Question: When the Xenomorph is mere inches from Ripley, how was it able to know there was a queen inside of her?
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Answer: Most likely by smell or other sensory perception. We already know that the aliens inside the hosts adapt and take on DNA and characteristics from them, like most being humanoid from the humans or the one in Alien 3 being more canine since it came from a dog. It's likely that the creatures inside also alter the host's body chemically to better suit their growth in such a short amount of time. This would also be necessary in other situations where the aliens are catching humans or the humans are being exposed to eggs, and the aliens wouldn't kill them or take them again knowing they already have a young one inside them. Now in Alien 3, it's not necessarily the case that the alien knew that it was actually a Queen inside Ripley, but at the very least, it knew one of its own kind was already inside her and knew not to harm her.
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