype maps are exponentially biased toward phenotypes with low descriptional complexity. A preference for symmetry is a special case of this bias… Lower descriptional complexity also correlates with higher mutational robustness, which may aid the evolution of complex modular assemblies of multiple components.”
Self-organisation
Complex biological structures, from proteins to organisms, have formed spontaneously due to evolution over millions of years. Their intricacy and functionality have led to claims of purpose and design. However, this is argued to be an “apparent” design, just like an economy whose self-organisation appears “as if” it is guided by an “invisible hand.”
Kauffman claimed that self-organisation is as important as natural selection in driving evolution.
Unpredictability
A contested question about evolution is the role of contingency (historical accidents) and whether the evolution of complex life forms, particularly humans, was an accident of history or inevitable.
Irreducibility
Until recently, evolutionary biology has been dominated by a reductionist gene-centric view, popularised by Dawkins. However, recent discussions about systems biology, evo-devo, and epigenetics have questioned this view. Some characterise these alternative views as a form of structuralism.
Complexity
An algorithmic picture of evolution suggests that simplicity spontaneously emerges as many genotype-phenotype maps may be biased towards phenotypes with low descriptional complexity.
Toy models
An earlier post discussed the key role that toy models, such as “bean bag” genetics, have played in evolutionary theory.
Cross-fertilisation of fields
Ideas from evolution have stimulated the development of genetic algorithms in computer science.
Drossel has reviewed connections between evolution and statistical physics, including a wide range of toy models. Examples include spin glass models that give rise to rugged landscapes for fitness and can describe hierarchical structures, comparable to Darwin’s tree of life. Goldenfeld and Woese argued that evolution can be viewed as a collective phenomenon far from equilibrium. The toy model central to their discussion is directed percolation.
Every person is unique. No two people are identical. We differ in physical appearance, personality, fingerprints, heartbeat, gait, and DNA. Such differences are used to identify criminals and in video surveillance of citizens by nation states. Yet in other ways all humans are the same. We all have brains, hearts, and lungs. All our bodies use the same biochemistry to stay alive: whether to breathe oxygen, digest food, or fight infections. On some level we have common aspirations: to survive, to be loved, to be happy, and to find meaning and purpose. Yet these aspirations find many expressions. Humans have certain universal qualities and properties, yet at a finer level of detail there is a particularity of each of these properties. They are at one level the same but are not the same at another level.
All academic disciplines search for universals; they develop categories, concepts, and theories that overarch particularities. Biologists classify species of plants and animals and types of cells and viruses. All biological systems use the same molecules (DNA, RNA, and proteins) and chemical reactions. The same genetic code uses the information encoded in a piece of DNA to make proteins with specific functions. Anthropologists study the immense diversity of human cultures and societies. This diversity can be described in terms of universal concepts such as kinship, family, ritual, community, economics, law, and morality. Linguists study the common structures and grammars of the thousands of different human languages. Although the world we live in is diverse, disciplines have each discovered some universals.
Condensed matter physicists study diverse states of matter and the transitions between them. A surprising discovery is that there is much more universality than might be expected, particularly given the chemical and structural diversity of materials. In this chapter, I will discuss the nature of this universality, how it emerges, and the length scales associated with transitions between different states of matter. Landau’s great insight was that many of the chemical and structural details of materials are irrelevant to understanding phase transitions. Furthermore, a precise classification of different types of phase transitions, into what are called universality classes, can be made. For example, superconducting, superfluid, and a subset of magnetic transitions are in the same class. The determinants of the universality classes are the symmetry of the state and the spatial dimensionality of the system. None of the other details matter.
Many phase diagrams (such as the Figure above) include a critical point, located at the end of a boundary between two different states of matter. A common example is the critical point that occurs at a specific temperature and pressure for a transition between a liquid and a gas. Understanding the physical properties of a material close to its critical point was a great challenge for theoretical physics, lasting a hundred years, and was only solved in the 1970s. The powerful theoretical ideas and techniques that were developed provide a quantitative way to relate the properties of a system at one length scale to properties at a different length scale. These techniques also have application to a wide range of other problems and fields including elementary particle physics, chaos theory, fractals, polymers, and machine learning. New insights were gained into universality and emergent phenomena.
An extract from "The Critical Point," chapter 6, Condensed Matter Physics: A Very Short Introduction
In computational quantum chemistry, the Born-Oppenheimer approximation (BOA) is used to determine potential energy surfaces (PES) for electronic states of molecules. It is standard practise to identify local minima on a PES with molecular structures. Molecular binding energies are identified with the difference in energy between these minima and the energies of the isolated atoms of which the molecule is composed.
A chemical reaction between two molecules A and B to produce C can be understood in terms of the PES for the composite system consisting of all the atoms in A and B. The dynamics of the chemical reaction can be described in terms of a path on the PES that goes from the local minimum associated with A and B infinitely far apart to the minimum associated with the structure C. The path will pass through a saddle point on the PES and this is identified with a transition state in the chemical reaction and its energy determines the activation energy for the chemical reaction. The local curvature of the PES near a minima can be used to determine force constants for harmonic motion and the associated vibrational frequencies of a molecule.
