The Hermetic Museum

The Hermetic Museum 

 

creatio ex deo vs creatio ex nihilo

**Creatio ex Deo vs. Creatio ex Nihilo**

*Creation Out of God's Own Substance vs. Creation From Nothing*

The doctrine of *creatio ex nihilo*, or creation out of nothing, has long dominated Christian theology. It proposes that when God created the heavens and the earth, He did not use any pre-existing material but brought everything into being from non-being—pure nothingness. While this might seem like a theological safeguard of God’s omnipotence and transcendence, it is a position that lacks biblical foundation and philosophical coherence.

The Scriptures are largely silent on *how* God created. They tell us *what* God created—"In the beginning God created the heavens and the earth" (Genesis 1:1), and "By faith we understand that the worlds were prepared by the word of God" (Hebrews 11:3)—but they do not specify the medium or substance through which this act of creation occurred. *Creatio ex nihilo*, then, is not a biblical doctrine, but one constructed later in response to competing cosmologies—particularly Gnostic dualism and various Platonic philosophies. As such, it became a reactionary doctrine rather than one organically derived from revelation.

If not out of nothing, then what? The alternative—often dismissed as heretical—is *creatio ex deo*: creation out of the very being, the corporeal spirit-substance, of God Himself. This does not mean that creation is God, nor that the universe is identical to God (pantheism), but that God emanated the world from His own essence—thus allowing for a distinction between Creator and creation while affirming their ontological connection. This view is better classified as panentheism: all things exist *in* God, though God is not reducible to them.

Scriptural testimony supports this. In Genesis 2:7, we read that “the LORD God formed man of dust from the ground, and breathed into his nostrils the breath of life; and the man became a living being.” The breath of God—the *ruach* or Spirit—is what animated man. This divine breath is not a metaphor for oxygen; it is God’s own emanation. Jesus reenacts this process in John 20:22: “He breathed on them and said, ‘Receive the Holy Spirit.’” This parallel is not coincidental—it is revelatory. The Spirit comes from within God’s own being and enters into humanity.

Further support comes from the Apostle Paul. In Acts 17:28, Paul proclaims, “In him we live and move and have our being,” quoting a Greek poet yet affirming it as true theology. Ephesians 4:6 declares that there is “One God and Father of all who is over all and through all and in all.” Colossians 3:11 states of Christ that he “is all, and in all.” These are not vague spiritual generalities; they are ontological claims. They affirm the immanence of God in creation and creation’s ongoing dependence upon Him.

If *creatio ex deo* is true, it means that creation was not an act of sheer externalization but of internal emanation—God drawing forth from Himself, forming creation out of His own spiritual-corporeal substance. This fits more coherently with how Genesis depicts creation: “God said, ‘Let there be light,’ and there was light.” But what is the word of God? According to John 1:1-3, “In the beginning was the Word, and the Word was with God, and the Word was God… Through him all things were made.” This Word is not some detached command—it is the mind, intention, and substance of God Himself, later “made flesh” in Jesus (John 1:14). The Word, then, is the divine pattern or blueprint emanating from within the being of God.

This concept helps us explain not only spiritual truths but physical ones. The first atoms of creation were not conjured from void, but issued from God’s own spirit-matter, giving rise to all subsequent matter. The Genesis narrative affirms that humanity was formed from *pre-existing* material: “the dust of the ground.” This is not insignificant. It reinforces that mankind is not created *ex nihilo*, but from created elements, which themselves ultimately came from the divine.

Scientifically, we understand that matter cannot be created from nothing. Even the Big Bang theory presupposes an initial singularity—something. The principle of conservation of energy asserts that energy can neither be created nor destroyed; it can only be transformed. If that is the case, and if God is the primal source of all that is, then the universe is a transformation, an emanation of God's own power and being into ordered complexity. The divine substance became the matrix from which time, space, matter, and life emerged.

Colossians 1:17 says of Christ, “He is before all things, and in him all things hold together.” The Word is the binding agent of reality—not just spiritually, but materially. God's presence is what sustains atomic cohesion, gravitational laws, and biological processes. The visible world is a continuous emanation of divine force, a structured outflow of God's own corporeal reality. Creation, then, is not something God *once* did but is something God continually upholds.

To summarize: *creatio ex deo* challenges the abstraction of *creatio ex nihilo* by grounding creation in the corporeal, spirit-substance of God. It finds stronger support in Scripture, aligns more closely with the scientific understanding of matter and energy, and deepens our sense of reverence for the material world—not as a detached other, but as something birthed from within God Himself. This worldview affirms the holiness of creation without collapsing Creator and creation into one and the same. It invites us to see the universe as sacred space—matter suffused with Spirit, atoms born from glory.

