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.