Biology is about emergence in subtle ways

Biology is a field that is all about emergence. It exhibits a hierarchy of structures from DNA to proteins to cells to organs to organisms. Phenotypes emerge from genotypes. At each level of the hierarchy (stratum) there are unique entities, phenomena, principles, methods, theories, and sub-fields. But there is more to the story. 

Philip Ball is probably my favourite science writer. Earlier this year, he gave a beautiful lecture at The Royal Institution, What is Life and How does it Work?

The lecture presents the main ideas in his recent book,  How Life Works: A User's Guide to the New Biology

Here are a few things that stood out for me from the lecture.

1. The question, "What is life?" has been and continues to be notoriously difficult to answer.

2. The Central Dogma of Molecular Biology is wrong.

It was originally stated by Francis Crick, and some commonly assumed corollaries of it are wrong. In simple terms, the Dogma states that DNA makes RNA and RNA makes proteins. This is a unique and unidirectional process. For example, a specific code (string of the letters A,G,T, and C) will produce a specific protein (sequence of amino acids) which will naturally fold into a unique structure with a specific biochemical function. 

The central dogma has undergirded the notion that genes determine everything in biology. Everything is bottom-up.

However, Ball gives several counterexamples.

A large fraction of our DNA does not code for proteins.

Many proteins are disordered, i.e., they do not have a unique folded structure.

Aside: An earlier failure of (some versions of) the central dogma was the discovery of reverse transcriptase by the obscure virus club, essential for the development of HIV drugs and covid-19 vaccines.

3. The role of emergence can be quantified in terms of information theory, helping to understand the notion of causal emergence: the cause of large-scale behaviour is not just a sum of micro-causes, i.e., the properties of and interactions between the constituents at smaller scales. Entities at the level of the phenomena are just as important as what occurs at lower levels.

(page 214 in the book). Causal emergence is concerned with fitting the scale of the causes to the scale of the effects.

The figure above is taken from this paper from 2021.

Evolution and emergence: higher order information structure in protein interactomes across the tree of life 

Brennan Klein, Erik Hoel, Anshuman Swain, Ross Griebenow, Michael Levin

The authors quantify casual emergence in protein networks in terms of mutual information (between large and small scales) and effective information (a measure of the certainty in the connectivity of a network).

Aside: These quantitative notions of emergence have been developed more in recent work by Fernando Rosas and collaborators and discussed in a Quanta article by Philip Ball.

4. Context matters.  A particular amino acid sequence does not define a unique protein structure and function. They may depend on the specific cell in which the protein is contained.

5. Causal spreading.  Causality happens at different levels. It does not always happen at the bottom (genetic level). Sometimes it happens at higher levels. And, it can flow up or down.

6. Levels of description matter. This is well illustrated by morphology and the reasons that we have five fingers. This is not determined by genes.

7. Relevance to medicine. There has been a focus on the genetic origin of diseases. However, many diseases, such as cancer, do not predominantly happen at the genetic level. There has been a prejudice to focus on the genetic level, partly because that is where most tools are available. For cancer, focussing on other levels, such as the immune system, may be more fruitful.

8. Metaphors matter. Biology has been dominated by  metaphors such as living things are "machines made from genes" and "computers running a code". However, metaphors are metaphors. They have limitations, particularly as we learn more. All models are wrong, but some are useful. Ball proposes that metaphors from life, including the notion of agency, may be more fruitful.

9. The wisdom of Michael Berry. Ball ends with Berry's saying that the biggest unsolved problem in physics is not about dark matter (or some similar problem), but rather, "If all matter can be described by quantum theory, where does the aliveness of living things come from?" In other words, "Why is living matter so different from other matter?"

There is also an interesting episode of the How To Academy podcast, where Ball is interviewed about the book.

Emergence in classical optics: caustics and rainbows

                                                                Photo by Chris Lawton on Unsplash

I love seeing patterns such as those above in bodies of water. I did not know that they are an example of emergence, according to Michael Berry, who states:

“A caustic is a collective phenomena, a property of a family of rays that is not present in any individual ray. Probably the most familiar example is the rainbow.”