Valentinian Cosmology in the Tripartite Tractate

Valentinian Cosmology in the Tripartite Tractate

the Tripartite Tractate Cosmology is very different to other Valentinian documents to have come down to us first there is no doctrine of an emanation of 30 aeons 

there no doctrine of the fall of Sophia instead it is the logos who falls 

The Aeons are emanations of the Divine Mind as well as Divine Beings
(For each of the aeons is a name corresponding to each of the Father's qualities and powers the Tripartite Tractate)

The Tripartite Tractate takes its cosmology from the gospel of John

The Head of Days

He existed before anything other than himself came into being. The Father is a single one, like a number, for he is the first one and the one who is only himself. Yet he is not like a solitary individual. Otherwise, how could he be a father? For whenever there is a "father," the name "son" follows. But the single one, who alone is the Father, is like a root, with tree, branches and fruit. It is said of him that he is a father in the proper sense, since he is inimitable and immutable. Because of this, he is single in the proper sense, and is a god, because no one is a god for him nor is anyone a father to him.

the Father is the Head of Days the head of the body 

Just as the Father exists in the proper sense, the one before whom there was no one else, and the one apart from whom there is no other unbegotten one, so too the Son exists in the proper sense, the one before whom there was no other, and after whom no other son exists. Therefore, he is a firstborn and an only Son, "firstborn" because no one exists before him and "only Son" because no one is after him. Furthermore, he has his fruit, that which is unknowable because of its surpassing greatness. Yet he wanted it to be known, because of the riches of his sweetness. And he revealed the unexplainable power, and he combined with it the great abundance of his generosity.

The son is the mind of the Father 

"Theos was the Logos."

In this text, then, there is ONE DEITY, and he is styled THE LOGOS. This word signifies, "the outward form by which the inward thought is expressed and made known; also, the inward thought or reason itself

No Logos, then there would be no Theos; and without Theos, the Logos could have no existence. This may be illustrated by the relation of reason, or intelligence and speech, to brain, as affirmed in the proposition, No brain, -- no thought, reason, nor intelligence. Call the brain Theos; and thought, reason, and understanding intelligently expressed, Logos; and the relation and dependence of Theos and Logos, in John's use of the terms, may readily be conceived. Brain-flesh is substance, or the hypostasis, that underlies thought; so Theos is substance which constitutes the substratum of Logos. Theos is the substance called Spirit; as it is written, "Theos is Spirit;" and he who uttered these words is declared to be himself both substance and spirit. Dr. John Thomas Eureka Volume 1 Of Deity Before Manifestation in Flesh.

Theos is the Brain, Logos is the Mind or thought

God came forth: the Son, Mind of the All, that is, it is from the Root of the All that even his Thought stems, since he had this one (the Son) in Mind. The Nag Hammadi Library A Valentinian Exposition

The son here is a personification of the mind of God or the Father's first thought. We will look more at personifications later. 

The Cosmology of creation begins and unfolds within the mind of the Father 

But furthermore (he says), "That which came into being in it was Life."[Jn 1:4] Here he discloses a pair. For he says that the entirety came into being through it, but Life is in it. Now, that which came into being in it more intimately belongs to it than what came into being through it: it is joined with it and through it it bears fruit. Indeed, inasmuch as he adds, "and Life was the light of human beings", [Jn 1:4] in speaking of human beings he has now disclosed also the Church by means of a synonym, so that with a single word he might disclose the partnership of the pair. For from the Word and Life, the Human Being and the Church came into being. And he called Life the light of human beings because they are enlightened by her, i.e. formed and made visible. Paul, too, says this: "For anything that becomes visible is light." [Eph 5:13] So since Life made the Human Being and the Church visible and engendered them, she is said to be their light.

the body

The Father

The Tripartite Tractate

This is the nature of the unbegotten one, which does not touch anything else; nor is it joined (to anything) in the manner of something which is limited. Rather, he possesses this constitution, without having a face or a form, things which are understood through perception, whence also comes (the epithet) "the incomprehensible. If he is incomprehensible, then it follows that he is unknowable, that he is the one who is inconceivable by any thought, invisible by any thing, ineffable by any word, untouchable by any hand. He alone is the one who knows himself as he is, along with his form and his greatness and his magnitude. And since he has the ability to conceive of himself, to see himself, to name himself, to comprehend himself, he alone is the one who is his own mind, his own eye, his own mouth, his own form, and he is what he thinks, what he sees, what he speaks, what he grasps, himself, the one who is inconceivable, ineffable, incomprehensible, immutable, while sustaining, joyous, true, delightful, and restful is that which he conceives, that which he sees, that about which he speaks, that which he has as thought. He transcends all wisdom, and is above all intellect, and is above all glory, and is above all beauty, and all sweetness, and all greatness, and any depth and any height.

The Son

the sole first one, the man of the Father, that is, the one whom I call

the form of the formless,

the body of the bodiless,

the face of the invisible,

the word of the unutterable,

the mind of the inconceivable,

the fountain which flowed from him,

the root of those who are planted,

and the god of those who exist,

the light of those whom he illumines,

the love of those whom he loved,

the providence of those for whom he providentially cares,

the wisdom of those whom he made wise,

the power of those to whom he gives power,

the assembly of those whom he assembles to him,

the revelation of the things which are sought after,

the eye of those who see,

the breath of those who breathe,

the life of those who live,

the unity of those who are mixed with the Totalities.