This picture is a completely classical one and so may motivate a claim that chemists mix classical and quantum concepts and calculations in an ad-hoc manner. (This kind of argument is often used by philosophers to claim that chemistry cannot be reduced to physics). This is unfair because a quantum description of the nuclear dynamics can be given in terms of quantum wave-packets, consistent with the Heisenberg uncertainty principle, and whose dynamics is defined by the quantum equation for nuclear motion that is given by the BOA. Furthermore, the dynamics of the centre of a wave-packet is given by classical equations of motion (Ehrenfest’s theorem). Thus, the classical language used by chemists can be viewed as a justified and compact version of a quantum description.
Structural isomers. Isomers are associated with different local minima on the electronic ground state potential energy surface for a given combination of atoms. To understand a quantum description of isomers, consider a reaction coordinate associated with an isomerisation reaction (i.e. conversion of one isomer to the other). There are three energy scales of relevance: the energy difference between the ground state energy of the two isomers, the magnitude of the barrier height (activation energy), and the quantum zero-point energy associated with vibrations in the direction of the reaction coordinate. Denote these energies as dE, Eb , and Ezp, respectively. If dE ~ Ezp << Eb then the nuclear probability density rho(R) for the vibrational ground state will have two local maxima, corresponding to the geometries of the two isomers. If dE >> Ezp then the nuclear probability density rho(R) for the vibrational ground state will have only one local maxima, corresponding to the lower energy isomer geometry. However, the geometry of the higher energy isomer can be found as a local maximum in the nuclear probability density rho(R) for one of the excited vibrational ground states.
Figure. Potential energy surface associated with the two structural isomers of HOCO. TS_n denote different transition states associated with the chemical reaction OH + CO -> H + CO2. Taken from Bui et al.
Adventures in Flatland
In everyday life we think of most objects as having three dimensions. But what would life be like in a two-dimensional world? For one thing, it would be harder to move around. We could no longer step over things but would have to move around them. In 1884 Edwin Abbott published Flatland: A Romance of Many Dimensions, under the pseudonym, A. Square, a satirical novella about social life in Victorian England. People are represented by geometrical objects. Men are represented by shapes such as triangles and hexagons. Women are represented by lines. The social status of men increases with the number sides that their shape has and how many of the sides are of the same length. Abbott’s book created limited interest and was largely forgotten by the 1920s. Interest revived when theoretical physicists started to think about worlds in different dimensions. This interest was stimulated by Albert Einstein’s theories of relativity, that proposed that we live in a four-dimensional world, not a three-dimensional one. Time is the fourth dimension, and there is an intimate and concrete connection between time and space. Attempts to unify gravity with other fundamental forces has led to physicists proposing and studying theories with more than four dimensions.
Changing the number of spatial dimensions leads to different physics because it changes what is mathematically possible. In three dimensions, there were only five highly symmetrical shapes known as Platonic solids (tetrahedron, cube, octahedron, icosahedron, and dodecahedron). In contrast, in two dimensions it is possible to make an infinite number of symmetrical shapes, known as regular polygons, shapes made of straight lines of equal length such as squares or hexagons. Similarly, the number of Bravais lattices differ in two and three dimensions. Changing the number of spatial dimensions changes both what is mathematically possible and what is physically possible.
What would condensed matter physics be like in Flatland? This question received limited attention before the 1970s. Occasionally, theoretical physicists would investigate mathematical models of crystals or magnets in one or two dimensions just because the mathematics was simpler and more tractable than in three dimensions. The goal was to obtain insight into physics in three dimensions. We will consider a famous example, the Ising model.
In the 1970s, several surprising developments led to significant interest in condensed matter physics in spatial dimensions different from the usual three. First, it became possible to make a wide range of material systems that were two-dimensional. Secondly, theoretical work showed that states of matter, and phase transitions between them, can be qualitatively different in one, two, and three spatial dimensions. And thirdly, considering different numbers of spatial dimensions turned out to be very fruitful for theory, particularly for understanding phase transitions near critical points.
An extract from "Adventures in Flatland," chapter 5 in Condensed Matter Physics: A Very Short Introduction
The order of things
Life and the world around us sometimes appears chaotic and random. We may feel this way about traffic, weather, economics, social change, politics, or our personal relationships. Perhaps that is why many yearn for regularity, predictability, order, and stability. Science is a search for patterns and order in the natural world. Condensed matter physics is about how order emerges from disorder.
This chapter explores how different states of matter are associated with different types of ordering of the atoms in the material. The symmetry of the state reflects the type of ordering, i.e., the patterns associated with the state. There is also a rigidity associated with the ordering and the rigidity determines the nature of the deviations from perfect ordering and results in entities such as vortices that are central to the physical properties of the state of matter.
