It depends on how empty you mean by empty. In a pure vacuum there’s no sound. Some black holes and star systems have enough gases around them that what might visibly look “empty” between the star and surrounding planets isn’t really empty. There, sound travels out in massive waves. Luckily our solar system lacks enough matter to transmit sound from our sun to our planet because it would be really frickin loud all the time if it did. Also, gravitational waves expand and compress space (and the matter within it) not too dissimilar from how sound travels through matter, but unlike audible sound waves, gravitational waves don’t require a physical medium. But this is how we can hear black holes. Also, they travel at the speed of light if I remember correctly.

Don’t forget the little holes on bones where blood vessels attached help us know what kind of blood flow the animal needed to oxygenate its organs. Combine that with what we know of the oxygen levels in its environment and you can accurately guess the mass that was supported along with whether it was endothermic or exothermic (warm or cold blooded). We compare these to bones of existing animals, along with brain size and shape of the inside of a skull to come up with stuff like “Allosaurus ate meat and likely had the metabolism of an ostrich and the hunting and eating behaviors of a crocodile”.

From the article: Fortunately, the AI didn't predict a deadly apocalypse or a robot takeover.

That’s exactly what an apocalyptic murderous AI would say.