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One achievement in Minecraft is called "The Lie", which includes making a cake. This is a nod to Portal's famous meme, "The Cake Is A Lie". Also, the achievement for entering the nether in the PC version is called "We Need To Go Deeper", which is a reference of the multi-layered dream based plot of "Inception".
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"Herobrine Removed" has been added to a number changelogs. Herobrine is a character from a Minecraft "creepypasta" who looks exactly like the player, but has white eyes. It is said that Herobrine is Notch's dead brother, although Notch said himself that he does not have a dead brother. Herobrine never appeared in the game, and it's likely that this line being added to the changelogs is just a joke with the community.
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Originally, zombies used to drop feathers when killed. This was the result of Notch, the developer of Minecraft at the time, not knowing what zombies should drop.
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"I don't have any modeling programs to do the models, I just write them in code. And I accidentally made them (the creepers) tall instead of long, so it was like a tall thing with four little feet. And that became the creeper. As opposed to a pig." - Minecraft creator 'Notch'
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The texts respectively read "Well Played Internets You Are Good", "These Names Will Be Random And Confusing" and "Each Spell Costs Experience Levels" describing the function of the enchantment table.
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Minecraft was originally called "Cave Game".
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Five humanoid mobs which were available in the Indev version were later removed. However, they can be found in the files of earlier versions of the game. The mobs were Beast Boy which resembles the DC comics character of the same name, Black Steve, humans which resemble the default player's character (later renamed 'Monsters'), Rana who is a little girl with a frog hat, and a different human also named Steve.
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