The association of a state of matter with a specific type of ordering is illustrated in Figure 15 by an analogue with the dodgem bumper cars at an amusement park. A quiet day at the park is not much fun as collisions between cars are rare. In other words, there is little correlation between the relative locations and speeds of the cars. In comparison, on a busy day at the park the spatial separation of the cars is small, and their positions and speeds are more correlated with one another than on a quiet day. But, in both cases, there is no ordered arrangement of the cars. In contrast, after the park closes the cars are parked and arranged in an orderly manner. There is a rigidity associated with their spatial arrangement. One car cannot be moved without moving others. These three states of the dodgem cars are an analogue of three states of matter: gas, liquid, and crystal.
Figure 15. A dodgem car analogue for the three states of matter: crystal, liquid, and gas. The only ordered arrangement is for the crystal (car park after hours) and this is associated with a specific symmetry and rigidity. The liquid and gas (busy and quiet day) only differ in density and the amount of correlation between the positions of the different atoms (dodgem cars).
In the dodgem car analogue, there are other possible types of ordering. In some amusement parks there is a track, and the cars are meant to all go in the same direction. The symmetry between clockwise and anti-clockwise of the track is then broken. In the car park, Figure 15 shows cars that are symmetrical with respect to front and back. However, real cars have a front and back, and so can be parked either front first or back first. Hence, several types of ordering are possible: all cars park back first, all cars park front first, cars are front first or back first at random, alternating patterns of front first and back first as one goes along a row, alternating rows of front first and back first, and so on. These different types of ordering in the car park all have analogues in different solid states of matter.
Liquid crystals involve unique types of ordering. These materials are composed of elongated organic molecules, such as those shown in Figure 16. At high temperatures the material is in a liquid state and the orientations and positions of the molecules are random. The liquid has both continuous translational and rotational symmetry. At low temperatures the molecules form a solid crystal without the continuous translational and rotational symmetry of the liquid state. As the crystal is heated the temperature increases and there is a phase transition to the liquid crystal state, in which all the molecules point in the same direction, but their positions are random. Hence, the liquid crystal state has the continuous translational symmetry of the liquid, but not its continuous rotational symmetry, like the crystal. As the temperature increases further there is a transition to the liquid state (Figure 16). In terms of the dodgem car analogue the liquid crystal state is similar to when cars park in a field all pointing in the same direction but there are no grid lines, and their positions are then random.
The existence of a state in between a liquid and crystal was first proposed in 1888 by botanist and chemist Friedrich Reinitzer who was doing research on cholesterol at the Institute for Plant Physiology in Prague. He performed a heating experiment similar to that described in Figure 4. Instead of one melting transition he observed transitions at two distinct temperatures.
Figure 16. Liquid crystals. (a) An example of the type of elongate organic molecule found in these materials. Each molecule can be represented by an oval shape. (b) In the nematic liquid crystal state, the molecules tend to point in the same direction, but their positions are random.
There are multiple alternative orderings for liquid crystals with names such as nematic, smectic, chiral nematic, discotic, and chlorestic. In the smectic phase molecules form layers of oriented molecules. The character of the liquid crystal state can be detected by shining polarised light on the material. Liquid crystal displays (LCDs) in electronic devices use the property that an electric field can orient the molecules, and this changes the interaction of the material with polarised light.
For solid crystals the nature of the ordering and the symmetry associated with a specific crystal structure is clear once the spatial arrangements of the atoms in the crystal are determined, such as by X-ray diffraction. For other states of matter, such as superconductors, superfluids, and antiferromagnets, the nature of the ordering and the symmetry is often not apparent and has only been determined with significant scientific insight.
An extract from "The order of things," chapter 4 in Condensed Matter Physics: A Very Short Introduction.
Most debates about the emergence of molecular structure centre around the issue of irreducibility. Specifically, can the existence of molecular structures be predicted from quantum theory without assuming their existence or invoking classical concepts?
Consider a molecule that contains Ne electrons and Nn atomic nuclei (ions). The full quantum-mechanical Hamiltonian for the system is
where e is the electronic charge, rj is the position of the j-th electron, Zi and Mi are the charge and mass, respectively, of the i’th ion with position co-ordinate Rj. This is the Hamiltonian that Laughlin and Pines dubbed “The Theory of Everything” because if the solution (i.e., eigenstates and eigenvalues of the Hamiltonian operator) could be found it would describe almost all of chemistry and materials science.
This Hamiltonian treats the electrons and nuclei on an equal footing.
For isomers, the Hamiltonian is identical. However, as will be discussed in a later post, that does not preclude solutions to the Hamiltonian that can describe isomers.
The Hamiltonian has global translational and rotational symmetry, where all the particles undergo the same rotation or translation. In contrast, molecular structures may have discrete rotational symmetries. However, this is not necessarily a problem, as an eigenstate of a quantum problem can transform according to a non-trivial irreducible representation of the symmetry. For example, except the s-orbitals all the orbitals of the hydrogen atom are spatially anisotropic.
