There are implications in all the Lost Experience videos that the real subject of the study was the vaccine. There is a reference to "innocent people" being used to test a vaccine who believe they are being innoculated against a disease carried by macaques. There are also several references to the vaccine in the series, and a new shipment of vaccine was included with the food drop.

Participants in the experiment may have been lured to the island for other reasons - for instance, to monitor a "psychological experiment" in the Pearl, or to prevent the electro magnetic pulse in the Swan. They are told that the island jungles breed an infection, and that they must inject themselves regularly with a vaccine to prevent it. There is, of course, no infection, as proven by Desmond's predecessor and by the many inhabitants of the island. So what is the purpose of the vaccine? Could it be part of the Dharma Initiative's quest to lengthen human life and cure war, disease and famine?

In fact, if the island has miraculously cured the various maladies of the crash survivors, and if Hurley isn't losing any weight despite not eating any less than anyone else, is it possible that they've succeeded?

The supposed disease that Desmond is afraid of is one method of controlling the marooned inhabitants - that is, the guinea pigs. The black cloud is another. Hallucinations may similarly be triggered by lacing the subjects' food or water supply, and Locke has discovered how to induce them intentionally. They may also be a method of control, or another experiment. The vaccine, however, seems to be a major focus.

Recent episodes of Lost further this particular theory. The "Others" clearly have contact with the outside world. Ben, however, appears to be the only one who has unmonitored contact, and he is likely a descendent of one of the original scientists. Juliette was invited to the Island on the pretense of being able to perform whatever medical/genetic experiments she desires. The Dharma Initiative is clearly not dead, as Juliette was invited to the island less than four years ago. It is, however, an extremely private organization for obvious reasons, given the highly risky and controversial nature of its experiments and lack of concern for human life. It is the job of the "Others" to manage the inhabitants of the Island, who are not going to be willing visitors and are therefore gathered through the Island's electromagnetic properties.