Challenging doctrine is always a dangerous proposition. Religious leaders don't especially like to be questioned. Followers are encouraged to blindly accept the teachings of their spiritual mentors and those who would ask questions or propose new theories, new explanations and new ideas are admonished, punished and sometimes killed.
Galileo Galilei challenged the widespread, papal-endorsed theory that we live in an Earth-centric system. He used observational astronomy to write about how, actually, the Earth and its sister planets all revolve around the sun. His ideas (which we're all taught about as second graders now) were revolutionary (excuse the pun) and (according to the church) dangerous. He challenged the status quo. Basically, he kind of made them look bad. One guy came up with a fact that God had apparently neglected to mention to all the other guys in charge. They didn't like this. When Galileo refused to recant his theories, he was sentenced to house arrest where he spent the remainder of his life.
Voyager basically retells Galileo's story. With dinosaurs:
Gegen is a scientist who challenges the doctrine of his people (the Voth) by proposing that they evolved in a distant quadrant of the galaxy (on Earth) rather than in the Delta Quadrant (which they believe they have a pre-destined, God-given claim over) and his ideas get him into serious trouble with the higher-ups. While the Voth hold Voyager hostage in their way bigger, way scarier ship, Chakotay works with Gegan to uphold the scientist's findings.
This episode is awesome. I mean, seriously awesome. Distant Origin is an example of what Star Trek has done (better than just about anyone else) since its inception. It presents a human problem through the lens of science fiction with a familiar and reliable cast of characters to relate the story. We end up spending time with Gegen via Chakotay and it's completely engrossing. Gegen's plight becomes more and more urgent and eventually Chakotay (in a scene that tears my heart right out of my chest) speaks up about the importance of questioning the status quo, pursuing scientific discovery, and fearlessness in the face of change.
From start to finish, Distant Origin is beautifully written, directed and acted. The premise (Dinosaur people evolved on Earth but no one will believe them) seems so silly. But, in practice, I think it's one of the best, most moving, most compelling episodes in all of Trek.