Physical Principles and Biology

24 Jul 2023 22:14

The construction of the universe is certainly very much easier to explain than is that of a plant ...
---Lichtenberg, Aphorisms J 4

I don't exactly mean biophysics in the usual sense (e.g. things like looking at the physical properties of proteins, or the other parts of what used to be molecular biology, before the DNA-sequencers pre-empted that name), interesting though that is. It's more like wondering how much of biology --- especially the Big Things, like evolution --- can be more or less directly explained by physics, or how tightly physics constrains biology. Physics constrains computation, (e.g., Landauer's principle: erasing a bit produces \( kT \ln{2} \) joules of waste heat) --- might it also constrain evolution in an analogous way? How useful are the mathematical tools physicists have come to know and love in understanding biology? And so on.

One long-running speculation along this line is that evolution has something or other to do with thermodynamics. It would be nice to think so, but I've never encountered any argument to this effect which is even remotely convincing; the most prominent one these days is that advanced by Brooks and Wiley in their book Evolution as Entropy: they claim that speciation and natural selection are instances of the increase of entropy. Unfortunately, they know squat-all about thermodynamics and statistical mechanics, and some of their examples lead me to think they don't really understand probability either. --- That said, I'd be willing to bet (in a very modest way) that some version of the thermodynamic formalism would actually be useful in describing evolution.

A nice symmetry to biologists who don't understand physics is physicists who don't understand biology: these also usually claim a connection between physics and evolution, only in the area of self-organized criticality and the supposed drive to the "edge of chaos." This involves less the active errors of people like Brooks and Wiley as sheer impatience with biological reality: as I heard one of its advocates put it memorably, "Details don't matter!" But of course they do. (My paper will Bill Tozier, below, is devoted to this critique.)

Pure mechanics seems to be much more successful at saying interesting things about biology; but much of this, like the square-cube law, is very old (that in fact goes back to Galileo). The work by James Brown (no relation), Geoff West et al., explaining "quarter-power" scaling laws in physiology, also looks reasonably solid (even though it's about circulatory systems).

Martin Barrett and Elliott Sober, "When and Why Does Entropy Increase?", pp. 230--255 in Steven Savitt, Time's Arrows Today: Recent Physical and Philosophical Work on the Direction of Time (Cambridge UP, 1995) [A very nice paper on arrows of time, considering both the 2nd law of thermodynamics and what Fisher called the "Fundamental Theorem of Natural Selection," which latter, unlike the 2nd law, almost never applies to real populations]
Freeman J. Dyson, "Time without end: Physics and biology in an open universe", Reviews of Modern Physics 51 (1979): 447--460
Lionel Harrison, The Kinetic Theory of Living Form [Inspired by Thompson, but much more chemical in approach, and much more at the cellular level]
D'Arcy Thompson, On Growth and Form [Physical constraints on the forms and development of organisms, and speculations on just how much of their shapes can be directly explained by physical forces. The edition edited by John Tyler Bonner has notes on how well Thompson's speculations have stood up under further research]
Geoffrey West, James H. Brown and Brian J. Enquist, "A General Model for the Origin of Allometric Scaling Laws in Biology", Science 276 (1997): 122--126 [PDF preprint as Santa Fe Institute Working Paper 97-03-019]

Cosma Rohilla Shalizi and William A. Tozier, "A Simple Model of the Evolution of Simple Models of Evolution", adap-org/9910002 [Rejected by Theoretical Population Biology for insufficient decorum.]