Bodies are not exclusively connected to the material world at the lowest level. The Father and the Son at the uppermost level of depth above the Pleroma can have bodies  

The church

Those which exist have come forth from the Son and the Father like kisses, because of the multitude of some who kiss one another with a good, insatiable thought, the kiss being a unity, although it involves many kisses. This is to say, it is the Church consisting of many men that existed before the aeons, which is called, in the proper sense, "the aeons of the aeons." This is the nature of the holy imperishable spirits, upon which the Son rests, since it is his essence, just as the Father rests upon the Son.

They were forever in thought, for the Father was like a thought and a place for them. When their generations had been established, the one who is completely in control wished to lay hold of and to bring forth that which was deficient in the [...] and he brought forth those [...] him. But since he is as he is, he is a spring, which is not diminished by the water which abundantly flows from it. While they were in the Father's thought, that is, in the hidden depth, the depth knew them, but they were unable to know the depth in which they were; nor was it possible for them to know themselves, nor for them to know anything else. That is, they were with the Father; they did not exist for themselves. Rather, they only had existence in the manner of a seed, so that it has been discovered that they existed like a fetus. Like the word he begot them, subsisting spermatically, and the ones whom he was to beget had not yet come into being from him. The one who first thought of them, the Father, - not only so that they might exist for him, but also that they might exist for themselves as well, that they might then exist in his thought as mental substance and that they might exist for themselves too, - sowed a thought like a spermatic seed. Now, in order that they might know what exists for them, he graciously granted the initial form, while in order that they might recognize who is the Father who exists for them, he gave them the name "Father" by means of a voice proclaiming to them that what exists, exists through that name, which they have by virtue of the fact that they came into being, because the exaltation, which has escaped their notice, is in the name.

The fall

Of all the Aeons only the first pair Mind and thought knew and comprehended the greatness of the self-existent Uncreated Eternal Spirit and could behold him but the last and youngest Aeon Logos or (Reason).

The intent, then, of this one who is the Logos, was good. When he had come forth, he gave glory to the Father, even if it led to something beyond possibility, since he had wanted to bring forth one who is perfect, from an agreement in which he had not been, and without having the command. and without the knowledge or consent of his female counterpart Sophia (wisdom) he projected from his own being a flawed emanation.

Thus the Logos motivated by abundant love and seeking only to give glory to the self-existent Uncreated Eternal Spirit creates other beings which are the seven archangels their leader is Michael who is the Demiurge the creator of the material cosmos or the physical heavens

But when the logos perceives that these are inferior to the emanations of the self-existent Uncreated Eternal Spirit indeed mere shadows and phantoms of them, lacking reason and light, dwelling in ignorance, bringing forth more and more defective creatures little weakling, hindered by the illnesses by which he too was hindered

This logos is the cause of the creation of the world and the lower beings including mankind but the logos is not the agent of creation the Demiurge is the agent of creation being used by the logos as a hand

This defective Logos is interceded for by his counterpart the Divine Logos or First Thought the Son in the Pleroma  

Logos and the Demiurge 

Over all the archons he appointed an Archon with no one commanding him. He is the lord of all of them, that is, the countenance which the Logos brought forth in his thought as a representation of the Father of the Totalities. Therefore, he is adorned with every <name> which <is> a representation of him, since he is characterized by every property and glorious quality. For he too is called "father" and god" and "demiurge" and "king" and "judge" and "place" and "dwelling" and "law."
The Logos uses him as a hand, to beautify and work on the things below, and he uses him as a mouth, to say the things which will be prophesied.
The things which he has spoken he does

The invisible spirit moved him in this way, so that he would wish to administer through his own servant, whom he too used, as a hand and as a mouth and as if he were his face, (and his servant is) the things which he brings, order and threat and fear, in order that those with whom he has done what is ignorant might despise the order which was given for them to keep, since they are fettered in the bonds of the archons, which are on them securely.


body--The outward expression of consciousness; the manifestation of the thinking part of man.
God creates the body thought, or divine reasoning, and man, by his thinking, makes it manifest depending upon the spiritual understanding of the individual whose mind it is. 

As God created man in His image and likeness by the power of His word, so man, as God's image and likeness, projects his body by the same power.


The Logos needs to use the Demiurge as body to interact with the world

Bodies are the way in which a being is perceived from, and interacts with a lower level

One (more actualised) being can be (function as) the body of another (less actualised)

The interaction downwards from the Father, Son, Logos, Demiurge and finally to the archons should be interpreted as a Body politic a divine corporation

The author of TT 100:31-33 wrote, “the Logos uses him [the Demiurge] as a hand, to beautify and work on the things below.” Also, see Exc 47:2, 49:1-2; Haer 1:5,1-4; 1:17,1; 2:6,3.

The cosmology of the Tripartite Tractate is one of a Corporeal conceptualisation: Body like that from Leviathan: Or the Matter, Forme and Power of a Commonwealth, Ecclesiasticall and Civil

Book by Thomas Hobbes

The tenth heaven

The tenth heaven

In the tenth Heaven, Aravoth, I saw the vision of the face of the Lord, like iron burnt in the fire, and brought forth and emitting sparks, and it burns. So I saw the face of the Lord; but the face of the Lord cannot be told. It is wonderful and awful, and very terrible.

