How can we trust the council of Nicea when it has been proven that there were many more holy books t

This is an involved question, to answer reasonably, in my estimation will require some detail I commonly avoid in this forum. Having said that, this first point that should be made surrounds which is a collection of Bible texts that were subject to a high level of skepticism while the canon of Scripture was being established. The word antilegomena literally means “spoken against” and was applied to those writings that were accepted by the majority of the early church but had more detractors than other books. Writings that were clearly seen as non-inspired or heretical were branded as such by the early church. Another group of writings, known as the homologumena, was recognized as inspired and enjoyed universal acceptance in the early church. The books classified as antilegomena were questioned in different ways and for different reasons than those that were rejected as non-canonical.

As the early church grew, it became important to distinguish between God’s Word and writings that were not God’s Word.

In short, books were recognized as canonical if they were written by an apostle or under and apostle’s direction as with Luke and Mark, written in both Hebrew and Koine Greek, positively explained true Christian doctrine, made some claim or connection to inspiration by the Holy Spirit, were accepted by the doctrinally loyal churches, and/or were suitable for public reading.

Using that criteria, the twenty-seven books of the New Testament quickly became accepted as the canon of Scripture.

However, seven of those twenty-seven books were subject to more debate than the others. Those seven were Hebrews, James, 2 Peter, 2 John, 3 John, Jude, and Revelation. Unlike the works that were rejected outright, these books contained no obvious disqualifiers. They did not present heresy, they were not clearly linked to a non-orthodox church, and so forth. Rather, each fell short in the minds of some early Christians, according to the criteria given above.

It must be emphasized that other categories of ancient writings, such as the pseudepigrapha and Apocrypha, were viewed in a completely different light as compared to the antilegomena. Even as the New Testament was being written, the church recognized the existence of false writings. “That ye be not soon shaken in mind, or be troubled, neither by spirit, nor by word, nor by letter as from us, as that the day of Christ is at hand”. 2 Thessalonians 2:2

This explains the abundance of caution the church used in officially recognizing works as inspired. The antilegomena were less readily accepted, not because they were flawed but because the early church was exceedingly careful in what it endorsed as inspired text.

The book of Hebrews was considered antilegomena because it is technically anonymous. Other New Testament books either clearly state their author or can be traced directly to an apostle. The book of Hebrews does neither, although it matches all of the other criteria for the biblical canon.

The book of James has always been subject to controversy, mostly because of its complex discussion of the relationship between saving faith and good works. For this reason, some in the early church hesitated to accept it, and it was classified as one of the antilegomena.

Second Peter is easily the most heavily disputed book of the antilegomena. More than anything else, the differences in style between 1 Peter and 2 Peter led to debates over whether or not it was legitimate. Over time, mounting evidence won over the skeptics, and 2 Peter was acknowledged to be canonical.

The letters of 2 John and 3 John do not identify their authors as clearly as other New Testament texts. In particular, they use the term elder rather than apostle, which led to some doubt concerning authorship. This wording was not uncommon for the apostles, however, and the short letters of John’s were never doubted to the same extent as 2 Peter.

Jude is an interesting member of the antilegomena. Jude was questioned for making explicit references to non-inspired works. Parts of the book of Jude allude to stories told in the non-canonical The Assumption of Moses and the Book of Enoch. However, because Jude does not endorse those writings as Scripture (Jude merely uses them as examples to support his points), this controversy was eventually settled.

Revelation has the distinction of being the most persistently questioned of the antilegomena. Though it was never questioned to the same degree as 2 Peter, critics continued to express doubts about it long after other books of the antilegomena had been widely accepted. Revelation’s biggest stumbling block was that its symbolism was open to such wide interpretation.

A few early sects attempted to use the book to justify bizarre doctrines, which made Revelation guilty by association in the eyes of some early church members.

Most books of the New Testament were accepted very soon after being written—the homologumena. Others—the antilegomena—were less readily accepted for various reasons.

