http://bactra.org/notebooks Cosma's Notebooks en http://bactra.org/notebooks/1994/10/03#molecular-biology <P>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 <em>works</em> so well it's almost scary, and really does get at how living things work. More: it lets us <em>change</em> 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, <cite>C. elegans,</cite> splice 'em into a vertebrate and have the critter come out normal. Dolly is <em>nothing.</em>) <P>So: the age of biology, prophesied since <a href="diderot.html">Diderot</a>, 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. <P>See also: <a href="bioinformatics.html">Bioinformatics</a>; <a href="biotechnology.html">Biotechnology</a>; <a href="gene-expression-data.html">Gene Expression Data Analysis</a>; <a href="signal-transduction.html">Signal Transduction, Gene Regulation, and Control of Metabolism</a>. <br>I need an immunology notebook. <ul>Recommended, large-scale: <li>Georgina Ferry, <cite>Dorothy Hodgkin: A Life</cite> <li>Gonnick and Wheelis, <cite>The Cartoon Guide to Genetics</cite> [I am utterly serious] <li>Horace Freeland Judson, <cite>The Eighth Day of Creation</cite> </ul> <ul>Recommended, details: <li>E. Shakhnovich, V. Abkevich and O. Ptitsyn, "Conserved residues and the mechanism of protein folding", <cite>Nature</cite> <strong>379</strong> (1996): 96--98 </ul> <ul>To read: <li>Alberts et al., <citE>Molecular Biology of the Cell</cite> <li>Jay Banavar, Amos Maritan, Cristian Micheletti and Flavio Seno, "Geometrical aspects of protein folding," <a href="http://arxiv.org/abs/cond-mat/0105209">cond-mat/0105209</a> <li>William Bechtel, <cite>Discovering Cell Mechanisms: The Creation of Modern Cell Biology: The Creation of Modern Cell Biology</cite> <li>Nathaniel C. Comfort, <cite>The Tangled Field: Barbara McClintock's Search for the Patterns of Genetic Control</cite> [<a href="http://www.hup.harvard.edu/catalog/COMTAN.html">Blurb</a>] <li>Enrico Di Cera, <cite>Thermodynamic Theory of Site-Specific Binding Processes in Biological Macromolecules</cite> <li>Nikolay V. Dokholyan and Eugene I. Shakhnovich, "Understanding hierarchical protein evolution from first principles," <a href="http://arxiv.org/abs/cond-mat/0104469">cond-mat/0104469</a> <li>Harrison Echols, <cite>Operators and Promoters: The Story of Molecular Biology and Its Creators</cite> <li>Ernest Fischer and Carol Lipson, <cite>Thinking about Science: Max Delbruck and the Origins of Molecular Biology</cite> <li>Donald Fleming, "Emigr&eacute; Physicists and the Biological Revolution," <cite>Perspectives in American History</cite> <strong>2</strong> (1968)152--89 <li>David S. Goodsell, <cite>Bionanotechnology: Lessons from Nature</cite> <li>Gregory M. Grason and Robijn F. Bruinsma, "Chirality and Equilibrium Biopolymer Bundles", <a href="http://dx.doi.org/10.1103/PhysRevLett.99.098101"><cite>Physical Review Letters</cite> <strong>99</strong> (2007): 098101</a> <li>Frederic Lawrence Holmes, <cite>Reconceiving the Gene: Seymour Benzer's Adventures in Phage Genetics</cite> [<a href="http://yalepress.yale.edu/yupbooks/book.asp?isbn=0300110782">Blurb</a>. Positive <a href="http://dx.doi.org/10.1038/443509a">review</a> in <cite>Nature</cite>] <li>Isaac A. Hubner, Eric J. Deeds, and Eugene I. Shakhnovich, "Understanding ensemble protein folding at atomic detail", <a href="http://dx.doi.org/10.1073/pnas.0605580103"><cite>Proceedings of the National Academy of Sciences</cite> (USA) <strong>103</strong> (2006): 