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According to orthodox Islamic belief, the Qur'an is the unchanging, eternal word of Allah, pre-existent before all time and space, handed to the prophet through divine revelation. The text of this final word of Allah is thus eternal and unchanging, as opposed to the previous revelations given to people of the book, which were changed and corrupted over the ages. This picture, though, is highly complicated by the fact that the Islamic tradition recognizes 7 historical reading traditions, each with two transmitters featuring different "harakat" or short vowels for the "rasm" or consonantal skeleton of the text. Recent work on the language of the Qur'an, extant manuscripts, and discoveries such as the Sana'a Manuscript complicate this picture significantly more. From the Sana'a palimpset it is apparent that the received text of the Qur'an at one point had variants which were not preserved in any of the 7 reading traditions, and the reading traditions themselves differ sometimes significantly in grammar and meaning. The Islamic tradition itself also complicates the picture. The below hadith traditions indicate that the complete, pristine text of the Qur'an did not make it out past the first generation of Muslims. According to the tradition, many of the Muslims who had memorized the entirety of the Qur'an were killed in battle before they could put their verses to writing, and some verses were lost with them; the ends and beginning of some of the suwar or chapters were in dispute, and several ahadith state that the entirety of the Qur'an was not passed down. Shi'ites in particular have traditions which claim that up to a quarter of the Qur'an was not passed down to the present day. Some hadith also claim that entire verses were "cancelled" or removed from the text for no apparent reason. All of these traditions were written down in or after the second Islamic century, so they likely reflect the thoughts and feelings of people alive at that time about the textual integrity of the Qur'an, which was by this time well known as the sacred text of the Muslims and their empire.
Difficulty in Collecting the Qur'anic Verses
Narrated Zaid bin Thabit Al-Ansari: who was one of those who used to write the Divine Revelation: Abu Bakr sent for me after the (heavy) casualties among the warriors (of the battle) of Yamama (where a great number of Qurra' were killed). 'Umar was present with Abu Bakr who said, 'Umar has come to me and said, The people have suffered heavy casualties on the day of (the battle of) Yamama, and I am afraid that there will be more casualties among the Qurra' (those who know the Qur'an by heart) at other battle-fields, whereby a large part of the Qur'an may be lost, unless you collect it. And I am of the opinion that you should collect the Qur'an." Abu Bakr added, "I said to 'Umar, 'How can I do something which Allah's Apostle has not done?' 'Umar said (to me), 'By Allah, it is (really) a good thing.' So 'Umar kept on pressing, trying to persuade me to accept his proposal, till Allah opened my bosom for it and I had the same opinion as 'Umar." (Zaid bin Thabit added:) Umar was sitting with him (Abu Bakr) and was not speaking. me). "You are a wise young man and we do not suspect you (of telling lies or of forgetfulness): and you used to write the Divine Inspiration for Allah's Apostle. Therefore, look for the Qur'an and collect it (in one manuscript). " By Allah, if he (Abu Bakr) had ordered me to shift one of the mountains (from its place) it would not have been harder for me than what he had ordered me concerning the collection of the Qur'an. I said to both of them, "How dare you do a thing which the Prophet has not done?" Abu Bakr said, "By Allah, it is (really) a good thing. So I kept on arguing with him about it till Allah opened my bosom for that which He had opened the bosoms of Abu Bakr and Umar. So I started locating Quranic material and collecting it from parchments, scapula, leaf-stalks of date palms and from the memories of men (who knew it by heart). I found with Khuzaima two Verses of Surat-at-Tauba which I had not found with anybody else, (and they were)...
Organization of the Qur'an
"Ibn ’Abbas said to ’Uthman, ‘What made you combine the chapter of the Anfal and the chapter of Tawba (repentance) without separating them by the verse, "In the name of God the compassionate, the Merciful"? (And why) did you put them among the seven long (chapters)?’ ’Uthman said, ‘The chapters used to be bestowed upon the apostle of God. The chapter of Anfal was among the early ones which were revealed in Medina and the chapter of Repentance was among the last revealed. Its story was similar to the early story (of the Anfal), so I thought that it was part of it. Then the apostle of God died without showing us that it was part of the (Anfal); thus, I combined them and did not write between them the verse, "In the name of God the Compassionate, the Merciful", and it is among the long ones."’