The electrons are identical particles and so have permutation symmetry. They are fermions with spin-1/2 and so any eigenstate must be antisymmetric under the exchange of two electrons. The energies associated with this exchange are crucial to the formation of chemical bonds and the stability of molecular structures.
If two or more atoms in the molecule are identical, then any exact eigenstate must be consistent with permutation symmetry. If a nucleus is composed of an even (odd) number of nucleons, then it is a boson (fermion) with integer (half-integer) spin, and eigenstates must be symmetric (antisymmetric) under exchange of identical nuclei. However, the corresponding exchange energies are relatively small (because the quantum delocalisation of the nuclei is small) and consequently most practical calculations of the eigenstates do not make this requirement of the eigenstates. Nevertheless, if the electrons and nuclei are treated on equal footing, this should be done. Although this is challenging, it has been done recently, as discussed below.
Full quantum solutions of the Hamiltonian
In most computational quantum chemistry, the Hamiltonian is solved in the Born-Oppenheimer approximation, which will be introduced and discussed later. This is a source of some confusion and contention in philosophical discussions about the emergence of molecular structure.
Due to advances in methodology and computational power over the past few decades, it has become possible in practise to solve the full quantum Hamiltonian for small molecules. There are three levels of complication associated with this: quantum nuclear motion, rotational symmetry, and some nuclei being identical particles. There are also two challenges: first, finding the eigenstates and second, deducing the molecular structure from the eigenstates.
To begin, I consider the simplest case and ignore the complications associated with rotational symmetry or identical nuclei. This provides some insight and undermines some objections in the philosophical literature.
The ground state eigenfunction can be written as
where r and R are 3Ne and 3Na -dimensional vectors, respectively. Note that this function will have a complicated structure as it will depend on the spin states of all the electrons, denoted by s.
A probability distribution (reduced density matrix) for the positions of the nuclei is given by
where the sum is over all the electron spin degrees of freedom.
For many molecules, but not all, this probability distribution will have a unique global maximum at the coordinates R_0. This set of coordinates defines the geometry of the molecular structure. The physics underlying the existence of well-defined maxima is that the mass of the nuclei is much larger than the mass of the electrons, and as a result, the zero-point motions of the nuclei are much smaller than the separation of the nuclei in the molecular structure.
Note that the nuclear probability distribution is regularly measured in scattering experiments (using X-rays, neutrons, or electrons), and its maxima are used to determine the structures of molecules and crystals. The Debye-Waller factor is a measure of the width of the probability distribution. At low temperatures, it is determined by quantum zero-point motion. In other words, it is well established experimentally that classical molecular structures are an approximation to a fluctuating quantum structure.
Not every molecule will have a probability distribution with a unique maximum. An example is ammonia. As discussed further below, it has two maxima; each represents an umbrella geometry, and they are related by an inversion symmetry. The ground state wavefunction of the whole system is a superposition of two quantum states, each being associated with one of the two umbrella geometries, and the electronic and nuclear degrees of freedom are entangled with one another.
A general quantum definition of molecular structure
Lang et al. have recently overcome the challenges mentioned above to determine molecular structure in a manner that treats the electrons and nuclei on an equal footing with regard to quantum theory. They have considered both rotational symmetry and nuclear permutation symmetry and given a general definition of molecular structure involving nuclear probability densities calculated from the full wavefunction. They have explicitly performed these calculations for D3+, (where D is deuterium). The result is that the molecule has the same triangular structure that is observed experimentally and calculated using the Born-Oppenheimer approximation. This work is significant because it explicitly shows that molecular structure can be predicted in practice, not just in principle, from quantum theory.
In a forthcoming post, I will discuss the Born-Oppenheimer approximation and some of the confusion associated with it.
Snowflakes form incredibly diverse structures, seen when they condense onto a plate of glass. Every snowflake is different. On the other hand, every snowflake is the same. They are all composed of ice, a solid state of water. Every snowflake is composed of units that have a six-fold symmetry (Figure 8). Every snowflake is composed solely of water molecules. This paradox of the particular and the universal is at the heart of condensed matter physics. Although diversity prevails anything is not possible. No snowflake has five-fold symmetry. Snowflakes have enchanted scientists for a long time. The astronomer Johannes Kepler studied them and in 1611 wrote a small book about them as a gift for his patron. Kepler suggested snowflakes provided clues to deeper questions about the composition of matter. Today, Kenneth Libbrecht, a physicist at Caltech, has spent most of his career studying snowflakes and has produced beautiful volumes of photographs of them.
Figure 8. A snowflake shows a six-fold symmetry, just like a hexagon. The snowflake appears identical when it is rotated by an angle of sixty degrees about an axis passing through its centre and perpendicular to the page.
Condensed matter physicists ask several questions about snowflakes. What is the reason for the six-fold symmetry of the snowflake? What is the connection between the macroscopic properties of snowflakes and the properties of the underlying microscopic constituents, molecules of H2O? How is the diversity of snowflake shapes possible? Is there a phase diagram that defines the external conditions under which the different shapes form?
