I'll put this in spoiler tags just in case anybody is worried about being spoiled about Abstergo's events throughout history. This info is revealed in the puzzle for Cluster 8.
Now perhaps I'm remembering incorrectly, but didn't Lucy say (in AC1) to Desmond that she designed the animus? And then in AC2, I could have sworn that it was mentioned that Baby ( Animus 2.0 ) was based on Lucy's design but upgraded.
Am I remembering this incorrectly? If not, they're retconning their own history. There's no way Lucy could have designed the animus prior to 1985 (that's probably around the time she was born).
Given our still-limited knowledge of the intricacies of DNA today and how much computer technology has advanced over the last 25 years, it's pretty silly to think that there could have been any kind of animus back in the early 80's. Using an apple to gain the knowledge to design an animus is one of those chicken/egg situations; if they had an apple and knew at the time what the best use for it was, they would have just asked the apple to show them where the other apples and PoE's were rather than designing a much more convoluted way of gathering the same information.
An apple being what gave the Templars the knowledge to design the animus is a pretty lame idea IMO. I really hope that's not what the writers are implying...
Anyways, I digress. Did Lucy not say that she designed the animus in AC1?
I don't really remember anything said about Lucy designing the Animus. Maybe she said she had installed it or something similar which would explain her extensive knowledge of the machine and the other hardware around, and as well, the animus shown is technically the Animus 1.28. Maybe Lucy made a hardware update to it on the events leading to AC1.
As to the Apple of Eden, did it said what number it was? Maybe it was the one destroyed in Denver, but maybe that doesn't change anything.
The most accurate thing Lucy EVER said was that she did research on the Animus Project. I don't think she said she designed it from scratch. After Vidic saved her, she was pretty much forced to do research. At the time, they didn't know she was an Assassin.