Caustics are envelopes of families of rays on which the intensity diverges. They occur in media where the refractive index is inhomogeneous. In the image above, there is an interplay of the uneven air-water interface and the difference in the refractive index between air and water. For rainbows, key parameters are the refractive index of the water droplets and the size of the droplets. The caustic is not the "rainbow", i.e., the spectrum of colours, but rather the large light intensity associated with the bow. The spectrum of colours arises because of dispersion (i.e., the refractive index of water depends on the wavelength of the light).

Caustics illustrate several characteristics of emergence properties: novelty, singularities, hierarchies, new scales, effective theories, and universality. 

Novelty. The whole system (a family of light rays) has a property (infinity intensity) that individual light rays do not.

Discontinuities. A caustic defines a spatial boundary across which there are discontinuities in properties.  

Irreducibility and singular limits. Caustics only occur in the theory of geometrical optics which corresponds to the limit where the wavelength of light goes to zero in a wave theory of light. Caustics (singularities) are not present in the wave theory.

Hierarchies. 

a. Light can be treated at the level of rays, scalar waves, and vector waves. At each level, there are qualitatively different singularities: caustics, phase singularities (vortices, wavefront dislocations, nodal lines), and polarisation singularities. 

b. Treating caustics at the level of wave theory, as pioneered by George Bidell Airy, reveals a hierarchy of non-analyticities, and an interference pattern, reflected in the supernumerary part of a rainbow.

New (emergent) scales. An example, is the universal angle of 42 degrees subtended by the rainbow, that was first calculated by Rene Descartes. Airy's wave theory showed that the spacing of the interference fringes shrinks as lambda^2/3.

Effective theories. At each level of the hierarchy, one can define and investigate effective theories. For ray theory, the effective theory is defined by the spatially dependent refractive index n(R)  and the ray action.

Universality. Caustics exist for any kind of waters: light, sound, and matter. They exhibit "structural stability". They fall into equivalence (universality) classes that are defined by the elementary catastrophes enumerated by Rene Thom and Vladimir Arnold and listed in the Table below. Any two members of a class can be smoothly deformed into one another.

The first column in the Table below is the name of the class given by Thom, and the second is the symbol used by Arnold. K is the number of parameters needed to define the class and the associated polynomial, which is given in the last column. 

For this post, I have drawn on several beautiful articles by Michael Berry.  A good place to start may be 

Nature's optics and our understanding of light (2015), which contains the figure I used above of the rainbow.

There is a beautiful description of some of the history and basic physics of the rainbow in Rainbows, Snowflakes, and Quarks: Physics and the World Around Us by Hans Christian Von Baeyer

Autobiography of John Goodenough (1922-2023)

 John Goodenough was an amazing scientist. He made important contributions to our understanding of strongly correlated electron materials, magnetism, solid state chemistry, and materials science and engineering. He developed materials that are widely used in computer RAMs and rechargeable lithium batteries. He kept working in the laboratory and writing papers into his early 90s. Goodenough was awarded the Nobel Prize in Chemistry in 2019. Here is his Nobel Lecture, including text, slides, and video.

In 2008 he published Witness to Grace, a brief autobiography that chronicles his personal, scientific, and spiritual journeys. It is a fascinating story. The book is now out of print and the publisher is out of business. I have scanned a copy. You can download it here. I thank David Purdy for bringing to my attention the need to preserve the book.

What symmetries distinguish liquids, crystals, glasses, and isotropic solids?

 One of the most important ideas in condensed matter physics is that different states of matter are associated with different symmetries. These different symmetries result in different types of elementary excitations such as the Goldstone bosons associated with continuous symmetry breaking. The symmetries of the low-lying excited states reflect the symmetries of the ground state.

For example, consider the transition from a liquid to a cubic crystal. The continuous rotational and translational symmetry of the liquid is broken to the discrete rotational and translational symmetry of the crystal. Long-wavelength sound waves reflect these changes in symmetry. In the crystal, there are three distinct sound waves: one longitudinal and two shear modes. In contrast, in the liquid, there are only longitudinal modes. 

An isotropic solid, such as studied in elasticity theory, supports two types of distortions: compression and shear. Consequently, there are three types of sound waves (longitudinal and transverse phonons. The latter can have two different polarisations). The isotropic solid has continuous, not discrete, rotational and translational symmetries. A glass is an example.

This leads to a fundamental question:

What is the difference between liquids and solids at the level of fundamental symmetries?

