Skaggs was born on 21 November 1911 in Trenton, Missouri. He grew up on a farm in northern Missouri. He attended a one-room schoolhouse and to get to high school, he had to ride a horse. Skaggs was the oldest of three children and his father planned for Skaggs to become a farmer. Instead, Skaggs had other interests and found amazement with tinkering, and enjoyed designing and building contraptions and made plans for a science career. He attended the University of Missouri and completed a B.S. in chemistry with a minor in mathematics in 1933 and M.S. in physics in 1934. He moved to Chicago in 1935, entered the University of Chicago and was accepted into the graduate program in nuclear physics. In 1939, Skaggs was awarded a Ph.D. in nuclear physics. At the University of Chicago, Skaggs had a post-doctoral fellowship in nuclear physics and secured part-time work at the Tumor Clinic at Michael Reese Hospital in radiation oncology. From 1941 – 1943, the war effort took him to Washington, D.C. where he served at the Carnegie Institution of Washington in the Department of Terrestrial Magnetism. Skaggs worked with physicist Nicholas Smith to design an airplane proximity detection system that utilized radio waves to locate and detonate anti-aircraft shells.