Evolution of Developmental Mechanisms
The close mapping between genotype and morphological phenotype in many modern metazoans has led to the general notion that the evolution of organismal form is a direct consequence of evolving genetic programs. This standard view has come into conflict with evidence on discordances between genotypic and phenotypic changes in both development and evolution. As an alternative to this view, we have been exploring the idea that the present relationship between genes and form is a highly derived condition, a product of evolution rather than its precondition. Prior to selection for the biochemical canalization of developmental pathways and the stabilization of phenotypes, interaction of multicellular organisms with their physico-chemical environments dictated a one-to-many mapping between genomes and forms. These forms would have been generated by epigenetic mechanisms: initially physical processes characteristic of condensed, chemically active materials, and later conditional, inductive interactions among the organism's constituent tissues. The concept that epigenetic mechanisms are the generative agents of body plan and morphological character origination helps to explain findings that are difficult to reconcile with the standard neo-Darwinian model, e.g., the burst of body plans in the early Cambrian, the origins of morphological innovation, homology, and rapid change of form.
Newman, S. A. (1994). Generic physical mechanisms of tissue morphogenesis: A common basis for development and evolution. J. Evolutionary Biology 7, 467-488. (PDF)
Newman, S. A. (1995). Interplay of genetics and physical processes of tissue morphogenesis in development and evolution: The biological fifth dimension. In "Interplay of Genetic and Physical Processes in the Development of Biological Form" (D. Beysens, G. Forgacs, and F. Gaill, Eds.), pp. 3-12. World Scientific, Singapore.
Newman, S. (1998). Epithelial morphogenesis: a physico-evolutionary interpretation. In "Molecular Basis of Epithelial Appendage Morphogenesis" (C.-M. Chuong, Ed.), pp. 341-358. R. G. Landes, Austin, TX.
Müller, G. B., and Newman, S. A. (1999). Generation, integration, autonomy: three steps in the evolution of homology. Novartis Found. Symp. 222, 65-73.
Newman, S. A., and Müller, G. B. (2000). Epigenetic mechanisms of character origination. J. Exp. Zool. B Mol. Dev. Evol. 288, 304-17. (PDF)
Salazar-Ciudad, I., Newman, S. A., and Solé, R. (2001). Phenotypic and dynamical transitions in model genetic networks. I. Emergence of patterns and genotype-phenotype relationships. Evolution & Development 3, 84-94. (PDF)
Salazar-Ciudad, I., Solé, R., and Newman, S. A. (2001). Phenotypic and dynamical transitions in model genetic networks. II. Application to the evolution of segmentation mechanisms. Evolution & Development 3, 95-103. (PDF)
Newman, S. A. (2002). Developmental mechanisms: putting genes in their place. J. Biosci. 27, 97-104. (PDF)
Müller, G. B., and Newman, S. A. (2003). Origination of organismal form: beyond the gene in developmental and evolutionary biology. MIT Press, Cambridge, MA. (link)
Salazar-Ciudad, I., Jernvall, J., and Newman, S. A. (2003). Mechanisms of pattern formation in development and evolution. Development 130, 2027-37. (PDF)
Newman, S. A. (2005). The pre-Mendelian, pre-Darwinian world: Shifting relations between genetic and epigenetic mechanisms in early multicellular evolution. J. Biosci. 30, 75-85. (PDF)
Müller, G. B., and Newman, S. A. (2005). The innovation triad: an EvoDevo agenda. J. Exp. Zool. B Mol. Dev. Evol. 304, 487-503. (PDF)
Newman, S. A., and Müller, G. B. (2005). Origination and innovation in the vertebrate limb skeleton: an epigenetic perspective. J. Exp. Zool. B Mol. Dev. Evol. 304, 593-609. (PDF)
Newman, S. A., Forgacs, G., and Müller, G. B. (2006). Before programs: The physical origination of multicellular forms. Int. J. Dev. Biol. 50, 289-99. (PDF)
Newman, S. A. (2006). The developmental-genetic toolkit and the molecular homology-analogy paradox. Biological Theory 1, 12-16. (link)
Newman, S. A. (2007). William Bateson's physicalist ideas. In "From Embryology to Evo-Devo: a History of Evolutionary Development" (M. Laubichler and J. Maienschein, Eds.), pp. 83-107. MIT Press, Cambridge, MA.
