I think i figured it out... Altair is in Desmonds head. He was able to use the apple to put his consciousness into the bloodline somehow... Maybe manually for the initial transition, to his son or grandson even... Thats how he could have cheated death as mentioned he might be doing in codex page 30. But from there traveled through procreation.. The animus only actually works because of what Altair did... or its a characteristic of the species.. the memories always stay in the DNA but if you choose to use the apple you can upload your consciousness. Minerva knew to talk to Desmond through Ezio. So it may be common knowledge. How she knew who Desmond is... IDK...  If Altair is in Desmonds mind, the bleeding effects are not Desmond being able to access the memories when he wants. but rather Altair showing Desmond the memories he wants him to see.  When he was bleeding he was seeing Altairs memories... and i'm playing the game a second time. with these ideas i got to the first bleeding memory again. I tried to see if there was anything that would support my theory..  and nothing really lol...  except.. and this could be just wishful thinking of me being right. and it would just be some cool trippy effect to enhance the memory. but there is definitely a voice whispering during the whole memory.. and again might be wishful thinking and i heard what i wanted to hear. but i could have sworn at one point it said, "We dont have much time" my girl and daughter both confirmed hearing it too. Maybe you guys can tell me if you hear anything if you play it again... Maybe if he is in his head.. he will be manifesting himself more through Desmond. telling Desmond where the Pieces of eden are. Helping him get them. and telling him where his old armor is stored. maybe even share desmonds body. thats how desmond would become the  "Ultimate assassin" In my opinion Altair is the ultimate assassin and if he had as many lifetimes over again of experience living in the minds of his descendants. He would naturally be.  It really seems to fit into everything if you think about it. Maybe the bad guy in the first game did the same as altair and is in the scientist of the first game, sorry i forget names but,  they both do look alike. maybe he created the animus all together to find altair and find where the apple is. To finish what he started... The ultimate assassin would need an ultimate templar to be an effective enemy hmmm?? But IDK in the end tho i really do hope i'm wrong.. because i do enjoy the games and would like to be surprised!! I still would like to know what you guys think of all this.