Verse of Rajam (Stoning)
The present day Qur’an does not contain the penalty of Rajm (stoning) for adulterers. But Sahih Hadiths testify that there was a verse in the Qur’an pertaining to the ‘Stoning Punishment’. Umar, the second Caliph of Islam, confirms the loss of this verse from the Qur’an:
Abdullah b. 'Abbas reported that 'Umar b. Khattab sat on the pulpit of Allah's Messenger (may peace be upon him) and said: Verily Allah sent Muhammad (may peace be upon him) with truth and He sent down the Book upon him, and the verse of stoning was included in what was sent down to him. We recited it, retained it in our memory and understood it. Allah's Messenger (may peace be upon him) awarded the punishment of stoning to death (to the married adulterer and adulteress) and, after him, we also awarded the punishment of stoning, I am afraid that with the lapse of time, the people (may forget it) and may say: We do not find the punishment of stoning in the Book of Allah, and thus go astray by abandoning this duty prescribed by Allah. stoning is a duty laid down in Allah's Book for married men and women who commit adultery when proof is established, or it there is pregnancy, or a confession.
It was narrated that 'Aishah said:
“The Verse of stoning
and of breastfeeding an adult ten times was revealed, and the paper was with me under my pillow. When the Messenger of Allah died, we were preoccupied with his death, and a tame sheep came in and ate it
Abd Allah Ibn Sa`d Ibn Abi Sarh and Verse 6:93
And who is more unjust than he who forges a lie against Allah, or says: It has been revealed to me; while nothing has been revealed to him, and he who says: I can reveal the like of what Allah has revealed? and if you had seen when the unjust shall be in the agonies of death and the angels shall spread forth their hands: Give up your souls; today shall you be recompensed with an ignominious chastisement because you spoke against Allah other than the truth and (because) you showed pride against His communications.
The scribes of Muhammad were 42 in number. `Abdallah Ibn Sarh al-`Amiri was one of them, and he was the first Quraishite among those who wrote in Mecca before he turned away from Islam. He started saying, "I used to direct Muhammad wherever I willed. He would dictate to me 'Most High, All-Wise', and I would write down 'All-Wise' only. Then he would say, 'Yes it is all the same'. On a certain occasion he said, 'Write such and such', but I wrote 'Write' only, and he said, 'Write whatever you like.'" So when this scribe exposed Muhammad, he wrote in the Qur'an, "And who does greater evil than he who forges against God a lie, or says, 'To me it has been revealed', when naught has been revealed to him."
So on the day Muhammad conquered Mecca, he commanded his scribe to be killed. But the scribe fled to `Uthman Ibn `Affan, because `Uthman was his foster brother (his mother suckled `Uthman). `Uthman, therefore, kept him away from Muhammad. After the people calmed down, `Uthman brought the scribe to Muhammad and sought protection for him. Muhammad kept silent for a long time, after which he said yes. When `Uthman had left, Muhammad said "I only kept silent so that you (the people) should kill him."
Al-Sira by al-'Iraqi
Some apologists claim that Abi Sarh returned to Islam under his own free will without pressure by citing al-Tabari's tafsir on 6:93, which says that Abi Sarh returned to Islam before the conquest of Mecca. However, Tabari's History and hadiths in Sunan Abu Dawud say that he returned to Islam on the same day that Mecca was taken (i.e. under pressure, when he was presented to Muhammad by his foster brother, `Uthman).
