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  • In Chapter 53 of Assassination Classroom, the English "monster" is covered with the words of the actual text of the question it represents, and the students' attacks leave an imprint in the form of their answers. Not only are the questions and answers written in perfectly grammatical English and Japanese, they match the explanation given for the reason behind their difference in effectiveness: Seo's answer is written in the sort of formal language you would expect to see on a test, while the question and Rio's answer are in Holden Caulfield's informal, slightly dated narration style.
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  • Billy Bat is chock full of references to American, animation and film culture and history. So are 20th Century Boys and Master Keaton. Perhaps historical references are Urasawa Naoki's Author Appeal.
  • The opening of The Melancholy of Haruhi Suzumiya depicts positronium, Lambda baryons, a benzene ring, cyclohexanes, an infinite number, the Titius-Bode law, Planck's constant, the Drake equation, the time-dependent Schrödinger equation, Hubble's law, an infinite product, the definition of information entropy, several large numbers, the time-independent Schrödinger equation, the theory of relativity, some probability axioms, the definition of Laplace operator, the wave equation in one space dimension, and several small numbers. In case you haven't noticed, the author likes math.
    • The Second Season (kind of...) continues this tradition, with Millennium Prize Problems, photons, quarks, electrons, tau neutrinos, gluons, M-theory, supersymmetric GUT, Tsuchinoko, and oddly enough some Nietzsche (Gott ist tot, ha-ah).
    • The books are even worse. In addition to the advanced mathematics and science references mentioned above, Kyon's narrative contains allusions to obscure science fiction novels, classical mythology, medieval Japanese history, and other highly esoteric topics. Also doubles as making him come across as, contrarily enough, a Book Dumb First-Person Smartass.
    • The later novels and the incredibly complicated Time Travel plot take the advanced mathematics from "Extra Credit" to "Required Courses".
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    • In the Deep-Immersion Gaming episode, Kyon makes reference to the philosopher Lacan when musing about being special because he's a completely normal person who's been able to cope with some pretty odd things.
    • Aside from the confusingly vast amount of scientific and mathemathic references, there are also a few philosophical and mythological ones. In the earlier parts, Kyon compares his life to Sisyphus' task in such a way that evokes Albert Camus.
    • In later novels, we see Sasaki, who talks about quantum physics with Kyon in middle school.
    • In The Day of Sagittarius, Nagato is seen to be wielding syntactically correct C Language and Windows command line arguments.note 
    • Nagato Yuki's alien incantations are shown in the anime as seemingly random high-speed gibberish. In the first light novel, during her confrontation with Asakura Ryoko, it's SQL code. And if you slow down the corresponding clip from the anime and play it in reverse, it is, in fact, SQL code (although, between the audio quality and the voice actor's accent, it's just barely identifiable as such).
  • Hunter × Hunter often contains very minor and obscure details that can actually completely change the perception one has of a character or event if one does get the reference. The most notable case is a dialogue scene in issue 10, chapter 84, between Feitan and Shalnark, where an attentive reader will notice that Feitan is reading a book from Trevor Brown, a Real Life, underground illustrator who specialized in such family friendly subjects as bondage, rape, torture, dismemberment, and pedophilia, all of this with a voluntarily uncanny style of drawing (his characters often look like puppets). So not only is Feitan a Psycho for Hire who completely lacks any kind of patience and uses torture on a regular basis, but he is also apparently a sick and sadistic pervert.
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    • The Chimera Ants' Royal Guards—Neferpitou, Shaiapouf, and Menthuthuyoupi—have some of the most obscure Theme Naming in fiction: The first half of their names are lesser-known Egyptian gods (Nefertem, Shai, and Montu), and the second half are characters from the French children's book series Caroline et ses Amis (Pitou, Pouf, and Youpi).
  • There are quite a few Genius Bonuses in Neon Genesis Evangelion. Some of these are just naming choices that require knowledge of biology to recognize but aren't overly meaningful or important, such as Central Dogma, the most important part of Nerv HQ, which is named after the central dogma in molecular biology, which deals with the way that DNA forms cellsnote  ,and the Pribnow Box, a testing facility in Nerv HQ named another after another concept in molecular biology that is part of the central dogma.
    • Some are more meaningful. The show contains many philosophical, mythological, psychological, and even political allusions, shout-outs to works of film, music and literature, and of course the famous obscure religious references that may or may not have a real symbolic deep meaning. Some scenes and episode names are incredibly confusing without, for example, knowledge of Freudian Pyschology, or Kabbalism.
    • All the angels' names come from Kabbalistic Mythology, and their names, which are only listed once in-show and which they are never referred to with in their debut episodes, tend to relate to their nature. For example, Israfel is the Angel of Music, and is defeated by Shinji and Asuka using a choreographed dance routine set to music in order to battle its two halves. Zeruel is the Angel of Might, the most physically powerful angel to appear, who breaches eighteen protective layers with a single shot and makes short work of every Eva sent against it until Unit-01 goes berserk and devours it. Its name also literally means 'Arm of God', and it uses its razor-sharp arms as one of its primary weapons.
