Pennock received his Ph.D. in the history and philosophy of science from the University of Pittsburgh, where he graduated summa cum laude. In 1997, he co-directed a National Science Foundation Chautauqua Workshop on the "Ethical Implications of the Human Genome Project." Pennock has served as president of the University of Texas at Austin Chapter of Sigma Xi and is a member of the American Philosophical Association, the National Center for Science Education and the American Association for the Advancement of Science.

Writing and speaking

He has written many books and articles critical of intelligent design, using the term methodological naturalism to emphasise that the scientific method inherently explains observable events in nature only by natural causes, without assuming the existence or non-existence of the supernatural, and is not based on dogmatic metaphysical naturalism as claimed by creationists. He has also been a featured speaker at atheist gatherings.

Kitzmiller v. Dover Area School District

Pennock testified as an expert witness at the Kitzmiller v. Dover Area School District was cited in the concluding memorandum by Judge John E. Jones III as evidence that "Methodological naturalism is a “ground rule” of science today which requires scientists to seek explanations in the world around us based upon what we can observe, test, replicate, and verify" contributing to the conclusion "that ID is an interesting theological argument, but that it is not science".

In 2009 Pennock received the American Institute of Biological Sciences's Outstanding Service Award, given "in recognition of an individual's (or organization's) noteworthy service to the biological sciences". Pennock has also received the "Friend of Darwin Award" from the National Center for Science Education. His book on creationism, Tower of Babel, was nominated for a Pulitzer Prize, National Book Award and PEN Award, and was a finalist for the ForeWord Book-of-the-Year. Pennock has also won several awards for his essays and teaching, including the Michael R. Bennett Prize, the Templeton Prize for Exemplary Paper in Theology and the Natural Sciences, Apple for the Teacher Award, and a Templeton Science & Religion Course Award. In 2006 Pennock was elected to the American Association for the Advancement of Science for "voicing the philosophical deficits in the pro-intelligent design argument and defending against its inclusion in science teaching" and in 2008 was designated a lifetime member of the National Research Council of the United States National Academy of Sciences.