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For many years Vaughn was managing editor of Prevention magazine, during which he co-edited The Complete Book of Vitamins and Minerals for Health and wrote Chilton's Guide to Home Energy Savings.

Vaughn's career at Prevention was followed by a stint as editor of Free Inquiry magazine, executive editor of the philosophy journal Philo, and executive editor of the medical journal The Scientific Review Of Alternative Medicine.

During this time Vaughn co-edited Science Meets Alternative Medicine: What the Evidence Says About Unconventional Treatments.

Vaughn is author of Thinking Outside the Box: Thinking Critically about Ordinary and Extraordinary Claims (Oxford University Press, forthcoming) and co-author of The Case for Humanism: An Introduction (Rowman & Littlefield), How to Think About Weird Things: Critical Thinking for a New Age (McGraw-Hill), and Doing Philosophy: An Introduction Through Thought Experiments (McGraw Hill).