Developmental Biology

25 Nov 2024 20:21

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.)

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]

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

Joseph Needham
- History of Embryology
- Order and Life
D'Arcy Wentworth Thompson, On Growth and Form

To read, history and historical interest:

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

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