The Bible's Shifting Canon
A common refrain among Atheists is that the oldest manuscripts of the Bible that we possess are copies of copies, often involving numerous scribal errors and mistranslations. A competing Christian claim is that the Bible as we have it today is virtually identical to the ancient manuscripts, and that the ancient manuscripts largely agree with one another. Where the two camps seem to generally agree is in the belief that there have been no modern changes to the Bible (save for the appearance of new translations). This seems to be an unspoken assumption on the part of both camps, with most people I've spoken to believing that the Bible was set in stone either at the Council of Nicea or with the publishing of the King James Bible.
This belief in the absence of modern changes is so pervasive that I've frequently seen Christians attempt to extend an olive branch to other denominations (especially Protestants reaching out to Catholics) by saying "we may disagree on some things, but ultimately we're all reading the same book!"
The truth is, of course, far more interesting, so I want to take this time to provide a brief history of the way that the Biblical canon has shifted over the years. Specifically, this will address the Biblical canon in Western Christianity, as Western Christianity has long held a binary view of the Biblical canon (i.e. a given text either was inspired by the Holy Spirit, or it was not). By contrast, Eastern Christianity (those denominations that typically have "orthodox" in their name) have largely not adopted this binary view, instead admitting of degrees of inspiration. While there were some books that they rejected for inclusion in their Bibles, they did not necessarily go so far as to say that they were not inspired at all. As such, Eastern Christianity typically hasn't made a big deal over the question of which books rightly belong in the Bible.
The Catholic Canon
First of all, to clear this up: No, the Council of Nicea did NOT determine what books would go in the Bible. That's a common misconception that may have started with Voltaire, and was popularized by Dan Brown's Da Vinci Code.
The Biblical Canon was actually established by the Council of Rome in 382 CE, at which time 73 books (the same books that presently make up the Catholic Bible) were declared canonical. In the same year, the Vulgate, a Latin translation of the Bible, was commissioned. Despite the Council of Rome having just decided on the 73 canonical books, the Vulgate also included the Prayer of Manasseh, which the Council had not declared canon.
Beyond that, in the 1200's, Vulgate Bibles printed in Paris began including the book of 1 Esdras, which was also not among the books that the Council of Rome had canonized.
Martin Luther
Fast forward to 1534 CE and Martin Luther has just finished putting the final touches on his German translation of the Bible. Luther disputed the canonicity of several books, relegating the books of Tobit, Judith, Baruch, Sirach, 1 Maccabees, 2 Maccabees, and Wisdom to a new section labeled "Apocrypha: These Books Are Not Held Equal to the Scriptures, but Are Useful and Good to Read," which he placed between the old and new testaments. He also included the Prayer of Manasseh in the Apocrypha. While Catholics had traditionally placed the book in the Old Testament at the end of 2 Chronicles, it was never "officially" canon, so this wasn't really a change, so to speak.He also omitted the Esther 10:4 – 16:24 as these verses are found in the Septuagint (the Greek translation of the Old Testament), but not in the Hebrew scriptures themselves. For this same reason, Luther also omitted Daniel 3:24–90 (renumbering verses 91-96 as verses 24-30 in the process), as well as omitting Daniel 13 and 14.
Finally, he moved the books of Hebrews and James to the back of the Bible, placing them just before Jude and Revelation, and included a preface to these books stating that - while he did not go so far as to remove them to the Apocrypha section as he had with so many others - he felt that there was strong reason to doubt the canonicity of these books.
The Council of Trent
In response to Martin Luther's work, and the growing popularity of Protestantism, the Catholic church held the Council of Trent in 1564, at which point it was re-affirmed that all 73 books from the Council of Rome were canonical in their entirety.
Despite this, in 1592, Pope Clement VIII published a revised edition of the Vulgate which included the Prayer of Manasseh, as well as 1 Esdras and 2 Esdras, none of which were in the Catholic canon. While Catholicism has officially held the same 73 books cannon for over 1,600 years, these 3 books indicate that the question of canon was not nearly so settled as the Catholic Church would have us believe.
The King James Version
Perhaps expectedly, the Catholic church insisting that they were absolutely right about the Biblical canon didn't satisfy Protestants since they no longer believed in the authority of the Catholic church. This was made evident again in 1604 when King James I of England (who needed to get the church off his back so that he could go be bisexual in peace) commissioned what would be the third English translation of the Bible (the first two being commissioned by King Henry VIII, and Queen Elizabeth I). The King James version was finally published in 1611 and almost immediately became the de facto standard for English-language Bibles.
As England was a Protestant nation, the committees in charge of translating and assembling the text followed many of the conventions of previous Protestant Bibles. As was the case with the Luther Bible, they relegated the books of Tobit, Judith, Baruch, Sirach, 1 Maccabees, 2 Maccabees, and Wisdom to the "Apocrypha" section. However, it also included the portions of Esther and Daniel that Luther had omitted, breaking them into 4 books and placing them in the Apocrypha, as well as including the Prayer of Manasseh, 1 Esdras, and 2 Esdras.
All told, the original 1611 King James Bible had 80 books: 39 in the Old Testament, 14 in the Apocrypha, and 27 in the New Testament.
In the interest of complete fairness, it's worth noting that these variations are almost universally minor, involving slight variations in spelling, omission or insertion of a small word such as "the," and so on. However, even D.A. Waite, in his book Defending the King James Bible, acknowledges the existence of 136 changes of "substance" between the original King James Bible and what is available today.

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