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Lateralus is an amazing album. It has many spiritual and deep references in it. I bet most of you never thought Tool’s music was this deep. I will try to analyze the songs and help you to better understand them. These are just my interpretations; so don't take offence if they differ from yours.
It would help greatly to read "Nothing in This Book Is True, But It's Exactly How Things Are" by Bob Frissell. This book is one of the keys to understanding most of Tool's music. Also read into the Tree Of Life or "Qabalah".

Take a good look at your Lateralus cd cover. It really is a spiritual masterpiece. Notice the flaming eyes? These are called Chakaras, energy vortexes on the body. Although Chakras can't be seen by the naked eye. They correspond to your glandular system and in this reality are seen there.
Next is the circle of eyes. I think this is a representation of the "Golden Mean Spiral" aka "The Spiral of love". The Fibonacci Sequence can help you to better understand it and also sacred geometry (see the geometry section).
The vertical tube has many names. I refer to it as the prana channel. Our soul breaths a substance called "prana". A combination of light and love. The Light hits your Chakras like prisms and emanates the energies that corespond to that chakra. He is also glowing. This is a representation of ones aura. The electro magnetic field of the body. It also consists of colors and corresponds to your mood, personality, state of mind etc.
There is also an image that resembles a cross on the backside of the cover. This is called a Dorje. Symbolically a dorje represents the "thunderbolt of enlightenment", that abrupt change in human consciousness which is recognised by all the great religions as a pivotal episode in the lives of mystics and saints. I also find it interesting that on the one before last page there is the word GOD written in the dissected man's brain. Is this a message? Possibly that god is just something we tell ourselves is real to attain a grasp on life, or that god is inside of us all, but we just need to "wake up" and find him/her.

I believe that every song has multiple meanings to it. They are all correct according to ones beliefs, feelings etc... And most importantly because true artists write from their heart. The heart does not lie and will always say what it intends.

The Grudge
A song about letting go of any negative feelings you may have against someone, something, or even yourself. "Forgive us our trespasses, as we forgive those who trespass against us". It's about forgiveness. The only way to truly change something is to understand its nature and tolerate its shortcomings with an open heart.
In reference to Qabalah. "Saturn ascends, choose one or ten. Hang on or be humbled again". "One" in the tree of life represents Keter. Heaven, our father, our spiritual right. "Ten" represents Malkuth. Earth, our mother, our hell. "Saturn" represents Da'at in Qabalah. It is the hidden sephiroth. Da'at represents knowledge. In order to get to this hidden knowledge, one must think with an open mind and heart. God is transmuting new knowledge to us at this time. We are in the Age of Aquarius. So listen up. The song literally means "sink or swim". Every time you act, think, or speak negatively you fall further from heaven and deeper into the dream which is reality.

Eon Blue Apocalypse
An Eon is defined as "An indefinitely long period of time; an age." I think Blue is used as dismal; dreary, like a blue day. We all know what an apocalypse is. So I think the meaning of this track is: A long and boring end. Possibly what our species will face.

The Patient
Be patient in life, for every beginning has an end. A man's unique outlook on life. He wants to have faith but it's hard when you have to go through so much pain here. Yet something inside is telling him to hold on.
The Buddhist religion teaches us that to be freed from the "cycle of life and death" one must attain spiritual enlightenment. Then and only then can one be free. I think the song is a reference to having faith in that. Time means nothing because it doesn't exist. So, Hold on!
Mantra is defined as: "A sacred verbal formula repeated in prayer, meditation, or incantation, such as an invocation of a god, a magic spell, or a syllable or portion of scripture containing mystical potentialities. " I think this song sounds like distorted whales. According to Drunvalo, whales are "The most intelligent, advanced, oldest life form on this planet" He also says that "The whales have been on this planet, conscious and alive for 500 million years. They hold the memory of the planet. " So your guess is as good as mine.

1."A separation or division into factions."
2."A formal breach of union within a Christian church."
a."The offense of attempting to produce such a breach."
3."Disunion; discord."

