In the early Beta version of Don't Starve, the game used a "Research Points" system, instead of prototyping. When Wilson examines the Science Machine, he states that "It breaks down items into their scientific components", which is a leftover dialogue script from when the game used Research Points.
The Science Machine appears at the top of the screen when the game "Autosaves".
There appears to be rope turning the wheels on the machine, while no rope is needed to build it.
The body of the Science Machine resembles the Companion Cube from Portal video game series.