There is a long history in art, architecture, philosophy, and science, of associating symmetry with beauty and perfection. The ancient Greek philosopher Plato was a proponent of this view. He studied a particular class of solid shapes: cube, tetrahedron, octahedron, icosahedron, and dodecahedron. Plato identified the first four shapes with the four “elements”: earth, wind, fire, and water, respectively, and the fifth with the heavens. Each of these solid shapes is highly symmetric. Every face of a Platonic solid is the same shape (square, triangle, pentagon,...) and each of those shapes has edges of equal length.
Like Plato, Kepler believed that “God is a geometer” and that God’s creation should reflect the perfection of God. These convictions led Kepler to propose in 1597 that the orbits of the planets around the Sun were circular and that the Platonic solids determined the relative size of the orbits. Later this model for the solar system was shown not to be true. In fact, Kepler himself became famous because he showed that the planets moved in elliptical, not circular orbits. Nevertheless, Kepler’s model was the beginning of a long history of successfully relating physical laws to symmetry and geometry.
A key discovery in physics from the past century is that symmetry is central to understanding a wide range of physical phenomena, whether colliding billiard balls, the allowed energies of an atom, the fundamental forces of nature, or different states of matter. Symmetries determine what is physically possible. For example, that energy cannot be created or destroyed is a consequence of the fact that physical laws do not change with time.
In this Chapter I explore three key ideas. First, transitions between different states of matter are associated with changes in symmetry. Thus, symmetry provides a criterion for specifying the qualitative difference between distinct states of matter. Second, for a specific state of matter the relevant symmetry constrains what is physically possible. Third, symmetry is central to making connections between the macroscopic and microscopic properties of a state of matter. The next chapter will explore how symmetry is associated with the type of ordering that occurs in a state of matter.
In discussions of emergence, particularly in chemistry, isomers are often given as an example of an emergent phenomenon. In Anderson's original "More is Different" article, he discussed the chirality of sugar molecules as an example of symmetry breaking. More recently, isomers (and the associated concept of molecular structure) are invoked to justify contentious claims about strong emergence and downward causality.
Here, I explain what isomers are and consider whether they are emergent in the sense of novelty, i.e., they have properties that are qualitatively different from their constituents.
In a later post, I hope to address the more general and knotty problems of molecular structure and the Born-Oppenheimer approximation.
Structural isomers
These occur when a specific collection of atoms (chemical formula) can have more than one molecular structure. An example, shown below, is C3H4.
Diamond and graphite are distinct solid states of carbon. They have qualitatively different physical properties, at both the microscopic and the macroscopic scale. Condensed matter physics is all about states of matter. In science classes at school, you were probably taught that there are only three states of matter: solid, liquid, and gas. Like other things you were told in school, this is incorrect. There are endless, unlimited, distinct states of matter.
Consider the “liquid crystals” that are the basis of LCDs (Liquid Crystal Displays) in the screens of televisions, computers, and smartphones. How can something be both a liquid and a crystal? A liquid crystal is a distinct state of matter. Solids can be found in many different states. We have already seen that there are two different solid states of carbon: graphite and diamond. In everyday life ice means simply solid water. But there are in fact eighteen different solid states of water, depending on the temperature of the water and the pressure that is applied to the ice. In each of these eighteen states there is a unique spatial arrangement of the water molecules and there are qualitative differences in the physical properties of the different solid states. Welcome to the world of condensed matter...
Extract from Chapter 1, Condensed Matter Physics: A Very Short Introduction
Classifying objects, people, and societies requires making qualitative distinctions. One book is easy to understand, and another is hard. One person is kind, and another is mean. One society is egalitarian, and another is not. Justifying such qualitative distinctions is hard. Not everyone will agree. Are there definitive criteria to justify a particular quality? Some claim they can quantify qualities such as these but that is contentious. In contrast, in condensed matter physics it is possible to give objective criteria that distinguish different states of matter. A state can only exist under specific external conditions, including defined ranges of parameters such as temperature and pressure. This chapter describes the clear signatures of transitions between different states that are observed as these parameters are varied. Some of the many known states of matter will be introduced including superconductors, superfluids, and magnets. On the way we will learn about “dry ice”, how to convert graphite into diamond, and how freeze-dried food is made.
Abrupt changes in properties
If you put some ice cubes in one empty glass and water in another, the ice does not change its shape, whereas water takes the shape of the glass. Solids are rigid and liquids are not. The distinct change from one state to another can be detected by observing an abrupt change or discontinuity in physical properties. For example, ice (solid water) has a different density to liquid water. This is evident because ice floats. The solid state of water has a lower density than the liquid state. To put it another way, water expands when it freezes. That’s why water pipes can burst if they freeze in cold weather.
