Molecular Biology
Last update: 28 Jul 2026 23:44First version: Before 13 March 1995; refurbished 27 July 2026
Original text from the '90s
I believe it was Watson who deeply offended many of his colleagues by saying that there is one biology, and it is molecular. This seems, alas, to be true --- not in the sense that simple DNA mongering is the heart of biology, but that the molecular, reductionist approach works so well it's almost scary, and really does get at how living things work. More: it lets us change how living things work. The possibilities it raises are enormous and to many minds obscene. (You can already take some key developmental genes out of a simple worm, C. elegans, splice 'em into a vertebrate and have the critter come out normal. Dolly is nothing.)
So: the age of biology, prophesied since Diderot, is coming upon us. We may as well enjoy it. I, frankly, am just glad that biologists will be the ones taking the rap for unleashing the apocalypse for the next half century or so, not physicists.
Update, July 2026
I am leaving the text above alone, except for adding some internal links, as I usually do, out of some hard-to-define (or defend) respect for my juvenalia. But, after some decades, I did decide to tidy this up, because I was reading my brother's book reviews (where your time, Dear Reader, would probably be better spent).
The "to many minds obscene" line above was a reference to Haldane's Daedalus: "every biological invention is a perversion".
Finally, my guess that the biologists would be taking the blame for screwing up the world was off the mark.
- See also:
- Biochemical Network Evolution
- Bioinformatics
- Biological Order
- Biotechnology
- Developmental Biology
- Gene Expression Data Analysis
- Historical Genetics
- The Physics of Molecular Machines
- Reductionism
- Signal Transduction, Gene Regulation, and Control of Metabolism
- Statistical Mechanics
- Recommended, large-scale:
- Georgina Ferry, Dorothy Hodgkin: A Life
- Gonnick and Wheelis, The Cartoon Guide to Genetics [I am utterly serious]
- Horace Freeland Judson, The Eighth Day of Creation
- Jacques Monod, Chance and Necessity: An Essay on the Natural Philosophy of Modern Biology [Review by Danny Yee]
- Michel Morange, A History of Biology
- Recommended, close-ups, with a more than usually strong "Rabbit's Friends and Relations" bias:
- Lauren W. Ancel and Walter Fontana, "Plasticity, Evolvability, and Modularity in RNA", Journal of Experimental Zoology (Molecular, Development and Evolutionary) 288 (2000): 242--283
- Nikolay V. Dokholyan and Eugene I. Shakhnovich, "Understanding hierarchical protein evolution from first principles," cond-mat/0104469
- Ivo L. Hofacker, Walter Fontana, Peter F. Stadler, L. S. Bonhoeffer, M. Tacker and Peter Schuster, "Fast Folding and Comparison of RNA Secondary Structures", Monatshefte füur Chemie 125 (1994): 167--188 [Abstract, PostScript preprint]
- Mihaela Oprea and Stephanie Forrest, "How the Immune System
Generates Diversity: Pathogen Space Coverage with Random and Evolved
Antibody Libraries",
pp. 1651--1656 in Wolfgang Banzhaf, Jason M. Daida, A. E. Eiben, Max H. Garzon and Vasant Honavar (eds.), Proceedings of the 1st Annual Conference on Genetic and Evolutionary Computation [GECCO '99],
SFI Working Paper 99-02-014
- Peter L. Privalov and Stanley J. Gill, "Stability of Protein Structure and Hydrophobic Interaction", Advances in Protein Chemistry 39 (1988): 191--234
- Peter Schuster, Walter Fontana, Peter F. Stadler and Ivo L. Hofacker, "From sequences to shapes and back: a case study in RNA secondary structures", Porceedings of the Royal Society B 255 (1994): 279--284
- E. Shakhnovich, V. Abkevich and O. Ptitsyn, "Conserved residues and the mechanism of protein folding", Nature 379 (1996): 96--98 [I retain vivid memories, decades later, of hearing Prof., Shakhnovich present this work at the UW-Madison physics seminar...]
