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In the Assassin's Creed series of games, protagonist Desmond enters a machine called the Animus, letting him view the lives of his Assassin ancestors. But how, exactly, is Desmond interacting with these lives?

It could be that Desmond has full and total control over, say, Altair, but if so, what if he does something Altair did not do, which would tamper with history (even if it was breathe at a time Altair did not)? A main element in AC is achieving full synchronization with the ancestor, and this would be near impossible if Desmond was in full control, as he would not know how exactly Altair did anything.

Or, it could be that Desmond is simply viewing Altair's life through his eyes. This would explain why he gets full synchronization, but if Desmond did nothing, there would be no need to. However, this would also explain how Desmond learned his free-running moves, as shown in II and Brotherhood.

Which is it? Or is it something different entirely?

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The short version from the wiki:

The corporation Abstergo Industries developed the Animus virtual machine explicitly to decode and render such memories in a three-dimensional feed, allowing the reliving of past events and the discovery of hidden information.

Basically the Animus is a massive VR engine with the notable ability to construct "levels" out of genetic memory. Desmond is reliving the memories of his ancestors. He's in full control of how is reliving them however, meaning he doesn't have to stick to the script. He is effectively having a lucid dream.

He can run around and slaughter a bunch of innocent people if he wants. He has that much control. He's not really altering history, because it is all in his head. However, the Animus can tell he is out of synch with Altair's memory and eventually he'll get kicked out. The Animus can't reveal what the memory is until Desmond relives it - but it can tell how close to the original he is playing it out. By playing it out closely, he achieves a higher synchronicity and the Animus operates with higher efficiency.

So the Animus can construct the backdrop for the memory, but without a subject following through the memory - one can't ascertain the important bits (like locations of certain artifacts). Basically it can provide the tape, but Desmond has to play through it to hear the song. If he gets too off key, the Animus has difficulty creating the level.

Note that the construct the Animus provides is not entirely authentic. This explains the HUD, the cryptograms, etc. Also remember that it can provide scenarios not based directly from memory like the training rooms, Animus Island, etc.

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    Awesome! Completely cleared that up for me, thanks. – PartyKingThrandeezy Jun 21 '14 at 21:44
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The Animus relies on the idea of Lamarckism, which was a theory proposed by Jean-Baptiste Lamarck (1744–1829) which stated that an individual's specific experiences & memories could be passed down to its offspring. If the theory were true (it was the popular theory until Darwin came along), then any one individual would retain at the genetic level the memories of every ancestor in their bloodline. This same deus ex machina is used in the Dune series of books, proposing that the Bene Gesserit along with any "pre-born" can access the memories & personalities of all people in their bloodline (give or take).

In both cases, the individual cannot directly access these "genetic memories" without assistance. In the Dune series, one must consume and survive the Water of Life, which then "unlocks" the memories. In the Assassin's Creed universe, it is accomplished via technology... a la the Animus.

I've only played the first two AC games, so I'm not sure if the premise is always the same. In those two, however, the protagonist was specifically sought out because he was a direct descendant of Altair. Therefore the antagonists believed that Altair's secrets were encoded in his DNA. So, to answer your question, the Animus uses an unknown process (chemical? biological?) to unlock Desmond's genetic memories. The Animus also appears to have the ability to "zero in" on a specific ancestor and force the individual to relive that ancestor's memories as if they were their own.

So basically, via the Animus, Desmond is taking a backseat to Altair's original memories, yet it's apparently a much more immersive experience than simply watching a movie. After unlocking the memories, he appears to be retaining some of the memory & skill even once he removes himself from the Animus device. This was actually the original idea behind Lamarckism - that skills & experiences (not to be confused with learned behavior) gained in a creature's lifetime could be passed down to future generations.

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Animus allows people to relive their ancestors lives, to see through their eyes and to think their thoughts. Desmond doesn't really "control" Altaïr, because you -- the player -- do. He is just sort of sitting at the backseat and watching events to unfold. When player screws up (does something irreversible that didn't happen; such as makes Altaïr meet his untimely demise) Desmond and Altaïr just go out of sync and player has to start over.

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Desmond is just reviewing the memories, he isn't actually in control. He isn't being sent back in the past, he is just searching the memories for information.

As for the assassination knowledge he gains, this is actually logical: he is reviewing the training, and the animus creates neural pathways for the skills gained. When he is outside of the animus and wants to free run or is fighting someone he can do everything that Altair could do because the neural pathways were created when he viewed the memories. This is the same reason you can ride a bike after not riding a bike for a decade.

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