Humans have polluted the galaxy with their religious nonsense and a quarantine is about to be established. People must decide whether to stay on Earth or in space, forever. The story was mentioned in Free Inquiry in the early 2000s. It's somewhat reminiscent of Lem. Actually, it's fairly humorous, as when one alien enthuses to another that the lights on the ship's console are "miraculously" the right wavelength for them to see. Could it be by George Zebrowski?

  • The first part almost reminds me of Christopher Anvil's novel "Pandora's Planet" - the populated alien worlds the story are very weak to human ideas and persuasive tactics (of all kinds, not just religion), and tend to get caught up in their fanaticism and other nonsense until disaster strikes. There's no quarantine, though, the nonsense is not inherently religious, and also no making people choose earth or space - so not a great match, in the end. – Megha Apr 9 '17 at 5:00

You may be thinking of Tom Flynn's Galactic Rapture. It was released in 2000, during which time Tom Flynn was editor for "Free Inquiry".

Galactic Rapture - Book Cover

If Thomas Pynchon wrote science fiction, "Galactic Rapture" might be the result. Earth in the year 2344 is a small player in a galaxy of some highly advanced planets – and some incredibly backward ones. A breathtakingly wealthy and sophisticated people, the Galactics keep 40,000 of their 42,000 planets in permanent quarantine, or 'Enclave', so their primitive inhabitants can serve as sources of entertainment. Now, called 'Terra', Earth has two lucrative exports: a perversely engaging mass entertainment medium known as 'senso' and Earth religions, of which the jaded Galactics can't get enough. Terra's greatest success story, the Universal (Roman) Catholic Church, has left its birth planet to thrive on one of its own, fittingly called Vatican, where priestly sex abuse and imperial corruption take on astonishing new forms. A theology called 'serial incarnation' teaches that God incarnates his son over and over, sending him to planet after planet. The Church has grown rich from this doctrine by charging huge fees to reveal to individual planets who their Messiah is and whether or not their historic religious leaders are genuine. All is well until celebrated mathematician and recent convert Fram Galbior is overheard telling the pope that his new formula can predict where God will send his son next – an Enclave planet where most Galactics, even those in power, are forbidden. Attention centres on the rumoured new Christ, named Arn Parek, a con-man who becomes hotly sought by the Galactics.

This novel is an iconoclastic, darkly hilarious epic, packed with hypocritical cardinals, scheming Mormons, religious bunco artists, and cynical media manipulators. Called a landmark in the new alternative science fiction, "Galactic Rapture" is an engaging satire on the power of religion, worship, and 'infotainment' in the future.

It had a sequel, Nothing Sacred. According to Wikipedia:

Nothing Sacred (Prometheus Books, 2004) is a sequel to Galactic Rapture set ten years after the conclusion of that novel. It features the Mormon comic villain from the first novel; Gram Enoda, a young Earthman on the make who has accidentally acquired a hugely powerful, self-aware digital assistant, and a darkly charismatic televangelist whose theology is drawn from 19th century German and Russian nihilism who wind up interfering in a top-secret government plan to quite literally save the Galaxy. It was reviewed by Towing Jehovah author James Morrow in "Free Inquiry".

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