A transition between two distinct states of matter is an example of a tipping point: a small change in a system variable can produce large changes in the system. For example, changing the temperature of water from +1 °C to -1 °C can produce a qualitative change in the system's properties. The water changes from liquid to solid. Tipping points occur in a wide range of physical, biological, and social systems. Examples include a stock market crash, the outbreak of an epidemic, and the operation of a room thermostat. Tipping points show that quantitative differences can become qualitative differences.
Extract from Chapter 2, Condensed Matter Physics: A Very Short Introduction
Every day we encounter a diversity of materials: liquids, glass, ceramics, metals, crystals, magnets, plastics, semiconductors, foams, … These materials look and feel different from one another. Their physical properties vary significantly: are they soft and squishy or hard and rigid? Shiny, black, or colourful? Do they absorb heat easily? Do they conduct electricity? The distinct physical properties of different materials are central to their use in technologies around us: smartphones, alloys, semiconductor chips, computer memories, cooking pots, magnets in MRI machines, LEDs in solid state lighting, and fibre optic cables. Consequently, the science of materials attracts researchers in a wide range of disciplines: physics, chemistry, biology, mathematics, and the varieties of engineering (electrical, chemical, mechanical, material…). But why do different materials have different physical properties?
There are more than one hundred different types of atoms, or chemical elements, in the universe. Any material is composed of a specific collection of different atoms, and they are arranged in a particular spatial pattern within the material. A central question is:
How are the physical properties of a material related to the properties of the atoms from which the material is made?
Extract from Chapter 1, Condensed Matter Physics: A Very Short Introduction
We are surrounded by scientific knowledge and have become so used to it that we often take science for granted. We may rarely reflect on the amazing revelations of science—and so miss the opportunity to recognize the awesome nature of the universe. Things that we know, learn, and do today in science would have been inconceivable decades, let alone centuries, ago.
Einstein said, “The most incomprehensible thing about the universe is that it is comprehensible.” For Einstein, the success of science was a wonderful mystery. As he wrote to his friend Maurice Solovine:
. . . I consider the comprehensibility of the world (to the extent that we are authorized to speak of such a comprehensibility) as a miracle or as an eternal mystery. Well, a priori, one should expect a chaotic world, which cannot be grasped by the mind in any way . . . the kind of order created by Newton’s theory of gravitation, for example, is wholly different.
There are several dimensions to the comprehensibility of the universe being mysterious. Einstein highlighted the first mystery, which is that there is order in the world, as reflected in scientific laws, such as Newton’s theory of gravity, and that this order can be succinctly stated in the language of mathematics. To the best of our knowledge, these laws hold for all time and everywhere in the universe. The existence of the orderly behaviour encoded in scientific laws is necessary for science to work, which leads to the second mystery. Why have we been able to discover these laws?
A second dimension that makes science possible is the intellectual abilities of humans. Humans not only have the rational ability to do science—to reason, to understand, to communicate—but also the ability to design instruments, such as telescopes and microscopes. There seems to be a connection between the rationality of the universe and human rationality. The idea that there may be harmony between the structures of the universe and those of the human mind has a long history. In the Renaissance, it was encapsulated in the metaphor of the “music of the spheres”. In his book, Harmonies of the World (1619), Johannes Kepler connected music and his explanations of planetary orbits. Einstein said that “Mozart’s music is so pure and beautiful that I see it as a reflection of the inner beauty of the universe.”
Humans might have been different. Suppose that the average human intelligence was lower than it is today, and the variation of human intelligence was smaller. Then, there might have been no Galileo, Isaac Newton, Robert Boyle, Charles Darwin, Albert Einstein, Richard Feynman, Phil Anderson, or Linus Pauling. Without these brilliant figures in scientific history, scientific progress would have been slow.
The third dimension is that human language enables scientists to formulate, represent, and communicate ideas, theories, and the results of scientific experiments. This language sometimes involves mathematics, graphs, or tables of data. Scientists can understand one another. Even though there can be misunderstandings, these can be resolved. There is a scientific culture that transcends the diversity of cultures associated with different countries, linguistic groups, and ethnicities.
The fourth dimension is the physical dexterity of humans. I am a theoretical physicist not an experimental physicist. I am “all thumbs” and not particularly good in the lab. Consequently, I have done no laboratory work since I was a Ph.D. student. In contrast, some gifted scientists have an ability to do things in a laboratory that most people cannot. Their manual dexterity allows them to fabricate precision instruments, grow pure crystals, blow exquisite glassware, see faint images, and fine-tune electronic instruments in extraordinary ways. If some humans did not have such amazing abilities, scientific progress would have been much slower—or possibly non-existent.
A fifth dimension that makes science possible is the availability and processability of materials that have been central to scientific progress. Making instruments requires specific materials, such as metals, glass, rubber, insulators, plastics, and semiconductors. If we lived in a world where some of these materials were very rare or could not be processed to the purity or malleability required for scientific instruments, we would not have supercomputers, electron microscopes, or the James Webb Space Telescope today. We might be struggling to make even the simple telescopes used by Galileo.