  • In the Kingdom Hearts manga adaptation of Chain of Memories, the female Nobody Larxene is seen in a library reading a book about the infamous French writer Marquis De Sade, the namesake of sadism, which is clearly related to her sadistic nature.
  • Lucky Star likes to hang lampshades on this trope, mainly in regards to otaku culture, which most of the characters don't get, but the minority understand all too well (* cough* Konata * cough* ).
  • Fullmetal Alchemist uses a large amount of alchemic symbolism with decent accuracy, for anyone who has ever studied that period of Western history in which alchemy was a legitimate form of science/mysticism. Accurate symbols for aspects of each element, the 'elements' known at the time (Edward in particular refers to Saltpetre and Ammonia in his list of the elements making up a human, compounds which were thought to be elements at the time) the 12 processes of alchemy, and various alchemic artworks. In particular, each alchemist's Gate of Truth has a different piece of real-life alchemic art on it, which can be related to aspects of their personality.
    • Large portions of random English seen in various books in the first anime are copypasted from third edition Dungeons & Dragons books (or online reviews of the same). The selection is completely meaningless, however, so its appropriateness to this trope is debatable.
    • Another surprising thing is OST in Russian. There is a song performed by boys chorus in a second episode of first FMA series which has meaningful text and perfect language.
    • Also, a joke for those who know Chinese - Ran Fan enjoys using explosives. "ran fang" is Chinese for "to light/set off (as firecrackers)". Technically, the actual pinyin is "Luan 4 fang4" which sounds similar, and it means "to randomly set off".
    • One combined with a Woolseyism: The English term for Xingese Alchemy is Alkahestry, which is named for a substance called the Alkahest, that was supposedly discovered by Paracelsus. Paracelsus' real name was Von Hohenheim, and in the series, Von Hohenheim is the inventor of Alkhahestry.
  • Black Lagoon:
    • The series includes loads of these. To name a few, several European/Asian dialects are used (from Russian to Romanian), quite a few old movie references are made ("This looks like a remake of the movie "The Last Command") as well as several obscure gun comments ("I mean he's Jewish, right? Of course he'd have an Israeli-made gun!"). References to various philosophers and their view on consequence ethics, like Kierkegaard and Sartre, are made by several of the characters.
  • When Minatsu teaches math in Seitokai no Ichizon, a proof of Euler's identity can be seen on the whiteboard behind her.
  • Mahou Sensei Negima! has tons of these in the Omake in the collected volumes; one needs a decent understanding of physics to understand the explanations of how the spells function. There are also a number of visual Shout Outs to famous architecture, such as the bell tower at Mahora being the bell tower on the Florence Cathedral, and the background of this page contains the Suleymaniye Mosque. It's strikingly realistic when compared to the actual landscape. And the spell incantations actually make a lot of sense if one has a familiarity with ancient Greek, Latin, and Greco-Roman Mythology.
    • Chisame's Deep Immersion Magical Hacker Battle in the Festival Arc displays realistic hacking techniques... visualized in bizarre ways (a SYN flood as a giant swarm of tuna fish, for example). When she incants "spells", she's actually reciting iptable syntax.
  • Yu-Gi-Oh! GX features references to alchemy, tarot cards, and various other subjects.
  • Sayonara, Zetsubou-Sensei ladles these on thick, primarily in the form of random scribbles on the ever-changing blackboard. Topics range from writer/illustrator Edward Gorey to philosophy to prominent (and obscure) works of Japanese and English literature. Even character names are not exempt ("Kafuka", anyone?).
  • On the surface, the concept of Strike Witches is just a shallow excuse for underage Fanservice, with storytelling chock full of Moe cliches. And yet it's littered with references to WWII events, figures, and especially technology down the the obscure, unimplemented aircraft designs. Basically, it inverts Getting Crap Past the Radar.
  • In Toward the Terra, when the first Mu baby is born by sexual reproduction, the mother is given a wreath of pea flowers. Gregor Mendel discovered heritability and genetics of sexual reproduction through his experiments with pollinating pea plants.
  • Poor Eureka Seven. Since the show is a massive sea of pop culture references with Fauxlosophic Narration, its surprisingly well-applied Buddhist elements are written off as equally shallow Faux Symbolism.
  • In Xam'd: Lost Memories, at the the climatic moment of she show (Nakiami reversing the Hiruken emperor's zone of darkness), the animation is a visual depiction of the solution to a (until it was solved) long standing topology problem: how to turn a sphere inside out without making any cusps, tears, or holes. A video of this can be found here: https://www.youtube.com/watch?v=R_w4HYXuo9M.
  • Surprisingly, Princess Tutu is rife with these. Naturally they're all ballet references, but it's still saying something when the translators compiled a list of notable references several pages long and it's likely they missed quite a few.