'Abdallah b. Sa'd b. Abi Sarh used to write for him. He apostatized from Islam and later returned to Islam on the day of the conquest of Mecca.
al-Tabari (d. 923), Ismail K. Poonawala, ed, The History of al-Tabari [Ta’rikh al-rusul wa’l-muluk], vol. IX, SUNY Press, p. 148, ISBN 0-88706-691-7, 1990, https://archive.org/details/HistoryAlTabari40Vol/History_Al-Tabari_10_Vol/page/n2267/mode/2up أبو جعفر الطبري, تاريخ الرسل والملوك, vol. 11, al-Maktabah al-Shamilah, p. 540, https://app.turath.io/book/9783
Narrated Sa'd: On the day when Mecca was conquered, the Apostle of Allah (peace be upon him) gave protection to the People except four men and two women and he named them. Ibn AbuSarh was one of them. He then narrated the tradition. He said: Ibn AbuSarh hid himself with Uthman ibn Affan. When the Apostle of Allah (peace be upon him) called the people to take the oath of allegiance, he brought him and made him stand before the Apostle of Allah (peace be upon him). He said: Apostle of Allah, receive the oath of allegiance from him. He raised his head and looked at him thrice, denying him every time. After the third time he received his oath. He then turned to his Companions and said: Is not there any intelligent man among you who would stand to this (man) when he saw me desisting from receiving the oath of allegiance, and kill him? They replied: We do not know, Apostle of Allah, what lies in your heart; did you not give us an hint with your eye? He said: It is not proper for a Prophet to have a treacherous eye.
"'To me it has been revealed', when naught has been revealed to him" refers to `Abdallah Ibn Sa`d Ibn Abi Sarh, who used to write for God's messenger. The verse (23:12) that says, "We created man of an extraction of clay" was revealed, and when Muhammad reached the part that says, "... thereafter We produced him as another creature (23:14), `Abdallah said, "So blessed be God the fairest of creators!" in amazement at the details of man's creation. The prophet said, "Write it down; for thus it has been revealed." `Abdallah doubted and said, "If Muhammad is truthful then I receive the revelation as much as he does, and if he is a liar, what I said is a good as what he said."
Surah of Repentance Lost 157 Verses
"Malik says that several verses from chapter 9 (Sura of Repentance) have been dropped from the beginning. Among them is, ‘In the name of God the compassionate, the Merciful’ because it was proven that the length of Sura of Repentance was equal to the length of the Sura of the Cow."
Narrated Ibn Abbas: Umar said, "Our best Qur'an reciter is Ubai and our best judge is 'Ali; and in spite of this, we leave some of the statements of Ubai because Ubai says, 'I do not leave anything that I have heard from Allah's Apostle while Allah:
"Whatever verse (Revelations) do We abrogate
or cause to be forgotten but We bring a better one or similar to it." (2.106)
’Ibn Umar al–Khattab: "Let no one of you say that he has acquired the entire Qur’an for how does he know that it is all? Much of the Qur’an has been lost, thus let him say, ‘I have acquired of it what is available"’
A’isha: "During the time of the prophet, the chapter of the Parties used to be two hundred verses when read. When Uthman edited the copies of the Qur’an, only the current (verses) were recorded"
Ubay ibn Ka’b: "This famous companion asked one of the Muslims, ‘How many verses in the chapter of the Parties?’ He said, ‘Seventy-two or seventy-three verses.’ He (Ubay) told him, ‘It used to be almost equal to the chapter of the Cow (about 286 verses) and included the verse of the stoning.’ The man asked, ‘What is the verse of the stoning?’ He said, ‘If an old man or woman committed adultery, stone them to death."’
Ibn Hazm: "’Ali Ibn Abi Talib said this has a reliable chain of authority."
"During the collection of the Qur’an, people used to come to Zayd Ibn Thabit (with the verses they memorized). He shunned recording any verse unless two witnesses attested to it. The last verse of chapter of Repentance was found only with Khuzayma Ibn Thabit. Zayd said, ‘Record it because the apostle of God made the testimony of Khuzayma equal to the testimony of two men.’ ’Umar came with the verse of the stoning but it was not recorded because he was the only witness to it."
A’isha: "Among the (verses) which were sent down, (the verse) of the ten breast feedings was abrogated by (a verse which calls for five breast feedings. The apostle of God died and this verse was still read as part of the Qur’an. This was related by Abu Bakr and ’Umar" 
Ibn Hazm: "The verses of stoning and breast feeding were in the possession of A’isha in a (Qur’anic) copy. When Muhammad died and people became busy in the burial preparations, a domesticated animal entered in and ate it."
