@Popehat It's hard to say where it began. Some say 4chan, but there were "glowing eye" memes on reddit before the anime incel edgelord identiarians picked it up. For example: 
@Popehat There's a lot of potential origins. Some people point to the Mass Effect "assuming control" meme with similar eyes. But it basically meant the person is supercharged with powerful energy, like going super saiyan:
@Popehat But like everything even remotely related to either anime or internet memes, the 4chan chuds had to ruin it. And for a while it became a thing for alt-right types to use glowing eyes, to signify the powerful energy of being red-pilled.
@Popehat The irony left was very late to the train on the glowing eyes avatars. And it seems to be a form of online cultural reappropriation. Not terribly unlike the (((echoes))) I guess. But IMHO it doesn't work. They just look like alt-right dorks.
@Popehat Also I'm embarrassed that I'm the go-to authority on the "asshole subset of the left," but I can't argue with it really.
