I think the meaning that lies behind the numbers is similar to the theory of Psychohistory that Isaac Asimov came up with in the Foundation series.
Read it if you haven't, but if you haven't, then the basic idea is that if some person or group was to compile literally all social cultural data from the entire course of human history, a distinct pattern would emerge that, given the right amount of skill and insight on the part of the researchers, could be used to predict the most likely course of the future. In the book, the guy who starts this project doesn't even believe it will work, but he is commissioned by the Emporer to complete the research anyway because it is theorized that the kingdom will fall, and the nobility think that by knowing the future, they can change it.
I think the Lost creators are recreating this idea on a non-universal scale to make it easier to understand. So...my theory is this: that the Valenzetti equation was created using the same technique of psychohistory, and that the "powers that be" heard that they could control the future with it. I think the people who made the equation are probably being misrepresented a little, if not a lot, by the way in which their research is coming to fruition.
In other words, I think the only "good and honorable" purposes that may have been there at the beginning of the project have by this point been completely subverted by various individuals and their personal motivations.