Developmental Biology

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.)

Evolutionary issues: Conservation of genes important in development, e.g. hox. Conservation of body plans, and whether this is any more than a statistical artifact (as G. C. Williams argues). To what extent is development constrained, and how much does this effect adaptive evolution? How do developmental programs themselves evolve? The developmental sequence as the thing-which-evolves and selection acts upon (Bonner, and earlier Woodger). Heterochrony. Von Baer's laws (roughly implying: the earlier the stage of development, the more members of two related species resemble each other.)

"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?

Philip Ball, The Self-Made Tapestry: Pattern Formation in Nature [Review: The Blind Snowflake-Maker]
John Tyler Bonner
- On Development: The Biology of Form
- The Evolution of Complexity, by Means of Natural Selection
Peter Dearden and Michael Akam, "Segmentation in silico," Nature 406 (2000): 131--132 [Commentary on von Dassow et al.]
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]
Arjumand Ghazi and K. VijayRaghavan, "Control by combinatorial codes," Nature 408 (2000): 419--420
Lionel G. Harrison, Kinetic Theory of Living Pattern
Stuart Kauffman, The Origins of Order [Interesting considerations on development; horrid writing; dodgy economics]
P. Z. Myers, Pharyngula [Weblog of a developmental biologist]
Joseph Needham
- History of Embryology
- Order and Life
Rudolf Raff, The Shape of Life: Genes, Development, and the Evolution of Animal Form [Actually, I'm only about half-way through this, but it's certainly worth recommending anyway. But really, he should've drunk more coffee while writing.]
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
D'Arcy Wentworth Thompson, On Growth and Form
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

Wallace Arthur
- Biased Embryos and Evolution
- The Origin of Animal Body Plans: A Study in Evolutionary Developmental Biology
Leo W. Buss, The Evolution of Individuality
Werner Callebaut and Diego Rasskin-Gutman (eds.), Modularity: Understanding the Development and Evolution of Natural Complex Systems [Blurb]
Sean B. Carroll, From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design
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 constraintts in a gene network model and pattern formation", q-bio.MN/0504005
Gunther Eble
- "The Role of Development in Evolutionary Radiations," in M. L. McKinney (ed.), Biodiversity Dynamics = SFI Working Paper 98-09-084
- "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 andStuart A. Newman, Biological Physics of the Developing Embryo [blurb]
Stephen Jay Gould, Ontogeny and Phylogeny
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 [Blurb]
Richard H. Kessin, Dictyostelium: Evolution, Cell Biology, and the Development of Multicellularity [Blurb]
Marc Kirschner and John Gerhart, The Plausibility of Life [Capsule review by Frenando Pereira]
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]
Volker Loeschcke, ed., Genetic Constraints on Adaptive Evolution
Alessandro Minelli, The Development of Animal Form: Ontogeny, Morphology and Evolution
Clara Pinto-Correia, The Ovary of Eve: Egg and Sperm and Preformation [Review by Danny Yee]
Raff and Kaufman, Embryoes, Genes and Evolution
Anne-Gaelle Rolland-Lagan, J. Andrew Bangham and Enrico Coen, "Growth dynamics underlying petal shape and symmetry," Nature 422 (2003): 161--163
Gerhard Schlosser and Gunter P. Wagner (eds.), Modules, Development and Evolution
Ricard V. Solé, Isaac Salazar-Ciudad and Jordi Garcia-Fernández, "Landscapes, Gene Networks and Pattern Formation: On the Cambrian Explosion," SFI Working Paper 00-08-046
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
Gunte P. Wagner, Chris Amemiya and Frank Ruddle, "How cluster duplications and the opportunity for evolutionary novelties", PNAS 100 (2003): 14603--14606
Steven D. Webb and Markus R. Own, "Oscillations and patterns in spatially discrete models for developmental intercellular signalling", Mathematical Biology 48 (2004): 444--476
Mary Jane West-Eberhard, Developmental Plasticity and Evolution
Adam S. Wilkins, The Evolution of Developmental Pathways
Lewis Wolpert and a cast of thousands, Principles of Development

Notebooks

Developmental Biology