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 Evol Biol 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. Evol & Devel 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. Evol & Devel 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 & Theory 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 a matter of 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)
Newman, S. A. (2014) Excitable media in medias res: how physics scaffolds metazoan development and evolution. In: "Developing scaffolds in evolution, culture, and cognition" (L. R. Caporael, J. R. Griesemer, W. C. Wimsatt, Eds.), pp. 109-123, MIT Press, Cambridge, Mass. (link)
Nanjundiah, V., Newman, S. A. (2014) Introduction: e pluribus unum. J Biosci 39, 171-6. (PDF)
Linde-Medina, M., Newman, S. A. (2014) Limb, tooth, beak: three modes of development and evolutionary innovation of form. J Biosci 39, 211-23. (PDF)
Newman, S. A. (2014) Physico-genetics of morphogenesis: the hybrid nature of developmental mechanisms. In: "Towards a theory of development" (A. Minelli, T. Pradeu, Eds.), pp. 95-113, Oxford University Press, Oxford. (link)
Newman, S. A., (2014) Form and function remixed: developmental physiology in the evolution of vertebrate body plans. J Physiol 592, 2403-2412. (PDF)
Newman, S. A. (2014) Development and evolution: the physics connection. In “Conceptual Change in Biology: Scientific and Philosophical Perspectives on Evolution and Development” (A. Love, Ed.), pp. 421-440. Springer, Berlin.
Newman, S. A. (2014) Physico-genetics of morphogenesis: the hybrid nature of developmental mechanisms. In “Towards a Theory of Development” (A. Minelli, T. Pradeu, Eds.), pp. 95-113. Oxford University Press, Oxford.
Newman, S. A. (2014) Why are there eggs? Biochem Biophys Res Commun 450, 1225-1230. (PDF)
Newman, S. A. (2014) Review of "In Search of Mechanisms: Discoveries across the Life Sciences", Notre Dame Philosophical Reviews. University of Notre Dame, Notre Dame, Indiana. (link)
Newman, S. A. (2015) The evolution of evolutionary mechanisms: a new perspective. In “Darwin in the Twenty-First Century: Nature, Humanity, and God” (Sloan, P. R., McKenny, G. P., Eggleson, K., Eds.), pp. 61-89. University of Notre Dame Press, Notre Dame, Indiana.
Moss, L., Newman, S. A. (2015) The grassblade beyond Newton: the pragmatizing of Kant for evolutionary-developmental biology Lebenswelt 7, 94-111. (PDF)
Newman, S. A. (2016) 'Biogeneric' developmental processes: drivers of major transitions in animal evolution. Philos Trans R Soc Lond B Biol Sci 371, 20150443.
Newman, S. A. (2016) Multicellularity, the emergence of animal body plans, and the stabilizing role of the egg. In “Multicellularity: Origins and Evolution" (Niklas, K.J., Newman, S.A., Eds.), pp. 225-246. MIT Press, Cambridge. Mass.
Newman, S. A. (2016) Origination, variation, and conservation of animal body plan development. Reviews in Cell Biology and Molecular Medicine 2, 130-162.
Niklas, K. J., Newman, S. A. (2016) “Multicellularity: Origins and Evolution" The MIT Press, Cambridge, MA.
Newman, S. A., Niklas, K. J., in press. Dynamical patterning modules link genotypes to morphological phenotypes in multicellular evolution. In Cells in Evolutionary Biology (Hall, B. K., Moody, S. A. (Eds.). CRC Press, Boca Raton, Florida.