Maybe, when you get all the way down to it, the problem I have with the bad history and magical artifacts and all that of a certain genre of adventure is that it is leaving out the good stuff.
This must be kept in mind because it is possible there is no really good reason not to do the kind of fake history a Dan Brown or Indiana Jones story depends on.
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First off, let's look at the Ancient Alien stuff. There's a reason why the candidates for this stuff fall into certain cultural and historical matrices. To be a good Ancient Alien artifact, it should be; 1) Superficially impressive (the Giza pyramid group), 2) The real background should be sufficiently obscure (at least to the average reader or movie-goer; Egyptologists are pretty comfortable on where the Giza group sits within the history and technology of Egypt), 3) Sufficiently exotic (Stonehenge gets a pass, but there is generally less interest in how medieval masons made cathedrals or whatever). And; 4) "Looks" alien. (Which is why the Rapa Nui statues are always showing up in these lists. And, no, they look a lot less menacing and inscrutable when their proper topknots are placed!)
By itself it is fairly insulting to the ancient culture as well as to modern researchers. It only gets really hinkey, though, when you look at it historically. Weird little long-headed alien guys mostly communicate that all of humanity are dullards. The historical theorizing about Great Zimbabwe, the Mound Builders, even the Greek Miracle is very specifically racial, or perhaps more properly nationalistic; "Our" kind of people built these, whether Dorians or Hebrew tribes or Solutreans.
I say it is more nationalist than racial in the context in which these were first proposed. And not at all unknown; there are a dozen different nationalist mythologies tying various civilizations back to Troy. Even England got in on that action.
Today it really does take the flavor of White People. Which is amusing and exasperating to any scholar of the ancient, hell, even the medieval world, as the peculiarities of recent American history create a mapping that had no real parallels earlier.
And lest we think this is an old forgotten history of bad ideas hidden behind the modern bad ideas, sorry, Von Danieken was openly racist, and there is very much a racial flavoring in much of the writing today. And I don't think you escape by recognizing that the outright White Power crowd are relatively small in number; because the much less outspoken biases are much more wide spread.
This is what I mean, specifically; there is direct, quite readable and obvious religious symbolism in King Pakal's coffin lid. Anyone who has studied the culture can recognize the lotus leaves, the Snake of Heaven, etc. The specific gesture by which this academic understanding is tossed aside (if it is considered in the first place) is "who cares what some backwards brown people thought they were painting? It's all primitive nonsense anyhow." (Ah, but aliens...that's a worthwhile discussion.)
And, yes, the bottom line is what is really moving this. Indiana Jones sells movies. Lara Croft sells games. Von Danieken sells books. And even the most die-hard racist web site still wants eyeballs (and maybe Patreon supporters or at least a few t-shirt sales).
Thing is, I can't decouple these in my mind. Sure, the purpose of creating yet another epic in which ignorant present-day people are saved by a (usually white) adventurer from some magical/alien/lost technology artifact the ignorant past people had hidden away in an elaborate booby-trapped temple (breathe!) is to make money. But you are selling poisoned narratives that do get into people's heads. It isn't "just entertainment" when there isn't another channel for facts -- not with the same popularity.
The Mound Builder myth wasn't just a fun tale for the salons. It guided Bloody, Bloody Andrew Jackson (he says so, in his letters) and ends in the Trail of Tears.
Right now Russia and Ukraine are trading historical narratives about how each of them is in the right because of past connections, past promises, past actions. This stuff doesn't just live inside the movie theater; the ideas get outside.
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But that still doesn't answer if changing history for a better story is itself a bad thing. Asked that way, I tend to think it isn't. I'm all up for Abraham Lincoln stalking vampires. I'm all up for steampunk Romans.
Is it bad (or worse) to do this and claim this is the historical truth? That's a little shakier. A lot of people think Braveheart is history. (A lot of people think The DaVinci Code is talking about real history within a clearly fictional adventure). And this is potentially damaging. It sure as hell is insulting.
