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It's instinct, and it controls the deer until the deer's brain has a chance to understand what a car's headlights means to the deer, and what the deer should do about it. Often, the deer doesn't get that time. The environment in which deer evolved did not have cars with headlights. So unless a deer has had a chance to learn about cars with headlights, it goes into the deer brain as "unknown possible danger" (UPD). Before cars, the safest thing any animal could do when faced with a UPD was to freeze. The is because the UPD is likely to be a predator, and predators have trouble seeing still objects while the most dangerous ones (wolves, big cats, bears) react to retreating animals by chasing them. If the UPD turns out to be a non-predator danger (fire, earthquake, falling tree) what's the point of running away until the deer can figure out which way to run? On the other hand, if the UPD turns out not to be dangerous, or another deer that wants to horn in on whatever the deer is eating, why waste energy running and giving up on whatever objective the deer was following. The UPD might even be something the deer wants to scare away--which they deer can do by stamping their front feet at or by charging at a smaller animal.

So evolution programmed in "freeze." when deer, squirrels and even humans are faced with a UPD. When the deer (or squirrel or human) has a chance to figure things out, it can use it's brain to pick an appropriate course of action and override the instinctive behavior. Unfortunately, cars can go faster than deer can figure things out, so freezing isn't always so helpful. Makes the deer seem stupid, huh.

But Deer aren't really that stupid. For example, you could train a deer to run back the way it came every time it sees a car with headlights, just like you can train a child to look both ways before it crosses the street. But who's going to train every deer in the world to do that?

It is also possible that the bright light of headlights momentarily causes a deer to be unable to see. Deers have very poor eyesight compared to humans even under ideal lighting conditions.

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