If humans were transplanted to a different Earth-like world that they didn't evolve on, how would they deduce how they came about?
I have a world where prehistoric humans were kidnapped and transported to another world. This other world is Earth-like, with mammals (also transported from Earth then later diversifying into other species), as well as some species that evolved on the planet itself. Apes were never transported to this world.
Those beings who transplanted the humans ended up having other concerns and long ago left the world alone. Humans ended up developing technology and science just like we have, and have reached a level of technology similar to our own.
However, their ability to deduce evolution is going to be made harder by the fact that there are so many missing links. Mammals from earth are very different from the native species of the planet they are on, and humans are fairly different from those mammals that were transplanted to the planet. There are also very few mammals, as only those deemed interesting/useful were transplanted, which leaves explaining their origin difficult. How would humans deduce what has happened?
I'm interested actually in two time periods. What would humans at roughly the technology level of Darwin, or slightly after, who didn't have access to carbon dating or as detailed a fossil record deduce, and what would 'modern' humans with better technology deduce?
There are no fossil records of the aliens who transported humans. Furthermore, humans were transplanted at a time of high geological turbulence, which may be used to explain the difficulty of finding fossils from that time.
I know that religion and intelligent design will come up, and likely be even more commonly believed than in our world, but I'm curious what scientists and atheists would deduce from the fossil record.
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(Regardless of what you believe in this Earth...)
You already answered (part of) your question; they'll believe in Intelligent Design¹. Genuine science does not a priori reject extraordinary explanations just because they are extraordinary. True scientists won't reject "IDESOT", especially since it happens to be correct.
What your "athiests" will do is another matter. "Atheism" (both in our world and in your context) is based on the a priori rejection of supernatural causes (which is, by definition, unscientific). Human nature being what it is, you will almost certainly have IDESOT deniers, just like we have crackpots that still insist the Earth is flat rather than (roughly) spherical. As to what they'll offer as an alternative theory... hard to say. We can say, however, that they will find a way to explain away any evidence contrary to their pet theory.
(¹ They might not call it "Intelligent Design", since technically it isn't "design". Maybe something like "Intelligence-Directed Extra-Solar Origination Theory".)
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