Developmental Biology

Last update: 21 Apr 2025 21:17
First version:

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The science formerly known as embryology.

Self-organization and pattern formation --- physico-chemical mechanisms; genetic markers; how the genes control the physical processes. Mathematical modelling in this field seems largely confined to the physical mechanisms of pattern formation; do we have any well-confirmed theories in this area? Do we have so much as a single pair of known Turing morphogens? (John Maynard Smith says we do not, and would almost certainly know.) (True in 1995 or 1996, when I wrote it, but not since 2012. It remains the case that Turing's mechanism doesn't seem to be much used by actual biology...)

Evolutionary issues: get their own notebook.

"Model systems" for developmental biology --- Drosophila, C. elegans, zebra fish, mice, frogs, sea urchins, salamanders, slime molds; what do plant or arthropod developmentalists study? Just how far can we extrapolate from these beasts to the other ~10^8 metazoan species? (That gets back to evolutionary issues.)

See also:
• Adaptation
• Biological order
• J. T. Bonner
• Evolution
• Evolution of Complexity
• Evolving Local Rules for Global Problems
• Evo-Devo
• Joseph Needham
• Pattern Formation
• Physical Principles in Biology
• Random Boolean Networks
• Self-organization
• Signal Transduction, Gene Regulation and Control of Metabolism
• Slime Molds, especially Dictyostelium
• D'Arcy Wentworth Thompson, 1860--1948

Recommended, big picture:
• Philip Ball, The Self-Made Tapestry: Pattern Formation in Nature [Review: The Blind Snowflake-Maker]
• John Tyler Bonner, On Development: The Biology of Form
• John Gerhart and Marc Kirschner, Cells, Embryos, and Evolution: Toward a Cellular and Developmental Understanding of Phenotypic Variation and Evolutionary Adaptability [Review by Danny Yee]
• Lionel G. Harrison, Kinetic Theory of Living Pattern
• Stuart Kauffman, The Origins of Order: Self-Organization and Selection in Evolution [Brief comments]

Recommended, close ups:
• Peter Dearden and Michael Akam, "Segmentation in silico," Nature 406 (2000): 131--132 [Commentary on von Dassow et al.]
• Andrew D. Economou, Atsushi Ohazama, Thantrira Porntaveetus, Paul T Sharpe, Shigeru Kondo, M. Albert Basson, Amel Gritli-Linde, Martyn T. Cobourne and Jeremy B. A. Green, "Periodic stripe formation by a Turing mechanism operating at growth zones in the mammalian palate", Nature Genetics 44 (2012): 348--351
• Arjumand Ghazi and K. VijayRaghavan, "Control by combinatorial codes," Nature 408 (2000): 419--420
• Thimo Rohlf and Stefan Bornholdt
  • "Self-organized pattern formation and noise-induced control from particle computation", cond-mat/0312366 [Short version]
  • "Morphogenesis by coupled regulatory networks", q-bio.MN/0401024 [Long version]
• Satoshi Sawai, Peter A. Thomason and Edward C. Cox, "An autoregulatory circuit for long-range self-organization in Dictyostelium cell populations", Nature 433 (2005): 323--326
• George von Dassow, Eli Meir, Edwin M. Munro and Garrett M. Odell, "The segment polarity network is a robust developmental module," Nature 406 (2000): 188--191

Recommended, big picture, but now of only historical interest:
• Joseph Needham
  • History of Embryology
  • Order and Life
• D'Arcy Wentworth Thompson, On Growth and Form

To read, history and historical interest:

