Bentley Layton writes (The Gnostic Scriptures, p. 26):
The manuscripts [three at Nag Hammadi, one elsewhere] and summary [in Irenaeus] attest the circulation of no less than four distinct editions of the Greek text in antiquity. Such a series of editions must have resulted from continual study and revision of AJn by gnostic teachers; it is a measure of the importance and timeliness of the work for ancient gnostic Christianity. These four ancient editions, usually called "versions," comprise the following.
1. The long version, which is represented by two virtually identical Coptic manuscripts, MSS NHC II and NHC IV, is the text translated here. When one of the two manuscripts is defective, its original reading can often be restored from the other. The most obvious difference between the long version and the short version is that the former contains a lengthy excerpt from a certain Book of Zoroaster (cf. 15:29-19:8f).
2. A short version, which is represented by Coptic MS NHC III, differs from the others in certain details of phraseology and systematic theology; as a Coptic translation it differs in style and vocabulary from all the other Coptic versions.
3. Another short version, which is represented by Coptic MS p. Berol. 8502, also differs in certain details of phraseology and systematic theology; as a Coptic translation it differs in style and vocabulary from all the other Coptic versions.
4. The summary of BJn in St. Irenaeus (IrG) is too brief and compressed to classify it as long or short, but in any case it shows certain minor differences that distinguish it from each of the three other versions.
The long version has been chosen for translation here because of its apparent coherence; however, scholars have not determined which version is the original.
Frederik Wisse writes (The Nag Hammadi Library in English, p. 104):
The Apocryphon of John is an important work of mythological Gnosticism. Using the framework of a revelation delivered by the resurrected Christ to John the son of Zebedee, this tractate offers a remarkably clear description of the creation, fall, and salvation of humanity; the mythological description is developed largely in terms of the early chapters of Genesis. Reports of the church fathers indicate that some of them were familiar with the contents of The Apocryphon of John: the teachings of certain Gnostics described by Irenaeus are very similar to the cosmological teachings of the present tractate. Though Irenaeus apparently did not know The Apocryphon of John in its present form, it is certain that the main teachings of the tractate existed before 185 C.E., the date of Irenaeus' work Against Heresies. The Apocryphon of John was still used in the eighth century by the Audians of Mesopotamia.
Kurt Rudolph writes (Gnosis, pp. 102-103):
In this document [Secret Book of John] too there is reference to the coming into being of three men: the psychic, the pneumatic and the earthly. Their binding together is once again portrayed in a very detailed but considered fashion. First of all we have the "psychic Adam", whom the demiurge Jaldabaoth with his "seven emissaries" (Genesis 1.26 is drawn upon here also) creates after the image, reflected in the water of chaos, of the "holy perfect Father, the first man in the form of a man". Thus the device of imitation is again made to serve the powers of darkness, but of necessity it must be imperfect and finally needs the help of the powers of light, who thereby are able to ensure the fulfilment of the secret purpose of the plan of salvation. Our text is a patricularly impressive example of the opposition of the two basic powers, since every move on the one side is matched by a countermove on the other, until in the course of the development a certain pendulum effect is established. Corresponding to the ancient idea of the part played by the planets in the formation of the psychic body of man, the seven powers contribute from their own elements the following "souls" for Adam: the "bone-soul", the "sinew-soul", the "flesh-soul", the "marrow-soul", the "blood-soul", the "skin-soul", and the "hair-soul". These "souls of the body" correspond, as is frequently the case in gnostic thought, to macrocosmic powers (providence, divinity, lordship, fire, kingdom, insight, wisdom). Behind this evidently lies the idea of the psychic capacities of man, belonging to the earthly intellectual (immaterial) sphere, in contrast to the supramundane intellectual element which is a gracious gift from the world above. In spit of the skill devoted to the formation of this psychic body it remains immobile and it is not possible to make him stand upright. This gives "Wisdom" (sophia) opportunity to intervene in order to win back the power which through her error she had lost to her son the Demiurge. She prays "the Father of the all" for help; he has recourse to deception (this is evidently quite permissible in dealing with the evil powers): "By a holy decree he sent the "self-originate" (autogenes) and the four lights in the form of the angels of the first archon. They gave him advice, that they might bring out from him the power of the mother. They said to him: "Breathe into his face (something) of the spirit (pneuma) which is in you, and the thing will raise itself up". "And (so) he breathed into him of his spirit—it is the power from the mother—into the body, and it moved at once . . . " In this way the pneumatic seed finds its way into the psychic Adam, and is thus no longer subject exclusively to the control of the powers of darkness.
The Secret Book of John is considered by sholars to be the locus classicus for the Gnostic mythological system and is the subject of Logan's book Gnostic Truth and Christian Heresy.
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