- 2 Enoch, Chapter XXII

This passage was translated into English from the Slavonic "Book of Enoch" in 1892. The word Aravoth is from the hebrew word "ערבות", which can be transliterated as "oraboth". This struck me as similiar to "Boraoth", one of the hidden names on the circumference of the Sigillum Dei, the letter B is in the middle of the word instead of the beginning. The enochian names have weird things around the use of the letter "B".

Aravoth is the 10th heaven were the throne of God resides, the Seraphim and Cherubim do serve the Almighty Lord shouting great praises to Him. They sing Holy Holy Holy is the Lord of Hosts, the world is full of His grace.

There is alot more need to know what happens on the 9th, 8th,7th up to the 1st heavens. 

Each level of heaven is designed for a purpose and it speaks God's glory.

And then the <seventh> heaven opened and we went up to the Ogdoad. And I saw the twelve apostles. They greeted me, and we went up to the ninth heaven. I greeted all those who were in the ninth heaven, and we went up to the tenth heaven. And I greeted my fellow spirits. The Nag Hammadi Library The Apocalypse of Paul

there are 14 levels, and Paul reached the tenth according to Apocalypse of Paul. Jesus/Osiris will be the 13th, and the 14th is the Father himself. Horemheb was he who built the tenth pylon/pillar at the Tempel of Karnak. It is still missing the 11th-13th pillar there.

I can before that time give you the information about the 1st to the 14th as a quote from NHL :)

The Apocalypse of Paul should be read as well to see what he thought abouth the 10th.

Now, the first kingdom says of the illuminator that he came from . . . a spirit . . . to heaven. He was nourished in the heavens. He received the glory of that one and the power. He came to the bosom of his mother, and in this way he came to the water.

And the second kingdom says of him that he came from a great prophet. And a bird came, took the child who was born, and brought him onto a high mountain. And he was nourished by the bird of heaven. An angel came forth there. He said to him, “Rise! God has given you glory.” He received glory and strength, and in this way he came to the water

The third kingdom says of him that he came from a virgin womb. He was cast out of his city, he and his mother; he was brought to a desert place. He was nourished there. He came and received glory and power, and in this way he came to the water.

The fourth kingdom says of him that he came from a virgin. . . . Solomon sought her, he and Phersalo and Sauel and his armies, which had been sent out. Solomon himself sent his army of demons to seek out the virgin. And they did not find the one whom they sought, but the virgin who was given to them. It was she whom they fetched. Solomon took her. The virgin became pregnant and gave birth to the child there. She nourished him on a border of the desert. When he was nourished, he received glory and power from the seed from which he was conceived, and in this way he came to the water.

And the fifth kingdom says of him that he came from a drop from heaven. He was thrown into the sea. The abyss received him, gave birth to him, and brought him to heaven. He received glory and power, and in this way he came to the water.

And the sixth kingdom says that one . . . came down to the realm that is below in order to gather flowers. She became pregnant from the desire of the flowers. She gave birth to him in that place. The angels of the flower garden nourished him. He received glory and power there, and in this way he came to the water.

And the seventh kingdom says of him that he is a drop and came from heaven to earth. Dragons brought him down to caves, and he became a child. A spirit came over him and raised him to the place from where the drop had come. He received glory and power there, and in this way he came to the water.

And the eighth kingdom says of him that a cloud came over the earth and enveloped a rock. He came from it. The angels above the cloud nourished him. He received glory and power there, and in this way he came to the water.

And the ninth kingdom says of him that from the nine muses one separated. She came to a high mountain and spent some time seated there, so that she desired her own body in order to become androgynous. She fulfilled her desire and became pregnant from her desire. He was born. The angels who were over the desire nourished him. And he received glory there and power, and in this way he came to the water.

The tenth kingdom says of him that his god loved a cloud of desire. He fathered him in his hand and cast upon the cloud above him some of the drop, and he was born. He received glory and power there, and in this way he came to the water.

And the eleventh kingdom says of him that the father desired his own daughter. She was pregnant from her father. She cast her child . . . tomb out in the desert. The angel nourished him there, and in this way he came to the water.

The twelfth kingdom says of him that he came from two luminaries. He was nourished there. He received glory and power, and in this way he came to the water.

And the thirteenth kingdom says of him that every birth of their ruler is a word. And this word received a mandate there. He received glory and power, and in this way he came to the water, that the desire of those powers might be satisfied.