Callebaut, W., Müller, G. B., and Newman, S. A. (2007). The organismic systems approach. Streamlining the naturalistic agenda. In "Integrating evolution and development. From theory to practice" (R. Sansom and R. N. Brandon, Eds.), pp. 25-92. MIT Press, Cambridge, MA.
Newman, S. A., and Bhat, R. (2008). Dynamical patterning modules: physico-genetic determinants of morphological development and evolution. Phys. Biol. 5, 15008. (PDF)
Mezentseva, N. V., Kumaratilake, J. S., and Newman, S. A. (2008). The brown adipocyte differentiation pathway in birds: an evolutionary road not taken. BMC Biol 6, 17. (link)
Newman, S. A., and Bhat, R. (2009). Dynamical patterning modules: a "pattern language" for development and evolution of multicellular form. Int. J. Dev. Biol. 53, 693-705 (link)
Bhat, R., and Newman, S. A. (2009). Snakes and ladders: the ups and downs of animal segmentation. J. Biosci. 34, 163-6 (link)
Newman, S. A., Bhat, R., and Mezentseva, N. V. (2009). Cell state switching factors and dynamical patterning modules: complementary mediators of plasticity in development and evolution. J. Biosci.34, 553-572 (link)
Newman, S. A., Müller, G. B. (2010). Morphological evolution: epigenetic mechanisms. Encyclopedia of Life Sciences. John Wiley & Sons, Chichester, U.K. doi: 10.1002/9780470015902.a0002100.pub2 (link)
Newman, S. A. (2010). Stuart A. Newman [respondent]. In "Evolutionary Theory: 5 Questions" (Oftedal, G., Friis, J. K. B. O., Roussel, P. and Norup, M. S., Eds.), pp. 125-142. Automatic Press, Copenhagen. (link)
Newman, S. A. (2010). Dynamical patterning modules. In "Evolution: the Extended Synthesis" (M. Pigliucci and G. B. Müller, Eds.) pp. 281-306. MIT Press, Cambridge, MA. (link)
Newman, S. A., Bhat, R. (2011). Lamarck's dangerous idea. In: "Transformations of Lamarckism: from subtle fluids to molecular biology" (S. Gissis, E. Jablonka, Eds.), pp. 157-169. MIT Press, Cambridge, MA. (link)
Newman, S. A. (2011). Thermogenesis, muscle hyperplasia, and the origin of birds. BioEssays 33, 653-6. (PDF)
Newman, S. A. (2011). The evolution of evolutionary mechanisms: a new perspective. In: "Biological evolution: facts and theories" (G. Auletta, M. Leclerc, R. A. Martinez, Eds.), pp. 169-191. Gregorian & Biblical Press, Rome. (PDF)
Newman, S. A. (2011). Animal egg as evolutionary innovation: a solution to the "embryonic hourglass" puzzle. J. Exp. Zool. B Mol. Dev. Evol. 316, 467-83. (PDF)
Newman, S. A. (2011). The developmental specificity of physical mechanisms. Ludus Vitalis 19, 343-351. (PDF)
Newman, S. A. (2012). What's new: Review essay on "The Origins of Evolutionary Innovations: A Theory of Transformative Change in Living Systems," by Andreas Wagner, Oxford University Press, 2011. Philos. Theor. Biol. 4, e304. (link)
Hernández-Hernández, V., Niklas, K. J., Newman, S. A., and Benítez, M. (2012). Dynamical patterning modules in plant development and evolution. Int. J. Dev. Biol. 56, 661-74. (link)
Newman, S. A. (2012). Physico-genetic determinants in the evolution of development. Science. 338, 217-9. (PDF)
Niklas, K. J., and Newman, S. A. (2013). The origins of multicellular organisms. Evol. Dev. 15, 41-52. (PDF)
Newman, S. A. (2013). Evolution is not mainly about genes. In "Genetic Explanations: Sense and Nonsense" (Krimsky, S. and Gruber, J. Eds.), pp. 26-33; 288-290. Harvard University Press, Cambridge, MA. (link)
Newman, S. A., and Linde-Medina, M. (2013). Physical determinants in the emergence and inheritance of multicellular form. Biological Theory 8, 274-285. (PDF)