Most activities grant you Experience Points (XP). Once you've gathered enough, you Level Up.
Levelling Up grants you Skill Points, which you can spend to learn new Perks at Shrines.
Most Perks have multiple Levels. Each Level has its own effect and cost in Skill Points. Learning advanced Perks also progresses Time.
Some Perks require reading a Manual to make the Perk available to learn. You can find Manuals by exploring the world.