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Be like Carl Sagan: do science!

Here are some games that, for the most part, focus on scientific things, and such fairly realistically. This is by no means a complete, list, only what has been able to be dug up as of right now. Additions are welcome and encouraged, as long as you follow a few basic rules:

1) The game should follow some sort of real-life science for the most part.
Pokemon Evolution is a no-go. Darwin's evolution is great!

2) If the game is made to be educational it should also be fun.
We're here for fun! If the game is boring and/or badly made it's still not worth it.

3) If it is a science fiction game it should be grounded in science for the period it was created in.
Firefly is a science fiction series with no aliens, no teleportation, and no un-realistic technology from a 2000's standpoint. A game set in Firefly's universe would be fine here. Star Wars with it's lazer swords, magical powers ("jedi"), and many alien races would not be allowed here.


Games

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Cover Title Discipline      Platforms      Description Link Screenshot
  Algodoo Physics Windows
macOS
iOS
The successor to Phun. Physics simulator in which you can draw objects and see how they behave in a realistic 2d physics engine. You can also create wheels and liquids. Link  
  Biogenesis Evolution Windows
Linux
Simulates evolution with various creatures mutating and evolving so they can better survive. The user can create custom creatures and can influence the environment by nourishing certain organisms. Technically an idle game, but still fun. Link  
  BoxCar 2D Evolution Flash Skip the single cellular life and give us cars! Vroom vroom! Evolve your car to go the furthest distance in the shortest amount of time. Technically an idle game, but still fun. Link  
  Conway's Game of Life Evolution
Mathematics
Computing
Web A 'cellular automaton' invented by mathematician John Conway in the 1970s. You set a bunch of cells on a grid, and watch them live, die, or multiply, according to mathematical rules. Link  
  EVE Online Space flight
Colonization
Trade
War
Windows
Linux
Mac
Easily one of the most infamous MMOs in the world due to the fact everything is realistic as possible. No aliens. No FTL travel. No joking. And the ships cost ACTUAL money. Yes, open your wallet for this one. Do you have the cash and the time to join in adventures on the final frontier? Link  
  Flow Evolution Flash
PlayStation 3
PlayStation 4
PSP
Vita
Direct your microorganism towards food, avoid predators, and evolve over time into something bigger and better within the vast ocean. This game is very soothing and is often compared to Flower. Flash version is free, paid advanced version for Sony machines. Link  
  Kerbal Space Program Space flight
Engineering
Windows
Linux
macOS
A relatively simple space sim with newtonian physics and custom spaceship construction. Uses whimiscal creatures as stand-ins for the actual astronauts and scientists who brought the world space flight, but otherwise is fairly accurate Link  
  Lunar Flight Space flight Windows
macOS
A modern take on the classic arcade game, Lunar Lander, Lunar Flight extends the experience to a fully fictionalized and accessible lunar module simulator. Link  
  Moonbase Alpha Space flight Windows AEIOU. Play as an astronaut on a moon base in this NASA sponsored game. Make the station work or just dick around with the text-to-speech funtion in the chat. Link  
  Orbiter: Space Flight Simulator Space flight Windows Fed up with space games that insult your intelligence and violate every law of physics? Orbiter is a simulator that gives you an idea what space flight really feels like - today and in the not so distant future. And best of all: you can download it for free!

(Not to be confused with the similarly named Orbiter: Space Shuttle Simulation for 80s computers.)

Link  
  Pioneer Space flight
Trade
Windows
Linux
Pioneer is a space adventure game set in our galaxy at the turn of the 33rd century. The game is open-ended, and you are free to eke out whatever kind of space-faring existence you can think of. Explore and trade between millions of star systems. Turn to a life of crime as a pirate, smuggler or bounty hunter. Travel through vast territories of various factions, experience beautiful scenery, be the first to witness foreign stars being eclipsed by alien worlds. The universe is whatever you make of it. Link  
  Spacechem Chemistry
Engineering
Windows
Linux
macOS
A puzzle game that tests and teaches basic concepts of computer engineering. Link  
  SpaceEngine Space flight Windows A space exploration game where one can explore the entire Virgo supercluster. Link  
  Space Station 13 Space flight Windows Space Station 13 is a community developed, multiplayer round-based role playing game, where players assume the role of a crewmember on a space station. Together they must keep the station running smoothly, whilst dealing with antagonistic forces who threaten to sabotage the mission. Link  
  The Powder Toy Physics Windows
Linux
macOS
Gives the user a big toybox of elements and lets him play with them as he wishes. Link  
  wxSand
(aka Owen Piette’s Falling Sand Game)
Physics Windows Sand. Link