But the generation without a king says that god chose him from all the eternal realms. He caused knowledge of the one of truth, who is undefiled, to reside in him. He said, “Out of a foreign air, from a huge eternal realm, the great illuminator appeared. And he made the generation of those people whom he had chosen for himself shine, so that they should shine on the whole eternal realm

The 12 Aeons Revelation 7

The 12 Aeons Revelation 7

7 After these things I saw four angels standing at the four corners of the earth, holding the four winds of the earth, that the wind should not blow on the earth, on the sea, or on any tree. 2 Then I saw another angel ascending from the east, having the seal of the living God. And he cried with a loud voice to the four angels to whom it was granted to harm the earth and the sea, 3 saying, “Do not harm the earth, the sea, or the trees till we have sealed the servants of our God on their foreheads.” 4 And I heard the number of those who were sealed. One hundred and forty-four thousand of all the tribes of the children of Israel were sealed:
5 of the tribe of Judah twelve thousand were sealed;
of the tribe of Reuben twelve thousand were [a]sealed;
of the tribe of Gad twelve thousand were sealed;
6 of the tribe of Asher twelve thousand were sealed;
of the tribe of Naphtali twelve thousand were sealed;
of the tribe of Manasseh twelve thousand were sealed;
7 of the tribe of Simeon twelve thousand were sealed;
of the tribe of Levi twelve thousand were sealed;
of the tribe of Issachar twelve thousand were sealed;
8 of the tribe of Zebulun twelve thousand were sealed;
of the tribe of Joseph twelve thousand were sealed;
of the tribe of Benjamin twelve thousand were sealed.




Then look at verse four. He says, “And I heard the number of the sealed, 144,000 sealed.” Some religious groups have picked up on this 144,000 and have attempted to say that this is the exact number that are going to be saved and going to be living in the kingdom of God and so forth, and folks, it just doesn’t make any sense. It isn’t logical. That’s what happens when you take things literally out of the scripture.

The 144,000 is simply symbolic. It means a wide number of people. It’s going to refer to both Jews and gentiles. Both Jewish Christians and gentile Christians. “A great multitude from every nation,” is what he says down here in verse nine. Go down to verse nine. “After this, I looked, and behold, a great multitude which no man could number from every nation, from all tribes and peoples and tongues, standing before the throne and before the lamb, clothed in white robes with palm branches in their hands.”

Peoples from all tribes and peoples and tongues. This includes the 144,000 as a reference to all the faithful who are going to be saved. And the symbology has to do with 12 times 12. The 12 tribes and the 12 apostles. 12 carries with it the idea of spiritual completeness. Spiritual completeness. The number of seven sort of carries the same idea; spiritual fulfillment or completion. But the number 12 really means completion in a broader sense, I suppose. Spiritual completion. And it’s simply a symbolic number.

If you take it literally, then we’re all in a lot of trouble, because there are a lot of souls running around on this plain and on other plains. If we say only 144,000 are going to make it, then that’s not very encouraging, is it? When we say that, we miss the whole point. He’s dealing with symbology here. The elect; the 144,000, okay? We see here a form of divine recognition for both the Jews and the gentiles.
The Aions are a symbol of the 12 followers of Jesus and the 12 tribes of Israel a symbol of the 12 Aions which emanated from the Deity Hebrews 11:1-4 cp 2tim 3:16 god breathed the Aions into existence from his substance heb 1:3 emanating forth from him

The Twelve Aions or 12 spiritual attributes of Consciousness

The names of the twelve sons of Jacob form a sentence, conveying an important message. Throughout the Scriptures they are set forth in various orders, changing the message of the names as this is done

The names of the tribes (vv. 5-8) form a sentence as follows:

Judah — Praise; praise Jehovah; meta. prayer and praise faculty.

Reuben — See a son; behold a vision of a son; meta. understanding through seeing.

Gad — Company pertaining to good fortune; meta. power on.the physical plane.

Asher — Blessed; straight forward; faculty of understanding.

Naphthali — Wrestling; wrestling; meta. elimination or renunciation.

Manasseh — Forgetting; out of the forgotten;

Simeon —Hearing; harkening, obeying; meta. understanding through hearing.

Levi — Joining; joining, clinging; meta. the love faculty in human consciousness.

Issachar —Reward; he will bring reward, he who brings recompense; meta. activated zeal.

Zebulun — Dwelling; habitation, dwelling; meta. order faculty.

Joseph —Adding; Joseph - Jehovah shall bring increase; meta. imagination.

Benjamin — Son of the right hand. son of good fortune; meta. active accomplishing faith.

The Pleroma the Waters Above the Heavens Genesis 1:7

The Pleroma the Waters Above the Heavens

An Opening reading from The Dialogue of the Savior

The Lord said, "When the Father established the cosmos, he [collected] water from it, and his Word came forth from it, and it experienced many [troubles]. It was more exalted than the path [of the starts] surrounds the entire earth.

[He continued] the collected water [above] is beyond the stars and beyond the water is  a great fire encircling them like a wall. [Periods of ] time began to be measured once many beings that were within had separated from the rest. When the [word] was established, he looked [down], and The Father said to him, 'Go, and [send something] from yourself, in order that [the earth] may not be in want from generation to generation, and from age to age.' 

The Hebrew shamayim (always in the plural), which is rendered “heaven(s),” seems to have the basic sense of that which is high or lofty. (Ps 103:11; Pr 25:3; Isa 55:9)

Genesis Verse 1  In the beginning God created the heavens (Heb. hushomayim – plural) and the earth. (Genesis 1)

If we read the history of the creation as a revelation to inhabitants of Earth we find it informs us of the order in which the things narrated would have developed themselves to our view if we had been placed on some projecting rock and observed the events revealed. We must remember this. The Mosaic account is not a revelation of the formation of the boundless universe to inhabitants on other planets removed from the Earth. Rather, it was given to humans as inhabitants of this terrestrial system. (1)

God existed before he created the Heavens and the earth. God exists outside of time and space in the Bythos or depth. 