These five dimensions are all required for humans to be able to do science. There are several additional mysteries of science. These can be divided into two classes: what science can do and what we can learn about the universe from science. Science allows us to know certain things about reality (epistemology) and also to understand the nature of that reality (ontology). In other words, science helps us make maps of physical reality. The terrain represented by those maps is amazing. And the fact that we can make the maps is amazing.
In 1994 superconductivity was discovered in strontium ruthenate (Sr2RuO4). This attracted considerable interest because it had a perovskite crystal structure, just like the cuprates. Furthermore, it was a stoichiometric compound and so not plagued by impurities like the cuprates.
In 1998, things got more interesting when NMR Knight shift measurements were interpreted as evidence for triplet superconductivity.
Analogues were made with triplet Cooper pairing in superfluid 3He mediated by ferromagnetic spin fluctuations.
Triplet pairing is associated with odd-parity (spatial) and time-reversal symmetry breaking. Evidence for the latter was claimed from muon spin relaxation (muSR) and the polar Kerr effect.
There are subtle questions about whether a bulk sample of a triplet superconductor exhibits spontaneous magnetisation. Leggett discussed this in an Appendix of his textbook. It turns out the magnetisation probably only exists on the edges.
Aside. The metallic phase is of interest because (unlike the cuprates) it is a Fermi liquid. More recently, it has been argued to be a Hund's metal.
Fueled by hype about topological quantum computing, the past two decades have seen even greater interest in the material due to proposals that it may be a topological superconductor. See for example, this paper.
Now we come to the disappointment. It turns out that the original Knight shift measurements were flawed, probably due to a problem with thermometry.
Recent, careful Knight shift measurements suggest spin-singlet pairing. They were described in a Physics Today article by Alex Lopatka in 2021, An unconventional superconductor isn’t so odd after all. The article describes all the intricacies and challenges of these measurements. Stuart Brown is to be commended for persisting with this problem.
What about the Kerr effect and muSR measurements suggesting time-reversal symmetry breaking?
The polar Kerr effect involves rotation of the plane of polarisation of the electromagnetic radiation by an angle of 65 nanoradians! There is only one group in the world (at Stanford) that can detect these ultra-minute rotations.
This post was stimulated by a helpful colloquium at UQ given recently by James Annett. He has worked on strontium ruthenate for many years and is a co-author of a relevant review article.
Update. 23 April. James Annett pointed out to me that the authors for the 1998 NMR published a paper in 2020 which acknowledges that their original paper was incorrect.
How is mental illness defined? What causes mental illness? How can a person be healed? Answering these questions will be influenced by our answer to the question of what a person is. Returning to the stratification of reality resulting from emergence, we see that there are social, psychological, neurological, physiological, and genetic dimensions to a person. To illustrate the complexity, I now take a brief tour of different university departments to get their unique perspective on mental health. Each represents a different tradition.
Biomedicine
The biomedical model for mental illness is based on the idea that brains are machines involving physical and chemical processes. Mental illness occurs when these processes do not function normally. Over the past few decades, brain imaging techniques have shown differences between the brains of healthy patients and those with mental illnesses such as depression, schizophrenia, and bipolar disorder. The best course of treatment is deemed to be drugs that target the parts of the brain or processes that are dysfunctional. Sometimes, physical interventions such as electrical shock therapies or surgeries are advocated. This biomedical model was embraced and promoted by most psychiatrists until relatively recently.
Antidepressant drugs have been widely prescribed, and now there are many studies examining their effectiveness, side effects, and biochemical mechanisms. I mention three scientific problems. First, there is a large placebo effect. This is found in studies where two groups of patients are told they are receiving an antidepressant drug. One group receive the actual drug, and the second group receives a placebo, a pill that, unknown to them, does not contain the drug. The proportion of patients reporting a significant improvement in mental health was about 25% for taking the actual drug compared to 10% for those taking the placebo. In other words, it seems that believing one will get better can lead to significant improvements in mental health.
Second, there is a large variation between patients concerning how effective the drugs are. Patients’ perceptions of change in their mental health range from getting slight worse to no change to large improvements. Third, the biochemical mechanism of the drugs has become controversial. When the class of drugs known as Selective Serotonin Reuptake Inhibitors (SSRIs) were introduced, psychiatrists were confident that they knew how they work. Depressed patients lacked serotonin. SSRIs blocked the reuptake of serotonin into neurons, increasing the levels of this neurotransmitter in the synaptic cleft. However, a recent meta-analysis concluded as follows.
“The main areas of serotonin research provide no consistent evidence of there being an association between serotonin and depression, and no support for the hypothesis that depression is caused by lowered serotonin activity or concentrations. Some evidence was consistent with the possibility that long-term antidepressant use reduces serotonin concentration.”
In her book, Mind Fixers: Psychiatry's Troubled Search for the Biology of Mental Illness, Anne Harrington, a historian of science at Harvard, commented.