To read:
• Werner Callebaut and Diego Rasskin-Gutman (eds.), Modularity: Understanding the Development and Evolution of Natural Complex Systems
• Elof Axel Carlson, The 7 Sexes: Biology of Sex Determination
• Guokai Chen, Olga Zhuchenko, and Adam Kuspa, "Immune-like Phagocyte Activity in the Social Amoeba", Science 317 (2007): 678--681
• Enrico Coen, The Art of the Genes
• Enrico Coen, Anne-Gaelle Rolland-Lagan, Mark Matthews, J. Andrew Bangham, and Przemyslaw Prusinkiewic, "The genetics of geometry", PNAS 10.1073/pnas.0306308101
• Eric Davidson
  • Genomic Regulatory Systems: Development and Evolution
  • The Regulatory Genome: Gene Regulatory Networks in Development and Evolution
• L. Diambra and Luciano da Fontoura, "Geometrical constraints in a gene network model and pattern formation", q-bio.MN/0504005
• Ana S. Dias, Irene de Almeida, Julio M. Belmonte, James A. Glazier, and Claudio D. Stern, "Somites Without a Clock", Science 343 (2014): 791--795
• Gunther Eble, "Theoretical Morphology: State of the Art," SFI Working Paper 00-08-45
• Jim Endersby, A Guinea Pig's History of Biology: The Plants and Animals who Taught Us the Facts of Life [Review by Georgina Ferry in The Guardian]
• Gabor Forgacs and Stuart A. Newman, Biological Physics of the Developing Embryo
• Lionel G. Harrison and Michael Lyons, Shaping of Life: The Generation of Biological Pattern
• Martin Howard and Pieter Rein ten Wolde, "Finding the Center Reliably: Robust Patterns of Developmental Gene Expression", Physical Review Letters 95 (2005): 208103
• Stephen H. Howell, Molecular Genetics of Plant Development
• Jack D. Hywood, Emily J. Hackett-Jones, and Kerry A. Landman, "Modeling biological tissue growth: Discrete to continuum representations", Physical Review E 88 (2013): 032704
• Richard H. Kessin, Dictyostelium: Evolution, Cell Biology, and the Development of Multicellularity
• Evelyn Fox Keller, Making Sense of Life: Explaining Biological Development with Models, Metaphors, and Machines
• Ioan Kosztin, Gordana Vunjak-Novakovic, and Gabor Forgacs, "Modeling the dynamics of multicellular systems: Application to tissue engineering", Reviews of Modern Physics 84 (2012): 1791
• Peter A. Lawrence, The Making of a Fly: The Genetics of Animal Design [Drosophila melanogaster, of course. --- Once, at an international conference on genetics, someone got up and read a paper on a human genetic disease. It had everything --- clever reasoning, subtle experiments, isolation of markers, it was written up like a detective story and delivered with gusto --- and at the end the presenter called for questions with no little confidence. From the back of the hall a Great Eminence slowly rose and demanded to know: "This is all very well, but what does it tell us about Drosophila?"]
• Michael Levine and Robert Tjian, "Transcription regulation and animal diversity", Nature 424 (2003): 147--151
• Armand Leroi, Mutants: On Genetic Variety and the Human Body
• Julian Lewis, "Autoinhibition with Transcriptional Delay: A Simple Mechanism for the Zebrafish Somitogenesis Oscillator", Current Biology 13 (2003): 1398--1408 [Thanks to Nadine Peyrieras for letting me know about this paper]
• Rob Morris, Ignacio Sancho-Martinez, Tatyana O. Sharpee, and Juan Carlos Izpisua Belmonte, "Mathematical approaches to modeling development and reprogramming", Proceedings of the National Academy of Sciences (USA) 111 (2014): 5076--5082
• Stuart A. Newman, "Cell differentiation: what have we learned in 50 years?", arxiv:1907.09551
• Clara Pinto-Correia, The Ovary of Eve: Egg and Sperm and Preformation [Review by Danny Yee]
• Anne-Gaelle Rolland-Lagan, J. Andrew Bangham and Enrico Coen, "Growth dynamics underlying petal shape and symmetry," Nature 422 (2003): 161--163
• J. Scott Turner, The Tinkerer's Accomplice: How Design Emerges From Life Itself [Apparently talks about "Bernard machines", which I thought was a phrase I coined!]
• Arjen vanOoyen (ed.), Modeling Neural Development
• Steven D. Webb and Markus R. Own, "Oscillations and patterns in spatially discrete models for developmental intercellular signalling", Mathematical Biology 48 (2004): 444--476
• Lewis Wolpert and a cast of thousands, Principles of Development

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Version history: 2004年01月20日 08:50; substantial changes and spin-offs in 2024-10 and and 2024-11

Notebooks :