In different words, what is the order parameter for the liquid-solid transition? A possible answer is the shear modulus G, which vanishes in the liquid state.

A related question is: What is the fate of the transverse phonons upon transitioning from the solid state to the liquid state?

I would have thought that these questions would have been settled decades ago. However, they have not. Just two years ago, Physical Review E published a 22 page article that aims to address the questions above.

Deformations, relaxation, and broken symmetries in liquids, solids, and glasses: A unified topological field theory

Matteo Baggioli, Michael Landry, and Alessio Zaccone

The paper immediately drew a Comment claiming the paper

"contradicts the known hydrodynamic theory of classical liquids." The authors have a Reply.

I do not have the expertise to give insight on the subtle technical issues in this debate. My only comment is that it is amazing how we are struggling to answer such basic questions.

I thank Jean-Noel Fuchs for getting me interested in these subtle questions. This happened when he kindly pointed out an error in Condensed Matter Physics: A Very Short Introduction. On page 40, I erroneously stated that shear sound waves exist in a liquid. This was part of a confused discussion about how sound waves can be used to distinguish different states of matter.  I have drafted a corrected paragraph and inserted it in my post listing the errors in my book.

I welcome any comments about the issues discussed above.

My mental health update

I have struggled with my mental health on and off since the time of my Ph.D. studies. Several readers have commented that has been helpful for them to hear my story. Here I give a small update on both my health and some recent reading.

I have been thinking about the issue more because I have been invited to give a talk in October for a research centre at UQ, as part of Mental Health Week. I may adapt a talk that I gave for a school colloquium at UQ six years ago. I welcome suggestions for things people think I should talk about.

My mental health is the best it has been for almost a decade. There are probably many reasons for this: retirement, managing stress, no international travel, being connected to a church community, and practising the basics (diet, exercise, less screen time, less caffeine, ...), ...

Until a year ago, I believed I would be on antidepressants for the rest of my life. But my doctor told me we should explore my getting off antidepressants. It is now the view of the medical establishment that there are too many people on them who do not need to be, there can be long-term complications, and that the longer a patient is on them the harder it is to get off them. Over the past 2 years, The Economist had helpful articles along these lines (see below).

In April we agreed that we would start the experiment of reducing my dose, following the now standard practice of slowly reducing the dose every three weeks. He warned me to look for side effects, such as random brain zaps. There were no side effects. I got to zero dosage a month ago.

Unfortunately, I am now experiencing one side effect which I have now learned is not uncommon: uncontrollable sobbing. The first instance was July 21 when I learned that Biden was not going to run again for President. The fact that this triggered ten minutes of sobbing shows there is something not quite right with my brain chemistry!

I had several other incidents with my family. The tears are out of proportion to the significance of the event that triggers them. Sometimes I choke up when talking to people I care about or on an issue that concerns me.

I had an appointment with my doctor this week and we agreed that for now, we would stay the course, not resume the medication, and monitor the situation.

How to make better use of antidepressants: Identify those who really need them, and wean other people off them

(The Economist, October 19, 2022)

Antidepressants are over-prescribed, but genuinely help some patients: In around 15% of cases, they offer large benefits

(The Economist, January 20, 2023)

The graphs above are amazing. They show several striking things.

1. There is a massive placebo effect for antidepressants. This is shown by the two coloured curves being almost identical.

2. There is a massive variation between patients with regard to how effective the drugs are. This is shown by the very broad distribution. It reminds me of journal impact factors: the distribution is so broad that discussions about the mean are meaningless.

Antidepressants can cause withdrawal symptoms – here’s what you need to know

(The Conversation, June 23, 2023)

Psychiatry’s Incurable Hubris: The biology of mental illness is still a mystery, but practitioners don’t want to admit it.

(The Atlantic, April 2019).

Disclaimer. I am not a mental health professional. Mental health is an incredibly complex issue. Everyone is different. Do not take any action based on what you read about my experience. I do not present my experience as an example others should follow. Rather I present my experience so others may know that mental health struggles are not unusual, including among those who may appear to have "successful" lives.

Do arrows of explanation point down or up?

The figure above shows the stratification of objects that interest physicists. As one goes down the chain length and time scales get smaller and energy scales get larger.

A reductionist seeks to explain the objects at each strata in terms of the objects that occur at the next lower strata.