“Today one is hard-pressed to find anyone knowledgeable who believes that the so-called biological revolution of the 1980’s made good on most or even any of its therapeutic and scientific promises. It is now increasingly clear to the general public that it overreached, overpromised, overdiagnosed, overmedicated and compromised its principles.”
Psychiatry is a tradition, for better or worse. Its proponents persist in their faith that the biomedical model has the best answers to mental illness, even though the evidence for this belief is ambiguous. Science can involve faith.
The stakes are high. If a patient takes medication, they may get better, worse, or experience no change. If they don’t take medication, they risk missing out on healing.
Psychology
Psychologists present a multitude of theories of and treatment plans for mental illnesses. The focus is not on biology but on mental processes. Some focus on the subconscious and others on thoughts we are aware of and can articulate. Some focus on current life experience and thinking patterns, whilst others delve into the past, including unresolved childhood conflict or trauma. Sigmund Freud, the founder of psychoanalysis, claimed that depression was due to aggression toward the self. A century later, there is no empirical evidence to support his claim. Other psychologists claim depression is predominantly a loss of hope. Opinion is divided about the best method of psychotherapy, where a patient has regular sessions with a trained professional to address unhelpful thoughts, emotions, and behaviours. Names for different methods include Cognitive Behavioural Therapy (CBT), Dialectical Behaviour Therapy (DBT), Psychodynamic Therapy, Humanistic Therapy, and Acceptance and Commitment Therapy (ACT). Central to CBT is the claim that "Irrational thinking is at the root of much emotional distress that people experience."
This diversity of perspectives and treatments highlights the level of scientific uncertainty about both causes and treatment.
I now mention three developments that are receiving increasing attention in psychology research and have a transcendent dimension.
Mindfulness practices. These involve training patients to focus their “attention on the present moment—thoughts, feelings, sensations, and environment—with an attitude of openness, curiosity, and non-judgment. It involves observing experiences directly, rather than overthinking or reacting impulsively. Key elements include breathing techniques, meditation, and bringing awareness to daily activities.” (Google AI overview).
Forgiveness. The American Psychological Association offers a continuing education article that cites studies showing that practising forgiveness can improve mental health.
Awe and wonder. Dacher Keltner has made extensive studies of the experience of awe and recounted them in a popular book. In a recent article with Maria Monroy, they: “review recent advances in the scientific study of awe, an emotion often considered ineffable and beyond measurement. Awe engages five processes—shifts in neurophysiology, a diminished focus on the self, increased prosocial relationality, greater social integration, and a heightened sense of meaning—that benefit well-being. We then apply this model to illuminate how experiences of awe that arise in nature, spirituality, music, collective movement, and psychedelics strengthen the mind and body.”
Integrated medicine
The past few decades have seen the rise of integrated medicine, which promotes the view that many diseases, both physical and mental, are best treated by a holistic approach that combines treatments from different specialists. For mental health, it proposes that treatments might include not just drug and talking therapies but also address lifestyle issues. This means considering the role of sleep, exercise, diet, stress reduction, connection to nature, and screen time. With regard to diet, this builds on recent research showing deep connections between what goes on in the gut and the brain. Perhaps this is not surprising because our brains are not disembodied. They are part of our bodies and are connected to our whole nervous system.
Sociology
Sociologists have investigated how mental illness can arise from social isolation. Emile Durkheim (1858-1917) was one of the founders of sociology. His book, Suicide: A Study in Sociology was published in 1897 and pioneered the scientific study of social phenomena. He proposed that suicide comes in four types, being distinguished by the level of imbalance of two social forces: social integration and moral regulation. Based on a detailed analysis of statistical data, Durkheim concluded that suicide was more likely in men than women, for single people than those who are married, for people without children than people with children, among Protestants than Catholics and Jews, among soldiers than civilians, and in times of peace than in times of war.
Since Durkheim, many more sociological studies suggest that social isolation and a lack of meaningful relationships can be a major contributing factor to depression. Some of this research has been reviewed in a popular book, Lost Connections: Uncovering the Real Causes of Depression and the Unexpected Solutions by Johann Hari. He was motivated by his own experience of being prescribed and taking antidepressants for many years without consideration of how his social isolation might be a contributing factor.
This short survey of the perspective on mental illness from a range of scientific disciplines illustrates the complexity of the issue, the multifaceted nature of reality, and scientific uncertainty.
Naturally, this survey of different scientific perspectives raises questions about my own experience. Why did the antidepressant drugs seem to work sometimes and not others? Did I experience a placebo effect? Why was mindfulness helpful to me two decades ago but not more recently? What was the role of stress, childhood experiences, social isolation, personal pride, or introversion in creating my mental illness? I simply don’t know the answers to these questions and don’t think I ever will. What does matter is that, somehow at different times, I did experience degrees of healing that allowed me to function, albeit sometimes at diminished levels. Regardless of which traditions you choose to guide your journey and whatever choices you make, trust (faith) is involved.