First of all the Pleroma did not always exist it was produced and formed by the Eternal Spirit this we call the emanation.

(He created the holy Pleroma in this way The Untitled Text in the Bruce Codex)

The word Pleroma means "fullness". It refers to all existence beyond visible universe. In other words it is the world of the Aeons, the heavens or spiritual universe. Bythos is the spiritual source of everything which emanates the pleroma,

The Pleroma is both the abode of and the essential nature of the True Ultimate Deity or Bythos.
The Pleroma as well as being the dwellings place of the Aeons is also a state of consciousness.

What does it mean by "in the beginning" you see some can argue that he means beginning as in God forever and eternal past but if that's the case there really is no beginning with God others might argue well beginning in the sense that when God conceived of creating the perfect sons and daughters of God the human beings whatever other beings he might have created in the universe that was the beginning

When this "beginning" was we are not told. But we are taught that wisdom was revealed in the acts of creation from the beginning. John states that "in the beginning" was the Word or Logos (John 1:1). Logos signifies the outward expression of inward thought or reason. It represents more than a mere word, for it incorporates the thought behind the word expressed. Elsewhere, we learn that wisdom was with God in the beginning, and was manifested in His acts of creation (Prov. 8:22). Hence, all that was done, was done with His ultimate purpose in mind, and not as the result of blind force or chance

atmospheric region or sky

Mat 6: 26 Observe intently the birds of heaven, because they do not sow seed or reap or gather into storehouses; still YOUR heavenly Father feeds them. Are YOU not worth more than they are?

Heavens of earth’s atmosphere. . “The sky” is sometimes meant, that is, the apparent or visual dome or vault arching over the earth.—Mt 16:1-3; Ac 1:10, 11.

After the very first verse of the Bible we are told that there is a body of ‘deep’ water presumably in or around the earth:

Genesis Verse 2  And the earth was without form, and void; and darkness was upon the face of the deep. And the Spirit of God moved upon the face of the waters. (Genesis 1)

This scripture also seems to be making a lot of play of the word ‘face’ or surface.

A little further on, God then made a firmament which divided the body of water into two bodies of water, one below and one above it: (2)

Genesis Verse 7  And God made the firmament, and divided the waters which were under the firmament from the waters which were above the firmament: and it was so. (Genesis 1)

This atmospheric region corresponds generally to the “firmament [Heb., raqia`]” formed during the second creative period, described at Genesis 1:6-8. It is evidently to this ‘heaven’ that Genesis 2:4; Exodus 20:11; 31:17 refer in speaking of the creation of ““the sky and the dry land. (3)

A typical dictionary definition of the word firmament is ‘expanse’ so this firmament would appear to be an expanse of space or sky surrounding the earth with a body of water on the earth and the other body of water sitting above the expanse of space.

Now it starts to get interesting. In verse 8 God now called the firmament ‘Heaven’. Whilst the word for heaven in verse 8 is also the plural ‘shomayim’ it does not contain the definite article as does the heavens in verse 1. OT Hebrew nouns without the definite article attached are likely to indicate a proper name, the ‘Sky’ or  atmospheric region it is the element of the heavens that mankind can see.

 The waters below the firmament are what formed the seas and the water in the earth’s atmosphere in the form of clouds and rainfall. So  the firmament is both the extent of the Earth’s atmosphere or sky and the visible universe therefore the firmament is intended to comprise both of these expanses: (4)

8  And God called the firmament Heaven. And the evening and the morning were the second day. (Genesis 1)

The firmament may have seemed like a glass dome.

“Let there be a firmament in the midst of the waters, the middle layer of water solidified,and the nether heavens and the uppermost heavens were formed. Rab said: [God's] handiwork [the heavens] was in fluid form, and on the second day it congealed; thus Let there be a firmament means ‘Let the firmament be made strong*. R. Judah b. R. Simon said: Let a lining be made for the firmament, as you read, And they did beat the gold into thin plates…R. Simon said: The fire came forth from above and burnished the face of the firmament.” Gen. Rab. 4:2

“R. Phinehas said in R. Oshaya’s name: As there is a void between the earth and the firmament, so is there a void between the firmament and the upper waters, as it is written, Let there be a firmament in the midst of the waters, meaning, midway between them. R. Tanhuma said: I will state the proof. If it said, And God made the firmament, and He divided between the waters . . . which are upon the firmament, I would say that the water lies directly upon the firmament itself.” Gen. Rab. 4:3

“But after that he makes the firmament, that is, the corporeal heaven. For every corporeal object is, without doubt, firm and solid; and it is this which “divides the water which is above heaven from the water which is below heaven.” Origen. Homily on Genesis

The firmament is the limit, the middle or boundary between the Physical Heavens and the spiritual heavens called the pleroma

Outer space. 