"Hamida, the daughter of Abi Yunis, said, ‘When my father was eighty years old, he read in the copy of A’isha, "God and His angels bless (literally pray for) the prophet Oh ye who believe, bless him and those who pray in the first rows." Then she said, "That was before ’Uthman changed the Qur’anic copies.""’
"Umar said to ’Abdul-Rahman Ibn ’Oaf, ‘Didn’t you find among the verses that we received one saying, "Strive as you strove at the first?" We do not locate it (any more).’ ’Abdul-Rahman Ibn ’Oaf told him, ‘This verse has been removed among those others which were removed from the Qur’an."’
"Maslama al-Ansar said to the companions of Muhammad, ‘Tell me about two verses which have not been recorded in the Qur’an which ’Uthman collected.’ They failed to do so. Maslama said, ‘Oh, ye who believed and immigrated and fought for the cause of God by (sacrificing) your properties and yourselves, you received the glad tidings, for you are prosperous. Also, those who sheltered them, aided them and defended them, against whom God (revealed) His wrath, no soul knows what is awaiting them as a reward for what they did."’
Ibn Kathir: "’Uthman burned the rest of the copies which were in the hands of the people because they disagreed on the (correct) reading and they fought among themselves. When they came to take ibn Mas’ud’s copy to bum it, he told them, ‘I know more than Zayd ibn Thabit (whom ’Uthman ordered to collect the copies of the Qur’an).’ ’Uthman wrote to ibn Mas’ud asking him to submit his copy for burning."
There is evidence to the cancellation of some verses from the Qur’an even though they were revealed to Muhammad and the people of his time had memorized them.
Narrated Anas: The Prophet sent seventy men from the tribe of Bani Salim to the tribe of Bani Amir. When they reached there, my maternal uncle said to them, "I will go ahead of you, and if they allow me to convey the message of Allah's Apostle (it will be all right); otherwise you will remain close to me." So he went ahead of them and the pagans granted him security But while he was reporting the message of the Prophet , they beckoned to one of their men who stabbed him to death. My maternal uncle said, "Allah is Greater! By the Lord of the Kaba, I am successful." After that they attached the rest of the party and killed them all except a lame man who went up to the top of the mountain. (Hammam, a sub-narrator said, "I think another man was saved along with him)." Gabriel informed the Prophet that they (i.e the martyrs) met their Lord, and He was pleased with them and made them pleased. We used to recite, "Inform our people that we have met our Lord, He is pleased with us and He has made us pleased " Later on this Quranic Verse was cancelled. The Prophet invoked Allah for forty days to curse the murderers from the tribe of Ral, Dhakwan, Bani Lihyan and Bam Usaiya who disobeyed Allah and his Apostle
Narrated Anas bin Malik: For thirty days Allah's Apostle invoked Allah to curse those who had killed the companions of Bir-Mauna; he invoked evil upon the tribes of Ral, Dhakwan, and Usaiya who disobeyed Allah and His Apostle. There was reveled about those who were killed at Bir-Mauna a Quranic Verse we used to recite, but it was cancelled later on. The Verse was: "Inform our people that we have met our Lord. He is pleased with us and He has made us pleased"
Narrated Anas: The people of the tribes of Ril, Dhakwan, 'Usiya and Bani Lihyan came to the Prophet and claimed that they had embraced Islam, and they requested him to support them with some men to fight their own people. The Prophet supported them with seventy men from the Ansar whom we used to call Al-Qurra'(i.e. Scholars) who (out of piety) used to cut wood during the day and pray all the night. So, those people took the (seventy) men till they reached a place called Bi'r-Ma'ana where they betrayed and martyred them. So, the Prophet invoked evil on the tribe of Ril, Dhakwan and Bani Lihyan for one month in the prayer. Narrated Qatada: Anas told us that they (i.e. Muslims) used to recite a Quranic Verse concerning those martyrs which was:-- "O Allah! Let our people be informed on our behalf that we have met our Lord Who has got pleased with us and made us pleased." Then the Verse was cancelled.
It is not clear who had decided to cancel them.
