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- Reed Richards in Fantastic Four does this all of the time.
- This angers Homer of all people in The Simpsons comic edition where Professor Frink uses his latest device to grant Homer increased intelligence. He rails on the impossibility of dinosaurs co-existing and fighting humans while watching a B-Movie, much to Bart's surprise.
- In Challenge Of The Super Friends: The End, Lex Luthor repeatedly underestimates The Benefactor's claims of ruling an entire universe, reasoning that the distances would be just too great. Apparently such claims are true.
- In the final chapter of Yabba Dabba Joes, a paleontologist working on Sue the T-Rex's skull before she goes on display goes into a temporary brain shutdown when he pulls a nine millimeter bullet out of a pockmark on Sue's jaw.
- Ritsuko in Shinji And Warhammer 40 K suffers a serious blow to her sanity after repeatedly witnessing Shinji playing Reality Warper with his AT-field wizardry and psyker abilities without finding ANY scientific explanation for it. She learned to cope via ranting and publishing scientific papers on the latest proof-by-Evangelion that physics don't work; the hate-mail keeps her going.
- In the Anime/Addventure thread "Switching Places/Eva", she has a similar reaction to Ranma. And to his habit (which most of the rest of the cast has picked up) of calling the Angels "kaiju."
- In Harry Potter and the Methods of Rationality, Harry took the revelation of the existence of magic in stride, because once he realised that magic follows certain rules he realised he could apply the scientific method to reconcile it with the known laws of physics. But when he sees Professor McGonagall turn into a housecat, which starts by breaking the Law of Conservation of Mass and just goes on from there, he tends to struggle a bit. (Presumably he's never read the Animorphs series, which did eventually get around to addressing the issue.)
- Ellie and Alan's miniature freakout the first time they see a dinosaur in Jurassic Park.
- In The Last Continent, Ponder Stibbons has some difficulty adjusting to the idea that the deserted island he and the rest of Unseen University's senior faculty are trapped on is actively supplying them with the means to live. Further, he's pretty disillusioned to learn that evolution isn't a wonderfully elegant self-driving force, but is driven by an inept god like everything else on the Disc.
- In Ted Chiang's story, Division by Zero, a mathematician tries to commit suicide after she proves that arithmetic is inconsistent and that through formal mathematics, one can make any two numbers equal each other.
- The short story "Flashes" by Robert J. Sawyer is about most of the scientific community of Earth being broken en masse by a broadcast of the Encyclopedia Galactica that claims that aliens have disproved many of Earth's established scientific theories. Why the scientists are not trying to repeat the aliens' experiments is not discussed in the story.
- Jules Verne's Journey to the Center of the Earth pits Crazy Awesome geologist Otto Lidenbrock (who clings to a hollow earth theory) against our narrator, Otto's nephew Axel (who knows that Science Has Marched On and that the Earth is heated from the inside, and thus that the journey makes absolutely no sense and will inevitably end in heat suffocation). Hilarity Ensues when Axel is forced to change his mind.
- This is actually a plot point quite often on Fringe. In a season 3 episode, Walter was confused and upset when the heaviest element was used by another scientist (who stumbled upon it and has no idea why it's doing this either) to make people float in the sky. Yes, it makes no sense. As it turns out, this lapse in the laws of physics is a sign that our universe is about to collide with another one and destroy them both.
- Hunter: The Vigil has Null Mysteriis, an academic organization devoted to the scientific study of supernatural creatures and phenomena, believing that things like vampires, werewolves, and mages all have rational, scientific explanations. Problem is, they live in the World of Darkness. Depending on the GM, either they're correct, and science simply hasn't advanced to the point where study of the supernatural is possible, or they have it all wrong, and the supernatural completely defies all attempts at explanation. Understandably, this tends to drive more than a few Null M. scientists insane.
- One of the planet travel guides in Tyrian reads "Many a scientist comes here after retirement to watch all their fundamental mathematical theorems fall apart as they watch the landmasses floating in apparent defiance to their life's work."
- El Goonish Shive
- A professor who starts crying whenever the laws of physics are violated hard enough. Whether he's actually present or not! The second link provides the alternate trope name (The Professor Is Crying Again).
- There's also a high school physics teacher named "Mr. Bleuel" who gets rather peeved when he spots one of his students floating down the hallway out of habit.
- The Infinite Summation Honeybee Professor in Problem Sleuth gets upset whenever the characters abuse the properties of windows in order to generate matter or discharge energy. Although that's partly because if it's done badly, it results in infinitely massive or infinitely dense objects and nasty things happen.
- In this "Something of that Ilk" comic, one man's refusal to believe in physics, and subsequent flying off, leaves the physics professor utterly speechless.
- Luckily for Dr. Lee in Skin Horse, the ancient, mystic order of notaries has a special couch just for scientists.
- xkcd 298 shows a scientist understandably shocked when Black Hat shoots lightning from his hands and hovers in the air, all while explaining that science doesn't actually work.
- This is what happens in Funny Business when a group of computer scientists learn of Jeanette's godlike powers. Tom is so shaken up by this that he goes on a lengthy rant about how useless his profession is if there exists a being who can ignore the laws of physics at will. It's not exactly "crying in the corner", but the effect is the same.
- In Welcome to Night Vale, poor, perfect Carlos seems to be a victim of this.
- An old Looney Tunes cartoon had a professor giving a lecture where he refuted the existence of UFO's and "Little green men". Just as he's laughing at the very idea, a flying saucer with a baby green Martian flies in and hovers before his face for a few moments, causing the laughter to turn into tears.
- Used twice in The Simpsons, once seriously with the curator for the Jebediah Springfield museum, was so dismayed upon finding evidence that Jebediah was actually a vicious pirate that he stole and hid the evidence to stop others from knowing the truth, and once more amusingly with science-minded Lisa Simpson when she discovered that apparently, rhinos are born from eggs when she sees it happen in Africa.
Lisa: Wait, rhinos aren't born from eggs!Homer: What did you just see, Lisa?Lisa: I know, but-Homer: What did you just see?!
- This actually has happened to a lesser extent with rival theories. One notable example was Fred Hoyle whose steady state theory was discredited once sufficient evidence was more accurately explained by the Big Bang theory. After it was proven, Fred Hoyle still wasn't in favor of it because he saw a universe with a finite beginning as bad due to the fact that it meant that the universe would also have a finite ending. (Admittedly, cosmologists have come to something resembling Hoyle's Steady State for other reasons.)