First Arrangement of the Holy Koran
"And We have sent down on you a Book in which is the clarification of all the things." (16:89)
There is no dispute among Muslim scholars, whether they are Sunni or Shia, concerning the fact that Ali possessed a special transcript of the text of Koran which he had collected himself, and he was the first who compiled Koran. Academics state that Ali compiled the Koran on the orders of Prophet Muhammad. There is also no disagreement among both Sunni and Shia Muslims that what we have with us today is the entire uncorrupted Koran as dictated by Mohammad.
The order in which Mohammad dictated is, however, not the same. Earliest chapters are written towards the end in the arrangement that exists today. Muslims clerics states there are a number of traditions which tell us that after the death of the Prophet in 632 C.E., Ali secluded himself in his house; and he told people that he had sworn an oath that he would not put on his outdoor clothes or leave his house until he collected together the Koran. [see, Fathul Bari by al Asqalani; Itqan by al Suyuti.]
Ali’s compilation was collected according to the order in which it had been sent down. Ibn Sireen (653-729) said he regretted that Ali’s transcript had not passed into the hands of the Muslims, and said: "If that transcript were in our hands, we would found a great knowledge in it." [see, Tabaqat by Ibn Saad; Ansab by Baladhuri; Istiab by Ibn Abdul Barr.]
Historians states that it is according to Ali’s transcript that most scholars claim that the first Chapter of Koran which was sent down to the Prophet was chapter 96 al-Iqra, also called al-Alaq. [Suyuti, Asqalani, Zarkashi, and Qastalani.]
Ali wanted to share knowledge of the Koran with the people. He often stated in her sermons: "Ask me before you lose me. By Allah, if you ask me about anything that could happen up to the Day of Judgment, I will tell you about it. Ask me, for, by Allah, you will not be able to ask me a question about anything without my informing you. Ask me about the Book of Allah, for by Allah, there is no verse about which I do not know whether it was sent down at night or during the day, or whether it was revealed on a plain or in a mountain." [Asqalani, Ibn Saad, and Suyuti.]
In present copies of Koran, Surah al-Alaq is not found at the beginning. Also one of the last verses to be revealed is verse of Surah al Maidah (5:3). Therefore, although we possess the complete Koran, it is not in the order that has been revealed. These few misplacements were done by some companions on purpose at worst, or out of ignorance at least.
Koran as collection by Ali contained commentary and interpretation (Tafsir and Tawil) from the Prophet himself some of which had been sent down as revelation but not as a part of the text of Koran. These pieces of information were the Divine commentary of the text of Koran which were revealed along its verses. Thus the verses of Koran and the verses of commentary could sum up to 17000 verses.
Muslims accept that Hadith al-Qudsi (the Hadith in which the speaker is Allah) is also direct revelation, but they are not a part of Koran. In fact Koran testifies that anything that Prophet said was (either direct or indirect) revelation. The direct revelation includes the interpretation/commentary of the Koran. (53:3-4)
Koran tells us that to follow only the clear verses and act upon them. It warns us not to dig into doubtful material in the book. See Surah Ale Imam (3:7). God had placed both type of verses to test the people of sincerity and people with devious aims. Ali’s unique transcript contained the information from the Holy Prophet as to which verses were clear (Muhkam) and which was ambiguous (Mutashabih), which verse was general and which was specific.
Ali’s transcript also contained references on additional information about verses. For example, it has information on persons and places about which the verses were revealed. This is called Asbab al Nazul, the “Occasions of Revelation”. Ali gave us all the particulars of all 6666 verses. Since Ali was aware of these facts, he frequently said:
"By Allah, no verse has been sent down without my knowing about for whom or for what it was revealed and where it was revealed. My Lord has gifted me with a mind which has a quick and retaining understanding, and a tongue which speaks eloquently." [Abu Nuaim, Ibn Saad, Haythami.]
After he compiled this transcript Ali took it and presented it to the rulers who came after the Holy Prophet, and said:
"Here is the book of Allah, your Lord, in the order that was revealed to your Prophet."
However, they did not accept it and replied:
"We have no need of this. We have with us what you possess."
Ali took the transcript back and informed them that they will never see it again. It is reported that Ali recited the latter part of the following verse of Koran:
"And when Allah took a Covenant from the People of the Book to clarify it to mankind and not to hide its (clarification); but they threw it away behind their backs and purchased with it some miserable gain! And what an evil was the bargain they made!" (3:187)
By "its clarification", Ali meant the unique divine commentaries.
It is said that Ali then concealed that transcript. After Ali, it was passed to the Imams. They also kept it hidden. They wanted there to be only one sequence of Koran among the Muslims. According to traditions in Usul al-Kafi, Ali’s hand written Koran contained "what can be understood of the universe", and "all the knowledge of the eternal book". This is because there were in Ali’s compilation commentaries and interpretations directly from the Holy Prophet.