The Seven Ahruf of the Qur'an
A number of hadiths narrate that the Qur'an was revealed to Muhammad in up to seven "ahruf" (literally "words" or "letters"), which has been variously interpreted by classical scholars to mean dialects, or ways of recitation, among other theories. The concept of seven ahruf is not to be confused with the seven (or ten) canonical qira'at, or readings of the Qur'an.
Narrated `Umar bin Al-Khattab:
I heard Hisham bin Hakim bin Hizam reciting Surat-al-Furqan in a way different to that of mine. Allah's Messenger (ﷺ) had taught it to me (in a different way). So, I was about to quarrel with him (during the prayer) but I waited till he finished, then I tied his garment round his neck and seized him by it and brought him to Allah's Messenger (ﷺ) and said, "I have heard him reciting Surat-al-Furqan in a way different to the way you taught it to me." The Prophet (ﷺ) ordered me to release him and asked Hisham to recite it. When he recited it, Allah s Apostle said, "It was revealed in this way." He then asked me to recite it. When I recited it, he said, "It was revealed in this way. The Qur'an has been revealed in seven different ways, so recite it in the way that is easier for you."
Narrated 'Abdullah bin 'Abbas: Allah's Apostle said, "Gabriel recited the Qur'an to me in one way. Then I requested him (to read it in another way), and continued asking him to recite it in other ways, and he recited it in several ways till he ultimately recited it in seven different ways."
Ubayy b. Ka'b reported that the Apostle of Allah (may peace be upon him) was near the tank of Banu Ghifar that Gabriel came to him and said: Allah has commanded you to recite to your people the Qur'an in one dialect. Upon this he said: I ask from Allah pardon and forgiveness. My people are not capable of doing it. He then came for the second time and said: Allah has commanded you that you should recite the Qur'an to your people in two dialects. Upon this he (the Holy prophet) again said: I seek pardon and forgiveness from Allah, my people would not be able to do so. He (Gabriel) came for the third time and said: Allah has commanded you to recite the Qur'an to your people in three dialects. Upon this he said: I ask pardon and forgiveness from Allah. My people would not be able to do it. He then came to him for the fourth time and said: Allah has commanded you to recite the Qur'an to your people in seven dialects, and in whichever dialect they would recite, they would be right.
"A great scholar, that is the Mawardi, said that Muhammad had permitted the reading (of the Qur’an) on the basis of any of the Seven Letters as it happened in the episodes of ’Umar. He also allowed replacing a letter with another letter."
"When the lads and their teachers fought against each other during the era of ’Uthman due to the difference in reading (the Qur’anic text), he (’Uthman) standardized the reading and made people recite it accordingly because he was afraid of riots since the Iraqis and the Damascenes disagreed on the dialect. But before that, the Qur’anic copies (used to be read) on the basis of the Seven Letters in which the Qur’an was given."
- ↑ "The Itqan" by Suyuti Part 1, Pages 172-173
- ↑ Is the Qur'an Infallible? by `Abdallah `Abd al-Fadi,
- ↑ Tafsir Anwar al-Tanzil wa Asrar al-Ta'wil by `Abdallah Ibn `Umar al-Baidawi
- ↑ "The Itqan" by Suyuti Part 3, Page 184
- ↑ 5.0 5.1 5.2 Suyuti, "The Itqan", part 3, p. 72
- ↑ The Sweetest [Al Mohalla] vol. 8, Part 11, pp. 234-235
- ↑ Suyuti, "The Itqan", part 1, p. 168
- ↑ Suyuti, "The Itqan", part 3, pp. 62-63
- ↑ Ibn Hazm Volume 8, Part II, Pages 235 and 236
- ↑ Suyuti, "The Itqan", part 3, p. 73
- ↑ 11.0 11.1 Suyuti, "The Itqan", part 3, p. 74
- ↑ "The Beginning and the End" Part 7, Page 218
- ↑ "The Itqan" by Suyuti Paragraph 1, Page 137. Ibid pages 141 and 142
- ↑ "The Itqan" by Suyuti Paragraph 1, Page 170 and 171