If the doctor became more ambitious, and decided to replace a species with 
a simulation, we have a ready example of what it might be like. Cars have 
replaced the functionality of horses in human society. They reproduce in a 
different, more centralized way, but otherwise they move around like 
horses, carry people and their possessions like horses, they even evolve 
into new styles over time. 

Notice, however, that despite our occasional use of a name like Pinto or 
Mustang, no horse-like properties have emerged from cars. They do not 
whinny or swat flies. They do not get spooked and send their drivers 
careening off of the road. They did not develop DNA. Certainly a car does 
not perform as many complex computations as a horse, but neither does it 
need to. The function of a horse really doesn't need to be very 
complicated. A Google self-driving car is a better horse for almost all 
practical purposes than a horse.

Maybe the doctor can replace all species with a functional equivalent? We 
could even do without all of the moving around and just keep the cars in 
the factory in which they are built and include a simulation screen on each 
windshield that interacts with Google Maps. With a powerful enough 
artificial intelligence, why not replace function altogether?

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