  • Revolutionary Girl Utena has the student council's speech in the elevator. It sounds like it's just some wordy nonsense, but it's actually a shout out to Herman Hesse's novel, Demian. The rest of the show benefits tremendously from knowledge of fairy tale tropes.
  • Fun game: try to recognize all of the Real Life people/events/spacecraft shown in the Planetes opening.
  • With Tears to Tiara, barring the obvious Arthur, Morgan, and Gaius, a lot of names and characters harken back to Welsh Mythology like Arawn, Rhiannon, Epona, Annwn, Pwyll, etc. Especially clever is the Sword in the Stone being named 'Durnwyn' rather than the generic Excalibur.
    • Myrddin is more of an Expy of Greek Titan Prometheus and has nothing in common with his Welsh namesake. The villains feel like a Gnostic Demiurge committee, being tasked by an aloof deity to create the world but failing at making it `perfect`... and not happy about it
    • Taliesin is named after a poet who supposedly lived during the time of King Arthur and wrote a bunch of poems about him.
  • Akagi is about a guy who plays mahjong, anyone can watch and enjoy it even if they haven't the slightest clue of how to play mahjong, however the author manages to make the games realistic. The point of view changes from time to time so at one round you can see the main character's tiles and next round you can only see his opponent's tiles. This will obviously mean nothing if you don't know about mahjong and can be easily ignored, but if you learn to play the game even at the most basic level, it instantly becomes way better because you understand what's going on, and you can finally understand why is Washizu in love with his 1-pin.
  • Tlön, Uqbar, Orbis Tertius is both the title of a story, and the incantation that Vamdemon uses to open the gate from the Digital World (where everything is made of computer data) to the Real world. One of the main themes of the story is that ideas (or data) ultimately manifest themselves in the physical world.
  • Heart Catch Pretty Cure is filled with stuff about flowers and just about every episode has Tsubomi (sometimes the other girls pitch in) talking about what their Heart Flower means in The Language of Flowers.
  • Cat Planet Cuties has quite a few references to obscure artistic films only a handful of film students and hardcore film enthusiasts will know.
  • Viewers of Puella Magi Madoka Magica with a knowledge of physics will be amused when they realize that Kyubey is Maxwell's demon. There's also the scene of Madoka's ascension to godhood and her wish being granted. Upon firing straight up to the sky, the pattern that forms for a split second is a map of the trail particles took in a particle accelerator. There's also the the overarching references to Faust, including Madoka's witch form being named Kriemhild Gretchen.
    • Though arguably here the Kriemhild part of the name is much more important being an allusion to Der Ring des Nibelungen by Richard Wagner where Kriemhild after the death of her husband goes insane and in revenge kills everyone ever so slightly involved.
  • A character in Problem Children Are Coming from Another World, Aren't They? is confident about the accuracy of a certain prophecy because it was made by the source of all prophecies: the Demon of Laplace.
  • Berserk has one of these in Meaningful Name form. Cute Witch Schierke may just have a random Germanic sounding name. Nope. Schierke is a mountain village in Germany right next to the Brocken - the mountain of witches.
  • The beginning of Galilei Donna shows workers harvesting methane hydrates, a real potential future energy source that Japan plans to begin mining a few years after the show's air date.
  • Code Geass usually gets its chess wrong, by using the game as a metaphor rather than caring about its strict regulations. The first episode demonstrates this with the line "If a king doesn't lead, how can he expect his subordinates to follow?" Good leadership, indeed, but terrible chess. Usually. But in the game featured in the first episode, the fastest win is in fact with the king, which forces mate in three more moves.
  • Fairy Tail: "Ankhseram" is actually a combination of two words. An Ankh is an ancient Egyptian symbol that, even today, represents life, or the creation of life. 'Seram' is the Malay/Indonesian word for 'horror.' It's the true name of Zeref's Death Magic, only it's not magic, but a Curse.
  • Dennou Coil has one right in the title- Dennou is the archaic Japanese term for Computer that has long fallen out of use. It literally means "electronic brain".
  • "Ame Ga Furu", a The Seven Deadly Sins theme song, mentions sleeves repeatedly drenched by rain. This is a reference to one of the oldest clichés in Japanese poetry- the image of lovers' tears drenching their sleeves as they part. And guess who's onscreen while the lyric is playing...
  • In Attack on Titan, while the soldiers are taking refuge in Castle Utgard, Ymir rummages through some boxes for food and finds a can of herring, declaring that it'll do despite not being her favorite. Reiner in turn asks if there's any more in there. Viewers with an understanding of Ichthyology will pick up on the fact that commercial herring are almost exclusive to ocean-dwelling species. Not only was this an incredibly subtle hint that both Ymir and Reiner are not from the Walls, but it also heavily foreshadowed a significant human presence beyond the Walls long before it was officially revealed.

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