17747--17752</a> [Open access] <li>Lawrence E. Hunter, <cite>The Processes of Life: An Introduction to Molecular Biology</cite> [<a href="http://mitpress.mit.edu/978-0-262-01305-5">blurb</a>] <li>Meyer B. Jackson, <cite>Molecular and Cellular Biophysics</cite> [<a href="http://cambridge.org/9780521624701">blurb</a>] <li>Karsten Kruse, Jean-Francois Joanny, Frank Julicher, Jacques Prost and Ken Sekimoto, "Generic theory of active polar gels: A paradigm for cytoskeletal dynamics", <a href="http://arxiv.org/abs/physics/0406058">physics/0406058</a> <li>Michal Kurzynski, <cite>The Thermodynamic Machinery of Life</cite> [<a href="http://www.springer.com/sgw/cda/frontpage/0,11855,4-10103-22-48659292-detailsPage%253Dppmmedia%257CaboutThisBook%257CaboutThisBook,00.html">Blurb</a>] <li>Pier Luigi Luisi, <cite>The Emergence of Life: From Chemical Origins to Synthetic Biology</cite> [<a href="http://www.cambridge.org/0521821177">Blurb</a><] <li>Cristian Micheletti, "Optimal prediction of folding rates and transition state placement from native state geometry," <a href="http://arxiv.org/abs/cond-mat/0202090">cond-mat/0202090</a> <li>Mihaela Oprea and Stephanie Forrest, "How the Immune System Generates Diversity: Pathogen Space Coverage with Random and Evolved Antibody Libraries," SFI Working Paper 99-02-014 <li>Alex Rosenberg, <cite>Darwinian Reductionism: Or, How to Stop Worrying and Love Molecular Biology</cite> [<a href="http://www.press.uchicago.edu/cgi-bin/hfs.cgi/00/193615.ctl">Blurb</a>] <li>Sahotra Sarkar <ul> <li><cite>Molecular Models of Life: Philosophical Papers on Molecular Biology</cite> [<a href="http://mitpress.mit.edu/0262195127">Blurb</a>] <li><cite>Genetics and Reductionism</cite> [<a href="http://cambridge.org/9780521637138">Blurb</a>] </ul> <li>Ora Schueler-Furman, Chu Wang, Phil Bradley, Kira Misura and David Baker, "Progress in Modeling of Protein Structures and Interactions", <a href="http://dx.doi.org/10.1126/science.1112160"><cite>Science</cite> <strong>310</strong> (2005): 638--642</a> <li>M. Sega, P. Faccioli, F. Pederiva, G. Garberoglio and H. Orland, "Quantitative Protein Dynamics from Dominant Folding Pathways", <a href="http://dx.doi.org/10.1103/PhysRevLett.99.118102"><cite>Physical Review Letters</cite> <strong>99</strong> (2007): 118102</a> <li>Kim Sneppen and Giovanni Zocchi, <cite>Physics in Molecular Biolgoy</cite> [<a href="http://cambridge.org/0521844193">Blurb</a> <li>R. H. Sprinkle, <cite>Profession of Conscience: The Making and Meaning of Life-Sciences Liberalism</cite> [<a href="http://pup.princeton.edu/titles/5617.html">Blurb</a>] <li>Chao Tang, "Simple Models of the Protein Folding Problem," <a href="http://arxiv.org/abs/cond-mat/9912450">cond-mat/9912450</a> <li>Guido Tiana, Boris E. Shakhnovich, Nikolay V. Dokholyan and Eugene I. Shakhnovich, "Imprint of evolution on protein structures", <a href="www.pnas.org/cgi/doi/10.1073/pnas.0306638101"><cite>PNAS</cite> 10.1073/pnas.0306638101</a> <li>Alessandro Torcini, Roberto Livi, and Antonio Politi, "A dynamical approach to protein folding," <a href="http://arxiv.org/abs/cond-mat/0103270">cond-mat/0103270</a> <li>D. E. Vance and J. Vance (eds.), <cite>Biochemistry of Lipids, Lipoproteins and Membranes</cite> [I have my reasons.] <li>David Wales, <cite>Energy Landscapes: Applications to Clusters, Biomolecules and Glasses</cite> [<a href="http://cambridge.org/0521814154">Blurb</a>] <li>James Watson, <cite>The Double Helix</cite> </ul>