The physical “heavens” extend through earth’s atmosphere and beyond to the regions of outer space with their stellar bodies, “all the army of the heavens”—sun, moon, stars, and constellations. (De 4:19; Isa 13:10; 1Co 15:40, 41; Heb 11:12 These heavens show forth God’s glory, even as does the expanse of atmosphere, being the work of God’s “fingers.” (Ps 8:3; 19:1-6)
The divinely appointed “statutes of the heavens” control all such celestial bodies. Astronomers, despite their modern equipment and advanced mathematical knowledge, are still unable to comprehend these statutes fully. (Job 38:33; Jer 33:25) Their findings, however, confirm the impossibility of man’s placing a measurement upon such heavens or of counting the stellar bodies. (Jer 31:37; 33:22;
Yet they are numbered and named by God.—Ps 147:4; Isa 40:26.

“Heavens of the heavens.

” The expression “heavens of the heavens” is considered to refer to the highest heavens and would embrace the complete extent of the physical heavens, however vast, since the heavens extend out from the earth in all directions.—De 10:14; Ne 9:6.

Solomon, the constructor of the temple at Jerusalem, stated that the “heavens, yes, the heaven of the heavens” cannot contain God. (1Ki 8:27)

27 “But will God truly dwell upon the earth? Look! The heavens, yes, the heaven of the heavens, themselves cannot contain you; how much less, then, this house that I have built!

Yahweh measures the physical heavens as easily as a man would measure an object by spreading his fingers so that the object lies between the tips of the thumb and the little finger. (Isa 40:12) Solomon’s statement does not mean that God has no specific place of residence.

Nor does it mean that he is omnipresent in the sense of being literally everywhere and in everything. This can be seen from the fact that Solomon also spoke of Yahweh as hearing “from the heavens, your established place of dwelling,” that is, the heavens of the pleroma the eternal realm.—1Ki 8:30, 39

. 30 And you must listen to the request for favor on the part of your servant and of your people Israel with which they pray toward this place; and may you yourself hear at the place of your dwelling, in the heavens, and you must hear and forgive.

, 39 then may you yourself hear from the heavens, your established place of dwelling, and you must forgive and act and give to each one according to all his ways, because you know his heart (for you yourself alone well know the heart of all the sons of mankind)

In Deuteronomy 10, we find the strongest evidence possible that there is more than one heaven. Verse 14 refers to the heavens in the plural but also references the heaven of the heavens. Whilst concordances and lexicons routinely consider the Hebrew word ‘shamay’ as an unused singular noun, this very rare form of the word for heaven in the OT scriptures does appear in this verse. This to my mind draws this specific word out with the special meaning of God’s home being singularly supreme and above the other heavens:

14 Behold,the heavens (Heb. Shamayim) and the heaven (Heb. Shamay – singular?) of heavens (Heb. Shamayim) is the LORD'S thy God, the earth also, with all that therein is. (Deuteronomy 10)

To further emphasise these points 1Kings Chapter 8 contains the same phraseology and Hebrew grammar:

27 But will God indeed dwell on the earth? behold, the heaven and heaven of heavens cannot contain thee; how much less this house that I have builded? (1Kings 8)

Nehemiah Chapter 9 but with one added ingredient. Here each heaven comes with its own host. This could be referring to the stars in the sky as well as the sons of God beyond the stars.

6 Thou, even thou, art Yahweh alone; thou hast made heaven, the heaven of heavens, with all their host, the earth, and all things that are therein, the seas, and all that is therein, and thou preservest them all; and the host of heaven worshippeth thee. (Nehemiah 9)

Psalm 33 paints a similar picture:

6 By the word of Yahweh were the heavens made; and all the host of them by the breath of his mouth. (Psalms 33)

1 Thus the heavens and the earth were finished, and all the host of them. (Genesis 2)

Spiritual Heavens.

James 1:17 Every good gift and every perfect present is from above, for it comes down from the Father of the [celestial] lights, and with him there is not a variation of the turning of the shadow.

the Father of the [celestial] lights, "Father of spirits" (Heb 12:9); "Father of the heavenly lights" (Jam 1:17

 The same original-language words used for the physical heavens are also applied to the spiritual heavens. As has been seen, Yahweh Elohim does not reside in the physical heavens, being a Spirit. However, since he is “the High and Lofty One” who resides in “the height” (Isa 57:15), the basic sense of that which is “lifted up” or “lofty” expressed in the Hebrew-language word makes it appropriate to describe God’s “lofty abode of holiness and beauty.” (Isa 63:15; Ps 33:13, 14; 115:3)

“army of the heavens,” often applied to the stellar creation, sometimes describes these angelic sons of God. (1Ki 22:19; compare Ps 103:20, 21; Da 7:10; Lu 2:13; Re 19:14.) So, too, “the heavens” are personified as representing this angelic organization, “the congregation of the holy ones.”—Ps 89:5-7; compare Lu 15:7, 10; Re 12:12.

12 Is not God in the height of heaven? (Heb. plural Shamayim) and behold the height of the stars, how high they are!
13 And thou sayest, How doth God know? can he judge through the dark cloud?
14 Thick clouds are a covering to him, that he seeth not; and he walketh in the circuit of heaven. (Job 22)

Job Chapter 22 teaches that God’s heaven is above the stars but that He can see through the darkness that covers Him from our sight.