I think schism has something to do with our creation and losing essential communication in a relationship. Maynard says something about a light that fueled our fire. A love that was once there but is now gone. "Doomed to crumble unless we grow, and strengthen our communication." Any of you who have had relationships know how this is. When you lose that essential communication everything just crumbles. In the video you see a man and a woman that may represent Adam and Eve. The man is desensitized to her because she has given him knowledge from the tree. She then is eaten by her guilt in betraying god. They are then cast out of Eden. In the end they "wake up" and realize that they are part of something greater and they then come together as one body, one consciousness. Also, at the end of the video you see a flame that starts as a spiral, this is the spiral of love. (Read more about the Fibonacci sequence.)

Parabol & Parabola
A Parable is a simple story illustrating a moral or religious lesson. I think this song is to tell us that we should enjoy life and live in harmony with one another.
A Parabola is an advanced mathamatical formula: y2 = 2 px
It is a plane curve formed by the intersection of a cone with a plane parallel to a straight line on the slanting surface of the cone.
"Remember, we are eternal. All this pain is an illusion". Once again a reference to reanimation into this world. Your body is just an instrument in which god works his magic upon this reality. The body means very little and a whole lot. It is the intermediary to this world and the worlds above and below it. We are light weavers. We are creaters of other worlds.
The mathamatical term Parabola to me is how this universe is able to exist and thus this reality. we are everything and we are nothing.

Ticks & Leaches
This song is unlike the rest of the album. It is one of Maynard's hardest performances ever. I think this song is about the kind of people who feed off of others.
Vampires do exist. yes, Spiritual vampires. The kind of people who feed off of your being. When you are around these people you often feel drained.

The term "Lateralus" to me means upward movement. Be it thinking, acting, feeling.
I think it's about realizing that the meaning of life is much more that you can imagine. There are infinite possibilities. "to bathe in the fountain, to swing on the spiral of our divinity and still be a human." I think that verse means that he is longing to be eternal and know all while he is human. The only way that can be obtained is to leg go of everything materialistic and know that you are a being of light and love.
Spirals are commonly found in nature. Galaxies, shells, plant growth, and yes, even human growth. Right down to our DNA structure.
The Axiom "As above, so below". The microcosm and the macrocosm. If you want to know anthing about the universe, yourself, plants, animals etc. All you have to do is look around you. Everything on this earth is a mirror image of the universe. I'll prove it.
Why are the planets here? Look down into Atomic structure. Notice any correlation. Ah, Yes something in the center (sun):(nucleus) (planets):(electrons) all down to the freakin magnetic fields of the planets have to do with this. It has been proven that Atoms are just a vibration of positive and negative charged particles. The subatomic particles are us and every living thing that creates energies. We are inside of another life form.

Disposition defined is "One's usual mood; temperament". In this case a saddning mood.
He wants to see proof that god exists so he is praying for the divine spirit to show him proof.

A song telling us how we are wasting our lives just admiring ourselves.
What we term "ourselves" is only a minute portion of what we really are. "And you will come to find that we are all one mind. Capable of all that's imagined and all conceivable. So let the light touch you so that the words spill through."
The light he is speaking of "the endless sheen" is the light that animates everything in existance. The white light that is encoded with the very fabric of our existance. You know that thing called the rainbow? Yeah, the light spectrum: Violet, Indego, Blue, Green, Yellow, Orange, Red. Everything that we can see with our eyes is encoded with this spectrum. The things we can't see in the spectrum are Ultraviolet rays, x-rays, Infared rays etc. Its the sprial that passes through us and connects us to everything.

Triad: "A group of three"
The Tree of Life comes in again. When two aspects of the Tree of Life come together to form one aspect. They are called Triads and represent you and every level of your existance.
I would have to write a book for you to explain exactly how. So, go and find a nice book on The tree of life or visit the Tree of life section of this site.

Faaip De Oiad (The Voice Of God)
It's pretty easy. It's about the aliens "Greys". They are interdimensional beings and they want to know what keeps us alive. It's because we can love and the ability is within us all to move up and take our rightful place in the universe.