While I have named numerous inanimate objects “Mr. Tock” through the years because of the genius & charm of the Professors Foglio, the origin of calling Pomodoros “tocks” is unrelated and slightly convoluted and boring 
~ “Every princess needs a battle axe!”
Here’s how I remember the convoluted boring story:
In grad school, before Kibotzer and before even the Voluntary Harassment Program predecessor of Beeminder, I made up a weight loss plan called The Rock Diet. The idea was to start with some number of pebbles/rocks in one pocket and for every 150-calorie serving of food you ate you’d move a rock to the other pocket. For every 150 calories burned you could move a rock in the other direction. We got used to talking about food and workouts in terms of rocks even though we switched to jelly bracelets moved between wrists to keep track. So that was in the water supply, so to speak. Also around that time I independently reinvented the pomodoro system and, being in grad school, I dubbed the 45-minute chunks of time “research rocks” which, absurdly, I abbreviated “chrocks”. That term actually stuck for years until at some point in the early Beeminder days (maybe around when I wrote my nominology treatise?) @bee and I decided it really wanted a better name and we thought of “tock” as in “tick-tock” and forced ourselves to stop saying “chrock”. I think we knew about pomodoros by then and we thought “tick” could be a synonym for a standard 25-minute pomodoro and “tock” for our 45-minute version. But “tick” doesn’t seem to have stuck.
And now you know the rest of the story.
Ok so what is girl genius?
It’s a long running sci-fi/comedy comic. Been published online for about a decade I think. I just recently reread it earlier this year.