4 Praise him, ye heavens of heavens, and ye waters that be above the heavens. (Psalms 148)

Now while ‘waters’ refers to God’s heavenly hosts or dwelling pleace that is the Pleroma in the symbolic meaning, the literal meaning would be the waters of the flood:

Ge 7:11 ¶ In the six hundredth year of Noah’s life, in the second month, the seventeenth day of the month, the same day were all the fountains of the great deep broken up, and the windows of heaven were opened.

4 Praise him, ye heavens of heavens, and ye waters that be above the heavens. (Psalms 148)

The allusion here is to the waters which are above the lower heaven, that is, the air or sky and outer space, this higher region where the waters are is a higher heaven called the upper waters or the Pleroma. (5)

Note the Pleroma and the Aeons are called the deep

The Pleroma is also called the ‘emanations of the Father’, the ‘treasuries of light’ and the ‘immeasurable deep’.

As the ‘immeasurable deep’: “After these things there is another place which is broad, having hidden within it a great wealth which supplies the All. This is the immeasurable deep.” (Untitled Text in the Bruce Codex)

The Upper Aeons are spiritual, invisible, immobile and are filled with light. They are described as ‘the Silence’ or a ‘watery light’ and contain archetypal images or reflections of the One. The Lower Aeons are material, visible, mutable and filled with darkness. They are described as ‘fiery’ and contain shadows, copies or images.

- Called ‘Watery light and life’, ‘water-light’, ‘light-water’, ‘Luminous Waters’, ‘Living Waters’, ‘the Silence’, ‘the silent Silence’, ‘the living Silence’, ‘the Treasure-House’, ‘the Store-House’, ‘the Dwelling-Place’, ‘crown’, ‘the kingless realm’.

- As water: “...the waters which are above.” (Melchizedek), “...the waters which are above matter.” (Apocryphon of John)

- As Living Water: “...the Aeons in the Living Water.” (Trimorphic Protennoia)

- As a watery light and life: “For it is he who looks at himself in his light which surrounds him, namely the spring of the water of life. And it is he who gives to all the aeons and in every way, (and) who gazes upon his image which he sees in the spring of the Spirit. It is he who puts his desire in his water-light which is in the spring of the pure light-water which surrounds him.” (Apocryphon of John)

They will receive you into aeonian dwellings (Luke 16: 9). We have a building from God, an aeonian house in heaven, not built by human hands (2 Cor 5: 1). I am going to prepare a place for you, so that you also may be where I am (John 14: 3). Ps 104:3  (103:3) Who covers his chambers with waters; who makes the clouds his chariot; who walks on the wings of the wind. LXX

3  Who frameth of the waters the beams of his upper-chambers; who maketh the clouds his chariot; who walketh along upon the wings of the wind:

Ps 104:3 Who layeth the beams of his chambers in the waters: who maketh the clouds his chariot: who walketh upon the wings of the wind:

     Who layeth the beams of his chambers in the waters The word here rendered “layeth” — from hrq — means properly to meet; then, in Hiphil, to cause to meet, or to fit into each other, as beams or joists do in a dwelling. It is a word which would be properly applied to the construction of a house, and to the right adjustment of the different materials employed in building it. The word rendered “beams” — hYli — means “an upper chamber, a loft,” such as rises, in Oriental houses, above the flat roof; in the New Testament, the υπερωον, rendered “upper room,” #Ac 1:13 9:37,39 20:8. It refers here to the chamber — the exalted abode of God — as if raised above all other heavens, or above the universe.

The house which covers, frameth and layeth in the upper waters is the Pleroma 

The word “waters” here refers to the description of the creation in #Ge 1:6,7 — the waters “above the firmament,” and the waters “below the firmament.” The allusion here is to the waters above the firmament; and the meaning is, that God had constructed the place of his own abode — the room where he dwells — in those waters; that is, in the most exalted place the Pleroma outside of our universe.

 It does not mean that he made it of the waters, but that his home — his dwelling-place — was in or above those waters, as if he had built his dwelling not on solid earth or rock, but in the waters, giving stability to that which seems to have no stability, and making the very waters a foundation for the structure of his abode. 

1. The earth is at the centre of the model;

2. The lower waters are upon and below the surface of the Earth in the form of its seas;

3. The outer surface of the sky (i.e. the outer edge of Earth’s atmosphere) being above the lower waters which were contained within Earth’s atmosphere either as clouds in the sky or on and below the Earth’s surface as the seas;

4. The heavenly bodies (stars, sun and moon) contained within the visible universe of outer space (the firmament) being above the outer surface of the Earth’s atmosphere; The waters below the firmament are what formed the seas and the water in the earth’s atmosphere in the form of clouds and rainfall

5. The upper waters being above the visible universe. On this basis we must reach the inescapable conclusion that the upper waters are the invisible heavens of God’s domain the Pleroma, outside of the physical universe.

The word Pleroma means "fullness". It refers to all existence beyond visible universe. In other words it is the world of the Aeons, the heavens or spiritual universe. 
Bythos is the spiritual source of everything which emanates the pleroma. 
The Pleroma is both the abode of and the essential nature of the True Ultimate God.