Howard C. Berg, Random Walks in Biology
William Bialek
- "Thinking about the brain," physics/0205030
- Biophysics: Searching for Principles
William Bialek and Sima Setayeshgar, "Physical limits to biochemical signaling," PNAS 102 (2005): 10040--10045, physics/0301001
James H. Brown and Geoffrey B. West (eds.), Scaling in Biology
Michael Burton, "Ecosystems, from life, to the Earth, to the Galaxy," astro-ph/0110694
William A. Calder III, Size, Function and Life History
Pierre-Henri Chavanis, "Phase separation of bacterial colonies in a limit of high degradation. Analogy with Jupiter's great red spot", physics/0607020
Peter Sheridan Dodds, "On the optimal form of branching supply and collection networks", arxiv:0909.1104
Sean Escola, Michael Eisele, Kenneth Miller and Liam Paninski, "Maximally Reliable Markov Chains Under Energy Constraints", Neural Computation 21 (2009): 1863--1912
Gabor Forgacs andStuart A. Newman, Biological Physics of the Developing Embryo
Joachim Hermisson, Oliver Redner, Holger Wagner and Ellen Baake, "Mutation-Selection Balance: Ancestry, Load, and Maximum Principle," cond-mat/0202432
I. R. Kennedy, Action in Ecosystems: Biothermodynamics for Sustainability
A. J. Lotka, Elements of Physical Biology [Dover reprint as Elements of Mathematical Biology]
Karo Michaelian, "A Non-equilibrium Thermodynamic Framework for the Dynamics and Stability of Ecosystems," physics/0204065 [I really want to read this, but the mere fact it's submitted to Phys. Rev. E, and not, say, The Journal of Theoretical Biology makes me skeptical.]
Philip Nelson, Physical Models of Living Systems, Second Edition: Probability, Simulation, Dynamics">Physical Models of Living Systems, Second Edition: Probability, Simulation, Dynamics
N. Rashevsky, Mathematical Bio-Physics
Glenn Rowe, Theoretical Models in Biology: The Origin of Life, the Immune System and the Brain
Schmidt-Nielsen, Scaling
Guy Sella and Aaron E. Hirsh, "The application of statistical physics to evolutionary biology", Proceedings of the National Academy of Sciences 102 (2005): 9541--9546
L. Sertorio and Giovanna Tinetti, "Available Energy for Life on a Planet, with or without Stellar Radiation," astro-ph/0107313
Eric Smith and Harold J. Morowitz, The Origin and Nature of Life on Earth: The Emergence of the Fouth Geosphere
Gasper Tkacik, "From statistical mechanics to information theory: understanding biophysical information-processing systems", arxiv:1006.4291
Erkan Tuzel and Ayse Erzan, "A Thermodynamic Model for Prebiotic RNA-Protein Co-evolution," cond-mat/0107315
Erik van Nimwegen, The Statistical Dynamics of Epochal Evolution [gzipped PostScript]
Steven Vogel
- Comparative Biomechanics: Life's Physical World
- Glimpses of Creatures in Their Physical Worlds
Volkstein, Physical Approaches to Biological Evolution
Muhammad H. Zaman (ed.), Statistical Mechanics of Cellular Systems and Processes

P. Ao, "Mathematical Structure of Evolutionary Theory", q-bio.QM/0403020 ["Here we postulate three laws which form a mathematical framework to capture the essence of Darwinian evolutionary dynamics. The second law is most quantitative and is explicitly expressed by a unique form of stochastic differential equation." Color me skeptical, but I haven't read beyond the abstract.]
Harold F. Blum, Time's Arrow and Evolution (1968)
Doriano Brogioli, "Marginally Stable Chemical Systems as Precursors of Life", Physical Review Letters 105 (2010): 058102
Debashish Chowdhury, Dietrich Stauffer and Ambarish Kunwar, "Unification of Small and Large Time Scales for Biological Evolution: Deviations from Power Law," Physical Review Letters 90 (2003): 068101
William Duncan, Fernando Antoneli, Janet Best, Martin Golubitsky, Jiaxin Jin, Fred Nijhout, Mike Reed, Ian Stewart, "Homeostasis Patterns", arxiv:2306.15145
Siegfried Fussy, Gerhard Groessing and Herbert Schwabl, "A Simple Model for the Evolution of Evolution," physics/0204070 = J. Biol. Systems 5 (1997): 341--357
Pankaj Mehta and David J. Schwab, "Energetic costs of cellular computation", Proceedings of the National Academy of Sciences(USA) 109 (2012): 17978--17982
Thierry Mora, William Bialek, "Are biological systems poised at criticality?", arxiv:1012.2242
Per Arne Rikvold and R. K. P. Zia, "Flicker Noise in a Model of Coevolving Biological Populations," nlin.AO/0303010
Hideaki Shimazaki and Ernst Niebur, "Bose-Einstein Condensation and the Principles of Competitive Process," cond-mat/0303298 [Sounds like a convoluted rediscovery of the replicator equation]
Weber, Depew and Smith (eds.), Entropy, Information, and Evolution: New Perspectives on Physical and Biological Evolution
Jeffrey Wicken, Evolution, Thermodynamics and Information: Extending the Darwinian Program