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.
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.
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