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The Islands Dead / Blakob (As there are currently no suggestions!?)
The Whispers are the Island's dead folk (who by 2007 are in their hundreds... Two Plane Crashes... Others... Freighter Folk) that can still exist on the Island due to the intriguing nature of time / electromagnetic properties. Even though they cannot be seen by the living members of the Island, their existence has been possible due to the above. Whoever these 'whisperers' are, they are observing events taking place on the Island - Survivors, Others, Dharma... and since main characters / supporting characters are killed off regularly perhaps their destiny once dead is to do work for The Man in Black / Jacob in manipulating / influencing the decisions each surviving character makes; conversations from whisper transcripts suggest this.
The transcripts suggest that the whisperers discuss the characters as if they are standing watching them. They often try to warn a character, or influence an event. Are these whispers the Man in Black and Jacob playing out their 'destiny' game?
Past and Present
The whispers are simply the past inhabitants of the Island from decades / centuries gone by e.g. The Black Rock Survivors... Dharma... that can sometimes be heard by the current survivors / Island folk and is a result of the end of Season 4 time shift Ben created when he turned the wheel - leaving a perma-electromagnetic anomoly allowing past to bleed in to present.