The Cerberus Theory

• Cerberus may have been partially designed as a weapon. Either as a side project as Hanso may have continued his weapons research partially to fund his Dharma project. Part of cerberus' design may have been that it could have uploaded itself with genetic code and/or memories from various species that would enhance it's function as a weapon. This would likely include Polar Bears and Sharks as they are such skilled hunters (this could also explain why the Polar Bears were required to adapt to the local conditions first).
  
  
• Following on from the above, there are two questions. Firstly was the project outside of the DI or was there a need for such a destructive thing inside the DI? If it was part of the DI then the answer to that could be that there was a need to eliminate life forms with a specific DNA component, like in Mittlewerks plan to eliminate 30% of the population. If the "Others" were in the target group perhaps these measures were taken because they refused to leave the island and turned hostile to the DI. Perhaps Cerberus was actually dormant and shut off until the Purge of the Others of failed and the DI activated it, with a new mission, before abandoning the island (save, perhaps for the Swan station).
  
  
• The second question is what went wrong? To me that seems likely to be part of the absorption process. If what Rousseau suggested about a virus turning people crazy is true then Cerberus may simply have caught this sickness or absorbed it from someone. Alternatively it may have simply absorbed too much. If Cerberus learned to upload DNA to itself then it may have just started uploading from all kinds of sources (including those paralysing spiders, which would explain why it was around with the swarm, if the first spider put out some kind of "call") and eventually turned generally hostile. Then again if it was a last ditch effort from the DI to stop the Hostiles, perhaps nothing went wrong at all.
  
  
• The Dharma Initiative project is a very volitile one. It requires a lot of logging and something has to store all the data tracking what goes on on the island. What the island really needs is a black box. Perhaps one of Cerberus' roles (or maybe it's main function) was to store information that would otherwise be lost, by scanning and storing the memories and perhaps the DNA of things that have died on the island. Remember that Dharma was very genetic concious, and don't forget that Dr. Mittlewerk wanted "The bodies of the Dead" to be scanned with his project as well.
  
  
• Okay now for some specifics. The smoke monster appeared to take the form of Yemi. But then Yemi was physically on the island. That would explain why Smokey seemed to recognise Eko and perhaps was what that supposed video footage of Eko's life was about. Notice that there seemed to be a flash of Eko in there. If it was Eko's mind being scanned, why would Eko have an image of himself in his own memory? Okay, it could be a mirror, but I don't buy that. More likely those were Yemi's memories.
  
  
• The way it acted toward Eko was like a confused creature and not a simple scanning judgement machine thing. Maybe it was the Yemi part that wanted to communicate with Eko, but another part that wanted to destroy him for not wishing forgiveness.
  
  
• More specifics. Remember how the whispers seemed strangely like they were the voices of people that had died on the island? Perhaps it is because Cerberus had absorbed their DNA and memories. Perhaps Cerberus can only upload from the dead.
  
  
• If Christian Shepard is actually dead, then it could be that Cerberus uploaded from him. Actually in truth I couldn't say if the subject needs to be dead to upload from and if Christian was in a "zombie" state then perhaps that was enough. So this doesn't have a bearing on that argument. But we do know Christian was almost certainly on the island and as such could well have been scanned and so his appearances to Jack was almost certainly Smokey and fits with this theory.
  
  
• Meanwhile there doesn't seem any reason that Sayid's cat or Kates horse would be scanned. This I still believe is a seperate mystery (along with Locke's father).