In 1987 Steven Weinberg gave a talk at the University of Cambridge at the Tercentenary Celebration of Newton's Principia.

The talk was published in Nature. Newtonianism, Reductionism, and the Art of Congressional Testimony

Part of the talk is about Weinberg's testimony to a US Congressional Committee making the case for the construction of the SSC (Superconducting Super Collider). Phil Anderson spoke against the SSC.

Weinberg argued that the SSC should be built because particle physics is "in some sense more fundamental than other areas of physics." He claims that this is because "the arrows of explanation point down", as in the diagram shown above.

A contrasting perspective is that of Andrew Steane. His book, Science and Humanity, contains the figure below.

In his picture of the explanatory relationship between physics, chemistry, and biology, Steane draws arrows pointing in both directions. The up arrow is denoted “supports [allows and physically embodies the expression of]” and the down arrow is denoted “enarches [exhibits the structures and behaviours that make sense in their own terms and are possible within the framework of].”

Weinberg's article is worth reading in full. It has many insights about science and physics worth considering, including the relationship between emergence and reductionism.

Aside: It is also reproduced in his book of essays, Facing Up: Science and Its Cultural Adversaries, published in 2001.

Emergence, structuralism, realism, and quarks

"Structuralism as an influential intellectual movement of the twentieth century has been advocated by Bertrand Russell, Rudolf Carnap, Nicholas Bourbaki, Noam Chomsky, Talcott Parsons, Claude Levi-Strauss, Jean Piaget, Louis Althusser, and Bas van Fraassen, among many others, and developed in various disciplines such as linguistics, mathematics, psychology, anthropology, sociology, and philosophy." 

In different words, structuralism and post-structualism have been and are still a really big deal in the humanities and social sciences. Structuralism is central to the rise and fall of a multitude of academic fashions, careers and reputations.  

"As a method of enquiry, it takes a structure as a whole rather than its elements as the major or even the only legitimate subject for investigations. Here, a structure is defined either as a system of stable relations among a set of elements, or as a self-regulated whole under transformations, depending on the specific subject under consideration. The structuralist maintains that the character or even the reality of a whole is mainly determined by its structuring laws, and cannot be reduced to its parts; rather, the existence and essence of a part in the whole can only be defined through its place in the whole and its relations with other parts."

In a sense, structuralism favours emergence over reductionism. But, note some of the strong exclusivist language highlighted in bold in the quote above. Structuralism seems to be an overreaction to extreme reductionism. 

Condensed matter physics has something concrete to contribute to these debates. Consider the case of Ising models defined on a range of lattices, as I discussed in a previous post. We do not have an exclusive interest in the whole system or in the parts of the system. Rather, we want to know the relationship between macroscopic properties [different ordered states], mesoscopic properties [domains, long-range correlations, networks], and microscopic properties [the individual spins and their local interactions].

That is the main point of this post. But for more context, keep reading.

The quotations above are taken from a book by Tian Yu Cao. 

From Current Algebra to Quantum Chromodynamics: A Case for Structural Realism

Cao is interested in a broad range of philosophical questions related to QCD, such as "If quarks cannot be observed in isolation should they be considered to be real?"

He continues:

In the epistemically interesting cases involving unobservable entities, the structuralist usually argues that it is only the structure and the structural relations of its elements, rather than the elements themselves (properties or entities with properties) that are empirically accessible to us. It is obvious that such an anti-reductionist holistic stance has lent some support to phenomenalism. 

However, as an effort to combat compartmentalization, which urge is particularly strong in mathematics, linguistics, and anthropology, the structuralist also tries to uncover the unity among various appearances, in addition to invariance or stable correlation under transformations, which can help discover the deep reality embodied in deep structures. Furthermore, if we accept the attribution of reality to structures, then the antirealist implications of the underdetermination thesis [which claims that since evidence cannot uniquely determine (or, worse, can even support conflicting) theoretical claims about certain unobservable entities, no theoretical entities should be taken as representation of reality], is somewhat neutralized, because then we can talk about the realism of structures, or the reality of the structural features of unobservable entities exhibited in evidence, although we cannot directly talk about the reality of the entities themselves that are engaged in the structural relations. In fact, this realist implication of structuralism was one of the starting points of current interests in structural realism.