1: I'm gonna say since they were on that Honey Moon after Christmas Carol.
1a: Known? I think he only knew for sure sometime towards the end of The Almost People. Suspected something was up, since he first got the old Schroedinger's pregnancy result from the TARDIS. He's been niggling away at that (and the whole "what are Amy and Rory hiding from me with those whispered conversations with River") since he first saw it. You don't drop mysteries like that in front of any of the Doctors and not have him work at them.
1) Exactly how long has Amy had a Ganger? Either since the white house bathroom incident or the three month gap in Day of the Moon but definitely before The Silence took her in the orphanage
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The switch probably happened either after the Doctor left her and Rory on Earth pre-Impossible Astronaut or during the three-month trip around America.
1a) How long has the Doctor known that this was Amy's Ganger, not her?
Who knows? I haven't been able to rewatch any of this season, but there's plenty of time in between episodes for him to put the pieces together.
2) Do we think the Doctor's Ganger survived the explosion?
No. But apparently the Flesh might be able to store his memories - except that the Flesh vat in the factory would have blown up, so maybe all Flesh everywhere had the same memories?
3) Do we know anything about The Flesh before Series 6?
No. Just because they used the same word in New Earth doesn't mean they're the same thing (it would be really stupid if they were using Gangers, because they'd want medical results replicable for any human, not just Flesh-built clones of specific patients).
3a) Is there a possible connection to "Flesh and Stone" from Series 5?
( ... )
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1a: Known? I think he only knew for sure sometime towards the end of The Almost People. Suspected something was up, since he first got the old Schroedinger's pregnancy result from the TARDIS. He's been niggling away at that (and the whole "what are Amy and Rory hiding from me with those whispered conversations with River") since he first saw it. You don't drop mysteries like that in front of any of the Doctors and not have him work at them.
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Also, the "Put some trousers on, Pond," throw-away punchline seems to have been taken very literally by Amy.
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The switch probably happened either after the Doctor left her and Rory on Earth pre-Impossible Astronaut or during the three-month trip around America.
1a) How long has the Doctor known that this was Amy's Ganger, not her?
Who knows? I haven't been able to rewatch any of this season, but there's plenty of time in between episodes for him to put the pieces together.
2) Do we think the Doctor's Ganger survived the explosion?
No. But apparently the Flesh might be able to store his memories - except that the Flesh vat in the factory would have blown up, so maybe all Flesh everywhere had the same memories?
3) Do we know anything about The Flesh before Series 6?
No. Just because they used the same word in New Earth doesn't mean they're the same thing (it would be really stupid if they were using Gangers, because they'd want medical results replicable for any human, not just Flesh-built clones of specific patients).
3a) Is there a possible connection to "Flesh and Stone" from Series 5? ( ... )
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