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Bonner is the George M. Moffett Professor Emeritus of Biology at Princeton University. He was trained at Harvard University between 1937 and 1947, aside from a stint in the United States Army Air Corps from 1942 to 1946. His PhD studies were interrupted by this stint in the Air Corps, so he completed his studies in an unusually short period of time. He soon joined the faculty of Princeton University, becoming the chairman of the Princeton Biology Department between 1966 and 1977, also in 1983-84 and 1987-88.

He holds three honorary doctorates and is a fellow of the American Association for the Advancement of Science. He was made a National Academy of Sciences fellow in 1973.

He was a visiting scholar at the Indian Institute of Science in 1993 and the Indian Academy of Sciences in 1990. He has also been visiting faculty at Brooklyn College, Williams College and University College, London. He also was a Sheldon Travelling Fellow in 1941 in Panama and Cuba while in graduate school, a Rockefeller Traveling Fellow 1953 in Paris, France, and held Guggenheim Fellowships in 1958 and from 1971-1972 in Edinburgh, Scotland. He held an National Science Foundation Senior Postdoctoral Fellowship in Cambridge, England in 1963. He also had Commonwealth Foundation Book Fund Fellowships in 1971 and between 1984 and in 1985 Edinburgh, Scotland and a Josiah Macy, Jr. Foundation Book Fund Fellowship in 1978 in Edinburgh, Scotland.

He has written an array of books on developmental biology and evolution, many scientific papers, and has produced a number of works in biology. Some of his books include:

• The Cellular Slime Molds
• The Evolution of Complexity by Means of Natural Selection [Review]
• The Evolution of Culture in Animals
• Life Cycles
• Morphogenesis: an Essay on Development
• On Development: The Biology of form, Harvard University Press
• Cells and Societies
• First Signals
• The Ideas of Biology
• Sixty Years of Biology
• Size and Cycle
• Why Size Matters: From Bacteria to Blue Whales
• Lives of a Biologist: Adventures in a Century of Extraordinary Science, Harvard University Press.

His autobiography, "Lives of a Biologist: Adventures in a Century of Extraordinary Science" winner of the 2002 ForeWord Magazine Book of the Year Award.

One of the earliest efforts to express support for evolution by scientists was organized by Nobel Prize winner German biologist Hermann J. Muller in 1966. Muller circulated a petition entitled: "Is Biological Evolution a Principle of Nature that has been well established by Science?", in May 1966.Bonner signed this manifesto, along with 176 other leading American biologists, including several Nobel Prize winners.

In the mid-1970s, Bonner corresponded with Talcott Parsons on the issue concerning the similaries and differences between biological and socio-cultural evolution.

He was born in 1920. He has 4 children. His wife is deceased. He has vacationed in Nova Scotia yearly for over 40 years.