Under Herod the Great in the 1st century BC the world mission called the New Israel was founded. It was intended to strengthen Judaism in the Diaspora in an updated form. Its Jewish identity was affirmed by having a new "Abraham, Isaac and Jacob". These men, members of Herod's court, established the positions that became the Pope (Father)and patriarchs of east and west.

The biblical Jacob had had a twin brother, Esau, who lost his birthright (Genesis 27). The name Didymus, given to a Thomas in the gospel period, means "Twin". It meant that he was an Esau of the New Israel who had lost his birthright. The description fitted one who had lost his right to inherit under Herod the Great. Thomas-Esau was the son of Herod and one of his nine wives, the wife called Mariamme II. She was the daughter of Simon Boethus, a resident of Jerusalem who was given the high priesthood by Herod in exchange for his daughter. By 5 BC Herod's increasing insanity was becoming a danger to the state, and Simon Boethus was involved in a plot to assassinate him. The plot was discovered, Simon Boethus was dismissed, Mariamme II was divorced, and her infant son disinherited, losing his birthright as a son of Herod. (Josephus, Antiquities 17, 77-78, Josephus, Wars 1, 600). He grew up to become Thomas Didymus, a contemporary of Jesus.

The original mission of the New Israel had originated from the benign influence of Hillel the Great, who was the "Abraham", the first Pope. Resident at first in Babylon, he had been willing to admit Gentiles as proselytes, for Diaspora Jews were attracting Gentiles by their high standards of theology and ethics. Proselytes were required to be circumcised, and some adopted the monastic way of life influenced by Essenes. In the Herodian court with its harem of wives there were eunuchs, who could be trusted with the women and in the king's bedchamber. They were normally non-Jews, and since they had to join in household worship they were made to become proselytes. The alienated "Esau" was the appropriate person to be the head of this class.

Thomas was, then, the superior of proselytes, and, as eventually emerged, was a suitable person to be in the company of literal eunuchs. He was a homosexual. He adopted the monastic way of life, and in the Book of Revelation is associated with Sodom.

In the list of people in Agrippa's house greeted by Paul in Romans 16:13 the name Rufus the Elect One (eklektos) appears. In Mark 15:21 two men were present on the way out to the crosses, called Alexander and Rufus. Simon of Cyrene, who was Simon Magus being prepared for crucifixion himself, is called the father of Alexander. Simon was to lift up the cross of Jesus, giving an allusion to Isaac who carried the wood for the sacrifice of himself (Genesis 22:1-14). Isaac was the father of Jacob and Esau. This combination of allusions makes Alexander a Jacob and Rufus an Esau. Alexander, from Alexandria in Egypt, was a title of the Chief Therapeut, named in 2 Timothy 4:14 and in Acts 19:33 The Chief Therapeut, who was Theudas in the gospel period, with Thomas-Esau, were in the area at Qumran where the crosses were erected, the southern esplanade loc.96, called " Salt" in the Copper Scroll (3Q15 3:8, 11). It was a very unclean place in the SW of the grounds, to which sinning monastics were at first excluded when they had committed breaches described in the Temple Scroll (11QT 45). In Revelation 11:8 a re-enactment of the crucifixion is described, in "Sodom and Egypt, where their Lord was crucified". Alexander of Egypt was of villager status only, so permitted in the unclean area as an "Egypt". Thomas-Rufus-Esau in the same area was in "Sodom". This detail in Revelation, a book vehemently opposed to homosexuality, is the most explicit evidence of Thomas' sexual orientation.

Thomas is named frequently in John's gospel, which was originally written for Gentile celibates. In John 20:24-29 he was found after the crucifixion, expressing doubt about whether Jesus could have actually survived in the flesh, thus earning the title of Doubting Thomas. The reason was that he was a gnostic with a monastic education, who would have preferred that Jesus had changed into a spiritual state, the concept found in the gnostic gospels (The Second Treatise of the Great Seth VII, 2, 55:15-56:20). When Jesus did join the sacred meal with him at Mird-Hyrcania on the Sunday after Good Friday, he insisted on the evidence that he was physically present, proof that he had survived the crucifixion. Thomas replied, "My Lord (ho kyrios mou). And my God (ho theos mou)." The word "and" indicates a new sentence in the pesher. There was a significant difference between ho theos with the definite article and theos without the article. Jesus is called theos without the article in John 1:1, and he is never called ho theos. He was only a "son of God", a deputy of the Annas priest who was believed to be an incarnation of God. In his reply, Thomas first addressed Jesus, for whom "Lord" was an acceptable title, then addressed Jonathan Annas who was also present, treating him as superior to Jesus.

In Acts 6:3-5 Jonathan Annas, under the title of Stephen the king-priest wearing the crown, selected six men, all with Greek names, to form an abbey. The number indicates that it was an abbey whose leaders corresponded to the days of the week, Jonathan being for Saturday. The last of them, for Friday, was Nicolaus the proselyte of Antioch. The Book of Revelation again gives the clue that Nicolaus was a despised proselyte, a homosexual like Thomas, the same as the eunuch Blastus who was admitted to the king's bedchamber and administered the poison that killed Agrippa I (Revelation 2:15; 3:14-18; Acts 12:20-23).

The Gentile abbey of Jonathan Annas had no objection to sodomy, and this was the reason why he was removed from office after only six months as high priest. Jonathan is also referred to as polloi, the Many, from the name Rabbim. It is Hebrew for the Many, the name of the Qumran monastic council (1QS 6:1). In Matthew 7:13-14 a sharp contrast is made between the Many, polloi, who go through the broad gate, and the Few (oligoi) who go through the narrow gate. The Many were called, and the Few chosen, Elect (eklektoi) (Matthew 22:14). The Many were liberal Sadducees like Jonathan Annas, while the Few were strict Sadducees like Matthew Annas, who founded the Gentile abbey that became fully Christian. Rufus is called the Elect One in the court of Agrippa II in the late 50's AD. He had, apparently, become strict in regard to his sexual practices, and was acceptable to Paul and other Christians in the court. He was responsible for the magnificent Gospel of Thomas that was found among the Nag Hammadi gnostic gospels.

Thomas, under his given name of Herod, figured in Josephus' narrative in another capacity. Herod the Great made plans for the continuation of his dynasty by arranging marriages between his offspring from different wives while they were still children. A granddaughter named Herodias, the full sister of the grandson who would become Agrippa I, was promised to his son Thomas soon after he was born. When he grew up Thomas married Herodias and they had a a daughter, but the marriage was failing. Herodias turned to another Herod relative, Antipas, and persuaded him to divorce his Arabian wife the daughter of the king of Arabia, thus causing a border war. (Josephus, Antiquities 18: 109-115). Herodias and Antipas remained a very influential couple in the gospel period, although condemned by John the Baptist on the grounds that Antipas had married the ex-wife of his half-brother Thomas (not Philip as in Mark 6:17. Herodias became a female co-worker with a Philip in the mission hierarchy. This fact is given in the pesher of Mark 12:19-27).

Doubting Thomas the Twin supplies a valuable source for the study of a question that still preoccupies parts of the Christian church.