The song have several parts.
first, it's about history, the past (without religion as an excuse/explanation/medecine), that explain why the person is very, very pessimist : it is a scientist, not a dreamer.
second, the present, a pessimist (realistic ?) description of the society, and the idea that it will become worst int he future.
Then, he ask to the markovian process to lead us : he hopes that the future will NOT follow the trajectory of the past (in the markovian process : the past is useless for predictions, only the last state is usefull, here it is the present. he says that we can make a future which will not be the continuity of the past : a positive future. then, this will be a proof even if we are dead, because we would have made it.
(we can think about politicians who prove only short-term promises because they don't care about next generations that will never vote for ... dead people).
This is my interpretation : sorry for my bad english, I will try to translate the song in french.

I'd say the song is about the destruction of the environment by mankind. What led me in that direction was the use of the word landscape, which seems to me to be a symbol of the environment. The phrase "today is a window/tomorrow the landscape" is both a metaphor for the Markovian process itself, and a symbol for the future of the environment.

He then later seems to talk about how environmental degradation will continue. Economic disparities between rich and poor, the common man's helplessness and inability to awaken intellectually, the way the earth is being destroyed, no one is doing enough, and our past actions have already put us on a dangerous course.

He then seems to make a prayer to the Markovian process to hold true in this circumstance, and show our children how we have destroyed the environment, and then let us die.

to me it seems like the first verse basically says: "hey, you may call me pessimist, but if you simply look at the facts we have today and leave your religious bullshit aside (gotta love the saying "they're not religious, they're for everyone") you will see that we have every reason to be pessimistic. In combination with the "today is a window..."-verse it goes quite well with the mathematical use of a markovian process, because these verses tell us to look at the current state to get an idea or even a detailed picture of what's going to happen next.
The third verse and "Markovian process, lead us not in vain" are fitting nicely with the biological term markovian process, even though this is maybe a bit contradictory to the mathematical use, as it means that a lot of things from the past affect our future and not only the current state.

I interpret the last to lines in the same way as susu.exp

To me greg always seemed to think that our past AND our present have a huge influence on our future and that only both together can provide a picture of how human existence will go on, but maybe the mathematical markovian process metaphor is used to show how we are not learning from the past so that only the present is needed to get this outlook into the future?

After reading everyone else's interpretations of this song. It seems to me that this song
is about de-evolution.

A Markovian process is a term from probability theory. It is the subclass of stochastic processes where the probabilities of states at time T only depend on the prior state at T-1 and not on the pathway that lead to it.

"Today is a window,
Tomorrow the landscape.
All you need to do is take a look outside
To know what we're bound to face." refers to this: We do not need to know how things got to the present state to make projections into the future.

The same holds for "Prove to our descendants what we did to them,
Then make us go away." Our descendent will only need to know the state they are in (i.e. what we did to them) and not that we did it (make us go away).

My interpretation of what Greg is trying to say is that the somewhat 'random' path of the Markov Processes have lead up to where we are now, a selfish, capitalist, and environmentally degrative society. Through 'Lead us not in vain' I believe he is trying to say that hopefully, through this infinite time-line, genetics and whatever factors that have brought us from the past to present states, will not repeat, as in history, rather, turning us back a step (in moving forward) to reclaim any responsibilty to the earth and society that we once had. This can also be seen through the line 'scathing trajectory from the past' in that the past with its values and morals and what-not have led us in the wrong direction, a 'scathing trajectory'. Additionally, references to poverty and the distribution of income and the inequalities/inequities of the current world state further highlight the fact that he is probably talking about how a dismal future is coming forth through our current practises....

I think this song is about extrapolation, or, that is, an inference of the unknown based on what's already known.
Greg is urging the listener to not be complacent when it comes to the issues of the day, because, if we do, than we risk losing it all.
He talks about his woldview. How nothing really looks like the hand of God to him, nor anything truly evil, but, rather, it is very bland and "sterile."
When he starts spouting off all these negative characteristics of the world that he can see he tells what is currently going.
"The level of disparity" = the myth of equality
"The manner of destruction of the native land" = Manifest Destiny, or, more currently, how we are sullying the skies, scrapping our forests clean of trees, and dumping toxins into our bodies of water
"The poverty of reprisal from all involved" = correlates to a line from "No Substance": "Forward is the hope; forget recompense."
"And the scathing trajectory from the past" = If you're not informed, we're doomed to make the same mistakes

A Markovian Process is when a species over evolves (such as humans) such that it extends it's natural boundaries. Then when the species dies out, evolution recognizes that as being over evolved and takes the species back an evolutionary step. Much like humans will be, or as individual humans are. Perhaps this is why we can't seem to make any progress. . .

I've read that the Markovian Process allows one to forecast the future based on the present state of things. 'Today is a window/Tomorrow the landscape.' Look at tomorrow through the window of today.

The markovian process is a biological term, meaning that we just didn't appear from nowhere. That we evolved, and from each parent race or whatever. We picked up some of their genes, they were passed through each generation, perhaps in small amounts, but they were still there. This provides less variety, but it follows the 'go with what works' way of thinking. That's my interpretation.

When an species becomes extinct, it's genes are removed from the gene pool. This is what biologists call the 'markovian process'. It's not very often we find Greg referring to himself, but for the first two lines he does. In the first half of the song, I think he is talking about how when he's long gone, there will be no more people that give a damn because people who care are no longer the majority. When the melody changes, he describes the people that will be left. In the last two lines: 'Prove to our descendants what we did to them, then make us go away' he's basically saying 'Hey look at what kind of genes we left for you!'

"I think this song is simply about the fact that human beings historically destroy the environment with no concern on how this could effect their descendents.