Are chemical isomers emergent?

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.

Each structure has different chemical and physical properties. Aggregates of each molecule can have different properties such as boiling and melting points.

Some isomers are more stable than others. They may be able to interconvert, but sometimes not on laboratory time scales.

From the point of view of a ground state potential energy surface, the different isomer structures correspond to different local minima on the surface.

Stereoisomers

The simplest example is HFClBr. There are two stable structures shown below. They are related by a chiral (mirror) symmetry. They differ physically in that they rotate the plane of polarisation of incident light in opposite directions. 

The isomers, known as enantiomers, have the same ground state energy. In terms of a potential energy surface, they correspond to two different minima and are separated by a high-energy barrier. In principle, the two forms can quantum-tunnel between each other.

Chemically, the two isomers differ in how they react with other chiral molecules.

Chirality is central to molecular biology. Proteins are made of amino acids, and in nature they all have the L-form. Most forms of DNA involve double helices with right-handed chirality. 

The chirality of drug molecules matters, as tragically found with thalidomide in the 1950s. 

Emergence?

The constituent components of these molecules can be viewed as electrons and atomic nuclei. Alternatively, the components could be viewed as the atoms they are made of. In both cases, the parts of the system do not have the structure and properties that the system does. The atoms, nuclei, and electrons all have spherical symmetry, whereas the molecules do not. In this sense, the molecular structures can be viewed as emergent. However,  this goes against the view that we generally associate emergence with systems with many interacting parts. If we take two massive particles interacting by gravity, they can form a stable orbit. Neither particle has this property, but we don't generally claim that such orbits are emergent.

[I am grateful to a commenter on an old post who pointed this out].

Isomers illustrate the diversity of forms often associated with emergence.

There are subtleties associated with the stability of enantiomers and the associated breaking of chiral symmetry. This is similar to the issue of ammonia having a stable pyramidal structure. (Also discussed by Anderson in "More is Different"). An isolated molecule in a vacuum will have no chirality. The ground state is a quantum superposition of both enantiomers. However, in the laboratory, the interaction of each molecule with its environment, such as other molecules, leads to decoherence that prevents quantum tunnelling. In that case, there are an infinite number of degrees of freedom associated with the environment, and they are crucial for the emergence of enantiomers.

How many states of matter are there?

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

What is condensed matter physics?

 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

A mystery about science is that humans can do it

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.

Scandals in Australian universities

In Australia, scandals about the management of public universities continue to be covered in the media. A recent one is the use of billions of dollars to pay consulting firms to tell management which staff to sack and courses to cut because they are not making a profit.

Below is a recent episode of an ABC (Australian equivalent of BBC or PBS in USA) show on the topic, Chaos on Campus.

I tend to avoid engaging too much with media lamenting the state of unversities as I find it too disturbing. However, I was asked to reference the show in something I was asked to write and so felt I should watch it. It was painful.

This is definitely a scandal. However, it got me reflecting on something that I think gets virtually no media coverage and when I talk to people outside the university, they are pretty surprised and shocked. Anecdotal evidence from my colleagues is that attendance at lectures is now typically around 10-30 per cent of enrolment. Even before COVID-19, lectures at UQ were all recorded. Faculty have no choice. But only a few per cent of students watch the videos. This is quite demoralising for faculty.

What does this low level of student engagement mean for learning outcomes?

What is happening elsewhere? 

Here are some links from Google AI. 

I did not find them that insightful.

One link is an article from The Guardian in Australia from last year. It highlights how moving things to online and lowering standards is driven by financial incentives. This ties in with the scandals in the video. The values of Australian universities are money, marketing, management, and metrics.

What is your own experience with the level of disengagement? How do you think this is affecting student learning? How are you and your colleagues adapting? Are academic standards being lowered? Any suggestions on ways forward?

The disappointing story of superconductivity in Strontium Ruthenate

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.

muSR may also be problematic. It is not really known where the implanted muon sits in the crystal or what effect it has on the surrounding crystal structure. In particular, these perturbations may produce a small local magnetic field which is nothing to do with the claimed global field due to the magnetism associated with the triplet superconductivity. A recent preprint by Warren Pickett considers some of the challenges associated with interpreting these experiments as evidence for time-reversal symmetry breaking.

What is disappointing about this?

Obviously, it would be nice to have a triplet superconductor and even more a topological one.

However, for me, the big disappointment is that it took almost thirty years for the original NMR measurements to be checked and shown to be wrong. This may reflect several sociological problems.

Kauzmann's maxim: people will tend to believe what they want to believe rather than what the evidence before them might suggest.

The condensed matter community tends to be infatuated with exotica.

There is not enough application of Occam's razor. Luxury journals don't want simple explanations or authors to raise doubts or ambiguities.

As far as I am aware, the 1998 Nature paper on the NMR Knight shift has still not been retracted.

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.

Reduction of the 17O Knight Shift in the Superconducting State and the Heat-up Effect by NMR Pulses on Sr2RuO4

A multi-disciplinary perspective on mental illness

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.