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In ID4 (Independence Day), there are 3 helicopters sent up to greet the alien craft. One of the copters is fitted with a set of light panels that flash the lights in a specific pattern/sequence. What is the significance of this? Is this something made up for the movie or is the light pattern/sequence meaningful in real life?

I'm looking for an answer on why would they choose to do such a thing and not expect to be received as hostile.

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Two different questions here. "What is the significance of this" It's an attempt to communicate with the aliens, and a homage to Close Encounters of the Third Kind. "Is the light pattern/sequence meaningful in real life?" - good question! Some googling done, but nothing I can quote yet, but looks like made up for movie. – AidanO May 23 '13 at 7:12
up vote 10 down vote accepted

I believe that it was a reference to the movie Close Encounters of the Third Kind. In that film (the scene is on YouTube) humans use a board with flashing lights (similar to the lights on the helicopters) and music to communicate with Aliens.

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I never imagined it to be a Close Encounters reference. I always imagined it was supposed to be the very same unknown government agency in charge of greeting aliens as depicted in Close Encounters. – wallyk May 23 '13 at 3:41

In-universe explanation

This is explained in the film's official novelisation, co-authored by Dean Devlin, ID4's producer.

The flashing lights were supposed to be an attempt to communicate with the aliens and to demonstrate our desire for peaceful co-existence:

The president picked up a remote control and switched on the television. The Apache had just reached the front of the huge spaceship and turned on its light boards. The powerful lights began to flash on and off, creating a repeating sequential pattern. The staff at SETI, alter several hours of furious on-line discussion and a blizzard of foxes, had come up with a simple mathematical progression, a message written in what they hoped would be a universally comprehensible language.

The entire sequence would repeat every three minutes, followed by a display of the word “peace”’ written in ten different earthly languages. It wasn’t much, but it was a beginning.

Out-of-universe explanation

Echoing djmadscribbler's answer, the effect was presumably a riff off the lightboard depicted in Close Encounters, a film that Dean Devlin described, in this interview as being one of his favourites:

Devlin: I don't know what the future holds. My passions have been for mainstream, popcorn movies. That's what I usually go to see on a Friday night. I fell in love with the movies by watching Star Wars, or Jaws, or Close Encounters of the Third Kind. One day, I hope to make a film as great as those.

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