The extreme caution exercised by the early church led to these seven books being more heavily examined prior to their eventual acceptance into the canon of Scripture.

The Council of Nicea took place in AD 325 by order of the Roman Emperor Caesar Flavius Constantine. Nicea was located in Asia Minor, east of Constantinople. At the Council of Nicea, Emperor Constantine presided over a group of church bishops and other leaders with the purpose of defining the nature of God for all of Christianity and eliminating confusion, controversy, and contention within the church.

The Council of Nicea overwhelmingly affirmed the deity and eternality of Jesus the Christ and defined the relationship between the Father and the Son as “of one substance.” It also affirmed the Trinity—the Father, Son, and Holy Spirit were listed as three co-equal and co-eternal Persons.

Constantine, who claimed conversion to Christianity, called for a meeting of bishops to be held in Nicea to resolve some escalating controversies among the church leadership. The issues being debated included the nature of Jesus the Christ, the proper date to celebrate Easter, and other matters. The failing Roman Empire, now under Constantine’s rule, could not withstand the division caused by years of hard-fought, “out of hand” arguing over doctrinal differences. The emperor saw the quarrels within the church not only as a threat to Christianity but as a threat to society as well. Therefore, at the Council of Nicea, Constantine encouraged the church leaders to settle their internal disagreements and become Christlike agents who could bring new life to a troubled empire. Constantine felt “called” to use his authority to help bring about unity, peace, and love within the church.

The main theological issue had always been about Christ. Since the end of the apostolic age, Christians had begun debating these questions: Who is the Christ? Is He more divine than human or more human than divine? Was Jesus created or begotten? Being the Son of God, is He co-equal and co-eternal with the Father, or is He lower in status than the Father? Is the Father the one true God, or are the Father, Son, and Spirit the one true God?

A priest named Arius presented his argument that Jesus the Christ was not an eternal being, that He was created at a certain point in time by the Father. Bishops such as Alexander and the deacon Athanasius argued the opposite position: that Jesus the Christ is eternal, just like the Father is. It was an argument pitting trinitarianismagainst monarchianism.

Constantine prodded the 300 bishops in the council make a decision by majority vote defining who Jesus Christ is. The statement of doctrine they produced was one that all of Christianity would follow and obey, called the “Nicene Creed.” This creed was upheld by the church and enforced by the Emperor. The bishops at Nicea voted to make the full deity of Christ the accepted position of the church. The Council of Nicea upheld the doctrine of Christ’s true divinity, rejecting Arius’s heresy. The council did not invent this doctrine. Rather, it only recognized what the Bible already taught.

The New Testament teaches that Jesus the Messiah should be worshipped, which is to say He is co-equal with God. The New Testament forbids the worship of angels (Colossians 2:18; Revelation 22:8, 9) but commands worship of Jesus. The apostle Paul tells us that “in Christ all the fullness of the Deity lives in bodily form” (Colossians 2:9; 1:19). Paul declares Jesus as Lord and the One to whom a person must pray for salvation (Romans 10:9-13; cf. Joel 2:32). “Jesus is God overall” (Romans 9:5) and our God and Savior (Titus 2:13). Faith in Jesus’ deity is basic to Paul’s theology.

John’s Gospel declares Jesus to be the divine, eternal Logos, the agent of creation and source of life and light (John 1:1-5,9); "the Way, the Truth, and the Life" (John 14:6); our advocate with the Father (1 John 2:1-2); the Sovereign (Revelation 1:5); and the Son of God from the beginning to the end (Revelation 22:13).

The author of Hebrews reveals the deity of Jesus through His perfection as the most high priest (Hebrews 1; Hebrews 7:1-3). The divine-human Savior is the Christian’s object of faith, hope, and love.

The Council of Nicea did not invent the doctrine of the deity of Christ. Rather, the Council of Nicea affirmed the apostles’ teaching of who Christ is—the one true God and the Second Person of the Trinity, with the Father and the Holy Spirit.

Why Christians Believe What They Believe 

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