- Einat Sprinzak, Shmuel Sattath and Hanah Margalit, "How Reliable are Experimental Protein-Protein Interaction Data", Journal of Molecular Biology 327 (2003): 919--923
- Ali Zarrinpar, Sang-Hyun Park and Wendell A. Lim, "Optimization of Specificity in a Cellular Protein Interaction Network by Negative Selection", Nature 426 (2003): 676--680
- To read, history and philosophy:
- William Bechtel, Discovering Cell Mechanisms: The Creation of Modern Cell Biology: The Creation of Modern Cell Biology
- Nathaniel C. Comfort, The Tangled Field: Barbara McClintock's Search for the Patterns of Genetic Control
- Soraya de Chadarevian, Designs for Life: Molecular Biology after World War II
- Harrison Echols, Operators and Promoters: The Story of Molecular Biology and Its Creators
- Ernest Fischer and Carol Lipson, Thinking about Science: Max Delbruck and the Origins of Molecular Biology [Review in Science]
- Donald Fleming, "Emigré Physicists and the Biological Revolution", pp. 152--189 in Donald Fleming and Bernard Bailyn (eds.), The Intellectual Migration: Europe and America, 1930--1960 (Harvard University Press, 1969)
- Frederic Lawrence Holmes, Reconceiving the Gene: Seymour Benzer's Adventures in Phage Genetics [Positive review in Nature]
- Alex Rosenberg, Darwinian Reductionism: Or, How to Stop Worrying and Love Molecular Biology
- Sahotra Sarkar
- Robert Hunt Sprinkle, Profession of Conscience: The Making and Meaning of Life-Sciences Liberalism
- William C. Summers, The American Phage Group: Founders of Molecular Biology
- James Watson, The Double Helix [To finish, one of these decades]
- To read, statistical mechanics of proteins, especially folding and evolution:
- Jay Banavar, Amos Maritan, Cristian Micheletti and Flavio Seno, "Geometrical aspects of protein folding," cond-mat/0105209
- Ken A. Dill and Justin L. MacCallum, "The Protein-Folding Problem, 50 Years On", Science 338 (2012): 1042--1046
- Isaac A. Hubner, Eric J. Deeds, and Eugene I. Shakhnovich, "Understanding ensemble protein folding at atomic detail", Proceedings of the National Academy of Sciences (USA) 103 (2006): 17747--17752 [Open access]
- Cristian Micheletti, "Optimal prediction of folding rates and transition state placement from native state geometry," cond-mat/0202090
- Ora Schueler-Furman, Chu Wang, Phil Bradley, Kira Misura and David Baker, "Progress in Modeling of Protein Structures and Interactions", Science 310 (2005): 638--642
- M. Sega, P. Faccioli, F. Pederiva, G. Garberoglio and H. Orland, "Quantitative Protein Dynamics from Dominant Folding Pathways", Physical Review Letters 99 (2007): 118102
- Chao Tang, "Simple Models of the Protein Folding Problem," cond-mat/9912450
- Guido Tiana, Boris E. Shakhnovich, Nikolay V. Dokholyan and Eugene I. Shakhnovich, "Imprint of evolution on protein structures", PNAS 10.1073/pnas.0306638101
- Alessandro Torcini, Roberto Livi, and Antonio Politi, "A dynamical approach to protein folding," cond-mat/0103270
- To read, other applications of physics:
- Enrico Di Cera, Thermodynamic Theory of Site-Specific Binding Processes in Biological Macromolecules
- Gregory M. Grason and Robijn F. Bruinsma, "Chirality and Equilibrium Biopolymer Bundles", Physical Review Letters 99 (2007): 098101
- Meyer B. Jackson, Molecular and Cellular Biophysics
- Karsten Kruse, Jean-Francois Joanny, Frank Julicher, Jacques Prost and Ken Sekimoto, "Generic theory of active polar gels: A paradigm for cytoskeletal dynamics", physics/0406058
- Michal Kurzynski, The Thermodynamic Machinery of Life
- Mark C. Leake, Single-Molecule Cellular Biophysics
- Kim Sneppen and Giovanni Zocchi, Physics in Molecular Biolgoy
- D. E. Vance and J. Vance (eds.), Biochemistry of Lipids, Lipoproteins and Membranes [For self-assembly]
- David Wales, Energy Landscapes: Applications to Clusters, Biomolecules and Glasses
- Muhammad H. Zaman (ed.), Statistical Mechanics of Cellular Systems and Processes
- To read, not otherwise, or not yet, classified:
- Alberts et al., Molecular Biology of the Cell
- David S. Goodsell, Bionanotechnology: Lessons from Nature
- Lawrence E. Hunter, The Processes of Life: An Introduction to Molecular Biology
- Pier Luigi Luisi, The Emergence of Life: From Chemical Origins to Synthetic Biology