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How could one distinguish a naturally evolved biosphere from one which has been manipulated in a subtle manner? Think slight genetic tweaks, targeted extinction events and so on. The process might have continued for hundreds of millions of years.

Assume that we know that one of several biospheres has been manipulated, but we need to find out which one. How could one tell, especially given that the creators tried to hide their work.

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    $\begingroup$ Hmm.. "Think slight genetic tweaks, targeted extinction events and so on. " please focus on one tampering measure.. The "and so on" part makes this very open end.. you could imagine any type of tampering involving a biosphere and show how that could be discovered afterward. Anything goes. $\endgroup$
    – Goodies
    May 21 at 10:21
  • $\begingroup$ Every event will have a different impact, meaning asking for any (and so every) of them will lead to very generic answers. Not sure any will suits you :/. Perhaps you're not sure what this tampering is yet perhaps. If this is the case, can it be interesting to work this first? $\endgroup$
    – Tortliena
    May 22 at 9:49

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You will end up finding species which have no reason to be there if one would follow only the historical evolution of the biosphere.

For example pigs or goats present on the atolls in the Pacific ocean: their ancestors evolved far from those places and there has never been contiguity with a continent to justify their presence on those remote islands. Therefore the only logical conclusion is that somebody must have brought and left them there.

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    $\begingroup$ Real historical examples: the sweet potato, an American plant, happily growing on tthe Pacific islands when the Europeans got around to discover them, clearly indicates that some people, at some time in the pre-European times, did somehow manage to cross the ocean; and similarly for the Asian chicken being part of the Inca menu. $\endgroup$
    – AlexP
    May 21 at 12:45
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Look for the same patterns of workmanship in the genome of different species. If the same genetic engineer manipulated different species, the genetic engineer might have done it the same way.

Say that the the extinct species S1 branched into the still existing species S2.0 and S3.0. By definition, S2.0 and S3.0 don't have fertile offsping, or they would not be different species. Now say that S2.0 develops into S2.1 and S3.0 develops into S3.1.

If the same, rather lengthy DNA sequence appears in S2.1 and S3.1, but not S2.0 and S3.0, scientists might wonder. Can viral transmission be excluded? Are S2.0 and S3.0 really not interfertile? Could it be convergent evolution?

And if the same pattern appears in even more species, again without being in the common ancestor, those other explanations become less plausible. It would also help if the investigators know many planets, so they can tell how common such similarities are.

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    $\begingroup$ I like this. The traces of the sorts of GMO tools used would show up in various species. Spymasters and schemers can fret about covering tracks but technicians like methods that reliably work above all else, and if they can hide their tracks from their own spymasters and schemers that is good enough. Technicians who come later may be more perceptive. $\endgroup$
    – Willk
    May 21 at 18:37
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Trace amounts of XXX

Subtle genetic manipulations can be detected by scanning for substances that do not otherwise occur on the planet.

For example gold molecules or new isotopes of carbon that occur in trace amounts in the animals' biology.

These are leftovers from whatever tools the engineers used to edit the DNA. Or whatever weapons they used to kill off unwanted species.

This way we can detect their meddling without saying exactly what modifications they made. That is much harder.

These markers would be invisible unless you can scan for life forms from the bridge of the USS Enterprise.

enter image description here

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    $\begingroup$ This could be used to identify migrated individuals, but how what if this was generations past? $\endgroup$
    – o.m.
    May 21 at 10:55
  • $\begingroup$ @o.m. The new isotopes or molecules are passed down the generations. $\endgroup$
    – Daron
    May 21 at 11:02
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    $\begingroup$ The genetic blueprint is passed down, but the atoms would mix with the rest of the ecosphere when the first generation dies. The second generation is made of atoms that are locally available. Yes, a few atoms might come from deceased immigrant individuals, but most is local. That's used when archaeologists analyze the isotopes in the teeth of a skeleton. $\endgroup$
    – o.m.
    May 21 at 11:27
  • $\begingroup$ @o.m. How would we overcome your proposed problem? $\endgroup$
    – Daron
    May 21 at 11:43
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    $\begingroup$ Difficult. Isotope ratios are good to spot individual immigrants. Check a real lot of fossils and find a few that differ? But that would always be 'ahh, that one sample must have been contaminated.' $\endgroup$
    – o.m.
    May 21 at 11:54

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