We discovered the electromagnetic force rather early on, though we didn’t know what it was that we were observing. Ancient Greeks noted that amber could attract small objects when rubbed with fir. We would later classify other objects with a similar attractive property as “electrica” based on the greek word for amber (elektron).
We then discovered the repulsive side. For example, if you rub glass with silk, then rub amber with wool, the glass will repel a charged gold leaf but the amber will attract it.
Ultimately, we would posit that all this rubbing action was causing a transfer of *something* from one object to another, and the attraction/repulsion was caused be a lack/excess of that something, respectively. Ben Franklin labeled the excess as being positive and the lack being negative, and posited that this substance, having a positive charge, is what was being transferred. However, others thought that there were two kinds of things involved, one wholly positive and one wholly negative.
We would eventually discover the electron. When you energized some cases, they would emit a stream of particles that could be influenced by a magnetic field. The manner that they were influenced was the same way as things which we had come to call as being negatively charged, based on Ben Franklin’s earlier categorization.
So, in short, with incomplete knowledge, we labeled things as being negatively or positively charged based on attraction or repulsion. When we managed to isolate electrons, we found that they behaved the same as the things we labeled as being negatively charged.
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