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One thing that comes into the mix when considering another "Lost Wickett of the Phoenicians" story is the level of detail. Face it, on paper, many adventure stories spend no more than a dozen words scene-setting modern Cairo or an Andean peak or wherever. The meat of the story is on the interchangeable ruffians/cultists/minions who are going to attack the hero next. Any description of the market is just there for color, not to learn about the dye trade.
Hollywood (or a game) gets a little more mileage out of the background of a two-minute chase scene. It can show you details about the people of the market. Are they poor? Dirty? Honest? Friendly? Intelligent? And more importantly, are these just colorful weirdoes for the background or do they share the essential humanity with us, the viewer?
The level of specificity matters here, too. In a lot of stories, "A street in Tokyo" is all you get. So you can very well paint it as clean and prosperous, narrow and threatening, whatever, because all of these can be true if you find the right street.
I tend to fault this both on humanistic grounds and on pure story-telling. Why hand-wave and do another quaint village full of ridiculous accents when thirty seconds on Google would turn up the real details of a real culture which not only has admirers (if not living members) who would be pleased as punch by your interest, but is probably going to be better and more interesting?
I give this advice to beginning fantasy writers on Quora; study history. The real world has created so much incredible stuff already, you can't help but make a better world of your own for being aware of it.
So I could make this a bone of contention but it isn't specific to the question posed. I dislike fiction that has generic towns or colorless dialog or blow-by-blow fight scenes or anything else which is stripped of all nuance and creativity. A book could have a totally original magic system but it could be -- and is, often enough to be disappointing -- shown in such a stripped-down and basic way the reader never gets a sense for what is is, how it works, what it looks and feels like.
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I can say there is one specific kind of bad history that annoys me when I see it in fiction. And that isn't things that are errors in research (well, those are annoying, but not in the same way). Or original mistakes, even. It is when a work repeats some tired old historical myth. It annoys me because this, then, isn't one more random wrong thing that becomes part of the noise floor. It is a specific support, an additional buttress, to an idea that is already out there.
Plus of course, if an idea is coming around that often it probably has some reason outside of the strictly historical for it. That it supports some narrative about how people want to view a different people, for instance. So when we hear the tired one about medieval people only drinking beer, we dislike it because that forms a pattern of seeing medieval life as being soaked in filth and ignorance.
And as I said above; many of these are nationalist or racist narratives. And not just lies about the Other. Every lie we tell about the medieval mind is a way we assure ourselves that we have grown beyond superstition, that we are now living in the best of all possible worlds. (In many ways, we are, but narratives that blind us to the problems and injustice that are still here are not helpful). And, yes, this goes way, way back; when Tacitus wrote about the German tribes, he was really writing about Romans (by contrasting them).
And that is one place where the Indiana Jones story and the Ancient Aliens beliefs combine, because the oft-repeated bad, from aliens building the Giza group to planes vanishing in the Bermuda Triangle, is already bad for lots of reasons but is already being supported and sold to people. Putting a UFO dragging limestone blocks around into a story isn't a neutral position because it doesn't occur in isolation. It becomes implicit support of a whole bunch of bad faith which is already out there.
And these specific bad ideas are so damnably pervasive. Half the juicy hidden histories you can dream up as a writer end up falling into a rathole of Templars or Jews. Pop-culture bogeymen like Rasputin or Tesla get even more attention. It is hard to stay away from these because, well, see above; your audience has heard of them already. It makes your job easier as a writer if you can drop a bit of Nazca Lines or Countess Bathory into the mix.
Hell, it is the same reason why the Usual Suspects keep showing up in historical novels. What's the fun of being in Montmartre in 1890 if you can't bump into a certain short-legged painter, absinthe drinker and rake?
So I am afraid I have no easy answers.
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Right after I wrote the above, I discovered where Bret Devereaux had captured the same idea but, of course, with much more flair:
For a great many people, Westeros will become the face of the European Middle Ages, further reinforcing distorting preconceptions about the period. How we view the past has a tremendous influence on what we think about the present. In particular, the tendency to view the distant past as a time of unrestrained barbarism provides us with both an unearned sense of superiority and often a dangerous hubris – ‘we’re not like that anymore, that can’t happen anymore – people in the past were just stupid.‘