"chaos is the score upon which reality is written" is an exact line from Henry Millers book, the tropic of cancer-1st chapter

This is a song about nihilism, disorder. We're all just made up of chemicals that keep us going til we die, who gives a shit about anything, none of it matters.

I believe they are taking that science a bit further and discussing more philosophical topics with it. I believe that line you mentioned earlier is trying to say that if what we know as 'real' or 'reality', is only based on our consciousness (electric reactions through the synapses in the body), then how do we know what we really are or where we are for that matter.

I believe this song is, at least partially, about evolution and the amazing yet very temporary coalescence of matter into a complex organism like a human being.

"Life is the sieve through which my anarchy strains, resolving itself into works." - He's saying that life represents a temporary change in the (apparently) inherent disorder of matter and energy; life is the process through which disorder (anarchy) is changed (resolved) into order (works).

"Chaos is the score upon which reality is written, the timeless, swirling, gyroscopic horde." - This is basically reiterating the message in the first line. Chaos is the original state of all things, but reality as we understand it involves order - so this order (reality) has to have developed (written) from disorder (chaos). The super particle that exploded in the Big Bang to create the universe as we know it could be thought of, from one point of view, as "a timeless, swirling, gyroscopic horde."

"Delirium of disorder" - I think Brett is just emphasizing how thinking about this concept can make you delirious.

"I am just an atom in an ectoplasmic sea without direction or a reason to exist." - The ectoplasmic sea is another name for what has been called the 'primordial soup'; basically it's the scum of increasingly complex molecules arranging themselves into stable patterns over hundreds of millions of years. An atom in this sea would not be a part of anything living (at least not living in the way we traditionally understand it) and therefore has no "direction or a reason to exist." I think Brett is just using the prebiotic atom as an analogy for his mental state - a feeling of purposelessness, loneliness, or apathy.

"The anechoic nebula rotating in my brain is persuading me contritely to persist." - Anechoic means without echoes; recording studios are usually anechoic chambers - they have foam padding on the walls to absorb sound. An "anechoic nebula rotating in my brain" might be a reference to an altered state caused by recreational drug use, although I am only speculating. It's well known that Brett had some addiction problems but I don't know whether they had begun by the time this song was written - it was released in 1988.

"Persuading me contritely to persist" means that he is going through the motions of his routine in life (persisting) motivated primarily by a sense of guilt or remorse (persuading me contritely).

All considered, I think the song is a very dark expression of existential angst that uses biopoeisis (the generation of organic, self-replicating molecules from inorganic molecules) as a metaphor for an emotional condition. I like to think there is also some hope in this song, because if the metaphor is extended, you can see that the disorder will not continue forever - even if it takes hundreds of millions of years, evolution by natural selection can eventually lead to astounding complexity. So, there may be something to look forward to after all.

I've always thought that this song is basically saying that 'consciousness' as we know it is little more than an extremely complex series of cause and effect events. "I am just an animated ectoplasmic sea without direction or a reason to exist." Ectoplasm is the dense outer layer of the cytoplasm in cells. I think this says that our actions, thoughts, and perhaps even our very sentience is just the product of the complex (but on the whole mechanic) interaction of our cells with each other and the world around us. A disconcerting thought to say the least.